WO2017218922A2 - Compositions and methods for the treatment of bacterial infections - Google Patents

Compositions and methods for the treatment of bacterial infections Download PDF

Info

Publication number
WO2017218922A2
WO2017218922A2 PCT/US2017/037924 US2017037924W WO2017218922A2 WO 2017218922 A2 WO2017218922 A2 WO 2017218922A2 US 2017037924 W US2017037924 W US 2017037924W WO 2017218922 A2 WO2017218922 A2 WO 2017218922A2
Authority
WO
WIPO (PCT)
Prior art keywords
optionally substituted
compound
acid
pharmaceutically acceptable
independently
Prior art date
Application number
PCT/US2017/037924
Other languages
French (fr)
Other versions
WO2017218922A3 (en
WO2017218922A8 (en
Inventor
James M. Balkovec
Daniel C. BENSEN
Timothy Blizzard
Allen Borchardt
Thomas P. Brady
Zhi-yong CHEN
Quyen-Quyen Thuy Do
Wanlong Jiang
Thanh Lam
Jeffrey B. Locke
Alain Noncovich
Original Assignee
Cidara Therapeutics, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Cidara Therapeutics, Inc. filed Critical Cidara Therapeutics, Inc.
Publication of WO2017218922A2 publication Critical patent/WO2017218922A2/en
Publication of WO2017218922A3 publication Critical patent/WO2017218922A3/en
Publication of WO2017218922A8 publication Critical patent/WO2017218922A8/en

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/50—Cyclic peptides containing at least one abnormal peptide link
    • C07K7/54—Cyclic peptides containing at least one abnormal peptide link with at least one abnormal peptide link in the ring
    • C07K7/60—Cyclic peptides containing at least one abnormal peptide link with at least one abnormal peptide link in the ring the cyclisation occurring through the 4-amino group of 2,4-diamino-butanoic acid
    • C07K7/62—Polymyxins; Related peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the disclosure relates to compounds, compositions, and methods for inhibiting bacterial growth (e.g., Gram-negative bacterial growth) and for the treatment of bacterial infections (e.g., Gram-negative bacterial infections).
  • bacterial growth e.g., Gram-negative bacterial growth
  • bacterial infections e.g., Gram-negative bacterial infections
  • such compounds contain dimers of cyclic heptapeptides, which bind to lipopolysaccharides (LPS) in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
  • LPS lipopolysaccharides
  • the disclosure features a compound described by formula (I):
  • M1 includes a first cyclic heptapeptide including a linking nitrogen and M2 includes a second cyclic heptapeptide including a linking nitrogen;
  • L' is a linker covalently attached to the linking nitrogen in each of M1 and M2, or a pharmaceutically acceptable salt thereof; wherein L' is not
  • L" is a remainder of L'; and each of R' L and R L is, independently, C1 -C10 alkyl.
  • L' in formula (I) is described by:
  • L is a remainder of L';
  • A1 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M1 or is absent; and
  • A2 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M2 or is absent.
  • the compound is described by formula (II):
  • L is a remainder of L'; each of each of R 1 , R 12 , R' 1 , and R' 12 is, independently, a lipophilic moiety, a polar moiety, or H; each of R 1 1 , R 13 , R 14 , R' 1 1 , R' 13 , and R' 14 is, independently, optionally substituted C1 - C5 alkamino, a polar moiety, a positively charged moiety, or H; each of R 15 and R' 15 is, independently, a lipophilic moiety or a polar moiety; each of R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R' 2 , R' 3 , R' 4 , R' 5 , R' 6 , R' 7 , R' 8 , R' 9 , and R' 10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, and
  • the compound includes at least one optionally substituted 5-8 membered ring formed by joining (i) R 2 , R 3 , and C 1 ; (ii) R 3 , R 4 , N 1 , and C 1 ; (iii) R 5 , R 6 , and C 2 ; (iv) R 6 , R 7 , N 2 , and C 2 ; (v) R 8 , R 9 , and C 3 ; (vi) R 9 , R 10 , N 3 , and C 3 ; (vii) R' 2 , R' 3 , and C' 1 ; (viii) R' 3 , R' 4 , N' 1 , and C' 1 ; (ix) R' 5 , R' 6 , and C' 2 ; (x) R' 6 , R' 7 , N' 2 , and C' 2 ; (xi) R' 8 , R' 9 , and C' 3 ; or (xii) R' 9 ,
  • L is a remainder of L'; or a pharmaceutically acceptable salt thereof.
  • each of R 1 , R 12 , R' 1 , and R' 12 is, independently, a lipophilic moiety; each of R 1 1 , R 13 , R 14 , R' 1 1 , R' 13 , and R' 14 is, independently, optionally substituted C1 -C5 alkamino, a polar moiety, or a positively charged moiety; and/or each of R 15 and R' 15 is, independently, a polar moiety.
  • each of R 1 , R 12 , R' 1 , and R' 12 is a lipophilic moiety.
  • each lipophilic moiety is, independently, optionally substituted C1 -C20 alkyl, optionally substituted C5-C1 5 aryl, optionally substituted C6-C35 alkaryl, or optionally substituted C3-C15 heteroaryl.
  • each lipophilic moiety is, independently, C1 -C8 alkyl, methyl substituted C2-C4 alkyl, (C1 - C10)alkylene(C6)aryl, phenyl substituted (C1 -C10)alkylene(C6)aryl, or alkyl substituted C4-C9 heteroaryl.
  • each lipophilic moiety is, independently, benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or methyl substituted indolyl.
  • each of R 1 1 , R 13 , R 14 , R' 1 1 , R' 13 , and R' 14 is independently optionally substituted C1 -C5 alkamino.
  • each of R 1 1 , R 13 , R 14 , R' 1 1 , R' 13 , and R' 14 is CH2CH2NH2.
  • each of R 15 and R' 15 is a polar moiety.
  • each polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group.
  • each polar moiety is hydroxyl substituted C1 -C4 alkyl.
  • each polar moiety is
  • the compound is described by formula (IV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (IV-1 ):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (V):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C
  • the compound is described by formula (V-1 ):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (V-2):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (V-3):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (V-4):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (V-5):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VI):
  • each of R' 1 and R 1 is, independently, benzyl or CH 2 CH(CH3)2; each of R 2 , R 6 , R 8 , R' 2 , R' 6 , and R' 8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally
  • the compound is described by formula (VI-1 ):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VI-2):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VI-3):
  • the compound is described by formula (VI-4):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VI-5):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VI-6):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VI-7):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (VII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-
  • the compound is described by formula (VIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C
  • the compound is described by formula (IX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or
  • the compound is described by formula (X):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically
  • the compound is described by formula (X-1 ):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • each of R 2 and R' 2 is optionally substituted C1 -C5 alkamino. In some embodiments, each of R 2 and R' 2 is CH2NH2 or CH2CH2NH2.
  • each of R 2 and R' 2 is a polar moiety.
  • each polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group.
  • each polar moiety is hydroxyl substituted C1 -C4 alkyl.
  • each polar moiety is CHCH3OH or CH2OH.
  • each of R 6 and R' 6 is a polar moiety.
  • the polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group.
  • the polar moiety is hydroxyl substituted C1 -C4 alkyl.
  • the polar moiety is CHCH3OH or CH2OH.
  • each of R 8 and R' 8 is optionally substituted C1 -C5 alkamino.
  • the optionally substituted C1 -C5 alkamino is In some embodiments, the compound is described by formula (XI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
  • L', L", or L includes one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, optionally substituted C3-C15 heteroarylene, O, S, NR', P, carbonyl, thiocarbonyl
  • the backbone of L', L", or L includes no more than 100 atoms.
  • the backbone of L', L", or L consists of one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, optionally
  • L is a bond. In some embodiments, L is capable of forming an amide, a carbamate, a sulfonyl, or a urea linkage.
  • L is described by formula (L-1 ):
  • I 1 is a bond attached to A2 or M2 if A2 is absent; I 2 is a bond attached to A1 or M1 if A1 is absent; each of U 1 , U 2 , U 3 , and U 4 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2- C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20
  • V 1 , V 2 , V 3 , V 4 , and V 5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C
  • L e.g., L of formula (L-1 )
  • each of U 1 , U 2 , U 3 , and U 4 in formula (L-1 ) is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, or optionally substituted C2-C20 heteroalkynylene; each of V 1 , V 2 , V 3 , V 4 , and V 5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-
  • L is N
  • heterocycloalkenyl optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C1 5 aryl, or optionally substituted C5-C15 heteroaryl; and each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
  • L is N
  • the disclosure features a compound of formula (XII):
  • each A 1 and A 2 is an independently selected amino acid
  • L is a linker that, when m is 1 , 2, 3, 4, or 5, is bound to a nitrogen atom in any A 1 and a nitrogen atom in any A 2
  • each m is independently 0, 1 , 2, 3, 4, or 5
  • Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of a natural amino acid, or a pharmaceutically acceptable salt thereof.
  • At least one of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
  • at least two of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
  • at least three of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non- natural amino acid, or a pharmaceutically acceptable salt thereof.
  • At least four of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, at least five of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, each of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
  • each Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
  • each of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
  • each of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, cyclohexylmethyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
  • the combination of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is selected from one of
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-
  • each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
  • the combination of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is selected from one of
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-
  • each m is 0, or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XIII):
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • m is 2, 3, or 4. In some embodiments of a compound of formula (XIV), m is 2. In some embodiments of a compound of formula (XIV), m is 3. In some embodiments of a compound of formula (XIV), m is 4.
  • d is 1 , 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XV):
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • X is absent, or a pharmaceutically acceptable salt thereof.
  • Y is -CH2-, or a pharmaceutically acceptable salt thereof.
  • Y is -C(O)-, or a pharmaceutically acceptable salt thereof.
  • X is O, or a pharmaceutically acceptable salt thereof.
  • each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • Y is -C(O)-, X is absent, and Z is CH, or a pharmaceutically acceptable salt thereof. In some embodiments, Y is -C(0)-,.X is absent, and Z is N, or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently threonine or 2,4-diaminobutyric acid; and m is 2 or 3; or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XVI):
  • each Y is independently -C(O)-, -S(O)-, -S(0) 2 -, or is absent;
  • R 1 is hydrogen, C1 -C10 alkyl, -N(R 3 R 4 ), or -OH;
  • R 2 is hydrogen, C1 -C10 alkyl, or -OH;
  • R 3 and R 4 are independently hydrogen or C1 -C10 alkyl; and
  • d is an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • CR 1 CR 2 -; R 1 is hydrogen or -NR 3 R 4 ; R 3 and R 4 are hydrogen; and d is 1 , 2, or 3; or a pharmaceutically acceptable salt thereof.
  • Y is -S(0)2-; X is -CH2-; and d is 1 , 2, or 3; or a pharmaceutically acceptable salt thereof.
  • Y is absent, X is -C(O)- and d is 1 , or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently threonine, 3-hydroxyalaline, 2,4-diaminobutyric acid, 3-hydroxyproline, 2-amino-4-(dimethylamino)butyric acid, and 2-aminooctanoic acid, or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XVII):
  • the compound is of the formula (XVII-1 ):
  • the compound is of the formula (XVII-2):
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2- piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcystein
  • each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2- piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylc
  • each A 1 and A 2 is independently threonine or 2,4-diaminobutyric acid, or a
  • the disclosure features a compound of formula (XVIII):
  • each A 1 and A 2 is an independently selected amino acid; e is an integer from 1 to 5; f is an integer from 1 to 5; each m is independently 0, 1 , 2, 3, 4, or 5; Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; and R 1 is hydrogen, C1 -C10 alkyl, -C(0)OR 2 , -C(0)-(CH 2 OCH2)d-heterocyclic, and -C(0)R 2 ; R 2 is C1 -C10 alkyl, benzyl, -CH 2 (biphenyl), -(CH2CH 2 0) g -R 3 ; R 3 is -(CH 2 )iNR 4 R 5 and -(CH 2 )i-(C 2 -C 8 alkynyl); R 4 is hydrogen or C1 -C10 alkyl; R 5 is hydrogen or C1 -C10 alkyl; and d is
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalan
  • each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
  • e and f are 1 , or a pharmaceutically acceptable salt thereof.
  • R 1 is hydrogen, or a pharmaceutically acceptable salt thereof.
  • R 1 is -C0 2 R 2 , or a pharmaceutically acceptable salt thereof.
  • R 1 is -C(0)R 2 , or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently threonine, 2,4-diaminobutyric acid, 2-aminooctanoic acid, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminodecanoic acid, O-allyl serine, tryptophan, and 3-(4,4'-biphenyl)alanine, or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XIX):
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-
  • d is 1 or 2
  • R 1 is hydrogen
  • R 2 is hydrogen, or a pharmaceutically acceptable salt thereof.
  • d is 1 . In some embodiments of a compound of formula (XIX), d is 2.
  • each A 1 and A 2 is independently 2,4- daminobutyric acid, threonine, or 4-aminoproline, or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-a
  • d is 1 , 2, or 3. In some embodiments, d is 1 and d' is 1 . In some embodiments, d is 1 and d' is 0. In some embodiments, d is 0 and d' is 1 . In some embodiments, d is 2 and d' is 2. In some embodiments, d is 2 and d' is 1 . In some embodiments, d is 1 and d' is 2. In some embodiments, d is 3 and d' is 0. In some embodiments, d is 0 and d' is 3.
  • R 1 is hydrogen, or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently 2,4- diaminobutyric acid or threonine, or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XXI):
  • each A 1 and A 2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-
  • each A 1 and A 2 is independently 2,4- diaminobutyric acid or threonine, or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine,
  • the disclosure features a compound of formula (XXIII):
  • each A 1 and A 2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine,
  • each A 1 and A 2 is an independently selected amino acid
  • R 1 is hydrogen or C1 -C10 alkyl
  • each m is independently 0, 1 , 2, 3, 4, or 5
  • Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid
  • d is an integer from 1 to 6; or a pharmaceutically acceptable salt thereof.
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalan
  • d is 1 , 2, or 3. In some embodiments, d is 3.
  • each A 1 and A 2 is independently 2,4- diaminobutyric acid, threonine, or 2-aminooctanoic acid, or a pharmaceutically acceptable salt thereof.
  • the disclosure features a compound of formula (XXV):
  • each A 1 and A 2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalan
  • each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
  • each Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a
  • each of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from C1 -C4 alkyi, C3-C6 cycloalkyi C1 -C4 alkyi, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, C6-C10 aryl, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
  • each of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, cyclohexylmethyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
  • the combination of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is selected from one of
  • the combination of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 is selected from one of
  • the compound is described by formula (XXVI):
  • each of R' 1 and R 1 is, independently, benzyl or CH 2 CH(CH 3 )2; each of R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R' 2 , R' 3 , R' 4 , R' 5 , R' 6 , R' 7 , R' 8 , R' 9 , and R' 10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C
  • heterocycloalkenyl optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring; each of a', b', c', a, b, and c is, independently, 0 or 1 ; each of N 1 , N 2 , N 3 , N 4 , N' 1 , N' 2 , N' 3 , and N' 4 is a nitrogen atom; each of C 1 , C 2 , C 3 , C' 1 , C' 2 , and C' 3 is a carbon atom; L is a linker comprising at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted
  • the compound comprises at least one optionally substituted 5-8 membered ring formed by joining (i) R 2 , R 3 , and C 1 ; (ii) R 3 , R 4 , N 1 , and C 1 ; (iii) R 5 , R 6 , and C 2 ; (iv) R 6 , R 7 , N 2 , and C 2 ; (v) R 8 , R 9 , and C 3 ; (vi) R 9 , R 10 , N 3 , and C 3 ; (vii) R' 2 , R' 3 , and C' 1 ; (viii) R' 3 , R' 4 , N' 1 , and C' 1 ; (ix) R' 5 , R' 6 , and C' 2 ; (x) R' 6 , R' 7 , N' 2 , and C' 2 ; (xi) R' 8 , R' 9 , and C' 3 ; or (xii) R' 9 ,
  • L is described by formula (L-2):
  • I 1 is a bond attached to N' 1 , N' 2 , N' 3 , or N' 4 ;
  • I 2 is a bond attached to N 1 , N 2 , N 3 , or N 4 ;
  • the compound is described by formula (XXVII):
  • each of R' 1 and R 1 is, independently, benzyl or CH 2 CH(CH 3 )2; each of R 2 , R 6 , R 8 , R' 2 , R' 6 , and R' 8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C
  • the compound is described by formula (XXVIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optional
  • the compound is described by formula (XXIX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6
  • the compound is described by formula (XXX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , and R 8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroal
  • the compound is described by formula (XXXI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C
  • the compound is described by formula (XXXII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 hetero
  • the compound is described by formula (XXXIII): H
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 and R 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a
  • the compound is described by formula (XXXIV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2;
  • R 2 is a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXVI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • L comprises at least one optionally substituted C3 cycloalkylene or at least one optionally substituted C3 heterocycloalkylene.
  • the compound is described by formula (XXXVII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXVIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • L is N
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L comprises at least one optionally substituted C5 cycloalkylene or at least one optionally substituted C5 heterocycloalkylene.
  • the compound is described by formula (XXXIX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXXI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXXII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • L comprises at least one optionally substituted pyrrolidine.
  • the pyrrolidine is substituted with an alkyne functional group, and azide functional group, a sulphone functional group, an amine functional group, or a fluorophore.
  • the fluorophore is fluorescein, rhodamine, coumarin, or a derivative thereof.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L is
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L comprises at least one optionally substituted 1 ,3-dioxolane.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L comprises at least one optionally substituted C6 cycloalkylene or at least one optionally substituted C6 heterocycloalkylene.
  • the compound is described by formula (XXXXIV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 cycloalkylene or an optionally substituted C6 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L comprises at least one optionally substituted C6 arylene or at least one optionally substituted C6 heteroarylene.
  • the compound is described by formula (XXXXV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXXVI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
  • the compound is described by formula (XXXXVII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L comprises at least two optionally substituted C6 arylene.
  • the compound is described by formula (XXXXVIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises at least two optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • L comprises at least one optionally substituted C5 arylene or at least one optionally substituted C5 heteroarylene.
  • the compound is described by formula (XXXXIX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 arylene or an optionally substituted C5 heteroarylene, or a pharmaceutically acceptable salt thereof.
  • each q is, independently, an integer from 1 to 1 1 , inclusive.
  • Non-natural amino acids that may be included in a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)), for example, in the polymyxin core portions (e.g., in the first cyclic heptapeptide and/or the second cyclic heptapeptide) and/or the linker portion of the compound, include, but are not limited to, , D-Ser, D-Pro, D-Leu, D-Nle (D-norleucine), D-Thr, D-Val, L-Abu (L-2- aminobutyric acid), 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4- diaminobutyric acid, 3-hydroxyproline, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2- piperazinecarboxylic acid, 2-amin
  • polymyxin core portions e.g., in the first cyclic heptapeptide and/or the second cyclic heptapeptide
  • polymyxin core portions include D-Ser, D-Pro, D-Leu, D-Nle, D-Thr, D-Val, and/or L-Abu.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX) and/or any one of compounds 1 -180, or a pharmaceutically acceptable salt thereof
  • the compound does not include any monosaccharide or oligosaccharide moieties.
  • the disclosure features any compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX) and/or any one of compounds 1 -180, or a pharmaceutically acceptable salt thereof).
  • the disclosure features a pharmaceutical composition including a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
  • the pharmaceutical composition further includes an antibacterial agent.
  • the antibacterial agent is selected from the group consisting of linezolid, tedizolid, posizolid, radezolid, rumblemulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem,
  • the antibacterial agent is linezolid or tedizolid phosphate.
  • the disclosure features a method of protecting against or treating a bacterial infection in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • the method further includes administering to the subject an antibacterial agent.
  • the disclosure features a method of protecting against or treating a bacterial infection in a subject by administering to the subject (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • an antibacterial agent e.g., a compound of any one of formulas (l)-(XXXXIX)
  • the bacterial infection is caused by Gram-negative bacteria. In some embodiments, the bacterial infection is caused by a resistant strain of bacteria. In some embodiments, the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance. In some embodiments, the resistant strain of bacteria is a resistant strain of E. coli.
  • the disclosure features a method of protecting against or treating sepsis in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
  • the method further includes administering to the subject an antibacterial agent.
  • the disclosure features a method of preventing LPS in Gram-negative bacteria, e.g., a resistant strain of Gram-negative bacteria.
  • the resistant strain of Gram- negative bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance.
  • the resistant strain of Gram-negative bacteria is a resistant strain of E. coli.
  • the method prevents LPS from activating a macrophage.
  • the method prevents LPS-induced nitroic oxide (NO) production from a macrophage.
  • the method further includes administering to the subject an antibacterial agent.
  • the compound and the antibacterial agent are administered substantially simultaneously.
  • the compound and the antibacterial agent are administered separately.
  • the compound is administered first, followed by administering of the antibacterial agent alone.
  • the antibacterial agent is administered first, followed by administering of the compound alone.
  • the compound and the antibacterial agent are administered substantially simultaneously, followed by administering of the compound or the antibacterial agent alone.
  • the compound or the antibacterial agent is administered first, followed by administering of the compound and the antibacterial agent substantially simultaneously.
  • administering the compound and the antibacterial agent together may lower the MIC of each of the compound and the antibacterial agent relative to the MIC of each of the compound and the antibacterial agent when each is used alone.
  • the compound and/or the antibacterial agent is administered intramuscularly, intravenously, intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally, locally, by inhalation, by injection, or by infusion.
  • the disclosure features a method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria.
  • the method includes contacting the bacteria or a site susceptible to bacterial growth with a compound described herein (e.g., a compound of any one of formulas (I)- (XXXXIX)).
  • the method further includes contacting the bacteria or the site susceptible to bacterial growth with an antibacterial agent, in addition to the compound.
  • the disclosure features a method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria by contacting the bacteria or a site susceptible to bacterial growth with (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
  • the bacteria is Gram-negative bacteria. In some embodiments, the bacteria is a resistant strain of bacteria. In some embodiments, the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance. In some embodiments, the resistant strain of bacteria is a resistant strain of E. coli.
  • the antibacterial agent is selected from the group consisting of linezolid, tedizolid, posizolid, radezolid, rumblemulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem, imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime,
  • acyl refers to a group having the structure: , wherein R z is an optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, alkaryl, alkamino, heteroalkyl, heteroalkenyl, heteroalkynyl, heterocycloalkyl, heterocycloalkenyl,
  • heterocycloalkynyl heteroaryl, heteroalkaryl, or heteroalkamino.
  • alkylene alkyl
  • alkenyl alkenylene
  • alkynyl alkynylene
  • an alkylene may contain, e.g., 1 - 20, 1 -1 8, 1 -16, 1 -14, 1 -12, 1 -10, 1 -8, 1 -6, 1 -4, or 1 -2 carbon atoms (e.g., C1 -C20, C1 -C18, C1 -C16, C1 - C14, C1 -C12, C1 -C1 0, C1 -C8, C1 -C6, C1 -C4, or C1 -C2).
  • an alkenylene or alkynylene may contain, e.g., 2-20, 2-1 8, 2-16, 2-14, 2-12, 2-10, 2-8, 2-6, or 2-4 carbon atoms (e.g., C2- C20, C2-C18, C2-C1 6, C2-C14, C2-C12, C2-C1 0, C2-C8, C2-C6, or C2-C4).
  • C1 -C20 alkyl means a fully saturated chain comprising from 1 to 20 carbons, which may be linear or branched.
  • Alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups include straight-chain and branched- chain forms, as well as combinations of these.
  • the divalency of an alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group does not include the optional substituents on the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group.
  • a first cyclic heptapeptide and a second cyclic heptapeptide may be attached to each other by way of a linker that includes alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene, or combinations thereof.
  • a linker that includes alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene, or combinations thereof.
  • Each of the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups in the linker is considered divalent with respect to the two attachments on either end of alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group.
  • a linker includes (optionally substituted alkylene) (optionally substituted alkenylene) or (optionally substituted alkylene)
  • the alkenylene is considered divalent with respect to its attachments to the two alkylenes at the ends of the linker.
  • the optional substituents on the alkenylene are not included in the divalency of the alkenylene.
  • alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group refers to both of the ends of the group and does not include optional substituents that may be present in an alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group.
  • Alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups can be substituted by the groups typically suitable as substituents for alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups as set forth herein.
  • HCR C ⁇ C may be considered as an optionally substituted alkynyl or alkynylene and is considered a divalent group even though it has an optional substituent, R.
  • alkamide refers to an amide group that is attached to an alkyl or alkylene (e.g., C1 -C5 alkylene), alkenyl or alkenylene (e.g., C2-C5 alkenylene), or alkynyl or alkynylene (e.g., C2-C5 alkenylene) group.
  • alkyl or alkylene e.g., C1 -C5 alkylene
  • alkenyl or alkenylene e.g., C2-C5 alkenylene
  • alkynyl or alkynylene e.g., C2-C5 alkenylene
  • the amide portion of an alkamide refers to -C(0)N(R X )2, where each R x is, independently, H, alkyl, alkenyl, alkynyl, aryl, alkaryl, cycloalkyl, or two R x combine to form a heterocycloalkyl.
  • the amide portion of an alkamide is-C(0)NH2.
  • An alkamide group may be -(CH2)2C(0)NH2, or -CH2C(0)NH2.
  • heteroalkamide group one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms selected from N, O, and S may be present in the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the heteroalkamide group.
  • an alkamide group may be optionally substituted.
  • the substituent may be present on the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the alkamide group and/or may be present on the amide portion of the alkamide group.
  • alkamino refers to an amino group, described herein, that is attached to an alkyl or alkylene (e.g., C1 -C5 alkylene), alkenyl or alkenylene (e.g., C2-C5 alkenylene), or alkynyl or alkynylene group (e.g., C2-C5 alkenylene).
  • alkyl or alkylene e.g., C1 -C5 alkylene
  • alkenyl or alkenylene e.g., C2-C5 alkenylene
  • alkynyl or alkynylene group e.g., C2-C5 alkenylene
  • amino portion of an alkamino refers to -N(R X )2 or -N + (R X )3, where each R x is, independently, H, alkyl, alkenyl, alkynyl, aryl, alkaryl, cycloalkyl, or two R x combine to form a
  • an alkamino group is C1 -C5 alkamino, e.g., C2 alkamino (e.g., CH2CH2NH2 or ChteChbNKCh ⁇ ).
  • a heteroalkamino group one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms selected from N, O, and S may be present in the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the heteroalkamino group.
  • an alkamino group may be optionally substituted.
  • the substituent may be present on the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the alkamino group and/or may be present on the amino portion of the alkamino group.
  • alkaryl refers to an aryl group that is connected to an alkyl, alkylene, alkenyl, alkenylene, alkynyl, or alkynylene group. In general, if a compound is attached to an alkaryl group, the alkyl, alkylene, alkenyl, alkenylene, alkynyl, or alkynylene portion of the alkaryl is attached to the compound.
  • an alkaryl is C6-C35 alkaryl (e.g., C6-C16, C6-C14, C6-C12, C6- C10, C6-C9, C6-C8, C7, or C6 alkaryl), in which the number of carbons indicates the total number of carbons in both the aryl portion and the alkyl, alkylene, alkenyl, alkenylene, alkynyl, or alkynylene portion of the alkaryl.
  • C6-C35 alkaryl e.g., C6-C16, C6-C14, C6-C12, C6- C10, C6-C9, C6-C8, C7, or C6 alkaryl
  • alkaryls include, but are not limited to, (C1 -C8)alkylene(C6-C12)aryl, (C2- C8)alkenylene(C6-C12)aryl, or (C2 C8)alkynylene(C6-C12)aryl.
  • an alkaryl is benzyl.
  • one or more heteroatoms selected from N, O, and S may be present in the alkylene, alkenylene, or alkynylene portion of the alkaryl group and/or may be present in the aryl portion of the alkaryl group.
  • the substituent may be present on the alkylene, alkenylene, or alkynylene portion of the alkaryl group and/or may be present on the aryl portion of the alkaryl group.
  • amino represents -N(R X )2 or -N + (R X )3, where each R x is,
  • H independently, H, alkyl, alkenyl, alkynyl, aryl, alkaryl, cycloalkyl, or two R x combine to form a
  • the amino group is NH2.
  • amino acid means naturally occurring amino acids and non-naturally occurring amino acids.
  • Naturally occurring amino acids means amino acids including Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, He, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, and Val.
  • non-naturally occurring amino acid means an alpha amino acid that is not naturally produced or found in a mammal.
  • non-naturally occurring amino acids include D-amino acids; an amino acid having an acetylaminomethyl group attached to a sulfur atom of a cysteine; a pegylated amino acid; the omega amino acids of the formula NH2(CH2)nCOOH where n is 2-6, neutral nonpolar amino acids, such as sarcosine, t-butyl alanine, t-butyl glycine, N-methyl isoleucine, and norleucine; oxymethionine; phenylglycine; citrulline; methionine sulfoxide; cysteic acid; ornithine;
  • diaminobutyric acid 3-aminoalanine; 3-hydroxy-D-proline; 2,4-diaminobutyric acid; 2-aminopentanoic acid; 2-aminooctanoic acid, 2-carboxy piperazine; piperazine-2-carboxylic acid, 2-amino-4-phenylbutanoic acid; 3-(2-naphthyl)alanine, and hydroxyproline.
  • amino acids are a-aminobutyric acid, a-amino-a- methylbutyrate, aminocyclopropane-carboxylate, aminoisobutyric acid, aminonorbornyl-carboxylate, L- cyclohexylalanine, cyclopentylalanine, L-N-methylleucine, L-N-methylmethionine, L-N-methylnorvaline, L- N-methylphenylalanine, L-N-methylproline, L-N-methylserine, L-N-methyltryptophan, D-ornithine, L-N- methylethylglycine, L-norleucine, a-methyl-aminoisobutyrate, a-methylcyclohexylalanine, D-a- methylalanine, D-a-methylarginine, D-a-methylasparagine, D-a-methylaspartate, D-a-methylcysteine
  • amino acid residues may be charged or polar.
  • Charged amino acids include alanine, lysine, aspartic acid, or glutamic acid, or non-naturally occurring analogs thereof.
  • Polar amino acids include glutamine, asparagine, histidine, serine, threonine, tyrosine, methionine, or tryptophan, or non-naturally occurring analogs thereof.
  • a terminal amino group in the amino acid may be an amido group or a carbamate group.
  • antibacterial agent refers to an agent that is used in addition to one or more of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) in methods of treating a bacterial infection (e.g., Gram-negative bacterial infection) and/or preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria.
  • a bacterial infection e.g., Gram-negative bacterial infection
  • An antibacterial agent may be an agent that prevents the entrance of a bacteria (e.g., a Gram-negative bacteria) into a subject's cells, tissues, or organs, inhibits the growth of a bacteria (e.g., a Gram-negative bacteria) in a subject's cells, tissues, or organs, and/or kills a bacteria (e.g., a Gram-negative bacteria) that is inside a subject's cells, tissues, or organs.
  • a bacteria e.g., a Gram-negative bacteria
  • Examples of antibacterial agents are described in detail further herein.
  • an antibacterial agent used in addition to a compound described herein is tedizolid (e.g., tedizolid phosphate), azithromycin, meropenem, amikacin, levofloxacin, rifampicin, linezolid, erythromycin, or solithromycin.
  • the antibacterial agent used in combination with a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • is tedizolid e.g., tedizolid phosphate
  • azithromycin meropenem
  • amikacin levofloxacin
  • aryl refers to any monocyclic or fused ring bicyclic or tricyclic system which has the characteristics of aromaticity in terms of electron distribution throughout the ring system, e.g., phenyl, naphthyl, or phenanthrene.
  • a ring system contains 5 1 5 ring member atoms or 5-10 ring member atoms.
  • An aryl group may have, e.g., between five to fifteen carbons (e.g., a C5-C6, C5-C7, C5-C8, C5-C9, C5-C10, C5-C1 1 , C5-C12, C5-C13, C5-C14, or C5-C15 aryl).
  • five to fifteen carbons e.g., a C5-C6, C5-C7, C5-C8, C5-C9, C5-C10, C5-C1 1 , C5-C12, C5-C13, C5-C14, or C5-C15 aryl.
  • arylene refers to a multivalent (e.g., divalent or trivalent) aryl group linking together multiple (e.g., two or three) parts of a compound. For example, one carbon within the arylene group may be linked to one part of the compound, while another carbon within the arylene group may be linked to another part of the compound.
  • An arylene may have, e.g., between five to fifteen carbons in the aryl portion of the arylene (e.g., a C5-C6, C5-C7, C5-C8, C5-C9.
  • arylene group can be substituted by the groups typically suitable as substituents for alkyl, alkenyl and alkynyl groups as set forth herein.
  • Heteroarylene refers to an aromatic group including one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S.
  • a heteroarylene group may have, e.g., between two to fifteen carbons (e.g., a C2-C3, C2-C4, C2-C5, C2-C6, C2-C7, C2- C8, C2-C9.
  • backbone refers to atoms comprising a linker of the compounds disclosed herein that together form the shortest path from one part of a compound to another part of the compound (e.g., the shortest path linking a first cyclic heptapeptide and a second cyclic heptapeptide).
  • bacteria infection refers to the invasion of a subject's cells, tissues, and/or organs by bacteria (e.g., Gram-negative bacteria), thus, causing an infection.
  • bacteria e.g., Gram-negative bacteria
  • the bacteria may grow, multiply, and/or produce toxins in the subject's cells, tissues, and/or organs.
  • a bacterial infection can be any situation in which the presence of a bacterial population(s) is latent within or damaging to a host body.
  • a subject is "suffering" from a bacterial infection when a latent bacterial population is detectable in or on the subject's body, an excessive amount of a bacterial population is present in or on the subject's body, or when the presence of a bacterial population(s) is damaging the cells, tissues, and/or organs of the subject.
  • bond refers to a chemical bond, e.g., an amide bond, a disulfide bond, a C-0 bond, a N-N bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation.
  • R and R ' are as defined for R 16 herein.
  • carbonyl refers to a group having the structure: .
  • covalently attached refers to two parts of a compound that are linked to each other by a covalent bond formed between two atoms in the two parts of the compound.
  • L is covalently attached to N' 4 , which means that when a' is 0, an atom in L forms a covalent bond with N' 4 in the compound.
  • cyclic heptapeptide refers to compounds having seven natural or non-natural a-amino acid residues, such as D- or L-amino acid residues, in a closed ring.
  • cyclic heptapeptides are formed by linking the a-carboxyl group of one amino acid to the a-amino group or the ⁇ -amino group of another amino acid and cyclizing.
  • the cyclic heptapeptide comprises a heterocycle comprising carbon and nitrogen ring members, which may be substituted, for example, with amino acid side chains.
  • One nitrogen from an a-amino group in the cyclic heptapeptide is not a ring member and is branched from a ring member of the heterocycle. Thus, this nitrogen is directly attached to a ring member, such as a carbon atom (e.g., an a-carbon atom).
  • This nitrogen atom serves as an attachment point for the cyclic heptapeptide to a linker and/or to a peptide (e.g., a peptide including 1 -5 amino acid residue(s)), and thus is referred to herein as a "linking nitrogen.”
  • the linking nitrogen is directly attached to the ring of the cyclic heptapeptide and is not derived from a side chain, such as an ethylamine side chain.
  • the linking nitrogens in a compound of, e.g., formula (II) or (III), are N 4 and N' 4 .
  • cyclic heptapeptides bind to lipopolysaccharides (LPS) in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
  • LPS lipopolysaccharides
  • a peptide including one or more (e.g., 1 -5; 1 , 2, 3, 4, or 5) amino acid residues may be covalently attached to a linking nitrogen (e.g., N 4 and/or N' 4 , the nitrogen from an a-amino group) in the cyclic heptapeptide ring.
  • Cyclic heptapeptides may be derived from polymyxins (e.g., naturally existing polymyxins and non-natural polymyxins) and/or octapeptins (e.g., naturally existing octapeptins and non-natural octapeptins).
  • polymyxins examples include, but are not limited to, polymyxin Bi , polymyxin B2, polymyxin B3, polymyxin B4, polymyxin B5, polymyxin ⁇ , polymyxin BHIe, polymyxin B2-lle, polymyxin Ci , polymyxin C2, polymyxin Si , polymyxin Ti, polymyxin T2, polymyxin Ai , polymyxin A2, polymyxin Di , polymyxin D2, polymyxin Ei (colistin A), polymyxin E2 (colistin B), polymyxin E3, polymyxin E 4 , polymyxin E7, polymyxin Ei-lle, polymyxin Ei-Val, polymyxin Ei-Nva, polymyxin E2-lle, polymyxin E2-Val, polymyxin E2-Nva, polymyxin Es-lle, polymyxin Mi , and polymyxin M2.
  • polymyxin Bi
  • cycloalkyl and cycloalkylene refer to a monovalent saturated or unsaturated non-aromatic cyclic alkyl group, wherein one carbon within the cyclokalkyl or cycloalkylene group may be linked to one part of the compound, while another carbon within the cycloalkyl or cycloalkylene group may be linked to another part of the compound.
  • a cycloalkyl may have, e.g., between three to twenty carbons (e.g., a C3-C7, C3-C8, C3-C9, C3-C10, C3-C1 1 , C3-C12, C3-C14, C3- C16, C3-C18, or C3-C20 cycloalkyl).
  • a C3-C20 cycloalkyl refers to a cycloalkyl group containing from 3 to 20 carbon atoms.
  • cycloalkyl and cycloalkylene groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.
  • Cycloalkyl and cycloalkylene groups also include cyclic compounds having bridged multicyclic structures in which one or more carbons bridges two non-adjacent members of a monocyclic ring, e.g., bicyclo[2.2.1 .]heptyl and adamantane. Cycloalkyl and cycloalkylene groups also include bicyclic, tricyclic, and tetracyclic fused ring structures, e.g., decalin and spiro cyclic compounds.
  • cycloalkenyl and cycloalkylene refer to a cyclic group comprising carbon atoms that includes at least one carbon-carbon double bond.
  • a cycloalkenyl or cycloalkenylene group may have, e.g., between four to twenty carbons in the cyclic portion of the cycloalkenyl or cycloalkenylene (e.g., a C4-C7, C4-C8, C4-C9. C4-C1 0, C4-C1 1 , C4-C12, C4-C14, C4-C16, C4-C18, or C4-C20 cycloalkenylene).
  • a C4-C20 cycloalkenyl or C4-C20 cycloalkenylene groups means a cycloalkenyl or cycloalkenylene group containing from 4 to 20 carbon atoms and includes at least one carbon-carbon double bond.
  • Exemplary cycloalkenyl groups include, but are not limited to, cyclopentenyl, cyclohexenyl, and cycloheptenyl.
  • cycloalkynyl and cycloalkynylene refer to a cyclic group comprising carbon atoms that contains at least one carbon-carbon triple bond.
  • a cycloalkynyl or cycloalkynylene group may have, e.g., between four to twenty carbons in the cyclic portion of the cycloalkynyl or cycloalkynylene (e.g., a C4-C7, C4-C8, C4-C9.
  • a C8-C20 cycloalkynyl group is a cyclic group containing from 8 to 20 carbon atoms and at least one carbon-carbon triple bond.
  • a cycloalkynyl or cycloalkynylene group can be substituted by the groups typically suitable as substituents for alkyl, alkenyl and alkynyl groups as set forth herein.
  • halo refers to any halogen atom, e.g., F, CI, Br, or I. Any one of the groups or moieties described herein may be referred to as a "halo moiety" if it contains at least one halogen atom, such as haloalkyl.
  • hetero refers to having at least one heteroatom that is not a carbon or a hydrogen, e.g., N, O, and S. Any one of the groups or moieties described above may be referred to as hetero if it contains at least one heteroatom.
  • a heterocycloalkyl, heterocycloalkenyl, or heterocycloalkynyl group refers to a cycloalkyl, cycloalkenyl, or cycloalkynyl group that has one or more heteroatoms independently selected from, e.g., N, O, and S.
  • An example of a heterocycloalkenyl group is a maleimido.
  • a heteroaryl group refers to an aromatic group that has one or more heteroatoms independently selected from, e.g., N, O, and S.
  • One or more heteroatoms may also be included in a substituent that replaced a hydrogen atom in a group or moiety as described herein.
  • the substituent may also contain one or more heteroatoms (e.g., methanol).
  • heteroalkyl refers to alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups including one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S.
  • a polyethylene glycol (PEG) polymer or a PEG unit -(CH2)2-0-in a PEG polymer is considered a heteroalkylene containing one or more oxygen atoms.
  • a C1 -C4 hydroxyalkyl is a heteroalkyl or heteroalkylene group.
  • heteroaryl refers to monocyclic or fused bicyclic ring systems containing one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms selected from O, S and N.
  • a heteroaryl group may have, e.g., between two to fifteen carbons (e.g., a C2-C3, C2-C4, C2-C5, C2-C6, C2-C7, C2- C8, C2-C9.
  • the inclusion of a heteroatom permits inclusion of 5 membered rings to be considered aromatic as well as 6 membered rings.
  • heteroaryl systems include, e.g., pyridyl, pyrimidyl, indolyl, benzimidazolyl, benzotriazolyl, isoquinolyl, quinolyl, benzothiazolyl, benzofuranyl, thienyl, furyl, pyrrolyl, thiazolyl, oxazolyl, isoxazolyl, benzoxazolyl, benzoisoxazolyl, and imidazolyl. Because tautomers are possible, a group such as phthalimido is also considered heteroaryl.
  • the aryl or heteroaryl group is a 5- or 6-membered aromatic rings system optionally containing 1 -2 nitrogen atoms.
  • the aryl or heteroaryl group is an optionally substituted phenyl, pyridyl, indolyl, pyrimidyl, pyridazinyl, benzothiazolyl, benzimidazolyl, pyrazolyl, imidazolyl, isoxazolyl, thiazolyl, or imidazopyridinyl.
  • the aryl group is phenyl.
  • an aryl group may be optionally substituted with a substituent such an aryl substituent, e.g., biphenyl.
  • heterocycloalkyl and “heterocycloalkylene” refer to a cyclic group comprising carbon atoms and one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S.
  • a tetrahydrofuran may be considered as a heterocycloalkylene.
  • heterocycloalkenyl and “heterocycloalkenylene,” as used herein, refer to a cyclic group comprising carbon atoms and one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S, and at least one carbon-carbon double bond.
  • heterocycloalkynl and “heterocycloalkynylene,” as used herein, refer to a cyclic group comprising carbon atoms and one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S, and at least one carbon-carbon triple bond.
  • heteroatoms e.g., N, O, and S
  • hydroxyl represents an -OH group.
  • amino represents the group having the structure: , wherein R is an optional substituent
  • linker refers to a covalent linkage or connection between two or more components in a compound (e.g., two cyclic heptapeptides in a cyclic heptapeptide dimer).
  • Molecules that may be used as linkers include at least two functional groups, which may be the same or different, e.g., two carboxylic acid groups, two amine groups, two sulfonic acid groups, a carboxylic acid group and an amine group, or a carboxy group and a sulfonic acid group.
  • the first functional group may form a covalent linkage with a first component in the compound and the second functional group may form a covalent linkage with the second component in the compound.
  • a linker may be a bivalent structure having two arms, in which each arm is conjugated to a component of the compound.
  • dicarboxylic acid molecules may be used as linkers, in which the first carboxylic acid may form a covalent linkage with one component in the compound and the second carboxylic acid may form a covalent linkage with another component in the compound. Examples of dicarboxylic acids are described further herein.
  • a molecule containing one or more sulfonic acid groups may be used as a linker, in which the sulfonic acid group may form a sulfonamide linkage with a component in the compound.
  • a molecule containing one or more isocyanate groups may be used as a linker, in which the isocyanate group may form a urea linkage with a component in the compound.
  • a molecule containing one or more haloalkyi groups may be used as a linker, in which the haloalkyi group may form a covalent linkage, e.g., C-N and C-0 linkages, with a component in the compound.
  • a linker provides space, rigidity, and/or flexibility between the two or more components.
  • a linker may be a bond, e.g., a covalent bond.
  • the term "bond" refers to a chemical bond, e.g., an amide bond, a disulfide bond, a C-0 bond, a N-N bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation.
  • a linker includes no more than 100 atoms.
  • a linker includes no more than 100 non- hydrogen atoms.
  • the backbone of a linker includes no more than 100 atoms.
  • the "backbone" of a linker refers to the atoms in the linker that together form the shortest path from one part of a compound to another part of the compound (e.g., the shortest path linking a first cyclic heptapeptide and a second cyclic heptapeptide).
  • the atoms in the backbone of the linker are directly involved in linking one part of a compound to another part of the compound (e.g., linking a first cyclic heptapeptide and a second cyclic heptapeptide).
  • hydrogen atoms attached to carbons in the backbone of the linker are not considered as directly involved in linking one part of the compound to another part of the compound.
  • a linker may comprise a synthetic group derived from, e.g., a synthetic polymer (e.g., a polyethylene glycol (PEG) polymer).
  • a linker may comprise one or more amino acid residues, such as D- or L-amino acid residues.
  • a linker may be a residue of an amino acid sequence (e.g., a 1 -25 amino acid, 1 -10 amino acid, 1 -9 amino acid, 1 -8 amino acid, 1 -7 amino acid, 1 -6 amino acid, 1 -5 amino acid, 1 -4 amino acid, 1 -3 amino acid, 1 -2 amino acid, or 1 amino acid sequence).
  • a linker may comprise one or more, e.g., 1 -100, 1 -50, 1 -25, 1 -10, 1 -5, or 1 -3, optionally substituted alkylene, optionally substituted heteroalkylene (e.g., a PEG unit), optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted cycloalkylene, optionally substituted heterocycloalkylene, optionally substituted cycloalkenylene, optionally substituted heterocycloalkenylene, optionally substituted cycloalkynylene, optionally substituted
  • heterocycloalkynylene optionally substituted arylene, optionally substituted heteroarylene (e.g., pyridine), O, S, NR' (R' is H, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted alkenyl, optionally substituted heteroalkenyl, optionally substituted alkynyl, optionally substituted heteroalkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted cycloalkenyl, optionally substituted heterocycloalkenyl, optionally substituted cycloalkynyl, optionally substituted heterocycloalkynyl, optionally substituted aryl, or optionally substituted heteroaryl), P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino.
  • R' is H, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted
  • a linker may comprise one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene (e.g. , a PEG unit), optionally substituted C2-C20 alkenylene (e.g., C2 alkenylene), optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20
  • heteroalkynylene optionally substituted C3-C20 cycloalkylene (e.g., cyclopropylene, cyclobutylene), optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene (e.g., C6 arylene), optionally substituted C3-C15 heteroarylene (e.g., imidazole, pyridine), O, S, NR' (R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2- C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C
  • lipophilic moiety refers to a portion, substituent, or functional group of a compound that is, in general, hydrophobic and non-polar.
  • a moiety is lipophilic if it has a hydrophobicity determined using a cLogP value of greater than 0, such as about 0.25 or greater, about 0.5 or greater, about 1 or greater, about 2 or greater, 0.25-5, 0.5-4 or 2-3.
  • cLogP refers to the calculated partition coefficient of a molecule or portion of a molecule.
  • the partition coefficient is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium (e.g., octanol and water) and measures the hydrophobicity or hydrophilicity of a compound.
  • cLogP can be determined using quantitative structure-property relationship algorithims known in the art (e.g., using fragment based prediction methods that predict the logP of a compound by determining the sum of its non-overlapping molecular fragments).
  • a moiety is considered lipophilic if it has a cLogP value described above in at least one of the above methods.
  • a lipophilic moiety having the stated cLogP value will be considered lipophilic, even though it may have a positive charge or a polar substituent.
  • a lipophilic moiety contains entirely hydrocarbons.
  • a lipophilic moiety may contain one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms independently selected from N, O, and S (e.g., an indolyl), or one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, halo groups, which, due to the structure of the moiety and/or small differences in electronegativity between the heteroatoms or halo groups and the hydrocarbons, do not induce significant chemical polarity into the lipophilic moiety.
  • a lipophilic moiety having, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms and/or, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, halo atoms may still be considered non-polar.
  • a lipophilic moiety may be optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heteroalkenyl, optionally substituted heteroalkynyl, or optionally substituted heteroaryl, or halo forms thereof, wherein the optional substituents are also lipophilic (such as alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, aryl, or heteroaryl) or are not lipophilic but do not change the overall lipophilic character of the moiety, i.e., the moiety has a cLogP value of greater than 0.
  • octanol contains a polar group, OH, but is still a lipophilic moiety.
  • a lipophilic moiety may be benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or substituted indolyl (e.g., alkyl substituted indolyl).
  • a lipophilic moiety may be the side chain of a hydrophobic amino acid residue, e.g., leucine, isoleucine, alanine, phenylalanine, valine, and proline, or groups such as methyl, ethyl, propyl, isopropyl, butyl, isobutyl, and pyrrolidinyl.
  • lipophilic moieties of the compounds described herein may interact with the hydrophobic portions of lipid A (e.g., fatty acid side chains of lipid A) when the compounds bind to the membrane of bacterial cells (e.g., Gram-negative bacterial cells). Due to its position on the cyclic heptapeptide, one or more of R 1 , R 12 , R 15 , R' 1 , R' 12 , and R' 15 may be a lipophilic moiety.
  • LPS-induced nitroic oxide (NO) production from a macrophage refers to the ability of the lipopolysaccharides (LPS) in Gram-negative bacteria to activate a macrophage and induce NO production from the macrophage.
  • NO production from a macrophage in response to LPS is a signal of macrophage activation, which may lead to sepsis in a subject, e.g., a Gram-negative bacteria infected subject.
  • the disclosure features compounds (e.g., compounds of any one of formulas (l)-(XXXXIX)) that are able to bind to LPS in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, thus neutralizing an immune response to LPS (see, e.g., Example 1 13).
  • NO production from a macrophage may be measured using available techniques in the art, e.g., a Griess assay, as demonstrated in Example 1 13.
  • N-protecting group represents those groups intended to protect an amino group against undesirable reactions during synthetic procedures. Commonly used N-protecting groups are disclosed in Greene, “Protective Groups in Organic Synthesis,” 5th Edition (John Wiley & Sons, New York, 2014), which is incorporated herein by reference.
  • N-protecting groups include, e.g., acyl, aryloyl, and carbamyl groups such as formyl, acetyl, propionyl, pivaloyl, t-butyl acetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthalyl, o-nitrophenoxyacetyl, a-chlorobutyryl, benzoyl, carboxybenzyl (CBz), 4 chlorobenzoyl, 4 bromobenzoyl, 4 nitrobenzoyl, and chiral auxiliaries such as protected or unprotected D, L or D, L-amino acid residues such as alanine, leucine, phenylalanine;
  • sulfonyl-containing groups such as benzenesulfonyl and p-toluenesulfonyl; carbamate forming groups such as benzyloxycarbonyl, p chlorobenzyloxycarbonyl, p methoxybenzyloxycarbonyl, p- nitrobenzyloxycarbonyl, 2 nitrobenzyloxycarbonyl, p bromobenzyloxycarbonyl, 3,4- dimethoxybenzyloxycarbonyl, 3,5 dimethoxybenzyl oxycarbonyl, 2,4-dimethoxybenzyloxycarbonyl, 4 methoxybenzyloxycarbonyl, 2 nitro-4,5-dimethoxybenzyloxycarbonyl, 3,4,5 trimethoxybenzyloxycarbonyl, 1 (p biphenylyl) 1 methylethoxycarbonyl, a,a-dimethyl-3,5 dimethoxybenzyloxycarbonyl, benzhydryloxy carbon
  • substituents include, but are not limited to, alkyl, alkenyl, alkynyl, aryl, alkaryl, acyl, heteroaryl, heteroalkyl, heteroalkenyl, heteroalkynyl, heteroalkaryl, halogen, oxo, cyano, nitro, amino, alkamino, hydroxy, alkoxy, alkanoyl, carbonyl, carbamoyl, guanidinyl, amidinyl, ureido, any of the groups or moieties described above, and hetero versions of any of the groups or moieties described above.
  • Substituents include, but are not limited to, F, CI, methyl, phenyl, benzyl, OR, NR 2 , SR, SOR, S0 2 R, OCOR, NRCOR, NRCONR2, NRCOOR, OCONR2, RCO, COOR, alkyl-OOCR, SO3R, CONR2, SO2NR2, NRSO2NR2, CN, CF 3 , OCF3, R3S1, and NO2, wherein each R is, independently, H, alkyl, alkenyl, aryl, heteroalkyl, heteroalkenyl, or heteroaryl, and wherein two of the optional substituents on the same or adjacent atoms can be joined to form a fused, optionally substituted aromatic or nonaromatic, saturated or unsaturated ring which contains 3-8 members, or two of the optional substituents on the same atom can be joined to form an optionally substituted aromatic or nonaromatic, saturated or unsaturated ring which contains 3-8 members.
  • an optionally substituted group or moiety refers to a group or moiety (e.g., any one of the groups or moieties described above) in which one of the atoms (e.g., a hydrogen atom) is optionally replaced with another substituent.
  • an optionally substituted alkyl may be an optionally substituted methyl, in which a hydrogen atom of the methyl group is replaced by, e.g., OH.
  • a substituent on a heteroalkyl or its divalent counterpart, heteroalkylene may replace a hydrogen on a carbon or a hydrogen on a heteroatom such as N.
  • group -R-NH-R- may be substituted with an alkamide substituent, e.g., -R-N[(CH 2 C(0)N(CH 3 )2]-R.
  • an optional substituent is a noninterfering substituent.
  • a “noninterfering substituent” refers to a substituent that leaves the ability of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) to either bind to LPS or to kill or inhibit the growth of Gram-negative bacteria qualitatively intact. Thus, in some embodiments, the substituent may alter the degree of such activity.
  • a noninterfering substituent leaves the ability of a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) to kill or inhibit the growth of Gram-negative bacteria qualitatively intact as determined by measuring the minimum inhibitory concentration (MIC) against at least one Gram-negative bacteria as known in the art, wherein the MIC is 32 ⁇ g/mL or less.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • a noninterfering substituent leaves the ability of a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) to bind to LPS from the cell membrane of Gram-negative bacteria qualitatively intact, as determined by an LPS binding assay (e.g., see Example 109), wherein the compound shows a value of about 10% or greater displacement of a fluorogenic substrate at 250 ⁇ of the compound.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • the term "pharmaceutical composition” refers to a medicinal or pharmaceutical formulation that contains at least one active ingredient (e.g., a compound of any one of formulas (I)- (XXXXIX)) as well as one or more excipients and diluents to enable the active ingredient suitable for the method of administration.
  • the pharmaceutical composition of the present disclosure includes pharmaceutically acceptable components that are compatible with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
  • a pharmaceutically acceptable carrier refers to an excipient or diluent in a pharmaceutical composition.
  • a pharmaceutically acceptable carrier may be a vehicle capable of suspending or dissolving the active compound (e.g., a compound of any one of formulas (I)- (XXXXIX)).
  • the pharmaceutically acceptable carrier must be compatible with the other ingredients of the formulation and not deleterious to the recipient.
  • the pharmaceutically acceptable carrier must provide adequate pharmaceutical stability to a compound described herein.
  • the nature of the carrier differs with the mode of administration. For example, for oral administration, a solid carrier is preferred; for intravenous administration, an aqueous solution carrier (e.g., WFI, and/or a buffered solution) is generally used.
  • pharmaceutically acceptable salt represents salts of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) that are, within the scope of sound medical judgment, suitable for use in methods described herein without undue toxicity, irritation, and/or allergic response.
  • Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in: Pharmaceutical Salts: Properties, Selection, and Use (Eds. P.H. Stahl and C.G. Wermuth), Wiley-VCH, 2008. The salts can be prepared in situ during the final isolation and purification of the compounds described herein or separately by reacting the free base group with a suitable organic acid.
  • phosphate represents the group having the structure:
  • phosphoryl represents the group having the structure:
  • polar moiety refers to a portion, substituent, or functional group of a compound that has a chemical polarity induced by atoms with different electronegativity.
  • the polarity of a polar moiety is dependent on the electronegativity between atoms within the moiety and the asymmetry of the structure of the moiety.
  • a polar moiety contains one or more (e.g., 1 -4, 1 -3, 1 , 2, 3, or 4) heteroatoms independently selected from N, O, and S, which may induce chemical polarity in the moiety by having different electronegativity from carbon and hydrogen.
  • a polar moiety interacts with other polar or charged molecules.
  • a polar moiety may be optionally substituted alkamino, optionally substituted heteroalkyl (e.g., N- and/or O-containing
  • heteroalkyl -(CH2)4-carboxylic acid, -(CH2)3-carboxylic acid, -(CH2)2-carboxylic acid, -CH2-carboxylic acid), optionally substituted heterocycloalkyl (e.g., N- and/or O-containing heterocycloalkyl), or optionally substituted heteroaryl (e.g., N- and/or O-containing heteroaryl).
  • a polar moiety may -CH(CH 3 )OH, -CH2OH , -(CH 2 ) 2 CONH2, -CH2CONH2, -CH2COOH , or -(CH 2 ) 2 COOH.
  • substituents may transform an otherwise lipophilic moiety such optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heteroalkenyl, optionally substituted heteroalkynyl, or optionally substituted heteroaryl, or halo forms thereof, to a polar moiety with the addition of a substituent that imparts polarity, such as OH, COOH, COOR, or CON R2, in which R is H or C1 -C4 alkyl.
  • a polar moiety may be the side chain or a polar or charged amino acid residue (e.g., threonine, serine, glutamine, asparagine, arginine, lysine histidine, aspartic acid, and glutamic acid).
  • a polar moiety is the side chain of threonine.
  • polar moieties of the compounds described herein interact with the negatively charged portions of lipid A (e.g., phosphates of lipid A) when the compounds bind to the membrane of bacterial cells (e.g., Gram-negative bacterial cells). Due to its position on the cyclic heptapeptide, one or more of R 1 , R 12 , R 15 , R' 1 , R' 12 , and R' 15 may be a polar moiety.
  • polymyxin core means a cyclic heptapeptide having the structure:
  • polymyxin core attachment of the polymyxin core to the remainder of the compounds disclosed herein, including the linker and the second polymyxin core (e.g., the second cyclic heptapeptide).
  • positively charged moiety refers to a portion, substituent, or functional group of a compound that contains at least one positive charge.
  • a positively charged moiety contains one or more (e.g., 1 -4, 1 -3, 1 , 2, 3, or 4) heteroatoms independently selected from N, O, and S, for example.
  • a positively charged moiety may possess a pH-dependent positive charge, e.g., the moiety becomes a positively charged moiety at physiological pH (e.g., pH 7), such as -NH 3 + , -(CH 2 ) 4 NH 2 , -(CH 2 ) 3 NH 2 , -(CH 2 ) 2 NH 2 , -CH 2 NH 2 , -(CH 2 ) 4 N(CH 3 ) 2 ,
  • a positively charged moiety may be optionally substituted alkamino, optionally substituted heteroalkyl (e.g., optionally substituted heteroalkyl containing 1 -3 nitrogens; -(CH 2 )4-guanidinium, -(CH 2 ) 3 -guanidinium, -(CH 2 ) 2 -guanidinium, -CH 2 -guanidinium), optionally substituted heterocycloalkyl (e.g., optionally substituted heterocycloalkyl containing 1 -3 nitrogens), or optionally substituted heteroaryl (e.g., optionally substituted heteroaryl containing 1 -3
  • a positively charged moiety may be pH independent such
  • substituents may transform an otherwise lipophilic moiety such as optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heteroalkenyl, optionally substituted heteroalkynyl, or optionally substituted heteroaryl, or halo forms thereof, to a positively charged moiety with the addition of a substituent that imparts a positive charge or a pH dependent positive charge, such as guanidinyl, -NH 3 + , -NH 2 , -NH(CH 3 ), -N(CH 3 ) 2 , and/or -N(CH 3 ) 3 + .
  • a positively charged moiety may be the side chain of an amino acid residue (e.g., a natural or non-natural amino acid residue, such as a D- or L-amino acid residue, that is positively charged at physiological pH (e.g., pH 7), such as the side chain of a basic amino acid residue
  • an amino acid residue e.g., a natural or non-natural amino acid residue, such as a D- or L-amino acid residue, that is positively charged at physiological pH (e.g., pH 7), such as the side chain of a basic amino acid residue
  • positively charged moieties of the compounds described herein interact with the negatively charged portions of lipid A (e.g., phosphates of lipid A) when the compounds bind to the membrane of bacterial cells (e.g., Gram-negative bacterial cells). Due to its position on the cyclic heptapeptide, one or more of R 1 1 , R 13 , R 14 , R' 1 1 , R' 13 , and R' 14 may be a positively charged moiety.
  • protecting against refers to preventing a subject from developing a bacterial infection (e.g., a Gram-negative bacterial infection) or decreasing the risk that a subject may develop a bacterial infection (e.g., a Gram-negative bacterial infection).
  • Prophylactic drugs used in methods of protecting against a bacterial infection in a subject are often administered to the subject prior to any detection of the bacterial infection.
  • a subject e.g., a subject at risk of developing a bacterial infection
  • a compound described herein e.g., a compound having any one of formulas (l)-(XXXXIX)
  • a compound described herein e.g., a compound having any one of formulas (l)-(XXXXIX)
  • resistant strain of bacteria refers to a strain of bacteria (e.g., Gram- negative or Gram-positive bacteria) that is refractory to treatment with an antibiotic, such as an antibiotic described in Section IV of Detailed Description.
  • an antibiotic such as an antibiotic described in Section IV of Detailed Description.
  • Resistance may arise through natural resistance in certain types of bacteria, spontaneous random genetic mutations, and/or by inter- or intra-species horizontal transfer of resistance genes.
  • a resistant strain of bacteria contains a mcr- 1 gene and/or a mcr-2 gene.
  • a resistant strain of bacteria contains a mcr- 1 gene and/or a mcr-2 gene in combination with other antibiotic resistance genes.
  • a resistant strain of bacteria is a resistant strain of E. co// (e.g., E. coli BAA-2469).
  • subject can be a human, non-human primate, or other mammal, such as but not limited to dog, cat, horse, cow, pig, turkey, goat, fish, monkey, chicken, rat, mouse, and sheep.
  • substantially simultaneously refers to two or more events that occur at the same time or within a narrow time frame of each other.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • an antibacterial agent e.g., Iinezolid or tedizolid
  • the compound and the antibacterial agent may be administered substantially simultaneously, which means that the compound and the antibacterial agent are administered together (e.g., in one pharmaceutical composition) or separately but within a narrow time frame of each other, e.g., within 10 minutes, e.g., 1 0, 9, 8, 7, 6, 5, 4, 3, 2, or 1 minute, or 45, 30, 15, or 10 seconds of each other.
  • sulfonyl represents the group having the structure: v 3 ⁇ 4 v° ⁇ .
  • terapéuticaally effective amount refers to an amount, e.g., pharmaceutical dose, effective in inducing a desired effect in a subject or in treating a subject having a condition or disorder described herein (e.g., a bacterial infection (e.g., a Gram-negative bacterial infection)). It is also to be understood herein that a “therapeutically effective amount” may be interpreted as an amount giving a desired therapeutic and/or preventative effect, taken in one or more doses or in any dosage or route, and/or taken alone or in combination with other therapeutic agents (e.g., an antibacterial agent described herein).
  • an effective amount of a compound is, for example, an amount sufficient to prevent, slow down, or reverse the progression of the bacterial infection as compared to the response obtained without administration of the compound.
  • thiocarbonyl refers to a group having the structure:
  • FIGS. 1 A, 1 B, and 1 C are graphs showing the inhibition of NO production by Compound 16, Compound 1 9, and Compound 30.
  • FIG. 2 is a schematic illustrating a 96-well checkerboard synergy MIC plate layout.
  • FIG. 3 is graph showing the activity of Compound 150 in a Mouse Thigh Infection Model. Detailed Description
  • the disclosure features compounds, compositions, and methods for the treatment of bacterial infections (e.g., Gram-negative bacterial infections).
  • the compounds disclosed herein include two cyclic heptapeptide cores (e.g., polymyxin cores) linked to each other through a linker and/or one or two peptides (e.g., a peptide including a 1 -5 amino acid residue(s)).
  • the compounds can be used in the treatment of bacterial infections caused by Gram-negative bacteria.
  • one or more of the compounds described herein are used in combination with an antibacterial agent (e.g., linezolid or tedizolid (e.g., tedizolid phosphate)).
  • Bacteria cause bacterial infections and diseases such as tuberculosis, pneumonia, and foodborne illnesses. Bacteria may be categorized into two major types: Gram-positive bacteria and Gram-negative bacteria. Gram-positive bacteria possess a thick cell wall containing multiple layers of peptidoglycan and teichoic acids, while Gram-negative bacteria have a relatively thin cell wall containing fewer layers of peptidoglycan that are surrounded by a second lipid membrane containing
  • LPS lipopolysaccharides
  • lipoproteins lipoproteins.
  • LPS also called endotoxins, are composed of
  • Gram-positive bacteria include, but are not limited to, bacteria in the genus Streptococcus (e.g., Streptococcus pyogenes), bacteria in the genus Staphylococcus (e.g., Staphylococcus cohnii), bacteria in the genus Corynebacterium (e.g., Corynebacterium auris), bacteria in the genus Listeria (e.g., Listeria grayi), bacteria in the genus Bacillus (e.g., Bacillus aerius), and bacteria in the genus Clostridium (e.g., Clostridium acetium).
  • Streptococcus e.g., Streptococcus pyogenes
  • Staphylococcus e.g., Staphylococcus cohnii
  • Corynebacterium e.g., Corynebacterium auris
  • Listeria e.g
  • Gram-negative bacteria examples include, but are not limited to, bacteria in the genus Escherichia (e.g., Escherichia coli), bacteria in the genus Klebsiella (e.g., Klebsiella granulomatis, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella terrigena, and Klebsiella variicola), bacteria in the genus Acinetobacter (e.g., Acinetobacter baumannii,
  • Acinetobacter ca!coaceticus, Acinetobacter kookii, and Acinetobacter junin bacteria in the genus Pseudomonas (e.g., Pseudomonas aeruginosa), bacteria in the genus Neisseria (e.g., Neisseria gonorrhoeae), bacteria in the genus Yersinia (e.g., Yersinia pestis), bacteria in the genus Vibrio (e.g., Vibrio cholerae), bacteria in the genus Campylobacter (e.g., Campylobacter jejuni), and bacteria in the genus Salmonella (e.g., Salmonella enterica).
  • Pseudomonas e.g., Pseudomonas aeruginosa
  • Neisseria e.g., Neisseria gonorrhoeae
  • Bacteria may evolve to become more or fully resistant to antibiotics. Resistance may arise through natural resistance in certain types of bacteria, spontaneous random genetic mutations, and/or by inter- or intra-species horizontal transfer of resistance genes. Resistant bacteria are increasingly difficult to treat, requiring alternative medications or higher doses, which may be more costly or more toxic.
  • MDR bacteria Bacteria resistant to multiple antibiotics are referred to as multidrug resistant (MDR) bacteria.
  • the mcr- 1 gene encodes a phosphoethanolamine transferase (MCR-1 ) which confers resistance to colistin, a natural polymyxin, through modification of LPS. This is the first known horizontally- transferable resistance determinant for the polymyxin class of antibiotics.
  • MCR-1 phosphoethanolamine transferase
  • colistin a natural polymyxin
  • LPS LPS
  • This the first known horizontally- transferable resistance determinant for the polymyxin class of antibiotics.
  • the mcr- 1 gene has also been found in bacterial strains which already possess resistance to other classes of antibiotics, such as in carbapenem-resistant Enterobacteriaceae (CRE).
  • CRE carbapenem-resistant Enterobacteriaceae
  • An mcr- 1 plasmid resistance plasmid refers to a bacterial plasmid that carries mcr- 1 alone or in combination with other antibiotic resistance genes.
  • a mcr- 1 resistance plasmid refers to a bacterial plasmid that carries one or more antibiotic resistance genes.
  • mcr- 1 resistance plasmids include, but are not limited to, pHNSHP45, pMR051 6mcr, pESTMCR, pAF48, pAF23, pmcr1 -lncX4, pmcr1 -lncl2, pA31 -12, pVT553, plCBEC72Hmcr, pE15004, pE1501 5, and pE15017.
  • the mcr-2 gene also confers resistance to colistin.
  • the mcr-2 gene was identified in porcine and bovine colistin-resistance E.coli that did not contain mcr- 1 (Xavier et al., Euro Surveill 2 ⁇ (27), 2016).
  • the mcr-2 gene is a 1 ,617 bp phspoethanolamine transferase harbored on an lncX4 plasmid.
  • the mcr-2 gene has 76.7% nucleotide identity to mcr- 1.
  • mcr-2 resistance plasmid refers to a bacterial plasmid that carries mcr-2 alone or in combination with other antibiotic resistance genes.
  • a mcr-2 resistance plasmid refers to a bacterial plasmid that carries one or more antibiotic resistance genes. Mcr-2 resistance plasmids include, but are not limited to, pKP37-BE and pmcr2-lncX4.
  • the mcr-3 gene also confers resistance to colistin.
  • the mcr-3 gene is considered to include variants which encode an MCR-3 protein that confers resistance to cholistin, such as mcr-3 which encodes a protein having an amino acid substitution at V413A.
  • the mcr-3 gene was identified in cholistin-resistant E.coli isolated from swine (Clemente et al., 27 th ECCMID, Vienna, Austria, 2017).
  • the mcr3 gene is harbored on an lncX4 plasmid. Analysis of mcr-3 harboring plasmids from E.coli isolates shows that the mobile element harboring mcr-3 is the IS26 element.
  • a mcr-3 resistance plasmid refers to a bacterial plasmid that carries one or more antibiotic resistance genes.
  • E. coli BAA-2469 possesses the New Delhi metallo-p-lactamase (NDM-1 ) enzyme, which makes bacteria resistant to a broad range of ⁇ -lactam antibiotics. Additionally, E. coli BAA-2469 is also known to be resistatnt to penicillins (e.g., ticarcillin, ticarcillin/clavulanic acid, piperacillin, ampicillin, and ampicillin/sulbactam), cephalosporins (e.g., cefalotin, cefuroxime, cefuroxime, cefotetan, cefpodoxime, cefotaxime, ceftizoxime, cefazolin, cefoxitin, ceftazidime, ceftriaxone, and cefepime), carbapenems (e.g., doripenem, meropenem, ertapenem, imipenem), quinolones (e.g., nalidixic
  • a resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance.
  • a resistant strain of bacteria is a resistant strain of E. coli (e.g., E. coli BAA-2469).
  • synthetic compounds useful in the treatment of bacterial infections e.g., Gram-negative bacterial infections.
  • the disclosure provides compounds including dimers of cyclic heptapeptides joined to each other by way of a linker and/or one or two peptides (e.g., each peptide including a 1 -5 amino acid residue(s)) (e.g., two polymyxin cores joined to each other by way of a linker and/or one or two peptides).
  • a cyclic heptapeptide or polymyxin core refers to certain compounds that bind to LPS in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
  • cyclic heptapeptide or polymyxin core refers to certain compounds that kill or inhibit the growth of Gram-negative bacteria as determined by measuring the minimum inhibitory concentration (MIC) against at least one Gram-negative bacteria as known in the art, wherein the MIC is 32 ⁇ g/mL or less.
  • Cyclic heptapeptides are composed of, at least, amino acid residues, each of which may, independently, have a D- or L- configuration, assembled as a cyclic heptapeptide ring.
  • a cyclic heptapeptide includes seven natural or non-natural amino acid residues attached to each other in a closed ring. The ring contains six bonds formed by linking the carbon in the a-carboxyl group of one amino acid residue to the nitrogen in the a-amino group of the adjacent amino acid residue and one bond formed by linking the carbon in the a-carboxyl group of one amino acid residue to the nitrogen in the ⁇ - amino group in the side chain of the adjacent amino acid residue.
  • the nitrogen in the a-amino group of this amino acid residue does not participate directly in forming the ring and serves as the linking nitrogen (thus, referred to as the "linking nitrogen” herein) that links one cyclic heptapeptide or polymyxin core to another cyclic heptapeptide or polymyxin core by way of a linker and/or one or two peptides (e.g., a peptide including 1 -5 amino acid residue(s)).
  • dimers of cyclic heptapeptides e.g., dimers of polymyxin cores
  • one or two peptides e.g., a peptide including 1 -5 amino acid residue(s)
  • a peptide including one or more (e.g., 1 -5; 1 , 2, 3, 4, or 5) amino acid residues may be covalently attached to the linking nitrogen of the cyclic heptapeptide or the polymyxin core.
  • Cyclic heptapeptides or polymyxin cores may be derived from polymyxins (e.g., naturally existing polymyxins and non-natural polymyxins) and/or octapeptins (e.g., naturally existing octapeptins and non-natural octapeptins).
  • cyclic heptapeptides may be compounds described in Gallardo-Godoy et al., J. Med. Chem. 59:1068, 2016 (e.g., compounds 1 1 -41 in Table 1 of Gallardo-Godoy et al.), which is incorporated herein by reference in its entirety. Examples of some naturally existing polymyxins and their structures are shown in Table 1 .
  • compounds described herein bind to the cell membrane of Gram-negative bacteria (e.g., bind to LPS in the cell membrane of Gram-negative bacteria) to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
  • the initial association of the compounds with the bacterial cell membrane occurs through electrostatic interactions between the compounds and the anionic LPS in the outer membrane of Gram-negative bacteria, disrupting the arrangement of the cell membrane.
  • compounds described herein may bind to lipid A in the LPS. More specifically, compounds described herein may bind to one or both phosphate groups in lipid A.
  • antibiotic- resistant bacteria e.g., antibiotic-resistant, Gram-negative bacteria
  • compounds described herein may bind to multiple Gram-negative bacterial cells at the same time.
  • the binding of the compounds described herein to the LPS may also displace Mg 2+ and Ca 2+ cations that bridge adjacent LPS molecules, causing, e.g., membrane permeabilization, leakage of cellular molecules, inhibition of cellular respiration, and/or cell death.
  • Compounds described herein include a first cyclic heptapeptide and a second cyclic heptapeptide linked to each other at their linking nitrogens by way of a linker and/or one or two peptides (e.g., a peptide including 1 -5 amino acid residue(s)), e.g., compounds of any one of formulas (l)-(XXXXIX).
  • the first and second cyclic heptapeptides are the same.
  • the first and second cyclic heptapeptides are different.
  • Compounds described herein may be synthesized using available chemical synthesis techniques in the art.
  • available functional groups in the first and second cyclic heptapeptides and the linker e.g., amines, carboxylic acids, and/or hydroxyl groups, may be used in making the compounds described herein.
  • the linking nitrogen in a cyclic heptapeptide may form an amide bond with the carbon in a carboxylic acid group in the linker.
  • a peptide including one or more (e.g., 1 -5; 1 , 2, 3, 4, or 5) amino acid residues may be also be covalently attached to the linking nitrogen of the cyclic heptapeptide through forming an amide bond between the carbon in a carboxylic acid group in the peptide and the linking nitrogen.
  • a molecule may be derivatized using conventional chemical synthesis techniques that are well known in the art.
  • the compounds described herein contain one or more chiral centers.
  • the compounds include each of the isolated stereoisomeric forms as well as mixtures of stereoisomers in varying degrees of chiral purity, including racemic mixtures. It also encompasses the various diastereomers, enantiomers, and tautomers that can be formed.
  • M1 includes a first cyclic heptapeptide including a linking nitrogen
  • M2 includes a second cyclic heptapeptide including a linking nitrogen
  • L' is a linker covalently attached to the linking nitrogen in each of M1 and M2, and in which L' is not
  • L" is a remainder of L', and each of R' L and R L is, independently, C1 -C10 alkyl.
  • L' in the compound described by formula M2-L'-M1 is described by: -A2— L— A1- in which L is a remainder of L'; A1 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M1 or is absent; and A2 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M2 or is absent.
  • the disclosure provides a compound, or a pharmaceutically acceptable salt thereof, described by formula (II)
  • each of R 2 , R 3 , and R 4 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
  • each of R 5 , R 6 , and R 7 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
  • each of R 8 , R 9 , and R 10 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
  • each of R' 2 , R' 3 , and R' 4 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
  • each of R' 5 , R' 6 , and R' 7 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
  • each of R' 8 , R' 9 , and R' 10 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
  • the compound of formula (II) has at least one optionally substituted 5-8 membered ring formed by joining (i) R 2 , R 3 , and C 1 ; (ii) R 3 , R 4 , N 1 , and C 1 ; (iii) R 5 , R 6 , and C 2 ; (iv) R 6 , R 7 , N 2 , and C 2 ; (v) R 8 , R 9 , and C 3 ; (vi) R 9 , R 10 , N 3 , and C 3 ; (vii) R' 2 , R' 3 , and C' 1 ; (viii) R' 3 , R' 4 , N' 1 , and C' 1 ; (ix) R' 5 , R' 6 , and C' 2 ; (x) R' 6 , R' 7 , N' 2 , and C' 2 ; (xi) R' 8 , R' 9 , and C' 3 ; or (xiii
  • each of R 2 , R 3 , and R 4 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
  • R 2 , R 3 , and C 1 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R 4 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted
  • cycloalkenylene optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
  • each of R 5 , R 6 , and R 7 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
  • R 5 , R 6 , and C 2 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R 7 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted
  • cycloalkenylene optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
  • each of R 8 , R 9 , and R 10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
  • R 8 , R 9 , and C 3 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R 10 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted
  • cycloalkenylene optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
  • each of R' 2 , R' 3 , and R' 4 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
  • R' 2 , R' 3 , and C' 1 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R' 4 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene,
  • cycloalkenylene optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
  • each of R' 5 , R' 6 , and R' 7 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
  • R' 5 , R' 6 , and C' 2 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R' 7 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene,
  • cycloalkenylene optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
  • each of R' 8 , R' 9 , and R' 10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
  • R' 8 , R' 9 , and C' 3 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R' 10 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene,
  • cycloalkenylene optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
  • the disclosure provides a compound, or a pharmaceutically acceptable salt thereof, described by formula (III)
  • each of R 1 , R 12 , R' 1 , and R' 12 is, independently, a lipophilic moiety; each of R 1 1 , R 13 , R 14 , R' 1 1 , R' 13 , and R' 14 is, independently, optionally substituted C1 -C5 alkamino, a polar moiety, or a positively charged moiety; and each of R 15 and R' 15 is, independently, a polar moiety.
  • a lipophilic moiety is optionally substituted C1 -C20 alkyl, optionally substituted C5-C15 aryl, optionally substituted C6-C35 alkaryl, or optionally C3-C1 5 substituted heteroaryl.
  • a lipophilic moiety is C1 -C8 alkyl, methyl substituted C2-C4 alkyl, (C1 - C10)alkylene(C6)aryl, phenyl substituted (C1 -C10)alkylene(C6)aryl, or alkyl substituted C4-C9 heteroaryl.
  • a lipophilic moiety is benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or methyl substituted indolyl.
  • optionally substituted C1 -C5 alkamino is CH2CH2NH2.
  • a polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group. In some embodiments, a polar moiety is hydroxyl substituted C1 -C4 alkyl. In some embodiments, a polar moiety is CHCH3OH.
  • the disclosure provides a compound described by formula (IV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (V):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C
  • the disclosure provides a compound described by formula (VI):
  • each of R' 1 and R 1 is, independently, benzyl or CH 2 CH(CH 3 )2; each of R 2 , R 6 , R 8 , R' 2 , R' 6 , and R' 8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or
  • the disclosure provides a compound described by formula (VII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-
  • the disclosure provides a compound described by formula (VIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalka
  • the disclosure provides a compound described by formula (IX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or
  • the disclosure provides a compound described by formula (X):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof
  • the disclosure provides a compound described by formula (XI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XII):
  • each A 1 and A 2 is an independently selected amino acid
  • L is a linker that, when m is 1 , 2, 3, 4, or 5, is bound to a nitrogen atom in any A 1 and a nitrogen atom in any A 2
  • each m is independently 0, 1 , 2, 3, 4, or 5
  • Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XIII):
  • the disclosure provides a compound described by formula (XIV):
  • the disclosure provides a compound described by formula (XV):
  • the disclosure provides a compound described by formula (XVI):
  • each Y is independently -C(O)-, -S(O)-, -S(0) 2 -, or is absent;
  • R 1 is hydrogen, C1 -C10 alkyl, -N(R 3 R 4 ), or -OH;
  • R 2 is hydrogen, C1 -C10 alkyl, or -OH;
  • R 3 and R 4 are independently hydrogen or C1 -C10 alkyl; and
  • d is an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XVII):
  • the disclosure provides a compound described by formula (XVIII):
  • each A 1 and A 2 is an independently selected amino acid; e is an integer from 1 to 5; f is an integer from 1 to 5; each m is independently 0, 1 , 2, 3, 4, or 5; Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; and R 1 is hydrogen, C1 -C10 alkyl, -C(0)OR 2 , -C(0)-(CH 2 OCH2)d-heterocyclic, and -C(0)R 2 ; R 2 is C1 -C10 alkyl, benzyl, -CH 2 (biphenyl), -(CH2CH 2 0) g -R 3 ; R 3 is -(CH 2 )iNR 4 R 5 and -(CH 2 )i-(C 2 -C 8 alkynyl); R 4 is hydrogen or C1 -C10 alkyl; R 5 is hydrogen or C1 -C10 alkyl; and d is
  • the disclosure provides a compound described by formula (XIX):
  • the disclosure provides a compound described by formula (XX):
  • the disclosure provides a compound described by formula (XXI):
  • each A 1 and A 2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXII):
  • each A 1 and A 2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXIII):
  • each A 1 and A 2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXIV):
  • each A 1 and A 2 is an independently selected amino acid
  • R 1 is hydrogen or C1 -C10 alkyl
  • each m is independently 0, 1 , 2, 3, 4, or 5
  • Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are each independently selected from the side chain of an amino acid
  • d is an integer from 1 to 6; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXV):
  • the disclosure provides a compound described by formula (XXVI):
  • each of R' 1 and R 1 is, independently, benzyl or CH 2 CH(CH 3 )2; each of R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R' 2 , R' 3 , R' 4 , R' 5 , R' 6 , R' 7 , R' 8 , R' 9 , and R' 10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted
  • heterocycloalkenyl optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring; each of a', b', c', a, b, and c is, independently, 0 or 1 ; each of N 1 , N 2 , N 3 , N 4 , N' 1 , N' 2 , N' 3 , and N' 4 is a nitrogen atom; each of C 1 , C 2 , C 3 , C' 1 , C' 2 , and C' 3 is a carbon atom; L is a linker comprising at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted
  • the disclosure provides a compound described by formula (XXVII):
  • each of R' 1 and R 1 is, independently, benzyl or CH 2 CH(CH 3 )2; each of R 2 , R 6 , R 8 , R' 2 , R' 6 , and R' 8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C
  • the disclosure provides a compound described by formula (XXVIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optional
  • the disclosure provides a compound described by formula (XXIX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R 8 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6
  • the disclosure provides a compound described by formula (XXX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , and R 8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroal
  • the disclosure provides a compound described by formula (XXXI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , R' 2 , and R' 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C
  • the disclosure provides a compound described by formula (XXXII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 , R 6 , and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 hetero
  • the disclosure provides a compound described by formula (XXXIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 and R 6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a
  • the disclosure provides a compound described by formula (XXXIV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; each of R 2 and R' 2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or
  • the disclosure provides a compound described by formula (XXXV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2;
  • R 2 is a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXVI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXVII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXVIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXIV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 cycloalkylene or an optionally substituted C6 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXV):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXVI):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXVII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXVIII):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises at least two optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
  • the disclosure provides a compound described by formula (XXXXIX):
  • each of R' 1 and R 1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 arylene or an optionally substituted C5 heteroarylene, or a pharmaceutically acceptable salt thereof.
  • a linker refers to a linkage or connection between two or more components.
  • the compounds described herein include a linker linking two cyclic heptapeptides in a cyclic heptapeptide dimer.
  • a linker provides space, rigidity, and/or flexibility between the two cyclic heptapeptides.
  • a linker may be a bond, e.g., a covalent bond, e.g., an amide bond, a disulfide bond, a N-N bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation.
  • a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXIX)) includes no more than 100 atoms (e.g., 1 -2, 1 -4, 1 -6, 1 -8, 1-10, 1 -12, 1 -14, 1 -16, 1-18, 1 -20, 1 -25, 1 -30,
  • a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas
  • (XXVI)-(XXXXIX)) includes no more than 100 non-hydrogen atoms (e.g., 1-2, 1-4, 1-6, 1-8, 1-10, 1-12, 1-
  • the backbone of a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXIX)) includes no more than 100 atoms (e.g., 1 -2, 1 -4, 1 -6, 1 -8, 1 -10, 1 -12, 1 -14, 1 -1 6, 1 -18, 1 -20, 1 -25, 1 -30, 1 -35, 1 -40, 1 -45, 1 -50, 1 -55, 1 -60, 1 -65, 1 -70, 1 -75, 1 -80, 1 -85, 1 -90, 1 -95, 1 -97, or 1 -99 atom(s); 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24, 22, 20, 18, 16, 14, 12,
  • the "backbone" of a linker refers to the atoms in the linker that together form the shortest path from one part of the compound to another part of the compound.
  • the atoms in the backbone of the linker are directly involved in linking one part of the compound to another part of the compound.
  • hydrogen atoms attached to carbons in the backbone of the linker are not considered as directly involved in linking one part of the compound to another part of the compound.
  • Molecules that may be used to make linkers (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) include at least two functional groups, e.g., two carboxylic acid groups.
  • the first functional group may form a covalent linkage with the first cyclic heptapeptide and the second functional group may form a covalent linkage with the second cyclic heptapeptide.
  • the linker when the first and/or second cyclic heptapeptide is attached to a peptide (e.g., a peptide including a 1 -5 amino acid residue(s)) at the linking nitrogen, the linker may form a covalent linkage with the peptide.
  • dicarboxylic acid molecules may be used as linkers (e.g., a dicarboxylic acid linker), in which the first carboxylic acid may form a covalent linkage with the linking nitrogen of the first cyclic heptapeptide and the second carboxylic acid may form a covalent linkage with the linking nitrogen of the second cyclic heptapeptide.
  • the first and/or second cyclic heptapeptide when the first and/or second cyclic heptapeptide is attached to a peptide (e.g., a peptide including a 1 -5 amino acid residue(s)) at the linking nitrogen, the first carboxylic acid in a dicarboxylic acid linker may form a covalent linkage with the terminal amine group at the end of the peptide that is attached to the first cyclic heptapeptide and the second carboxylic acid in the dicarboxylic acid linker may form a covalent linkage with the terminal amine group at the end of the peptide that is attached to the second cyclic heptapeptide.
  • a peptide e.g., a peptide including a 1 -5 amino acid residue(s)
  • a molecule containing one or more sulfonic acid groups may be used to form a linker, in which the sulfonic acid group may form a sulfonamide linkage with the linking nitrogen in a cyclic heptapeptide.
  • a molecule containing one or more isocyanate groups may be used to form a linker, in which the isocyanate group may form a urea linkage with the linking nitrogen in a cyclic heptapeptide.
  • a molecule containing one or more haloalkyl groups may be used to form a linker, in which the haloalkyl group may form a covalent linkage, e.g., C-N and C-0 linkages, with a cyclic heptapeptide.
  • a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXIX)) may comprise a synthetic group derived from, e.g., a synthetic polymer (e.g., a polyethylene glycol (PEG) polymer).
  • a linker may comprise one or more amino acid residues.
  • a linker may be an amino acid sequence (e.g., a 1 -25 amino acid, 1 -10 amino acid, 1 -9 amino acid, 1 -8 amino acid, 1 -7 amino acid, 1 -6 amino acid, 1 -5 amino acid, 1 -4 amino acid, 1 -3 amino acid, 1 -2 amino acid, or 1 amino acid sequence).
  • amino acid sequence e.g., a 1 -25 amino acid, 1 -10 amino acid, 1 -9 amino acid, 1 -8 amino acid, 1 -7 amino acid, 1 -6 amino acid, 1 -5 amino acid, 1 -4 amino acid, 1 -3 amino acid, 1 -2 amino acid, or 1 amino acid sequence.
  • a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) may include one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene (e.g., a PEG unit), optionally substituted C2-C20 alkenylene (e.g., C2 alkenylene), optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20
  • heteroalkynylene optionally substituted C3-C20 cycloalkylene (e.g., cyclopropylene, cyclobutylene), optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene (e.g., C6 arylene), optionally substituted C3-C15 heteroarylene (e.g., imidazole, pyridine), O, S, NR' (R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C2- C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C
  • each of U 1 , U 2 , U 3 , and U 4 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2- C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C
  • L in any one of formulas (XXVI)-(XXXXIX) is described by formula (L-2):
  • I 1 is a bond attached to N' 1 , N' 2 , N' 3 , or N' 4 ;
  • I 2 is a bond attached to N 1 , N 2 , N 3 , or N 4 ;
  • Covalent conjugation of two or more components in a compound using a linker may be accomplished using well-known organic chemical synthesis techniques and methods.
  • Complementary functional groups on two components may react with each other to form a covalent bond.
  • Examples of complementary reactive functional groups include, but are not limited to, e.g., amine and activated carboxylic acid, thiol and maleimide, activated sulfonic acid and amine, isocyanate and amine, azide and alkyne, and alkene and tetrazine.
  • amino-reactive acylating groups include, e.g., (i) an isocyanate and an isothiocyanate; (ii) a sulfonyl chloride; (iii) an acid halide; (iv) an active ester, e.g., a nitrophenylester or N- hydroxysuccinimidyl ester; (v) an acid anhydride, e.g., a mixed, symmetrical, or N-carboxyanhydride; (vi) an acylazide; and (vii) an imidoester. Aldehydes and ketones may be reacted with amines to form Schiff's bases, which may be stabilized through reductive amination.
  • one or more antibacterial agents may be administered in combination (e.g., administered substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions) or administered separately at different times) with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
  • Antibacterial agents may be grouped into several classes, e.g., quinolones, carbapenems, macrolides, DHFR inhibitors, aminoglycosides, ansamycins (e.g., geldanamycin, herimycin, and rifaximin), carbacephem (e.g., loracarbef), cephalosporins (e.g., cefadroxil, cefaolin, cefalotin, cefalothin, cephalexin, e.g., cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefdinir, cefditoren,
  • quinolones e.g., geldanamycin, herimycin, and rifaximin
  • carbacephem e.g., loracarbef
  • cephalosporins e.g., cefadroxil, cefaolin, ce
  • cefoperazone cefotaxime, cefpodoxime, ceftazidime, and ceftobiprole
  • glycopeptides e.g., teicoplanin, vancomycin, telavancin, dalbavancin, and oritavancin
  • lincosamides e.g., clindamycin and lincomycin
  • lipopeptides e.g., daptomycin
  • monobactams e.g., aztreonam
  • nitrofurans e.g., furazolidone and nitrofurantoin
  • oxazolidinones pleuromutilins
  • penicillins , sulfonamides, and tetracyclines (e.g., eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, and tetracycline).
  • Quinolones include, but are not limited to, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, and temafloxacin.
  • Carbapenems include, but are not limited to, ertapenem, doripenem,
  • Macrolides include, but are not limited to, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, and spiramycin.
  • a macrolide is solithromycin.
  • DHFR inhibitors include, but are not limited to, diaminoquinazoline, diaminopyrroloquinazoline, diaminopyrimidine, diaminopteridine, and diaminotriazines.
  • Aminoglycosides include, but are not limited to, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, and spectinomycin.
  • Oxazolidinones include, but are not limited to, Iinezolid, tedizolid, posizolid, radezolid, and furazolidone.
  • Pleuromutilins include, but are not limited to, rumblemulin, valnemulin, tiamulin, azamulin, and lefamulin.
  • Penicillins include, but are not limited to, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, penicillin G, temocillin, and ticarcillin.
  • Sulfonamides include, but are not limited to, mafenide,
  • sulfacetamide sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (Co-trimoxazole) (TMP-SMX), and sulfonamidochrysoidine.
  • TMP-SMX trimethoprim-sulfamethoxazole
  • the antibacterial agent used in combination with a compound described herein is selected from the group consisting of Iinezolid, tedizolid, posizolid, radezolid, rumblemulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem,
  • the antibacterial agent used in combination with a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • solithromycin e.g., a compound of any one of formulas (l)-(XXXXIX)
  • Methods described herein include, e.g., methods of protecting against or treating a bacterial infection (e.g., a Gram-negative bacterial infection) in a subject and methods of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria (e.g., Gram-negative bacteria).
  • a method of treating a bacterial infection (e.g., a Gram-negative bacterial infection) in a subject includes administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof.
  • the bacterial infection is caused by Gram- negative bacteria.
  • the bacterial infection is caused by a resistant strain of bacteria.
  • the resistant strain of bacteria is a resistant strain of E. coli.
  • a method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria includes contacting the bacteria (e.g., Gram-negative bacteria) or a site susceptible to bacterial growth (e.g., Gram-negative bacterial growth) with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof.
  • the bacteria in this method is Gram-negative bacteria.
  • the bacteria in this method is a resistant strain of bacteria.
  • methods described herein also include methods of protecting against or treating sepsis in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)). In some embodiments, the method further includes administering to the subject an antibacterial agent. Methods described herein also include methods of preventing LPS in Gram- negative bacteria (e.g., a resistant strain of Gram-negative bacteria or a resistant strain of E. coli (e.g., E. coli BAA-2469)) from activating a immune system in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
  • Gram- negative bacteria e.g., a resistant strain of Gram-negative bacteria or a resistant strain of E. coli (e.g., E. coli BAA-2469)
  • the method prevents LPS from activating a macrophage. In some embodiments, the method further includes administering to the subject an antibacterial agent.
  • a compound used in any methods described herein e.g., a compound of any one of formulas (l)-(XXXXIX) may bind to LPS in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
  • the methods described herein may further include administering to the subject an antibacterial agent in addition to a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
  • Methods described herein also include methods of protecting against or treating a bacterial infection in a subject by administering to the subject (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
  • Methods described herein also include methods of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria, by contacting the bacteria or a site susceptible to bacterial growth with (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • the compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • the antibacterial agent is administered first, followed by administering of the compound described herein alone.
  • the compound described herein and the antibacterial agent are administered substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions).
  • the compound described herein or the antibacterial agent is administered first, followed by administering of the compound described herein and the antibacterial agent substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions).
  • the compound described herein and the antibacterial agent are administered first substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions), followed by administering of the compound described herein or the antibacterial agent alone.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • an antibacterial agent e.g., a compound of any one of formulas (l)-(XXXXIX)
  • the MIC of each of the compound and the antibacterial agent may be lower than the MIC of each of the compound and the antibacterial agent when each is used alone in a treatment regimen.
  • a compound described herein may be formulated in a pharmaceutical composition for use in the methods described herein.
  • a compound described herein may be formulated in a pharmaceutical composition alone.
  • a compound described herein may be formulated in combination with an antibacterial agent in a pharmaceutical composition.
  • the pharmaceutical composition includes a compound described herein (e.g., a compound described by any one of formulas (l)-(XXXXIX)) and pharmaceutically acceptable carriers and excipients. Acceptable carriers and excipients in the pharmaceutical compositions are nontoxic to recipients at the dosages and concentrations employed.
  • Acceptable carriers and excipients may include buffers such as phosphate, citrate, HEPES, and TAE, antioxidants such as ascorbic acid and methionine, preservatives such as hexamethonium chloride, octadecyldimethylbenzyl ammonium chloride, resorcinol, and benzalkonium chloride, proteins such as human serum albumin, gelatin, dextran, and immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acid residues such as glycine, glutamine, histidine, and lysine, and carbohydrates such as glucose, mannose, sucrose, and sorbitol.
  • buffers such as phosphate, citrate, HEPES, and TAE
  • antioxidants such as ascorbic acid and methionine
  • preservatives such as hexamethonium chloride, octadecyldimethylbenzyl ammonium chloride,
  • excipients examples include, but are not limited to, antiadherents, binders, coatings, compression aids, disintegrants, dyes, emollients, emulsifiers, fillers (diluents), film formers or coatings, flavors, fragrances, glidants (flow enhancers), lubricants, sorbents, suspensing or dispersing agents, or sweeteners.
  • excipients include, but are not limited to: butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, croscarmellose, crosslinked polyvinyl pyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine,
  • BHT butylated hydroxytoluene
  • the compounds herein may have ionizable groups so as to be capable of preparation as pharmaceutically acceptable salts.
  • These salts may be acid addition salts involving inorganic or organic acids or the salts may, in the case of acidic forms of the compounds herein be prepared from inorganic or organic bases.
  • the compounds are prepared or used as pharmaceutically acceptable salts prepared as addition products of pharmaceutically acceptable acids or bases.
  • Suitable pharmaceutically acceptable acids and bases are well-known in the art, such as hydrochloric, sulphuric, hydrobromic, acetic, lactic, citric, or tartaric acids for forming acid addition salts, and potassium hydroxide, sodium hydroxide, ammonium hydroxide, caffeine, various amines, and the like for forming basic salts. Methods for preparation of the appropriate salts are well-established in the art.
  • Representative acid addition salts include, but are not limited to, acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate,
  • alkali or alkaline earth metal salts include, but are not limited to, sodium, lithium, potassium, calcium, and magnesium, as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, and ethylamine.
  • a compound e.g., a compound of any one of formulas (l)-(XXXXIX)
  • a pharmaceutical composition thereof may be formulated to be administered intramuscularly, intravenously (e.g., as a sterile solution and in a solvent system suitable for intravenous use), intradermal ⁇ , intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleural ⁇ , intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally (e.g., a tablet, capsule, caplet, gelcap, or syrup), topically (e.g., as a cream, gel,
  • a compound herein or a pharmaceutical composition thereof may be in the form of, e.g., tablets, capsules, pills, powders, granulates, suspensions, emulsions, solutions, gels including hydrogels, pastes, ointments, creams, plasters, drenches, osmotic delivery devices, suppositories, enemas, injectables, implants, sprays, preparations suitable for iontophoretic delivery, or aerosols.
  • the compositions may be formulated according to conventional pharmaceutical practice.
  • a compound described herein may be formulated in a variety of ways that are known in the art.
  • a compound described herein can be formulated as pharmaceutical or veterinary compositions.
  • a compound described herein is formulated in ways consonant with these parameters.
  • a summary of such techniques is found in Remington: The Science and Practice of Pharmacy, 22nd Edition, Lippincott Williams & Wilkins (2012); and Encyclopedia of Pharmaceutical Technology, 4th Edition, J. Swarbrick and J. C. Boylan, Marcel Dekker, New York (2013), each of which is incorporated herein by reference.
  • Formulations may be prepared in a manner suitable for systemic administration or topical or local administration.
  • Systemic formulations include those designed for injection (e.g., intramuscular, intravenous or subcutaneous injection) or may be prepared for transdermal, transmucosal, or oral administration.
  • the formulation will generally include a diluent as well as, in some cases, adjuvants, buffers, and preservatives.
  • the compounds can be administered also in liposomal compositions or as microemulsions.
  • Systemic administration may also include relatively noninvasive methods such as the use of suppositories, transdermal patches, transmucosal delivery and intranasal administration.
  • Oral administration is also suitable for compounds herein. Suitable forms include syrups, capsules, and tablets, as is understood in the art.
  • compositions can be administered parenterally in the form of an injectable formulation.
  • Pharmaceutical compositions for injection can be formulated using a sterile solution or any pharmaceutically acceptable liquid as a vehicle.
  • Formulations may be prepared as solid forms suitable for solution or suspension in liquid prior to injection or as emulsions.
  • Pharmaceutically acceptable vehicles include, but are not limited to, sterile water, physiological saline, and cell culture media (e.g., Dulbecco's Modified Eagle Medium (DMEM), a-Modified Eagles Medium (a-MEM), F-12 medium).
  • DMEM Dulbecco's Modified Eagle Medium
  • a-MEM a-Modified Eagles Medium
  • F-12 medium e.g., F-12 medium.
  • Such injectable compositions may also contain amounts of nontoxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, such as sodium acetate and sorbitan monolaurate.
  • Formulation methods are known in the art, see e.g
  • compositions can be prepared in the form of an oral formulation.
  • Formulations for oral use include tablets containing the active ingredient(s) in a mixture with non-toxic pharmaceutically acceptable excipients.
  • excipients may be, for example, inert diluents or fillers (e.g., sucrose, sorbitol, sugar, mannitol, microcrystalline cellulose, starches including potato starch, calcium carbonate, sodium chloride, lactose, calcium phosphate, calcium sulfate, or sodium phosphate); granulating and disintegrating agents (e.g., cellulose derivatives including microcrystalline cellulose, starches including potato starch, croscarmellose sodium, alginates, or alginic acid); binding agents (e.g., sucrose, glucose, sorbitol, acacia, alginic acid, sodium alginate, gelatin, starch, pregelatinized starch, microcrystalline cellulose, magnesium aluminum silicate, carboxymethylcellulose sodium,
  • inert diluents or fillers e.g.
  • methylcellulose hydroxypropyl methylcellulose, ethylcellulose, polyvinylpyrrolidone, or polyethylene glycol
  • lubricating agents e.g., magnesium stearate, zinc stearate, stearic acid, silicas, hydrogenated vegetable oils, or talc.
  • Formulations for oral use may also be provided as chewable tablets, or as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin), or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example, peanut oil, liquid paraffin, or olive oil.
  • an inert solid diluent e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin
  • water or an oil medium for example, peanut oil, liquid paraffin, or olive oil.
  • Powders, granulates, and pellets may be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, e.g., a mixer, a fluid bed apparatus or a spray drying equipment.
  • compositions for oral formulations include, but are not limited to, colorants, flavoring agents, plasticizers, humectants, and buffering agents.
  • Formulations for oral use may also be provided as chewable tablets, or as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin), or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example, peanut oil, liquid paraffin, or olive oil.
  • Powders, granulates, and pellets may be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, e.g., a mixer, a fluid bed apparatus or a spray drying equipment.
  • Dissolution or diffusion controlled release of a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • a pharmaceutical composition thereof can be achieved by appropriate coating of a tablet, capsule, pellet, or granulate formulation of the compound, or by incorporating the compound into an appropriate matrix.
  • a controlled release coating may include one or more of the coating substances mentioned above and/or, e.g., shellac, beeswax, glycowax, castor wax, carnauba wax, stearyl alcohol, glyceryl monostearate, glyceryl distearate, glycerol palmitostearate, ethylcellulose, acrylic resins, dl-polylactic acid, cellulose acetate butyrate, polyvinyl chloride, polyvinyl acetate, vinyl pyrrolidone, polyethylene, polymethacrylate, methylmethacrylate, 2-hydroxymethacrylate, methacrylate hydrogels, 1 ,3 butylene glycol, ethylene glycol methacrylate, and/or polyethylene glycols.
  • the matrix material may also include, e.g., hydrated
  • methylcellulose methylcellulose, carnauba wax and stearyl alcohol, carbopol 934, silicone, glyceryl tristearate, methyl acrylate-methyl methacrylate, polyvinyl chloride, polyethylene, and/or halogenated fluorocarbon.
  • the pharmaceutical composition may be formed in a unit dose form as needed.
  • the amount of active component, e.g., a compound described herein, included in the pharmaceutical compositions are such that a suitable dose within the designated range is provided (e.g., a dose within the range of 0.01 - 100 mg/kg of body weight).
  • compounds herein may be administered by any appropriate route for treating or protecting against a bacterial infection (e.g., a Gram-negative bacterial infection), or for preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria (e.g., Gram- negative bacteria).
  • a bacterial infection e.g., a Gram-negative bacterial infection
  • Compounds described herein may be administered to humans, domestic pets, livestock, or other animals with a pharmaceutically acceptable diluent, carrier, or excipient.
  • administering comprises administration of any of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) or compositions intramuscularly, intravenously (e.g., as a sterile solution and in a solvent system suitable for intravenous use), intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleural ⁇ , intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally (e.g., a tablet, capsule, caplet, gelcap, or syrup), topically (e.g., as a cream, gel, lotion, or ointment), locally, by inhalation, by injection, or by in
  • the dosage of a compound described herein e.g., a compound of any one of formulas (I)- (XXXXIX)
  • a pharmaceutical compositions thereof depends on factors including the route of administration, the disease to be treated (e.g., the extent and/or condition of the bacterial infection), and physical characteristics, e.g., age, weight, general health, of the subject.
  • the amount of the compound or the pharmaceutical composition thereof contained within a single dose may be an amount that effectively prevents, delays, or treats the bacterial infection without inducing significant toxicity.
  • a pharmaceutical composition may include a dosage of a compound described herein ranging from 0.01 to 500 mg/kg (e.g., 0.01 , 0.1 , 0.2, 0.3, 0.4, 0.5, 1 , 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 200, 250, 300, 350, 400, 450, or 500 mg/kg) and, in a more specific embodiment, about 0.1 to about 30 mg/kg and, in a more specific embodiment, about 1 to about 30 mg/kg.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • an antibacterial agent are administered together (e.g., substantially simultaneously in the same or separate
  • the dosage needed of the compound described herein may be lower than the dosage needed of the compound if the compound was used alone in a treatment regimen.
  • a compound described herein e.g., a compound of any one of formulas (l)-(XXXXIX)
  • a pharmaceutical composition thereof may be administered to a subject in need thereof, for example, one or more times (e.g., 1 -10 times or more; 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 times) daily, weekly, monthly, biannually, annually, or as medically necessary. Dosages may be provided in either a single or multiple dosage regimens. The timing between administrations may decrease as the medical condition improves or increase as the health of the patient declines. The dosage and frequency of administration may be adapted by the physician in accordance with conventional factors such as the extent of the infection and different parameters of the subject.
  • Cyclic heptapeptides that comprise residues M1 and M2 may be prepared by synthesis using solid phase peptide methods or by solution phase methods. Alternately, the cyclic heptapeptides that comprise residues M1 and M2 may be derived from certain compounds known as polymyxins or from octapeptins which may be derived from fermentation sources or be synthetic. The protected M1 and M2 residues may be obtained by first protection of the polymyxin or octapeptin followed by enzymatic hydrolysis (e.g. with savinase or other enzymes known to those skilled in the art).
  • the cyclic heptapeptides may be optionally derivatized with 1 , 2 or 3 amino acids which may be the same or different.
  • a suitable linker group L the two halves which may be the same or different, may be coupled and after deprotection, give the compounds of the immediate disclosure.
  • the linker group L' may be prepared from the individual amino acid groups and L by methods known to those in the art. L' may be built up sequentially or by a convergent synthesis and then coupled to the cyclic heptapeptides that comprise the residues M1 and M2. After deprotection, the compounds of the immediate disclosure may be obtained.
  • A1 -M1 or A2-M2 may be derived from a polymyxin or octapeptin precursor by first protection followed by enzymatic hydrolysis (e.g. with papain). Subsequent coupling with L provides the compounds of the immediate disclosure.
  • the cyclic heptapeptides that comprise the residues M1 and M2 may be coupled directly with L to give the compounds of the immediate disclosure.
  • Preparative HPLC was performed using the following: Teledyne Isco HP C18, 50g column. Eluent: CH3CN/H2O/ 0.1 % formic acid or 0.1 % trifluoroacetic acid; various linear gradients as necessary at 40 mL/min on an Isco Combiflash Rf LC unit, or Isco EZ prep HPLC, with UV Detection at 220 and 254 nm on a Luna 5 micron C18, 100 A, AXIA 100 x 30 mm.
  • HRES-LC/MS High resolution liquid chromatography mass spectrometry
  • a gradient of 0.1 % formic acid in water (A) and 0.1 % formic acid in acetonitrile (B) was run from 15%B to 95% over 10 min using a 1 00 x 2.1 mm 1 .7 ⁇ Phenomenex Kinetex C18 column at 40 °C.
  • Liquid chromatography mass spectrometry was performed using an Agilent 6120 mass spectrometer an electrospray probe coupled with an Agilent 1260 HPLC system with a variable wavelength detector set to either 220 nm or 254 nm.
  • a gradient of 0.1 % formic acid in water (A) and 0.1 % formic acid in acetonitrile (B) was run from 15%B to 99% over 3.5 min using a 50x3.0 mm 2.6 ⁇ Phenomenex Gemini-NX column at 30 °C.
  • Colistin sulfate (5.0 g, 3.95 mmol) was dissolved in acetonitrile (50 mL) and water (25 mL) and stirred at room temperature for 10 minutes. Triethylamine (3.2 mL, 23.0 mmol) was added and the mixture stirred for a further 10 minutes. Di-tert-butyl dicarbonate (5.0 g, 23.0 mmol) was subsequently added in one portion and the mixture stirred for 16 hours. Savinase (Novozymes) (15 mL) was then added, followed by 4 M sodium hydroxide solution (0.5 mL) and the reaction mixture stirred at room temperature for 5 days. The mixture was diluted with ethyl acetate and water.
  • Colistin sulfate (50.0 g, 39.5 mmol) was dissolved in acetonitrile (500 mL, 10V) and water (250 mL, 5V) and stirred at room temperature for 10 mins.
  • TEA (24.2 g, 6.0eq) was added and the mixture stirred for a further 10 mins.
  • Di-tert-butyl dicarbonate (52.2 g, 6.0 eq) was subsequently added in one portion and the mixture stirred for 29 hrs.
  • LCMS showed material no being detected.
  • Savinase 150 mL was then added. The pH of the resulting mixture was adjusted to 9.0 with aq 4M sodium hydroxide solution (5 mL) and the reaction mixture stirred at 25°C.
  • Polymyxin B (100 g, 72.2 mmol) was dissolved in acetonitrile (1000 mL, 10V) and water (500 mL, 5V) and stirred at room temperature for 10 mins.
  • TEA 58.5 g, 8.0 eq
  • Di-tert-butyl dicarbonate (94.6 g, 6.0eq) was subsequently added in one portion and the mixture stirred for 6 hrs at 20 °C.
  • Savinase (300 mL) was then added. The pH of the resulting mixture was adjusted to 9.0 with aq 4M sodium hydroxide solution (1 0 mL) and the reaction mixture stirred at 25°C.
  • lnt-5 was prepared from lnt-3 and Z-Thr-OH in a manner similar to that described for lnt-6. Yield 73%.
  • LC/MS ((M+2H)/2) 565.8 (loss of 2 Boc groups on LC/MS).
  • Colistin sulfate (5 g) was dissolved in phosphate buffer (1 liter, pH 7, 25 mM), and KCI (1 .5g), EDTA (500 mg), Cysteine-HCI (2g) and Immobilised papain (10 mL, Thermofisher, 16-40 BAEE/mg before immobilisation) was added then the pH was brought back to 7 with potassium phosphate, dibasic. The reaction was shaken at 37 S C for 72 hours. The solids were removed by filtration and the aqueous reaction mixture was lyophilized.
  • Step b Selective protection of polymyxin E nonapeptide to tetra-Boc polymyxin E nonapeptide (lnt-5)
  • LC/MS ((M+2H)/2) 649.4 (Cbz protected intermediate, loss of 2 boc groups on LC/MS).
  • the Cbz protected intermediate was taken up in methanol (10 mL) and stirred in the presence of 5% Pd/C (40 mg) under 1 atmosphere of hydrogen gas for 45 minutes.
  • the mixture was filtered and applied to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient).
  • the pure fractions were lyophilized to afford 0.187 g of the title compound as a white solid. Yield: 78%, 2 steps.
  • LC/MS ((M+2H)/2) 582.4 (artefactual loss of 2 Boc groups on LC/MS).
  • Tetra-Boc polymyxin B nonapeptide may be prepared from polymyxin B via polymyxin B nonapeptide (PMBN) in a manner similar to that described in Example 5, Procedure B.
  • PMBN polymyxin B nonapeptide
  • Penta-Boc polymyxin E decapeptide was prepared analogously to penta-Boc polymyxin B decapeptide (see Example 8), except that polymyxin E was substituted for polymyxin B as the starting material.
  • Penta-Boc polymyxin E undecapeptide was prepared analogously to penta-Boc polymyxin B undecapeptide (see Example 1 0), except that polymyxin E decapeptide was substituted for polymyxin B decapeptide as the starting material.
  • Step c Preparation of dibenzyl 14-(2-(dimethylamino)-2-oxoethyl)-4,12,16,24-tetraoxo-8,20- dioxa-5,1 1 ,14,17,23-pentaazaheptacosane-1 ,27-dioate
  • Step b Synthesis of 2,2'-((2-(octylamino -2-oxoethyl)azanediyl)diacetic acid
  • Step c Synthesis of dibenzyl 14-(2-(octylamino)-2-oxoethyl)-4,12,16,24-tetraoxo-8,20- dioxa-5,11 ,14, -pentaazaheptacosane-1 ,27-dioate
  • 2,2'-((2-(octylamino)-2-oxoethyl)azanediyl)diacetic acid 150 mg, 0.5 mmol
  • aminoethoxyethyl 4- (benzyloxy)-4-oxobutanoic amide 200 mg, 1 mmol
  • EDC 200 mg, 1 mmol
  • HOBt 150 mg, 1 mmol
  • TEA 0.14 mL, 1 mmol

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Oncology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Communicable Diseases (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Peptides Or Proteins (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

Compositions and methods for the treatment of bacterial infections include compounds containing dimers of cyclic heptapeptides. In particular, compounds can be used in the treatment of bacterial infections caused by Gram-negative bacteria.

Description

COMPOSITIONS AND METHODS FOR THE TREATMENT OF BACTERIAL INFECTIONS
Background
The need for novel antibacterial treatments for bacterial infections is significant and especially critical in the medical field. Antibacterial resistance is a serious global healthcare threat. Polymyxins are a class of antibiotics that exhibit potent antibacterial activities against Gram-negative bacteria. However, the use of polymyxins as an antibiotic has been limited due to the associated toxicity and adverse effects (e.g., nephrotoxicity). Moreover, mcr- 1, a plasmid-borne gene conferring bacterial resistance to polymyxins, has a high potential for dissemination and further threatens the efficacy of this class of antibiotics.
Because of the shortcomings of existing antibacterial treatments, combined with the emergence of multidrug-resistant Gram-negative bacteria, there is a need in the art for improved antibacterial therapies having greater efficacy, bioavailability, and reduced toxicity.
Summary
The disclosure relates to compounds, compositions, and methods for inhibiting bacterial growth (e.g., Gram-negative bacterial growth) and for the treatment of bacterial infections (e.g., Gram-negative bacterial infections). In particular, such compounds contain dimers of cyclic heptapeptides, which bind to lipopolysaccharides (LPS) in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
In one aspect, the disclosure features a compound described by formula (I):
M2-U-M1
(I)
wherein M1 includes a first cyclic heptapeptide including a linking nitrogen and M2 includes a second cyclic heptapeptide including a linking nitrogen; L' is a linker covalently attached to the linking nitrogen in each of M1 and M2, or a pharmaceutically acceptable salt thereof; wherein L' is not
Figure imgf000002_0001
wherein L" is a remainder of L'; and each of R'L and RL is, independently, C1 -C10 alkyl. In some embodiments, L' in formula (I) is described by:
\— A2— L— A1— \
wherein L is a remainder of L'; A1 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M1 or is absent; and A2 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M2 or is absent.
In some embodiments, the compound is described by formula (II):
Figure imgf000003_0001
(II)
wherein L is a remainder of L'; each of each of R1 , R12, R'1 , and R'12 is, independently, a lipophilic moiety, a polar moiety, or H; each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is, independently, optionally substituted C1 - C5 alkamino, a polar moiety, a positively charged moiety, or H; each of R15 and R'15 is, independently, a lipophilic moiety or a polar moiety; each of R2, R3, R4, R5, R6, R7, R8, R9, R10, R'2, R'3, R'4, R'5, R'6, R'7, R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3- C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring; each of a', b', c', a, b, and c is, independently, 0 or 1 ; each of N1 , N2, N3, N4, N'1 , N'2, N'3, and N'4 is a nitrogen atom, each of C1 , C2, C3, C'1 , C'2, and C'3 is a carbon atom, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound includes at least one optionally substituted 5-8 membered ring formed by joining (i) R2, R3, and C1 ; (ii) R3, R4, N1 , and C1 ; (iii) R5, R6, and C2; (iv) R6, R7, N2, and C2; (v) R8, R9, and C3; (vi) R9, R10, N3, and C3; (vii) R'2, R'3, and C'1 ; (viii) R'3, R'4, N'1 , and C'1 ; (ix) R'5, R'6, and C'2; (x) R'6, R'7, N'2, and C'2; (xi) R'8, R'9, and C'3; or (xii) R'9, R'10, N'3, and C'3. In some embodiments, the compound is described by formula (III)
Figure imgf000004_0001
(III)
wherein L is a remainder of L'; or a pharmaceutically acceptable salt thereof.
In some embodiments, each of R1 , R12, R'1 , and R'12 is, independently, a lipophilic moiety; each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is, independently, optionally substituted C1 -C5 alkamino, a polar moiety, or a positively charged moiety; and/or each of R15 and R'15 is, independently, a polar moiety.
In some embodiments, each of R1 , R12, R'1 , and R'12 is a lipophilic moiety. In particular, each lipophilic moiety is, independently, optionally substituted C1 -C20 alkyl, optionally substituted C5-C1 5 aryl, optionally substituted C6-C35 alkaryl, or optionally substituted C3-C15 heteroaryl. In some embodiments, each lipophilic moiety is, independently, C1 -C8 alkyl, methyl substituted C2-C4 alkyl, (C1 - C10)alkylene(C6)aryl, phenyl substituted (C1 -C10)alkylene(C6)aryl, or alkyl substituted C4-C9 heteroaryl. In particular, each lipophilic moiety is, independently, benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or methyl substituted indolyl.
In some embodiments, each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is independently optionally substituted C1 -C5 alkamino. In particular, each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is CH2CH2NH2.
In some embodiments, each of R15 and R'15 is a polar moiety. In some embodiments, each polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group. In particular, each polar moiety is hydroxyl substituted C1 -C4 alkyl. In particular, each polar moiety is
In some embodiments, the compound is described by formula (IV):
Figure imgf000004_0002
(IV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (IV-1 ):
Figure imgf000005_0001
(IV-1 ),
or formula (IV-2):
Figure imgf000005_0002
(IV-2)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (V):
Figure imgf000005_0003
(V)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (V-1 ):
Figure imgf000006_0001
(V-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (V-2):
Figure imgf000006_0002
(V-2)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (V-3):
Figure imgf000006_0003
(V-3)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof. In some embodiments, the compound is described by formula (V-4):
Figure imgf000007_0001
(V-4)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (V-5):
Figure imgf000007_0002
(V-5)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI):
Figure imgf000007_0003
(VI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, R'6, and R'8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-1 ):
Figure imgf000008_0001
(VI-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-2):
Figure imgf000008_0002
(VI-2)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-3):
Figure imgf000008_0003
(VI-3) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-4):
Figure imgf000009_0001
(VI-4)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-5):
Figure imgf000009_0002
(VI-5)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-6):
Figure imgf000009_0003
(VI-6)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VI-7):
Figure imgf000010_0001
(VI-7)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VII):
(VII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (VIII):
Figure imgf000010_0003
(VIII) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (IX):
Figure imgf000011_0001
(IX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (X):
Figure imgf000011_0002
(X) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (X-1 ):
Figure imgf000012_0001
(X-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments of the compounds described herein, each of R2 and R'2 is optionally substituted C1 -C5 alkamino. In some embodiments, each of R2 and R'2 is CH2NH2 or CH2CH2NH2.
In some embodiments of the compounds described herein, each of R2 and R'2 is a polar moiety. In some embodiments, each polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group. In some embodiments, each polar moiety is hydroxyl substituted C1 -C4 alkyl. In particular, each polar moiety is CHCH3OH or CH2OH.
In some embodiments of the compounds described herein, each of R6 and R'6 is a polar moiety. In some embodiments, the polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group. In some embodiments, the polar moiety is hydroxyl substituted C1 -C4 alkyl. In particular, the polar moiety is CHCH3OH or CH2OH.
In some embodiments of the compounds described herein, each of R8 and R'8 is optionally substituted C1 -C5 alkamino. In some embodiments, the optionally substituted C1 -C5 alkamino is
Figure imgf000012_0002
In some embodiments, the compound is described by formula (XI):
Figure imgf000013_0001
(XI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
In some embodiments of the compounds described herein, L', L", or L includes one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, optionally substituted C3-C15 heteroarylene, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino, wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl.
In some embodiments of the compounds described herein, the backbone of L', L", or L includes no more than 100 atoms. In some embodiments, the backbone of L', L", or L consists of one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, optionally substituted C3-C15 heteroarylene, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino, wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl.
In some embodiments of the compounds described herein, L is a bond. In some embodiments, L is capable of forming an amide, a carbamate, a sulfonyl, or a urea linkage.
In some embodiments of the compounds described herein, L is described by formula (L-1 ):
l1-(V1)f-(U1 )g-(V2)h-(U2)i-(V3)j-(U3)k-(V4)|-(U4)m-(V5)n-l2
(L-1 )
wherein I1 is a bond attached to A2 or M2 if A2 is absent; I2 is a bond attached to A1 or M1 if A1 is absent; each of U1 , U2, U3, and U4 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2- C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20
heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C1 5 heteroarylene; each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl; and each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
In some embodiments of the compounds described herein, L (e.g., L of formula (L-1 )) is
Figure imgf000014_0001
In some embodiments, each of U1 , U2, U3, and U4 in formula (L-1 ) is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, or optionally substituted C2-C20 heteroalkynylene; each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl ; and each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
In some embodiments, L is
Figure imgf000015_0001
Figure imgf000016_0001
In some embodiments, each of U1 , U2, U3, and U4 is, independently, optionally substituted C3- C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, or optionally substituted C3-C1 5 heteroarylene; each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20
heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C1 5 aryl, or optionally substituted C5-C15 heteroaryl; and each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
In some embodiments, L is
Figure imgf000016_0002
Figure imgf000017_0001
In another aspect, the disclosure features a compound of formula (XII):
Figure imgf000017_0002
(XII)
wherein each A1 and A2 is an independently selected amino acid; L is a linker that, when m is 1 , 2, 3, 4, or 5, is bound to a nitrogen atom in any A1 and a nitrogen atom in any A2; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of a natural amino acid, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), at least one of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, at least two of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, at least three of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non- natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, at least four of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, at least five of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof. In some embodiments, each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, cyclohexylmethyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000018_0001
Figure imgf000019_0001
In some embodiments of a compound of formula (XII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently selected from 1 , 2, 3, 4, or 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XII), the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000019_0003
Figure imgf000019_0002
In some embodiments of a compound of formula (XII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3 or 4; and the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000020_0003
Figure imgf000020_0001
In some embodiments of a compound of formula (XII), each m is 0, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XIII):
Figure imgf000020_0002
(XIII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 is hydrogen, C1-C10 alkyl, or -CH2C(0)NR2R3; R2 is hydrogen or C1-C10 alkyl; R3 is hydrogen or C1-C10 alkyl; and each d is independently an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XIII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XIII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; R1 is hydrogen; each m is independently 1 , 2, 3 or 4; and the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000021_0003
Figure imgf000021_0001
In another aspect, the disclosure features a compound of formula (XIV):
Figure imgf000021_0002
(XIV)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and each d is independently an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XIV), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); and d is an integer from 1 to 5; or a pharmaceutically acceptable salt thereof. In some embodiments of a compound of formula (XIV), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3 or 4; d is an integer from 1 to 5; and the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000022_0003
Figure imgf000022_0001
In some embodiments of a compound of formula (XIV), m is 2, 3, or 4. In some embodiments of a compound of formula (XIV), m is 2. In some embodiments of a compound of formula (XIV), m is 3. In some embodiments of a compound of formula (XIV), m is 4.
In some embodiments of a compound of formula (XIV), d is 1 , 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XV):
Figure imgf000022_0002
(XV)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; X is O or is absent; each Y is independently -CH2- or -C(O)-; and each Z is independently N or CH; or a pharmaceutically acceptable salt thereof. In some embodiments of a compound of formula (XV), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), X is absent, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), Y is -CH2-, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), Y is -C(O)-, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), X is O, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3 or 4; and the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000023_0002
Figure imgf000023_0001
pharmaceutically acceptable salt thereof. In some embodiments, Y is -C(O)-, X is absent, and Z is CH, or a pharmaceutically acceptable salt thereof. In some embodiments, Y is -C(0)-,.X is absent, and Z is N, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XV), each A1 and A2 is independently threonine or 2,4-diaminobutyric acid; and m is 2 or 3; or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XVI):
Figure imgf000024_0001
(XVI)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; X is - CR1 R2-, -C(R1)=C(R2)-, -CH2OCH2-, -C(O)-, or is absent; each Y is independently -C(O)-, -S(O)-, -S(0)2-, or is absent; R1 is hydrogen, C1 -C10 alkyl, -N(R3R4), or -OH; R2 is hydrogen, C1 -C10 alkyl, or -OH; R3 and R4 are independently hydrogen or C1 -C10 alkyl; and d is an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVI), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVI), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3 or 4; and the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000025_0003
or
Figure imgf000025_0001
CR1=CR2-; R1 is hydrogen or -NR3R4; R3 and R4 are hydrogen; and d is 1 , 2, or 3; or a pharmaceutically acceptable salt thereof. In some embodiments, Y is -S(0)2-; X is -CH2-; and d is 1 , 2, or 3; or a pharmaceutically acceptable salt thereof. In some embodiments, Y is absent, X is -C(O)- and d is 1 , or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVI), each A1 and A2 is independently threonine, 3-hydroxyalaline, 2,4-diaminobutyric acid, 3-hydroxyproline, 2-amino-4-(dimethylamino)butyric acid, and 2-aminooctanoic acid, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XVII):
Figure imgf000025_0002
(XVII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and each Y is independently -CH2-, -C(O)-, -S(O)-, or -S(0)2-; or a pharmaceutically acceptable salt thereof. In some embodiments of a compound of formula (XVII), the compound is of the formula (XVII-1 ):
Figure imgf000026_0001
(XVII-1 )
narmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVII), the compound is of the formula (XVII-2):
Figure imgf000026_0002
(XVII-3)
or a pharmaceutically acceptable salt thereof. In some embodiments of a compound of formula (XVII) (e.g., a compound of any one of formulas (XVII-1 )-(XVII-3)), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2- piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVII) (e.g., a compound of any one of formulas (XVII-1 )-(XVII-3)), each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVII) (e.g., a compound of any one of formulas (XVII-1 )-(XVII-3)), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2- piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3 or 4; and the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000027_0002
or
Figure imgf000027_0001
is 2, 3 or 4, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVII) (e.g., a compound of any one of formulas (XVII-1 )-(XVII-3)), each A1 and A2 is independently threonine or 2,4-diaminobutyric acid, or a
pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XVIII):
Figure imgf000028_0001
(XVIII)
wherein each A1 and A2 is an independently selected amino acid; e is an integer from 1 to 5; f is an integer from 1 to 5; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and R1 is hydrogen, C1 -C10 alkyl, -C(0)OR2, -C(0)-(CH2OCH2)d-heterocyclic, and -C(0)R2; R2 is C1 -C10 alkyl, benzyl, -CH2(biphenyl), -(CH2CH20)g-R3; R3 is -(CH2)iNR4R5 and -(CH2)i-(C2-C8 alkynyl); R4 is hydrogen or C1 -C10 alkyl; R5 is hydrogen or C1 -C10 alkyl; and d is an integer from 1 to 10; g is an integer from 1 to 10; and i is an integer from 1 to 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVIII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2- amino-5-methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha- neopentylglycine, 3-aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5- methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVIII), each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVIII), e and f are 1 , or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVIII), R1 is hydrogen, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVIII), R1 is -C02R2, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XVIII), R1 is -C(0)R2, or a pharmaceutically acceptable salt thereof. In some embodiments of a compound of formula (XVIII), each A1 and A2 is independently threonine, 2,4-diaminobutyric acid, 2-aminooctanoic acid, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminodecanoic acid, O-allyl serine, tryptophan, and 3-(4,4'-biphenyl)alanine, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XIX):
Figure imgf000029_0001
(XIX)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 and R2 are independently hydrogen, C1 -C10 alkyl, or -C(0)OR3; R3 is hydrogen C1 -C10 alkyl, or benzyl; and d is an integer from 1 to 4; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XIX), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XIX), d is 1 or 2, R1 is hydrogen, and R2 is hydrogen, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XIX), d is 1 . In some embodiments of a compound of formula (XIX), d is 2.
In some embodiments of a compound of formula (XIX), each A1 and A2 is independently 2,4- daminobutyric acid, threonine, or 4-aminoproline, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure featuers a compound of formula (XX):
Figure imgf000030_0001
(XX)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 is hydrogen or C1 -C10 alkyl; and d and d' are, independently, an integer from 1 to 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XX), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XX), d is 1 , 2, or 3. In some embodiments, d is 1 and d' is 1 . In some embodiments, d is 1 and d' is 0. In some embodiments, d is 0 and d' is 1 . In some embodiments, d is 2 and d' is 2. In some embodiments, d is 2 and d' is 1 . In some embodiments, d is 1 and d' is 2. In some embodiments, d is 3 and d' is 0. In some embodiments, d is 0 and d' is 3.
In some embodiments of a compound of formula (XX), R1 is hydrogen, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XX), each A1 and A2 is independently 2,4- diaminobutyric acid or threonine, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XXI):
Figure imgf000031_0001
(XXI)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXI), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXI), each A1 and A2 is independently 2,4- diaminobutyric acid or threonine, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XXII):
Figure imgf000031_0002
(XXII) wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2- carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2- naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4- amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S- methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5- methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3- aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'- biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XXIII):
Figure imgf000032_0001
(XXIII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXIII), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine,
, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t- butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4- methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2- aminodecanoic acid, and O-allyl serine; and each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XXIV):
Figure imgf000033_0001
(XXIV)
wherein each A1 and A2 is an independently selected amino acid; R1 is hydrogen or C1 -C10 alkyl; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and d is an integer from 1 to 6; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXIV), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2- amino-5-methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha- neopentylglycine, 3-aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5- methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3, 4, or 5 (e.g., 2, 3, or 4); d is an integer from 1 to 2; and or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXIV), d is 1 , 2, or 3. In some embodiments, d is 3.
In some embodiments of a compound of formula (XXIV), each A1 and A2 is independently 2,4- diaminobutyric acid, threonine, or 2-aminooctanoic acid, or a pharmaceutically acceptable salt thereof.
In another aspect, the disclosure features a compound of formula (XXV):
Figure imgf000033_0002
(XXV) wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; d and d' are, independently 0, 1 , or 2; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 is hydrogen, C1 -C10 alkyi, -(CH2)d-R2 or -C(0)(CH2)d-R2; d and d' are, independently, 0, 1 , or 2; R2 is aryl, C1 -C10 alkyi, -NR3R4, or -OR4; and R3 and R4 are independently hydrogen or C1 -C10 alkyi; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXV), each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3-hydroxyproline, threonine, 2-amino-4- phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2- aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2- amino-5-methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha- neopentylglycine, 3-aminoproline, 4-aminoproline, 2-amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2-aminopentanoic acid, alanine, 4-methylpentanoic acid, 5- methylhexanoic acid, 2-aminoheptanoic acid, 2-aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; each m is independently 1 , 2, 3, 4, or 5; or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of formula (XXV), each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of any one of formulas (XIII)-(XXV), each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a
pharmaceutically acceptable salt thereof.
In some embodiments of a compound of any one of formulas (XIII)-(XXV), each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyi, C3-C6 cycloalkyi C1 -C4 alkyi, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, C6-C10 aryl, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of any one of formulas (XIII)-(XXV), each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, cyclohexylmethyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of any one of formulas (XIII)-(XXV), the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000034_0001
Figure imgf000035_0001
or a pharmaceutically acceptable salt thereof.
In some embodiments of a compound of any one of formulas (XIII)-(XXV), the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000035_0003
Figure imgf000035_0002
In some embodiments, the compound is described by formula (XXVI):
Figure imgf000036_0001
(XXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R3, R4, R5, R6, R7, R8, R9, R10, R'2, R'3, R'4, R'5, R'6, R'7, R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20
heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring; each of a', b', c', a, b, and c is, independently, 0 or 1 ; each of N1 , N2, N3, N4, N'1 , N'2, N'3, and N'4 is a nitrogen atom; each of C1 , C2, C3, C'1 , C'2, and C'3 is a carbon atom; L is a linker comprising at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, or optionally substituted C3-C15 heteroarylene; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound comprises at least one optionally substituted 5-8 membered ring formed by joining (i) R2, R3, and C1 ; (ii) R3, R4, N1 , and C1 ; (iii) R5, R6, and C2; (iv) R6, R7, N2, and C2; (v) R8, R9, and C3; (vi) R9, R10, N3, and C3; (vii) R'2, R'3, and C'1 ; (viii) R'3, R'4, N'1 , and C'1 ; (ix) R'5, R'6, and C'2; (x) R'6, R'7, N'2, and C'2; (xi) R'8, R'9, and C'3; or (xii) R'9, R'10, N'3, and C'3.
In some embodiments L is described by formula (L-2):
l1-(V1)f-(U1 )g-(V2)h-(U2)i-(V3)j-(U3)-(V4)k-(U4)|-(V5)m-(U5)n-(V6)o-l2
(L-2)
wherein I1 is a bond attached to N'1 , N'2, N'3, or N'4; I2 is a bond attached to N1 , N2, N3, or N4; U3 comprises at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C1 5 heteroarylene; each of U1 , U2, U4, and U5 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene; each of V1 , V2, V3, V4, V5, and V6 is, independently, O, S, NR\ P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl; and each of f, g, h, i, j, k, I, m, n, and o is, independently, 0 or 1 .
In some embodiments, the compound is described by formula (XXVII):
Figure imgf000037_0001
(XXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, R'6, and R'8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXVIII):
Figure imgf000037_0002
(XXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXIX):
Figure imgf000038_0001
(XXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXX):
Figure imgf000038_0002
(XXX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, and R8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXI):
Figure imgf000039_0001
(XXXI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXII):
Figure imgf000039_0002
(XXXII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXIII): H
N
Figure imgf000040_0001
(XXXIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXIV):
Figure imgf000040_0002
(XXXIV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof. In some embodiments, the compound is described by formula (XXXV):
Figure imgf000041_0001
(XXXV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; R2 is a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXVI):
Figure imgf000041_0002
(XXXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, L comprises at least one optionally substituted C3 cycloalkylene or at least one optionally substituted C3 heterocycloalkylene.
In some embodiments, the compound is described by formula (XXXVII):
Figure imgf000041_0003
(XXXVII) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXVIII):
Figure imgf000042_0001
(XXXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, L is
Figure imgf000042_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments, L comprises at least one optionally substituted C5 cycloalkylene or at least one optionally substituted C5 heterocycloalkylene.
In some embodiments, the compound is described by formula (XXXIX):
Figure imgf000042_0003
(XXXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXX):
Figure imgf000043_0001
(XXXX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXXI):
Figure imgf000043_0002
(XXXXI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXXII):
Figure imgf000043_0003
(XXXXII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof. In some embodiments, the compound is described by formula (XXXXIII):
Figure imgf000044_0001
(XXXXIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, L comprises at least one optionally substituted pyrrolidine. In some embodiments, the pyrrolidine is substituted with an alkyne functional group, and azide functional group, a sulphone functional group, an amine functional group, or a fluorophore. In some embodiments the fluorophore is fluorescein, rhodamine, coumarin, or a derivative thereof.
In some embodiments L is
Figure imgf000044_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments L is
Figure imgf000044_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments L is
Figure imgf000044_0004
wherein each q is, independently, an integer from 1 to 1 1 , inclusive. In some embodiments L is
Figure imgf000045_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
Figure imgf000045_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments, L comprises at least one optionally substituted 1 ,3-dioxolane.
Figure imgf000045_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
Figure imgf000046_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments, L comprises at least one optionally substituted C6 cycloalkylene or at least one optionally substituted C6 heterocycloalkylene.
In some embodiments, the compound is described by formula (XXXXIV):
Figure imgf000046_0002
(XXXXIV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 cycloalkylene or an optionally substituted C6 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments L is
Figure imgf000046_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments, L comprises at least one optionally substituted C6 arylene or at least one optionally substituted C6 heteroarylene.
In some embodiments, the compound is described by formula (XXXXV):
Figure imgf000046_0004
(XXXXV) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXXVI):
Figure imgf000047_0001
(XXXXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the compound is described by formula (XXXXVII):
Figure imgf000047_0002
(XXXXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
Figure imgf000047_0003
Figure imgf000048_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments, L comprises at least two optionally substituted C6 arylene.
In some embodiments, the compound is described by formula (XXXXVIII):
Figure imgf000048_0002
(XXXXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises at least two optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
In some embodiments L is
Figure imgf000048_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
In some embodiments, L comprises at least one optionally substituted C5 arylene or at least one optionally substituted C5 heteroarylene.
In some embodiments, the compound is described by formula (XXXXIX):
Figure imgf000049_0001
(XXXXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 arylene or an optionally substituted C5 heteroarylene, or a pharmaceutically acceptable salt thereof.
Figure imgf000049_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
Non-natural amino acids that may be included in a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)), for example, in the polymyxin core portions (e.g., in the first cyclic heptapeptide and/or the second cyclic heptapeptide) and/or the linker portion of the compound, include, but are not limited to, , D-Ser, D-Pro, D-Leu, D-Nle (D-norleucine), D-Thr, D-Val, L-Abu (L-2- aminobutyric acid), 3-(2H-tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4- diaminobutyric acid, 3-hydroxyproline, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2- piperazinecarboxylic acid, 2-aminooctanoic acid, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S-propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5-methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2-amino-4- (dimethylamino)butyric acid, 3-(4,4'-biphenyl)alanine, 2-aminopentanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine. In some embodiments, polymyxin core portions (e.g., in the first cyclic heptapeptide and/or the second cyclic heptapeptide) of the compound include D-Ser, D-Pro, D-Leu, D-Nle, D-Thr, D-Val, and/or L-Abu.
In some embodiments of a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX) and/or any one of compounds 1 -180, or a pharmaceutically acceptable salt thereof), the compound does not include any monosaccharide or oligosaccharide moieties. In another aspect, the disclosure features any compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX) and/or any one of compounds 1 -180, or a pharmaceutically acceptable salt thereof).
In another aspect, the disclosure features a pharmaceutical composition including a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition further includes an antibacterial agent.
In some embodiments, the antibacterial agent is selected from the group consisting of linezolid, tedizolid, posizolid, radezolid, retapamulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem,
imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime, cefpodoxime, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, dalbavancin, oritavancin, clindamycin, lincomycin, daptomycin, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, spiramycin, aztreonam, furazolidone, nitrofurantoin, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin g, penicillin v, piperacillin, penicillin g, temocillin, ticarcillin, amoxicillin clavulanate, ampicillin/sulbactam,
piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, temafloxacin, mafenide, sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (tmp-smx), sulfonamidochrysoidine, eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, clofazimine, dapsone, capreomycin, cycloserine, ethambutol(bs), ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, streptomycin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, trimethoprim, prodrugs thereof, and pharmaceutically acceptable salts thereof. In particular, a prodrug of tedizolid is tedizolid phosphate.
In some embodiments, the antibacterial agent is linezolid or tedizolid phosphate.
In another aspect, the disclosure features a method of protecting against or treating a bacterial infection in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
In some embodiments of the method, the method further includes administering to the subject an antibacterial agent.
In another aspect, the disclosure features a method of protecting against or treating a bacterial infection in a subject by administering to the subject (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
In some embodiments of the methods described herein, the bacterial infection is caused by Gram-negative bacteria. In some embodiments, the bacterial infection is caused by a resistant strain of bacteria. In some embodiments, the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance. In some embodiments, the resistant strain of bacteria is a resistant strain of E. coli.
In another aspect, the disclosure features a method of protecting against or treating sepsis in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)). In some embodiments, the method further includes administering to the subject an antibacterial agent.
In another aspect, the disclosure features a method of preventing LPS in Gram-negative bacteria, e.g., a resistant strain of Gram-negative bacteria. In some embodiments, the resistant strain of Gram- negative bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance. In some embodiments, the resistant strain of Gram-negative bacteria is a resistant strain of E. coli. In some embodiments, the method prevents LPS from activating a macrophage. In some embodiments, the method prevents LPS-induced nitroic oxide (NO) production from a macrophage. In some embodiments, the method further includes administering to the subject an antibacterial agent.
In some embodiments of the methods described herein, the compound and the antibacterial agent are administered substantially simultaneously.
In some embodiments of the methods described herein, the compound and the antibacterial agent are administered separately. In some embodiments, the compound is administered first, followed by administering of the antibacterial agent alone. In some embodiments, the antibacterial agent is administered first, followed by administering of the compound alone. In some embodiments, the compound and the antibacterial agent are administered substantially simultaneously, followed by administering of the compound or the antibacterial agent alone. In some embodiments, the compound or the antibacterial agent is administered first, followed by administering of the compound and the antibacterial agent substantially simultaneously.
In some embodiments of the methods described herein, administering the compound and the antibacterial agent together may lower the MIC of each of the compound and the antibacterial agent relative to the MIC of each of the compound and the antibacterial agent when each is used alone.
In some embodiments of the methods described herein, the compound and/or the antibacterial agent is administered intramuscularly, intravenously, intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally, locally, by inhalation, by injection, or by infusion.
In another aspect, the disclosure features a method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria. The method includes contacting the bacteria or a site susceptible to bacterial growth with a compound described herein (e.g., a compound of any one of formulas (I)- (XXXXIX)).
In some embodiments, the method further includes contacting the bacteria or the site susceptible to bacterial growth with an antibacterial agent, in addition to the compound. In another aspect, the disclosure features a method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria by contacting the bacteria or a site susceptible to bacterial growth with (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
In some embodiments, the bacteria is Gram-negative bacteria. In some embodiments, the bacteria is a resistant strain of bacteria. In some embodiments, the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance. In some embodiments, the resistant strain of bacteria is a resistant strain of E. coli.
In some embodiments of these methods, the antibacterial agent is selected from the group consisting of linezolid, tedizolid, posizolid, radezolid, retapamulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem, imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime, cefpodoxime, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, dalbavancin, oritavancin, clindamycin, lincomycin, daptomycin, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, spiramycin, aztreonam, furazolidone, nitrofurantoin, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin g, penicillin v, piperacillin, penicillin g, temocillin, ticarcillin, amoxicillin clavulanate, ampicillin/sulbactam,
piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, temafloxacin, mafenide, sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (tmp-smx), sulfonamidochrysoidine, eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, clofazimine, dapsone, capreomycin, cycloserine, ethambutol(bs), ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, streptomycin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, and trimethoprim. In some embodiments, a prodrug of tedizolid is tedizolid phosphate. In some embodiments, the antibacterial agent is linezolid or tedizolid phosphate.
Definitions:
The term "about," as used herein, indicates a deviation of ±5%. For example, about 10% refers to from 9.5% to 10.5%.
The term "acyl," as used herein, refers to a group having the structure:
Figure imgf000052_0001
, wherein Rz is an optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, alkaryl, alkamino, heteroalkyl, heteroalkenyl, heteroalkynyl, heterocycloalkyl, heterocycloalkenyl,
heterocycloalkynyl, heteroaryl, heteroalkaryl, or heteroalkamino. The terms "alkylene," "alkyl," "alkenyl," "alkenylene," "alkynyl," and "alkynylene," as used herein, refer to divalent groups having a specified size. In some embodiments, an alkylene may contain, e.g., 1 - 20, 1 -1 8, 1 -16, 1 -14, 1 -12, 1 -10, 1 -8, 1 -6, 1 -4, or 1 -2 carbon atoms (e.g., C1 -C20, C1 -C18, C1 -C16, C1 - C14, C1 -C12, C1 -C1 0, C1 -C8, C1 -C6, C1 -C4, or C1 -C2). In some embodiments, an alkenylene or alkynylene may contain, e.g., 2-20, 2-1 8, 2-16, 2-14, 2-12, 2-10, 2-8, 2-6, or 2-4 carbon atoms (e.g., C2- C20, C2-C18, C2-C1 6, C2-C14, C2-C12, C2-C1 0, C2-C8, C2-C6, or C2-C4). For example, C1 -C20 alkyl means a fully saturated chain comprising from 1 to 20 carbons, which may be linear or branched.
Alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups include straight-chain and branched- chain forms, as well as combinations of these. The divalency of an alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group does not include the optional substituents on the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group. For example, a first cyclic heptapeptide and a second cyclic heptapeptide may be attached to each other by way of a linker that includes alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene, or combinations thereof. Each of the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups in the linker is considered divalent with respect to the two attachments on either end of alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group. For example, if a linker includes (optionally substituted alkylene) (optionally substituted alkenylene) or (optionally substituted alkylene), the alkenylene is considered divalent with respect to its attachments to the two alkylenes at the ends of the linker. The optional substituents on the alkenylene are not included in the divalency of the alkenylene. The divalent nature of an alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group (e.g., an alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group in a linker) refers to both of the ends of the group and does not include optional substituents that may be present in an alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene group. Because they are divalent, they can link together multiple (e.g., two) parts of a compound, e.g., a first cyclic heptapeptide and a second cyclic heptapeptide. Alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups can be substituted by the groups typically suitable as substituents for alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups as set forth herein. For example, C=0 is a C1 alkyl or alkylene that is substituted by an oxo (=0). For example, HCR C≡C may be considered as an optionally substituted alkynyl or alkynylene and is considered a divalent group even though it has an optional substituent, R.
The term "alkamide," as used herein, refers to an amide group that is attached to an alkyl or alkylene (e.g., C1 -C5 alkylene), alkenyl or alkenylene (e.g., C2-C5 alkenylene), or alkynyl or alkynylene (e.g., C2-C5 alkenylene) group. In general, if a compound is attached to an alkamide group, the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the alkamide is attached to the compound. The amide portion of an alkamide refers to -C(0)N(RX)2, where each Rx is, independently, H, alkyl, alkenyl, alkynyl, aryl, alkaryl, cycloalkyl, or two Rx combine to form a heterocycloalkyl. In some embodiment, the amide portion of an alkamide is-C(0)NH2. An alkamide group may be -(CH2)2C(0)NH2, or -CH2C(0)NH2. In a heteroalkamide group, one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms selected from N, O, and S may be present in the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the heteroalkamide group. In some embodiments, an alkamide group may be optionally substituted. In a substituted alkamide group, the substituent may be present on the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the alkamide group and/or may be present on the amide portion of the alkamide group.
The term "alkamino," as used herein, refers to an amino group, described herein, that is attached to an alkyl or alkylene (e.g., C1 -C5 alkylene), alkenyl or alkenylene (e.g., C2-C5 alkenylene), or alkynyl or alkynylene group (e.g., C2-C5 alkenylene). In general, if a compound is attached to an alkamino group, the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the alkamino is attached to the compound. The amino portion of an alkamino refers to -N(RX)2 or -N+(RX)3, where each Rx is, independently, H, alkyl, alkenyl, alkynyl, aryl, alkaryl, cycloalkyl, or two Rx combine to form a
heterocycloalkyl. In some embodiment, the amino portion of an alkamino is -NH2. An example of an alkamino group is C1 -C5 alkamino, e.g., C2 alkamino (e.g., CH2CH2NH2 or ChteChbNKCh ^). In a heteroalkamino group, one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms selected from N, O, and S may be present in the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the heteroalkamino group. In some embodiments, an alkamino group may be optionally substituted. In a substituted alkamino group, the substituent may be present on the alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene portion of the alkamino group and/or may be present on the amino portion of the alkamino group.
The term "alkaryl," as used herein, refers to an aryl group that is connected to an alkyl, alkylene, alkenyl, alkenylene, alkynyl, or alkynylene group. In general, if a compound is attached to an alkaryl group, the alkyl, alkylene, alkenyl, alkenylene, alkynyl, or alkynylene portion of the alkaryl is attached to the compound. In some embodiments, an alkaryl is C6-C35 alkaryl (e.g., C6-C16, C6-C14, C6-C12, C6- C10, C6-C9, C6-C8, C7, or C6 alkaryl), in which the number of carbons indicates the total number of carbons in both the aryl portion and the alkyl, alkylene, alkenyl, alkenylene, alkynyl, or alkynylene portion of the alkaryl. Examples of alkaryls include, but are not limited to, (C1 -C8)alkylene(C6-C12)aryl, (C2- C8)alkenylene(C6-C12)aryl, or (C2 C8)alkynylene(C6-C12)aryl. In some embodiments, an alkaryl is benzyl. In a heteroalkaryl, one or more heteroatoms selected from N, O, and S may be present in the alkylene, alkenylene, or alkynylene portion of the alkaryl group and/or may be present in the aryl portion of the alkaryl group. In an optionally substituted alkaryl, the substituent may be present on the alkylene, alkenylene, or alkynylene portion of the alkaryl group and/or may be present on the aryl portion of the alkaryl group.
O
The term "amido" as used herein, refers to a group having the formula R' , wherein R and R' are as defined for R16 herein.
The term "amino," as used herein, represents -N(RX)2 or -N+(RX)3, where each Rx is,
independently, H, alkyl, alkenyl, alkynyl, aryl, alkaryl, cycloalkyl, or two Rx combine to form a
heterocycloalkyl. In some embodiment, the amino group is NH2.
The term "amino acid," as used herein, means naturally occurring amino acids and non-naturally occurring amino acids.
The term "naturally occurring amino acids," as used herein means amino acids including Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, He, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, and Val. The term "non-naturally occurring amino acid," as used herein, means an alpha amino acid that is not naturally produced or found in a mammal. Examples of non-naturally occurring amino acids include D-amino acids; an amino acid having an acetylaminomethyl group attached to a sulfur atom of a cysteine; a pegylated amino acid; the omega amino acids of the formula NH2(CH2)nCOOH where n is 2-6, neutral nonpolar amino acids, such as sarcosine, t-butyl alanine, t-butyl glycine, N-methyl isoleucine, and norleucine; oxymethionine; phenylglycine; citrulline; methionine sulfoxide; cysteic acid; ornithine;
diaminobutyric acid; 3-aminoalanine; 3-hydroxy-D-proline; 2,4-diaminobutyric acid; 2-aminopentanoic acid; 2-aminooctanoic acid, 2-carboxy piperazine; piperazine-2-carboxylic acid, 2-amino-4-phenylbutanoic acid; 3-(2-naphthyl)alanine, and hydroxyproline. Other amino acids are a-aminobutyric acid, a-amino-a- methylbutyrate, aminocyclopropane-carboxylate, aminoisobutyric acid, aminonorbornyl-carboxylate, L- cyclohexylalanine, cyclopentylalanine, L-N-methylleucine, L-N-methylmethionine, L-N-methylnorvaline, L- N-methylphenylalanine, L-N-methylproline, L-N-methylserine, L-N-methyltryptophan, D-ornithine, L-N- methylethylglycine, L-norleucine, a-methyl-aminoisobutyrate, a-methylcyclohexylalanine, D-a- methylalanine, D-a-methylarginine, D-a-methylasparagine, D-a-methylaspartate, D-a-methylcysteine, D- a-methylglutamine, D-a-methylhistidine, D-a-methylisoleucine, D-a-methylleucine, D-a-methyllysine, D-a- methylmethionine, D-a-methylornithine, D-a-methylphenylalanine, D-a-methylproline, D-a-methylserine, D-N-methylserine, D-a-methylthreonine, D-a-methyltryptophan, D-a-methyltyrosine, D-a-methylvaline, D- N-methylalanine, D-N-methylarginine, D-N-methylasparagine, D-N-methylaspartate, D-N-methylcysteine, D-N-methylglutamine, D-N-methylglutamate, D-N-methylhistidine, D-N-methylisoleucine, D-N- methylleucine, D-N-methyllysine, N-methylcyclohexylalanine, D-N-methylornithine, N-methylglycine, N- methylaminoisobutyrate, N-(1 -methylpropyl)glycine, N-(2-methylpropyl)glycine, D-N-methyltryptophan, D- N-methyltyrosine, D-N-methylvaline, γ-aminobutyric acid, L-t-butylglycine, L-ethylglycine, L- homophenylalanine, L-a-methylarginine, L-a-methylaspartate, L-a-methylcysteine, L-a-methylglutamine, L-a-methylhistidine, L-a-methylisoleucine, L-a-methylleucine, L-a-methylmethionine, L-a-methylnorvaline, L-a-methylphenylalanine, L-a-methylserine, L-a-methyltryptophan, L-a-methylvaline, N-(N-(2,2- diphenylethyl) carbamylmethylglycine, 1 -carboxy-1 -(2,2-diphenyl-ethylamino) cyclopropane, 4- hydroxyproline, ornithine, 2-aminobenzoyl (anthraniloyl), D-cyclohexylalanine, 4-phenyl-phenylalanine, L- citrulline, a-cyclohexylglycine, L-1 ,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, L-thiazolidine-4- carboxylic acid, L-homotyrosine, L-2-furylalanine, L-histidine (3-methyl), N-(3-guanidinopropyl)glycine, O- methyl-L-tyrosine, O-glycan-serine, meta-tyrosine, nor-tyrosine, L-N,N',N"-trimethyllysine, homolysine, norlysine, N-glycan asparagine, 7-hydroxy-1 ,2,3,4-tetrahydro-4-fluorophenylalanine, 4- methylphenylalanine, bis-(2-picolyl)amine, pentafluorophenylalanine, indoline-2-carboxylic acid, 2- aminobenzoic acid, 3-amino-2-naphthoic acid, asymmetric dimethylarginine, L-tetrahydroisoquinoline-1 - carboxylic acid, D-tetrahydroisoquinoline-1 -carboxylic acid, 1 -amino-cyclohexane acetic acid, D/L- allylglycine, 4-aminobenzoic acid, 1 -amino-cyclobutane carboxylic acid, 2 or 3 or 4-aminocyclohexane carboxylic acid, 1 -amino-1 -cyclopentane carboxylic acid, 1 -aminoindane-1 -carboxylic acid, 4-amino- pyrrolidine-2-carboxylic acid, 2-aminotetraline-2-carboxylic acid, azetidine-3-carboxylic acid, 4-benzyl- pyrolidine-2-carboxylic acid, tert-butylglycine, b-(benzothiazolyl-2-yl)-alanine, b-cyclopropyl alanine, 5,5- dimethyl-1 ,3-thiazolidine-4-carboxylic acid, (2R,4S)4-hydroxypiperidine-2-carboxylic acid, (2S,4S) and (2S,4R)-4-(2-naphthylmethoxy)-pyrolidine-2-carboxylic acid, (2S,4S) and (2S,4R)4-phenoxy-pyrrolidine-2- carboxylic acid, (2R,5S)and(2S,5R)-5-phenyl-pyrrolidine-2-carboxylic acid, (2S,4S)-4-amino-1 -benzoyl- pyrrolidine-2-carboxylic acid, t-butylalanine, (2S,5R)-5-phenyl-pyrrolidine-2-carboxylic acid, 1 - aminomethyl-cyclohexane-acetic acid, 3,5-bis-(2-amino)ethoxy-benzoic acid, 3,5-diamino-benzoic acid, 2- methylamino-benzoic acid, N-methylanthranylic acid, L-N-methylalanine, L-N-methylarginine, L-N- methylasparagine, L-N-methylaspartic acid, L-N-methylcysteine, L-N-methylglutamine, L-N- methylglutamic acid, L-N-methylhistidine, L-N-methylisoleucine, L-N-methyllysine, L-N-methylnorleucine, L-N-methylornithine, L-N-methylthreonine, L-N-methyltyrosine, L-N-methylvaline, L-N-methyl-t- butylglycine, L-norvaline, a-methyl-Y-aminobutyrate, 4,4'-biphenylalanine, a-methylcylcopentylalanine, a- methyl-a-napthylalanine, a-methylpenicillamine, N-(4-aminobutyl)glycine, N-(2-aminoethyl)glycine, N-(3- aminopropyl)glycine, N-amino-a-methylbutyrate, a-napthylalanine, N-benzylglycine, N-(2- carbamylethyl)glycine, N-(carbamylmethyl)glycine, N-(2-carboxyethyl)glycine, N-(carboxymethyl)glycine, N-cyclobutylglycine, N-cyclodecylglycine, N-cycloheptylglycine, N-cyclohexylglycine, N-cyclodecylglycine, N-cylcododecylglycine, N-cyclooctylglycine, N-cyclopropylglycine, N-cycloundecylglycine, N-(2,2- diphenylethyl)glycine, N-(3,3-diphenylpropyl)glycine, N-(3-guanidinopropyl)glycine, N-(1 - hydroxyethyl)glycine, N-(hydroxyethyl))glycine, N-(imidazolylethyl))glycine, N-(3-indolylyethyl)glycine, N- methyl-Y-aminobutyrate, D-N-methylmethionine, N-methylcyclopentylalanine, D-N-methylphenylalanine, D-N-methylproline, D-N-methylthreonine, N-(1 -methylethyl)glycine, N-methyl-napthylalanine, N- methylpenicillamine, N-(p-hydroxyphenyl)glycine, N-(thiomethyl)glycine, penicillamine, L-a-methylalanine, L-a-methylasparagine, L-a-methyl-t-butylglycine, L-methylethylglycine, L-a-methylglutamate, L-a- methylhomophenylalanine, N-(2-methylthioethyl)glycine, L-a-methyllysine, L-a-methylnorleucine, L-a- methylornithine, L-a-methylproline, L-a-methylthreonine, L-a-methyltyrosine, L-N-methyl- homophenylalanine, N-(N-(3,3-diphenylpropyl) carbamylmethylglycine, L-pyroglutamic acid, D- pyroglutamic acid, O-methyl-L-serine, O-methyl-L-homoserine, 5-hydroxylysine, a-carboxyglutamate, phenylglycine, L-pipecolic acid (homoproline), L-homoleucine, L-lysine (dimethyl), L-2-naphthylalanine, L- dimethyldopa or L-dimethoxy-phenylalanine, L-3-pyridylalanine, L-histidine (benzoyloxymethyl), N- cycloheptylglycine, L-diphenylalanine, O-methyl-L-homotyrosine, L-p-homolysine, O-glycan-threoine, Ortho-tyrosine, L-N,N'-dimethyllysine, L-homoarginine, neotryptophan, 3-benzothienylalanine, isoquinoline-3-carboxylic acid, diaminopropionic acid, homocysteine, 3,4-dimethoxyphenylalanine, 4- chlorophenylalanine, L-1 ,2,3,4-tetrahydronorharman-3-carboxylic acid, adamantylalanine, symmetrical dimethylarginine, 3-carboxythiomorpholine, D-1 ,2,3,4-tetrahydronorharman-3-carboxylic acid, 3- aminobenzoic acid, 3-amino-1 -carboxymethyl-pyridin-2-one, 1 -amino-1 -cyclohexane carboxylic acid, 2- aminocyclopentane carboxylic acid, 1 -amino-1 -cyclopropane carboxylic acid, 2-aminoindane-2-carboxylic acid, 4-amino-tetrahydrothiopyran-4-carboxylic acid, azetidine-2-carboxylic acid, b-(benzothiazol-2-yl)- alanine, neopentylglycine, 2-carboxymethyl piperidine, b-cyclobutyl alanine, allylglycine, diaminopropionic acid, homo-cyclohexyl alanine, (2S,4R)- 4-hydroxypiperidine-2-carboxylic acid, octahydroindole-2- carboxylic acid, (2S,4R) and (2S,4R)-4-(2-naphthyl), pyrrolidine-2-carboxylic acid, nipecotic acid, (2S,4R)and (2S,4S)-4-(4-phenylbenzyl) pyrrolidine-2-carboxylic acid, (3S)-1 -pyrrolidine-3-carboxylic acid, (2S,4S)-4-tritylmercapto-pyrrolidine-2-carboxylic acid, (2S,4S)-4-mercaptoproline, t-butylglycine, N,N- bis(3-aminopropyl)glycine, 1 -amino-cyclohexane-1 -carboxylic acid, N-mercaptoethylglycine, and selenocysteine. In some embodiments, amino acid residues may be charged or polar. Charged amino acids include alanine, lysine, aspartic acid, or glutamic acid, or non-naturally occurring analogs thereof. Polar amino acids include glutamine, asparagine, histidine, serine, threonine, tyrosine, methionine, or tryptophan, or non-naturally occurring analogs thereof.
It is specifically contemplated that in some embodiments, a terminal amino group in the amino acid may be an amido group or a carbamate group.
The term "antibacterial agent," as used herein, refers to an agent that is used in addition to one or more of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) in methods of treating a bacterial infection (e.g., Gram-negative bacterial infection) and/or preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria. An antibacterial agent may be an agent that prevents the entrance of a bacteria (e.g., a Gram-negative bacteria) into a subject's cells, tissues, or organs, inhibits the growth of a bacteria (e.g., a Gram-negative bacteria) in a subject's cells, tissues, or organs, and/or kills a bacteria (e.g., a Gram-negative bacteria) that is inside a subject's cells, tissues, or organs. Examples of antibacterial agents are described in detail further herein. In some embodiments, an antibacterial agent used in addition to a compound described herein is tedizolid (e.g., tedizolid phosphate), azithromycin, meropenem, amikacin, levofloxacin, rifampicin, linezolid, erythromycin, or solithromycin. In some embodiments, the antibacterial agent used in combination with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) is tedizolid (e.g., tedizolid phosphate), azithromycin, meropenem, amikacin, or levofloxacin.
The term "aryl," as used herein, refers to any monocyclic or fused ring bicyclic or tricyclic system which has the characteristics of aromaticity in terms of electron distribution throughout the ring system, e.g., phenyl, naphthyl, or phenanthrene. In some embodiments, a ring system contains 5 1 5 ring member atoms or 5-10 ring member atoms. An aryl group may have, e.g., between five to fifteen carbons (e.g., a C5-C6, C5-C7, C5-C8, C5-C9, C5-C10, C5-C1 1 , C5-C12, C5-C13, C5-C14, or C5-C15 aryl).
The term "arylene," as used herein, refers to a multivalent (e.g., divalent or trivalent) aryl group linking together multiple (e.g., two or three) parts of a compound. For example, one carbon within the arylene group may be linked to one part of the compound, while another carbon within the arylene group may be linked to another part of the compound. An arylene may have, e.g., between five to fifteen carbons in the aryl portion of the arylene (e.g., a C5-C6, C5-C7, C5-C8, C5-C9. C5-C10, C5-C1 1 , C5-C12, C5-C13, C5-C14, or C5-C15 arylene). An arylene group can be substituted by the groups typically suitable as substituents for alkyl, alkenyl and alkynyl groups as set forth herein. Heteroarylene refers to an aromatic group including one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S. A heteroarylene group may have, e.g., between two to fifteen carbons (e.g., a C2-C3, C2-C4, C2-C5, C2-C6, C2-C7, C2- C8, C2-C9. C2-C10, C2-C1 1 , C2-C12, C2-C13, C2-C14, or C2-C15 heteroarylene).
The term "backbone," as used herein, refers to atoms comprising a linker of the compounds disclosed herein that together form the shortest path from one part of a compound to another part of the compound (e.g., the shortest path linking a first cyclic heptapeptide and a second cyclic heptapeptide).
The term "bacterial infection," as used herein, refers to the invasion of a subject's cells, tissues, and/or organs by bacteria (e.g., Gram-negative bacteria), thus, causing an infection. In some embodiments, the bacteria may grow, multiply, and/or produce toxins in the subject's cells, tissues, and/or organs. In some embodiments, a bacterial infection can be any situation in which the presence of a bacterial population(s) is latent within or damaging to a host body. Thus, a subject is "suffering" from a bacterial infection when a latent bacterial population is detectable in or on the subject's body, an excessive amount of a bacterial population is present in or on the subject's body, or when the presence of a bacterial population(s) is damaging the cells, tissues, and/or organs of the subject.
The term "bond," as used herein, refers to a chemical bond, e.g., an amide bond, a disulfide bond, a C-0 bond, a N-N bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation.
The term "carbamate," as used herein refers to a group having the structure
Figure imgf000058_0001
wherein R and R' are as defined for R16 herein.
The term "carbonyl," as used herein, refers to a group having the structure:
Figure imgf000058_0002
.
The term "covalently attached" refers to two parts of a compound that are linked to each other by a covalent bond formed between two atoms in the two parts of the compound. For example, in the compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)), when a' is 0, L is covalently attached to N'4, which means that when a' is 0, an atom in L forms a covalent bond with N'4 in the compound. Similarly, when a' is 1 and b' is 0, L is covalently attached to N'1 ; when b' is 1 , and c' is 0, L is covalently attached to N'2; when c' is 1 , L is covalently attached to N'3; when a is 0, L is covalently attached to N4; when a is 1 and b is 0, L is covalently attached to N1 ; when b is 1 , and c is 0, L is covalently attached to N2; and when c is 1 , L is covalently attached to N3.
The term "cyclic heptapeptide" or "cycloheptapeptide," as used herein, refers to compounds having seven natural or non-natural a-amino acid residues, such as D- or L-amino acid residues, in a closed ring. Generally, cyclic heptapeptides are formed by linking the a-carboxyl group of one amino acid to the a-amino group or the γ-amino group of another amino acid and cyclizing. The cyclic heptapeptide comprises a heterocycle comprising carbon and nitrogen ring members, which may be substituted, for example, with amino acid side chains. One nitrogen from an a-amino group in the cyclic heptapeptide, however, is not a ring member and is branched from a ring member of the heterocycle. Thus, this nitrogen is directly attached to a ring member, such as a carbon atom (e.g., an a-carbon atom). This nitrogen atom serves as an attachment point for the cyclic heptapeptide to a linker and/or to a peptide (e.g., a peptide including 1 -5 amino acid residue(s)), and thus is referred to herein as a "linking nitrogen." The linking nitrogen is directly attached to the ring of the cyclic heptapeptide and is not derived from a side chain, such as an ethylamine side chain. The linking nitrogens in a compound of, e.g., formula (II) or (III), are N4 and N'4. In some embodiments, cyclic heptapeptides bind to lipopolysaccharides (LPS) in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
In some embodiments, a peptide including one or more (e.g., 1 -5; 1 , 2, 3, 4, or 5) amino acid residues (e.g., natural and/or non-natural amino acid residues) may be covalently attached to a linking nitrogen (e.g., N4 and/or N'4, the nitrogen from an a-amino group) in the cyclic heptapeptide ring. Cyclic heptapeptides may be derived from polymyxins (e.g., naturally existing polymyxins and non-natural polymyxins) and/or octapeptins (e.g., naturally existing octapeptins and non-natural octapeptins).
Examples of naturally existing polymyxins include, but are not limited to, polymyxin Bi , polymyxin B2, polymyxin B3, polymyxin B4, polymyxin B5, polymyxin Ββ, polymyxin BHIe, polymyxin B2-lle, polymyxin Ci , polymyxin C2, polymyxin Si , polymyxin Ti, polymyxin T2, polymyxin Ai , polymyxin A2, polymyxin Di , polymyxin D2, polymyxin Ei (colistin A), polymyxin E2 (colistin B), polymyxin E3, polymyxin E4, polymyxin E7, polymyxin Ei-lle, polymyxin Ei-Val, polymyxin Ei-Nva, polymyxin E2-lle, polymyxin E2-Val, polymyxin E2-Nva, polymyxin Es-lle, polymyxin Mi , and polymyxin M2. In other embodiments, a cyclic heptapeptide may be entirely synthetic and prepared by standard peptide methodology as known in the art.
The terms "cycloalkyl" and "cycloalkylene," as used herein, refer to a monovalent saturated or unsaturated non-aromatic cyclic alkyl group, wherein one carbon within the cyclokalkyl or cycloalkylene group may be linked to one part of the compound, while another carbon within the cycloalkyl or cycloalkylene group may be linked to another part of the compound. A cycloalkyl may have, e.g., between three to twenty carbons (e.g., a C3-C7, C3-C8, C3-C9, C3-C10, C3-C1 1 , C3-C12, C3-C14, C3- C16, C3-C18, or C3-C20 cycloalkyl). For example, a C3-C20 cycloalkyl refers to a cycloalkyl group containing from 3 to 20 carbon atoms. Examples of cycloalkyl and cycloalkylene groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl. Cycloalkyl and cycloalkylene groups also include cyclic compounds having bridged multicyclic structures in which one or more carbons bridges two non-adjacent members of a monocyclic ring, e.g., bicyclo[2.2.1 .]heptyl and adamantane. Cycloalkyl and cycloalkylene groups also include bicyclic, tricyclic, and tetracyclic fused ring structures, e.g., decalin and spiro cyclic compounds.
The terms "cycloalkenyl" and "cycloalkylene," as used herein, refer to a cyclic group comprising carbon atoms that includes at least one carbon-carbon double bond. A cycloalkenyl or cycloalkenylene group may have, e.g., between four to twenty carbons in the cyclic portion of the cycloalkenyl or cycloalkenylene (e.g., a C4-C7, C4-C8, C4-C9. C4-C1 0, C4-C1 1 , C4-C12, C4-C14, C4-C16, C4-C18, or C4-C20 cycloalkenylene). For example, a C4-C20 cycloalkenyl or C4-C20 cycloalkenylene groups means a cycloalkenyl or cycloalkenylene group containing from 4 to 20 carbon atoms and includes at least one carbon-carbon double bond. Exemplary cycloalkenyl groups include, but are not limited to, cyclopentenyl, cyclohexenyl, and cycloheptenyl.
The terms "cycloalkynyl" and "cycloalkynylene," as used herein, refer to a cyclic group comprising carbon atoms that contains at least one carbon-carbon triple bond. A cycloalkynyl or cycloalkynylene group may have, e.g., between four to twenty carbons in the cyclic portion of the cycloalkynyl or cycloalkynylene (e.g., a C4-C7, C4-C8, C4-C9. C4-C1 0, C4-C1 1 , C4-C12, C4-C14, C4-C1 6, C4-C18, or C8-C20 cycloalkynyl or cycloalkynylene). For example, a C8-C20 cycloalkynyl group is a cyclic group containing from 8 to 20 carbon atoms and at least one carbon-carbon triple bond. A cycloalkynyl or cycloalkynylene group can be substituted by the groups typically suitable as substituents for alkyl, alkenyl and alkynyl groups as set forth herein.
The terms "halo" or "halogen," as used herein, refer to any halogen atom, e.g., F, CI, Br, or I. Any one of the groups or moieties described herein may be referred to as a "halo moiety" if it contains at least one halogen atom, such as haloalkyl. The term "hetero," as used herein, when used to describe a chemical group or moiety, refers to having at least one heteroatom that is not a carbon or a hydrogen, e.g., N, O, and S. Any one of the groups or moieties described above may be referred to as hetero if it contains at least one heteroatom. For example, a heterocycloalkyl, heterocycloalkenyl, or heterocycloalkynyl group refers to a cycloalkyl, cycloalkenyl, or cycloalkynyl group that has one or more heteroatoms independently selected from, e.g., N, O, and S. An example of a heterocycloalkenyl group is a maleimido. For example, a heteroaryl group refers to an aromatic group that has one or more heteroatoms independently selected from, e.g., N, O, and S. One or more heteroatoms may also be included in a substituent that replaced a hydrogen atom in a group or moiety as described herein. For example, in an optionally substituted heteroaryl group, if one of the hydrogen atoms in the heteroaryl group is replaced with a substituent (e.g., methyl), the substituent may also contain one or more heteroatoms (e.g., methanol).
The terms "heteroalkyl," "heteroalkylene," "heteroalkenyl," "heteroalkenylene," "heteroalkynyl," and/or "heteroalkynylene," as used herein, refer to alkylene, alkyl, alkenyl, alkenylene, alkynyl, and alkynylene groups including one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S. For example, a polyethylene glycol (PEG) polymer or a PEG unit -(CH2)2-0-in a PEG polymer is considered a heteroalkylene containing one or more oxygen atoms. In some embodiments, a C1 -C4 hydroxyalkyl is a heteroalkyl or heteroalkylene group.
The terms "heteroaryl," as used herein, refer to monocyclic or fused bicyclic ring systems containing one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms selected from O, S and N. A heteroaryl group may have, e.g., between two to fifteen carbons (e.g., a C2-C3, C2-C4, C2-C5, C2-C6, C2-C7, C2- C8, C2-C9. C2-C10, C2-C1 1 , C2-C12, C2-C13, C2-C14, or C2-C15 heteroaryl). The inclusion of a heteroatom permits inclusion of 5 membered rings to be considered aromatic as well as 6 membered rings. Thus, typical heteroaryl systems include, e.g., pyridyl, pyrimidyl, indolyl, benzimidazolyl, benzotriazolyl, isoquinolyl, quinolyl, benzothiazolyl, benzofuranyl, thienyl, furyl, pyrrolyl, thiazolyl, oxazolyl, isoxazolyl, benzoxazolyl, benzoisoxazolyl, and imidazolyl. Because tautomers are possible, a group such as phthalimido is also considered heteroaryl. In some embodiments, the aryl or heteroaryl group is a 5- or 6-membered aromatic rings system optionally containing 1 -2 nitrogen atoms. In some embodiments, the aryl or heteroaryl group is an optionally substituted phenyl, pyridyl, indolyl, pyrimidyl, pyridazinyl, benzothiazolyl, benzimidazolyl, pyrazolyl, imidazolyl, isoxazolyl, thiazolyl, or imidazopyridinyl. In some embodiments, the aryl group is phenyl. In some embodiments, an aryl group may be optionally substituted with a substituent such an aryl substituent, e.g., biphenyl.
The terms "heterocycloalkyl" and "heterocycloalkylene" refer to a cyclic group comprising carbon atoms and one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S. A tetrahydrofuran may be considered as a heterocycloalkylene.
The terms "heterocycloalkenyl" and "heterocycloalkenylene," as used herein, refer to a cyclic group comprising carbon atoms and one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S, and at least one carbon-carbon double bond.
The terms "heterocycloalkynl" and "heterocycloalkynylene," as used herein, refer to a cyclic group comprising carbon atoms and one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms, e.g., N, O, and S, and at least one carbon-carbon triple bond. The terms "hydroxyl" and "hydroxyl," as used herein, represents an -OH group.
The term "imino," as used herein, represents the group having the structure:
Figure imgf000061_0001
, wherein R is an optional substituent
The terms "linker," "Ι_'," "L"," and "L," as used herein, refer to a covalent linkage or connection between two or more components in a compound (e.g., two cyclic heptapeptides in a cyclic heptapeptide dimer). Molecules that may be used as linkers include at least two functional groups, which may be the same or different, e.g., two carboxylic acid groups, two amine groups, two sulfonic acid groups, a carboxylic acid group and an amine group, or a carboxy group and a sulfonic acid group. The first functional group may form a covalent linkage with a first component in the compound and the second functional group may form a covalent linkage with the second component in the compound. In some embodiments, a linker may be a bivalent structure having two arms, in which each arm is conjugated to a component of the compound. In some embodiments, dicarboxylic acid molecules may be used as linkers, in which the first carboxylic acid may form a covalent linkage with one component in the compound and the second carboxylic acid may form a covalent linkage with another component in the compound. Examples of dicarboxylic acids are described further herein. In some embodiments, a molecule containing one or more sulfonic acid groups may be used as a linker, in which the sulfonic acid group may form a sulfonamide linkage with a component in the compound. In some embodiments, a molecule containing one or more isocyanate groups may be used as a linker, in which the isocyanate group may form a urea linkage with a component in the compound. In some embodiments, a molecule containing one or more haloalkyi groups may be used as a linker, in which the haloalkyi group may form a covalent linkage, e.g., C-N and C-0 linkages, with a component in the compound.
In some embodiments, a linker provides space, rigidity, and/or flexibility between the two or more components. In some embodiments, a linker may be a bond, e.g., a covalent bond. The term "bond" refers to a chemical bond, e.g., an amide bond, a disulfide bond, a C-0 bond, a N-N bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation. In some embodiments, a linker includes no more than 100 atoms. In some embodiments, a linker includes no more than 100 non- hydrogen atoms. In some embodiments, the backbone of a linker includes no more than 100 atoms. The "backbone" of a linker refers to the atoms in the linker that together form the shortest path from one part of a compound to another part of the compound (e.g., the shortest path linking a first cyclic heptapeptide and a second cyclic heptapeptide). The atoms in the backbone of the linker are directly involved in linking one part of a compound to another part of the compound (e.g., linking a first cyclic heptapeptide and a second cyclic heptapeptide). For examples, hydrogen atoms attached to carbons in the backbone of the linker are not considered as directly involved in linking one part of the compound to another part of the compound.
In some embodiments, a linker may comprise a synthetic group derived from, e.g., a synthetic polymer (e.g., a polyethylene glycol (PEG) polymer). In some embodiments, a linker may comprise one or more amino acid residues, such as D- or L-amino acid residues. In some embodiments, a linker may be a residue of an amino acid sequence (e.g., a 1 -25 amino acid, 1 -10 amino acid, 1 -9 amino acid, 1 -8 amino acid, 1 -7 amino acid, 1 -6 amino acid, 1 -5 amino acid, 1 -4 amino acid, 1 -3 amino acid, 1 -2 amino acid, or 1 amino acid sequence). In some embodiments, a linker may comprise one or more, e.g., 1 -100, 1 -50, 1 -25, 1 -10, 1 -5, or 1 -3, optionally substituted alkylene, optionally substituted heteroalkylene (e.g., a PEG unit), optionally substituted alkenylene, optionally substituted heteroalkenylene, optionally substituted alkynylene, optionally substituted heteroalkynylene, optionally substituted cycloalkylene, optionally substituted heterocycloalkylene, optionally substituted cycloalkenylene, optionally substituted heterocycloalkenylene, optionally substituted cycloalkynylene, optionally substituted
heterocycloalkynylene, optionally substituted arylene, optionally substituted heteroarylene (e.g., pyridine), O, S, NR' (R' is H, optionally substituted alkyl, optionally substituted heteroalkyl, optionally substituted alkenyl, optionally substituted heteroalkenyl, optionally substituted alkynyl, optionally substituted heteroalkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted cycloalkenyl, optionally substituted heterocycloalkenyl, optionally substituted cycloalkynyl, optionally substituted heterocycloalkynyl, optionally substituted aryl, or optionally substituted heteroaryl), P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino. For example, a linker may comprise one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene (e.g. , a PEG unit), optionally substituted C2-C20 alkenylene (e.g., C2 alkenylene), optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20
heteroalkynylene, optionally substituted C3-C20 cycloalkylene (e.g., cyclopropylene, cyclobutylene), optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene (e.g., C6 arylene), optionally substituted C3-C15 heteroarylene (e.g., imidazole, pyridine), O, S, NR' (R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2- C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C1 5 aryl, or optionally substituted C5-C15 heteroaryl), P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino.
The term "lipophilic moiety," as used herein, refers to a portion, substituent, or functional group of a compound that is, in general, hydrophobic and non-polar. A moiety is lipophilic if it has a hydrophobicity determined using a cLogP value of greater than 0, such as about 0.25 or greater, about 0.5 or greater, about 1 or greater, about 2 or greater, 0.25-5, 0.5-4 or 2-3. As used herein, the term "cLogP" refers to the calculated partition coefficient of a molecule or portion of a molecule. The partition coefficient is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium (e.g., octanol and water) and measures the hydrophobicity or hydrophilicity of a compound. A variety of methods are available in the art for determining cLogP. For example, in some embodiments, cLogP can be determined using quantitative structure-property relationship algorithims known in the art (e.g., using fragment based prediction methods that predict the logP of a compound by determining the sum of its non-overlapping molecular fragments). Several algorithims for calculating cLogP are known in the art including those used by molecular editing software such as CHEMDRAW® Pro, Version 12.0.2.1 092 (Camrbridgesoft, Cambridge, MA) and MARVINSKETCH® (ChemAxon, Budapest, Hungary). A moiety is considered lipophilic if it has a cLogP value described above in at least one of the above methods. A lipophilic moiety having the stated cLogP value will be considered lipophilic, even though it may have a positive charge or a polar substituent.
In some embodiments, a lipophilic moiety contains entirely hydrocarbons. In some embodiments, a lipophilic moiety may contain one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms independently selected from N, O, and S (e.g., an indolyl), or one or more, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, halo groups, which, due to the structure of the moiety and/or small differences in electronegativity between the heteroatoms or halo groups and the hydrocarbons, do not induce significant chemical polarity into the lipophilic moiety. Thus, in some embodiments, a lipophilic moiety having, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, heteroatoms and/or, e.g., 1 -4, 1 -3, 1 , 2, 3, or 4, halo atoms may still be considered non-polar. In some embodiments, a lipophilic moiety may be optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heteroalkenyl, optionally substituted heteroalkynyl, or optionally substituted heteroaryl, or halo forms thereof, wherein the optional substituents are also lipophilic (such as alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, aryl, or heteroaryl) or are not lipophilic but do not change the overall lipophilic character of the moiety, i.e., the moiety has a cLogP value of greater than 0. For example, octanol contains a polar group, OH, but is still a lipophilic moiety. In some embodiments, a lipophilic moiety may be benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or substituted indolyl (e.g., alkyl substituted indolyl). In some embodiments, a lipophilic moiety may be the side chain of a hydrophobic amino acid residue, e.g., leucine, isoleucine, alanine, phenylalanine, valine, and proline, or groups such as methyl, ethyl, propyl, isopropyl, butyl, isobutyl, and pyrrolidinyl. In some embodiments, lipophilic moieties of the compounds described herein may interact with the hydrophobic portions of lipid A (e.g., fatty acid side chains of lipid A) when the compounds bind to the membrane of bacterial cells (e.g., Gram-negative bacterial cells). Due to its position on the cyclic heptapeptide, one or more of R1 , R12, R15, R'1 , R'12, and R'15 may be a lipophilic moiety.
The phrase "LPS-induced nitroic oxide (NO) production from a macrophage," as used herein, refers to the ability of the lipopolysaccharides (LPS) in Gram-negative bacteria to activate a macrophage and induce NO production from the macrophage. NO production from a macrophage in response to LPS is a signal of macrophage activation, which may lead to sepsis in a subject, e.g., a Gram-negative bacteria infected subject. The disclosure features compounds (e.g., compounds of any one of formulas (l)-(XXXXIX)) that are able to bind to LPS in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, thus neutralizing an immune response to LPS (see, e.g., Example 1 13). NO production from a macrophage may be measured using available techniques in the art, e.g., a Griess assay, as demonstrated in Example 1 13.
The term "N-protecting group," as used herein, represents those groups intended to protect an amino group against undesirable reactions during synthetic procedures. Commonly used N-protecting groups are disclosed in Greene, "Protective Groups in Organic Synthesis," 5th Edition (John Wiley & Sons, New York, 2014), which is incorporated herein by reference. N-protecting groups include, e.g., acyl, aryloyl, and carbamyl groups such as formyl, acetyl, propionyl, pivaloyl, t-butyl acetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthalyl, o-nitrophenoxyacetyl, a-chlorobutyryl, benzoyl, carboxybenzyl (CBz), 4 chlorobenzoyl, 4 bromobenzoyl, 4 nitrobenzoyl, and chiral auxiliaries such as protected or unprotected D, L or D, L-amino acid residues such as alanine, leucine, phenylalanine;
sulfonyl-containing groups such as benzenesulfonyl and p-toluenesulfonyl; carbamate forming groups such as benzyloxycarbonyl, p chlorobenzyloxycarbonyl, p methoxybenzyloxycarbonyl, p- nitrobenzyloxycarbonyl, 2 nitrobenzyloxycarbonyl, p bromobenzyloxycarbonyl, 3,4- dimethoxybenzyloxycarbonyl, 3,5 dimethoxybenzyl oxycarbonyl, 2,4-dimethoxybenzyloxycarbonyl, 4 methoxybenzyloxycarbonyl, 2 nitro-4,5-dimethoxybenzyloxycarbonyl, 3,4,5 trimethoxybenzyloxycarbonyl, 1 (p biphenylyl) 1 methylethoxycarbonyl, a,a-dimethyl-3,5 dimethoxybenzyloxycarbonyl, benzhydryloxy carbonyl, t-butyloxycarbonyl (BOC), diisopropylmethoxycarbonyl, isopropyloxycarbonyl, ethoxycarbonyl, methoxycarbonyl, allyloxycarbonyl, 2,2,2,-trichloroethoxycarbonyl, phenoxycarbonyl, 4-nitrophenoxy carbonyl, fluorenyl-9-methoxycarbonyl (Fmoc), cyclopentyloxycarbonyl, adamantyloxycarbonyl, cyclohexyloxycarbonyl, and phenylthiocarbonyl; alkaryl groups such as benzyl, triphenylmethyl, and benzyloxymethyl; and silyl groups such as trimethylsilyl.
The term "optionally substituted," as used herein, refers to having 0, 1 , or more substituents, such as 0-25, 0-20, 0-10 or 0-5 substituents. Substituents include, but are not limited to, alkyl, alkenyl, alkynyl, aryl, alkaryl, acyl, heteroaryl, heteroalkyl, heteroalkenyl, heteroalkynyl, heteroalkaryl, halogen, oxo, cyano, nitro, amino, alkamino, hydroxy, alkoxy, alkanoyl, carbonyl, carbamoyl, guanidinyl, amidinyl, ureido, any of the groups or moieties described above, and hetero versions of any of the groups or moieties described above. Substituents include, but are not limited to, F, CI, methyl, phenyl, benzyl, OR, NR2, SR, SOR, S02R, OCOR, NRCOR, NRCONR2, NRCOOR, OCONR2, RCO, COOR, alkyl-OOCR, SO3R, CONR2, SO2NR2, NRSO2NR2, CN, CF3, OCF3, R3S1, and NO2, wherein each R is, independently, H, alkyl, alkenyl, aryl, heteroalkyl, heteroalkenyl, or heteroaryl, and wherein two of the optional substituents on the same or adjacent atoms can be joined to form a fused, optionally substituted aromatic or nonaromatic, saturated or unsaturated ring which contains 3-8 members, or two of the optional substituents on the same atom can be joined to form an optionally substituted aromatic or nonaromatic, saturated or unsaturated ring which contains 3-8 members.
An optionally substituted group or moiety refers to a group or moiety (e.g., any one of the groups or moieties described above) in which one of the atoms (e.g., a hydrogen atom) is optionally replaced with another substituent. For example, an optionally substituted alkyl may be an optionally substituted methyl, in which a hydrogen atom of the methyl group is replaced by, e.g., OH. As another example, a substituent on a heteroalkyl or its divalent counterpart, heteroalkylene, may replace a hydrogen on a carbon or a hydrogen on a heteroatom such as N. For example, the hydrogen atom in the
group -R-NH-R- may be substituted with an alkamide substituent, e.g., -R-N[(CH2C(0)N(CH3)2]-R.
Generally, an optional substituent is a noninterfering substituent. A "noninterfering substituent" refers to a substituent that leaves the ability of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) to either bind to LPS or to kill or inhibit the growth of Gram-negative bacteria qualitatively intact. Thus, in some embodiments, the substituent may alter the degree of such activity. However, as long as the compound retains the ability to bind to LPS and/or to kill or inhibit the growth of Gram-negative bacteria, the substituent will be classified as "noninterfering." In some aspects, a noninterfering substituent leaves the ability of a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) to kill or inhibit the growth of Gram-negative bacteria qualitatively intact as determined by measuring the minimum inhibitory concentration (MIC) against at least one Gram-negative bacteria as known in the art, wherein the MIC is 32 μg/mL or less. In some aspects, a noninterfering substituent leaves the ability of a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) to bind to LPS from the cell membrane of Gram-negative bacteria qualitatively intact, as determined by an LPS binding assay (e.g., see Example 109), wherein the compound shows a value of about 10% or greater displacement of a fluorogenic substrate at 250 μΜ of the compound.
The term "oxo," as used herein, refers to a substituent having the structure =0, where there is a double bond between an atom and an oxygen atom.
As used herein, the term "pharmaceutical composition" refers to a medicinal or pharmaceutical formulation that contains at least one active ingredient (e.g., a compound of any one of formulas (I)- (XXXXIX)) as well as one or more excipients and diluents to enable the active ingredient suitable for the method of administration. The pharmaceutical composition of the present disclosure includes pharmaceutically acceptable components that are compatible with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
As used herein, the term "pharmaceutically acceptable carrier" refers to an excipient or diluent in a pharmaceutical composition. For example, a pharmaceutically acceptable carrier may be a vehicle capable of suspending or dissolving the active compound (e.g., a compound of any one of formulas (I)- (XXXXIX)). The pharmaceutically acceptable carrier must be compatible with the other ingredients of the formulation and not deleterious to the recipient. In the present disclosure, the pharmaceutically acceptable carrier must provide adequate pharmaceutical stability to a compound described herein. The nature of the carrier differs with the mode of administration. For example, for oral administration, a solid carrier is preferred; for intravenous administration, an aqueous solution carrier (e.g., WFI, and/or a buffered solution) is generally used.
The term "pharmaceutically acceptable salt," as used herein, represents salts of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) that are, within the scope of sound medical judgment, suitable for use in methods described herein without undue toxicity, irritation, and/or allergic response. Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in: Pharmaceutical Salts: Properties, Selection, and Use (Eds. P.H. Stahl and C.G. Wermuth), Wiley-VCH, 2008. The salts can be prepared in situ during the final isolation and purification of the compounds described herein or separately by reacting the free base group with a suitable organic acid.
The term "phosphate," as used herein, represents the group having the structure:
Figure imgf000065_0001
The term "phosphoryl," as used herein, represents the group having the structure:
Figure imgf000066_0001
or
O
s i '
|— 0-p-o—
R
The term "polar moiety," as used herein, refers to a portion, substituent, or functional group of a compound that has a chemical polarity induced by atoms with different electronegativity. The polarity of a polar moiety is dependent on the electronegativity between atoms within the moiety and the asymmetry of the structure of the moiety. In some embodiments, a polar moiety contains one or more (e.g., 1 -4, 1 -3, 1 , 2, 3, or 4) heteroatoms independently selected from N, O, and S, which may induce chemical polarity in the moiety by having different electronegativity from carbon and hydrogen. In general, a polar moiety interacts with other polar or charged molecules. In some embodiments, a polar moiety may be optionally substituted alkamino, optionally substituted heteroalkyl (e.g., N- and/or O-containing
heteroalkyl; -(CH2)4-carboxylic acid, -(CH2)3-carboxylic acid, -(CH2)2-carboxylic acid, -CH2-carboxylic acid), optionally substituted heterocycloalkyl (e.g., N- and/or O-containing heterocycloalkyl), or optionally substituted heteroaryl (e.g., N- and/or O-containing heteroaryl). In some embodiments, a polar moiety may -CH(CH3)OH, -CH2OH , -(CH2)2CONH2, -CH2CONH2, -CH2COOH , or -(CH2)2COOH. Thus, substituents may transform an otherwise lipophilic moiety such optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heteroalkenyl, optionally substituted heteroalkynyl, or optionally substituted heteroaryl, or halo forms thereof, to a polar moiety with the addition of a substituent that imparts polarity, such as OH, COOH, COOR, or CON R2, in which R is H or C1 -C4 alkyl. In some embodiments, a polar moiety may be the side chain or a polar or charged amino acid residue (e.g., threonine, serine, glutamine, asparagine, arginine, lysine histidine, aspartic acid, and glutamic acid). In some embodiments, a polar moiety is the side chain of threonine. In some embodiments, polar moieties of the compounds described herein interact with the negatively charged portions of lipid A (e.g., phosphates of lipid A) when the compounds bind to the membrane of bacterial cells (e.g., Gram-negative bacterial cells). Due to its position on the cyclic heptapeptide, one or more of R1 , R12, R15, R'1 , R'12, and R'15 may be a polar moiety.
The term "polymyxin core," as used herein means a cyclic heptapeptide having the structure:
Figure imgf000066_0002
wherein Q1 , Q2 and Q3 are as follows:
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
attachment of the polymyxin core to the remainder of the compounds disclosed herein, including the linker and the second polymyxin core (e.g., the second cyclic heptapeptide).
The term "positively charged moiety," as used herein, refers to a portion, substituent, or functional group of a compound that contains at least one positive charge. In some embodiments, a positively charged moiety contains one or more (e.g., 1 -4, 1 -3, 1 , 2, 3, or 4) heteroatoms independently selected from N, O, and S, for example. In some embodiments, a positively charged moiety may possess a pH- dependent positive charge, e.g., the moiety becomes a positively charged moiety at physiological pH (e.g., pH 7), such as -NH3 +, -(CH2)4NH2, -(CH2)3NH2, -(CH2)2NH2, -CH2NH2, -(CH2)4N(CH3)2,
-(CH2)3N(CH3)2, -(CH2)2N(CH3)2, -CH2N(CH3)2, -(CH2)4NH(CH3), -(CH2)3NH(CH3),-(CH2)2NH(CH3), and -CH2NH(CH3). In some embodiments, a positively charged moiety may be optionally substituted alkamino, optionally substituted heteroalkyl (e.g., optionally substituted heteroalkyl containing 1 -3 nitrogens; -(CH2)4-guanidinium, -(CH2)3-guanidinium, -(CH2)2-guanidinium, -CH2-guanidinium), optionally substituted heterocycloalkyl (e.g., optionally substituted heterocycloalkyl containing 1 -3 nitrogens), or optionally substituted heteroaryl (e.g., optionally substituted heteroaryl containing 1 -3
nitrogens; -(CH2)4-imidazole, -(CH2)3-imidazole, -(CH2)2-imidazole, -CH2-imidazole). In some
embodiments, a positively charged moiety may be pH independent such
as -CH2N(CH3)3 +, -(CH2)2N(CH3)3 +, -(CH2)3N(CH3)3 +, or -(CH2)4N(CH3)3 +. Thus, substituents may transform an otherwise lipophilic moiety such as optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heteroalkenyl, optionally substituted heteroalkynyl, or optionally substituted heteroaryl, or halo forms thereof, to a positively charged moiety with the addition of a substituent that imparts a positive charge or a pH dependent positive charge, such as guanidinyl, -NH3 +, -NH2, -NH(CH3), -N(CH3)2, and/or -N(CH3)3 +. In some embodiments, a positively charged moiety may be the side chain of an amino acid residue (e.g., a natural or non-natural amino acid residue, such as a D- or L-amino acid residue, that is positively charged at physiological pH (e.g., pH 7), such as the side chain of a basic amino acid residue
(e.g., arginine, lysine, histidine, ornithine, diaminobuteric acid, or diaminopropionic acid). In some embodiments, positively charged moieties of the compounds described herein interact with the negatively charged portions of lipid A (e.g., phosphates of lipid A) when the compounds bind to the membrane of bacterial cells (e.g., Gram-negative bacterial cells). Due to its position on the cyclic heptapeptide, one or more of R1 1 , R13, R14, R'1 1 , R'13, and R'14 may be a positively charged moiety.
The term "protecting against," as used herein, refers to preventing a subject from developing a bacterial infection (e.g., a Gram-negative bacterial infection) or decreasing the risk that a subject may develop a bacterial infection (e.g., a Gram-negative bacterial infection). Prophylactic drugs used in methods of protecting against a bacterial infection in a subject are often administered to the subject prior to any detection of the bacterial infection. In some embodiments of methods of protecting against a bacterial infection, a subject (e.g., a subject at risk of developing a bacterial infection) may be administered a compound described herein (e.g., a compound having any one of formulas (l)-(XXXXIX)) to prevent the bacterial infection development or decrease the risk of the bacterial infection development.
The term "resistant strain of bacteria," as used herein, refers to a strain of bacteria (e.g., Gram- negative or Gram-positive bacteria) that is refractory to treatment with an antibiotic, such as an antibiotic described in Section IV of Detailed Description. Antibiotics that a strain of bacteria is resistant to do not include the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)).
Resistance may arise through natural resistance in certain types of bacteria, spontaneous random genetic mutations, and/or by inter- or intra-species horizontal transfer of resistance genes. In some embodiments, a resistant strain of bacteria contains a mcr- 1 gene and/or a mcr-2 gene. In some embodiments, a resistant strain of bacteria contains a mcr- 1 gene and/or a mcr-2 gene in combination with other antibiotic resistance genes. In some embodiments, a resistant strain of bacteria is a resistant strain of E. co// (e.g., E. coli BAA-2469).
The term "subject," as used herein, can be a human, non-human primate, or other mammal, such as but not limited to dog, cat, horse, cow, pig, turkey, goat, fish, monkey, chicken, rat, mouse, and sheep.
The term "substantially simultaneously," as used herein, refers to two or more events that occur at the same time or within a narrow time frame of each other. As disclosed herein, a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and an antibacterial agent (e.g., Iinezolid or tedizolid) may be administered substantially simultaneously, which means that the compound and the antibacterial agent are administered together (e.g., in one pharmaceutical composition) or separately but within a narrow time frame of each other, e.g., within 10 minutes, e.g., 1 0, 9, 8, 7, 6, 5, 4, 3, 2, or 1 minute, or 45, 30, 15, or 10 seconds of each other.
The term "sulfonyl," as used herein, represents the group having the structure: v ¾ v° ^ .
The term "therapeutically effective amount," as used herein, refers to an amount, e.g., pharmaceutical dose, effective in inducing a desired effect in a subject or in treating a subject having a condition or disorder described herein (e.g., a bacterial infection (e.g., a Gram-negative bacterial infection)). It is also to be understood herein that a "therapeutically effective amount" may be interpreted as an amount giving a desired therapeutic and/or preventative effect, taken in one or more doses or in any dosage or route, and/or taken alone or in combination with other therapeutic agents (e.g., an antibacterial agent described herein). For example, in the context of administering a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) that is used for the treatment of a bacterial infection, an effective amount of a compound is, for example, an amount sufficient to prevent, slow down, or reverse the progression of the bacterial infection as compared to the response obtained without administration of the compound. The term "thiocarbonyl," as used herein, refers to a group having the structure:
Figure imgf000072_0001
Definitions of abbreviations used in the disclosure are provided in Table A below:
Table A
Figure imgf000072_0002
Other features and advantages of the compounds described herein will be apparent from the following detailed description and the claims.
Description of the Drawings
FIGS. 1 A, 1 B, and 1 C are graphs showing the inhibition of NO production by Compound 16, Compound 1 9, and Compound 30.
FIG. 2 is a schematic illustrating a 96-well checkerboard synergy MIC plate layout.
FIG. 3 is graph showing the activity of Compound 150 in a Mouse Thigh Infection Model. Detailed Description
The disclosure features compounds, compositions, and methods for the treatment of bacterial infections (e.g., Gram-negative bacterial infections). The compounds disclosed herein include two cyclic heptapeptide cores (e.g., polymyxin cores) linked to each other through a linker and/or one or two peptides (e.g., a peptide including a 1 -5 amino acid residue(s)). In particular, the compounds can be used in the treatment of bacterial infections caused by Gram-negative bacteria. In some embodiments, one or more of the compounds described herein are used in combination with an antibacterial agent (e.g., linezolid or tedizolid (e.g., tedizolid phosphate)).
I. Bacterial Infections
Pathogenic bacteria cause bacterial infections and diseases such as tuberculosis, pneumonia, and foodborne illnesses. Bacteria may be categorized into two major types: Gram-positive bacteria and Gram-negative bacteria. Gram-positive bacteria possess a thick cell wall containing multiple layers of peptidoglycan and teichoic acids, while Gram-negative bacteria have a relatively thin cell wall containing fewer layers of peptidoglycan that are surrounded by a second lipid membrane containing
lipopolysaccharides (LPS) and lipoproteins. LPS, also called endotoxins, are composed of
polysaccharides and lipid A. These differences in bacterial cell wall structure can produce differences in antibiotic susceptibility. Examples of Gram-positive bacteria include, but are not limited to, bacteria in the genus Streptococcus (e.g., Streptococcus pyogenes), bacteria in the genus Staphylococcus (e.g., Staphylococcus cohnii), bacteria in the genus Corynebacterium (e.g., Corynebacterium auris), bacteria in the genus Listeria (e.g., Listeria grayi), bacteria in the genus Bacillus (e.g., Bacillus aerius), and bacteria in the genus Clostridium (e.g., Clostridium acetium). Examples of Gram-negative bacteria include, but are not limited to, bacteria in the genus Escherichia (e.g., Escherichia coli), bacteria in the genus Klebsiella (e.g., Klebsiella granulomatis, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella terrigena, and Klebsiella variicola), bacteria in the genus Acinetobacter (e.g., Acinetobacter baumannii,
Acinetobacter ca!coaceticus, Acinetobacter kookii, and Acinetobacter junin, bacteria in the genus Pseudomonas (e.g., Pseudomonas aeruginosa), bacteria in the genus Neisseria (e.g., Neisseria gonorrhoeae), bacteria in the genus Yersinia (e.g., Yersinia pestis), bacteria in the genus Vibrio (e.g., Vibrio cholerae), bacteria in the genus Campylobacter (e.g., Campylobacter jejuni), and bacteria in the genus Salmonella (e.g., Salmonella enterica).
Bacteria may evolve to become more or fully resistant to antibiotics. Resistance may arise through natural resistance in certain types of bacteria, spontaneous random genetic mutations, and/or by inter- or intra-species horizontal transfer of resistance genes. Resistant bacteria are increasingly difficult to treat, requiring alternative medications or higher doses, which may be more costly or more toxic.
Bacteria resistant to multiple antibiotics are referred to as multidrug resistant (MDR) bacteria. For example, the mcr- 1 gene encodes a phosphoethanolamine transferase (MCR-1 ) which confers resistance to colistin, a natural polymyxin, through modification of LPS. This is the first known horizontally- transferable resistance determinant for the polymyxin class of antibiotics. The mcr- 1 gene has also been found in bacterial strains which already possess resistance to other classes of antibiotics, such as in carbapenem-resistant Enterobacteriaceae (CRE). An mcr- 1 plasmid resistance plasmid refers to a bacterial plasmid that carries mcr- 1 alone or in combination with other antibiotic resistance genes. A mcr- 1 resistance plasmid refers to a bacterial plasmid that carries one or more antibiotic resistance genes. Examples of mcr- 1 resistance plasmids include, but are not limited to, pHNSHP45, pMR051 6mcr, pESTMCR, pAF48, pAF23, pmcr1 -lncX4, pmcr1 -lncl2, pA31 -12, pVT553, plCBEC72Hmcr, pE15004, pE1501 5, and pE15017.
In another example, the mcr-2 gene also confers resistance to colistin. The mcr-2 gene was identified in porcine and bovine colistin-resistance E.coli that did not contain mcr- 1 (Xavier et al., Euro Surveill 2~\ (27), 2016). The mcr-2 gene is a 1 ,617 bp phspoethanolamine transferase harbored on an lncX4 plasmid. The mcr-2 gene has 76.7% nucleotide identity to mcr- 1. Analysis of mcr-2 harboring plasmids from E.coli isolates shows that the mobile element harboring mcr-2 is an IS element of the IS1595 superfamily, which are distinguished by the presence of an ISX02-like transposase domain (Xavier et al., supra). The MCR-2 protein was predicted to have two domains, with domain 1 (1 -229 residues) as a transporter and domain 2 (230-538 residues) as a transferase domain. An mcr-2 resistance plasmid refers to a bacterial plasmid that carries mcr-2 alone or in combination with other antibiotic resistance genes. A mcr-2 resistance plasmid refers to a bacterial plasmid that carries one or more antibiotic resistance genes. Mcr-2 resistance plasmids include, but are not limited to, pKP37-BE and pmcr2-lncX4.
In a further example, the mcr-3 gene also confers resistance to colistin. The mcr-3 gene is considered to include variants which encode an MCR-3 protein that confers resistance to cholistin, such as mcr-3 which encodes a protein having an amino acid substitution at V413A. The mcr-3 gene was identified in cholistin-resistant E.coli isolated from swine (Clemente et al., 27th ECCMID, Vienna, Austria, 2017). The mcr3 gene is harbored on an lncX4 plasmid. Analysis of mcr-3 harboring plasmids from E.coli isolates shows that the mobile element harboring mcr-3 is the IS26 element. A mcr-3 resistance plasmid refers to a bacterial plasmid that carries one or more antibiotic resistance genes.
Furthermore, resistant strain E. coli BAA-2469 possesses the New Delhi metallo-p-lactamase (NDM-1 ) enzyme, which makes bacteria resistant to a broad range of β-lactam antibiotics. Additionally, E. coli BAA-2469 is also known to be resistatnt to penicillins (e.g., ticarcillin, ticarcillin/clavulanic acid, piperacillin, ampicillin, and ampicillin/sulbactam), cephalosporins (e.g., cefalotin, cefuroxime, cefuroxime, cefotetan, cefpodoxime, cefotaxime, ceftizoxime, cefazolin, cefoxitin, ceftazidime, ceftriaxone, and cefepime), carbapenems (e.g., doripenem, meropenem, ertapenem, imipenem), quinolones (e.g., nalidixic acid, moxifloxacin, norfloxacin, ciprofloxacin, and levofloxacin), aminoglycosides (e.g., amikacin, gentamicin, and tobramycin), and other antibiotics (e.g., tetracycline, tigecycline, nitrofurantoin, aztreonam, trimethoprim/sulfamethoxazole).
In some embodiments, a resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, and/or a chromosomal mutation conferring polymyxin resistance. In some embodiments, a resistant strain of bacteria is a resistant strain of E. coli (e.g., E. coli BAA-2469).
II. Compounds of the Disclosure
Provided herein are synthetic compounds useful in the treatment of bacterial infections (e.g., Gram-negative bacterial infections). The disclosure provides compounds including dimers of cyclic heptapeptides joined to each other by way of a linker and/or one or two peptides (e.g., each peptide including a 1 -5 amino acid residue(s)) (e.g., two polymyxin cores joined to each other by way of a linker and/or one or two peptides). In some aspects, a cyclic heptapeptide or polymyxin core, as used herein, refers to certain compounds that bind to LPS in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics. In some aspects, cyclic heptapeptide or polymyxin core, as used herein, refers to certain compounds that kill or inhibit the growth of Gram-negative bacteria as determined by measuring the minimum inhibitory concentration (MIC) against at least one Gram-negative bacteria as known in the art, wherein the MIC is 32 μg/mL or less. Cyclic heptapeptides are composed of, at least, amino acid residues, each of which may, independently, have a D- or L- configuration, assembled as a cyclic heptapeptide ring. A cyclic heptapeptide includes seven natural or non-natural amino acid residues attached to each other in a closed ring. The ring contains six bonds formed by linking the carbon in the a-carboxyl group of one amino acid residue to the nitrogen in the a-amino group of the adjacent amino acid residue and one bond formed by linking the carbon in the a-carboxyl group of one amino acid residue to the nitrogen in the γ- amino group in the side chain of the adjacent amino acid residue. For the amino acid residue whose nitrogen in the γ-amino group in the side chain participates in forming the ring, the nitrogen in the a-amino group of this amino acid residue does not participate directly in forming the ring and serves as the linking nitrogen (thus, referred to as the "linking nitrogen" herein) that links one cyclic heptapeptide or polymyxin core to another cyclic heptapeptide or polymyxin core by way of a linker and/or one or two peptides (e.g., a peptide including 1 -5 amino acid residue(s)). Compounds described herein are dimers of cyclic heptapeptides (e.g., dimers of polymyxin cores) that are linked to each other at their linking nitrogens through a linker and/or one or two peptides (e.g., a peptide including 1 -5 amino acid residue(s)).
In some embodiments, a peptide including one or more (e.g., 1 -5; 1 , 2, 3, 4, or 5) amino acid residues (e.g., natural and/or non-natural amino acid residues) may be covalently attached to the linking nitrogen of the cyclic heptapeptide or the polymyxin core. Cyclic heptapeptides or polymyxin cores may be derived from polymyxins (e.g., naturally existing polymyxins and non-natural polymyxins) and/or octapeptins (e.g., naturally existing octapeptins and non-natural octapeptins). In some embodiments, cyclic heptapeptides may be compounds described in Gallardo-Godoy et al., J. Med. Chem. 59:1068, 2016 (e.g., compounds 1 1 -41 in Table 1 of Gallardo-Godoy et al.), which is incorporated herein by reference in its entirety. Examples of some naturally existing polymyxins and their structures are shown in Table 1 .
Table 1 . Natural polymyxins and their structures
Figure imgf000076_0001
Figure imgf000077_0001
Without being bound by theory, in some aspects, compounds described herein bind to the cell membrane of Gram-negative bacteria (e.g., bind to LPS in the cell membrane of Gram-negative bacteria) to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics. In some embodiments, the initial association of the compounds with the bacterial cell membrane occurs through electrostatic interactions between the compounds and the anionic LPS in the outer membrane of Gram-negative bacteria, disrupting the arrangement of the cell membrane.
Specifically, compounds described herein may bind to lipid A in the LPS. More specifically, compounds described herein may bind to one or both phosphate groups in lipid A. In some embodiments, antibiotic- resistant bacteria (e.g., antibiotic-resistant, Gram-negative bacteria) has one phosphate group in lipid A. In some embodiments, compounds described herein may bind to multiple Gram-negative bacterial cells at the same time. The binding of the compounds described herein to the LPS may also displace Mg2+ and Ca2+ cations that bridge adjacent LPS molecules, causing, e.g., membrane permeabilization, leakage of cellular molecules, inhibition of cellular respiration, and/or cell death.
Compounds described herein include a first cyclic heptapeptide and a second cyclic heptapeptide linked to each other at their linking nitrogens by way of a linker and/or one or two peptides (e.g., a peptide including 1 -5 amino acid residue(s)), e.g., compounds of any one of formulas (l)-(XXXXIX). In some embodiments, the first and second cyclic heptapeptides are the same. In some embodiments, the first and second cyclic heptapeptides are different. Compounds described herein may be synthesized using available chemical synthesis techniques in the art. In some embodiments, available functional groups in the first and second cyclic heptapeptides and the linker, e.g., amines, carboxylic acids, and/or hydroxyl groups, may be used in making the compounds described herein. For example, the linking nitrogen in a cyclic heptapeptide may form an amide bond with the carbon in a carboxylic acid group in the linker. A peptide including one or more (e.g., 1 -5; 1 , 2, 3, 4, or 5) amino acid residues (e.g., natural and/or non- natural amino acid residues) may be also be covalently attached to the linking nitrogen of the cyclic heptapeptide through forming an amide bond between the carbon in a carboxylic acid group in the peptide and the linking nitrogen. In cases where a functional group is not available for conjugation, a molecule may be derivatized using conventional chemical synthesis techniques that are well known in the art. In some embodiments, the compounds described herein contain one or more chiral centers. The compounds include each of the isolated stereoisomeric forms as well as mixtures of stereoisomers in varying degrees of chiral purity, including racemic mixtures. It also encompasses the various diastereomers, enantiomers, and tautomers that can be formed.
The disclosure provides a compound, or a pharmaceutically acceptable salt thereof, described by formula (I):
M2-L'-M1
(I)
in which M1 includes a first cyclic heptapeptide including a linking nitrogen and M2 includes a second cyclic heptapeptide including a linking nitrogen, and L' is a linker covalently attached to the linking nitrogen in each of M1 and M2, and in which L' is not
Figure imgf000078_0001
in which L" is a remainder of L', and each of R'L and RL is, independently, C1 -C10 alkyl.
In some embodiments, L' in the compound described by formula M2-L'-M1 is described by: -A2— L— A1- in which L is a remainder of L'; A1 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M1 or is absent; and A2 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M2 or is absent.
In some embodiments, the disclosure provides a compound, or a pharmaceutically acceptable salt thereof, described by formula (II)
Figure imgf000079_0001
(ll)
in which L is a reminder of L'; each of each of R1 , R12, R'1 , and R'12 is, independently, a lipophilic moiety, a polar moiety, or H; each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is, independently, optionally substituted C1 - C5 alkamino, a polar moiety, a positively charged moiety, or H; each of R15 and R'15 is, independently, a lipophilic moiety or a polar moiety; each of R2, R3, R4, R5, R6, R7, R8, R9, R10, R'2, R'3, R'4, R'5, R'6, R'7, R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3- C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring; each of a', b', c', a, b, and c is, independently, 0 or 1 ; each of N1 , N2, N3, N4, N'1 , N'2, N'3, and N'4 is a nitrogen atom, and each of C1 , C2, C3, C'1 , C'2, and C'3 is a carbon atom.
In some embodiments, when R2, R3, and C1 together form an optionally substituted 5-8 membered ring or when R3, R4, N1 , and C1 together form an optionally substituted 5-8 membered ring, each of R2, R3, and R4 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
In some embodiments, when R5, R6, and C2 together form an optionally substituted 5-8 membered ring or when R6, R7, N2, and C2 together form an optionally substituted 5-8 membered ring, each of R5, R6, and R7 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
In some embodiments, when R8, R9, and C3 together form an optionally substituted 5-8 membered ring or when R9, R10, N3, and C3 together form an optionally substituted 5-8 membered ring, each of R8, R9, and R10 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
In some embodiments, when R'2, R'3, and C'1 together form an optionally substituted 5-8 membered ring or when R'3, R'4, N'1 , and C'1 together form an optionally substituted 5-8 membered ring, each of R'2, R'3, and R'4 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
In some embodiments, when R'5, R'6, and C'2 together form an optionally substituted 5-8 membered ring or when R'6, R'7, N'2, and C'2 together form an optionally substituted 5-8 membered ring, each of R'5, R'6, and R'7 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
In some embodiments, when R'8, R'9, and C'3 together form an optionally substituted 5-8 membered ring or when R'9, R'10, N'3, and C'3 together form an optionally substituted 5-8 membered ring, each of R'8, R'9, and R'10 is, independently, optionally substituted C1 -C20 alkylene or optionally substituted C1 -C20 heteroalkylene.
In some embodiments, the compound of formula (II) has at least one optionally substituted 5-8 membered ring formed by joining (i) R2, R3, and C1 ; (ii) R3, R4, N1 , and C1 ; (iii) R5, R6, and C2; (iv) R6, R7, N2, and C2; (v) R8, R9, and C3; (vi) R9, R10, N3, and C3; (vii) R'2, R'3, and C'1 ; (viii) R'3, R'4, N'1 , and C'1 ; (ix) R'5, R'6, and C'2; (x) R'6, R'7, N'2, and C'2; (xi) R'8, R'9, and C'3; or (xii) R'9, R'10, N'3, and C'3.
In some embodiments, when a is 1 in the compound of formula (II), (i) each of R2, R3, and R4 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (ii) R2, R3, and C1 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R4 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (iii) R3, R4, N1 , and C1 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted heterocycloalkyi comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, or optionally substituted heteroaryl comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, and R2 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
In some embodiments, when b is 1 in the compound of formula (II), (i) each of R5, R6, and R7 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (ii) R5, R6, and C2 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R7 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (iii) R6, R7, N2, and C2 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted heterocycloalkyi comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, or optionally substituted heteroaryl comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, and R5 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
In some embodiments, when c is 1 in the compound of formula (II), (i) each of R8, R9, and R10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (ii) R8, R9, and C3 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R10 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (iii) R9, R10, N3, and C3 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted heterocycloalkyi comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, or optionally substituted heteroaryl comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, and R8 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
In some embodiments, when a' is 1 in the compound of formula (II), (i) each of R'2, R'3, and R'4 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (ii) R'2, R'3, and C'1 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R'4 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (iii) R'3, R'4, N'1 , and C'1 together form a ring (e.g., an optionally substituted 5- 8 membered ring) comprising optionally substituted heterocycloalkyi comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, or optionally substituted heteroaryl comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, and R'2 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
In some embodiments, when b' is 1 in the compound of formula (II), (i) each of R'5, R'6, and R'7 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (ii) R'5, R'6, and C'2 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R'7 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (iii) R'6, R'7, N'2, and C'2 together form a ring (e.g., an optionally substituted 5- 8 membered ring) comprising optionally substituted heterocycloalkyi comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, or optionally substituted heteroaryl comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, and R'5 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
In some embodiments, when c' is 1 in the compound of formula (II), (i) each of R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (ii) R'8, R'9, and C'3 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted cycloalkyl, optionally substituted heterocycloalkyi comprising 1 or 2 heteroatoms independently selected from N, O, and S, and R'10 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl ; or (iii) R'9, R'10, N'3, and C'3 together form a ring (e.g., an optionally substituted 5-8 membered ring) comprising optionally substituted heterocycloalkyi comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, or optionally substituted heteroaryl comprising an N heteroatom and additional 0-2 heteroatoms independently selected from N, O, and S, and R'8 is a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted alkamino, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted
cycloalkenylene, optionally substituted cycloalkynylene, optionally substituted aryl, optionally substituted heteroalkyl, optionally substituted heterocycloalkyi, optionally substituted heterocycloalkenylene, optionally substituted heterocycloalkynylene, optionally substituted heteroaryl, optionally substituted alkaryl, or optionally substituted heteroalkaryl.
In some embodiments, the disclosure provides a compound, or a pharmaceutically acceptable salt thereof, described by formula (III)
Figure imgf000084_0001
(III)
in which each of R1 , R12, R'1 , and R'12 is, independently, a lipophilic moiety; each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is, independently, optionally substituted C1 -C5 alkamino, a polar moiety, or a positively charged moiety; and each of R15 and R'15 is, independently, a polar moiety.
In some embodiments, a lipophilic moiety is optionally substituted C1 -C20 alkyl, optionally substituted C5-C15 aryl, optionally substituted C6-C35 alkaryl, or optionally C3-C1 5 substituted heteroaryl. In some embodiments, a lipophilic moiety is C1 -C8 alkyl, methyl substituted C2-C4 alkyl, (C1 - C10)alkylene(C6)aryl, phenyl substituted (C1 -C10)alkylene(C6)aryl, or alkyl substituted C4-C9 heteroaryl. In some embodiments, in particular, a lipophilic moiety is benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or methyl substituted indolyl.
In some embodiments, optionally substituted C1 -C5 alkamino is CH2CH2NH2.
In some embodiments, a polar moiety includes a hydroxyl group, a carboxylic acid group, an ester group, or an amide group. In some embodiments, a polar moiety is hydroxyl substituted C1 -C4 alkyl. In some embodiments, a polar moiety is CHCH3OH.
In some embodiments, a compound provided herein is described by any one of formulas (IV)-
(XXV).
In some embodiments, the disclosure provides a compound described by formula (IV):
Figure imgf000084_0002
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof. In some embodiments, the disclosure provides a compound described by formula (V):
Figure imgf000085_0001
(V)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (VI):
Figure imgf000085_0002
(VI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, R'6, and R'8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (VII):
Figure imgf000086_0001
(VII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (VIII):
Figure imgf000086_0002
(VIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (IX):
Figure imgf000087_0001
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (X):
Figure imgf000087_0002
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3- C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XI):
Figure imgf000088_0001
(XI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XII):
Figure imgf000088_0002
wherein each A1 and A2 is an independently selected amino acid; L is a linker that, when m is 1 , 2, 3, 4, or 5, is bound to a nitrogen atom in any A1 and a nitrogen atom in any A2; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XIII):
Figure imgf000088_0003
(XIII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 is hydrogen, C1-C10 alkyl, or -CH2C(0)NR2R3; R2 is hydrogen or C1-C10 alkyl; R3 is hydrogen or C1-C10 alkyl; and each d is independently an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XIV):
Figure imgf000089_0001
(XIV)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and each d is independently an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XV):
Figure imgf000089_0002
(XV)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; X is O or is absent; each Y is independently -CH2- or -C(O)-; and each Z is independently N or CH; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XVI):
Figure imgf000089_0003
(XVI)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; X is - CR1 R2-, -C(R1)=C(R2)-, -CH2OCH2-, -C(O)-, or is absent; each Y is independently -C(O)-, -S(O)-, -S(0)2-, or is absent; R1 is hydrogen, C1 -C10 alkyl, -N(R3R4), or -OH; R2 is hydrogen, C1 -C10 alkyl, or -OH; R3 and R4 are independently hydrogen or C1 -C10 alkyl; and d is an integer from 1 to 10; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XVII):
Figure imgf000090_0001
(XVII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and each Y is independently -CH2-, -C(O)-, -S(O)-, or -S(0)2-; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XVIII):
Figure imgf000090_0002
(XVIII)
wherein each A1 and A2 is an independently selected amino acid; e is an integer from 1 to 5; f is an integer from 1 to 5; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and R1 is hydrogen, C1 -C10 alkyl, -C(0)OR2, -C(0)-(CH2OCH2)d-heterocyclic, and -C(0)R2; R2 is C1 -C10 alkyl, benzyl, -CH2(biphenyl), -(CH2CH20)g-R3; R3 is -(CH2)iNR4R5 and -(CH2)i-(C2-C8 alkynyl); R4 is hydrogen or C1 -C10 alkyl; R5 is hydrogen or C1 -C10 alkyl; and d is an integer from 1 to 10; g is an integer from 1 to 10; and i is an integer from 1 to 5; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XIX):
Figure imgf000091_0001
(XIX)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 and R2 are independently hydrogen, C1 -C10 alkyl, or -C(0)OR3; R3 is hydrogen C1 -C10 alkyl, or benzyl; and d is an integer from 1 to 4; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XX):
Figure imgf000091_0002
(XX)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 is hydrogen or C1 -C10 alkyl; and d and d' are, independently, an integer from 1 to 5; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXI):
Figure imgf000092_0001
(XXI)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXII):
Figure imgf000092_0002
(XXII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXIII):
Figure imgf000092_0003
(XXIII)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; and Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof. In some embodiments, the disclosure provides a compound described by formula (XXIV):
Figure imgf000093_0001
(XXIV)
wherein each A1 and A2 is an independently selected amino acid; R1 is hydrogen or C1 -C10 alkyl; each m is independently 0, 1 , 2, 3, 4, or 5; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and d is an integer from 1 to 6; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXV):
Figure imgf000093_0002
(XXV)
wherein each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5; d and d' are, independently, 0, 1 , or 2; Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; R1 is hydrogen, C1 -C10 alkyl, -(CH2)d-R2 or -C(0)(CH2)d-R2; d is an integer from 1 to 10; R2 is aryl, C1 -C10 alkyl, -NR3R4, or -OR4; and R3 and R4 are independently hydrogen or C1 -C10 alkyl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXVI):
Figure imgf000093_0003
(XXVI) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R3, R4, R5, R6, R7, R8, R9, R10, R'2, R'3, R'4, R'5, R'6, R'7, R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20
heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring; each of a', b', c', a, b, and c is, independently, 0 or 1 ; each of N1 , N2, N3, N4, N'1 , N'2, N'3, and N'4 is a nitrogen atom; each of C1 , C2, C3, C'1 , C'2, and C'3 is a carbon atom; L is a linker comprising at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, or optionally substituted C3-C15 heteroarylene; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXVII):
Figure imgf000094_0001
(XXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, R'6, and R'8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXVIII):
Figure imgf000095_0001
(XXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXIX):
Figure imgf000095_0002
(XXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R8, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXX):
Figure imgf000096_0001
(XXX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, and R8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXI):
Figure imgf000096_0002
(XXXI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXII):
Figure imgf000097_0001
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2, R6, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXIII):
Figure imgf000097_0002
(XXXIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXIV):
Figure imgf000098_0001
(XXXIV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXV):
Figure imgf000098_0002
(XXXV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; R2 is a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXVI):
Figure imgf000099_0001
(XXXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXVII):
Figure imgf000099_0002
(XXXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXVIII):
Figure imgf000099_0003
(XXXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
Figure imgf000100_0001
(XXXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXX):
Figure imgf000100_0002
(XXXX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXI):
Figure imgf000100_0003
(XXXXI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXII):
Figure imgf000101_0001
(XXXXII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXIII):
Figure imgf000101_0002
(XXXXIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXIV):
Figure imgf000101_0003
(XXXXIV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 cycloalkylene or an optionally substituted C6 heterocycloalkylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXV):
Figure imgf000102_0001
(XXXXV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXVI):
Figure imgf000102_0002
(XXXXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXVII):
Figure imgf000102_0003
(XXXXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof. In some embodiments, the disclosure provides a compound described by formula (XXXXVIII):
Figure imgf000103_0001
(XXXXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises at least two optionally substituted C6 arylene, or a pharmaceutically acceptable salt thereof.
In some embodiments, the disclosure provides a compound described by formula (XXXXIX):
Figure imgf000103_0002
(XXXXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 arylene or an optionally substituted C5 heteroarylene, or a pharmaceutically acceptable salt thereof.
III. Linkers
A linker refers to a linkage or connection between two or more components. The compounds described herein include a linker linking two cyclic heptapeptides in a cyclic heptapeptide dimer. In some embodiments, a linker provides space, rigidity, and/or flexibility between the two cyclic heptapeptides. In some embodiments, a linker may be a bond, e.g., a covalent bond, e.g., an amide bond, a disulfide bond, a N-N bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation. In some embodiments, a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) includes no more than 100 atoms (e.g., 1 -2, 1 -4, 1 -6, 1 -8, 1-10, 1 -12, 1 -14, 1 -16, 1-18, 1 -20, 1 -25, 1 -30,
1-35, 1-40, 1-45, 1-50, 1-55, 1-60, 1-65, 1-70, 1-75, 1-80, 1-85, 1-90, 1-95, 1-97, or 1-99 atom(s); 95, 90,
85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24, 22, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, or
1 atom(s)). In some embodiments, a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas
(XXVI)-(XXXXIX)) includes no more than 100 non-hydrogen atoms (e.g., 1-2, 1-4, 1-6, 1-8, 1-10, 1-12, 1-
14, 1-16, 1-18, 1-20, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, 1-60, 1-65, 1-70, 1-75, 1-80, 1-85, 1-90, 1-
95, 1-97, or 1-99 non-hydrogen atom(s); 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24,
22, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 non-hydrogen atom(s)). In some embodiments, the backbone of a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) includes no more than 100 atoms (e.g., 1 -2, 1 -4, 1 -6, 1 -8, 1 -10, 1 -12, 1 -14, 1 -1 6, 1 -18, 1 -20, 1 -25, 1 -30, 1 -35, 1 -40, 1 -45, 1 -50, 1 -55, 1 -60, 1 -65, 1 -70, 1 -75, 1 -80, 1 -85, 1 -90, 1 -95, 1 -97, or 1 -99 atom(s); 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24, 22, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 atom(s)). The "backbone" of a linker refers to the atoms in the linker that together form the shortest path from one part of the compound to another part of the compound. The atoms in the backbone of the linker are directly involved in linking one part of the compound to another part of the compound. For examples, hydrogen atoms attached to carbons in the backbone of the linker are not considered as directly involved in linking one part of the compound to another part of the compound.
Molecules that may be used to make linkers (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) include at least two functional groups, e.g., two carboxylic acid groups. The first functional group may form a covalent linkage with the first cyclic heptapeptide and the second functional group may form a covalent linkage with the second cyclic heptapeptide. In some
embodiments, when the first and/or second cyclic heptapeptide is attached to a peptide (e.g., a peptide including a 1 -5 amino acid residue(s)) at the linking nitrogen, the linker may form a covalent linkage with the peptide. In some embodiments, dicarboxylic acid molecules may be used as linkers (e.g., a dicarboxylic acid linker), in which the first carboxylic acid may form a covalent linkage with the linking nitrogen of the first cyclic heptapeptide and the second carboxylic acid may form a covalent linkage with the linking nitrogen of the second cyclic heptapeptide. In some embodiments, when the first and/or second cyclic heptapeptide is attached to a peptide (e.g., a peptide including a 1 -5 amino acid residue(s)) at the linking nitrogen, the first carboxylic acid in a dicarboxylic acid linker may form a covalent linkage with the terminal amine group at the end of the peptide that is attached to the first cyclic heptapeptide and the second carboxylic acid in the dicarboxylic acid linker may form a covalent linkage with the terminal amine group at the end of the peptide that is attached to the second cyclic heptapeptide.
Examples of dicarboxylic acids molecules that may be used to form linkers include, but are not limited to,
Figure imgf000104_0001
Figure imgf000105_0001
In some embodiments, a molecule containing one or more sulfonic acid groups may be used to form a linker, in which the sulfonic acid group may form a sulfonamide linkage with the linking nitrogen in a cyclic heptapeptide. In some embodiments, a molecule containing one or more isocyanate groups may be used to form a linker, in which the isocyanate group may form a urea linkage with the linking nitrogen in a cyclic heptapeptide. In some embodiments, a molecule containing one or more haloalkyl groups may be used to form a linker, in which the haloalkyl group may form a covalent linkage, e.g., C-N and C-0 linkages, with a cyclic heptapeptide.
In some embodiments, a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) may comprise a synthetic group derived from, e.g., a synthetic polymer (e.g., a polyethylene glycol (PEG) polymer). In some embodiments, a linker may comprise one or more amino acid residues. In some embodiments, a linker may be an amino acid sequence (e.g., a 1 -25 amino acid, 1 -10 amino acid, 1 -9 amino acid, 1 -8 amino acid, 1 -7 amino acid, 1 -6 amino acid, 1 -5 amino acid, 1 -4 amino acid, 1 -3 amino acid, 1 -2 amino acid, or 1 amino acid sequence). In some embodiments, a linker (L or L' as shown in any one of formulas (l)-(XII) or formulas (XXVI)-(XXXXIX)) may include one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene (e.g., a PEG unit), optionally substituted C2-C20 alkenylene (e.g., C2 alkenylene), optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20
heteroalkynylene, optionally substituted C3-C20 cycloalkylene (e.g., cyclopropylene, cyclobutylene), optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene (e.g., C6 arylene), optionally substituted C3-C15 heteroarylene (e.g., imidazole, pyridine), O, S, NR' (R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C2- C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C1 5 aryl, or optionally substituted C5-C15 heteroaryl), P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino.
In some embodiments, L in any one of formulas (ll)-(XII) is described by formula (L-1 ):
l1-(V1)f-(U1 )g-(V2)h-(U2)i-(V3)j-(U3)k-(V4)|-(U4)m-(V5)n-l2
(L-1 )
in which I1 is a bond attached to A2 or M2 if A2 is absent; I2 is a bond attached to A1 or M1 if A1 is absent; each of U1 , U2, U3, and U4 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2- C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C1 5 heteroarylene; each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR' (R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl), P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; and each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
In some embodiments, L in any one of formulas (XXVI)-(XXXXIX) is described by formula (L-2):
l1-(V1)f-(U1 )g-(V2)h-(U2)i-(V3)j-(U3)-(V4)k-(U4)|-(V5)m-(U5)n-(V6)o-l2
(L-2)
wherein I1 is a bond attached to N'1 , N'2, N'3, or N'4; I2 is a bond attached to N1 , N2, N3, or N4; U3 comprises at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C1 5 heteroarylene; each of U1 , U2, U4, and U5 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene; each of V1 , V2, V3, V4, V5, and V6 is, independently, O, S, NR\ P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C15 heteroaryl; and each of f, g, h, i, j, k, I, m, n, and o is, independently, 0 or 1 .
Covalent conjugation of two or more components in a compound using a linker may be accomplished using well-known organic chemical synthesis techniques and methods. Complementary functional groups on two components may react with each other to form a covalent bond. Examples of complementary reactive functional groups include, but are not limited to, e.g., amine and activated carboxylic acid, thiol and maleimide, activated sulfonic acid and amine, isocyanate and amine, azide and alkyne, and alkene and tetrazine.
Other examples of functional groups capable of reacting with amino groups include, e.g., alkylating and acylating agents. Representative alkylating agents include: (i) an a-haloacetyl group, e.g., XCH2CO- (where X=Br, CI, or I); (ii) a N-maleimide group, which may react with amino groups either through a Michael type reaction or through acylation by addition to the ring carbonyl group; (iii) an aryl halide, e.g., a nitrohaloaromatic group; (iv) an alkyl halide; (v) an aldehyde or ketone capable of Schiff's base formation with amino groups; (vi) an epoxide, e.g., an epichlorohydrin and a bisoxirane, which may react with amino, sulfhydryl, or phenolic hydroxyl groups; (vii) a chlorine-containing of s-triazine, which is reactive towards nucleophiles such as amino, sufhydryl, and hydroxyl groups; (viii) an aziridine, which is reactive towards nucleophiles such as amino groups by ring opening; (ix) a squaric acid diethyl ester; and (x) an a-haloalkyl ether.
Some examples of amino-reactive acylating groups include, e.g., (i) an isocyanate and an isothiocyanate; (ii) a sulfonyl chloride; (iii) an acid halide; (iv) an active ester, e.g., a nitrophenylester or N- hydroxysuccinimidyl ester; (v) an acid anhydride, e.g., a mixed, symmetrical, or N-carboxyanhydride; (vi) an acylazide; and (vii) an imidoester. Aldehydes and ketones may be reacted with amines to form Schiff's bases, which may be stabilized through reductive amination.
It will be appreciated that certain functional groups may be converted to other functional groups prior to reaction, for example, to confer additional reactivity or selectivity. Examples of methods useful for this purpose include conversion of amines to carboxyls using reagents such as dicarboxylic anhydrides; conversion of amines to thiols using reagents such as N-acetylhomocysteine thiolactone, S- acetylmercaptosuccinic anhydride, 2-iminothiolane, or thiol-containing succinimidyl derivatives;
conversion of thiols to carboxyls using reagents such as a -haloacetates; conversion of thiols to amines using reagents such as ethylenimine or 2-bromoethylamine; conversion of carboxyls to amines using reagents such as carbodiimides followed by diamines; and conversion of alcohols to thiols using reagents such as tosyl chloride followed by transesterification with thioacetate and hydrolysis to the thiol with sodium acetate.
IV. Antibacterial Agents
In some embodiments, one or more antibacterial agents may be administered in combination (e.g., administered substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions) or administered separately at different times) with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)).
Antibacterial agents may be grouped into several classes, e.g., quinolones, carbapenems, macrolides, DHFR inhibitors, aminoglycosides, ansamycins (e.g., geldanamycin, herimycin, and rifaximin), carbacephem (e.g., loracarbef), cephalosporins (e.g., cefadroxil, cefaolin, cefalotin, cefalothin, cephalexin, e.g., cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefdinir, cefditoren,
cefoperazone, cefotaxime, cefpodoxime, ceftazidime, and ceftobiprole), glycopeptides (e.g., teicoplanin, vancomycin, telavancin, dalbavancin, and oritavancin), lincosamides (e.g., clindamycin and lincomycin), lipopeptides (e.g., daptomycin), monobactams (e.g., aztreonam), nitrofurans (e.g., furazolidone and nitrofurantoin), oxazolidinones, pleuromutilins, penicillins , sulfonamides, and tetracyclines (e.g., eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, and tetracycline). Quinolones include, but are not limited to, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, and temafloxacin. Carbapenems include, but are not limited to, ertapenem, doripenem,
imipenem/cilastatin, and meropenem. Macrolides include, but are not limited to, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, and spiramycin. In some embodiments, a macrolide is solithromycin. DHFR inhibitors include, but are not limited to, diaminoquinazoline, diaminopyrroloquinazoline, diaminopyrimidine, diaminopteridine, and diaminotriazines. Aminoglycosides include, but are not limited to, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, and spectinomycin.
Oxazolidinones include, but are not limited to, Iinezolid, tedizolid, posizolid, radezolid, and furazolidone. Pleuromutilins include, but are not limited to, retapamulin, valnemulin, tiamulin, azamulin, and lefamulin. Penicillins include, but are not limited to, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, penicillin G, temocillin, and ticarcillin. Sulfonamides include, but are not limited to, mafenide,
sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (Co-trimoxazole) (TMP-SMX), and sulfonamidochrysoidine.
In some embodiments, the antibacterial agent used in combination with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) is selected from the group consisting of Iinezolid, tedizolid, posizolid, radezolid, retapamulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem,
imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime, cefpodoxime, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, dalbavancin, oritavancin, clindamycin, lincomycin, daptomycin, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, spiramycin, aztreonam, furazolidone, nitrofurantoin, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin g, penicillin v, piperacillin, penicillin g, temocillin, ticarcillin, amoxicillin clavulanate, ampicillin/sulbactam,
piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, temafloxacin, mafenide, sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (tmp-smx), sulfonamidochrysoidine, eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, clofazimine, dapsone, capreomycin, cycloserine, ethambutol(bs), ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, streptomycin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, trimethoprim, prodrugs thereof, and pharmaceutically acceptable salts thereof.
In some embodiments, the antibacterial agent used in combination with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) is tiamulin. In some embodiments, the antibacterial agent used in combination with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) is solithromycin.
V. Methods
Methods described herein include, e.g., methods of protecting against or treating a bacterial infection (e.g., a Gram-negative bacterial infection) in a subject and methods of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria (e.g., Gram-negative bacteria). A method of treating a bacterial infection (e.g., a Gram-negative bacterial infection) in a subject includes administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof. In some embodiments, the bacterial infection is caused by Gram- negative bacteria. In some embodiments, the bacterial infection is caused by a resistant strain of bacteria. In some embodiments, the resistant strain of bacteria is a resistant strain of E. coli. A method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria (e.g., Gram-negative bacteria) includes contacting the bacteria (e.g., Gram-negative bacteria) or a site susceptible to bacterial growth (e.g., Gram-negative bacterial growth) with a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof. In some embodiments, the bacteria in this method is Gram-negative bacteria. In some embodiments, the bacteria in this method is a resistant strain of bacteria.
Moreover, methods described herein also include methods of protecting against or treating sepsis in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)). In some embodiments, the method further includes administering to the subject an antibacterial agent. Methods described herein also include methods of preventing LPS in Gram- negative bacteria (e.g., a resistant strain of Gram-negative bacteria or a resistant strain of E. coli (e.g., E. coli BAA-2469)) from activating a immune system in a subject by administering to the subject a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)). In some embodiments of the method, the method prevents LPS from activating a macrophage. In some embodiments, the method further includes administering to the subject an antibacterial agent. In some embodiments, a compound used in any methods described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) may bind to LPS in the cell membrane of Gram-negative bacteria to disrupt and permeabilize the cell membrane, leading to cell death and/or sensitization to other antibiotics.
In some embodiments, the methods described herein may further include administering to the subject an antibacterial agent in addition to a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)). Methods described herein also include methods of protecting against or treating a bacterial infection in a subject by administering to the subject (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent. Methods described herein also include methods of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria, by contacting the bacteria or a site susceptible to bacterial growth with (1 ) a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and (2) an antibacterial agent.
In some embodiments, the compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) is administered first, followed by administering of the antibacterial agent alone. In some embodiments, the antibacterial agent is administered first, followed by administering of the compound described herein alone. In some embodiments, the compound described herein and the antibacterial agent are administered substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions). In some embodiments, the compound described herein or the antibacterial agent is administered first, followed by administering of the compound described herein and the antibacterial agent substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions). In some embodiments, the compound described herein and the antibacterial agent are administered first substantially simultaneously (e.g., in the same pharmaceutical composition or in separate pharmaceutical compositions), followed by administering of the compound described herein or the antibacterial agent alone. In some embodiments, when a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and an antibacterial agent are
administered together (e.g., substantially simultaneously in the same or separate pharmaceutical compositions, or separately in the same treatment regimen), the MIC of each of the compound and the antibacterial agent may be lower than the MIC of each of the compound and the antibacterial agent when each is used alone in a treatment regimen.
VI. Pharmaceutical Compositions and Preparations
A compound described herein may be formulated in a pharmaceutical composition for use in the methods described herein. In some embodiments, a compound described herein may be formulated in a pharmaceutical composition alone. In some embodiments, a compound described herein may be formulated in combination with an antibacterial agent in a pharmaceutical composition. In some embodiments, the pharmaceutical composition includes a compound described herein (e.g., a compound described by any one of formulas (l)-(XXXXIX)) and pharmaceutically acceptable carriers and excipients. Acceptable carriers and excipients in the pharmaceutical compositions are nontoxic to recipients at the dosages and concentrations employed. Acceptable carriers and excipients may include buffers such as phosphate, citrate, HEPES, and TAE, antioxidants such as ascorbic acid and methionine, preservatives such as hexamethonium chloride, octadecyldimethylbenzyl ammonium chloride, resorcinol, and benzalkonium chloride, proteins such as human serum albumin, gelatin, dextran, and immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acid residues such as glycine, glutamine, histidine, and lysine, and carbohydrates such as glucose, mannose, sucrose, and sorbitol.
Examples of other excipients include, but are not limited to, antiadherents, binders, coatings, compression aids, disintegrants, dyes, emollients, emulsifiers, fillers (diluents), film formers or coatings, flavors, fragrances, glidants (flow enhancers), lubricants, sorbents, suspensing or dispersing agents, or sweeteners. Exemplary excipients include, but are not limited to: butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, croscarmellose, crosslinked polyvinyl pyrrolidone, citric acid, crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine,
methylcellulose, methyl paraben, microcrystalline cellulose, polyethylene glycol, povidone, pregelatinized starch, propyl paraben, retinyl palmitate, shellac, silicon dioxide, sodium carboxymethyl cellulose, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, stearic acid, sucrose, talc, titanium dioxide, vitamin A, vitamin E, vitamin C, and xylitol.
The compounds herein may have ionizable groups so as to be capable of preparation as pharmaceutically acceptable salts. These salts may be acid addition salts involving inorganic or organic acids or the salts may, in the case of acidic forms of the compounds herein be prepared from inorganic or organic bases. Frequently, the compounds are prepared or used as pharmaceutically acceptable salts prepared as addition products of pharmaceutically acceptable acids or bases. Suitable pharmaceutically acceptable acids and bases are well-known in the art, such as hydrochloric, sulphuric, hydrobromic, acetic, lactic, citric, or tartaric acids for forming acid addition salts, and potassium hydroxide, sodium hydroxide, ammonium hydroxide, caffeine, various amines, and the like for forming basic salts. Methods for preparation of the appropriate salts are well-established in the art.
Representative acid addition salts include, but are not limited to, acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate,
camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, toluenesulfonate, undecanoate, and valerate salts. Representative alkali or alkaline earth metal salts include, but are not limited to, sodium, lithium, potassium, calcium, and magnesium, as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, and ethylamine.
Depending on the route of administration and the dosage, a compound herein or a
pharmaceutical composition thereof used in the methods described herein will be formulated into suitable pharmaceutical compositions to permit facile delivery. A compound (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof may be formulated to be administered intramuscularly, intravenously (e.g., as a sterile solution and in a solvent system suitable for intravenous use), intradermal^, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleural^, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally (e.g., a tablet, capsule, caplet, gelcap, or syrup), topically (e.g., as a cream, gel, lotion, or ointment), locally, by inhalation, by injection, or by infusion (e.g., continuous infusion, localized perfusion bathing target cells directly, catheter, lavage, in cremes, or lipid compositions). Depending on the route of administration, a compound herein or a pharmaceutical composition thereof may be in the form of, e.g., tablets, capsules, pills, powders, granulates, suspensions, emulsions, solutions, gels including hydrogels, pastes, ointments, creams, plasters, drenches, osmotic delivery devices, suppositories, enemas, injectables, implants, sprays, preparations suitable for iontophoretic delivery, or aerosols. The compositions may be formulated according to conventional pharmaceutical practice.
A compound described herein may be formulated in a variety of ways that are known in the art. For use as treatment of human and animal subjects, a compound described herein can be formulated as pharmaceutical or veterinary compositions. Depending on the subject (e.g., a human) to be treated, the mode of administration, and the type of treatment desired, e.g., prophylaxis or therapy, a compound described herein is formulated in ways consonant with these parameters. A summary of such techniques is found in Remington: The Science and Practice of Pharmacy, 22nd Edition, Lippincott Williams & Wilkins (2012); and Encyclopedia of Pharmaceutical Technology, 4th Edition, J. Swarbrick and J. C. Boylan, Marcel Dekker, New York (2013), each of which is incorporated herein by reference.
Formulations may be prepared in a manner suitable for systemic administration or topical or local administration. Systemic formulations include those designed for injection (e.g., intramuscular, intravenous or subcutaneous injection) or may be prepared for transdermal, transmucosal, or oral administration. The formulation will generally include a diluent as well as, in some cases, adjuvants, buffers, and preservatives. The compounds can be administered also in liposomal compositions or as microemulsions. Systemic administration may also include relatively noninvasive methods such as the use of suppositories, transdermal patches, transmucosal delivery and intranasal administration. Oral administration is also suitable for compounds herein. Suitable forms include syrups, capsules, and tablets, as is understood in the art.
The pharmaceutical compositions can be administered parenterally in the form of an injectable formulation. Pharmaceutical compositions for injection can be formulated using a sterile solution or any pharmaceutically acceptable liquid as a vehicle. Formulations may be prepared as solid forms suitable for solution or suspension in liquid prior to injection or as emulsions. Pharmaceutically acceptable vehicles include, but are not limited to, sterile water, physiological saline, and cell culture media (e.g., Dulbecco's Modified Eagle Medium (DMEM), a-Modified Eagles Medium (a-MEM), F-12 medium). Such injectable compositions may also contain amounts of nontoxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, such as sodium acetate and sorbitan monolaurate. Formulation methods are known in the art, see e.g., Pharmaceutical Preformulation and Formulation, 2nd Edition, M. Gibson, Taylor & Francis Group, CRC Press (2009).
The pharmaceutical compositions can be prepared in the form of an oral formulation.
Formulations for oral use include tablets containing the active ingredient(s) in a mixture with non-toxic pharmaceutically acceptable excipients. These excipients may be, for example, inert diluents or fillers (e.g., sucrose, sorbitol, sugar, mannitol, microcrystalline cellulose, starches including potato starch, calcium carbonate, sodium chloride, lactose, calcium phosphate, calcium sulfate, or sodium phosphate); granulating and disintegrating agents (e.g., cellulose derivatives including microcrystalline cellulose, starches including potato starch, croscarmellose sodium, alginates, or alginic acid); binding agents (e.g., sucrose, glucose, sorbitol, acacia, alginic acid, sodium alginate, gelatin, starch, pregelatinized starch, microcrystalline cellulose, magnesium aluminum silicate, carboxymethylcellulose sodium,
methylcellulose, hydroxypropyl methylcellulose, ethylcellulose, polyvinylpyrrolidone, or polyethylene glycol); and lubricating agents, glidants, and antiadhesives (e.g., magnesium stearate, zinc stearate, stearic acid, silicas, hydrogenated vegetable oils, or talc). Formulations for oral use may also be provided as chewable tablets, or as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin), or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example, peanut oil, liquid paraffin, or olive oil. Powders, granulates, and pellets may be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, e.g., a mixer, a fluid bed apparatus or a spray drying equipment. Other pharmaceutically acceptable excipients for oral formulations include, but are not limited to, colorants, flavoring agents, plasticizers, humectants, and buffering agents. Formulations for oral use may also be provided as chewable tablets, or as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin), or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example, peanut oil, liquid paraffin, or olive oil. Powders, granulates, and pellets may be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, e.g., a mixer, a fluid bed apparatus or a spray drying equipment.
Dissolution or diffusion controlled release of a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof can be achieved by appropriate coating of a tablet, capsule, pellet, or granulate formulation of the compound, or by incorporating the compound into an appropriate matrix. A controlled release coating may include one or more of the coating substances mentioned above and/or, e.g., shellac, beeswax, glycowax, castor wax, carnauba wax, stearyl alcohol, glyceryl monostearate, glyceryl distearate, glycerol palmitostearate, ethylcellulose, acrylic resins, dl-polylactic acid, cellulose acetate butyrate, polyvinyl chloride, polyvinyl acetate, vinyl pyrrolidone, polyethylene, polymethacrylate, methylmethacrylate, 2-hydroxymethacrylate, methacrylate hydrogels, 1 ,3 butylene glycol, ethylene glycol methacrylate, and/or polyethylene glycols. In a controlled release matrix formulation, the matrix material may also include, e.g., hydrated
methylcellulose, carnauba wax and stearyl alcohol, carbopol 934, silicone, glyceryl tristearate, methyl acrylate-methyl methacrylate, polyvinyl chloride, polyethylene, and/or halogenated fluorocarbon.
The pharmaceutical composition may be formed in a unit dose form as needed. The amount of active component, e.g., a compound described herein, included in the pharmaceutical compositions are such that a suitable dose within the designated range is provided (e.g., a dose within the range of 0.01 - 100 mg/kg of body weight).
VII. Routes of Administration and Dosages
In any of the methods described herein, compounds herein may be administered by any appropriate route for treating or protecting against a bacterial infection (e.g., a Gram-negative bacterial infection), or for preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria (e.g., Gram- negative bacteria). Compounds described herein may be administered to humans, domestic pets, livestock, or other animals with a pharmaceutically acceptable diluent, carrier, or excipient. In some embodiments, administering comprises administration of any of the compounds described herein (e.g., compounds of any one of formulas (l)-(XXXXIX)) or compositions intramuscularly, intravenously (e.g., as a sterile solution and in a solvent system suitable for intravenous use), intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleural^, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally (e.g., a tablet, capsule, caplet, gelcap, or syrup), topically (e.g., as a cream, gel, lotion, or ointment), locally, by inhalation, by injection, or by infusion (e.g., continuous infusion, localized perfusion bathing target cells directly, catheter, lavage, in cremes, or lipid compositions). In some embodiments, if an antibacterial agent is also administered in addition to a compound described herein, the antibacterial agent or a pharmaceutical composition thereof may also be administered in any of the routes of administration described herein.
The dosage of a compound described herein (e.g., a compound of any one of formulas (I)- (XXXXIX)) or a pharmaceutical compositions thereof depends on factors including the route of administration, the disease to be treated (e.g., the extent and/or condition of the bacterial infection), and physical characteristics, e.g., age, weight, general health, of the subject. Typically, the amount of the compound or the pharmaceutical composition thereof contained within a single dose may be an amount that effectively prevents, delays, or treats the bacterial infection without inducing significant toxicity. A pharmaceutical composition may include a dosage of a compound described herein ranging from 0.01 to 500 mg/kg (e.g., 0.01 , 0.1 , 0.2, 0.3, 0.4, 0.5, 1 , 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 200, 250, 300, 350, 400, 450, or 500 mg/kg) and, in a more specific embodiment, about 0.1 to about 30 mg/kg and, in a more specific embodiment, about 1 to about 30 mg/kg. In some embodiments, when a compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) and an antibacterial agent are administered together (e.g., substantially simultaneously in the same or separate
pharmaceutical compositions, or separately in the same treatment regimen), the dosage needed of the compound described herein may be lower than the dosage needed of the compound if the compound was used alone in a treatment regimen.
A compound described herein (e.g., a compound of any one of formulas (l)-(XXXXIX)) or a pharmaceutical composition thereof may be administered to a subject in need thereof, for example, one or more times (e.g., 1 -10 times or more; 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 times) daily, weekly, monthly, biannually, annually, or as medically necessary. Dosages may be provided in either a single or multiple dosage regimens. The timing between administrations may decrease as the medical condition improves or increase as the health of the patient declines. The dosage and frequency of administration may be adapted by the physician in accordance with conventional factors such as the extent of the infection and different parameters of the subject.
EXAMPLES
General Schemes
The compounds of the disclosure and their precursors may be synthesized by a number of methods known to those skilled in the art. The following scheme illustrates several methods and strategies that may employed. Cyclic heptapeptides that comprise residues M1 and M2 may be prepared by synthesis using solid phase peptide methods or by solution phase methods. Alternately, the cyclic heptapeptides that comprise residues M1 and M2 may be derived from certain compounds known as polymyxins or from octapeptins which may be derived from fermentation sources or be synthetic. The protected M1 and M2 residues may be obtained by first protection of the polymyxin or octapeptin followed by enzymatic hydrolysis (e.g. with savinase or other enzymes known to those skilled in the art).
The cyclic heptapeptides may be optionally derivatized with 1 , 2 or 3 amino acids which may be the same or different. Using a suitable linker group L, the two halves which may be the same or different, may be coupled and after deprotection, give the compounds of the immediate disclosure. Alternatively, the linker group L' may be prepared from the individual amino acid groups and L by methods known to those in the art. L' may be built up sequentially or by a convergent synthesis and then coupled to the cyclic heptapeptides that comprise the residues M1 and M2. After deprotection, the compounds of the immediate disclosure may be obtained.
Alternatively, when a, b, a', and b' are 1 , A1 -M1 or A2-M2 may be derived from a polymyxin or octapeptin precursor by first protection followed by enzymatic hydrolysis (e.g. with papain). Subsequent coupling with L provides the compounds of the immediate disclosure.
Alternatively, when a, b, c, a', b' and c' are 0, the cyclic heptapeptides that comprise the residues M1 and M2 may be coupled directly with L to give the compounds of the immediate disclosure.
Other methods known by those skilled in the art may be employed to prepare symmetric compounds (i.e. those where A1 and A2 are the same and M1 and M2 are the same), or asymmetric compounds where A1 -M1 is different from A2-M2.
Figure imgf000117_0001
General Methods
Preparative HPLC was performed using the following: Teledyne Isco HP C18, 50g column. Eluent: CH3CN/H2O/ 0.1 % formic acid or 0.1 % trifluoroacetic acid; various linear gradients as necessary at 40 mL/min on an Isco Combiflash Rf LC unit, or Isco EZ prep HPLC, with UV Detection at 220 and 254 nm on a Luna 5 micron C18, 100 A, AXIA 100 x 30 mm. Eluent: CH3CN/H2O/ 0.1 % formic acid or 0.1 % trifluoroacetic acid; various linear gradients as necessary at 25 mL/min on the Gilson System ; 215 Liquid Handler, Gilson UV-VIS 155, Gilson 305 pump and Detector. UV detection at 220 and 254 nm.
Analytical LC/MS: High resolution liquid chromatography mass spectrometry (HRES-LC/MS) was performed using a Waters Q-TOF Premier mass spectrometer with an electrospray probe coupled with a Waters Acquity H-class UPLC system with a diode array detector set to collect from 210 nm to 400 nm. A gradient of 0.1 % formic acid in water (A) and 0.1 % formic acid in acetonitrile (B) was run from 15%B to 95% over 10 min using a 1 00 x 2.1 mm 1 .7 μ Phenomenex Kinetex C18 column at 40 °C.
Liquid chromatography mass spectrometry was performed using an Agilent 6120 mass spectrometer an electrospray probe coupled with an Agilent 1260 HPLC system with a variable wavelength detector set to either 220 nm or 254 nm. A gradient of 0.1 % formic acid in water (A) and 0.1 % formic acid in acetonitrile (B) was run from 15%B to 99% over 3.5 min using a 50x3.0 mm 2.6μ Phenomenex Gemini-NX column at 30 °C.
1 H-NMR (1 H NMR) spectra were acquired on a Bruker 300 MHz system using a 5 mm QNP probe and chemical shifts are reported as ppm (δ) downfield from tetramethylsilane.
Compounds herein may be made using synthetic methods known in the art, including procedures analogous to those disclosed below. Exemplary protocols, techniques, reagents, and solvents for synthetic methods known in the art are provided, for example, in Caren, S., Practical Synthetic Organic Chemistry: Reactions, Principles, and Techniques. Wiley, 201 1 , and Benoiton, N.L., Chemistry of Peptide Synthesis. CRC Press, 2005, each of which is incorporated by reference in their entirety.
Example 1. Degradation of polymyxin E to tri-Boc polymyxin E cycloheptapeptide (lnt-2)
Figure imgf000118_0001
colistin sulfate
Procedure A
Colistin sulfate (5.0 g, 3.95 mmol) was dissolved in acetonitrile (50 mL) and water (25 mL) and stirred at room temperature for 10 minutes. Triethylamine (3.2 mL, 23.0 mmol) was added and the mixture stirred for a further 10 minutes. Di-tert-butyl dicarbonate (5.0 g, 23.0 mmol) was subsequently added in one portion and the mixture stirred for 16 hours. Savinase (Novozymes) (15 mL) was then added, followed by 4 M sodium hydroxide solution (0.5 mL) and the reaction mixture stirred at room temperature for 5 days. The mixture was diluted with ethyl acetate and water. After separation of the layers, the organic phase was washed with 0.1 M sodium hydroxide solution (x2), then water. The organic layer was dried over magnesium sulfate, filtered and the solvent evaporated at reduced pressure. The residue was purified by reversed phase chromatography (10-95% acetonitrile/di water containing 0.1 % formic acid: 25 minute gradient). The pure fractions were pooled and lyophilized to afford title compound lnt-2 as a formate salt, white powder. (2.28 g, 56%). m/z 1 028, [MH]+
Procedu e B
Colistin sulfate (50.0 g, 39.5 mmol) was dissolved in acetonitrile (500 mL, 10V) and water (250 mL, 5V) and stirred at room temperature for 10 mins. TEA (24.2 g, 6.0eq) was added and the mixture stirred for a further 10 mins. Di-tert-butyl dicarbonate (52.2 g, 6.0 eq) was subsequently added in one portion and the mixture stirred for 29 hrs. LCMS showed material no being detected. Savinase (150 mL) was then added. The pH of the resulting mixture was adjusted to 9.0 with aq 4M sodium hydroxide solution (5 mL) and the reaction mixture stirred at 25°C. Additional savinase (50 mL, 1 V) was added after 79 hrs, and another quantity of savinase (50 mL, 1 V) was added after 103 hrs. After an overall reaction time of 162 hrs, the mixture was diluted with EA (1 000 mL, 20V). After separation of the layers, the organic phase was washed with 0.1 M NaOH solution (500 mL x2, 10V x2 ), then water(500 mL, 10V). The organic layer was dried over anhydrous Na2S04, filtered and the solvent evaporated at reduced pressure. The residue was purified by silica gel chromatography eluting with 80%
(EtOAc:MeOH:NH4OH=40:10:1 ) in ethyl acetate to give the title compound lnt-2 (20.2 g, 49.3%). LCMS: m/z (M + H)+ calcd for C47H85Ni i Oi4:1 027.63; found:1 028.5.
Example 2. Degradation of polymyxin B to tri-Boc polymyxin B cycloheptapeptide (lnt-1)
Figure imgf000119_0001
Polymyxin B (100 g, 72.2 mmol) was dissolved in acetonitrile (1000 mL, 10V) and water (500 mL, 5V) and stirred at room temperature for 10 mins. TEA (58.5 g, 8.0 eq) was added and the mixture stirred for a further 10 mins. Di-tert-butyl dicarbonate (94.6 g, 6.0eq) was subsequently added in one portion and the mixture stirred for 6 hrs at 20 °C. Savinase (300 mL) was then added. The pH of the resulting mixture was adjusted to 9.0 with aq 4M sodium hydroxide solution (1 0 mL) and the reaction mixture stirred at 25°C. Additional savinase (100 mL, 1 V) was added after 17 hrs, and another quantity of savinase (100 mL x2, 1 VX2) was added after 26 hrs. After an overall reaction time of 80 hrs, the mixture was diluted with EA (2000 mL, 20V). After separation of the layers, the organic phase was washed with 0.1 M NaOH solution (1000 mL x2, 10V x2), then water(1000 mL, 10V). The organic layer was dried over anhydrous Na2S04, filtered and the solvent evaporated at reduced pressure. The residue was purified by silica gel chromatography eluting with 80% (EtOAc : MeOH : Η2ΟΝΗ3 = 40:10:1 ) in ethyl acetate to give the title compound lnt-1 (49.8 g, 65.0%).
LCMS: m/z (M + H)+ calcd for CsoHeaNnOuil 061 .61 ; found:1062.5
Example 3. Preparation of tetra-Boc Dab-polymyxin E cycloheptapeptide (lnt-3)
Step a. Synthesis of Cbz-L- -(lnt-2)
Figure imgf000120_0001
lnt-2 (0.20 g, 0.195 mmol) , Z-L-Dab(Boc)-OH-DCHA (dicyclohexylamine) (0.124 g, 0.233 mmol), and HOBT (0.029 g, 0.214 mmol) were dissolved in DMF (2 mL) and EDC (0.041 g, 0.214 mmol) was added and the reaction was stirred for 2 hours. The mixture was applied directly to reversed phase HPLC (25-95% acetonitrile in Dl water containing 0.1 % formic acid:20 minute gradient). The pure fractions were lyophilized to afford 0.197g of the title compound as a white solid. Yield: 74%. LC/MS((M+2H+)/2)= 682.0.
Step b. Synthesis of lnt-3
Figure imgf000120_0002
The Cbz-L-Dab-(lnt-2) (0.197 g, 0.194 mmol) was stirred in methanol (15 ml) in the presence of 5% Pd/C (50 mg) under 1 atm of hydrogen gas for 45 minutes. The mixture was filtered, concentrated and applied to reversed phase HPLC (25-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were lyophilized to afford 0.140 g of the title compound as a white solid. Yield: 72%. LC/MS [M+2H/2]= 565.0 (loss of 1 Boc in LC/MS). Example 4. Preparation of tetra-Boc Dab- polymyxin B cycloheptapeptide (lnt-4) Step a. Synthesis of Cbz- -Dab-(lnM)
Figure imgf000121_0001
lnt-1 (2 g, 1 .88 mmol) , Z-L-Dab(Boc)-OH-DCHA (1 .20 g, 2.33 mmol), and N-methylmorpholine (0.62 ml_, 5.65 mmol) were dissolved in DMF (6 mL) and HATU (1 -[Bis(dimethylamino)methylene]-1 H- 1 ,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate) (0.858 g, 2.25 mmol) was added and the reaction was stirred for 45 minutes. The mixture was applied directly to reversed phase HPLC (25-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were lyophilized to afford 2.1 g of the title compound as a white solid. Yield: 79%. LC/MS [M+2H/2] = 599.0 (Cbz protected intermediate, - loss of 2 Boc groups on LC/MS).
Step b. Preparation of lnt-4
Figure imgf000121_0002
The Cbz-L-Dab-(lnM ) (2.1 g, 1 .50 mmol) was stirred in methanol (25 ml) in the presence of 5% Pd/C (125 mg) under 1 atm of hydrogen gas for 45 minutes. The mixture was filtered, concentrated and applied to reversed phase HPLC (25-95% acetonitrile in Dl water: 20 minute gradient). The pure fractions were lyophilized to afford 1 .92 g of lnt-4 as a white solid. Yield: 96%. LC/MS ((M+2H)/2)=532.0 (loss of 2 Boc groups on LC/MS).
Example 5. Synthesis of lnt-5 (tetra-Boc polymyxin E nonapeptide)
Figure imgf000121_0003
Procedu e A
lnt-5 was prepared from lnt-3 and Z-Thr-OH in a manner similar to that described for lnt-6. Yield 73%. LC/MS ((M+2H)/2) = 565.8 (loss of 2 Boc groups on LC/MS).
Procedure B
Step a. Enzymatic hydrolysis of colistin to polymyxin E nonapeptide (PMEN)
Colistin sulfate (5 g) was dissolved in phosphate buffer (1 liter, pH 7, 25 mM), and KCI (1 .5g), EDTA (500 mg), Cysteine-HCI (2g) and Immobilised papain (10 mL, Thermofisher, 16-40 BAEE/mg before immobilisation) was added then the pH was brought back to 7 with potassium phosphate, dibasic. The reaction was shaken at 37 SC for 72 hours. The solids were removed by filtration and the aqueous reaction mixture was lyophilized. The white solids were dissolved in 1 N HCI and purified (in 3 aliquots) by reversed phase HPLC (5-50% acetonitrile in Dl water containing 0.1 % TFA: 20 minute gradient). Pure fractions were pooled and lyophilized to afford the product as a white solid. LC/MS 929.5 (M+H) and 465.0 (M+2H/2).
Step b. Selective protection of polymyxin E nonapeptide to tetra-Boc polymyxin E nonapeptide (lnt-5)
The title compound is prepared in a manner similar to the following literature procedure: O'Dowd, et al. Tetrahedron Letters, Volume 48, Issue 1 1 , 12 March 2007, Pages 2003-2005.
Example 6. Synthesis of lnt-6 (t )
Figure imgf000122_0001
Procedure A
lnt-4 (0.22 g, 0.174 mmol) , Z-Thr-OH (0.053 g, 0.209 mmol), and N-methylmorpholine (57 uL, 5.65 mmol) were dissolved in DMF (6 mL) and HATU (0.070 g, 0.209 mmol) was added and the reaction was stirred for 45 minutes. The mixture was applied directly to reversed phase HPLC (25-95% acetonitrile in Dl water containing 0.1 % formic acid:20 minute gradient). The pure fractions were lyophilized to afford 0.21 g of the title compound as a white solid. LC/MS ((M+2H)/2) = 649.4 (Cbz protected intermediate, loss of 2 boc groups on LC/MS). The Cbz protected intermediate was taken up in methanol (10 mL) and stirred in the presence of 5% Pd/C (40 mg) under 1 atmosphere of hydrogen gas for 45 minutes. The mixture was filtered and applied to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were lyophilized to afford 0.187 g of the title compound as a white solid. Yield: 78%, 2 steps. LC/MS ((M+2H)/2) = 582.4 (artefactual loss of 2 Boc groups on LC/MS).
Procedu e B
Tetra-Boc polymyxin B nonapeptide may be prepared from polymyxin B via polymyxin B nonapeptide (PMBN) in a manner similar to that described in Example 5, Procedure B.
Example 7. Synthesis of lnt-7 (penta-Boc polymyxin E decapeptide)
Figure imgf000123_0001
Penta-Boc polymyxin E decapeptide was prepared analogously to penta-Boc polymyxin B decapeptide (see Example 8), except that polymyxin E was substituted for polymyxin B as the starting material.
Example 8. Synthesis of lnt-8 (penta-Boc polymyxin B decapeptide)
Figure imgf000123_0002
Step a. Synthesis of Cbz-penta-Boc polymyxin B decapeptide
Figure imgf000123_0003
A solution of lnt-1 (2.25 g, 2.18 mmol), (2S)-2-[(N-{(2S)-2-{[(benzyloxy)carbonyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid (1 .36 g, 2.08 mmol), and DIEA (1 .20 mL, 6.87 mmol), in DMF (5mL), were treated with HATU (0.831 g, 2.1 8 mmol), while stirring at room temperature. After 30 minutes, the product was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 20% to 100% methanol and water, using no modifier. Yield 2.50 g, 72% yield, lon(s) found by LCMS: (M + 2H)/2 = 799.5 (loss of 1 Boc group), (M + 2H)/2 = 749.5 (loss of two Boc groups).
Step b. Synthesis of penta-Boc polymyxin B decapeptide lnt-8)
Figure imgf000124_0001
A solution of Cbz-penta-Boc polymyxin B decapeptide (2.5 g, 1 .47 mmol) dissolved in methanol (10 mL), was treated with 5% Pd/C (0.5 g), flushed with hydrogen and stirred for 12 hr. The reaction was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 1 .98 g, 86% yield, lon(s) found by LCMS: (M + 2H)/2 = 732.4 (loss of 1 Boc group)
Example 9. Synthesis of lnt-9 (penta-Boc polymyxin E undecapeptide)
Figure imgf000124_0002
Penta-Boc polymyxin E undecapeptide was prepared analogously to penta-Boc polymyxin B undecapeptide (see Example 1 0), except that polymyxin E decapeptide was substituted for polymyxin B decapeptide as the starting material. LCMS: [(M-2Boc)+2H]/2 = 737.3, [(M-3Boc)+2H]/2 = 677.3
Figure imgf000125_0001
A solution of penta-Boc polymyxin B decapeptide (prepared as described in Example 8) (1 .31 g, 0.838 mmol), (2S)-2-{[(benzyloxy)carbonyl]amino}octanoic acid (0.25 g, 0.880 mmol), and DIEA (0.46 mL, 2.64 mmol), in DMF (5ml_), were treated with HATU (0.334 g, 0.880 mmol), while stirring at room temperature. After 30 minutes, the product was used in the next step without isolation, lon(s) found by LCMS: [(M-1 Boc)+2H]/2 = 870.0, [(M-2Boc)+2H]/2 = 820.0
Step b. Synthesis of penta-Boc polymyxin B undecapeptide
Figure imgf000125_0002
A solution of Cbz penta-Boc polymyxin B undecapeptide dissolved in DMF (crude, 5 mL, from previous step), was treated with 5% Pd/C (0.5g), flushed with hydrogen and stirred for 2hr. The reaction was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.83 g, 58% yield, lon(s) found by LCMS: [(M-1 Boc)+2H]/2 = 803.0, [(M-2Boc)+2H]/2 = 753.0
Example 11. Synthesis of lnt-11 (H-Thr-YBoc-Dab-OMe)
Procedu
Figure imgf000126_0001
Step a. Preparation of Cbz-Thr-YBoc-Dab-OMe
NH2-Dab(Boc)-OMe (HCI salt) (5.000 g, 1 eq.), Z-NH-L-Thr-OH (5.049 g, 1 .05eq.), EDCI (5.350 g, 1 .5eq.), HOBt (3.733 g, 1 .5eq.) and NaHC03 (3.095 g, 2eq.) were weighed into a 100-mL round bottom flask. 24 mL of DCM/DMF (dicloromethane/dimethylformamide) (4:1 ) was added into the flask. The mixture was stirred at room temperature for about 3 hrs. (TLC or LC/MS monitoring). After the completion, EtOAc (200 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated
NaHC03 and brine. Dried with Na2S04 and condensed. The residue was purified with normal phase silica (2-7% MeOH/DCM) to give 8.24 g pure desired product (>95%).
Figure imgf000126_0002
Step b. Removal of the Cbz Group
Cbz-Thr-yBoc-Dab-OMe (8.24 g) was dissolved in 100 mL of MeOH/EtOAc and 5% Pd/C (3.75 g, 0.1 eq.) was added. Under H2 balloon, the reaction mixture was stirred for 2h. When the reaction was judged complete by TLC and LC/MS, it was filtered through Celite with several MeOH washes. The filtrate was concentrated and dried to give 5.87 g of free amine (>99%). The material may be used in the next step without purification.
Procedure B
Figure imgf000126_0003
Z-Thr-OH (2.0 g, 7.9 mmol), methyl (2S)-2-amino-4-[(tert-butoxymethyl)amino]butanoate hydrochloride (2.2 g, 8.7 mmol), HOBt (1 .2 g, 8.7 mmol), EDC (1 .7 g, 8.7 mmol) and DIEA (2.0 g, 16 mmol) were stirred in DMF (15 mL) at ambient temperature for 2 hours. The mixture was diluted with ethyl acetate (30 mL) and aqueous 1 N HCI (50 mL). The aqueous phase was extracted with ethyl acetate (3x, 30 mL) and the combined organic extracts were dried over sodium sulfate, filtered and concentrated. The crude dipeptide was stirred in a methanol (50 mL) under 1 atmosphere of hydrogen gas in the presence of 5% Pd/C (200 mg) for 45 minutes. The mixture was filtered, concentrated and purified by reversed phase HPLC (5 to 75% acetonitrile in Dl water containing 0.1 % TFA: 20 minute gradient). The pure fractions were pooled and lyophilized to afford H-Thr-YBoc-Dab-OMe as a white solid. Yield: 82%. LC/MS [M+H+]+ 334.8.
Figure imgf000127_0001
Figure imgf000127_0002
Step a. Synthesis of Bis13-(1-(9H-fluoren-9-yl)-3,11 -dioxo-2,7-dioxa-4,10-diazadodecan-12- yl)-1-(9H-flu
Figure imgf000127_0003
Fmoc-PEG1 -NH2 (650 mg, 2 mmol) and 2,2',2"-nitrilotriacetic acid (2 g, 1 0 mmol) in DMF (5 mL) was added EDC (600 mg, 3 mmol), HOBT (450 mg, 3 mmol), N-methyl morpholine (2.8 mL, 20 mmol) at room temperature. The solution was stirred overnight. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. 13-(1 -(9H-fluoren-9-yl)-3,1 1 -dioxo-2,7-dioxa-4,10-diazadodecan-12-yl)-1 -(9H-fluoren-9-yl)-3,1 1 - dioxo-2,7-dioxa-4,1 0,13-triazapentadecan-15-oic acid was isolated and confirmed structure By LC/MS [M]+1 808.4. Step b. Synthesis of bis((9H-fluoren-9-yl)methyl) (9-(2-(dimethylamino)-2-oxoethyl)-7,11 - dioxo-3,15-dioxa-6,9,12-triazaheptadecane-1 ,17-diyl)dicarbamate
Figure imgf000128_0001
To bisl 3-(1 -(9H-fluoren-9-yl)-3,1 1 -dioxo-2,7-dioxa-4,1 0-diazadodecan-12-yl)-1 -(9H-fluoren-9-yl)- 3,1 1 -dioxo-2,7-dioxa-4,1 0,13-triazapentadecan-15-oic acid (400 mg, 0.5 mmol) in DMF (5 mL) and N,N- dimethyl amine HCI (200 mg, 2.5 mmol) was added EDC (200 mg, 1 mmol), HOBT (150 mg, 1 mmol), N- methyl morpholine (1 .4 mL, 10 mmol) at room temperature. The solution was stirred overnight. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Ν,Ν-dimethyl Bis-Fmoc-PEG1 -NH2-2,2'nitrilotriacetamide-N-acetamide was isolated and confirmed structure By LC/MS (M+H) 835.4.
Step c. Preparation of dibenzyl 14-(2-(dimethylamino)-2-oxoethyl)-4,12,16,24-tetraoxo-8,20- dioxa-5,1 1 ,14,17,23-pentaazaheptacosane-1 ,27-dioate
Figure imgf000128_0002
bis((9H-fluoren-9-yl)methyl) (9-(2-(dimethylamino)-2-oxoethyl)-7,1 1 -dioxo-3,15-dioxa-6,9,12- triazaheptadecane-1 ,1 7-diyl)dicarbamate (240 mg, 0.3 mmol) was treated with 5 mL DBU 1 % in DMF for 2hour, then 4-(benzyloxy)-4-oxobutanoic acid ( 200 mg, 1 mmol), EDC(200 mg, 0.1 mmol), HOBt (150 mg, 0.1 mmol) and TEA(0.14 mL, 1 mmol) were added to above solution at room temperature respectively. The solution was stirred for overnight. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Dibenzyl 14-(2- (dimethylamino)-2-oxoethyl)-4,12,16,24-tetraoxo-8,20-dioxa-5,1 1 ,14,17,23-pentaazaheptacosane-1 ,27- dioate was isolated and confirmed structure By LC/MS [M]+1 771 .4
Figure imgf000129_0001
Dibenzyl 14-(2-(dimethylamino)-2-oxoethyl)-4,12,1 6,24-tetraoxo-8,20-dioxa-5,1 1 ,14,17,23- pentaazaheptacosane-1 ,27-dioate (80 mg, 0.1 mmol) was dissolved into 2 ml_ MeOH and 2 ml_ ethyl acetate, then 50 mg of 5% Palladium on charcoal was added above solution, and the mixture was stirred at room temperature under the hydrogen atmosphere for overnight. The palladium charcoal was removed by filtration after completed the reaction by LCMS. The filtrate was concentrated and used for next step without any purification. LC/MS [M]+1 591 .3.
The above debenzylation product (30 mg, 0.05 mmol), triethylamine (0.14 ml_, 1 mmol) and lnt-6 (200 mg 0.15m ml_) in 5 mL DMF was added HATU (38 mg, 0.1 mmol). the reaction solution was stirred for 1 hour, and the resulted solution was concentrated and purified by reversed phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of product, 35 mg, 40% yield.
The per-Boc product from previous step was treated in 2 mL DCM and 2 mL TFA at room temperature, the solution was stirred 1 0 min, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 15 mg, 65% yield, lon(s) found by LCMS: (M+2H)/2 = 1240.7, (M+3H)/3 = 827.5, (M+4H)/4 =620.8.
Figure imgf000129_0002
Synthesis of diethyl 2,2'-((2-(octylamino)-2-oxoethyl)azanediyl)diacetate
Figure imgf000130_0001
To the solution octyl amine (650 mg, 5 mmol) and 2-(bis(2-ethoxy-2-oxoethyl)amino)acetic acid (1 .5 g, 6 mmol) in DMF (30 mL) was added EDC (1 .2 g, 6 mmol), HOBT (900 mg, 6 mmol), DIPEA (1 .4 mL, 10 mmol) at room temperature. The solution was stirred for overnight. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of oil product 1 .6 g, 85% yield. LC/MS 359.3 [M+H]+
Step b. Synthesis of 2,2'-((2-(octylamino -2-oxoethyl)azanediyl)diacetic acid
Figure imgf000130_0002
Lithium hydroxide (72 mg, 3 mmol) in 3 mL H2O was added to the solution of diethyl 2,2'-((2- (octylamino)-2-oxoethyl)azanediyl)diacetate (360 mg, 1 mmol) in mix solvent of 3 mL MeOH and 3 mL THF. The resulted solution was stirred for 1 hours at room temperature. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoro-acetic acid as the modifier. Yield of oil product, 270 mg 90% yield. LC/MS [M]+1 303.2
Step c. Synthesis of dibenzyl 14-(2-(octylamino)-2-oxoethyl)-4,12,16,24-tetraoxo-8,20- dioxa-5,11 ,14, -pentaazaheptacosane-1 ,27-dioate
Figure imgf000130_0003
2,2'-((2-(octylamino)-2-oxoethyl)azanediyl)diacetic acid (150 mg, 0.5 mmol), aminoethoxyethyl 4- (benzyloxy)-4-oxobutanoic amide ( 200 mg, 1 mmol), EDC (200 mg, 1 mmol), HOBt (150 mg, 1 mmol) and TEA(0.14 mL, 1 mmol) were dissolved into 5 mL DMF and the solution was stirred for overnight. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier dibenzyl 14-(2-(octylamino)-2-oxoethyl)-4,12,16,24-tetraoxo-8,20- dioxa-5,1 1 ,14,17,23-pentaazaheptacosane-1 ,27-dioate was isolated and confirmed structure By LC/MS [M]+1 855.5.
Figure imgf000131_0001
The title compound was prepared analogously to Compound 1 . lon(s) found by LCMS: (M+2H)/2 = 1282.8, (M+3H)/3 = 855.5, (M+4H)/4 =641 .90, (M+5H)/5 =513.7.
E
Figure imgf000131_0002
lnt-6 (80 mg, 58 mmol) and bis-PEG1 -NHS-ester (10 mg, 28 mmol) were stirred together in DMF (1 mL) at room temperature for 2 hours. The mixture was applied directly to reversed phase HPLC (30- 95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized and the resulting white solid was stirred in a 1 /1 mixture of TFA/DCM containing 0.1 % thioanisole (4 mL) at room temperature for 30 minutes. The solvent was removed by rotovap, azeotroped twice with toluene. The residue was dissolved in Dl water (1 mL) and applied to reversed phase HPLC (0-35% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield: 50 %, 2 steps. LC/MS [M+3H/3] = 684.9.
Example 15. Synthesis of Compound 4
Figure imgf000131_0003
Compound 4 was prepared analogously to Compound 3 from lnt-6 and bis-PEG2-NHS-ester. Yield: 59 %, 2 steps. LC/MS [M+3H/3] = 699.6. Example 16. Synthesis of Compound 5
Figure imgf000132_0001
Compound 5 was prepared analogously to Compound 3 from lnt-6 and bis-PEG3-NHS-ester. Yield: 55 %, 2 steps. LC/MS [M+3H/3] = 714.4.
E
Figure imgf000132_0002
Compound 6 was prepared analogously to Compound 3 from lnt-6 and bis-PEG4-NHS-ester. Yield: 53 %, 2 steps. LC/MS [M+3H/3] = 728.7.
Figure imgf000132_0003
Compound 7 was prepared analogously to Compound 2 using lnt-5 as the starting material. lon(s) found by LCMS: (M+2H)/2 = 1248.8, (M+3H)/3 = 832.8, (M+4H)/4 =624.9, (M+5H)/5 =500.1 .
Example 1
Figure imgf000132_0004
lnt-6 (120 mg, 0.088 mmol) and the 4-formyl-phenoxy benzaldehyde (10 mg, 0.044 mmol) were stirred in ethanol (5 mL) at room temperature for 30 minutes. Sodium triacetoxyborohydride (37 mg, 177 mmol) was added and the reaction was stirred for an additional 12 hours. The reaction was quenched with water (1 mL), concentrated and applied to reversed phase HPLC (30-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized and the resulting white solid was stirred in a 1 /1 mixture of TFA/DCM containing 0.1 % thioanisole (4 mL) at room temperature for 30 minutes. The solvent was removed by rotovap, azeotroped twice with toluene. The residue was dissolved in Dl water (1 mL) and applied to reversed phase HPLC (0-35% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield: 33 %, 2 steps. LC/MS [M+3H/3] = 707.4.
Ex
Figure imgf000133_0001
lnt-6 (107 mg, 0.079 mmol) and TEA ( 14 mg, 0.140 mmol) were dissolved in DMF (2 mL) and [1 ,1 '-biphenyl]-4,4'-dicarbonyl dichloride (10 mg, 0.036 mmol) was added . The reaction was stirred for 2 hours at room temperature. The mixture was applied directly to reversed phase HPLC (30-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized and the resulting white solid was stirred in a 1 /1 mixture of TFA/DCM containing 0.1 % thioanisole (4 mL) at room temperature for 30 minutes. The solvent was removed by rotovap, azeotroped twice with toluene. The residue was dissolved in Dl water (1 mL) and applied to reversed phase HPLC (0- 35% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield: 56 %, 2 steps. LC/MS [M+3H/3] = 71 1 .6. Example 21. Synthesis of Compound 10
Figure imgf000134_0001
This compound was prepared from lnt-6 and 4,4'-chlorocarbonyl-1 ,1 '-biphenyl ether as described for the synthesis of Compound 9. Yield: 51 %, 2 steps. LC/MS [M+3H/3] = 716.9.
Example 22: Synthesis of Compound 11
Figure imgf000134_0002
Step a. Synthesis of dimethyl (2S,5S,8S,16S,19S,22S)-12-[(benzyloxy)carbonyl]-2,8,16,22- tetrakis{2-[(tert-butoxycarbonyl)amino]ethyl}-5,19-bis[(1 R)-1-hydroxyethyl]-4,7,10,14,17,20- hexaoxo-3,6,9,12, -heptaazatricosane-1 ,23-dioate
Figure imgf000135_0001
A stirring solution of methyl (2S)-2-[(N-{(2S)-2-amino-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate (0.399 g, 0.748 mmol), 2,2'- {[(benzyloxy)carbonyl]azanediyl}diacetic acid (0.100, 0.374 mmol), and DIEA (0.261 mL, 1 .50 mmol), in DMF (1 mL), were treated with a solution of HATU (0.285 g, 0.748 mmol), dropwise over 30 minutes, at room temperature. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.200 g, 41 %. lon(s) found by LCMS: (M+H)+ = 1298.7
Step b. Synthesis of (2S,5S,8S,16S,19S,22S)-12-[(benzyloxy)carbonyl]-2,8,16,22-tetrakis{2- [(tert-butoxycarbonyl)amino]ethyl}-5,19-bis[(1 R)-1-hydroxyethyl]-4,7,10,14,17,20-hexaoxo- 3,6,9,12,15,18,21 -heptaazatricosane-1 ,23-dioic acid
Figure imgf000135_0002
A solution of dimethyl (2S,5S,8S,16S,19S,22S)-12-[(benzyloxy)carbonyl]-2,8,16,22-tetrakis{2- [(tert-butoxycarbonyl)amino]ethyl}-5,19-bis[(1 R)-1 -hydroxyethyl]-4,7,10,14,17,20-hexaoxo- 3,6,9,12,15,18,21 -heptaazatricosane-1 ,23-dioate (0.380 g, 0.242 mmol), in methanol (1 mL) was treated with a solution of lithium hydroxide (0.028 g, 1 .171 mmol), in water (1 mL), then stirred at room temperature for 30 minutes. The reaction was made slightly acidic (pH=5) with concentrated HCI (few drops). The desired product was isolated directly by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, using no modifier. Yield 0.164 g, 44%. lon(s) found by LCMS: [(M-2Boc)+2H]/2 = 535.8, [(M-3Boc)+2H]/2 =485.8 Step
Figure imgf000136_0001
A solution of (2S,5S,8S,1 6S,19S,22S)-12-[(benzyloxy)carbonyl]-2,8,16,22-tetrakis{2-[(tert- butoxycarbonyl)amino]ethyl}-5,19-bis[(1 R)-1 -hydroxyethyl]-4,7,10,14,17,20-hexaoxo-3, 6,9,12,15,18,21 - heptaazatricosane-1 ,23-dioic acid (0.164 g, 0.129 mmol), lnt-1 (0.329 g, 0.31 0 mmol), DIEA(0.146 mL, 0.839 mmol), and DMF (1 mL), was treated with a solution of HATU (0.175 g, 0.460 mmol) in DMF (1 mL), dropwise over 30 minutes. The crude reaction mixture was taken on to the next step without purification, lon(s) found by LCMS: [(M-2Boc)+3H]/3 = 1053.3, [(M-3Boc)+3H]/3 = 1019.9, [(M- 4Boc)+3H]/3 = 986.6.
Step
Figure imgf000136_0002
Crude Cbz-deca-Boc-(Compound 1 1 ) (DMF solution) was diluted with methanol (10 mL), charged with 5%Pd/C (0.150g), and hydrogen from a balloon. The reaction was monitored by LCMS. After 2hr the mixture was filtered through celite, concentrated and purified by reversed phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 0.252 g, 61 % (two steps), lon(s) found by LCMS: (M+3H)/3 = 1075.3
Step
Figure imgf000136_0003
Deca-Boc-(Compound 1 1 ) (0.030 g, 0.0093 mmol), was suspended in DCM (1 mL) and treated with TFA (1 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% acetonitrile and water, using formic acid(0.1 %) as the modifier. Yield 0.022 g, 86%. lon(s) found by LCMS: (M+3H)/3 = 741 .8, (M+4H)/4 =556.6,
Figure imgf000137_0001
Step a. Synthesis of dimethyl (2S,5S,8S,15S,18S,21S)-2,8,15,21-tetrakis{2-[(tert- butoxycarbonyl)amino]ethyl}-5,18-bis[(1 R)-1-hydroxyethyl]-4,7,10,13,16,19-hexaoxo-3,6,9,14,17,20- hexaazadocosane-1 ,22-dioate
Figure imgf000137_0002
A solution of methyl (2S)-2-[(N-{(2S)-2-amino-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate (0.150 g, 0.281 mmol), and 1 ,1 '-[(1 ,4- dioxobutane-1 ,4-diyl)bis(oxy)]di(pyrrolidine-2,5-dione) (0.044 g, 0.141 mmol), in DMF (1 mL) were stirred at room temperature for 1 hr. Reaction progress was monitored by LCMS. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using formic acid(0.1 %) as the modifier. Yield 0.069 g, 43%. lon(s) found by LCMS: (M+H)+ = 1 149.6 Step b. Synthesis of (2S,5S,8S,15S,18S,21S)-2,8,15,21-tetrakis{2-[(tert- butoxycarbonyl)amino]ethyl}-5,18-bis[(1 R)-1-hydroxyethyl]-4,7,10,13,16,19-hexaoxo-3,6,9,14,17,20- hexaazadocosane-1 ,22-dioic
Figure imgf000138_0001
A solution of dimethyl (2S,5S,8S,15S,18S,21 S)-2,8,15,21 -tetrakis{2-[(tert- butoxycarbonyl)amino]ethyl}-5,18-bis[(1 R)-1 -hydroxyethyl]-4,7,10,13,16,19-hexaoxo-3, 6,9,14,17,20- hexaazadocosane-1 ,22-dioate (0.069 g, 0.060 mmol), in methanol(2 ml_), was treated with a solution of LiOH (0.0043 g, 0.1 80 mmol) in water (1 ml_). LCMS after 30 minutes indicates complete conversion. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.048 g, 71 %. lon(s) found by LCMS: (M+H)+ = 1 121 .6
Step c.
Figure imgf000138_0002
A solution of (2S,5S,8S,1 5S,18S,21 S)-2,8,1 5,21 -tetrakis{2-[(tert-butoxycarbonyl)amino]ethyl}- 5,18-bis[(1 R)-1 -hydroxyethyl]-4,7,1 0,13,1 6,19-hexaoxo-3, 6,9,14,17,20-hexaazadocosane-1 ,22-dioic acid(0.048 g, 0.043 mmol), lnt-1 (0.100 g, 0.094 mmol), and DIEA (0.049 mL, 0.283 mmol), in DMF (1 mL), was treated with COMU ((1 -Cyano-2-ethoxy-2-oxoethylidenaminooxy)dimethylamino-morpholino- carbenium hexafluorophosphate) (0.0422 g, 0.098 mmol), while stirring at room temperature. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, using formic acid as the modifier. Yield 0.042 g, 31 %. lon(s) found by LCMS: [(M-3Boc)+3H]/3 = 970.3, [(M-4Boc)+3H]/3 = 936.9, [(M- 5Boc)+3H]/3 = 903.6
Step d.
Figure imgf000138_0003
Deca-Boc-(Compound 12) (0.042 g, 0.013 mmol) was dissolved in DCM (1 mL) and treated with TFA (1 mL), while stirring at room temperature. After 30 minutes, the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.006 g, 21 % yield, lon(s) found by LCMS: (M+4H)/4 = 552.8, (M+5H)/5 = 442.5, (M+6H)/6 = 368.9
Example 24. Synthesis of Compound 13
Step a. Synthesis of linker
Figure imgf000139_0001
Benzene-1 ,4-dicarbonyl dichloride (60 mg, 0.296 mmol) in DMF (0.5 mL) was added dropwise to a stirring mixture H-Thr-YBoc-Dab-OMe (lnt-1 1 ) (197 mg, 0.591 mmol) and DIEA in DMF (1 .5 mL). The mixture was stirred for 1 hour and then applied directly to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled, concentrated and stirred in a 1 /1 /2 mixture of methanol/THF/DI water (8 mL) containing lithium hydroxide (0.42 g, 1 .77 mmol) at room temperature for 2 hours. The mixture was neutralized with 1 N HCL aqueous, extracted into ethyl acetate, concentrated and applied to reversed phase HPLC (5-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford (2S,2'S)-2,2'-(1 ,4-phenylenebis{carbonylazanediyl[(2S,3R)-3-hydroxy-1 -oxobutane-2,1 - diyl]azanediyl})bis{4-[(tert-butoxycarbonyl)amino]butanoic acid} as a white solid. Yield: 55 %, 2 steps. LC/MS [m-H+
Figure imgf000139_0002
Step b. Coupling to cycloheptapeptide lnt-1
HATU (63 mg, 0.166 mmol) was added to a stirring mixture of (2S,2'S)-2,2'-(1 ,4- phenylenebis{carbonylazanediyl[(2S,3R)-3-hydroxy-1 -oxobutane-2,1 -diyl]azanediyl})bis{4-[(tert- butoxycarbonyl)amino]butanoic acid} (60 mg, 0.0.75 mmol), lnt-1 (176 mg, 166 mmol), and DIEA (58 mg, 0.451 mmol) in DMF (4 mL). The mixture was stirred for 30 minutes and then applied directly to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and concentrated and the resulting white solid was stirred in a 1 /1 mixture of TFA/DCM containing 0.1 % thioanisole (4 mL) at room temperature for 30 minutes. The solvent was removed by rotovap, azeotroped twice with toluene. The residue was dissolved in Dl water (1 mL) and applied to reversed phase HPLC (0-35% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford N~1 ~,N~4~-bis[(2S,3R)-1 -{[(2S)-4- amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 - hydroxyethyl]-12-(2-methylpropyl)-2,5,8, 1 1 ,14,17,20-heptaoxo-1 , 4,7,1 0,13,16, 19-heptaazacyclotricosan- 21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]benzene-1 ,4-dicarboxamide (Compound 13) as a white solid. Yield: 61 %, 2 steps. LC/MS [M+3H/3] = 686.1 .
Example 25. Synthesis of Compound 14
Figure imgf000140_0001
Step a. Synthesis of linker
Figure imgf000140_0002
(2S,2'S)-2,2'-(1 ,3-phenylenebis{carbonylazanediyl[(2S,3R)-3-hydroxy-1 -oxobutane-2,1 - diyl]azanediyl})bis{4-[(tert-butoxycarbonyl)amino]butanoic acid} was prepared from benzene-1 ,3- dicarbonyl dichloride and H-Thr-YBoc-Dab-OMe (lnt-1 1 ) as described in Example 24, Step a. Step b. Coupling to cycloheptapeptide lnt-1
N~1 ~,N~3~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2- yl]benzene-1 ,3-dicarboxamide (Compound 14) was prepared from (2S,2'S)-2,2'-(1 ,3- phenylenebis{carbonylazanediyl[(2S,3R)-3-hydroxy-1 -oxobutane-2,1 -diyl]azanediyl})bis{4-[(tert- butoxycarbonyl)amino]butanoic acid} and lnt-1 as described in Example 24, Step b. Yield: 63 %, 2 steps. LC/MS [M+3H/3]= 686.3.
Example 26. Synthesis of Compound 15
Step a. Synthesis of linke
Figure imgf000141_0001
HATU (222 mg, 0.495 mmol) was added to a stirring mixture of [2,2'-bipyridine]-5,5'-dicarboxylic acid (55 mg, 0.225 mmol), H-Thr-YBoc-Dab-OMe (lnt-1 1 ) (150 mg, 0.450 mmol), DIEA (174 mg, 1 .35 mmol) in DMF (4 mL). The mixture was stirred for 30 minutes and then applied directly to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were concentrated and stirred in a 1 /1 /2 mixture of methanol/THF/DI water (15 mL) containing lithium hydroxide (32 mg, 1 .35 mmol) at room temperature for 2 hours. The mixture was neutralized with 1 N HCL aqueous and extracted into ethyl acetate, concentrated and applied to reversed phase HPLC (10-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford (2S,2'S)-2,2'-([2,2'-bipyridine]-5,5'-diylbis{carbonylazanediyl[(2S,3R)-3- hydroxy-1 -oxobutane-2,1 -diyl]azanediyl})bis{4-[(tert-butoxycarbonyl)amino]butanoic acid} as a white solid. Yield: 67 %, 2 steps. LC/MS [m+H+] = 847.6.
Step b. Coupling to cycloheptapeptide lnt-1
Figure imgf000141_0002
N~5~,N~5'~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl][2,2'- bipyridine]-5,5'-dicarboxamide (Compound 15) was prepared from (2S,2'S)-2,2'-([2,2'-bipyridine]-5,5'- diylbis{carbonylazanediyl[(2S,3R)-3-hydroxy-1 -oxobutane-2,1 -diyl]azanediyl})bis{4-[(tert- butoxycarbonyl)amino]butanoic acid} and lnt-1 as described in Example 24, step b. Yield: 47 %, 2 steps. LC/MS [M+3H/3]= 712.3.
Example 27: Synthesis of Compound 16
du e A.
Figure imgf000142_0001
Step a. Synthesis of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2- {[(benzyloxy)carbonyl]amino}octanoyl]amino}-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate
Figure imgf000142_0002
A stirring solution of methyl (2S)-2-[(N-{(2S)-2-amino-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate (0.300 g, 0.562 mmol),(2S)-2-
{[(benzyloxy)carbonyl]amino}octanoic acid (0.1 65 g, 0.562 mmol), and DIEA (0.294 mL, 1 .69 mmol), in
DMF (1 mL), were treated with HATU (0.235 g, 0.618 mmol) at room temperature. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% acetonitrile and water, using 0.1 % TFA as the modifier. Yield 0.296 g, 65%. lon(s) found by LCMS: (M+H)+ = 809.5
Step b. Synthesis of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2-aminooctanoyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate
Figure imgf000143_0001
A solution of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2-{[(benzyloxy)carbonyl]amino}octanoyl]amino}-4- [(tert-butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate (1 .1 60 g, 1 .433 mmol) (material from multiple batches), in methanol (5 mL), was charged with 5%Pd/C (0.400 g), and hydrogen gas from a balloon. When the reaction was complete by LCMS (1 hr), the mixture was filtered through celite, concentrated and taken-on to the next step without purification. Yield 0.630 g, 65%. lon(s) found by LCMS: (M+H)+ = 675.4
Step c. Synthesis of dimethyl (2S,5S,8S,11 S,19S,22S,25S,28S)-15-[(benzyloxy)carbonyl]- 2,8,22,28-tetrakis{2-[(tert-butoxycarbonyl)amino]ethyl}-11 ,19-dihexyl-5,25-bis[(1 R)-1- hydroxyethyl]-4,7,10,13,17,20,23,26-octaoxo-3,6,9,12,15,18,21 ,24,27-nonaazanonacosane-1 ,29- dioate
Figure imgf000143_0002
A solution of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2-aminooctanoyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate (0.626 g, 0.928 mmol), 2,2'-{[(benzyloxy)carbonyl]azanediyl}diacetic acid (0.124 g, 0.464 mmol), and DIEA (0.364 mL, 2.088 mmol) in DMF (3 mL), were treated with a solution of HATU (0.362 g, 0.951 mmol) in DMF (1 mL), dropwise over 15 minutes. The desired product was isolated by reversed phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 0.383 g, 52%. lon(s) found by LCMS: [(M-2Boc)+2H]/2 =690.9, [(M-4Boc)+2H]/2 = 590.9 Step d. Synthesis of (2S,5S,8S,11S,19S,22S,25S,28S)-15-[(benzyloxy)carbonyl]-2,8,22,28- tetrakis{2-[(tert-butoxycarbonyl)amino]ethyl}-11 ,19-dihexyl-5,25-bis[(1 R)-1-hydroxyethyl]-
4,7,10,13,17,20,23,26-octaoxo-3,6,9,12,15,18,21 ,24,27-nonaazanonacosane-1 ,29-dioic acid
Figure imgf000144_0001
A solution of dimethyl (2S,5S,8S,1 1 S,19S,22S,25S,28S)-15-[(benzyloxy)carbonyl]-2,8,22,28- tetrakis{2-[(tert-butoxycarbonyl)amino]ethyl}-1 1 ,19-dihexyl-5,25-bis[(1 R)-1 -hydroxyethyl]- 4,7,1 0,13,17,20,23,26-octaoxo-3, 6,9,12,15,18,21 ,24,27-nonaazanonacosane-1 ,29-dioate (0.383 g, 0.242 mmol), in methanol (10 mL, warmed to promote dissolution) was treated with a solution of lithium hydroxide (0.0232 g, 0.969 mmol), in water (2 mL), while stirring at room temperature. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.340 g, 90%. lon(s) found by LCMS: [(M-1 Boc)+2H]/2 = 726.9, [(M-2Boc)+2H]/2 =676.9
Figure imgf000144_0002
Procedu e A
A solution of (2S,5S,8S,1 1 S,19S,22S,25S,28S)-1 5-[(benzyloxy)carbonyl]-2,8,22,28-tetrakis{2- [(tert-butoxycarbonyl)amino]ethyl}-1 1 ,19-dihexyl-5,25-bis[(1 R)-1 -hydroxyethyl]-4,7,10,13,17,20,23,26- octaoxo-3,6,9, 12, 15,18,21 ,24,27-nonaazanonacosane-1 ,29-dioic acid (0.34 g, 0.230 mmol), lnt-1 (0.488 g, 0.460 mmol), DIEA (0.1 91 mL, 1 .095 mmol), and DMF (5 mL), was treated with HATU (0.175 g, 0.460 mmol). The crude reaction mixture was taken on to the next step without purification, lon(s) found by LCMS: [(M-3Boc)+3H]/3 = 1 1 14.0
Procedure B
A solution of lnt-10 (2.23 g, 1 .308 mmol), 2,2'-{[(benzyloxy)carbonyl]azanediyl}diacetic acid
(0.175 g, 0.654 mmol), DIEA (0.718 mL, 4.12 mmol), and DMF (10 mL), was treated with a solution HATU (0.522 g, 1 .373 mmol) in DMF (3 mL) via syringe pump over 1 hr, while stirring at room temperature. The crude reaction mixture was taken on to the next step without purification, lon(s) found by LCMS: [(M- 3Boc)+3H]/3 = 1 1 14.0
Figure imgf000145_0001
Procedu e A
Crude Cbz-deca-Boc-(Compound 1 6) (from Procedure A, Step e.) was diluted with methanol (10 mL), charged with 5%Pd/C (0.250 g), and hydrogen from a balloon. The reaction was monitored by LCMS. After 2hr the mixture was filtered through celite, concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.139 g, 18% (two steps), lon(s) found by LCMS: [(M- 2Boc)+3H]/3 = 1 1 02.6
Procedure B
Crude Cbz-deca-Boc-(Compound 1 6) (from Procedure B, Step e.) in DMF, was charged with 5%Pd/C (1 .0 g), and hydrogen gas from a balloon. The reaction was monitored by LCMS. After 2hr the mixture was filtered through celite, concentrated and purified by C1 8 reverse phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 20% to 1 00% methanol and water, using no modifier. Yield 1 .46 g, 64% (two steps), lon(s) found by LCMS: [(M- 2Boc)+3H]/3 = 1 1 02.6
Figure imgf000145_0002
Deca-Boc-(Compound 16) (0.070 g, 1 .020 mmol), was dissolved in DCM (1 mL) and treated with TFA (1 mL), while stirring at room temperature. After 15 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.024 g, 40%. lon(s) found by LCMS: (M+3H)/3 = 835.8, (M+4H)/4 =627.1 , (M+5H)/5 =501 .9
Example 28. Synthesis of Compound 17
Step a. Synthesis of D-ser-(lnM)
Figure imgf000146_0001
lnt-1 (500 mg, 0.47 mmol), HOBt (68 mg, 0.50 mmol), EDC (96 mg, 0.50 mmol), DIEA (130 mg, 1 mmol) and CBZ-(D)-Ser-OH (0.50 mmol) were stirred in DMF (3 mL) at room temperature for 2 hours. The mixture was applied directly to reversed phase HPLC (25-95% acetonitrile in Dl water containing 0.1 % TFA: 20 minute gradient). The pure fractions were pooled, concentrated and directly taken up in methanol (10 mL) and stirred in the presence of 5% Pd/C (75 mg) under 1 atmosphere of hydrogen gas for 1 hour. The mixture was filtered, concentrated and purified by reversed phase HPLC (10-95% acetonitrile in Dl water, no modifier: 20 minute gradient). The pure fractions were pooled and lyophilized to afford tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-17-[(1 R)-1 -hydroxyethyl]-8-(2- methylpropyl)-3, 6,9, 12,15, 1 8,23-heptaoxo-22-(D-serylamino)-1 , 4,7,10,13, 16,19-heptaazacyclotricosane- 2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate (D-ser-(lnM )) as a white solid. Yield: 83%. LC/MS [m- boc/2+H+]+ 525.6.
Step b. Synthesis of L-thr-D-ser-(lnM)
Figure imgf000146_0002
L-threonyl-N-[(3S,6S,9S,12S,15R,18S.21 S)-15-benzyl-6,9,1 8-tris{2-[(tert- butoxycarbonyl)amino]ethyl}-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-D-serinamide (L-thr-D-ser-(lnt-1 )) was prepared from tri- tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)- 3,6,9 ,12 ,15 ,18,23-heptaoxo-22-(D-serylamino)-1 ,4,7 ,10 ,13 ,16,19-heptaazacyclotricosane-2,1 1 ,14- triyl]tri(ethane-2,1 -diyl)}triscarbamate (D-ser-(lnt-l )) and Z-Thr-OH as described in Example 28, Step a. Yield: 81 %. LC/MS [m-2 boc/2+H+]+ 525.8.
Figure imgf000147_0001
HATU (62 mg, 0.16 mmol, in 0.75 mL DMF) was added dropwise over 45 minutes to a stirring mixture of L-threonyl-N-[(3S,6S,9S,12S,15R,18S,21 S)-15-benzyl-6,9,18-tris{2-[(tert- butoxycarbonyl)amino]ethyl}-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-D-serinamide (203 mg, 0.16 mmoL), fumaric acid (9 mg. 0.077 mmol), and triethylamine (31 mg, 0.31 mmol) in DMF (1 .5 mL). The reaction was stirred for an additional 30 minutes then applied directly to reversed phase HPLC (35-95% methanol in Dl water containing 0.1 % TFA: 20 minute gradient). The pure fractions were pooled and concentrated. The Boc- protected intermediate was stirred in a 1 /1 mixture of DCM/TFA containing thioanisole (77 mg, 0.62 mmoL) at room temperature for 20 minutes. The solvent was removed on the rotary evaporator and the crude product was dried under high vacuum for 1 hour. The crude residue was taken up in a 9/1 mixture of Dl water and methanol (2 mL) and applied to reversed phase HPLC (0-45% methanol in Dl water containing 0.1 % TFA: 30 minute gradient). The pure fractions were pooled and lyophilized to afford (2R,5S,8E,12S,1 5R)-5,12-bis[(1 R)-1 -hydroxyethyl]-2,15-bis(hydroxymethyl)-4,7,10,13-tetraoxo- N~1 ~,N~16~-bis(3S,6S,9S,12S,15R,18S.21 S)[6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 - hydroxyethyl]-12-(2-methylpropyl)-2,5,8, 1 1 ,14,17,20-heptaoxo-1 , 4,7,1 0,13, 16,19-heptaazacyclotricosan- 21 -yl]-3,6,1 1 ,14-tetraazahexadec-8-ene-1 ,16-diamide (Compound 17) as a white solid. Yield: 63%. LC/MS ((M+2H)/2)+ 990.6.
Example 29. Synthesis of Compound 18 (Mixture of diastereomers)
Step
Figure imgf000147_0002
The cyclopropane bis-amide (mixture of diastereomers at the cyclopropane chiral centers) was prepared from racemic trans-cyclopropane-1 ,2-dicarboxylic acid and H-Thr-yBoc-Dab-OMe (lnt-1 1 ) by a procedure analogous to that described in Example 26, Step a.
Step
Figure imgf000148_0001
Compound 1 8 (mixture of diastereomers at cyclopropane chiral centers) was prepared from the cyclopropane bis-amide from Step a. and lnt-1 as described in Example 24, Step b. Yield: 40%, 2 steps. LC/MS [M+3H/3]= 674.2.
Example 30: S
Figure imgf000148_0002
Figure imgf000148_0003
Step a. Sy
Figure imgf000149_0001
A stirring solution of lnt-7 (0.150 g, 0.098 mmol), fumaric acid (0.0057 g, 0.049 mmol), and DIEA (0.051 mL, 0.294 mmol), dissolved in DMF (1 mL), was treated with a solution of HATU (0.037 g, 0.098 mmol) in DMF(0.5 mL), dropwise over 15 minutes. After 1 hour the product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.108 g, 70% yield, lon(s) found by LCMS: [(M- 3Boc)+3H]/3 = 947.0, [(M-4Boc)+3H]/3 = 913.6, [(M-5Boc)+3H]/3 = 880.3
Step b. Sy
Figure imgf000149_0002
A stirring solution of deca-Boc-(Compound 19) (0.1 08 g, 0.034 mmol), dissolved in DCM (2 mL), was treated with TFA (0.5 mL) at room temperature. After 30 minutes, the crude reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 1 00% acetonitrile and water, using formic acid as the modifier. Yield 0.037 g, 50% yield, lon(s) found by LCMS: Exact Mass: 2137.3, (M+2H)/2 = 1069.6, (M+3H)/3 = 713.4, (M+4H)/4 =535.3
Example 31 : Synt
Figure imgf000149_0003
Figure imgf000150_0001
Compound 20 (mixture of diastereomers at the cyclopropane chiral centers) was prepared analogously to Compound 19, where (racemic)-trans-cyclopropane-l ,2-dicarboxylic acid, was substituted for fumaric acid in the first step of the sequence, lon(s) found by LCMS: (M+3H)/3 = 718.4
Example 32: Synthe
Figure imgf000150_0002
3,3'-oxybis{N-[(3S,6S,9S,12S,1 5R,1 8S.21 S)-6,9,18-tris(2-aminoethyl)-1 5-benzyl-3-[(1 R)-1 - hydroxyethyl]-12-(2-methylpropyl)-2,5,8, 1 1 ,14,17,20-heptaoxo-1 , 4,7,1 0,13, 16,19-heptaazacyclotricosan- 21 -yl]propanamide} was prepared from lnt-1 and bis-PEG1 -NHS-ester as described in Example 14. Yield: 61 %, 2 steps. LC/MS [M+3H/3] = 686.1 .
Figure imgf000150_0003
Figure imgf000150_0004
Figure imgf000151_0001
A stirring solution of lnt-7 (0.200 g, 0.131 mmol), Cbz-L-aspartic acid (0.017 g, 0.065 mmol), and DIEA (0.068 mL, 0.392 mmol), dissolved in DMF (1 mL), was treated with a solution of HATU (0.050 g, 0.0131 mmol) in DMF (1 .0 mL), dropwise over 30 minutes. After 1 hour the product was taken on to the next step without further purification lon(s) found by LCMS: [(M-3Boc)+3H]/3 = 997.3, [(M-4Boc)+3H]/3 = 964.0, [(M-5Boc)+3H]/3 = 930.6
Figure imgf000151_0002
A solution of Cbz-deca-Boc-(Compound 22) (0.131 mmol) dissolved in methanol (5 mL), was charged with 5% Pd/C (0.050 g), flushed with hydrogen from a balloon, and stirred under a hydrogen atmosphere until Cbz removal was complete by LCMS (-0.5 hr). The crude product was isolated by filtration through celite, then concentrated to an oil, which was purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield for two steps 0.147 g, 71 % yield, lon(s) found by LCMS: [(M-3Boc)+3H]/3 = 952.6, [(M-4Boc)+3H]/3 = 919.3
Figure imgf000152_0001
A stirring solution of deca Boc-(Compound 22) (0.042 g, 0.013 mmol), dissolved in DCM (1 mL), was treated with TFA (1 mL) at room temperature. After 30 minutes, the crude reaction was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 0.010 g, 35% yield, lon(s) found by LCMS: (M+4H)/4 =539.6, (M+5H)/5 =431 .9
Example 34: Synthesis of Compound 23
Figure imgf000152_0002
Compound 23 was prepared analogously to Example 30, where glutaric acid, was substituted for fumaric acid in the first step of the sequence, lon(s) found by LCMS: (M+2H)/2 = 1077.7, (M+3H)/3 = 718.8, (M+4H)/4 =539.3
Example 35: Synthesis of Compound 24
Figure imgf000152_0003
Compound 24 was prepared analogously to Example 30, where 2,2'-oxydiacetic acid, was substituted for fumaric acid in the first step of the sequence, lon(s) found by LCMS: (M+2H)/2 = 1078.6, (M+3H)/3 = 71 9.4, (M+4H)/4 =539.8, (M+5H)/5 =432.1 Example 36: Synthesis of Compound 25
Step a. Preparatio
Figure imgf000153_0001
lnt-1 (2 g, 1 .88 mmol), Z-L-Dab(Boc)-OH-DCHA (1 .20 g, 2.33 mmol), and N-methylmorpholine (0.62 mL, 5.65 mmol) were dissolved in DMF (6 mL) and HATU (0.858 g, 2.25 mmol) was added and the reaction was stirred for 45 minutes. The mixture was applied directly to reversed phase HPLC (25-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were lyophilized to afford 2.1 of the title compound as a white solid. Yield: 79%. LC/MS ((M+2H)/2) = 599.0 (CBZ protected intermediate, loss of 2 boc groups on LC/MS).
Step b. Removal of the CBz group
Figure imgf000153_0002
Cbz-INT-4 (2.1 g, 1 .50 mmol) was stirred in methanol (25 mL) in the presence of 5% Pd/C (125 mg) under 1 atm of hydrogen gas for 45 minutes. The mixture was filtered, concentrated and applied to reversed phase HPLC (25-95% acetonitrile in Dl water: 20 minute gradient). The pure fractions were lyophilized to afford 1 .92 g of INT-4 as a white solid. Yield: 96%. LC/MS ((M+2H)/2)=532.0. Step
Figure imgf000154_0001
Compound 25 was prepared from INT-4 and bis-PEG1 -NHS-ester as described in Example 14. Yield: 43%. LC/MS[M+3H/3] + 617.5.
Example 37: Synthesis of Compound 26
Figure imgf000154_0002
Compound 26 was prepared as described in Example 14 from lnt-6 and bis-PEG2-NHS-ester. Yield: 59 %, 2 steps. LC/MS [M+3H/3] = 699.6.
Exam
Figure imgf000154_0003
Step a. Synthesis of Benzyl-deca-Boc-(Compound 27)
Figure imgf000155_0001
Benzyl-deca-Boc-(Compound 27) was prepared analogously as in Example 30 (step a), where 1 - benzyl-3,3-azetidinedicarboxylic acid, was substituted for fumaric acid, lon(s) found by LCMS: [(M- 2Boc)+3H]/3 = 1020.0, [(M-3Boc)+3H]/3 = 986.6
Step b. S
Figure imgf000155_0002
A solution of benzyl-deca-Boc-(Compound 27) (0.175 g, 0.537 mmol) dissolved in methanol (5 mL), was charged with 5% Pd/C (0.050 g), flushed with hydrogen gas from a balloon, and stirred under a hydrogen atmosphere until debenzylation was complete by LCMS (~2hr). The crude product was isolated by filtration through celite, then concentrated to an oil, and used in the next step without further purification.
S
Figure imgf000155_0003
A solution of crude deca-Boc-(Compound 27) (0.025 g, 0.00767 mmol) in DCM (1 mL), was treated with TFA(1 mL), while stirring at room temperature. After 5min the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 0.010 g, 58%. lon(s) found by LCMS: (M+2H)/2 = 1084.2, (M+3H)/3 = 723.1 . Examp
Figure imgf000156_0001
(2S,5R,15R,18S)-2,18-bis(2-aminoethyl)-5,1 5-bis[(1 S)-1 -hydroxyethyl]-4,7,13,16-tetraoxo-N~1 ~- [(3S,6S,9S,12S,15R,18S.21 R)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2, 5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-N~19—
[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2, 5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-10-oxa- -tetraazanonadecane-1 ,19-diamide
Figure imgf000156_0002
Step a. Synthesis of Cbz-D-T -Dab(Boc)-OH
Figure imgf000156_0003
(2S)-2-({N-[(benzyloxy)carbonyl]-D-threonyl}amino)-4-[(tert-butoxycarbonyl)amino]butanoic acid
Cbz-D-Thr-OH (commercial) (1 .924 g, 7.37 mmol), Dab(Boc)-OMe (commercial) (2.000 g, 7.37 mmol), EDCI (4.263 g, 1 1 .05 mmol), HOBt (1 .493 g, 1 1 .05 mmol) and NaHCOs (1 .238 g, 14.74 mmol) were weighed into a 100- mL round bottom flask. 50 mL of DCM/DMF (4:1 ) was added into the flask. The mixture was stirred at room temperature for overnight (TLC or LC/MS monitoring). After completion, EtOAc (200 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated NaHC03 and brine. Dried with Na2S04 and condensed. The residue was purified with normal phase silica (2-7% MeOH/DCM) to give 3.000g pure desired product as a white solid (87%). Ions were found as: positive charge (M-Boc+H+: 368.2), negative charge (M-H+: 467.2). The solid was dissolved in 10 mL of THF/water (1 :1 ) and treated with LiOH (0.95 equiv.) for 30 minutes at room temperature. The reaction mixture was acidified to pH~2 with 1 N aqueous HCI. THF was removed under reduced pressure. The residue was extracted with EtOAc. After drying and condensation Cbz-D-Thr-Dab(Boc)-OH was obtained in quantitative yield. Ions were found as: positive charge (M-Boc+H+: 354.2), negative charge (M-H+: 452.2).
Step b. Synthesis of -Thr-Dab-tri-Boc-PMBH
Figure imgf000157_0001
(2S)-2-({N-[(benzyloxy)carbonyl]-D-threonyl}amino)-4-[(tert-butoxycarbonyl)amino]butanoic acid- tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-22-{[(2R)-4-[(tert-butoxycarbonyl)amino]-2-(D- threonylamino)butanoyl]amino}-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3,6,9,12,15,18,23-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosane-2, 1 1 , 14-triyl]tri(ethane-2, 1 -diyl)}triscarbamate
lnt-1 (1 .595 g, 1 .502 mmol) and Cbz-D-Thr-Dab(Boc)-OH (0.715 g, 1 .577 mmol) were dissolved in 10 mL of DMF at room temperature followed by addition of DIPEA (0.52 mL, 3.00 mmol). To this mixture was slowly added HATU (1 .142 g, 3.00 mmol) in 5 mL of DMF. After stirring overnight at room temperature, the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C18 with acetonitrile/water (0.1 % TFA) to give 1 .800 g of protected intermediate (80%). Ion was found as ((M+2H+)/2: 748.4). Cbz protecting group was removed with 5%Pd/C in MeOH/EtOAc (1 :1 , 10 mL) under hydrogen balloon pressure at room temperature for 2 hours. Celite filtration gave D- Thr-Dab(Boc)-PMBH(tri-Boc) in quantitative yield. Ion was found as ((M+2H+)/2: 632.6).
Step c. Synthesis of D-Thr-Dab-PMBH PEG1 Dimer-(Compound 28)
D-Thr-Dab(Boc)-PMBH(tri-Boc) (0.200 g, 0.147 mmol) was dissolved in 2 mL of DMF followed by addition of DIPEA (0.037 mL, 0.21 1 mmol) and bis-PEG1 -NHS-ester (commercial, 0.025 g, 0.070 mmol). The reaction mixture was stirred at room temperature for 2 hours, then the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C18 with acetonitrile/water (0.1 %TFA) to give per-Boc-(Compound 28). Ion was found as ((M+2H+)/2: 1427.5). The Boc groups were removed by treating with TFA/DCM (1 :2) for about 2 hours. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with acetonitrile/water (0.1 % TFA). The pure Compound 28 was collected and lyophilized to give white powder. Ion was found as ((M+3H+)/3: 685.4).
Example
Figure imgf000158_0001
(1 R*,2R*)-N~1 ~-[(2R,3S)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S.21 R)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]- N~2~-[(2R,3S)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15- benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]cyclopropane-1 ,2- dicarboxa
Figure imgf000158_0002
(1 S*,2S*)-N~1 ~-[(2R,3S)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S.21 R)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]- N~2~-[(2R,3S)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15- benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]cyclopropane-1 ,2- dicarboxamide (Compound 29b) (* indicates racemix mixture)
Figure imgf000159_0001
Compound 29b or Compound 29a
D-Thr-Dab(Boc)-PMBH(tri-Boc) (compound from Example 39, step b) (0.174 g, 0.128 mmol) was dissolved in 2 mL of DMF followed by addition of racemic cyclopropane-trans-1 ,2-dicarboxylic acid (0.008 g, 0.06 mmol) and DIPEA (0.032 mL, 0.18 mmol). To this mixture was added HATU (0.058 g, 0.15 mmol) in 3 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C18 with
acetonitrile/water (0.1 %TFA) to give two isomers of per-Boc-(Compound 29a) and per-Boc-(Compound 29b). Ions were found as ((M-2Boc+3H+)/3: 841 .1 ) for both two isomers. The Boc groups for both isomers were removed by treating with TFA/DCM (1 :1 ) for less than 1 hour. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with acetonitrile/water (0.1 % TFA). The pure Compound 29a and Compound 29b fractions were collected and lyophilized to give white powders. Compound 29a was the more polar product. Ions were found as ((M+4H+)/4: 506.0) for both diastereomers.
Examp
Figure imgf000160_0001
A solution of Cbz-deca-Boc-(Compound 1 1 ) (0.030 g, 0.00893 mmol) in DCM (1 ml_) was treated with TFA (1 ml_), while stirring at room temperature for 5 minutes. The product was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier to afford the title compound, lon(s) found by LCMS: (M+2H)/2 = 1 179.2, (M+3H)/3 = 786.4
Example
Figure imgf000160_0002
Step a. Synthesis of linker
HATU (613 mg, 1 .61 mmol, in 1 ml_ DMF) was added to a stirring mixture of methyl (4S)-4-[(tert- butoxycarbonyl)amino]-L-prolinate (394 mg, 1 .61 mmol), racemic trans-cyclopropane-1 ,2-dicarboxylic acid, (1 00 mg, 0.769 mmol) and diisopropylethylamine (397 mg, 3.07 mmol), in DMF (1 .5 mL) dropwise over a period of 30 minutes. The reaction was stirred for an additional 30 minutes then applied directly to reversed phase HPLC (5-95% acetonitrile in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled and lyophilized and taken directly to the next step.
Dimethyl ester (mixture of diastereomers at the cyclopropane chiral centers) from the step above (250 mg, 0.43 mmol) was stirred in a 1 /1 /2 mixture of THF/Methanol/DI water (10 mL) containing lithium hydroxide (1 10 mg, 4.6 mmol) for 20 minutes. The mixture was acidified with TFA (~1 mL) and the volume was concentrated by half on the rotary evaporator. The mixture was applied to reversed phase HPLC (0-70% acetonitrile in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled and lyophilized to afford the dicarboxylic acid (mixture of diastereomers) as a white solid. Yield: 45%, 2 steps. LC/MS [M-H]- = 553.6.
Figure imgf000161_0001
HATU (60 mg, 0.159 mmol, in 0.5 mL DMF) was added to a stirring mixture of tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-22-{[(2S)-4-{[(benzyloxy)carbonyl]amino}-2-(L- threonylamino)butanoyl]amino}-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3,6,9,12,15,18,23-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate (lnt-6) (222 mg, 0.159 mmol), the diacid (mixture of diastereomers) from Step a. (40 mg, 0.072 mmol) and
diisopropylethylamine (55 mg, 0.433 mmol), in DMF (1 mL) dropwise over a period of 30 minutes. The reaction was stirred for an additional 30 minutes, diluted with methanol (2 mL) and 5% Pd/C (35 mg) was added and the mixture was stirred under 1 atmosphere of hydrogen gas for 1 hour. The mixture was filtered, concentrated and applied to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % TFA: 25 minute gradient). The pure fractions were pooled and lyophilized to afford product as a white solid which was immediately stirred in a 1 /1 mixture of TFA/DCM (5 mL) containing thioanisole (27 mg, 0.216 mmol) for 30 minutes. The mixture was concentrated, dried under high vacuum then purified by reversed phase HPLC (0-70% acetonitrile in Dl water containing 0.1 % TFA: 20 minute gradient). The pure fractions were pooled and lyophilized to afford Compound 31 (as a mixture of diastereomers at the cyclopropane chiral centers) as a white solid. Yield: 49%, 3 steps. LC/MS [M+4H/4]+ 562.2.
Example 43: Synthesis of Compound 32
Step a. Preparation of N-benzyl-(L)-threonine tert-butyl ester
Figure imgf000162_0001
Sodium triacetoxyborohydride (3 g, 14.3 mmol) was added in 4 portions, to a stirring solution of tert-butyl L-threoninate-hydrochloride (1 g, 5.71 mmol), benzaldehyde (0.67 g, 6.28 mmol), and diisopropylethylamine (0.81 g, 6.28 mmoL) in methanol (40 mL). The reaction was stirred for 12 hours at which point Dl water (~5 mL) was added and the solvent was reduced to 20 mL on the rotary evaporator. The crude mixture was purified by reversed phase HPLC (0-70% acetonitrile in Dl water with no modifier: 20 minute gradient). The pure fractions were pooled and lyophilized to afford tert-butyl N-benzyl-L- threoninate as a clear oil. Yield: 73%. LC/MS [M+H+]+ 266.4.
Step b. Preparation of the li
Figure imgf000162_0002
Benzene-1 ,4-dicarbonyl dichloride (1 50 mg, 0.739 mmol) in DMF (2 mL) was added dropwise to a stirring mixture tert-butyl N-benzyl-L-threoninate (431 mg, 0.591 mmol) and diisopropylethylamine (381 mg, 2.96 mmol) in DMF (4 mL). The mixture was stirred for 1 hour and then applied directly to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled, concentrated and stirred in TFA (15 mL) at 50°C for 4 hours. The mixture was concentrated and applied to reversed phase HPLC (1 0-95% acetonitrile in Dl water containing 0.1 % formic acid: 20 minute gradient). The pure fractions were pooled and lyophilized to afford (2S,3R,2'S,3'R)- 2,2'-{1 ,4-phenylenebis[carbonyl(benzylazanediyl)]}bis(3-hydroxybutanoic acid) as a clear oil. Yield: 69%, 2 steps. LC/MS [M-H+]- 547.4. Step c.
Figure imgf000163_0001
N~1 ~,N~4~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]- N~1 ~,N~4~-dibenzylbenzene-1 ,4-dicarboxamide was prepared from lnt-4 and (2S,3R,2'S,3'R)-2,2'-{1 ,4- phenylenebis[carbonyl(benzylazanediyl)]}bis(3-hydroxybutanoic acid) as described in Example 24, step b. Yield: 35%, 2 steps. LC/MS [M+3H/3]= 746.2.
Exa
Figure imgf000163_0002
Step a
Figure imgf000164_0001
A solution of deca-Boc-(Compound 1 1 ) (prepared as in Example 22, Step d) (0.135 g, 0.042 mmol), 3-(2-{2-[2-(2,5-dioxo-2,5-dihydro-1 H-pyrrol-1 -yl)ethoxy]ethoxy}ethoxy)propanoic acid (0.015 g, 0.050 mmol), and DIEA (0.026 mL, 0.150 mmol), in DMF (1 mL), were treated with HATU (0.01 9 g, 0.050 mmol), while stirring at room temperature. After 30 minutes, the product was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.1 12 g, 76% yield, lon(s) found by LCMS: [(M- 3Boc)+3H]/3 = 1069.6, [(M-4Boc)+3H]/3 = 1036.3, [(M-5Boc)+3H]/3 = 1003.0
Step
Figure imgf000164_0002
A solution of deca-Boc-(Compound 33) (0.1 12 g, 0.032 mmol), dissolved in DCM (1 mL), was treated with TFA (1 mL), while stirring at room temperature. After 5 minutes, the product was
concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 1 00% acetonitrile and water, using formic acid as the modifier. Yield 0.071 g, 88% yield, lon(s) found by LCMS: (M+3H)/3 = 836.1 , (M+4H)/4 =627.3, (M+5H)/5 = 502.1 .
Figure imgf000165_0001
Compound 34 (mixture of diastereomers at the cyclobutane chiral centers) was prepared analogously to Compound 19, where racemic (trans)-cyclobutane-l ,2-dicarboxylic acid, was substituted for fumaric acid and INT-8 was substituted for INT-7 in the first step of the sequence, lon(s) found by LCMS: (M+3H)/3 = 745.4, (M+4H)/4 = 559.3, (M+5H)/5 = 447.7 (* indicates racemic mixture)
Example 46: Syn
Figure imgf000165_0002
Compound 35 (mixture of diastereomers at the cyclobutane chiral centers) was prepared from trans-cyclobutane-1 ,2-dicarboxylic acid (racemic) and lnt-4 in a manner similar to that as described in Example 24, Step b. Yield: 51 %, 2 steps. LC/MS [M+4H/4]+ 509.3.
Example 47:
Figure imgf000166_0001
(1 R,2S)-N~1 ~,N~2~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)- 6,9, 1 8-tris(2-aminoethyl)-1 5-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2, 5,8, 1 1 , 14,17,20- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan- 2-yl]cyclopropane-1 ,2-dicarboxamide was prepared from cis-cyclopropane-1 ,2-dicarboxylic acid in a manner analogous to that described in Example 24, Step b. Yield: 59%, 2 steps. LC/MS [M+4H/4]+ 506.0.
Example 48: Synthesis of Compound 37 (Mixture of diastereomers)
Figure imgf000166_0002
Step a. Preparation of the linker
The linker (mixture of diastereomers at the cyclopropane chiral centers) was prepared from racemic trans-cyclopropane-1 ,2-dicarboxylic acid and H-Thr-yBoc-Dab-OMe (lnt-1 1 ) similarly to the procedure described in Example 26, Step a.
Figure imgf000167_0001
Step b. Coupling of cycloheptapeptide lnt-1 to give Compound 37 (mixture of
diastereomers)
Compound 37 (mixture of diastereomers at the cyclopropane chiral centers) was prepared from the linker from Step a. and lnt-1 as described in Example 24, Step b. Yield: 40 %, 2 steps. LC/MS
[M+3H/3]= 674.2.
Example 49:
Figure imgf000167_0002
Compound 38 was prepared analogously to Compound 33, where octanoic acid, was substituted for3-(2-{2-[2-(2,5-dioxo-2,5-dihydro-1 H-pyrrol-1 -yl)ethoxy]ethoxy}ethoxy)propanoic acid in the first step of the sequence, lon(s) found by LCMS: (M+2H)/2 = 1 175.2, (M+3H)/3 = 783.8, (M+4H)/4 = 588.1
Figure imgf000168_0001
Step a. Synthesis of deca-Boc-(Compound 39)
Figure imgf000168_0002
A solution of lnt-7 (0.1 00 g, 0.065 mmol), bis(pentafluorophenyl) carbonate (0.013g, 0.033mmol), and DIEA (0.012 mL, 0.065 mmol) in DMF (1 mL), were stirred at room temperature for 12 hours. The product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.027 g, 27% yield, lon(s) found by LCMS: [(M-3Boc)+3H]/3 = 928.9, [(M-4Boc)+3H]/3 = 895.6
Step b. Synthesis of Compound 39
Figure imgf000168_0003
Deca-Boc-(Compound 39) (0.027 g, 0.0088 mmol) was dissolved in DCM (1 mL) and treated with TFA(1 mL), while stirring at room temperature. After 5 minutes, the reaction was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.012 g, 66% yield, lon(s) found by LCMS: (M+2H)/2 = 1042.6, (M+3H)/3 = 695.4, (M+4H)/4 = 521 .8
Figure imgf000169_0001
Step a. Synthesis of tert-butyl (2S)-2-[(tert-butoxycarbonyl)amino]-4- (dimethylamino)butanoate
Figure imgf000169_0002
A solution of tert-butyl (2S)-4-amino-2-[(tert-butoxycarbonyl)amino]butanoate(1 .00 g, 3.65 mmol), 37% aqueous formaldehyde(1 .357 mL, 18.22 mmol), DIEA(0.781 mL,0 437 mmol), dissolved in DCM(10 mL), was treated with sodium triacetoxy borohydride(3.862 g, 1 8.22 mmol), while stirring at room temperature. After overnight, the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% acetonitrile and water, using formic acid(0.1 %) as the modifier. Yield 0.469 g, 43%. lon(s) found by LCMS: [M+H]+ = 275.2
Step b. Synthesis of (2S)-2-amino-4-(dimethylamino)butanoic acid
Figure imgf000169_0003
A solution of tert-butyl (2S)-2-[(tert-butoxycarbonyl)amino]-4-(dimethylamino)butanoate (0.469 g, 1 .55 mmol) dissolved in DCM (2 mL), was treated with 4M HCI in dioxane (3 mL), and stirred at room temperature for 30 minutes. The crude reaction was concentrated and used in the next step without further purification. Step c. Synthesis of (2S)-2-{[(benzyloxy)carbonyl]amino}-4-(dimethylamino)butanoic acid
Figure imgf000170_0001
A solution of crude (2S)-2-amino-4-(dimethylamino)butanoic acid (1 .553 mmol), and lithium hydroxide(0.167 g,6.988 mmol), dissolved in water(5 mL), was treated with a solution of 1 - {[(benzyloxy)carbonyl]oxy}pyrrolidine-2,5-dione(0.580 g, 2.329 mmol), dissolved in THF(5 mL). After stirring for 1 hr at room temperature, the mixture was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 0.340 g, 78%. lon(s) found by LCMS: [M+H]+ = 281 .3
Step d. Synthesis of tri-tert-butyl {[(2S,5R,8S,11S,14S,17S,22S)-5-benzyl-22-({(5S,8S,11S)- 11-{2-[(tert-butoxycarbonyl)amino]ethyl}-5-[2-(dimethylamino)ethyl]-8-[(1 R)-1-hydroxyethyl]- 3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10-triazadodecan-12-yl}amino)-17-[(1 R)-1-hydroxyethyl]-8-(2- methylpropyl)-3,6,9,12,15,18,23-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosane-2,11 ,14- triyl]tri(ethane-2,1-diyl)}triscarbamate
Figure imgf000170_0002
A solution of (2S)-2-{[(benzyloxy)carbonyl]amino}-4-(dimethylamino)butanoic acid (0.045 g, 0.161 mmol, lnt-6 (0.200 g, 0.147 mmol), DIEA (0.084 mL, 0.484 mmol), and DMF (1 mL) were treated with HATU (0.061 g, 0.161 mmol) slowly over 30 minutes, while stirring at room temperature. After 1 hour, the reaction was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.1 50 g, 63% yield, lon(s) found by LCMS: (M+2H)/2 = 813.5, [(M-1 Boc)+2H]/2 = 763.5
Step e. Synthesis of tri-tert-butyl {[(2S,5R,8S,11S,14S,17S,22S)-22-({(2S)-2-({N-[(2S)-2- amino-4-(dimethylamino)butanoyl]-L-threonyl}amino)-4-[(tert- butoxycarbonyl)amino]butanoyl}amino)-5-benzyl-17-[(1 R)-1-hydroxyethyl]-8-(2-methylpropyl)- 3,6,9,12,15,18,23-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosane-2,11 ,14-triyl]tri(ethane-2,1- diyl)}triscarbamate
Figure imgf000171_0001
A solution of Cbz protected intermediate (0.150 g, 0.0922 mmol) dissolved in methanol (1 mL), was treated with 5% Pd/C (0.075g), flushed with hydrogen and stirred for 1 hr. The reaction was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.135 g, 98% yield, lon(s) found by LCMS: (M+2H)/2 = 746.4, [(M-1 Boc)+2H]/2 = 696.4
Step f. Synthesis of Octa-Boc-(Compound 40)
Figure imgf000171_0002
A solution of amino intermediate (0.135 g, 0.090 mmol), fumaric acid (0.0053 g, 0.0452 mmol), DIEA (0.047 mL, 0.271 mmol), and DMF (1 mL) were treated with a solution of HATU (0.034 g, 0.090 mmol) in DMF (0.5 mL) slowly over 30 minutes, while stirring at room temperature. After 1 hour, the reaction was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.079 g, 57% yield, lon(s) found by LCMS: (M+2H)/2 = 1531 .9, [M-1 (Boc)/3]+1 = 988.2
Figure imgf000172_0001
Octa-Boc-(Compound 40) (0.079 g, 0.0257 mmol) was dissolved in DCM (1 ml_) and treated with TFA (1 ml_), while stirring at room temperature. After 5minutes, the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid(0.1 %) as the modifier. Yield 0.033 g, 56% yield, lon(s) found by LCMS: (M+2H)/2 = 1 131 .7, (M+3H)/3 = 754.8, (M+4H)/4 = 566.3
Exampl
Figure imgf000172_0002
N~1 ~-[(2S)-4-amino-1 -{[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18- tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2- yl]amino}-1 -oxobutan-2-yl]-N~4~-[(2S)-4-amino-1 -{[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 - {[(2S,5S,8S,13S,16S,1 9R,22R)-2,5,16-tris(2-aminoethyl)-19-benzyl-8-[(1 R)-1 -hydroxyethyl]-22-(2- methylpropyl)-3,6,9,14,17,20,23-heptaoxo-1 ,4,7,10,1 5,18-hexaazacyclotricosan-13-yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]amino}-1 -oxobutan-2-yl]-N~1 ~,N~4~-dibenzylbenzene-1 ,4- dicarboxamide was prepared from lnt-1 and (2S,3R,2'S,3'R)-2,2'-{1 ,4- phenylenebis[carbonyl(benzylazanediyl)]}bis(3-hydroxybutanoic acid) as described in Example 24, Step b. Yield: 39%, 2 steps. LC/MS [M+4H/4]= 610.0. Example 5
Figure imgf000173_0001
Compound 42 was prepared analogously to Compound 33, where (4-Biphenylyl)acetic acid, was substituted for 3-(2-{2-[2-(2,5-dioxo-2,5-dihydro-1 H-pyrrol-1 -yl)ethoxy]ethoxy}ethoxy)propanoic acid. lon(s) found by LCMS: (M+2H)/2 = 1078.6, (M+3H)/3 = 719.4, (M+4H)/4 =539.8, (M+5H)/5 =432.1
Exa
Figure imgf000173_0002
Compound 43 was prepared analogously to Compound 19, where lnt-8, was substituted for lnt-7 in the first step of the sequence, lon(s) found by LCMS: (M+2H)/2 = 1209.2, (M+3H)/3 = 806.5, (M+4H)/4 = 605.1
Example 55:
Figure imgf000173_0003
(2S,5S,8E,12S,15S)-2,15-bis(2-aminoethyl)-5,12-bis[(1 R)-1 -hydroxyethyl]-4,7,10,13-tetraoxo- N~1 ~,N~16~-bis(3S,6S,9S,12S,15R,18S.21 S)[6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 - hydroxyethyl]-12-(2-methylpropyl)-2,5,8 ,1 1 ,14 ,17,20-heptaoxo-1 ,4,7 ,1 0 ,13 ,16 ,19-heptaazacyclotricosan- 21 -yl]-3,6,1 1 ,14-tetraazahexadec-8-ene-1 ,16-diamide (Compound 44) was prepared from fumaric acid and lnt-1 as described in Example 24, Step b. Yield: 57%, 2 steps. LC/MS [M+3H/3]+ 669.4.
Exam
Figure imgf000174_0001
The title compound was prepared analogously to Compound 1 6. lon(s) found by HRMS: [M+H]+
Exampl
Figure imgf000174_0002
The title compound was prepared analogously to Compound 1 6. lon(s) found by HRMS: [M + H]+
= 2669.
Examp
Figure imgf000174_0003
Compound 47 was prepared analogously to Compound 19, where succinic acid, was substituted for fumaric acid in the first step of the sequence, and lnt-9 was substituted for lnt-7 in the first step of the sequence, lon(s) found by LCMS: (M+3H)/3 = 808.2, (M+4H)/4 = 606.4, (M+5H)/5 = 485.3
E
Figure imgf000175_0001
Compound 48 was prepared analogously to Compound 19, where lnt-9 was substituted for lnt-7 in the first step of the sequence, lon(s) found by LCMS: (M+3H)/3 = 807.5, (M+4H)/4 = 605.9, (M+5H)/5 = 484.9
Ex
Figure imgf000175_0002
Compound 49 (mixture of diastereomers at the cyclopropane chiral centers) was prepared analogously to Compound 19, where (racemic)-trans-l ,2-cyclopropanedicarboxylic acid, was substituted for fumaric acid in the first step of the sequence, and lnt-9 was substituted for lnt-7 in the first step of the sequence, lon(s) found by LCMS: (M+3H)/3 = 812.2, (M+4H)/4 = 609.4, (M+5H)/5 = 487.7 Exa
Figure imgf000176_0001
(2S,5S,8E,12S,15S)-2,1 5-bis(2-aminoethyl)-5,12-bis[(1 R)-1 -hydroxyethyl]-4,7,1 0,13-tetraoxo- N~1 ~,N~16~-bis(3S,6S,9S,12S,15R,18S,21 S)[6,9,18-tris(2-aminoethyl)-3-[(1 R)-1 -hydroxyethyl]-12,15- bis(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]- 3,6,1 1 ,14-tetraazahexadec-8-ene-1 ,16-diamide (Compound 50) was prepared from fumaric acid and lnt-5 as described in Example 24, Step b. Yield: 33%, 2 steps. LC/MS [M+3H/3]+ 647.0.
Example
Figure imgf000176_0002
(1 R,2R)-N~1 ~,N~2~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)- 6,9,1 8-tris(2-aminoethyl)-3-[(1 R)-1 -hydroxyethyl]-12,15-bis(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2- yl]cyclopropane-1 ,2-dicarboxamide and (1 S,2S)-N~1 ~,N~2~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-3-[(1 R)-1 -hydroxyethyl]-12,15-bis(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]cyclopropane-1 ,2-dicarboxamide were prepared from racemic trans- cyclopropane-1 ,2-dicarboxylic acid and lnt-5 as described in Example 24, Step b and the diastereomers were separated by reversed phase HPLC (5-95% acetonitrile in Dl water containing 0.1 % formic acid: 40 minute gradient). Yield (combined): 61 %. LC/MS [M+3H/3]+ 651 .6. Compound 51 a is the more polar diastereomer relative to Compound 51 b.
Example 63. Synthesis of Compound 52
Figure imgf000177_0001
Step a. Synthesis of bis(4-nitrophenyl) 2-oxoimidazolidine-1 ,3-dicarboxylate
Figure imgf000177_0002
To the solution of ethane-1 ,2-diamine (120 mg, 2 mmol) in 2 ml_ pyridine and 4 ml_ DCM was added 4-nitrophenyl carbonochloridate (1 . g, 5 mmol), the reaction was stirred for overnight and concentrated. The resulted solution was concentrated and purified by reversed phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of product, 140 mg 15% yield. 1 H NMR (300 MHz, DMSO-de) δ 8.36 (d, J = 9.0 Hz, 4H), 7.57 (d, J = 8.9 Hz, 4H), 4.01 (s, 4H). LC/MS [M]+1 416.1 .
Step b. Synthesis of Compound 52
N1 ,N3-bis((2S,3R)-1 -(((S)-4-amino-1 -oxo-1 -(((3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-((R)-1 -hydroxyethyl)-12-isobutyl-2,5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21 -yl)amino)butan-2-yl)amino)-3-hydroxy-1 -oxobutan-2-yl)-2-oxoimidazolidine-1 ,3- dicarboxamide
To lnt-6 (140 mg 0.1 mmol) in 4 mL DMF and (0.07 mL, 0.5 mmol) TEA was added bis(4- nitrophenyl) 2-oxoimidazolidine-1 ,3-dicarboxylate (20 mg, 0.05 mmol). The reaction solution was stirred for overnight, and the resulting solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and w 5 mg, 25% yield.
Figure imgf000177_0003
The per-Boc-(Compound 52) from the previous step was treated in 2 ml_ DCM and 2 ml_ TFA at room temperature, the solution was stirred 10 min, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 15 mg, 65% yield, lon(s) found by LCMS: (M+2H)/2 = 1033.2, (M+3H)/3 = 689.1 , (M+4H)/4 =51 7.1 .
Example 64.
Figure imgf000178_0001
The title compound was prepared analogously to Compound 1 6. lon(s) found by HRMS: [M + H]+
= 2595.
Exampl
Figure imgf000178_0002
3,3'-oxydipropanoic acid-(2S,5R,8S,1 8S.21 R,24S)-2,8,18,24-tetrakis(2-aminoethyl)-5,21 - bis[(1 S)-1 -hydroxyethyl]-4,7,10,16,19,22-hexaoxo-N~1 ~-[(3S,6S,9S,12S,15R,18S.21 R)-6,9,1 8-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-N~25~-[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,1 1 ,14,17,20-heptaoxo- 1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-13-oxa-3,6,9,17,20,23-hexaazapentacosane-1 ,25- diamide
Figure imgf000179_0001
methyl (2S)-2-({N-[(benzyloxy)carbonyl]-D-threonyl}amino)-4-[(tert- butoxycarbonyl)amino]butanoate (product from 39, Step a)
Step a. Synthesis of D-Thr-Dab(Boc)-OMe
Figure imgf000179_0002
Methyl (2S)-2-({N-[(benzyloxy)carbonyl]-D-threonyl}amino)-4-[(tert- butoxycarbonyl)amino]butanoate--methyl (2S)-4-[(tert-butoxycarbonyl)amino]-2-(D- threonylamino)butanoate (D-Thr-Dab(Boc)-OMe) was obtained by hydrogenolysis of the -ester intermediate from Example 39, Step a. in quantitative yield. Ion was found as (M+H+: 334.2).
Figure imgf000179_0003
(2S)-2-[(N-{(2S)-2-{[(benzyloxy)carbonyl]amino}-4-[(tert-butoxycarbonyl)amino]butanoyl}-D- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid
D-Thr-Dab(Boc)-OMe (0.713 g, 2.14 mmol), Z-NH-Dab(Boc)-OH (DCHA salt) (1 .1 99 g, 2.25 mmol), EDCI (0.615 g, 3.21 mmol), HOBt (0.433 g, 3.21 mmol) and NaHC03 (0.359 g, 4.28 mmol) were weighed into a 100- mL round bottom flask. 20 mL of DCM/DMF (4:1 ) was added into the flask. The mixture was stirred at room temperature for overnight. After completion, EtOAc (1 00 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated NaHCCb and brine. Dried with Na2S04 and condensed. The residue was purified with normal phase silica (2-7% MeOH/DCM) to give 1 .1 86 g pure desired product Cbz-Dab(Boc)-D-Thr-Dab(Boc)-OMe as a white solid (83%). Ion was found as (M- Boc+H+: 568.2). This white solid was dissolved in 10 mL of THF/water (1 :1 ) and treated with LiOH (1 .05 equiv.) for half hour at room temperature. The reaction mixture was acidified to pH~2 with 1 N aqueous HCI. THF was removed under reduced pressure. The residue was extracted with EtOAc. After drying and condensation Cbz-Dab(Boc)-D-Thr-Dab(Boc)-OH was obtained in quantitative yield. Ions were found as: positive charge (M-Boc+H+: 554.2), negative charge (M-H+: 653.2).
Step b. Synthesis of -D-Thr-Dab(Boc)-tri-Boc-PMBH
Figure imgf000180_0001
(2S)-2-[(N-{(2S)-2-{[(benzyloxy)carbonyl]amino}-4-[(tert-butoxycarbonyl)amino]butanoyl}-D- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid-tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S.22S)- 22-({(8S,1 1 R,14S)-8-amino-14-{2-[(tert-butoxycarbonyl)amino]ethyl}-1 1 -[(1 S)-1 -hydroxyethyl]-2,2- dimethyl-4,9,12,1 5-tetraoxo-3-oxa-5,10,13-triazapentadecan-15-yl}amino)-5-benzyl-17-[(1 R)-1 - hydroxyethyl]-8-(2-methylpropyl)-3,6,9,12,15,18,23-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosane- 2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate (Dab(Boc)-D-Thr-Dab(Boc)-tri-Boc-PMBH)
lnt-1 (0.709 g, 0.668 mmol) and Cbz-Dab(Boc)-D-Thr-Dab(Boc)-OH (0.502 g, 1 .577 mmol) were dissolved in 10 mL of DMF at room temperature followed by adding DIPEA (0.23 mL, 1 .34 mmol). To this mixture was slowly added HATU (0.305 g, 0.801 mmol) in 1 .2 mL of DMF via syringe pump. After overnight of stirring at room temperature, the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C18 with acetonitrile/water (0.1 %TFA) to give 1 .039 g of Cbz-protected Dab(Boc)-D-Thr-Dab(Boc)-tri-Boc-PMBH. Ion was found as ((M-2Boc+2H+)/2: 749.6). The Cbz protecting group was removed with 5% Pd/C in MeOH/EtOAc (1 :1 , 10 mL) under hydrogen balloon pressure at room temperature for 2 hours. Celite filtration gave Dab(Boc)-D-Thr-Dab(Boc)-PMBH(tri-Boc) in quantitative yield. Ion was found as ((M+2H+)/2: 782.4).
Figure imgf000180_0002
3,3'-oxydipropanoic acid
Step c. Synthesis of Dab-D-Thr-Dab-PMBH PEG1 Dimer Compound 54a
Dab(Boc)-D-Thr-Dab(Boc)-PMBH(tri-Boc) (0.145 g, 0.0925 mmol) was dissolved in 2 mL of DMF followed by addition of 3,3'-oxydipropanoic acid (Bis-PEG1 acid, commercial) (0.0073 g, 0.045 mmol) and DIPEA (0.024 mL, 0.14 mmol). To this mixture was added HATU (0.043 g, 0.1 1 mmol) in 1 .2 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C1 8 with acetonitrile/water (0.1 %TFA) to give per-Boc-(Compound 54a). The Boc groups were removed by treating with TFA/DCM (1 :1 ) for about 1 hour. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with acetonitrile/water (0.1 % TFA). The purified Compound 54a fractions were collected and lyophilized to give a white powder. Ions were found as ((M+3H+)/3: 752.4).
Figure imgf000181_0001
Compound 54b was prepared analogously to Compound 19, where
[(carboxymethyl)(benzyloxycarbonyl)amino]acetic acid, was substituted for fumaric acid in the first step of the sequence, and lnt-9 was substituted for lnt-7 in the first step of the sequence, lon(s) found by LCMS: (M+3H)/3 = 813.2, (M+4H)/4 = 610.1 , (M+5H)/5 = 488.3
Example 66: Synthesis of Compound 55
Figure imgf000181_0002
Compound 55 was prepared analogously to Compound 19, where bicyclo[1 .1 .1 ]pentane-1 ,3- dicarboxylic acid, was substituted for fumaric acid in the first step of the sequence, and lnt-8 was substituted for lnt-7 in the first step of the sequence, lon(s) found by LCMS: (M+4H)/4 = 562.3, (M+5H)/5 = 450.0, (M+6H)/6 = 375.2 Example 67. Synthesis of Compound 56
Step a. Synthesis of protected tripeptide
Figure imgf000182_0001
HATU (379 mg, 0.845 mmol, in 0.75 ml_ DMF) was added to a stirring mixture of methyl (2S)-2- [(N-{(2S)-2-amino-4-[(tert-butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert- butoxycarbonyl)amino]butanoate (41 0 mg, 0.768 mmol), (2S)-2-{[(benzyloxy)carbonyl]amino}-4- phenylbutanoic acid (264 mg, 0.845 mmol) and triethylamine (155 mg, 1 .54 mmol), in DMF (3 mL) dropwise over a period of 30 minutes. The reaction was stirred for an additional 30 minutes then applied directly to reversed phase HPLC (30-95% acetonitrile in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled and lyophilized then stirred in a 1 /1 /2 mixture of
THF/methanol/DI water (10 mL) containing lithium hydroxide (46 mg, 1 .92 mmol) for 20 minutes. The mixture was acidified with TFA (~1 mL) and the volume was concentrated by half on the rotary evaporator. The mixture was applied to reversed phase HPLC (20-95% acetonitrile in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled and lyophilized to afford (2S)-2-[(N-{(2S)- 2-{[(2S)-2-{[(benzyloxy)carbonyl]amino}-4-phenylbutanoyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid as a white solid. Yield: 48%, 2 steps. LC/MS [M-H]- = 813.8.
Step b. Synthesi
Figure imgf000182_0002
HATU (169 mg, 0.378 mmol, in 1 ml_ DMF) was added dropwise, over 45 minutes, to a stirring mixture of (2S)-2-[(N-{(2S)-2-{[(2S)-2-{[(benzyloxy)carbonyl]amino}-4-phenylbutanoyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid (280 mg, 0.344 mmol), lnt-1 (401 mg, 0.377 mmol), and triethylamine (69 mg, 0.687 mmol) in DMF (1 .5 ml_). The reaction was stirred for an additional 20 minutes then applied directly to reversed phase HPLC (30-95% acetonitrile in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled, concentrated then stirred in methanol (20 mL) containing 5% Pd/C (250 mg) under 1 atmosphere of hydrogen gas for 10 hours. The mixture was filtered and concentrated to afford tri-tert-butyl
{[(2S,5R,8S,1 1 S,14S,17S,22S)-22-({(8S,1 1 S,14S)-8-{[(2S)-2-amino-4-phenylbutanoyl]amino}-14-{2-[(tert- butoxycarbonyl)amino]ethyl}-1 1 -[(1 R)-1 -hydroxyethyl]-2,2-dimethyl-4,9,12,15-tetraoxo-3-oxa-5,10,13- triazapentadecan-15-yl}amino)-5-benzyl-1 7-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3,6,9,12,1 5,1 8,23- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate as a white solid. Yield: 81 %, 2 steps. LC/MS [M+2H/2]+863.2.
Figure imgf000183_0001
(2S,5S,8S,1 1 S,14E,18S.21 S,24S,27S)-2,8,21 ,27-tetrakis(2-aminoethyl)-5,24-bis[(1 R)-1 - hydroxyethyl]-4,7,10,13,16,19,22,25-octaoxo-1 1 ,18-bis(2-phenylethyl)-N~1 ~,N~28~- bis(3S,6S,9S,12S,1 5R,1 8S,21 S)[6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2, 5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]- 3,6,9,12,17,20,23,26-octaazaoctacos-14-ene-1 ,28-diamide was prepared from fumaric acid and tri-tert- butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-22-({(8S,1 1 S,14S)-8-{[(2S)-2-amino-4-phenylbutanoyl]amino}-14-{2- [(tert-butoxycarbonyl)amino]ethyl}-1 1 -[(1 R)-1 -hydroxyethyl]-2,2-dimethyl-4,9,12,1 5-tetraoxo-3-oxa- 5,10,13-triazapentadecan-1 5-yl}amino)-5-benzyl-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)- 3,6,9,12,15,18,23-heptaoxo-1 ,4,7,10,13,1 6,1 9-heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 - diyl)}triscarbamate as described in Example 24, Step b. Yield: 8%, 2 steps. LC/MS [M+4H/4]+632.6. Example 68. Synthesis of Comp
Figure imgf000184_0001
Figure imgf000184_0002
Step a. Synthesis of propane-1 ,3-disulfonyl-Y-Boc-L-Dab-OMe
Figure imgf000184_0003
To the solution of propane-1 ,3-disulfonyl dichloride (240 mg, 1 mmol) in 5 mL pyridine was added γ-Boc-L-Dab-OMe (500 mg, 2 mmol), the reaction was stirred for overnight and concentrated. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoro-acetic acid as the modifier. Yield of product, 420 mg 71 % yield. 1 H NMR (300 MHz, Methanol-dt) 5 4.1 0 (dd, J = 9.1 , 4.7 Hz, 1 H), 3.78 (s, 2H), 3.36 (s, OH), 3.34 - 3.08 (m, 3H), 2.33 (p, J = 7.6 Hz, 1 H), 2.03 (d, = 10.7 Hz, 1 H), 1 .91 - 1 .72 (m, 1 H), 1 .45 (s, 9H), 1 .44 - 1 .27 (m, 1 H). LC/MS [M]+1 633.2.
Step b. Synthesis of propane-1 ,3-disulfonyl-Y-Boc-L-Dab-OH
Figure imgf000184_0004
Lithium hydroxide (12 mg, 0.5 mmol) in 3 mL H2O was added to the solution of of propane-1 ,3- disulfonyl-Y-Boc-L-Dab-OMe(150 mg, 0.025 mmol) in mix solvent of 3 mL MeOH and 3 mL THF. The resulted solution was stirred for 1 hours at room temperature. The resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of oil product, 90 mg 62% yield. LC/MS [M]+1 605.2. Step c.
Figure imgf000185_0001
To the solution of propane-1 ,3-disulfonyl-Y-Boc-L-Dab-OH (28 mg, 0.048 mmol), triethylamine (0.07 mL, 0.5 mmol) and lnt-6 (140 mg, 0.1 mmol) in 5 mL DMF was added HATU(38 mg, 0.1 mmol) in 1 mL DMF by syringe pump over 1 hour, the reaction was stirred for 1 hr and then the resulted solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of product, 40 mg, 35% yield.
Per-Boc product from previous step was treated in 2 mL DCM and 2 mL TFA at room
temperature, the solution was stirred 1 0 min, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 10 mg, 35% yield, lon(s) found by LCMS: (M+2H)/2 = 1 147.6, (M+3H)/3 = 765.4, (M+4H)/4 =574.3.
Example 69: Synthesis of Compound 58
Figure imgf000185_0002
Step a. Synthesis of methyl (2S)-2-{2-[(1S)-1-methoxycarbonyl-3-(tert- butoxycarbonylamino)propylamino]-2-oxoacetylamino}-4-(tert-butoxycarbonylamino)butyrate
Figure imgf000185_0003
A solution of diethyl oxalate (0.186 mL, 1 .369 mmol), methyl (2S)-2-amino-4-(ferf- butoxycarbonylamino)butyrate (0.919 g, 3.42 mmol), and DIEA (0.71 5 mL, 4.106 mmol) in DMF (2 mL) were heated in a 120°C oil bath for 12h. The reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% acetonitrile and water, using formic acid as the modifier. Yield 0.207 g, 29% yield, lon(s) found by LCMS: [M+H]+ = 519.6
Step b. Synthesis of (2S)-2-{2-[(1S)-1-Carboxy-3-(tert-butoxycarbonylamino)propylamino]- 2-oxoacetylamino}-4-(tert-butoxycarbonylamino)butyric acid
Figure imgf000186_0001
A solution of methyl (2S)-2-{2-[(1 S)-1 -methoxycarbonyl-3-(tert- butoxycarbonylamino)propylamino]-2-oxoacetylamino}-4-(tert-butoxycarbonylamino)butyrate(0.270 g, 0.521 mmol) dissolved in methanol(1 mL) and THF(4 mL) was treated with a solution of lithium hydroxide(0.031 g, 1 .30 mmol) in water(1 mL). After stirring for 1 hour at room temperature, the reaction was made slightly acidic (pH=4-5) by adding concentrated HCI. The reaction was then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.1 97 g, 77% yield, lon(s) found by LCMS: [M-H]- = 489.5
Step c. Synthesis of deca-Boc-(Compound 58)
Figure imgf000186_0002
A solution of (2S)-2-{2-[(1 S)-1 -carboxy-3-(tert-butoxycarbonylamino)propylamino]-2- oxoacetylamino}-4-(tert-butoxycarbonylamino)butyric acid(0.037 g, 0.0752 mmol), lnt-5 (0.200 g, 0.151 mmol), and DIEA (0.083 mL, 0.474 mmol) in DMF (4 mL) was treated dropwise over 30 minutes with a solution of HATU (0.0601 g, 0.1 58 mmol) dissolved in DMF (1 mL). After 1 hour, the reaction was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.150 g, 64%. lon(s) found by LCMS: [(M-3Boc)+3H]/3 = 938.3, [(M-4Boc)+3H]/3 = 904.9 Step d
Figure imgf000187_0001
A solution of deca-Boc-(Compound 58) (0.096 g, 0.0308 mmol), dissolved in DCM(1 mL), was treated with TFA(1 mL), while stirring at room temperature. After 5 minutes, the product was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 0.048 g, 73% yield, lon(s) found by LCMS: (M+4H)/4 = 528.8, (M+5H)/5 = 423.3, (M+6H)/6 = 352.9
Example 70. Synthesis of Compound 59 (Mixture of diastereomers)
Step a. Synthesis of protected linear peptide
Figure imgf000187_0002
(5S,8S,1 1 S,14S,1 7R,20S,23S,26S,29S)-1 1 -(2-aminoethyl)-8,14,23,26-tetrakis(2- {[(benzyloxy)carbonyl]amino}ethyl)-17-[([1 ,1 '-biphenyl]-4-yl)methyl]-1 -(9H-fluoren-9-yl)-5,29-bis[(1 R)-1 - hydroxyethyl]-20-(2-methylpropyl)-3,6,9,12,15,18,21 ,24,27-nonaoxo-2-oxa-4,7,10,13,16,19,22,25,28- nonaazatriacontan-30-oic acid was prepared on an automated peptide synthesizer: Model Symphony (Protein Technologies, Inc.) using 2-chlorotrityl chloride, 1 % DVB (Advanced ChemTech, Inc). Conditions: 2-chlorotrityl chloride resin (1 .1 mmol/g substitution) was stirred with the FMOC amino acid (FMOC-L- threonine) and DIEA in DCM for 4 hours the washed with methanol. FMOC-protected amino acids were coupled in 0.2 M HCTU (2-(6-Chlor-1 H-benzotriazol-1 -yl)-1 ,1 ,3,3-tetramethylaminium- hexafluorophosphat) in DMF. The FMOC groups were removed by stirring in 20% piperidine in DMF (2x, 5 minutes). The peptide was cleaved by stirring in a mixture of 90% TFA/5%thioanisole/2.5% EDT/2.5% Dl water for 15 minutes. Step b. Cycliz
Figure imgf000188_0001
HATU (1 15 mg, 0.302 mmol, in 1 mL DMF) was added to a stirring mixture of
(5S,8S,1 1 S,14S,1 7R,20S,23S,26S,29S)-1 1 -(2-aminoethyl)-8,14,23,26-tetrakis(2- {[(benzyloxy)carbonyl]amino}ethyl)-17-[([1 ,1 '-biphenyl]-4-yl)methyl]-1 -(9H-fluoren-9-yl)-5,29-bis[(1 R)-1 - hydroxyethyl]-20-(2-methylpropyl)-3,6,9,12,15,18,21 ,24,27-nonaoxo-2-oxa-4,7,10,13,16,19,22,25,28- nonaazatriacontan-30-oic acid (500 mg, 0.275 mmol), and triethylamine (70 mg, 0.688 mmol) in DMF (3 mL). The mixture was stirred for 20 minutes (monitored by LC/MS) then applied directly to reversed phase HPLC (30-95% methanol in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled, concentrated then stirred in a mixture of 20% piperidine in DMF (6 mL) for 20 minutes. The mixture was applied directly to reversed phase HPLC (30-95% acetonitrile in Dl water containing 0.1 % TFA:20 minute gradient). The pure fractions were pooled and lyophilized to afford tribenzyl
{[(2S,5R,8S,1 1 S,14S,17S,22S)-22-{[(2S)-4-{[(benzyloxy)carbonyl]amino}-2-(L- threonylamino)butanoyl]amino}-5-[([1 ,1 '-biphenyl]-4-yl)methyl]-17-[(1 R)-1 -hydroxyethyl]-8-(2- methylpropyl)-3, 6,9,12,15,1 8,23-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosane-2,1 1 ,14- triyl]tri(ethane-2,1 -diyl)}triscarbamate as a white solid. Yield: 32%, 2 steps. LC/MS ((M+2H)/2)+ 788.8.
Figure imgf000188_0002
Figure imgf000189_0001
Step c. Synthesis of Compound 59 (Mixture if diastereomers)
Compound 59 (mixture of diastereomers at the cyclopropane chiral centers) was prepared from racemic trans-cyclopropane-1 ,2-dicarboxylic acid and tribenzyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-22-{[(2S)- 4-{[(benzyloxy)carbonyl]amino}-2-(L-threonylamino)butanoyl]amino}-5-[([1 ,1 '-biphenyl]-4-yl)methyl]-17- [(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3,6,9,12,1 5,1 8,23-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate as described in Example 24, Step b. Yield: 2%, 2 steps. LC/MS ((M+2H)/2)+ 1086.6.
Example 71.
Figure imgf000189_0002
The title compound was prepared analogously to Compound 1 6. lon(s) found by LCMS: (M+3H)/3 = 807, (M+4H)/4 = 606, (M+5H)/5 = 485, (M+6H)/6 = 404.
Example 72. Synthesis of Compound 61
Figure imgf000189_0003
lnt-5 (180 mg, 0.135 mmol), pthalic anhydride (10 mg, 0.068 mmol), and triethylamine (20 mg, 0.202 mmol) were stirred together in DMF (3 ml_) for 30 minutes at which point HATU (25 mg, 0.068 mmol, in 0.5 mL of DMF) was added, dropwise over 15 minutes to the stirring reaction mixture. The reaction was stirred for an additional 30 minutes and then applied directly to reversed phase HPLC (30- 95% methanol in Dl water containing 0.1 % TFA: 20 minute gradient). The pure fractions were pooled, concentrated and then stirred in a 1 /1 mixture of TFA/DCM (5 mL) containing thioanisole (50 mg, 0.405 mmol) for 20 minutes. The mixture was concentrated on the rotary evaporator and purified by reversed phase HPLC (0-35% acetonitrile in Dl water containing 0.1 % TFA: 20 minute gradient). The pure fractions were pooled and lyophilized to afford N~1 ~,N~2~-bis[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-3-[(1 R)-1 -hydroxyethyl]-12,15-bis(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]benzene-1 ,2-dicarboxamide as a white solid. Yield: 58%, 2 steps. LC/MS [M+3H/3]+ 663.8.
Example 73. Synthesis of Compound 62
Step a. Synthesis of tri-tert-butyl {[(2S,5R,8S,11S,14S,17S,22S)-5-benzyl-22-(4-[(tert- butoxycarbonyl)amino]-2-{[(3S)-3-hydroxy-D-prolyl]amino}butanamido)-17-[(1 R)-1-hydroxyethyl]- 8-(2-methylpropyl)-3,6,9,12,15,18,23-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosane-2,11 ,14- triyl]tri(ethane-2,1-diyl)}trisca
Figure imgf000190_0001
Tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-22-(4-[(tert-butoxycarbonyl)amino]-2-{[(3S)- 3-hydroxy-D-prolyl]amino}butanamido)-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3, 6,9,12,15,18,23- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate was prepared from lnt-4 and (3S)-1 -[(benzyloxy)carbonyl]-3-hydroxy-D-proline similar to the procedure for the synthesis of lnt-6. Yield: 61 %, 2 steps. LC/MS [M-boc/2+H+]+ 638.4.
Figure imgf000190_0002
(2R,3S)-N-(4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl- 3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2, 5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21 -yl]amino}butan-2-yl)-1 -[(2E)-4-{(2R,3S)-2-[(4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl)carbamoyl]-3-hydroxypyrrolidin-1 -yl}-4-oxobut-2-enoyl]-3-hydroxypyrrolidine-2-carboxamide
(Compound 62) was prepared from tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-22-(4-[(tert- butoxycarbonyl)amino]-2-{[(3S)-3-hydroxy-D-prolyl]amino}butanamido)-17-[(1 R)-1 -hydroxyethyl]-8-(2- methylpropyl)-3, 6,9,12,15,1 8,23-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosane-2,1 1 ,14- triyl]tri(ethane-2,1 -diyl)}triscarbamate and fumaric acid as described in Example 24, Step b. Yield: 52%, 2 steps. LC/MS [M+3H/3]+ 677.6.
Exampl
Figure imgf000191_0001
Step a. Synthesis of per-Boc-(Compound 63)
Sebacoyl chloride (28 mg, 0.1 1 mmol) and lnt-6 (320 mg, 0.23 mmol) were mixed into 3 mL pyridine, the resulted solution was stirred overnight, and then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of product, 40 mg, 25% yield.
Step b. Deprotection to give Compound 63
Per-Boc-(Compound 63) from previous step was treated with 2 mL TFA in 2 mL DCM at room temperature. The solution was stirred 10 min, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 10 mg, 35% yield, lon(s) found by LCMS: (M+2H)/2 = 1046.6, (M+3H)/3 = 698.1 , (M+4H)/4 =523.8. Example 75. Preparation of INT-12
Figure imgf000192_0001
INT-12 was prepared from lnt-1 and Z-D-Ser-OH in an analogous manner as described in Example 4. Yield: 81 %. LC/MS ((M+2H)/2) = 525.6 (artefactual loss of 1 Boc group).
Example 76. Preparation of INT-13
Figure imgf000192_0002
INT-13 was prepared from INT-12 and Z-Thr-OH in an analogous manner as described in Example 6. Yield: 66%. LC/MS ((M+2H)/2) = 525.8 (artefactual loss of 2 Boc groups).
Example 77. Preparation of INT-14
Figure imgf000192_0003
INT-14 was prepared from lnt-13 and Z-(Y-Boc)-Dab-OH in an analogous manner as described in Example 8. Yield: 78%. LC/MS [M+2H/2] 676.2 (artefactual loss of 1 Boc group). Example 78. Preparation of INT-15
Figure imgf000193_0001
INT-15 was prepared from lnt-14 and Z-Norleu-OH in an analogous manner as described in Example 10. Yield: 67%. LC/MS [M+2H/2] 682.6 (artefactual loss of 2 Boc groups).
Example 79. Preparation of INT-1
Figure imgf000193_0002
HATU (6.3 g, 16.5 mmol) in DMF (4 mL) was added, dropwise, to a stirring mixture of (2,2'- {[(benzyloxy)carbonyl]azanediyl}diacetic acid (2.1 g, 7.9 mmol), Norleucine methyl ester hydrochloride salt (2.9 g, 16.5 mmol), and triethylamine (6.3 g, 62.9 mmol) in DMF (6 mL) over a period of 20 minutes. The reaction was stirred for an additional 1 5 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 5% to 95% acetonitrile and water using 0.1 % TFA as modifier. The pure fractions were pooled and lyophilized to afford methyl 8-[(benzyloxy)carbonyl]-4,12-dibutyl-3,6,10-trioxo-2-oxa-5,8,1 1 -triazatridecan-13-oate as a white solid. The di-ester was stirred in a 1 /1 /2 THF/methanol/water (15 mL) containing LiOH (0.76 g, 31 .4 mmol) at room temperature for 20 minutes. The mixture was applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 5% to 95% acetonitrile and water using 0.1 % TFA as modifier. The pure fractions were pooled and lyophilized to afford 2,2'-({[(benzyloxy)carbonyl]azanediyl}bis[(1 -oxoethane-2,1 -diyl)azanediyl])dihexanoic acid as a white solid. Yield: 37%, 2 steps. LC/MS [M-H]- = 492.2.
Example 80. Preparation of INT-17
Figure imgf000193_0003
HATU (3.2 g, 8.4 mmol)in DMF (3 mL) was added, dropwise, to a stirring mixture of norleucoine methylester-hydrochloride (1 .3 g, 8.8 mmol), and trans (racemic)-1 -benzylpyrrolidine-3,4-dicarboxylic acid (1 g, 4.0 mmol) and triethylamine (2 g, 20 mmol) in DMF (4 mL) over a period of 20 minutes. The reaction was stirred for an additional 20 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 95% acetonitrile and water using 0.1 % TFA as modifier. The pure fractions were pooled and lyophilized to afford the product as a clear oil. The diester intermediate was stirred in a 1 /1 /2 mixture of methanol/THF/water (25 mL) containing lithium hydroxide (3.1 g, 12 mmol) at ambient temperature for 30 minutes. The reaction mixture was applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0% to 55% acetonitrile and water using no modifier. Yield 57%, 2 steps. LC/MS [M+H]+ = 476.4.
Figure imgf000194_0001
HATU (in DMF, 0.75 ml) was added, dropwise via syringe over a 45 minute period, to a stirring mixture of fumaric acid (9 mg, 0.08 mmol), lnt-13 (204 mg, 0.16 mmol) and triethylamine (31 mg, 0.31 mmol) in DMF (1 .5 mL). The mixture was stirred for another 20 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 100% methanol and water using no modifier. The pure fractions were pooled and lyophilized. The boc protected intermediate was stir in a 1 /1 mixture of TFA/DCM containing thioanisole (77 mg, 0.62 mmol) ( 5 mL). The solvent was removed and the residue was dried under high vac. The crude was dissolved in water (2 mL) and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0% to 35% acetonitrile and water using TFA (0.1 %) as modifier. The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield: 63%, 2 steps. LC/MS ((M+2H)/2) = 990.6.
Figure imgf000195_0001
Step a. Preparation of per-Boc-Compound 65
Sebacoyl chloride (24mg, 0.1 mmol) was dissolved into 5 mL INT-8 (320 mg, 0.2 mmol) solution in pyridine, the resulting solution was stirred overnight, then the solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoro-acetic acid as the modifier. Yield: 160mg 45% yield.
Step b. Removal of the Boc groups
The product from Step a was dissolved in 2 mL DCM and 2ml TFA at room temperature, the solution was stirred 10 min, then concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 45 mg, 34% yield, lon(s) found by LCMS: (M+3H)/3 = 742.1 , (M+4H)/4 =556.8, (M+5H)/5=445.7.
Example 83
Figure imgf000195_0002
The title compound was prepared analogously to Compound 1 1 . Ions found by LCMS: (M+2H)/2 = 1 183, (M+3H)/3 = 789, (M+4H)/4 = 592, (M+5H)/5 = 473, (M+6H)/6 = 395. Example 84: S
Figure imgf000196_0001
The title compound was prepared analogously to Compound 1 1 . Ions found by LCMS: (M+4H)/4 = 613, (M+5H)/5 = 490, (M+6H)/6 = 409.
Example 85
Figure imgf000196_0002
Step a. Synthesis of L-homoleu-INT-8
Figure imgf000196_0003
A mixture of Fmoc-L-homoleucine (47.8 mg, 0.13 mmol) and HOBT hydrate (23 mg, 0.15 mmol) was dissolved in anhydrous DMF (0.5 ml) and added with EDC-HCI (28.8 mg, 0.15 mmol). The resulting mixture was stirred for 20 minutes, then added with a solution of INT-8 (167 mg, 0.1 mmol) in DMF (1 ml) and DIPEA (39 mg, 0.3 mmol). After the mixture was stirred for 1 hour, it was added with piperidine (2 drops) and stirred for 2 hours. The product was then purified through RPLC (50 g, 30 to 100 % MeOH and water). Yield 139 mg, 82.3 %. LCMS: [(M - Boc)/2]+1 = 796. Step b. Synthesis of deca-Boc-Compound 68 precursor
Figure imgf000197_0001
To a mixture of diethyl 2,2'-{[(benzyloxy)carbonyl]azanediyl}diacetate (8 mg, 0.03 mmol) and L- homoleu-INT-8 (106 mg, 0.0627 mmol) in anhydrous DMF (0.5 ml) and DIPEA (65 mg, 0.5 mmol) was added with a solution of HATU (26.2 mg, 0.069 mmol) in DMF (1 ml) via syringe pump at 0.5 ml/hr rate. After the addition, the mixture was stirred for one more hour (LCMS: [(M-3Boc)+3H]/3 = 04,
[(M63Boc)/3]+1 = 1 004) and then added with Pd/C and EtOAc (~ 1 0 ml). The resulting mixture was stirred under hydrogen for 4 hours. Pd/C was filtered off, and the filtrate was concentrate. The residue was purified through RPLC (50 g, 20 to 100 % MeOH and water, using 0.1 % formic acid as modifier). Yield 59.2 mg, 56.7 %). Ions found by LCMS: [(M-2Boc)+3H]/3 = 1 093, [(M-3Boc)+3H]/3 = 1060, [(M- 4Boc)+3H]/3 = 1026, [(M-5Boc)+3H]/3 = 993.
Step c. Removal of the Boc groups
The step-b product (59.2 mg, 0.017 mmol) was re-dissolved in TFA/DCM (-1 :1 , 0.8 ml). After the solution was stirred for 1 5 minutes, it was concentrated and purified though HPLC (5 to 22 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 17.8 mg, 28 % (Compound 68). Ions found by LCMS: (M+2H)/2 = 1239, (M+3H)/3 = 826, (M+4H)/4 = 620, (M+5H)/5 = 496, (M+6H)/6 = 413.
Figure imgf000197_0002
Step a. Acylation of INT-8
Racemic-frans-3,6-endomethylene-1 ,2,3,6-tetrahydrophthaloyl chloride (22 mg, 0.1 mmol) was dissolved into 5mL of a solution of INT-8 (320 mg, 0.2 mmol) in pyridine, the resultant solution was stirred overnight, then the solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoro-acetic acid as the modifier. Yield of product, 160 mg 45% yield.
Step b. Removal of the Boc groups
The product from Step a was dissolved in 2 ml_ DCM and 2 ml TFA at room temperature, the solution was stirred 10 min, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield (mixture of diastereomers) 65 mg, 43% yield, lon(s) found by LCMS: (M+3H)/3 = 758.1 , (M+4H)/4 =568.8, (M+5H)/5=455.3.
Example 8
Figure imgf000198_0001
Step a. Acylation of INT-15
HATU (24 mg, 0.063 mmol, in DMF, 0.5 mL) was added, dropwise via syringe over a 45 minute period, to a stirring mixture of 2,2'-{[(benzyloxy)carbonyl]azanediyl}diacetic acid (8 mg, 0.03 mmol), lnt-15 (98 mg, 0.063 mmol) and triethylamine (12 mg, 0.12 mmol) in DMF (1 .5 mL). The mixture was stirred for another 20 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 20% to 100% methanol and water using no modifier. The pure fractions were pooled and lyophilized to afford the CBZ-protected intermediate as a white solid. LC/MS [M+3H/3] 1020.0 (CBZ intermediate, loss of 2 boc). The CBZ-protected intermediate was stirred in methanol (10 ml) containing 5% Pd/C (30 mg) under 1 atmosphere of hydrogen gas for 45 minutes. The mixture was filtered and concentrated then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 95% acetonitrile and water using no modifier. The pure fractions were pooled and lyophilized to afford the Boc-protected intermediate as a white solid. Yield: 69%, 2 steps. LC/MS [M+2H/2] = 1562.6 (CBZ de-protected, artefactual loss of 1 boc group).
Figure imgf000198_0002
Step b. Removal of the Boc groups
The product from Step a (55 mg, 0.017 mmol) was stirred in a 1 /1 mixture of DCM/TFA (5 mL) containing thioanisole (17 mg, 0.37 mmol) at ambient temperature for 15 minutes. The solvent was removed by rotovap and the crude residue was dried under high vacuum than applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0% to 35% acetonitrile and water using 0.1 % TFA as modifier. The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield: 63%. LC/MS [M+3H/3] = 808.4.
Example 8
Figure imgf000199_0001
Step a. Synthesis of methyl (2R)-2-({N-[(benzyloxy)carbonyl]-L-allothreonyl}amino)-4-[(tert- butoxycarbonyl)amino]butanoate
NH2-D-Dab(Boc)-OMe (HCI salt) (1 .000 g, 3.688 mmol), Z-NH-Thr-OH (1 .019 g, 3.872 mmol), EDCI (1 .071 g, 5.531 mmol), HOBt (0.747 g, 5.531 mmol) and NaHCOs (0.620 g, 7.375 mmol) were weighed into a 100-mL round bottom flask. 20 mL of DCM/DMF (4:1 ) was added into the flask. The mixture was stirred at room temperature for less than 3 hrs. (TLC or LC/MS monitoring). After the completion, EtOAc (200 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated NaHCCb and brine. Dried with Na2S04 and condensed. The residue was purified with normal phase silica (2-7% MeOH/DCM) to give 1 .64 g pure desired product (95% isolated yield). Mass showed a strong detectable positive charge signal at tr=4.1 0 min (found M-Boc+H+: 368.2). Step b. Synthesis of (2R)-2-({N-[(benzyloxy)carbonyl]-L-allothreonyl}amino)-4-[(tert- butoxycarbonyl)amino]butanoic acid
Z-Thr-D-Dab(Boc)-OMe (0.820 g, 1 .754 mmol) was dissolved in THF/H2O (1 :1 , 20 mL) followed by adding Lithium hydroxide (0.0420 g, 1 .701 mmol, 0.97 eq.). The mixture was stirred at room temperature for less than 1 hr. After the completion, the reaction mixture was acidified with 1 N aq. HCI to pH=2~3. Most of THF was removed by rotovap followed by EtOAc (200 mL) extraction Dried with Na2S04 and condensed. The white foam (0.79 g, 99%) was obtained. Mass showed strong detectable positive/negative charge signals at tr=4.10 min (found Positive ion M-Boc+H+: Negative ion 354.2; M-H+: 452.2).
Step c. Synthesis of tri-tert-butyl {[(2S,5R,8S,11S,14S,17S,22S)-5-benzyl-22-{[(2R)-4-[(tert- butoxycarbonyl)amino]-2-(L-threonylamino)butanoyl]amino}-17-[(1 R)-1-hydroxyethyl]-8-(2- methylpropyl)-3,6,9,12,15,18,23-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosane-2,11 ,14- triyl]tri(ethane-2,1-diyl)}triscarbamate
Z-Thr-D-Dab(Boc)-OH (0.398 g, 0.878 mmol) and INT-1 (0.888 g, 0.836 mmol) was dissolved in 4 mL of DMF followed by addition of DIPEA (0.22 mL, 1 .25 mmol). To this mixture was added HATU (0.477 g, 1 .25 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C18 with ACN/water (0.1 %TFA) to give the desired product. Ion was found as ((M-2Boc+2H+)/2: 649.2). The Cbz group was removed by adding Pd/C/H2 to the reaction mixture and stirring for less than 2 hour. Celite filtration and solvents were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with ACN/water (0.1 % TFA). The purified product was collected to give white powders. Ion was found as ((M-Boc+2H+)/2: 632.4).
Step d: Synthesis of Compound 71.
Tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-22-{[(2R)-4-[(tert-butoxycarbonyl)amino]-2- (L-threonylamino)butanoyl]amino}-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3, 6,9,12,15,18,23- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate (0.300 g, 0.220 mmol) was dissolved in 5 mL of DMF followed by addition of fumaric acid (0.013 g, 0.1 1 mmol) and DIPEA (0.048 mL, 0.28 mmol). To this mixture was added HATU (0.0627 g, 0.165 mmol) in 1 .5 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reverse phase C18 with ACN/water (0.1 %TFA) to give per-Boc dimer. Ion was found as ((M+2H+)/2: 1404.3). The Boc groups were removed by treating with TFA/DCM (1 :1 ) for less than 1 hour. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with ACN/water (0.1 % TFA). The pure product (Compound 71 ) was collected and lyophilized to give white powders. Ion was found as ((M+4H+)/4: 502.4). Example 89:
Figure imgf000201_0001
Compound 72 was prepared analogously to the compopund of Example 27 (procedure B), where 1 -[(benzyloxy)carbonyl]piperidine-2,6-dicarboxylic acid, was substituted for 2,2'- {[(benzyloxy)carbonyl]azanediyl}diacetic acid in the first step of the sequence, lon(s) found by LCMS: (M+2H)/2 = 1273.3, (M+3H)/3 = 849.2, (M+4H)/4 = 637.1
Example
Figure imgf000201_0002
The title compound was prepared analogously to Compound 68. Ions found by LCMS: (M+4H)/4 = 622, (M+5H)/5 = 497, (M+6H)/6 = 415.
Example 91
Figure imgf000201_0003
Step a. Synthesis of methyl (2S)-4-[(tert-butoxycarbonyl)amino]-2-(octylamino)butanoate
Figure imgf000201_0004
A flame-dried reaction flask was filled with N2 and charged with a mixture of (S)-methyl 2-amino-
4-((tert-butoxycarbonyl)amino)butanoate HCI (806.2 mg, 3 mmol), EtOH (9 ml), and octanal (423.1 g, 3.3 mmol). The mixture was dissolved by gently heated with a heat gun. After cooled to room temperature, it was added with sodium triacetoxyborohydride (636 mg, 3 mmol) by portions over 20 minutes. The suspension was stirred for 3 hours, then added with an additional amount of NaHB(OAc)3 (318 mg). The reaction was continued for 4 more hours. The solid was filtered off, and the filtrate was concentrated and purified through RPLC (150 g, 1 0 to 80 % MeOH and water, set collect all). Yield 340 mg, 32.9 %. Ions found by LCMS: [M + H]+ = 345.
Step b. Synthesis of (2E)-4-[{(2S)-4-[(tert-butoxycarbonyl)amino]-1-methoxy-1-oxobutan-2- yl}(octyl)amino]-4-oxobut-2-enoic aci
Figure imgf000202_0001
A flamed-dried reaction flask was filled with N2 and charged with the step-a product (340 mg, 0.987 mmol), CHCI3 (10 ml), and DIPEA (520 mg, 4 mmol). After the mixture was cooled in an ice-water bath, it was added with a solution of fumaryl chloride (90 mg, 0.59 mmol) in CHCI3 (1 ml) via syringe pump at a rate of 0.4 ml/hr. An additional amount of DIPEA (260 mg, 2 mmol) was added after 0.5 ml of the fumaryl chloride solution was added. Upon the completion of the fumaryl chloride addition, the reaction was stirred for one more hour, then quenched by water (1 0 ml) and stirred overnight. CHCI3 was removed by rotary evaporation to precipitate the product. The solid was collected by vacuum filtration and purified through RPLC (50g, 20 to 100 % MeOH and water). Yield 45 mg, 10.3%. Ion found by LCMS: [M- Boc]+1 = 343.
Step c. Synthesis of dimethyl (8S,11 E,15S)-2,2,21 ,21-tetramethyl-9-octyl-4,10,13,19- tetraoxo-3,20-dioxa-5,9,14,18-tetraazadocos-11-ene-8,15-dicarboxylate
Figure imgf000202_0002
To mixture of the step-b product (45 mg, 0.106 mmol) in anhydrous DMF (0.5 ml) was added DIPEA (26 mg, 0.2 mmol) followed by HATU (44.5 mg, 0.1 17 mmol). After the resulting mixture was stirred for 10 minutes, it was added with (S)-methyl-2-amino-4-(tert-butoxycarbonyl)amino)butanoate HCI (34.9 mg, 0.23 mmol) and DIPEA (26 mg). The reaction was stirred for 1 hour and directly purified through RPLC (50 g, 20 to 100 % MeOH and water). Yield 53.8 mg, 80.7%. Ion found by LCMS: [M- Boc]+1 = 557. Step d. Synthesis of (8S,11 E,15S)-15-{2-[(tert-butoxycarbonyl)amino]ethyl}-8-carboxy-2,2- dimethyl-9-octyl-4,10,13-trioxo-3-oxa-5,9,14-triazahexadec-11-en-16-oic acid
Figure imgf000203_0001
The step-c product (53.8 mg, 0.086 mmol) was dissolved in MeOH (~ 2 ml) and THF (~4 ml). The solution was cooled in an ice-water bath and added with a solution of LiOH (8 mg, 0.33 mmol) in water (1 ml). The mixture was stirred for 4 hours, then slowly treated with a 4N HCI solution in dioxane (0.1 ml). It was then directly purified through RPLC (50 g, 20 to 100 % MeOH and water). Yield 51 mg, 94.3 %. Ion found by LCMS: [M-Boc]+1 = 529.
Step e. Synthesis of deca-Boc Compound 74 precursor
To a mixture of the step-d product (51 mg, 0.081 mmol) and INT-6 (281 .4 mg, 0.206 mmol) in anhydrous DMF (1 ml) and DIPEA (130 mg, 1 mmol) was added a solution of HATU (78.3 mg, 0.206 mmol) in DMF (1 ml) via syringe pump at a rate of 0.5 ml/hr. After the addition, the reaction was stirred overnight then directly purified through RPLC (20 to 100 % MeOH and water). Yield 59.7 mg, 19.1 %. Ion found by LCMS: [(M-3Boc)+3H]/3 = 1007.
Step f. Removal of the Boc groups
The step-e product (59.7 mg, 0.018 mmol) was re-dissolved in TFA (~ 0.5 ml). The solution was stirred for 15 minutes, then directly purified through HPLC (5 to 20 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 1 1 .5 mg, 18.4 % (Compound 74). Ions found by LCMS: (M+4H)/4= 580, (M+5H)/5 = 464, (M+6H)/6 = 387.
Figure imgf000203_0002
The product from Example 93, Step b (0.319 g, 0.204 mmol) was dissolved in 5 mL of DMF followed by addition of fumaric acid (0.0121 g, 0.1 02 mmol) and DIPEA (0.045 mL, 0.25 mmol). To this mixture was added HATU (0.0582 g, 0.153 mmol) in 1 .5 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reversed phase C18 with ACN/water (0.1 %TFA) to give per-Boc dimer (0.214 g, 65% isolated yield). Ions were found as ((M-Boc+2H+)/2: 1553.5, (M-2Boc+2H+)/2: 1 504.0, (M-4Boc+3H+)/3: 951 .1 ). The Boc groups were removed by treating with TFA/DCM (1 :1 ) for less than 1 hour. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with ACN/water (0.1 % TFA). The pure product was collected and lyophilized to give white powders. Ions were found as ((M+3H+)/3: 736.2, (M+4H+)/4: 552.5).
Figure imgf000204_0001
Step a. Synthesis of (2R)-2-[(N-{(2S)-2-{[(benzyloxy)carbonyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-allothreonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid
Z-Thr-D-Dab(Boc)-OMe (0.824 g, 1 .76 mmol) was dissolved in 16 mL of MeOH/EtOAc. And 5%Pd/C (0.375 g, 0.176 mmol) was added. Under H2 balloon, the reaction mixture was stirred for 2hrs. Check TLC and LC/MS. Celite filtration, MeOH wash and dried gave 0.587 g of free amine (>99%). Used it for next step without purification. Mass showed a strong detectable positive/negative charge signal at tr=1 .131 min (found Positive M+H+: 334.2; Negative M-H+: 332.2).
NH2-Thr-D-Dab(Boc)-OMe (0.587 g, 1 .76 mmol), Z-NH-Dab(Boc)-OH(DCHA salt) (0.987 g, 1 .85 mmol),
EDCI (0.506 g, 2.64 mmol), HOBt (0.357 g, 2.64 mmol) and NaHC03 (0.296, 3.52 mmol) were weighed into a 50-mL round bottom flask. 10 mL of DCM/DMF (4:1 ) was added into the flask. The mixture was stirred at room temperature for convenience overnight) with TLC or LC/MS monitoring. After completion,
EtOAc (50 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated NaHCOe and brine. Dried with Na2S04 and condensed. The residue was purified with normal phase silica (2-7%
MeOH/DCM) to give 0.886 g pure desired product (z-Dab(Boc)-Thr-D-Dab(Boc)-OMe, >75% isolated yield). Mass showed a strong detectable positive charge signal at tr=4.980 min (found M+H+: 668.4, M- Boc+H+: 568.2). Z-Dab(Boc)-Thr-D-Dab(Boc)-OMe (0.400 g, 0.599 mmol) was dissolved in THF/H2O (1 :1 , 10 mL) followed by adding Lithium hydroxide (0.0156 g, 0.630 mmol). The mixture was stirred at room temperature for less than 1 hr. After the completion, the reaction mixture was acidified with 1 N aq. HCI to pH=2~3. Most of THF was removed by rotovap followed by EtOAc (50 mL x 2) extraction, dried with Na2S04 and condensed. The white foam (0.390g, 99%) was obtained. Mass showed strong detectable positive/negative charge signals at tr=4.748 min (found Positive M-Boc+H+: 554.2; Negative M-H+: 652.2).
Step b. Synthesis of tri-tert-butyl {[(2S,5R,8S,11S,14S,17S,22S)-22-({(8S,11S,14R)-8-amino- 14-{2-[(tert-butoxycarbonyl)amino]ethyl}-11-[(1 R)-1-hydroxyethyl]-2,2-dimethyl-4,9,12,15-tetraoxo- 3-oxa-5,10,13-triazapentadecan-15-yl}amino)-5-benzyl-17-[(1 R)-1-hydroxyethyl]-8-(2-methylpropyl)- 3,6,9,12,15,18,23-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosane-2,11 ,14-triyl]tri(ethane-2,1- diyl)}triscarbamate
(2R)-2-[(N-{(2S)-2-{[(benzyloxy)carbonyl]amino}-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- allothreonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoic acid (0.203 g, 0.31 1 mmol) and INT-1 (0.333 g, 0.282 mmol) were dissolved in 4 mL of DMF followed by addition of DIPEA (0.074 mL, 0.42 mmol). To this mixture was added HATU (0.0547 g, 0.424 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reverse phase C18 with ACN/water (0.1 %TFA) to give the desired product. Ion was found as ((M-2Boc+2H+)/2: 749.2). The Cbz group was removed by adding Pd/C/hb to the reaction mixture and stirring for less than 2 hour. Celite filtration and solvents were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with ACN/water (0.1 % TFA). The purified product Dab(Boc)-Thr-D-Dab(Boc)-PMBH(tri-Boc) was collected to give white powders (0.318 g, 72%). Ion was found as ((M-Boc+2H+)/2: 733.0, M-Boc+2H+)/2: 682.6).
Step c. Synthesis of Compound 76a and Compound 76b
Dab(Boc)-Thr-D-Dab(Boc)-PMBH(tri-Boc) (0.540 g, 0.345 mmol) was dissolved in 5 mL of DMF followed by addition of racemic cyclopropane-trans-1 ,2-dicarboxylic acid (0.0229 g, 0.1 73 mmol) and DIPEA (0.075 mL, 0.43 mmol). To this mixture was added HATU (0.0985 g, 0.259 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reverse phase C18 with ACN/water (0.1 %TFA) to give two isomers of per-Boc Compound 76a (more polar peak) and Compound 76b (less polar peak). Ions were found as ((M+4H+)/4: 782.2) for both two isomers. The Boc groups for each isomer were removed by treating with TFA/DCM (1 :1 ) for less than 1 hour. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with ACN/water (0.1 % TFA). The purified (1 R,2R)-N~1 ~,N~2~-bis[(2S)-4-amino-1 -{[(2S,3R)-1 -{[(2R)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]amino}-1 -oxobutan-2-yl]cyclopropane-1 ,2-dicarboxamide and (1 S,2S)-N~1 ~,N~2~-bis[(2S)-4-amino-1 -{[(2S,3R)-1 -{[(2R)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]amino}-1 -oxobutan-2-yl]cyclopropane-1 ,2-dicarboxamide were collected and lyophilized to give white powders. Ions were found as ((M+4H+)/4: 556.0) for both diastereomers Compound 76a (more polar) and Compound 76b (less polar).
Example 94. Syn
Figure imgf000206_0001
The title compound was prepared analogously to Compound 68. Ions found by LCMS: [M/3]+= 854, [M/4]+= 641 , [M/5]+= 513, [M/6]+= 427.
Example 95. Synthesis of Compound 78
Figure imgf000206_0002
The title compound was prepared analogously to Compound 68. Ions found by LCMS: {M/3]+ 825, [M/4]+ = 619.3, [M/5]+ = 495.6, [M/6]+ = 413.2
Example 96. Synthesis of Compound 79
Figure imgf000206_0003
Step a. Synthesis of deca-Boc Compound 79 benzyl ester
Deca-Boc Compound 79 benzyl ester was prepared analogously as the Compound of Example 27 (procedure B), where racemic (1 R,2R)-3-[(benzyloxy)carbonyl]cyclopropane-1 ,2-dicarboxylic acid, was substituted for 2,2'-{[(benzyloxy)carbonyl]azanediyl}diacetic acid in the first step of the sequence, lon(s) found by LCMS: [(M-1 Boc)+3H]/3 = 1 1 12.4, [(M-2Boc)+3H]/3 = 1079.0, [(M-3Boc)+3H]/3 = 1045.7
Step b. Synthesis of deca-Boc Compound 79
Crude deca-Boc Compound 79 benzyl ester (0.373g, 0.103 mmol) from Step a (DMF solution) was charged with 5% Pd/C (0.200 g), and hydrogen from a balloon. The reaction was monitored by LCMS. After 12 hr the mixture was filtered through celite, concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.295 g, 81 % (two steps), lon(s) found by LCMS: [(M- 3Boc)+3H]/3 = 1083.0, [(M-4Boc)+3H]/3 = 1049.7, [(M-5Boc)+3H]/3 = 1016.3
Step c. Synthesis of Compound 79
A solution of deca-Boc Compound 79 (0.234 g, 0.0659 mmol), dissolved in DCM (5 mL), was treated with TFA (5 mL), while stirring at room temperature. After 5 minutes, the product was
concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 1 00% acetonitrile and water, using formic acid as the modifier. Yield 0.149 g, 88% yield, lon(s) found by LCMS: (M+3H)/3 = 850.0, (M+4H)/4 = 637.8, (M+5H)/5 = 51 0.4.
E
Figure imgf000207_0001
tri-tert-butyl {[(2S,5R,8S,1 1 S,14S,17S,22S)-5-benzyl-22-{[(2R)-4-[(tert-butoxycarbonyl)amino]-2- (L-threonylamino)butanoyl]amino}-17-[(1 R)-1 -hydroxyethyl]-8-(2-methylpropyl)-3, 6,9,12,15,18,23- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosane-2,1 1 ,14-triyl]tri(ethane-2,1 -diyl)}triscarbamate (0.400 g, 0.293 mmol) was dissolved in 5 mL of DMF followed by addition of cyclopropane-trans-1 ,2-dicarboxylic acid (racemic, 0.0195 g, 0.167 mmol) and DIPEA (0.064 mL, 0.37 mmol). To this mixture was added HATU (0.0837 g, 0.220 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reverse phase C18 with ACN/water (0.1 %TFA) to give two isomers of per-Boc Compound 80a (more polar peak) and Compound 80b (less polar peak). Ions were found as ((M+4H+)/4: 707.8) for both two isomers. The Boc groups for each isomer were removed by treating with TFA/DCM (1 :1 ) for less than 1 hour. TFA/DCM were removed and the residue was dissolved in minimum amount NMP and loaded to Prep HPLC with ACN/water (0.1 % TFA). The pure (1 S,2S)-N~1 ~,N~2~-bis[(2S,3R)-1 -{[(2R)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]cyclopropane-1 ,2-dicarboxamide and (1 R,2R)-N~1 ~,N~2~- bis[(2S,3R)-1 -{[(2R)-4-amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl- 3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2, 5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]cyclopropane-1 ,2- dicarboxamide were collected and lyophilized to give white powders. Ions were found as ((M+4H+)/4: 506.0 and (M+3H+)/3:674.2) for both Compound 80a (more polar) and Compound 80b (less polar).
Figure imgf000208_0001
Step a. Synthesis of ethyl 32-(2-ethoxy-2-oxoethyl)-3,31 -dioxo-1 -phenyl- 2,7,10,13,16,19,22,25,28-nonaoxa-4,32-diazatetratriacontan-34-oate
To the solution of 3-oxo-1 -phenyl-2, 7, 10, 13, 16,1 9,22,25, 28-nonaoxa-4-azahentriacontan-31 -oic acid (1 g, 2.5 mmol) in DMF (20 ml_) were added diethyl 2,2'-azanediyldiacetate (0.71 g, 3.7 mmol), EDC (600mg, 3mmol), HOBT (0.45g, 3.0mmol), Hunigs base (0.7 ml_, 5mmol) at room temperature. The solution was stirred overnight. The resultant solution was removed DMF and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of oil product, 1 .2 g, 65% yield. LC/MS 747.4 [M+H]
Step b. Synthesis of 32-(carboxymethyl)-3,31 -dioxo-1 -phenyl-2,7,10,13,16,19,22,25,28- nonaoxa-4,32-diazatetratriacontan-34-oic acid
Lithium hydroxide (50 mg, 2 mmol) in 2 mL H2O was added to the solution of ethyl 32-(2-ethoxy-2- oxoethyl)-3,31 -dioxo-1 -phenyl-2,7,10,13,1 6,1 9,22,25,28-nonaoxa-4,32-diazatetratriacontan-34-oate (800mg, 1 mmol) in mix solvent of 2 mL H2O, 2ml MeOH and 2ml THF. The resulting solution was stirred for 1 hour at room temperature. The resulted solution was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoro-acetic acid as the modifier. LC/MS 691 .3 [M+H]+
Step c. Synthesis of Bis (penta-Boc-polymyxin B decapeptide)-32-(carboxymethyl)-3,31- dioxo-1 -phenyl-2,7,10,13,16,19,22 ,25,28-nonaoxa-4,32-diazatetratriacontan-34-amide
To a solution of 32-(carboxymethyl)-3,31 -dioxo-1 -phenyl-2,7,10,13,16,19,22,25,28-nonaoxa-4,32- diazatetratriacontan-34-oic acid (70 mg, 0.1 mmol), triethyl amine (0.14 mL, 1 mmol) and penta-Boc- polymyxin B decapeptide (300 mg, 0.2 mmol) in 5 mL DMF was added HATU (80 mg, 0.2 mmol) in 1 mL DMF by syringe pump over 1 hour. The resultant solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of product, 230 mg, 70% yield.
Step d. Synthesis of deca-Boc-Compound 81
The Cbz-protected product from Step c (120 mg, 0.03 mmol) was dissolved into a mixture of 2 mLs of MeOH and 2 mLs of ethyl acetate, then 100 mg of 5% palladium on charcoal was added to the above solution, and the mixture was stirred at room temperature under the hydrogen atmosphere overnight. The palladium charcoal was removed by filtration after completion of the reaction as indiciated by HPLC. The filtrate was concentrated and used next step without any purification.
Step e. Synthesis of Compound 81
Compound 81 was prepared by removal of the Boc groups from the deca-Boc-Compound 81 using trifluoroacetic acid, lon(s) found by LCMS: (M+3H)/3 = 883.2, (M+4H)/4 =662.6, (M+5H)/5=530.3. E
Figure imgf000210_0001
Step a. Coupling of INT-10 with sebacoyl chloride
Sebacoyl chloride (24 mg, 0.1 mmol) was added to a solution of INT-10 (350 mg, 0.2 mmol) solution in 5 mL of pyridine, the resultant solution was stirred overnight, then the solution was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using 0.1 % trifluoro-acetic acid as the modifier. Yield of product, 160 mg 45% yield.
Step b. Removal of the Boc groups
The compound from Step a was dissolved in a mixture of 2 mL of DCM and 2 mL of TFA at room temperature, the solution was stirred 1 0 min, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 70 mg, 45% yield, lon(s) found by LCMS: (M+3H)/3 = 858.9, (M+4H)/4 =644.4, (M+5H)/5=515.7.
Example 1 rily)
Figure imgf000210_0002
Thr-D-Dab(Boc)-PMBH(tri-Boc) (0.364 g, 0.270 mmol) was dissolved in 5 mL of DMF followed by addition of 3-[(benzyloxy)carbonyl]cyclopropane-trans-1 ,2-dicarboxylic acid (racemic, 0.0352 g, 0.133 mmol) and DIPEA (0.058 mL, 0.33 mmol). To this mixture was added HATU (0.0761 g, 0.200 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. Then the reaction mixture was condensed under reduced pressure. The residue was purified with reverse phase C1 8 with ACN/water (0.1 %TFA) to give a mixture of two isomers of per-Boc Compound 83 and per-Boc Compound 84. Ions were found as ((M-3Boc+3H+)/3: 886.4, tr=4.10 min. for Peak 1 ; (M-3Boc+3H+)/3: 886.6, tr=4.26 min. for Peak 2). The Boc groups were removed by treating with TFA/DCM (1 :1 ) for less than 1 hour. TFA/DCM were removed and the residue was dissolved in a minimal amount NMP and loaded onto Prep HPLC with ACN/water (0.1 % TFA). The pure Compound 83 and Compound 84 fractions were collected and lyophilized to give white powders. Ions were found as ((M+3H+)/3: 719.0) for benzyl (2R,3R)-2,3-bis{[(2S,3R)-1 -{[(2R)-4- amino-1 -oxo-1 -{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 - hydroxyethyl]-12-(2-methylpropyl)-2,5,8, 1 1 ,14,17,20-heptaoxo-1 , 4,7,1 0,13,16, 19-heptaazacyclotricosan- 21 -yl]amino}butan-2-yl]amino}-3-hydroxy-1 -oxobutan-2-yl]carbamoyl}cyclopropane-1 -carboxylate and ((M+4H+)/4: 539.5) for benzyl (2S,3S)-2,3-bis{[(2S,3R)-1 -{[(2R)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]carbamoyl}cyclopropane-1 -carboxylate (structures assigned arbitrarily).
Example 101 : Synthesis of Compound 85a and Compound 85b
Figure imgf000211_0001
Step a. Coupling of INT-13 and racemic trans-cyclopropane-1 ,2-dicarboxylic acid
HATU (92 mg, 0.24 mmol, in DMF, 0.75 ml) was added, dropwise via syringe over a 45 minute period, to a stirring mixture of racemic trans-cyclopropane-1 ,2-dicarboxylic acid (15 mg, 0.12 mmol), Int- 13 (303 mg, 0.24 mmol) and triethylamine (58 mg, 0.58 mmol) in DMF (2 mL). The mixture was stirred for another 20 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 20% to 100% methanol and water using 0.1 % TFA as modifier. The pure fractions were pooled and lyophilized to afford the Boc-protected intermediate as a white solid.
Step b. Removal of the Boc groups
The Boc-protected intermediate from Step a was stirred in a 1 /1 mixture of DCM/TFA containing thioanisole (86 mg, 0.59 mmol) for 20 minutes at ambient temperature. The mixture was filtered and concentrated then dried under high vacuum . The crude material was purified by to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0% to 35% acetonitrile and water using 0.1 % TFA as modifier at which point the diastereomers were separated. The pure fractions were pooled as either the polar (Compound 85a) or less polar (Compound 85b) samples and lyophilized to afford the solid products. Yield (combined) : 55%, 2 steps. LC/MS [M+2H/2] = 997.8.
Example 102: Synthesis of Compound 86
Figure imgf000212_0001
Step a. Preparation of Compound 86 Precursor
HATU (0.69 g , 1 .53 mmol) in DMF (2 mL) was added, dropwise, to a stirring mixture of INT-14 (2.2 g, 1 .53 mmol), INT-1 6 (0.36 g , 0.73 mmol), and triethylamine (0.44 g, 4.38 mmol) in DMF (4 mL) over a period of 20 minutes. The reaction was stirred for an additional 1 5 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 30% to 1 00% methanol and water using 0.1 % TFA as modifier. The pure fractions were pooled, concentrated and stirred in methanol in the presence of 5% Pd/C (1 g) under 1 atmosphere of hydrogen gas for 2 hours. The mixture was filtered and concentrated and then purified by reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 30% to 1 00% acetonitrile and water using no modifier. The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield : 40%, 2 steps. LC/MS [M+3H/3]+ 975.6 (artefactual loss of 2 bocs). Step b. Preparation of Compound 86
HATU (56 mg, 0.15 mmol) in DMF (1 ml_) was added, dropwise, to a stirring mixture of
Compound 86 precursor (345 mg, 0.107 mmol), 4,7,10,13-tetraoxahexadec-15-yn-1 -oic acid (42 mg, 0.16 mmol), and trimethylamine (32 mg, 0.32 mmol) in DMF (2 ml_) over a period of 20 minutes. The reaction was stirred for an additional 15 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 30% to 100% methanol and water using 0.1 % TFA as modifier. The pure fractions were pooled, concentrated and dried under high vacuum. The boc-protected intermediate was stirred in a 1 /1 mixture of TFA/DCM (5 mL) containing thioanisole (106 mg, 0.86 mmol) at room temperature for 20 minutes. The mixture was concentrated on the rotovap then dried under high vacuum and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0% to 50% acetonitrile and water using 0.1 % TFA as modifier. The pure fractions were pooled and lyophilized to afford the title compound as a white solid. Yield: 36%, 2-steps. LC/MS [M+4H/4]+ = 667.2.
Figure imgf000213_0001
Step a. Synthesis of deca-Boc Compound 87
A stirring solution of INT-8 (0.250 g, 0.160 mmol), mesaconic acid (0.0099 g, 0.0761 mmol), and DIEA (0.084 mL, 0.480 mmol) in DMF (1 mL), was treated with a solution of HATU (0.0607 g, 0.1 60 mmol) in DMF (1 mL), dropwise over 60 minutes. After 1 .5 hour the product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.172 g, 70% yield, lon(s) found by LCMS: [(M- 3Boc)+3H]/3 = 974.3
Step b. Synthesis of Compound 87
A solution of deca-Boc-(Compound 87) (0.172 g, 0.053 mmol), dissolved in DCM (1 mL), was treated with TFA (1 mL), while stirring at room temperature. After 5 minutes, the product was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 1 00% acetonitrile and water, using formic acid as the modifier. Yield 0.056 g, 47% yield, lon(s) found by LCMS: (M+3H)/3 = 740.8, (M+4H)/4 = 555.8, (M+5H)/5 = 444.9, (M+6H)/6 = 370.9
Example 104
Figure imgf000214_0001
A mixture of acetylenedicarboxylic acid (3.7 mg, 0.0324 mmol) and hydroxysuccinimide (15 mg, 0.13 mmol) in anhydrous DMF (0.5 ml) was cooled in an ice-water bath and added with EDC-HCI (13. 8 mg, 0.72 mmol). The resulting mixture was stirred for 30 minutes, then added with a solution of INT-8 (130.9 mg, 0.078 mmol) in DMF (1 ml) and pyridine (84 mg). After stirring at 0 °C to room temperature for 3 days, the mixture was purified through RPLC (50 g, 20 to 95 % MeOH and water). The collected fractions were concentrated by rotary evaporation to obtain a white solid (LCMS: [(M-2Boc)/3]+ = 1 008, [(M-3Boc)/3]+ = 975, [(M-4Boc)/3]+ = 942). The material was re-dissolved in a 1 :1 mixture of DCM:TFA (~1 ml). The solution was stirred for 15 minutes and purified through HPLC (5 to 10 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 9.6 mg, 3.7 % over two steps. Ions found by LCMS: [M/3]+ = 741 , [M/4]+ = 556, [M/5]+ = 445, [M/6]+ = 371 .
Example 105: S
Figure imgf000214_0002
The title compound was prepared from INT-8 and hexylpropanedioic acid in a procedu logous to that used in Example 14. Yield; 33%, 2 steps. LC/MS [M+3H/3]+ = 759.9 Example 106: Sy
Figure imgf000215_0001
Compound 90 was prepared from INT-8 and INT-17 in a manner to that described for Example 14. Yield; 45%, 2 steps. LC/MS [M+3H/3]+ = 856.0.
E
Figure imgf000215_0002
Step a. Synthesis of Deca-Boc Compound 91
A mixture of lnt-10 (0.140 g, 0.0821 mmol), 1 ,4-bis(bromomethyl)benzene (0.0108g, 0.041 1 ), and cesium carbonate (0.0401 g, 0.123 mmol), were stirred in DMF(1 ml_) at room temperature for 24h. The product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.037 g, 25% yield, lon(s) found by LCMS: [(M-1 Boc)+3H]/3 = 1 137.7
Step b. Synthesis of Compound 91
A solution of deca-Boc Compound 91 (0.037 g, 0.0105 mmol), dissolved in DCM (1 mL), was treated with TFA (1 mL), while stirring at room temperature. After 5 minutes, the product was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 1 00% acetonitrile and water, using formic acid as the modifier. Yield 0.026 g, 83% yield, lon(s) found by LCMS: (M+2H)/2 = 1255.8, (M+3H)/3 = 837.5, (M+4H)/4 = 628.4, (M+5H)/5 = 502.9
Example 108. Syn
Figure imgf000216_0001
Preparation of Compound 92-lnt-A-polar isomer and Compound 92-lnt-A-hydrophobic isomer
Figure imgf000216_0002
To a solution of racemic-trans1 -(tert-butoxycarbonyl)pyrrolidine-3,4-dicarboxylic acid (0.1 g, 0.39 mmol), H-Norleu-OMe-hydrochloride (0.15 g, 0.80 mmol), and diisopropylethylamine (0.22 g, 1 .74 mmol) in DMF (2 mL) was added a solution of HATU (0.29 g, 0.77 mmol) in DMF (1 mL) via a syringe pump at a rate of 2.5 mL/hr. After the addition, the reaction mixture was stirred for an additional of 1 h at room temperature. The reaction mixture was applied directly to reversed phase liquid chromatography (5-45% acetonitrile and water with 0.1 % TFA as modifier) to yield two diastereomers: polar diastereomer (a) (92.4 mg, 47%) and less polar diastereomer (b) (71 .2 mg, 36%). LC/MS [M-boc+H] = 414.2 (artefactual loss of 1 boc group) for both boc-protected intermediates (methyl 2-[((3R,4R)-4-{N-[(1 S)-1 - (methoxycarbonyl)pentyl]carbamoyl}-1 [(tert-butyl)oxycarbonyl]pyrrolidin-3-yl)carbonylamino](2S). Note: the isomers were taken forward separately in subsequent synthesis. Preparati
Figure imgf000217_0001
Note: Only the polar diastereomer was carried on to the hydrolysis step. A solution of methyl 2- [((3R,4R)-4-{N-[(1 S)-1 -(methoxycarbonyl)pentyl]carbamoyl}-1 [(tert-butyl)oxycarbonyl]pyrrolidin-3- yl)carbonylamino](2S)hexanoate (Compound 92-lnt-A-polar isomer) 92.4 mg, 3.56 mmol) and LiOH (256.0 mg, 10.69 mmol) was stirred in THF:MeOH:H20 (6 mL, 1 :1 :2) at room temperature for 3 hour. After the reaction was completed, the reaction mixture was neutralized with acetic acid to pH 6 then purified directly by reversed phase liquid chromatography (0-40% of acetonitrile and water with 0.1 % TFA as modifier: 30 minute gradient) to yield the title compound (72.1 mg, 42%) as white solid. LC/MS [M- boc+H]+ = 386.2.
Preparation of Compound 92
Figure imgf000217_0002
A solution of HATU (61 .3 mg, 0.16 mmol) in DMF (0.4mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of Compound 92-lnt-B(polar isomer) (34.5 mg, 0.07 mmol), (pentaboc)- PMBD (240.0 mg, 0.1 5 mmol) and diisopropylethylamine (63.8 mg, 0.49 mmol) in DMF (1 .1 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (30-100% of methanol in Dl water with 0.1 % TFA as modifier: 30 minute gradient) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (5-40% acetonitrile and water with 0.1 % TFA as modifier: 30 minute gradient) to yield the title compound (142.4 mg, 54%). LC/MS [M/3+H] 826.6. Example 109. Binding of Selected Compounds from Examples 12-74, 81-107 and 134-136 to Lipopolysaccharide (LPS)
Binding of compounds to LPS derived from Pseudomonas aeruginosa (ATCC 27316) was determined according to the following procedure. LPS from other strains of bacteria may be substituted to determine binding of compounds with any particular LPS sample.
Figure imgf000218_0001
Step a. Synthesis of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2- {[(benzyloxy)carbonyl]amino}octanoyl]amino}-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate
Figure imgf000218_0002
A solution of methyl (2S)-2-[(N-{(2S)-2-amino-4-[(tert-butoxycarbonyl)amino]butanoyl}-L- threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate(0.600 g, 1 .124 mmol),(2S)-2- {[(benzyloxy)carbonyl]amino}octanoic acid (0.330 g, 1 .124 mmol), and DIEA(0.59 mL, 3.37 mmol) in DMF(4 mL), was treated with HATU (0.470 g, 1 .24 mmol), and stirred for 30 minutes. The reaction was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.726 g, 79% yield, lon(s) found by LCMS: (M+H)+ = 809.5 Step b. Synthesis of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2-aminooctanoyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate
Figure imgf000219_0001
A mixture of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2-{[(benzyloxy)carbonyl]amino}octanoyl]amino}-4- [(tert-butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate (0.300 g, 0.371 mmol), 5%Pd/C(0.150g), and methanol(4 mL), were charged with hydrogen from a balloon. After 2hr the product was filtered through celite, concentrated, and used in the next step without further purification. Mass recovery 0.250 g, quantitative, lon(s) found by LCMS: (M+H)+ = 675.4
Step c. Synthesis of methyl (2S)-4-[(tert-butoxycarbonyl)amino]-2-({N-[(2S)-4-[(tert- butoxycarbonyl)amino]-2-{[(2S)-2-{[5-(dimethylamino)naphthalene-1- sulfonyl]amino}octanoyl]amino}butanoyl]-L-threonyl}amino)butanoate
Figure imgf000219_0002
A solution of methyl (2S)-2-[(N-{(2S)-2-{[(2S)-2-aminooctanoyl]amino}-4-[(tert- butoxycarbonyl)amino]butanoyl}-L-threonyl)amino]-4-[(tert-butoxycarbonyl)amino]butanoate(), and dansyl chloride (0.1 10 g, 0.408 mmol), in NMP (1 .5 mL) was treated with N-methylmorpholine (0.081 mL, 0.741 mmol). After 30 minutes the product was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.336 g, 85% yield, lon(s) found by LCMS: (M+H)+ = 908.5
Step d. Synthesis of (2S)-4-[(tert-butoxycarbonyl)amino]-2-({N-[(2S)-4-[(tert- butoxycarbonyl)amino]-2-{[(2S)-2-{[5-(dimethylamino)naphthalene-1- sulfonyl]amino}octanoyl]amino}butanoyl]-L-threonyl}amino)butanoic acid
Figure imgf000219_0003
A solution of methyl (2S)-4-[(tert-butoxycarbonyl)amino]-2-({N-[(2S)-4-[(tert- butoxycarbonyl)amino]-2-{[(2S)-2-{[5-(dimethylamino)naphthalene-1 - sulfonyl]amino}octanoyl]amino}butanoyl]-L-threonyl}amino)butanoate (0.285 g, 0.314 mmol), in methanol(10 mL), was treated with lithium hydroxide (0.050 g, 2.1 mmol) in water(1 mL), while stirring at room temperature. After 30 minutes the mixture was titrated with concentrated HCI(aq.) until slightly acidic by pH paper, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% acetonitrile and water, using no modifier. Yield 0.267 g, 95% yield, lon(s) found by LCMS: LCMS: (M+H)+ = 894.5
Step e. Synthesis of penta-Boc-(Compound 93)
Figure imgf000220_0001
A solution of (2S)-4-[(tert-butoxycarbonyl)amino]-2-({N-[(2S)-4-[(tert-butoxycarbonyl)amino]-2- {[(2S)-2-{[5-(dimethylamino)naphthalene-1 -sulfonyl]amino}octanoyl]amino}butanoyl]-L- threonyl}amino)butanoic acid(0.267 g, 0.299 mmol), lnt-1 (0.349 g, 0.328 mmol), and DIEA (0.172 ml_, 0.985 mmol) in DMF (1 ml_), was treated with HATU (0.129 g, 0.328 mmol), while stirring at room temperature. The product was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.267 g, 46% yield, lon(s) found by LCMS: (M+2H)/2 = 969.5, [(M-1 Boc)+2H]/2 = 919.5, [(M-2Boc)+2H]/2 = 869.5
Step f. Syn
Figure imgf000220_0002
Penta-Boc-(Compound 93) (0.267 mg, 0.138 mmol) was treated with TFA (3 mL) for 15 minutes, then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco
CombiFlash liquid chromatograph eluted with 0% to 1 00% acetonitrile and water, using formic acid as the modifier. The appropriate fractions were collected, pooled and concentrated to give after drying and lyophilization, Compound 93. Yield 0.053 g, 27% yield, lon(s) found by LCMS: [(M-3Boc)+2H]/2 = 719.4 Part 2. Binding assay
The LPS binding of compounds was measured by fluorescence of a compound bound to LPS using a Tecan Infinite Pro fluorescence spectrophotometer set at an excitation wavelength of 340 nm and emission wavelength of 485 nm. Displacement assays were performed by recording the fluorescence after the addition of inhibitors at 250 μΜ final concentration. Assays were performed in 96-well microtiter plates using 4 μg of P. aeruginosa LPS (ATCC 27316) and 6 μΜ Compound 93 in 10 mM HEPES buffer (pH 7.5). Percent displacement is expressed relative to a no inhibitor control and corrected for intrinsic inhibitor fluorescence.
Part 3. Results
Table 2. % Displacement of Fluorescent Probe Compound 93 from P. aeruginosa LPS
Figure imgf000221_0001
Compound % Displacement Compound % Displacement
Compound 23 79.3 Compound 70 76.6
Compound 24 87.3 Compound 71 88.2
Compound 26 49.1 Compound 72 96.6
Compound 25 72.0 Compound 73 89.4
Compound 27 91 .4 Compound 74 94.6
Compound 28 69.0 Compound 75 96
Compound 29a 67.0 Compound 76a 80.1
Compound 30 95.4 Compound 76b 86.7
Compound 31 71 .0 Compound 77 99.8
Compound 32 81 .0 Compound 78 92.2
Compound 33 98.3 Compound 79 97.1
Compound 34 86.4 Compound 80a 77.9
Compound 46 96.2 Compound 80b 89
Compound 47 92.0 Compound 81 80.7
Compound 50 62.9 Compound 82 98.8
Compound 51 a 55.0 Compound 83 95.1
Compound 51 b 59.7 Compound 84 93.4
Compound 52 69.9 Compound 85a 44.3
Compound 53 94.2 Compound 85b 41 .3
Compound 54a 79.1 Compound 86 78.1
Compound 54b 84.7 Compound 87 92.4
Compound 55 88.9 Compound 88 88.2
Compound 56 96.1 Compound 89 94.7
Compound 57 90.1 Compound 90 95.6
Compound 58 78.9 Compound 94 94.5
Compound 59 95.5 Compound 95 98.1 Compound % Displacement Compound % Displacement
Compound 60 88.9 Compound 96 96.9
Compound 61 57.5
Compound 62 77.7
Example 110. Antibacterial Activity of Selected Compounds from Examples 12-74, 81-107, 134-200 and 202
Part 1. Methods
Generation of E. coli BW25113 + pUC18-mcr-1. An mcr- 1 expression plasmid was constructed (GenScript; Piscataway, NJ) using the pUC1 8 high copy number plasmid (Yanisch-Perron, et al., 1985). A 1649-bp fragment was synthesized containing, in order from 5' to 3': EcoR1 restriction site (5'- GAATTC-3'), a ribosomal binding site (5'-AGGAGG-3'), a 5-bp native start codon upstream sequence (5'- TTCTC-3') from the mcr- 7 -bearing plasmid pHNSHP45 (Liu, YY, et al., 201 5; GenBank Accession # KP347127), the 1626-bp mcr- 1 open reading frame with stop codon ("orf00073" of GenBank Accession # KP347127), and finally an Xbs\ restriction site sequence (5'-TCTAGA-3'). Restriction digestion and subsequent ligation into the multiple cloning site of the pUC18 backbone resulted in directional integration of the mcr- 1 gene. The pUC18-mcr-1 plasmid was transformed into chemically-competent E. coli BW251 13 (Coli Genetic Stock Center #7636) as described previously (Chung, et al., 1989), recovered for 1 h shaking at 37°C in Super Optimal broth with Catabolite repression (SOC) media and then aliquots were plated on Luria-Bertani (LB) media containing 100 μg/mL of carbenicillin. Putative transformant colonies were then verified in MIC assays.
Strains and culture conditions. Bacterial strains were stored as glycerol stocks at -80 °C prior to culturing on cation-adjusted Mueller-Hinton agar (MHA; BD cat. no. 21 1438) or in cation-adjusted Mueller-Hinton broth (MHB; BD cat. no.212322) cultured at 37°C. Antibacterial activity was assessed against a strain panel consisting of Escherichia coli BW251 13 wild-type (Coli Genetic Stock Center #7636), BW251 13 + pUC18-mcr-1 , BW251 13 COLr 4X-12 mutant (an uncharacterized, spontaneous mutant selected by plating BW251 13 on MHA containing 1 μg/ml COL (colistin), or 4X the MIC value), and ATCC BAA-2469 (ATCC - American Type Culture Collection), Acinetobacter baumannii ATCC A5075 (ATCC), Pseudomonas aeruginosa PA01 (ATCC BAA-47, ATCC), and Klebsiella pneumoniae ATCC 10031 (ATCC).
MIC assays. MIC assays were performed according to CLSI broth microdilution guidelines (M07- A9, M100-S23) with the exception of using a 100 μί assay volume and preparing stock compounds at 50X final concentration. Briefly, stock solutions of all antibacterial agents were prepared fresh in appropriate solvents (i.e. DMSO, Dl water, ethanol, etc.). Stock concentrations were made at 50X the highest final assay concentration and serially diluted 2-fold, 12 times in a 96-well PCR plate (VWR cat. no. 83007-374). Bacterial cell suspensions generated from MHA plate cultures were prepared in 0.85% saline and adjusted to -0.1 OD600 nm. Next, cell suspensions were diluted 1 :200 in MHB (BD cat. no. 212322) to a concentration of ~5 x 105 CFU/mL. Ninety-eight microliters of each cell suspension in MHB were added to test wells in a 96-well assay plate (Costar cat. no. 3370). A Beckman Multimek 96 liquid handling robot was used to dispense 2 μΙ_ of each 50X stock compound into the plate containing 98 μΙ_ of each strain in MHB (2% final solvent concentration). Plates were shaken then incubated at 37°C overnight (16-20 h). MIC values were read visually at 100% growth inhibition for all compounds.
Part 2. Results
Table 3. MICs ^g/mL)
Figure imgf000224_0001
Figure imgf000225_0001
Figure imgf000226_0001
Figure imgf000227_0001
Figure imgf000228_0001
Figure imgf000229_0001
Figure imgf000230_0001
*: ND: not determined
Example 111. Synergistic Activity of Selected Compounds from Examples 12-74, 81-107 and 134- 143
Fixed concentration synergy MIC assays. The synergistic potential of test compounds was investigated through assessment of MIC values in the presence of a fixed concentration of erythromycin (ERY; Sigma cat. no. E5389). The test compound was run as a dilution series as performed under the CLSI-based conditions described in Example 1 10 for single agents using E. coli BW251 13 (or E. coli BW251 13 + pUC18-mcr-1 ), however each well was stamped a subsequent time with Beckman Multimek 96 liquid handling robot to aliquot a 2 μΙ_ volume of 0.05 mg/mL ERY (solubilized in 50% ethanol) across the 12-point, 2-fold dilution series to give a resulting concentration of ~1 μg/mL ERY. MIC values for the test compounds alone were compared with those containing the fixed concentration of ERY to determine if the polymyxin-based compound increased the susceptibility of the strain to ERY.
Table 4. MICs in combination/absence of 1 μg/mL erythromycin and resultant fold-synergy
Figure imgf000231_0001
E. coli + 1 E. coli + 1
Fold Fold
Compound E. coli Mg/mL E. coli Mg/mL
Synergy Synergy erythromycin erythromycin
BW251 13 + BW251 13 +
Strain BW251 13 BW251 13
pUC18-mcr-1 pUC18-mcr-1
Compound 15 0.5 0.5 1 .0 16 0.5 32.0
Compound 18 0.25 0.25 1 .0 4 0.5 8.0
Compound 19 0.125 0.125 1 .0 2 0.5 4.0
Compound 20 0.125 0.125 1 .0 2 0.25 8.0
Compound 21 32 0.25 128.0 64 2 32.0
Compound 22 0.25 0.125 2.0 4 0.5 8.0
Compound 23 0.25 0.25 1 .0 16 2 8.0
Compound 25 64 1 64.0 64 32 2.0
Compound 26 128 16 8.0 128 128 1 .0
Compound 27 1 0.5 2.0 128 64 2.0
Compound 28 64 1 64.0 64 1 64.0
Compound 29a 64 1 64.0 32 2 16.0
Compound 29b 32 2 16.0 64 2 32.0
Compound 31 32 1 32.0 128 128 1 .0
Compound 32 2 2 1 .0 16 2 8.0
Compound 33 2 2 1 .0 128 4 32.0
Compound 35 0.5 0.5 1 .0 8 4 2.0
Compound 36 8 2 4.0 32 8 4.0
Compound 39 0.5 0.5 1 .0 16 8 2.0
Compound 42 2 1 2.0 4 2 2.0
Compound 44 0.5 0.5 1 .0 4 2 2.0
Compound 47 2 1 2.0 2 2 1 .0
Compound 52 16 0.5 32.0 128 2 64.0 E. coli + 1 £. coli + 1
Fold Fold
Compound E. coli Mg/mL E. coli Mg/mL
Synergy Synergy erythromycin erythromycin
BW25113 + BW25113 +
Strain BW25113 BW25113
pUC18-mcr-1 pUC18-mcr-1
Compound 55 1 1 1.0 4 2 2.0
Compound 57 0.25 0.25 1.0 16 4 4.0
Compound 58 4 4 1.0 16 8 2.0
Compound 59 1 1 1.0 4 2 2.0
Compound 60 16 1 16.0 128 16 8.0
Compound 61 32 1 32.0 64 1 64.0
Compound 62 1 1 1.0 4 1 4.0
Compound 64 1 1 1.0 2 2 1.0
Compound 65 1 1 1.0 4 2 2.0
Compound 66 2 1 2.0 2 2 1.0
Compound 67 4 2 2.0 4 2 2.0
Compound 68 2 2 1.0 2 4 0.5
Compound 69 4 2 2.0 8 8 1.0
Compound 70 1 1 1.0 2 1 2.0
Compound 71 1 1 1.0 1 1 1.0
Compound 72 2 2 1.0 2 2 1.0
Compound 73 1 1 1.0 1 2 0.5
Compound 74 2 1 2.0 2 2 1.0
Compound 75 1 0.5 2.0 4 4 1.0
Compound 76a 0.5 0.5 1.0 1 0.5 2.0
Compound 76b 0.5 1 0.5 2 0.5 4.0
Compound 77 4 4 1.0 8 4 2.0
Compound 78 1 1 1.0 4 1 4.0 £. co/ + 1 £. co// + 1
Fold Fold
Compound E. coli Mg/mL E. coli Mg/mL
Synergy Synergy erythromycin erythromycin
BW25113 + BW25113 +
Strain BW25113 BW25113
pUC18-mcr-1 pUC18-mcr-1
Compound 79 1 0.5 2.0 2 2 1.0
Compound 80a 1 0.5 2.0 1 1 1.0
Compound 80b 2 1 2.0 2 1 2.0
Compound 81 1 1 1.0 256 32 8.0
Compound 82 2 2 1.0 4 2 2.0
Compound 83 2 2 1.0 8 2 4.0
Compound 84 2 2 1.0 4 2 2.0
Compound 85a 1 1 1.0 2 1 2.0
Compound 85b 1 1 1.0 8 4 2.0
Compound 86 2 2 1.0 2 2 1.0
Compound 87 2 1 2.0 8 8 1.0
Compound 88 2 1 2.0 16 16 1.0
Compound 89 2 2 1.0 8 2 4.0
Compound 90 2 2 1.0 2 2 1.0
Compound 91 2 1 2.0 2 2 1.0
Compound 94 4 4 1.0 4 4 1.0
Compound 95 8 8 1.0 4 4 1.0
Compound 96 0.5 0.5 1.0 1 1 1.0
Compound 98 2 2 1.0 2 2 1.0
Compound 99 2 2 1.0 2 2 1.0
Compound 100 2 2 1.0 4 2 2.0
Compound 101 4 4 1.0 4 4 1.0
Compound 102 2 1 2.0 1 1 1.0
Compound 103 4 4 1.0 2 4 0.5
Compound 104 2 2 1.0 4 4 1.0 E. coli + 1 E. coli + 1
Fold Fold
Compound E. coli Mg/mL E. coli Mg/mL
Synergy Synergy erythromycin erythromycin
BW251 13 + BW251 13 +
Strain BW251 13 BW251 13
pUC18-mcr-1 pUC18-mcr-1
Compound 105 1 1 1 .0 1 1 1 .0
Compound 106 1 1 1 .0 1 1 1 .0
Example 112. Synergistic Activity of Selected Compounds from Examples 12-74 and 81-107
Checkerboard synergy assays. Checkerboard synergy assays were performed as previously described (Eliopoulos, G.M. and R.C. Moellering, 1996; Moody, J., 2004). In master stock plates the stocks of two compounds ("Compound A" - test compound, and "Compound B" - a known antibacterial agent) for synergistic evaluation were prepared. A liquid stock of Compound A was prepared fresh in Dl water to a concentration 50X the desired final synergy assay concentration. Into wells A1 through H1 (vertical, Y-axis column on left edge of plate) of a 96-well PCR plate (VWR cat. no. 83007-374)
Compound A was aliquoted in 100 μΙ_ volumes. To all other wells on the plate, with the exception of A12 through H12, 50 μΙ_ of Dl water was added. A multichannel pipette was then used to transfer 50 μΙ_ from column A1 -H1 to column A2-H2. Following mixing, tips were discarded and the process was repeated across the plate to create a series of 1 1 , serial two-fold dilutions spanning columns 1 through 1 1 .
A stock of Compound B was prepared in a similar fashion in the appropriate solvent (DMSO, Dl water, ethanol, etc.) at 50X the desired final synergy assay concentration. In a separate 96-well PCR plate, 1 00 μΙ_ aliquots of Compound B were added to wells in the top row of the plate spanning A1 through A12. In all other wells, excluding the bottom row (H1 -H12), 50 μΙ_ of the corresponding
Compound B solvent were added. In a similar fashion to Compound A, Compound B was serially diluted, two-fold down the plate using a multichannel pipette, resulting in 7 rows comprised of 12 wells with 50 μΙ_ diluted Compound B.
Checkerboard synergy assays were performed using the same assay setup as the standard MIC assays previously described previously herein (i.e. inoculum, media, volume, 96-well assay plates, incubation time, incubation temperature, 100% inhibition assay endpoint, etc.). However, rather than a single addition of 2 μΙ_ of 50X stock compound solution to the assay plate containing MHB pre-inoculated with bacterial cells using the Multimek 96 liquid handling robot, two sequential additions were made (one from the Compound A 50X stock plate and one from the Compound B 50X stock plate). The resulting checkerboard plates contained a 7 x 1 1 -well grid (A1 -G1 x A1 -A1 1 ) of synergy wells containing varying proportions of Compounds A and B, an 1 1 -point dilution series of Compound A alone (wells H1 -H1 1 , assay concentration range 1 X to 1 /1024X), a 7-point dilution series of Compound B alone (wells A12- G12, assay concentration range 1 X to 1 /64X) and a positive growth control well containing no drug (well H12) (FIG. 2).
Following overnight incubation, checkerboard synergy plates were read visually at 100% growth inhibition. MIC values for Compound A and B were recorded from their respective single-drug dilution series wells and an optimal synergy well (or wells) was identified as that for which growth inhibition was achieved using a combination of the lowest possible concentrations of both drugs. The fraction inhibitory concentration (FIC) was calculated for each compound by dividing the combination MIC value in the optimal synergy well by the MIC value for the compound alone. The summation of the FIC values for Compounds A and B was then used to calculate the fractional inhibitory concentration index (FIG) and synergy was defined as an FICI value of <0.50.
FIC Compound A = MIC of Compound A in combination/MIC of Compound A alone
FIC Compound B = MIC of Compound B in combination/MIC of compound B alone
Figure imgf000236_0001
Example 113. LPS Neutralization by Selected Compounds from Examples 12-74 and 81 -107
Part a. Method
Murine macrophage cells (RAW 264.7, ATCC, TIB-71 ) were grown to 70-90 % confluency in DMEM + 10 % FBS in T75 cm2 flasks at 37 °C / 5 % C02 for 2-3 days. Cells are washed once with 10 mL DPBS and scraped into 5 mL of media. After centrifugation at 800 rpm for 5 min, the cells were counted with a hemocytometer after 1 :10 dilution in media with 0.04 % trypan blue. Cells were adjusted to 2E6/mL in DMEM + 10 % FBS. Seed 100 iL medium containing 2E5 RAW per well and incubate overnight at 37°C / 5% C02.
RAW 264.7 cells were added to a 96-well plate at 2 x 105 cells per well in 100 μΙ in DMEM + 10 % FBS. The plate was incubated for 24 h at 37°C / 5% CO2 and the medium was aspirated and cells washed once with 200 μί DPBS Test reagents and media only control were prepared in RPMI without phenol red + 5% FBS.
Table 5. Test article preparation
Test Compounds Polymyxin B LPS (positive control)
5 μg/mL· 5 μg/mL· 10 g/mL
7.5 μΐ 15 μL· Polymyxin B 1 μΐ LPS
(2 mg/mL) (1 mg/mL) (1 mg/mL)
1492.5 μΐ media 1485 μί μί media 999 μί media
1 .5 mL 1 .5 mL 1 mL
100 it of reagents were added to wells at 0.5 and 5 μg/mL final concentrations. The cells were incubated with reagents for 1 h at 37°C + 5% CO2. After 15 min, 100 μί medium was added without LPS and with LPS at 0.001 , 0.01 , 0.1 , 1 and 10 μg/mL to appropriate wells and the plates were incubated for 24 h at 37°C + 5% CO2. After 24h, 150 μΙ of each supernatant was transferred to a new 96 well FLAT bottom plate. 50 μί of the transferred supernatant was transferred for a Griess assay (measurement of nitric oxide (NO) production). The remainder was stored at 4 °C for ELISA. A Griess assay was performed according to manufacturer's (Promega) instructions: a. Prepare the sodium nitrite standard curve: 1 mL of a 100 μΜ Nitrite Solution by diluting the nitrite standard from the kit 1 :1 ,000 which is 1 μΙ_ in 999 μΙ_ media (same as samples in RPMI without phenol red + 5 % FBS).
b. Add 100 [it of the 100 μΜ Nitrite Solution perform serial 2-fold dilutions of the standard from
100 μΜ down to 1 .56 μΜ in RPMI (without phenol red + 5 % FBS) by taking 50 μΙ_ from the 100 μΜ wells into the next well; the last 50 μΙ_ from the 1 .56 μΜ wells are discarded
c. Dispense 50 μΙ_ of the Sulfanilamide Solution to wells containing samples or standard d. Incubate at room temperature, protected from light, for 10 min
e. Dispense 50 μΙ_ of the NED Solution to wells containing samples or standard
f. Incubate at room temperature, protected from light, for 5 min at RT (purple/magenta color will begin to form immediately; note: color fade after 30 min)
The absorbance at 540 nm was read and NO production in μΜ was calculated by linear regression analysis of the NO standard curve using Graphpad Prism 6 software.
Part b. Results: Inhibition of NO production by Selected Compounds from Examples 12- 74 and 81-107 in RAW cells stimulated with LPS
NO production in response to LPS (endotoxin) is a signal of macrophage activation which may lead to sepsis in an infected host. Inhibition of NO production through LPS binding and neutralization is demonstrated by the compounds Compound 16, Compound 19, and Compound 30 of the present disclosure (FIGS. 1 A, 1 B, and 1 C) at clinically relevant concentrations of LPS that have been correlated with sepsis in humans which is less than 1 ng/mL in the plasma (see, e.g., Opal et al., J. Infect. Dis. 180:1584-9, 1999).
Example 114. In vivo activity in mouse model of bacterial sepsis for selected compounds
Mouse strain. Experiments utilized female C57BI/6 mice (18 - 22 grams) from Charles River
Laboratories (Wilmington, Massachusetts) and were allowed to acclimate for 5 days prior to start of study.
Animals were housed 6 per cage with free access to food and water.
Inoculum preparation and infection.
E. coli ATCC25922 was obtained from the American Type Culture Collection (Manassas, Va) and was prepared for infection from an overnight plate culture (Trypicase Soy agar media). A portion of the plate was re-suspended in sterile saline and adjusted to an OD of 0.1 at 625 nm. The adjusted bacterial suspension was further diluted in 5% hog gastric mucin to target an infecting inoculum of 1 .0x103 CFU/mouse. Plate counts of the inoculum were performed to confirm inoculum concentration. To initiate the infection, mice were injected with 0.5 ml of the suspension intraperitoneally (IP).
Treatment/Efficacy.
Beginning at one hour post infection, mice were dosed with either vehicle, colistin, meropenem or Compound 1 6. Vehicle/diluent was sterile 0.9% saline for all test articles. All animals were dosed IP at 10 mL/kg. Mice were euthanized at 16 hours post infection. Kidneys were aseptically removed, weighed, homogenized, serially diluted and plated. The CFUs were enumerated after overnight incubation. The average and standard deviations for each group were determined via standard methodology. Results.
Table 6. Survival and CFU reduction in kidneys of mice infected with E. co//' and treated with colistin or
Compound
Figure imgf000238_0001
Example 115. Antibacterial Activity of Compound 16
Part 1. Methods
Generation of E. co/ BW25113 + pUC18-mcr-2. An mcr-2 expression plasmid was constructed (GenScript; Piscataway, NJ) using the pUC1 8 high copy number plasmid (Yanisch-Perron, et al., 1985). A 1640-bp fragment was synthesized containing, in order from 5' to 3': EcoR1 restriction site (5'- GAATTC-3'), a ribosomal binding site (5'-AGGAGG-3'), a 5-bp native start codon upstream sequence (5'- TTTCT-3') from the mcr-2-bearing plasmid pKP37-BE (Xavier et al., Euro Surveill A (27), 2016;
GenBank Accession # LT598652), the 1617-bp mcr-2 open reading frame with stop codon (locus tag # A7J1 1_03753), and finally an Xbs\ restriction site sequence (5'-TCTAGA-3'). Restriction digestion and subsequent ligation into the multiple cloning site of the pUC18 backbone resulted in directional integration of the mcr-2 gene. The pUC18-mcr-2 plasmid was transformed into chemically-competent E. coli BW251 13 (Coli Genetic Stock Center #7636) as described previously (Chung, et al., 1989), recovered for 1 h shaking at 37°C in Super Optimal broth with Catabolite repression (SOC) media and then aliquots were plated on Luria-Bertani (LB) media containing 100 μg/mL of carbenicillin. Putative transformant colonies were then verified in MIC assays. Susceptibility of Compound 16, COL (colistin), and PMB (polymyxin B) were then assessed vs. WT E. coli BW251 13 and the pUC18-mcr-2 transformant strain.
Strains and culture conditions. Bacterial strains were stored as glycerol stocks at -80 °C prior to culturing at 37°C on cation-adjusted Mueller-Hinton agar (MHA; BD cat. no. 21 1438) or in cation- adjusted Mueller-Hinton broth (MHB; BD cat. no. 212322). Antibacterial activity was assessed against Escherichia coli BW251 13 wild-type (Coli Genetic Stock Center #7636), BW251 13 + pUC18-mcr-1 , BW251 13 + pUC18-mcr-2, BW251 13 COLr 4X-12 mutant (an uncharacterized, spontaneous mutant selected by plating BW251 13 on MHA containing 1 ig/m\ COL (colistin), or 4X the MIC value), ATCC BAA-2469 (ATCC - American Type Culture Collection), ATCC25922, and ATCC25922+50%FBS, and Acinetobacter baumannii ATCC A5075 (ATCC), Pseudomonas aeruginosa PA01 (ATCC BAA-47, ATCC), and Klebsiella pneumoniae ATCC 1 0031 (ATCC). Additionally MIC90 assays were run on panels of COL-S (colistin-susceptible) clinical isolates collected from US sites between 2012 and 2016 for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii (n=20/species) as well as a panel of COL-R (colistin-resistant) isolates (n=25, composed of a mixture of K. pneumoniae, P. aeruginosa and A. baumannii). Finally, E. coli ATCC 25922 WT and a panel of spontaneous mutants selected with Compound 16 and COL were assessed for changes in susceptibility to selecting drugs and a panel of compounds to assess cross-resistance.
MIC (Minimum Inhibitory Concentration) assays. MIC assays were performed according to CLSI broth microdilution guidelines (M07-A9, M100-S23) with the exception of using a 100 μί assay volume and preparing stock compounds at 50X final concentration. Briefly, stock solutions of all antibacterial agents were prepared fresh in appropriate solvents (i.e. DMSO, Dl water, ethanol, etc.). Stock concentrations were made at 50X the highest final assay concentration and serially diluted 2- fold, 12 times in a 96-well PCR plate (VWR cat. no. 83007-374). Bacterial cell suspensions generated from MHA plate cultures were prepared in 0.85% saline and adjusted to -0.1 Οϋβοο nm. Next, cell suspensions were diluted 1 :200 in MHB (BD cat. no. 212322) to a concentration of ~5 x 105 CFU (Colony- Forming Units)/mL. Ninety-eight microliters of each cell suspension in MHB were added to test wells in a 96-well assay plate (Costar cat. no. 3370). A Beckman Multimek 96 liquid handling robot was used to dispense 2 μί of each 50X stock compound into the plate containing 98 μί of each strain in MHB (2% final solvent concentration). Plates were shaken then incubated at 37°C overnight (16-20 h). MIC values were read visually at 1 00% growth inhibition for all compounds. Part 2. Results
Table 8 (MIC g/mL))
Figure imgf000240_0001
Table 9. MIC90 analysis of Compound 1 6 (CMP 1 6), COL, PMB, MERO (meropenem), and TIG (tigecycline) against COL-S E. coli, K. pneumoniae, P. aeruginosa, and A. baumannii clinical isolates panels
Figure imgf000240_0002
Table 10. MIC90 analysis of Compounds 16 (CMP 16), COL, PMB, MERO, CAZ (ceftazidime), AZT (aztreonam), AMIK (amikacin), LEVO (levofloxacin), and TIG against COL-R clinical isolate panels
Figure imgf000240_0003
Example 116. MIC50 and MIC90 Determination of Selected Compounds from Examples 139, 143-145, and 187
Using the methodology for the MIC assays described in Example 1 15, the following MIC50S and MIC90S were obtained. MIC90 analysis of Compounds against COL-S E. coli, K. pneumoniae, P. aeruginosa, and A.
baumannii clinical isolate panels
Figure imgf000241_0001
Table 12. MIC90 analysis of Compounds against a COL-R clinical isolate panel
Figure imgf000241_0002
Example 117. Immune-Competent Mouse Septicemia Model
The antibacterial activity was evaluated in vivo using an acute disseminated E. coli mouse septicemia model with Compound 44, Compound 51 a, Compound 85a and Compound 85b and colistin. Efficacy was determined using both survival and bacterial burden in the kidneys. Mice (n=5 or 6) were infected with E. coli 25922 and given a single intraperitoneal dose of Test Article at either 0.3, 1 or 3 mg/kg as indicated. After 16 h, survival was recorded and mice were euthanized and kidneys aseptically removed and enumerated for bacterial burden.
The results shown in Table 13 demonstrate that Compound 44, Compound 51 a, Compound 85a and Compound 85b possess antibacterial activity at doses of 0.3 and 3 mg/kg, except Compound 44 which failed to show a benefit at the 0.3 mg/kg dose. Survival was equivalent for all compounds versus a 1 .0 mg/kg dose of colistin at 3 mg/kg and reduction in bacterial burden was similar.
Table 13. In Vivo Activity of Compounds in a Mouse Septicemia Model
Figure imgf000241_0003
3.0 5/5 3.30 0.97 -4.41
Compound 51a 0.3 5/6 5.33 1 .64 -2.38
3.0 5/5 2.93 0.90 -4.78
Compound 85a 0.3 4/6 4.16 0.81 -3.55
3.0 5/5 3.33 0.69 -4.38
Compound 85b 0.3 3/6 6.44 2.18 -1 .27
3.0 5/5 2.64 0.37 -5.07
Example 118. Activity in an ImmunoSuppressed Mouse Thigh Infection Model with Colistin- Resistant E. coli
Mice (n=6 / group) were immunosuppressed (IP cyclophosphamide, 150 mg/kg at day -4 and 100 mg/kg at day -1 ) and infected with E. coli (CDC AR-0349 which expesses the MCR-1 plasmid which renders the bacteria resistant to colistin, day 0) directly into the thigh muscle. Mice were dosed with PBS (bid, IP), imipenem 30 mg/kg (bid, SC), colistin 10 mg/kg (bid, SC), Compound 150 15 mg/kg (qd, IP) or Compound 1 50 1 0 mg/kg (bid, IP) 1 h (qd) or 1 h and 6h (bid) after infection. 26 h post-infection, the mice were euthanized and thigh muscle was surgically removed and enumerated for bacteria.
Figure 3 shows significant growth of bacteria in the thigh of mice receiving PBS control injections while those receiving imipenem showed a substantial reduction in bacterial burden. Colisitn was less effective in controlling the infection while Compound 1 50 given at 10 mg/kg (bid, IP) produced superior results. These data demonstrate that Compound 150 is effective at controlling infection by colistin- resistant E. coli containing the mcr-1 plasmid in a mouse model of infection.
Example 119. Preparation of INT-18. Synthesis of Trans-cyclopentane-(Bis-norleu-YBocDab-Thr) linker
Figure imgf000242_0001
Note: The absolute configuration of the trans-cyclopentane dicarboxylate is arbitrarily assigned but the product is derived from the more polar trans-cyclopentane-(bis-norleu methyl ester) Step a. Synthesis of Trans-cyclopentane-(Bis-norleu methyl ester)
To a mixture of racemic trans-1 ,2-cyclopentanedicarboxylic acid (1 g, 6.323 mmol) and L- norleucine methyl ester hydrochloride (2.544 g, 14 mmol) in anhydrous DMF (7 mL) was added DIPEA (5.46 g, 14 mmol) , followed by drop-wise added of a solution of HATU (5.32 g, 14 mmol) in DMF (14 mL) via syringe pump at a rate of 30 mL/hr. After the addition, the reaction mixture was partitioned between water (100 mL) and EtOAc (100 mL). The organic layer was concentrated by rotary evaporation, and the residue was purified by RPLC (10 to 72 % acetonitrile and water). 1 .16 g of the more polar product was obtained in 44.3 % yield. MS: [M+H]+ = 413.
Step b. Hydrolysis of Trans-cyclopentane-(Bis-norleu methyl ester)
The step-a product (1 .16 g, 2.8 mmol) was dissolved in a minimal volume of 1 :1 MeOH:THF. The solution was cooled in an ice-water bath and a solution of LiOH (168 mg, 6.73 mmol) in water (10 mL) was added. The reaction was stirred for 6 hours, then acidified by 4N HCI solution in dioxane (2 mL). It was then extracted with EtOAc (100 mL). The aqueous layer was back extracted with 1 :1 EtOAc/hexane (60 mL). The combined organic layers were concentrated by rotary evaporation, and the residue was purified byby RPLC (5 to 45 % acetonitrile and water). Yield (INT-26) 965.1 mg, 89.6 %. MS: [M+H]+ = 385.
Step c. Synthesis of Trans-cyclopentane-(Bis-norleu-YBocDab methyl ester)
To a mixture of Step-b product (682 mg, 1 .77 mmol) and (S)-methyl-2-amino-4-((ter- butoxycarbonylamino)butanoate hydrochloride (1 .05 g, 3.9 mmol) in anhydrous DMF (4 mL) was added DIPEA (1 .01 g, 7.8 mmol), followed by drop-wise added of a solution of HATU (1 .48 g, 3.9 mmol) in DMF (4 mL) via syringe pump at a rate of 8 mL/hr. After the addition, the reaction mixture was extracted with water (100 mL) and EtOAc (100 mL X 2). The organic layer was concentrated by rotary evaporation, and the residue was purified by RPLC (150 g, 1 0 to 100 % acetonitrile and water). Yield 1 .4 g, 97.3 %. MS: [M+H]+ = 813, [(M - Boc)+H]+ = 713.
Step d. Hydrolysis of Trans-cyclopentane-(Bis-norleu-YBocDab methyl ester)
Step-c product (1 .4 g, 1 .722 mmol) was dissolved in THF (15 mL) and MeOH (5 mL). The mixture was cooled in an ice-water bath, as a solution of LiOH monohydrate (220 mg, 5.2 mmol) in water (2 mL) was added. The resulting mixture was stirred for 2 hours then extracted with water (50 mL), 1 .5 mL of 4N HCI in dioxane, and EtOAc/Hexane (1 :1 , 150 mL x 2). The combined organic layers were washed with water (30 mL), dried over Na2S04, and concentrated by rotary evaporation to dryness. Yield 1 .3 g, 96.3 % crude product. MS: [(M - Boc)+H]+ = 685.
Step e. Synthesis of Trans-cyclopentane-(Bis-norleu-YBocDab-Thr carboxylic acid) (INT-18)
To a mixture of step-d product (1 .3 g, 1 .658 mmol) and L-Threonine hydrochloride (678.4 g, 4 mmol) in anhydrous DMF (4 mL) was added DIPEA (1 .3 g, 10 mmol), followed by drop-wise addition of a solution of HATU (1 .41 g, 3.7 mmol) in DMF (4 mL) via syringe pump at a rate of 8 mL/hr. After the addition, the reaction mixture was extracted with water (100 mL) and EtOAc (150 mL X 2). The organic layer was concentrated by rotary evaporation to afford the crude product as a yellow solid. MS: [(M - 2Boc + 2H)/2]+ = 408. The material was re-dissolved in MeOH (30 mL) and THF (50 mL) and a solution of LiOH monohydrate (205 mg, 4.88 mmol) was added. The resulting mixture was stirred for 4 hours then 4N HCI (1 mL) in dioxane was added. The organic solvent was partially removed by rotary evaporation at room temperature. The remaining was poured into water (50 mL), and the precipitate was collected by filtration. It was then purified by RPLC (5 to 55 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 1 .26 g, 77 %. MS: [(M-2Boc+2H)/2]+ = 394.
Example 120. Preparation of INT-19 and INT-20
Figure imgf000244_0001
Peak-2 (more polar trans- cyclopropane stereochemistry
randomly assigned)
Step a. Synthesis of dimethyl (2S,2'S)-2,2'-[(1S,2S)-cyclopropane-1 ,2- diylbis(carbonylazanediyl)]dioctanoate and dimethyl (2S,2'S)-2,2'-[(1 R,2R)-cyclopropane-1 ,2- diylbis(carbonylazanediyl)]dioctanoate
Racemic-trans-cyclopropane-1 ,2-dicarboxylic acid (0.675 g, 5.187 mmol), methyl (2S)-2- aminooctanoate HCI salt (2.285 g, 1 0.89 mmol), EDCI (2.486 g, 12.97 mmol), HOAt (1 .765 g, 12.97 mmol) and NaHC03 (1 .743 g, 20.75 mmol) were weighed into a 100- mL round bottom flask. 50 mL of DCM/DMF (4:1 ) was added into the flask. The mixture was stirred at room temperature for 3 hrs.
(monitored by TLC and LC/MS). After completion, EtOAc (200 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated NaHCCb and brine. Organic layer was dried with Na2S04 and condensed. The residue was purified by reversed phase C18 chromatography to give 2.012 g of desired product (as an inseparable mixture of a pair of diastereomers, 88% isolated yield). Mass showed a strong detectable positive charge signal at tr = 3.14 min with 5 min (40-95%) gradient (reverse phase C18 with ACN/water (0.1 %TFA)) (found M+H+: 441 .0).
Step b. Synthesis of dimethyl (2S,2'S)-2,2'-[(1S,2S)-cyclopropane-1 ,2- diylbis{carbonylazanediyl[(2S)-1-oxooctane-2,1-diyl]azanediyl}]bis{4-[(tert- butoxycarbonyl)amino]butanoate}
and dimethyl (2S,2'S)-2,2'-[(1 R,2R)-cyclopropane-1 ,2-diylbis{carbonylazanediyl[(2S)-1-oxooctane- 2,1-diyl]azanediyl}]bis{4-[(tert-butoxycarbonyl)amino]butanoate}
The diastereomeric mixture of dimethyl esters (from Step a, 0.510 g, 1 .16 mmol) was dissolved in THF/H2O (1 :1 , 20 mL) followed by adding lithium hydroxide (0.0582 g, 2.43 mmol). The mixture was stirred at room temperature for 2 hrs. After completion, the reaction mixture was acidified with 1 N aq. HCI to pH=2~3. Most of the THF was removed by rotary evaporation followed by EtOAc (200 mL) extraction, dried with Na2S04 and concentrated. A white foam (0.436 g, 91 %) was obtained. Mass showed strong detectable positive/negative charge signals at tr = 4.97 min and 5.12 min (found Positive ion M+H+: 413.2; Negative ion 354.2; M-H+: 41 1 .2). The product was used in next step without purification.
The diastereomeric mixture of dicarboxylic acids (0.436 g, 1 .06 mmol), NH2-Dab(Boc)-OMe HCI salt (0.596 g, 2.22 mmol), EDCI (0.506 g, 2.64 mmol), HOAt (0.360 g, 2.64 mmol) and NaHC03 (0.355 g, 4.23 mmol) were weighed into a 100- mL round bottom flask. 20 mL of DCM/DMF (4:1 ) was added into the flask. The mixture was stirred at room temperature for 3 hrs. (monitored by TLC and/or LC/MS). After completion, EtOAc (1 50 mL) was added to dilute the reaction mixture and washed with 1 N aq. HCI, saturated NaHCOe and brine. The organic layer was dried with Na2S04 and condensed. The residue was purified with normal phase silica to give Peak-1 (less polar) 0.370 g pure desired product (83% isolated yield) and Peak-2 (more polar) 0.310 g pure desired product (70% isolated yield). Mass showed strong detectable positive charge signals at tr = 3.35 min [found (M - 2Boc + 2H+)/2: 321 .0 and M-Boc + H+: 742.4 for Peak-1 and at tr=3.56 min [found (M - 2Boc + 2H+)/2: 321 .0 and M-Boc + H+: 742.4 for Peak-2.
Step c. Synthesis of (2S,2'S)-2,2'-[(1S,2S)-cyclopropane-1 ,2- diylbis{carbonylazanediyl[(2S)-1-oxooctane-2,1-diyl]azanediyl}]bis{4-[(tert- butoxycarbonyl)amino]butanoic acid} and (2S,2'S)-2,2'-[(1 R,2R)-cyclopropane-1 ,2- diylbis{carbonylazanediyl[(2S)-1-oxooctane-2,1-diyl]azanediyl}]bis{4-[(tert- butoxycarbonyl)amino]butanoic acid}
The dimethyl ester (Peak-1 from Step b, 0.370 g, 0.440 mmol) was dissolved in THF/H2O (1 :1 , 10 mL) and lithium hydroxide (0.0221 g, 0.924 mmol) was added. The mixture was stirred at room temperature for 2 hrs. After completion, the reaction mixture was acidified with 1 N aq. HCI to pH=2~3. Most of THF was removed by rotary evaporation followed by EtOAc (200 mL) extraction, dried with Na2S04 and concentrated. A white foam (0.355 g, 98%) was obtained. Mass showed strong detectable positive signal at tr= 3.24 min (found positive ion M-Boc+H+: 713.4. The desired diacid product (INT-19) was used without purification. The stereochemistry of the trans-cyclopropane is unknown and is arbitrarily assigned.
The dimethyl ester (Peak-2 from Step b, 0.310 g, 0.369 mmol) was dissolved in THF/H2O (1 :1 , 10 mL) followed by adding Lithium hydroxide (0.0185 g, 0.774 mmol). The mixture was stirred at room temperature for 2 hrs. After the completion, the reaction mixture was acidified with 1 N aq. HCI to pH=2~3. Most of THF was removed by rotovap followed by EtOAc (200 mL) extraction, dried with Na2S04 and concentrated. A white foam (0.21 1 g, 70%) was obtained. Mass showed strong detectable positive charge signal at tr= 2.97 min (found Positive ion M-Boc+H+: 713.4). The desired diacid product (INT-20) was used without purification. The absolute stereochemistry of the trans-cyclopropane is unknown and is arbitrarily assigned.
Example 121. Synthesis of INT-21 and INT-22
Figure imgf000246_0001
To a solution of racemic-trans1 -(tert-butoxycarbonyl)pyrrolidine-3,4-dicarboxylic acid (0.1 g, 0.39 mmol), L-Norleu-OMe-hydrochloride (0.15 g, 0.80 mmol), and diisopropylethylamine (0.22 g, 1 .74 mmol) in DMF (2 mL) was added a solution of HATU (0.29 g, 0.77 mmol) in DMF (1 mL) via a syringe pump at a rate of 2.5 mL/hr. After the addition, the reaction mixture was stirred for an additional of 1 h at room temperature. The reaction mixture was applied directly to reversed phase liquid chromatography (5-45% acetonitrile and water with 0.1 % TFA as modifier) to yield two diastereomers: polar diastereomer (INT-21 ) (92.4 mg, 47%) and less polar diastereomer (INT-22) (71 .2 mg, 36%). LC/MS [M-Boc+H]+ = 414.2 for both boc-protected intermediates (methyl 2-[((3R,4R)-4-{N-[(1 S)-1 -(methoxycarbonyl)pentyl]carbamoyl}- 1 [(tert-butyl)oxycarbonyl]pyrrolidin-3-yl)carbonylamino](2S). Note: the isomers were taken forward separately in subsequent synthesis. Example 122. Synthesis of INT-23
Figure imgf000247_0001
Note: Only the polar diastereomer (INT-21 ) was carried on to the hydrolysis step. A solution of methyl 2-[((3R,4R)-4-{N-[(1 S)-1 -(methoxycarbonyl)pentyl]carbamoyl}-1 [(tert-butyl)oxycarbonyl]pyrrolidin- 3-yl)carbonylamino](2S)hexanoate (INT-21 ) 92.4 mg, 3.56 mmol) and LiOH (256.0 mg, 10.69 mmol) was stirred in THF:MeOH:H20 (6 mL, 1 :1 :2) at room temperature for 3 hours. After the reaction was completed, the reaction mixture was neutralized with acetic acid to pH 6 then purified directly by reversed phase liquid chromatography (0-40% of acetonitrile and water with 0.1 % TFA as modifier: 30 minute gradient) to yield the title compound (72.1 mg, 42%) as white solid. LC/MS [M-boc+H]+ = 386.2.
Example 123.
Figure imgf000247_0002
The synthesis of INT-24 and INT-25 was analogous to the procedure described for INT-21 and INT-22. Note: the isomers were taken forward separately in subsequent syntheses. Example 124. Preparation of INT-26 and INT-27
Figure imgf000248_0001
Step a. Coupling of Trans-Cyclopentane Dicarboxylic Acid with L-nor-Leucine Methyl Ester
HATU (10.6 g, 27.8 mmol) in DMF (5 mL) was added, dropwise over 30 minutes to a mixture of racemic 1 ,2-trans-cyclopentane dicarboxylic acid (2.0 g, 12.6 mmol), L-norleucine-methyl ester hydrochloride, and triethylamine in DMF (5 mL). The mixture was stirred for an additional 30 minutes then applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 95% acetonitrile and water using 0.1 % TFA modifier. The two diastereomers were separated, fractions pooled and lyophilized separately to give the more polar diastereomer (a) and the less polar diastereomer (b): LC/MS [m+H]+ = 413.4 for both intermediates. Total yield 76%.
Step b. Hydrolysis of the Methyl Esters
Diastereomer (a) (polar isomer) (2.0 g, 4.8 mmol) was hydrolyzed by stirring in a 1 /1 /2 mixture of methanol/THF/DI water (~1 5 mL) containing LiOH (0.72 g, 30 mmol) for 30 minutes. The mixture was adjusted to pH 5 with acetic acid then concentrated and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 95% acetonitrile and water using 0.1 % TFA modifier. The pure fractions were concentrated to afford the product (INT-26) as a white solid. Yield: 66%, 2 steps. LC/MS [M+H]+ = 385.6. In a similar fashion, INT-27 is obtained from the less polar diastereomer.
Note: The trans-cyclopentane stereochemistry of INT-26 and INT-27 was arbitrarily assigned to the product
Example 125. Synthesis of INT-28 and INT-29
Figure imgf000249_0001
INT-29
HATU (3.1 g, 8.1 mmol) in DMF (5 mL) was added, dropwise, to a solution of racemic-trans-1 - (ferf-butoxycarbonyl)pyrrolidine-3,4-dicarboxylic acid (1 g, 3.9 mmol), L-Norleu-OMe-hydrochloride (1 .5 g, 8.1 mmol), and triethylamine (4.0 g, 39.5 mmol) in DMF (10 mL) over a period of 20 minutes. The mixture was stirred for an additional 20 minutes then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 95% acetonitrile and water using 0.1 % TFA modifier. The two diastereomers were separated and pooled and lyophilized separately to afford a more polar diastereomer and a less polar diastereomer: LC/MS [M-Boc+H]+ = 414.2 for both Boc-protected intermediates. Each Boc-protected diastereomer was stirred in a 1 /1 mixture of DCM/TFA (8 mL) for 20 minutes then concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0% to 75% acetonitrile and water using no modifier to afford, after lyophilization each product as its TFA salt as a hygroscopic white solid (INT-28 and INT-29). Yield: 88%, 2 steps. LC/MS [m+H]+ = 414.2.
Note: The configuration of the diastereomers has been arbitrarily assigned to the more and less polar diastereomers
Example 126. Synthesis of INT-30
Figure imgf000249_0002
Cbz-NHS ester (227 mg, 0.91 mmol) was added to a stirring mixture of INT-28 (400 mg, 0.76 mmol) and triethylamine in DMF (10 mL). The mixture was stirred for 4 hours and then applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 5% to 95% acetonitrile and using 0.1 % THFA modifier. The solvent was removed by rotovap and the di- ester was hydrolyzed stirring in a 1 /1 /2 mixture of methanol/THF/DI water (5 mL) containing LiOH (0.72 g, 30 mmol) for 30 minutes. The mixture was adjusted to pH 5 with acetic acid then concentrated and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 10% to 95% acetonitrile and water using 0.1 % TFA modifier. The pure fractions were lyophilized to afford the product as a white solid. Yield: 78%, 2 steps. LC/MS [M+H]+ = 520.2.
Example 127. Synthesis of INT-31
Figure imgf000250_0001
Step a. Coupling of INT-30 and INT-7
A solution of HATU (161 .0 mg, 0.423 mmol) in DMF (1 .0 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-30 (100.2 mg, 0.19 mmol), INT-7 (647.74 mg, 0.42 mmol) and diisopropylethylamine (149.1 mg, 1 .15 mmol) in DMF (1 .2 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-35-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the title compound (279.5 mg, 41 %). LC/MS [(M- 3Boc)+3H)]/3 747.8, [(M-4Boc)+4H)]/4 536.1 , [(M-5Boc)+5H)]/5 409.1 , [(M-6Boc)+6H)]/6 324.4.
Step b. Synthesis of INT-31
The product from Step a. (279.5 mg, 0.079 mmol) was dissolved in methanol (21 mL) and DMF (7 mL) was added to increase solubility. To this solution, 5% Pd/C (16.8 mg, 0.008 mmol) and H2 gas balloon were charged. The reaction mixture was stirred at room temperature for 16 hours. After the reaction was completed, the reaction mixture was filtered through a pad of Celite® and washed with methanol then concentrated under reduced pressure. The residue was purified by reverse phase liquid chromatography (5-25-100% of methanol in Dl water without modifier) to yield the title compound as white solid (>95%). LC/MS [(M-6Boc)+6H)]/6 469.2. Example 1 -32
Figure imgf000251_0001
Step a. Coupling of Cyclohexane Dicarboxylic Acid with L-nor-Leucine Methyl Ester
A solution of HATU (4.87 g, 12.82 mmol) in DMF (20.5 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of (cis-cyclohexane-1 ,2-dicarboxylic acid (1 .00 g, 5.82 mmol), L-Norleu- OMe-hydrochloride (2.33 g, 12.82 mmol), and diisopropylethylamine (4.53 g, 35.02 mmol) in DMF (8.3 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-50% of acetonitrile in Dl water with 0.1 % TFA as modifier) to yield the title compound (1 .29 g, 52%). MS [M+H] 428.35.
Step b. Hydrolysis of the Methyl Esters
To a solution of INT-32 in THF:MeOH:H20 (1 :1 :2, 30 mL) was added LiOH (217.29 mg, 9.07 mmol). The reaction mixture was stirred at room temperature for 3 hours. After the reaction was completed. The reaction mixture was quenched with acetic acid to pH4 then concentrated under reduced presssure. The residue was purified by reverse phase liquid chromatography (Isco, 0-50% ACN/H20 with 0.1 % TFA; P came at 38%) to yield the title compound as white solid (1 .22 g, 100%). MS [M+H] 399.2.
Example 129. Synthesis of INT-33
Figure imgf000251_0002
HATU (644 mg, 1 .69 mmol), in DMF (2 ml_) was added, dropwise over 10 minutes, to a stirring mixture of INT-8 (2.65 g, 1 .69 mmol), INT-30 (400 mg, 0.77 mmol), and triethylamine (466 mg, 4.62 mmol) in DMF (6 mL) and the reaction was stirred for an additional 30 minutes. Acetic acid (2 ml_) was added, followed by 5% Pd/C (400 mg) and the mixture was stirred under an atmosphere of hydrogen for 12 hours. The mixture was filtered through celite and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 35 % to 95% acetonitrile and water using 0.1 % TFA modifier to give INT-33 after lyophilization. Yield: 35%. MS [(M-2Boc+3H)/3]+ =1092.8.
Example 130. Preparation of INT-34
Figure imgf000252_0001
4-Biphenylboronic acid (4.1 g, 20.8 mmol), 5-bromo-1 ,3-benzenedicarboxylic acid (3.50 g, 19.9 mmol), sodium carbonate (5.96 g, 56.8 mmol), and tetrakis(triphenylphosphine)palladium(0) (1 .53 g, 1 .31 mmol) were stirred in a 1 /9 mixture of Dl water and ethanol (200 mL) at reflux for 2 hours under an atmosphere of nitrogen. The reaction mixture was cooled, diluted with DCM, and neutralized with 1 N aqueous HCI. The aqueous layer was extracted into DCM, dried, filtered and concentrated. The product was crystallized from hexanes and ethyl acetate. Yield: 83.9%. MS [M+H]+ = 31 9.1 .
Example 131. Preparation of INT-35
Figure imgf000252_0002
INT-35
The title compound was prepared from L-norleucine methyl ester hydrochloride and 1 ,3- benzenedicarboxylic acid in an analogous fashion as described for procedure to prepare INT-32. Yield: 72 %, 2 steps. MS [M+H]+ = 393.2. Example 132. Preparation of INT-36
Figure imgf000253_0001
HATU (150 mg, 0,40 mmol), in DMF (1 mL) was added, dropwise over 10 minutes, to a stirring mixture of INT-13 (450 mg, 0.36 mmol), CBZ-protected-2S-amino-decanoic acid (1 50 mg, 046 mmol), and triethylamine (120 mg, 1 .18 mmol) in DMF (4 mL) and the reaction was stirred for an additional 30 minutes. The mixture was applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 35 % to 95% acetonitrile and water using 0.1 % TFA modifier. The pure fractions were concentrated and taken up in methanol (150 mL), 5% Pd/C (100 mg) was added and the mixture was stirred under an atmosphere of hydrogen for 3 hours. The mixture was filtered through celite and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 35 % to 95% acetonitrile and water using 0.1 % TFA modifier to give INT-36 after lyophilization. Yield: 47%. LC/MS [(M-Boc+2H)/2]+ =660.4.
Example 133. Preparation of INT-37
Figure imgf000253_0002
In a procedure analogous to that described for INT-15, INT-37 was prepared using (S)-2- aminooctanoic acid in place of Z-Norleu-OH to obtain the title compound. LCMS: [(M+H]/2 = 779.5, [(M- 2Boc)+2H]/2 =729.5, [(M-3Boc)+2H]/2 =679.5
Example 134: Synthesis of Compound 94
Figure imgf000253_0003
Step a. Synthesis of deca-Boc-(Compound 94)
A solution of deca-Boc-(Compound 1 1 ) (0.750 g, 0.214 mmol, Example 22), maleimide-Peg-8- acid (0.139 g, 0.235 mmol), DIEA (0.123 mL, 0.706 mmol), and DMF (5 mL), was treated with HATU (0.089 g, 0.235 mmol), then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.856 g, 98%.
Step b. Deprotection to Compound 94
Deca-Boc-(Compound 94) (0.856 g, 0.210 mmol), was suspended in DCM (3 mL) and treated with TFA (3 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.518 g, 58%. MS: (M+3H)/3 = 1 027.3, (M+4H)/4 =770.5, , (M+5H)/5 =616.7
Example 135: Synthes
Figure imgf000254_0001
Step a. Synthesis of deca-Boc-(Compound 95)
A solution of deca-Boc-(Compound 1 1 ) (0.125 g, 0.036 mmol, Example 22, step d), hexanoic acid (0.0049 mL, 0.039 mmol), DIEA(0.020 mL, 0.1 1 8 mmol), and DMF (1 mL), was treated with HATU (0.015 g, 0.039 mmol), then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 0.1 14 g, 89% after lyophilization.
Step b. Deprotection to Compound 95
Deca-Boc-(Compound 95) (0.1 14 g, 0.032 mmol), was suspended in DCM (1 mL) and treated with TFA (1 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% acetonitrile and water, using formic acid (0.1 %) as the modifier. Yield 0.077 g, 79%. MS: (M+3H)/3 = 868.5, (M+4H)/4 =651 .6, (M+5H)/5 =521 .5 Example 136. Synthesis of Compound 96 and Compound 97
Figure imgf000255_0001
Step a. Synthesis of ethyl N-({(8S,11S,14S,17R)-8-{[(3S,6S,9S,12S,15R,18S,21 S)-15-benzyl- 6,9,18-tris{2-[(tert-butoxycarbonyl)amino]ethyl}-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)- 2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]carbamoyl}-14-{2-[(tert- butoxycarbonyl)amino]ethyl}-11-[(1 R)-1-hydroxyethyl]-2,2-dimethyl-4,10,13,16-tetraoxo-3-oxa- 5,9,12,15-tetraazatricosan-17-yl}carbamoyl)glycinate
Ethyl isocyanoacetate (60 mg, 0.5 mmol) was added into the solution of INT-10 (340 mg, 0.2mmol) and triethylamine (0.14mmol, 1 mmol) in 5 mL DMF at room temperature, the reaction was stirred for overnight, then concentrated and the residue was purified by reversed phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 260 mg, 75%. MS: [(M-2Boc)+2H]/2 = 817.5, [(M- 3Boc)+2H]/2 =767.5.
Step b. Synthesis of N-({(8S,11S,14S,17R)-8-{[(3S,6S,9S,12S,15R,18S,21 S)-15-benzyl-6,9,18- tris{2-[(tert-butoxycarbonyl)amino]ethyl}-3-[(1 R)-1-hydroxyethyl]-12-(2-methylpropyl)- 2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosan-21-yl]carbamoyl}-14-{2-[(tert- butoxycarbonyl)amino]ethyl}-11-[(1 R)-1-hydroxyethyl]-2,2-dimethyl-4,10,13,16-tetraoxo-3-oxa- 5,9,12,15-tetraazatricosan-17-yl}carbamoyl)glycine
A solution of ethyl N-({(8S,1 1 S,14S,17R)-8-{[(3S,6S,9S,12S,15R,18S.21 S)-15-benzyl-6,9,18- tris{2-[(tert-butoxycarbonyl)amino]ethyl}-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2, 5,8, 1 1 , 14,17,20- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosan-21 -yl]carbamoyl}-14-{2-[(tert- butoxycarbonyl)amino]ethyl}-1 1 -[(1 R)-1 -hydroxyethyl]-2,2-dimethyl-4,10,13,1 6-tetraoxo-3-oxa-5,9,12,15- tetraazatricosan-17-yl}carbamoyl)glycinate (0.20 g, 0.12 mmol), in methanol (1 mL) was treated with a solution of lithium hydroxide (0.024 g, 1 .0 mmol), in water (1 mL) and THF (1 mL), then stirred at room temperature for 30 minutes. The reaction was quenched by drops of acetic acid. The desired product was isolated directly by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield 0.150 g, 75%.
Step c. Synthesis of (2S,5S,8S,11S,18S,21S,24S,27S)-2,8,21 ,27-tetrakis(2-aminoethyl)- 11 ,18-dihexyl-5,24-bis[(1 R)-1-hydroxyethyl]-4,7,10,13,16,19,22,25-octaoxo-N~1 ~,N~28~- bis(3S,6S,9S,12S,15R,18S,21 S)[6,9,18-tris(2-am inoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]- 3,6,9, 12, 14,17,20,23,26-nonaazaoctacosane-1 ,28-diamide (Compound 96 and Compound 97)
To the solution of N-({(8S,1 1 S,14S,17R)-8-{[(3S,6S,9S,12S,15R,18S.21 S)-1 5-benzyl-6,9,18- tris{2-[(tert-butoxycarbonyl)amino]ethyl}-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2, 5,8, 1 1 , 14,17,20- heptaoxo-1 ,4,7,10,13,1 6,19-heptaazacyclotricosan-21 -yl]carbamoyl}-14-{2-[(tert- butoxycarbonyl)amino]ethyl}-1 1 -[(1 R)-1 -hydroxyethyl]-2,2-dimethyl-4,10,13,1 6-tetraoxo-3-oxa-5,9,12,15- tetraazatricosan-17-yl}carbamoyl)glycine (85 mg, 0.05 mmol), triethylamine (0.15 mL, 1 mmol) and INT-10 (170 mg, 0.1 mmol) in 5 mL DMF was added HATU(40 mg, 0.1 mmol) in 1 mL DMF by syringe pump over 1 hour. Then the resulting solution was concentrated and purified by reverse phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield of product, 130 mg, 87% yield.
Step d. Removal of the Boc Groups
Per-Boc-(Compound 96) from previous step was treated in 2 mL DCM and 2 mL TFA at room temperature, the solution was stirred 1 0 min, then concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using formic acid as the modifier. Yield 85 mg, 75% yield. MS: [(M+3H)/3]+ = 831 .2, [(M+4H)/4]+ =623.6, [(M+5H)/5]+=499.1 , [(M+6H)/6]+=416.1 . A small amount of an isomer was also obtained (Compound 97). Ex
Figure imgf000257_0001
Step a. Synthesis of dimethyl (3R,4R)-1-benzylpyrrolidine-3,4-dicarboxylate
To a solution of dimethyl fumarate (1 .44 g, 10 mmol) in acetonitrile (40 mL) was added N- (methoxymethyl)-N-(trimethylsilylmethyl)benzylamine (2.37 g, 1 0 mmol) followed by lithium fluoride (410 mg, 15.8 mmol). The mixture was stirred for 1 .5 days, then concentrated by rotary evaporation. The residue was purified by RPLC (150 g, 0 to 35 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 3.0 g, 76.7 %. MS: [M+H]+ = 278.
Step b. Synthesis of (3R,4R)-1-benzylpyrrolidine-3,4-dicarboxylic acid
The step-a product (3 g, 7.67 mmol) was dissolved in 1 :1 mixture of MeOH/THF (16 mL). The solution was cooled in an ice-water bath and added with a solution of LiOH (384 mg, 15.3 mmol) in water (10 mL). The mixture was stirred overnight, then added with an additional amount of LiOH (300 mg) in water (3 mL). The reaction was continued at ~ 5-10 °C for 6 hours. The pH was adjusted to ~ 6 by a solution of 4N HCI in dioxane (3 mL). The organic solvent was removed by rotary evaporation, and the aqueous solution was purified by RPLC (150 g, 0 to 50 % acetonitrile and water). Yield 1 .57 g, 82 %. MS: [M+H]+ = 250. Step c. Synthesis of dimethyl (2S,2'S)-2,2'-{[(3R,4R)-1-benzylpyrrolidine-3,4- diyl]bis(carbonylazanediyl)}dioctanoate
A mixture of step-b product (290 mg, 1 .163 mmol) and tert-butyl (2S)-2-aminooctanoate HCI (654.7 mg, 2.6 mmol) was dissolved in anhydrous DMF (2 mL) and DIPEA (650 mg, 5 mmol). The resulting mixture was added with a HATU solution (988 mg, 2.6 mmol) in DMF (4 mL) via syringe pump at a rate of 4 mL/hr. After the addition, the reaction was directly purified by RPLC (150 g, 10 to 70 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 226.8 mg of the product that is the more polar isomer, 34.8 %. MS: [M+H]+ = 644. The stereochemistry of trans-pyrrolidine dicarboxylate was arbitrarily assigned but corresponds to the more polar isomer. This material was used in subsequent reactions
Step d. Hydrolysis of dimethyl (2S,2'S)-2,2'-{[(3R,4R)-1-benzylpyrrolidine-3,4- diyl]bis(carbonylazanediyl)}dioctanoate
The step-c product (226.8 mg, 0.352 mmol) was dissolved in TFA (~ 3 mL) and thioanisole (0.3 mL). After the mixture was stirred for 1 day, it was concentrated by rotary evaporation and purified by RPLC (100 g, 10 to 60 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 170.3 mg, 91 %. MS: [M+H]+ = 532.
Step e. Synthesis of Bis-(Thr-Dab)-intermediate
A mixture of step-d product (53.2 mg, 0.1 mmol) and (YNH2)Dab-Thr-C02Me (70 mg, 0.21 mmol) was dissolved in anhydrous DMF (0.5 mL) and DIPEA (65 mg, 0.5 mmol). After cooled in an ice-water bath, the solution was drop-wise added with a solution of HATU (79.8 mg, 0.21 mmol) in DMF (0.5 mL) at a rate of 1 mL/hr. After the addition, the mixture was stirred for 30 more minutes and directly purified by RPLC (100 g, 5 to 80 % acetonitrile and water). Yield 87.7 mg, 75.5 %. MS: [(M-Boc+2H)/2]+ = 531 .
Step f. Hydrolysis of Bis-(Thr-Dab)-intermediate
Step-e product (87.7 mg, 0.0755 mmol) was dissolved in MeOH (~ 1 mL) and THF (4 mL). The solution was cooled in an ice-water bath and slowly added with a solution of LiOH (12.5 mg, 0.5 mmol) in water (1 .5 mL) over 15 minutes. The reaction was stirred for 2 hours, then purified by HPLC (5 to 62 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 72.1 mg, 76.5 %. MS: [(M-Boc+2H)/2]+ = 518.
Step g. Synthesis of Asn-lnt-1
A mixture of Z-L-Asn-OH (87.9 mg, 0.33 mmol) and HOBT hydrate (70.7 mg, 0.463 mmol) was dissolved in anhydrous DMF (1 mL) and cooled in an ice-water bath. EDC-HCI (76.8 mg, 0.4 mmol) was added, and the resulting mixture was stirred for 15 minutes. It was then added with a solution of lnt-1 (31 9 mg, 0.3 mmol) in anhydrous DMF (1 mL) and DIPEA (130 mg, 1 mmol). The reaction mixture was stirred for 1 hour and directly purified by C18 RPLC (50 g, 10 to 90 % MeOH and water). The collected fractions were concentrated to a white solid (LCMS: [(M-2Boc)/2]+ = 555). The material was re-dissolved in MeOH (~ 10 mL), and the solution was added with Pd/C. The resulting mixture was stirred under hydrogen for 4 hours. Pd/C was filtered off, and the filtrate was concentrated by rotary evaporation and further dried in high vacuum to afford the title product as a white solid (185.2 mg, 52.5 %). MS: [(M+2H)/2]+ = 538. Step h. Synthesis of octa-Boc-(Compound 98) precursor
A mixture of the step-f product (72.1 mg, 0.0578 mmol) and step-g product (1 65 mg, 0.14 mmol) was dissolved in anhydrous DMF (1 mL) and DIPEA (78 mg, 0.6 mmol). After cooled in an ice-water bath, the solution was drop-wise added with a solution of HATU (53.2 mg, 0.14 mmol) in DMF (0.5 mL) at a rate of 1 mL/hr. After the addition, the mixture was stirred for 30 more minutes and directly purified by RPLC (100 g, 20 to 100 % acetonitrile and water, using 0.1 % formic acid as modifier). Yield 56.8 mg, 28.5 %. MS: [(M-2Boc+3H)/3]+ = 1084.4, [(M-3Boc+3H)/3]+ = 1 051 , [(M-4Boc+3H)/3]+ = 1076.
Step i. Removal of the Boc groups
The step-h product (56.8 mg, 0.0165 mmol) was dissolved in TFA (~ 1 mL). The solution was stirred for 15 minutes, then directly purified by HPLC (5 to 35 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 24.4 mg, 39 %. MS: [(M+4H)/4]+ = 663, [(M+5H)/5]+ = 531 , [(M+6H)/6]+ = 442,
[(M+7H)/7]+ = 379.
Example
Figure imgf000259_0001
Synthesis of (7S,10R,13R,16R)-18-amino-3-[(4S,7S,10S,13S)-15-amino-7-(2-aminoethyl)-4- hexyl-10-[(1 R)-1-hydroxyethyl]-2,5,8,11-tetraoxo-13-{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1-hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo- 1 ,4,7, 10, 13,16,19-heptaazacyclotricosan-21-yl]carbamoyl}-3,6,9,12-tetraazapentadecan-1-yl]-10-(2- aminoethyl)-7-hexyl-13-[(1S)-1-hydroxyethyl]-5,8,11 ,14-tetraoxo-16-{[(3R,6R,9R,12R,15S,18R,21 R)- 6,9,18-tris(2-am inoethyl)-15-benzyl-3-[(1 S)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20- heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21-yl]carbamoyl}-3,6,9,12,15- pentaazaoctadecan-1-oic acid (Compound 99)
The products were obtained using a procedure analogous to the preparation of Compound 1 1 0. MS: [(M+3H)/3]+ = 855.2, [(M+4H)/4]+ =641 .6, [(M+5H)/5]+ =513.5 , [(M+6H)/6]+ =428.1 .
(2R,5R,8R,1 1 S)-14-{4-[(2S)-1 -{[(2S)-4-amino-1 -{[(2S,3R)-1 -{[(2S)-4-amino-1 -oxo-1 - {[(3S,6S,9S,12S,15R,18S.21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]amino}butan-2- yl]amino}-3-hydroxy-1 -oxobutan-2-yl]amino}-1 -oxobutan-2-yl]amino}-1 -oxooctan-2-yl]-3,5-dioxopiperazin- 1 -yl}-2,8-bis(2-aminoethyl)-1 1 -hexyl-5-[(1 S)-1 -hydroxyethyl]-4,7,1 0,13-tetraoxo-N- [(3R,6R,9R,12R,15S,18R,21 R)-6,9,1 8-tris(2-aminoethyl)-15-benzyl-3-[(1 S)-1 -hydroxyethyl]-12-(2- methylpropyl)-2, 5,8,1 1 ,14,1 7,20-heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-3,6,9,12- tetraazatetradecan-1 -amide (Compound 1 00) was obtained as a by-product in the reaction. MS:
[(M+3H)/3]+ = 849.2, [(M+4H)/4]+ =637.1 , [(M+5H)/5]+ =509.9 , [(M+6H)/6]+ =425.1 .
Example 1
Figure imgf000260_0001
HATU (43 mg, 0.1 1 mmol), in DMF (1 ml_) was added, dropwise over 20 minutes, to a stirring mixture of INT-8 (179, mg, 0.1 1 mmol), INT-26 (20 mg, 0.052 mmol), and triethylamine (32 mg, 0.31 mmol) in DMF (2 ml_). The reaction was stirred for 30 additional minutes and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 30% to 100% methanol and water using 0.1 % TFA modifier. The pure fractions were concentrated to afford the product as a white solid. Yield: 52%, 2 steps. LC/MS [(M+6H)/6]+ = 413.4 , LC/MS [(M+5H)/5]+ = 495.9 , LC/MS [(M+4H)/4]+ = 619.6 . Example 140: Synthesis of Compound 103
Figure imgf000261_0001
Step a. Synthesis of deca-Boc-Cbz- precursor
A solution of deca-Boc-(Compound 106) (0.300 g, 0.085 mmol, Example 143), Cbz-Peg-8-acid (0.049 g, 0.085 mmol), DIEA(0.049 mL, 0.085 mmol), and DMF (5 mL), was treated with HATU (0.036 g, 0.093 mmol), then stirred for 30 minutes. The desired product was taken on to the next step without purification.
Step b. Synthesis of deca-Boc-amino precursor
Crude deca-Boc-Cbz-precursor in DMF was treated with 5% Pd/C (0.35g), vacuum flushed with hydrogen, and stirred under a hydrogen atmosphere for 3h. The solution was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water. Yield for two steps 0.315g, 93% yield. MS: [(M-2Boc)+2H]/2 = 1252.4
Step c. Synthesis of bissulfone deca-Boc precursor
A solution of deca-Boc-amino precursor (0.315 g, 0.080 mmol), bis-sulfone acid (0.044 g, 0.088 mmol), N-methylmorpholine (0.019 mL, 0.175 mmol), and DMF (5 mL), was treated with HATU (0.033 g, 0.088 mmol), then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 0.243 g, 69%. Step d. Deprotection to Compound 103
Bis-sulfone deca-Boc precursor (0.216 g, 0.049 mmol), was suspended in DCM (2 mL) and treated with TFA (2 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% acetonitrile and water, using TFA (0.1 %) as the modifier. Yield 0.226 g, 1 01 %. MS: (M+3H)/3 = 1 146.3, (M+4H)/4 =860.0, (M+5H)/5 =688.2
Example 141 : Synthesis of Compound 104
Figure imgf000262_0001
Step a. Synthesis of Cbz-PEG-PMB
A solution of lnt-10 (0.700 g, 0.41 1 mmol), Cbz-Peg-8-acid (0.260 g, 0.452 mmol), DIEA (0.235 mL, 1 .355 mmol), and DMF (10 mL), was treated with HATU (0.172 g, 0.452 mmol), then stirred for 30 minutes. The desired product was taken on to the next step without purification.
Step b. Synthesis of amino-PEG-PMB
Crude Cbz-PEG-PMB in DMF was treated with 5% Pd/C (0.45g), vacuum flushed with hydrogen, and stirred under a hydrogen atmosphere for 3h. The solution was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, no modifier. Yield for two steps 0.746g, 88% yield. MS: (M+2H)/2 = 1 064.6
Step c. Synthesis of Cbz-amino-PEG-PMB dimer
A solution of amino-PEG-PMB (0.746 g, 0.350 mmol), Cbz-imino-diacetic acid (0.046 g, 0.171 mmol), DIEA(0.197 mL, 1 .13 mmol), and DMF (5 mL), was treated with a solution of HATU (0.133 g, 0.350 mmol) in DMF (2 mL) over 30 minutes, then stirred for 30 minutes. The desired product was taken on to the next step without purification.
Step d. Synthesis of amino-PEG-PMB dimer
Crude Cbz-amino-PEG-PMB dimer in DMF was treated with 5% Pd/C (0.35g), vacuum flushed with hydrogen, and stirred under a hydrogen atmosphere for 3h. The solution was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, no modifier. Yield for two steps 0.465g, 62%. MS: [(M-2Boc) +3H]/3 = 1384.8, [(M-3Boc)+3H]/3 = 1351 .5
Step e. Synthesis of deca-Boc-(Compound 104)
A solution of amino-PEG-PMB dimer (0.315g, 0.072 mmol), bis-sulfone acid (0.072 g,
0.145mmol), N-methylmorpholine (0.048 mL, 0.434 mmol), and DMF (5 mL), was treated with HATU (0.055 g, 0.145 mmol), then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.325 g, 93%
Step f. Deprotection to Compound 104
Deca-Boc-(Compound 104) (0.325 g, 0.067 mmol), was suspended in DCM (4 mL) and treated with TFA (4 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.099 g, 30%. MS: (M+3H)/3 = 1278.7, (M+4H)/4 =959.3, (M+5H)/5 =767.6.
Figure imgf000264_0001
Step a. Preparation of the azido dicarboxylic acid
EDC (135 mg. 0.70 mmol) was added to INT-28 (polar isomer) (265 mg, 0.64 mmol), Azido- PEG4-Carboxy (about 1 eq) and triethylamine (85 mg, 0.83 mmol) in DMF (3 mL) and the mixture was stirred for 3 hours then applied directly to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 5% to 95% acetonitrile and water using 0.1 % TFA modifier The pure fractions were concentrated and then hydrolyzed by stirring in a 1 /1 /2 mixture of
methanol/THF/DI water containing LiOH (46 mg, 1 .90 mmol) for 30 minutes. The mixture was adjusted to pH 5 with acetic acid then concentrated and applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 5% to 95% acetonitrile and water using 0.1 % TFA modifier. The pure fractions were concentrated to afford the product as an oil. Yield: 54%, 2 steps. LC/MS [M+H]+ = 659.4
Step b. Coupling to INT-8
The title compound was prepared from INT-8 and the product of Step a. in a similar fashion as described by the procedure for Compound 102. LC/MS [(M+3H)/3]+ = 91 7.2. Example 143. Synthesis of Compound 106
Figure imgf000265_0001
A solution of HATU (61 .3 mg, 0.16 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-23 (34.5 mg, 0.07 mmol), INT-8 (240.0 mg, 0.15 mmol) and diisopropylethylamine (63.8 mg, 0.49 mmol) in DMF (1 .1 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (30-100% of methanol in Dl water with 0.1 % TFA as modifier: 30 minute gradient) to yield the Boc-protected intermediate. The Boc- protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (5-40% acetonitrile and water with 0.1 % TFA as modifier: 30 minute gradient) to yield the title compound (142.4 mg, 54%). LCMS (M+3H)/3 826.2, (M+4H)/4 620.2, (M+5H)/5 496.2, (M+6H)/6 413.7.
Figure imgf000265_0002
A solution of HATU (44.5 mg, 0.12 mmol) in DMF (0.5 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-26 (30.0 mg, 0.078 mmol), INT-7 (358.12 mg, 0.23mmol) and diisopropylethylamine (25.7 mg, 0.20 mmol) in DMF (3.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-25-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid
chromatography (0-30% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (1 1 .4 mg, 6%). LC/MS (M+5H)/5 482.30 and (M+6H)/6 401 .9. Example 145. Synthesis of Compound 108
Figure imgf000266_0001
A solution of HATU (71 .36 mg, 0.19 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-23 (37.5 mg, 0.077 mmol), INT-7 (255.19 mg, 0.17 mmol) and diisopropylethylamine (59.8 mg, 0.46 mmol) in DMF (1 .3 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-30-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (2:1 , 3 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid
chromatography (5-50% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (150.7 mg, 41 %). LC/MS (M+4H)/4 603.0, (M+5H)/5 482.60 and (M+6H)/6 402.4.
Figure imgf000266_0002
Step a. Synthesis of (S)-methyl 2-aminooctanoate
A stirring mixture of (2S)-2-aminooctanoic acid (1 .592 g, 10.0 mmol) in methanol (25 mL) and sulfuric acid (1 .0 mL, 98%) was heated at 75 in a sealed tube overnight. The reaction mixture was then added dropwise to a saturated solution of sodium bicarbonate (50 mL) under vigorous stirring. Upon gas evolution ceased (bubbler monitoring), the mixture was reduced in volume (about 25 mL) by rotatory evaporation. This concentrate was extracted with ethyl acetate (3 x 30 mL. The combined organics were dried with brine and solid magnesium sulfate. After filtration through a short Celite pad, the volatiles were evaporated. The residue was taken up in a minimum amount of hexanes (about 5 mL) and filtered through a 0.5 μΜ disposable filter in order to get rid of the fine insoluble particulate. Yield 1 .62 g, 93% (92+% purity, as confirmed per 1 H-NMR and LC-MS analysis). MS: (M+H)+ = 174.1 ; 1 H NMR (DMSO-afe) δ: 3.60 (s, 3H), 3.27 (dd, J = 7.3, 5.7 Hz, 1 H), 1 .70 (br s, 2H), 1 .60 - 1 .13 (m, 10H), 0.93 - 0.79 (m, 3H).
Step b. Synthesis of 1 ,3-Phenylene ditriflate
To a 0°C stirring solution of resorcinol (2.20 g, 20.0 mmol) and 1 ,1 ,1 -trifluoro-N-phenyl-N- (trifluoromethanesulfonyl)methanesulfonamide (14.65 g, 41 .0 mmol) in N,N-dimethylformamide (20 mL) it was added triethylamine (5.85 mL, 42 mmol) and 4-dimethylaminopyridine (0.073 g, 0.600 mmol). The temperature was raised to ambient after 10 minutes and stirring was continued until complete disappearance of resorcinol by LC-MS analysis. All the volatiles were removed per rotatory evaporation. The residue was taken up in ethyl acetate and washed with a saturated solution of ammonium chloride, then brine and finally treated with solid sodium sulfate. Upon filtration, all the volatiles were evaporated. The desired product was isolated by normal phase liquid chromatography using an Isco CombiFlash liquid chromatograph eluted with 1 % to 20% hexanes and ethyl acetate. Yield 6.82 g, 91 %. 1 H NMR (DMSO-afe) δ: 8.01 (t, J = 2.4 Hz, 1 H), 7.84 - 7.68 (m, 3H).
Step c. Synthesis of N,N-1 ,3-Phenylene bis-(methyl-2-aminooctanoate)
Under nitrogen, in a round bottom flask equipped with a stir bar and rubber septum was charged sequentially with (S)-methyl 2-aminooctanoate (0.550 g, 3.175 mmol), 1 ,3-phenylene ditriflate (0.594 g, 1 .587 mmol), the palladium catalyst listed in the Scheme above (see: Org. Lett. 2016, 18, 4128-4131 ) (0.135 g, 0.159 mmol), and cesium carbonate (6.202 g, 9.524 mmol). The reaction test tube was capped and then evacuated and backfilled with argon by piercing with a needle attached to a Schlenk line (this process was repeated a total of three times). 2-methyltetrahydrofuran was added and the reaction vessel was placed in an oil bath that had been preheated to 50 °C. The reaction mixture was stirred and heated at 50 °C until full conversion of the starting material per HPLC analysis. The reaction mixture was allowed to cool over 20 min to rt. The cooled product mixture was diluted with dichloromethane, filtered through Celite and concentrated to dryness. The desired product was isolated by normal phase liquid
chromatography using an Isco CombiFlash liquid chromatograph eluted with 1 % to 50% hexanes and ethyl acetate. 1 H NMR analysis of the desired fractions showed racemization of the chiral centers, and this isomeric mixture was used in the next step. Yield 0.225 g, 41 %. MS: (M+H)+ = 421 .3.
Step d. Synthesis of N,N-1 ,3-Phenylene bis-(2-aminooctanoic acid)
To a stirring solution of N,N-1 ,3-Phenylene bis-(methyl-2-aminooctanoate) (0.020 g, 0.048 mmol) in tetrahydrofuran (2.0 mL) and water (2.0 mL) it was added lithium hydroxide (0.024 g, 0.480 mmol) and stirring was continued overnight. The reaction was concentrated to about half of its volume per rotatory evaporation. Ethyl acetate (10 mL) was added and subsequently a 1 .0 M solution of sulfuric acid (1 .0 mL), while the mixture was stirred vigorously for 10 minutes. The organic phase was separated and then washed with water (10 mL) and brine (10 mL). The organic layer was then dried with sodium sulfate, filtered, and concentrated to dryness. Yield was considered quantitative and the material used in the next step without further purification. MS: (M-H)- = 391 .2. Step e. Synthesis of deca-Boc-(Compound 109)
A stirring solution of INT-8 (0.149 g, 0.095 mmol), N,N-1 ,3-Phenylene bis-(2-aminooctanoic acid) (0.018 g, 0.048 mmol), and 2,4,6-trimethylpyridine (0.026 mL, 0.200 mmol) in DMF (1 mL), was treated with a solution of HATU (0.038 g, 0.100 mmol) in DMF (1 mL), dropwise over 30 minutes. After 1 .5 hour, all the volatiles were evaporated. The desired product was isolated by reversed phase liquid
chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 50% to 1 00% methanol and water, using no modifier. Yield 0.089 g, 54% yield. MS: [(M-3Boc)+3H]/3 = 796.4
Step f. Synthesis Compound 109
A solution of deca-Boc-(Compound 109) (0.089 g, 0.029 mmol), dissolved in DCM (4 mL), was treated with TFA (2 mL), while stirring at room temperature. After 30 minutes, all the volatiles were evaporated per vacuum techniques. The desired product was isolated as a dodeca-TFA salt by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% methanol and water, using TFA as the modifier. Yield 0.051 g, 61 % yield. MS: (M+3H)/3 = 828.3, (M+4H)/4 = 621 .5, (M+5H)/5 = 497.3.
Figure imgf000268_0001
Step a. Coupling of INT-10
trans-Aziridine-2,3-dicarboxylic acid (13 mg, 0.1 mmol) , triethylamine (0.15 mL, 1 mmol) and INT-10 (340 mg, 0.2mmol) in 10 mL DMF was added HATU (80 mg, 0.2mmol) in 1 mL DMF by syringe pump over 1 hour. Then the resulted solution was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield of product, 260 mg, 74% yield.
Step b. Removal of Boc Groups to give (2R,3R)-N~2~,N~3~-bis[(2S)-1-{[(2S)-4-amino-1- {[(2S,3R)-1-{[(2S)-4-amino-1-oxo-1-{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15- benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21-yl]amino}butan-2-yl]amino}-3-hydroxy-1-oxobutan-2-yl]amino}-1- oxobutan-2-yl]amino}-1-oxooctan-2-yl]aziridine-2,3-dicarboxamide
The product from Step a. was treated in 2 mL DCM and 2 mL TFA at room temperature, the solution was stirred 10 min, then concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 % to 100% acetonitrile and water, using formic acid as the modifier. Yield 0.120g, 65% yield. MS: [(M+4H)/4]+=626.6, [(M+5H)/5]+=501 .5, [(M+6H)/6]+=418.1 ..
Figure imgf000269_0001
Compound 1 05 (30 mg, 0.01 1 mmol) and DBCO-Peg4-Carboxy Rhodanine 1 1 0 (from Click Chemistry Tools) (1 1 mg, 0.12 mmol) were stirred together in ethanol (5 mL) for 12 hours. The mixture was applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 5% to 95% acetonitrile and water using 0.1 % TFA modifier. Yield: 58%. LC/MS [(M+5H)/5]+ = 726.6.
Example 149. Synthesis of Compound 112
Figure imgf000270_0001
EDC (12 mg, 0.062 mmol) was added to a stirring mixture of INT-33 (76 mg, 0.021 mmol), 2H-1 - Benzopyran-4-acetic acid, 7-(dimethylamino)-2-oxo- (26 mg, 0.10 mmol), and triethylamine (4.2 mg, 0.040 mmol) and the mixture was stirred for 4 hours. The mixture was applied to reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 35 % to 95% acetonitrile and water using 0.1 % TFA modifier. The pure fractions were lyophilized and then stirred in a 1/1 mixture of DCM/TFA for 30 minutes. The solvent was removed by rotovap and the product was purified by reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0 % to 75% acetonitrile and water using 0.1 % TFA modifier. The pure fractions were lyophilized to afford the product as a yellow solid. Yield: 36%. LC/MS [(M+3H)/3]+ =902.2.
Figure imgf000270_0002
Figure imgf000271_0001
Step a. Synthesis of Cbz-(PEG4)2-PMB dimer
A solution of lnt-10 (0.500 g, 0.291 mmol), Cbz-(PEG4)2-acid (0.089 g, 0.138 mmol), DIEA (0.167 mL, 0.960 mmol), and DMF (10 mL), was treated with a solution of HATU (0.172 g, 0.452 mmol) in DMF over 30 minutes. After stirring for 30 minutes the crude product was taken on to the next step without purification.
Step b. Synthesis of amino-(PEG4)2-PMB dimer
The crude Cbz-(PEG4)2-PMB dimer in DMF from Step a, was treated with 5% Pd/C (0.50g), vacuum flushed with hydrogen, and stirred under a hydrogen atmosphere for 3h. The solution was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, no modifier. Yield for two steps 0.212g, 37% yield. MS: [(M-3Boc) +4H]/4 = 897.3, [(M-4Boc)+4H]/4 = 872.3, [(M- 5Boc)+4H]/4 = 847.3
Step c. Synthesis of deca-Boc-(Compound 113)
A solution of amino-(PEG4)2-PMB dimer (0.212g, 0.055 mmol), bis-sulfone acid (0.033 g, 0.065mmol), N-methylmorpholine (0.022 mL, 0.196 mmol), and DMF (3 mL), was treated with HATU (0.025 g, 0.065 mmol), then stirred for 30 minutes. The crude product was stripped of DMF and taken forward without purification.
Step d. Deprotection to Compound 113
Crude deca-Boc-(Compound 1 13) was dissolved in DCM(10 mL), treated with TFA(10 mL) for 5 minutes, concentrated to an oil, then purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.099 g, 40%. MS: (M+3H)/3 = 1 123.3, (M+4H)/4 =842.7, (M+5H)/5 =674.4
Figure imgf000272_0001
Compound 1 14 was prepared from INT-33 and Boc-protected -3-amino propanoic acid as described in procedure (Compound 1 12).Yield: 36%. MS [(M+3H)/3]+ = 849.6.
Figure imgf000272_0002
A solution of HATU (6.33 mg, 0.017 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-31 (52.0 mg, 0.015 mmol), 3-[(tert- butoxy)carbonylamino]propanoic acid (2.7 mg, 0.014 mmol) and diisopropylethylamine (5.4 mg, 0.042 mmol) in DMF (1 .0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-30-1 00% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (23.5 mg, 19%). MS (M+4H)/4 620.5, (M+5H)/5 496.8 and (M+6H)/6 414.2.
Figure imgf000273_0001
A solution of HATU (20.65 mg, 0.054 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-31 (154.3 mg, 0.015 mmol), 3-[(tert- butoxy)carbonylamino]cyclobutanecarboxylic acid (1 1 .69 mg, 0.054 mmol) and diisopropylethylamine (17.5 mg, 0.14 mmol) in DMF (2.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-30-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 2 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (79.0 mg, 47%). MS (M+4H)/4 627.3, (M+5H)/5 502.2 and (M+6H)/6 418.6.
Example 154. Synthesis of Compound 117
Figure imgf000273_0002
A solution of HATU (5.5 mg, 0.014 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-31 (50.2 mg, 0.014 mmol), 2-[(tert-butoxy)carbonylamino]acetic acid (2.1 mg, 0.012 mmol) and diisopropylethylamine (4.64 mg, 0.036 mmol) in DMF (1 .0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-30-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc- protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (6.3 mg, 14%). MS (M+4H)/4 634.2, (M+5H)/5 507.5 and (M+6H)/6 423.2.
Figure imgf000274_0001
Compound 1 18 was prepared from INT-33 and c/'s-3-[[(1 ,1 -dimethylethoxy)carbonyl]amino]- cyclobutane carboxylic acid in a similar manner as described in the procedure to prepare Compound 1 12.Yield: 36%. MS [(M+3H)/3]+ = 858.6.
Figure imgf000274_0002
A solution of HATU (5.8 mg, 0.015 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-31 (50.2 mg, 0.014 mmol), 3-(2-{2-[(tert- butoxy)carbonylamino]ethoxy}ethoxy)propanoic acid (4.3 mg, 0.01 5 mmol) and diisopropylethylamine (7.23 mg, 0.056 mmol) in DMF (1 .0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (10-30-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (13.0 mg, 24%). MS (M+4H)/4 660.2, (M+5H)/5 528.71 and (M+6H)/6 440.3.
Figure imgf000275_0001
The title compound was prepared from INT-8 and [[1 1 ,21 :24,31-terphenyl]-13,15-dicarboxylic acid ■34) in an analogous procedure as described for Compound 102. MS [(M+3H)/3]+ = 803.5.
Figure imgf000275_0002
Step a. Preparation of the dicarboxylic acid
34-propoxy[1 1 ,21 :24,31-terphenyl]-13,15-dicarboxylic acid was prepared from 5-bromo-1 ,3- benzenedicarboxylic acid and 4-n-isopropyl-biphenyl-boronic acid in a similar fashion as described in the procedure for INT-34. Yield: 72.1 %. LC/MS [M+H]+ = 377.4.
Step b. Coupling to INT-8 and deprotection
The title compound was prepared from INT-8 and 34-propoxy[1 1 ,21 :24,31-terphenyl]-13,15- dicarboxylic acid (Step a.) in a similar procedure as described for Compound 102. LC/MS [(M+3H)/3]+ = 822.4. Example 159. Synthesis of Compound 122
Figure imgf000276_0001
A solution of HATU (26.25 mg, 0.069 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-33 (50.2 mg, 0.014 mmol), 2-{2-[(tert- butoxy)carbonylamino]ethoxy}acetic acid (1 5.13 mg, 0.069 mmol) and diisopropylethylamine (20.43 mg, 0.16 mmol) in DMF (1 .5 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (10-35-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (18.0 mg, 33%). MS (M+5H)/5 516.5 and (M+6H)/6 430.4.
Example 160: Synthesis of Compound 123
Figure imgf000276_0002
The title compound was prepared analogously to Compound 94 where DBCO-PEG5-acid was substituted for maleimide-PEG-8-acid in the first step of the sequence. MS: (M+3H)/3 = 1028.4, (M+4H)/4 =771 .7, (M+5H)/5 =617.6
Figure imgf000277_0001
The dicarboxylic acid INT-19 (0.1 1 68 g, 0.144 mmol) and INT-6 (0.41 14 g, 0.302 mmol) were dissolved in 5 mL of DMF followed by addition of DIPEA (0.075 mL, 0.43 mmol). To this mixture was added HATU (0.1366 g, 0.359 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. After completion of HATU addition, the reaction mixture was stirred for 1 hr at room temperature. Then the reaction mixture was concentrated under reduced pressure. The residue was purified by reversed phase C18 with ACN/water (0.1 %TFA) to give the per-Boc product. The mass spectrum showed a strong detectable positive charge signal at tr = 2.82 min with 7 min (60-95%) gradient (reverse phase C18 with ACN/water (0.1 %TFA)) [found positive ions (M-3Boc+H+)/3: 1067.0, (M-4Boc+H+)/5: 602.2]. The Boc groups were removed by treating with TFA for less than 1 hour. Most of the TFA was removed and the residue was dissolved in a minimum amount of NMP and loaded onto a Preparative HPLC with
ACN/water (0.1 % TFA). The desired product was collected and lyophilized to give the product as a TFA salt, isolated as a white powder. MS: [(M+6H+)/6: 418.2), (M+5H+)/5: 501 .6), (M+4H+)/4: 626.6).
Figure imgf000277_0002
The dicarboxylic acid INT-20 (0.1020 g, 0.125 mmol) and INT-6 (0.3593 g, 0.263 mmol) were dissolved in 5 mL of DMF followed by addition of DIPEA (0.066 mL, 0.38 mmol). To this mixture was added HATU (0.1 193 g, 0.314 mmol) in 2 mL of DMF via syringe pump in 2 hours at room temperature. After completion of HATU addition, the reaction mixture was stirred for 1 hr at room temperature. Then the reaction mixture was concentrated under reduced pressure. The residue was purified by reversed phase C18 with ACN/water (0.1 % TFA) to give the per-Boc product. The mass spectrum showed a strong detectable positive charge signal at tr = 2.78 min with 7 min (60-95%) gradient (reverse phase C18 with ACN/water (0.1 %TFA)) [found positive ion (M-4Boc+H+)/5: 602.6. The Boc groups were removed by treating with TFA for less than 1 hour. Most of the TFA was removed under reduced pressure and the residue was dissolved in a minimum amount of NMP and loaded onto a Preparative HPLC column with ACN/water (0.1 % TFA). The product was collected and lyophilized to give the desired product as a TFA salt, isolated as a white powder. MS: [(M+6H+)/6: 418.0), (M+5H+)/5: 501 .2), (M+4H+)/4: 626.2).
Figure imgf000278_0001
The title compound was prepared analogously to Compound 94 where ethyne-PEG4-acid was substituted for maleimide-PEG-8-acid in the first step of the sequence. MS: (M+3H)/3 = 916.4, (M+4H)/4 =687.6, (M+5H)/5 =550.3
Figure imgf000278_0002
Step a. Synthesis of amino-PEG4-deca-Boc-(Compound 16)
A stirring solution of previously described deca-Boc-(Compound 16) (1 .03 g, 0.294 mmol), Cbz- N-amido-PEG4-acid (0.1 17 g, 0.294 mmol), and DIPEA (0.1 07 mL, 0.61 6 mmol) in DCM (15 mL) and DMF (5 mL), was treated with a solution of HATU (0.1 17 g, 0.308 mmol) in DMF (2.5 mL), dropwise over 30 minutes. After 1 .5 hour, all the volatiles were evaporated. This residue was taken up in methanol (25 mL) and suspended with 5% Pd on charcoal (1 .0 g) under hydrogen atmosphere (~1 atm). When all the starting material was consumed by HPLC analysis, the mixture was filtered through a short Celite pad, and all the volitales were evaporated. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 50% to 1 00% methanol and water, using no modifier. Yield 0.450 g, 41 % yield. MS: (M+3H)/3 = 864.3.
Step b. Synthesis of deca-Boc- Compound 127
A stirring solution of amino-PEG4-deca-Boc-(Compound 16) (0.450 g, 0.1 14 mmol), 4-(3-tosyl-2- (tosylmethyl)propanoyl)benzoic acid (0.057 g, 0.1 14 mmol), and 4-methylmorpholine (0.025 mL, 0.229 mmol) in DCM (5 mL) and DMF (5 mL), was treated with a solution of HATU (0.043 g, 0.1 14 mmol) in DMF (2 mL), dropwise over 30 minutes. After 1 .5 hour, all the volatiles were evaporated. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 50% to 100% methanol and water, using no modifier. Yield 0.158 g, 31 % yield. Diagnostic peaks for 1 H NMR (Methanol-ck) δ: 7.83 (d, J = 8.3 Hz, 2H), 7.62 (d, J = 8.1 Hz, 4H), 7.57 (d, J = 8.4 Hz, 2H), 7.43 (4, J = 8.1 Hz, 4H), 7.34 - 7.15 (m, 10H), 2.64 (br s, 1 H), 2.50 (s, 3H), 0.89 (br s, 6H), 0.71 (br d, J = 16.9 Hz, 12H).
Step c. Synthesis of Compound 127
A solution of deca-Boc-(Compound 127) (0.158 g, 0.037 mmol), dissolved in DCM (4 mL), was treated with TFA (2 mL), while stirring at room temperature. After 30 minutes, all the volatiles were evaporated. The desired product was isolated as a dodeca-TFA salt by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% methanol and water, using TFA as the modifier. Yield 0.047 g, 27% yield. MS: (M+4H)/4 = 809.5, (M+5H)/5 = 647.7.
Example 165: Synthesis of
Figure imgf000279_0001
Step a. Synthesis of methyl (2S)-2-({[(2S)-6-{[(benzyloxy)carbonyl]amino}-1-fer^utoxy-1- oxohexan-2-yl]carbamoyl}amino)octanoate
The methyl (2S)-2-isocyanatooctanoate (200 mg, 1 mmol) was added into the solution of tert- butyl /^-[(benzyloxyJcarbonylJ-L-lysinate (340 mg, 1 mmol) and triethylamine(0.28m mL, 2mmol) in 5 mL DMF at room temperature, the reaction was stirred for overnight, then concentrated and the residue was purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield 460 mg, 75%. MS: M+H = 536.3.
Step b. Synthesis of methyl (2S)-2-[({(9S,12S,15S,18S,21 /¾-21- {[(3S,6S,9S,12S,15/?,18S,21 ¾-15-benzyl-6,9,18-tris{2-[(fert-butoxycarbonyl)amino]ethyl}-3-[(1 /¾-1- hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 ,4,7,10,13,16,19- heptaazacyclotricosan-21-yl]carbamoyl}-15-{2-[(fert-butoxycarbonyl)amino]ethyl}-12-hexyl-18- [(1 /¾-1-hydroxyethyl]-27,27-dimethyl-3,10,13,16,19,25-hexaoxo-1-phenyl-2,26-dioxa- 4, 11 , 14, 17,20,24-hexaazaoctacosan-9-y I }carbamoy l)am i no]octanoate
Methyl (2S)-2-({[(2S)-6-{[(benzyloxy)carbonyl]amino}-1 -ferf-butoxy-1 -oxohexan-2- yl]carbamoyl}amino)octanoate (55 mg, 0.1 mmol) was treated with TFA and stirred for half hour and then concentrated and dried under high vacuum used for next step without purification.
The de-butylated products from above step dissolved into 5 mL DMF, and then INT-10 (170 mg, 0.1 mmol) in 5 mL DMF was added HATU(40 mg, 0.1 mmol) in 1 mL DMF by syringe pump over 1 hour. Then the resulted solution was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted 10% to 100% methanol and water, using no modifier. Yield of desired product, 130 mg, 87% yield.
Step c. Synthesis of (2S)-2-[({(9S,12S,15S,18S,21 /¾-21-{[(3S,6S,9S,12S,15/?,18S,21 ¾-15-benzyl-
6,9,18-tris{2-[(ferf-butoxycarbonyl)amino]ethyl}-3-[(1 fl)-1-hydroxyethyl]-12-(2-methylpropyl)- 2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosan-21-yl]carbamoyl}-15-{2-[(fert- butoxycarbonyl)amino]ethyl}-12-hexyl-18-[(1 /¾-1-hydroxyethyl]-27,27-dimethyl-3,10,13,16,19,25- hexaoxo-1-phenyl-2,26-dioxa-4,11 ,14,17,20,24-hexaazaoctacosan-9-yl}carbamoyl)amino]octanoic acid
A solution of methyl (2S)-2-[({(9S,12S,1 5S,18S.21 fl)-21 -{[(3S,6S,9S,12S,15fl,18S.21 S)-15- benzyl-6,9,18-tris{2-[(ferf-butoxycarbonyl)amino]ethyl}-3-[(1 fi)-1 -hydroxyethyl]-12-(2-methylpropyl)- 2,5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,1 6,1 9-heptaazacyclotricosan-21 -yl]carbamoyl}-15-{2-[(ferf- butoxycarbonyl)amino]ethyl}-12-hexyl-18-[(1 R)-1 -hydroxyethyl]-27,27-dimethyl-3,1 0,13,16,19,25- hexaoxo-1 -phenyl-2,26-dioxa-4,1 1 ,14,17,20,24-hexaazaoctacosan-9-yl}carbamoyl)amino]octanoate (0.10 g, 0.05 mmol), in methanol (1 mL) was treated with a solution of lithium hydroxide (0.024 g, 1 .0 mmol), in water (1 mL) and THF (1 mL), then stirred at room temperature for 30 minutes. The reaction was quenched by drops of acetic acid. The desired product was isolated directly by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 1 00% methanol and water, using no modifier. Yield 0.90 g, 90%.
Step d. Synthesis of full protected Compound 128
To the solution of (2S)-2-[({(9S,12S,15S,18S,21 fl)-21 -{[(3S,6S,9S,12S,15fl,18S,21 S)-15-benzyl- 6,9,1 8-tris{2-[(ferf-butoxycarbonyl)amino]ethyl}-3-[(1 R)-1 -hydroxyethyl]-12-(2-methylpropyl)- 2,5,8,1 1 ,14,17,20-heptaoxo-1 ,4,7,10,13,1 6,1 9-heptaazacyclotricosan-21 -yl]carbamoyl}-15-{2-[(ferf- butoxycarbonyl)amino]ethyl}-12-hexyl-18-[(1 R)-1 -hydroxyethyl]-27,27-dimethyl-3,1 0,13,16,19,25- hexaoxo-1 -phenyl-2,26-dioxa-4,1 1 ,14,17,20,24-hexaazaoctacosan-9-yl}carbamoyl)amino]octanoic acid (85 mg, 0.05 mmol), triethylamine (0.15 mL, 1 mmol) and INT-8(80 mg, 0.05mmol) in 5 mL DMF was added HATU(40 mg, 0.1 mmol) in 1 mL DMF by syringe pump over 1 hour. Then the resulted solution was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, using no modifier. Yield of product, 130 mg, 87% yield.
Step e. Synthesis of (2S)-2-{[(2S,6S,9S,12S,15S)-17-amino-2-(4-aminobutyl)-9-(2- aminoethyl)-6-hexyl-12-[(1 R)-1-hydroxyethyl]-4,7,10,13-tetraoxo-15-{[(3S,6S,9S,12S,15R,18S,21S)- 6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1-hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20- heptaoxo-1 ,4,7,10,13,16,19-heptaazacyclotricosan-21-yl]carbamoyl}-3,5,8,11 ,14- pentaazaheptadecanan-1-oyl]amino}-N-[(2S)-4-amino-1-{[(2S,3R)-1-{[(2S)-4-amino-1-oxo-1- {[(3S,6S,9S,12S,15R,18S,21S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1-hydroxyethyl]-12-(2- methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosan-21 - yl]amino}butan-2-yl]amino}-3-hydroxy-1-oxobutan-2-yl]amino}-1-oxobutan-2-yl]octanamide (Compound 128)
Per-Boc-(Compound 128) (100 mg, 0.03mmol) was dissolved into 5 mL 5% H20 in MeOH, then 20 mg of 5% Palladium on charcoal was added above solution, and the mixture was stirred at room temperature under the hydrogen atmosphere for 2hours. The palladium charcoal was removed by filtration. The residue was treated in 2 mL DCM and 2 mL TFA at room temperature, the solution was stirred 10 min, then concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 1 00% acetonitrile and water, using formic acid as the modifier. Yield 35 mg, 45% yield. MS: [(M+3H)/3]+ = 854.9, [(M+4H)/4]+ =641 .4,
[(M+5H)/5]+=513.3, [(M+6H)/6]+=427.9.
Figure imgf000282_0001
A solution of HATU (26.56 mg, 0.070 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-33 (50.6 mg, 0.015 mmol), 1 -[(tert-butyl)oxycarbonyl]azetidine-3- carboxylic acid (14.06 mg, 0.07 mmol) and diisopropylethylamine (20.67 mg, 0.16 mmol) in DMF (1 .5 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (1 0-35-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc- protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (45.0 mg, 81 %). MS (M+3H)/3 853.4, (M+4H)/4 640.4, (M+5H)/5 512.4 and (M+6H)/6 427.4.
Figure imgf000282_0002
A solution of HATU (26.46 mg, 0.070 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-33 (50.4 mg, 0.014 mmol), 3-[(tert- butoxy)carbonylamino]cyclobutane carboxylic acid (14.98 mg, 0.07 mmol) and diisopropylethylamine (20.59 mg, 0.1 6 mmol) in DMF (1 .5 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (10-35-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (44.0 mg, 79%). MS (M+4H)/4 643.9, (M+5H)/5 51 5.3 and (M+6H)/6 429.6.
Figure imgf000283_0001
Step a. Synthesis of hexa-Boc-(Compound 131)
A solution of lnt-1 (0.500 g, 0.471 mmol), Cbz-imino-diacetic acid (0.046 g, 0.171 mmol), DIEA(0.197 mL, 1 .13 mmol), and DMF (5 mL), was treated with a solution of HATU (0.188 g, 0.494 mmol) in DMF (2 mL) over 30 minutes, then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.496g, 90%.
Step b. Deprotection to Compound 131
Hexa-Boc-(Compound 131 ) (0.496 g, 0.212 mmol), was suspended in DCM (3 mL) and treated with TFA (3 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.427 g, 82%. MS: (M+2H)/2 =877.8, (M+3H)/3 =585.6, (M+4H)/4 =439.4
Figure imgf000283_0002
The title compound was prepared from INT-33 and Peg4-alkynyl-acid in a similar manner as described for Compound 1 12. Yield: 61 %. LC/MS [(M+3H)/3]+ = 906.8.
Figure imgf000284_0001
A solution of HATU (1 1 .02 mg, 0.029 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-33 (50.4 mg, 0.014 mmol), (1 S,3S)-3-[(tert- butoxy)carbonylamino]cyclopentane carboxylic acid (6.65 mg, 0.029 mmol) and diisopropylethylamine (5.6 mg, 0.43 mmol) in DMF (1 .0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (10-35-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-35% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (15.1 mg, 27%). LC/MS (M+4H)/4 647.6, (M+5H)/5 518.2 and (M+6H)/6 432.2.
Figure imgf000284_0002
A solution of Compound 131 (0.200g, 0.082 mmol) dissolved in methanol (5 mL) was treated with 5% Pd/C (0.400g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 2h. The solution was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.165g, 83% yield. LCMS: (M+3H)/3 = 540.8, (M+4H)/4 = 406.0.
Figure imgf000285_0001
Step a. Synthesis of Cbz-D-Ser-lnt-1
A solution of lnt-1 (0.500 g, 0.471 mmol), Cbz-D-Ser (0.046 g, 0.171 mmol), DIEA (0.197 mL, 1 .13 mmol), and DMF (5 mL), was treated with HATU (0.124 g, 0.518 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification.
Step b. Synthesis of D-Ser-lnt-1
Crude Cbz-D-Ser-lnt-10 in DMF (from Step a), was charged with 5% Pd/C (0.5g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 2h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, using no modifier. Yield 0.242 g, 54%. MS: [(M-1 Boc)+2H]/2 = 525.2, [(M-2Boc)+2H]/2 = 475.2, [(M-3Boc)+2H]/2 = 425.2
Step c. Synthesis of Hexa-Boc-(Compound 135)
A solution of D-Ser-lnt-1 (0.142 g, 0.124 mmol), Cbz-imino-diacetic acid (0.016 g, 0.059 mmol), DIEA(0.068 mL, 0.389 mmol), and DMF (3 mL), was treated with a solution of HATU (0.049 g, 0.130 mmol) in DMF (1 mL) over 30 minutes, then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.138g, 88%
Step d. Deprotection to Compound 135
Hexa-Boc-(Compound 135) (0.138 g, 0.055 mmol), was suspended in DCM (2 mL) and treated with TFA (2 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.1 15 g, 80%. MS: (M+3H)/3 =643.6, (M+4H)/4 =483.0, (M+5H)/5 =386.6
Figure imgf000286_0001
A solution of Compound 135 (0.200g, 0.082mmol) dissolved in methanol (5 mL) was treated with 5% Pd/C (0.200g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 2h. The solution was filtered through celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.021 g, 1 7% yield. MS: (M+3H)/3 =599.3, (M+4H)/4 =449.4, (M+5H)/5 =359.8
Example 174: Synthesis of Compound 137
Figure imgf000286_0002
Step a. Synthesis of methyl 3-(aminomethyl)-5-bromobenzoate
In a sealed tube, a stirring mixture of methyl 3-bromo-5-(bromomethyl)benzoate (3.08 g, 1 0.00 mmol) and sodium azide (0.715 g, 1 1 .00 mmol) in DMF (10 mL) was heated at 80 °C for 1 h, when HPLC analysis showed full conversion of the bromide. All the volatiles were evaporated. The residue was taken up in DCM (40 mL) and water (40 mL). The water layer was washed with additional DCM (2 x 30 mL). The combined organic layers were dried with brine and solid sodium sulfate. Upon filtration, all the volatiles were evaporated, affording 2.73 g of the crude azide derivative in high purity, as confirmed by 1 H-NMR and LC-MS analysis. Ή NMR (DMSO-afe) δ: 8.03 (t, J = 1 .6 Hz, 1 H), 7.98 - 7.93 (m, 1 H), 7.90 (t, J = 1 .5 Hz, 1 H), 4.60 (s, 2H), 3.88 (s, 3H). This azide (2.73 g) was dissolved under stirring in THF (30 mL) and water (2 mL), and triphenylphosphine (3.148 g, 12.00 mmol) was added. The reaction was stirred at room temperature overnight, allowing gas evolution through a bubbler. All the volatiles were evaporated. The desired product was isolated by normal phase liquid chromatography using an Isco CombiFlash liquid chromatograph eluted with 1 % to 20% hexanes and ethyl acetate. From the appropriate fractions, the desired compound was obtained still contaminated with triphenylphenylphosphine oxide. This material was dissolved in DCM (50 mL) and extracted with an acidic solution (12 mL of 1 .0 M hkSC and 30 mL of water). The water layer was added dropwise to a vigorously stirring solution of saturated sodium bicarbonate (60 mL) and stirring was continued overnight. The obtained mixture was extracted with DCM (3 x 30 mL). The combined organic layers were dried with brine and solid sodium sulfate. Upon filtration, all the volatiles were evaporated, affording 1 .31 g, 54% of the title compound. MS: (M+H)+ = 244.0; 246.0.
Step b. Synthesis of methyl 3-((N-(1 '-(3'-carboxymethyl-5- bromo)phenylene)methylene)methyl)-5-bromobenzoate
A solution of methyl 3-(aminomethyl)-5-bromobenzoate (1 .306 g, 5.350 mmol) and methyl 3- bromo-5-formylbenzoate (1 .238 g, 5.096 mmol) in DCM (10 mL) was evaporated per vacuum techniques and left over high vacuum overnight. The residue was taken up in THF (30 mL) and treated under vigorous stirring with sodium triacetoxyborohydride (3.240 g, 1 5.29 mmol). This mixture was quenched after 18 h by the addition of a saturated aqueous solution of ammonium chloride (50 mL). The obtained mixture was extracted with DCM (3 x 30 mL). The combined organic layers were dried with brine and solid sodium sulfate. Upon filtration, all the volatiles were evaporated. The desired product was isolated by normal phase liquid chromatography using an Isco CombiFlash liquid chromatograph eluted with 1 % to 50% hexanes and ethyl acetate. Yield 1 .61 1 g, 67%. MS: (M+H)+ = 470.0, 472.1 , 474.0.
Step c. Synthesis of N-Cbz protected methyl 3-((N-(1 '-(3'-carboxymethyl-5- bromo)phenylene)methylene)methyl)-5-bromobenzoate
To a 0°C stirring solution of methyl 3-((N-(1 '-(3'-carboxymethyl-5- bromo)phenylene)methylene)methyl)-5-bromobenzoate (1 .61 1 g, 3.419 mmol) and DIPEA (0.953 mL, 5.471 mmol) in THF (20 mL) it was added Cbz-CI (0.732 mL, 5.129 mmol) dropwise. The temperature was raised to ambient after 10 minutes and stirring was continued until complete disappearance of the starting amine by LC-MS analysis. All the volatiles were removed by rotatory evaporation. The desired product was isolated by normal phase liquid chromatography using an Isco CombiFlash liquid
chromatograph eluted with 1 % to 20% hexanes and ethyl acetate. Yield 2.070 g, quant. MS: (M+H)+ = 603.0, 605.0, 607.0.
Step d. Synthesis of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5- phenyl)phenylene)methylene)methyl)-5-phenylbenzoic acid
Under nitrogen, in a capped microwave reaction vessel stirring mixture of N-Cbz protected methyl 3-((N-
(1 '-(3'-carboxymethyl-5-bromo)phenylene)methylene)methyl)-5-bromobenzoate (0.299 g, 0.494 mmol), potassium phenyltrifluoroborate (0.200 g, 1 .087 mmol), sodium carbonate (0.209 g, 1 .976 mmol) and bis(triphenylphosphine)palladium (II) dichloride (0.035 g, 0.049 mmol) in MeCN (4 mL) and water (4 mL) were irradiated with microwaves for 10 mim at 130 °C. Upon cooling, the reaction was treated under stirring with SiliaMetS® (0.200 g, 0.240 mmol) for 1 h, and TFA was added (0.380 mL, 5.0 mmol). Upon filtration, all the volatiles were evaporated per vacuum techniques. The desired product was isolated as a dodeca-TFA salt by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% methanol and water, using TFA as the modifier. Yield 0.072 g, 25% yield. Ή NMR (0.500 mL Chloroform-d + 0.050 mL TFA) δ: 8.18 (d, J = 5.5 Hz, 2H), 7.82 (d, J = 16.6 Hz, 2H), 7.60 (d, J = 33.5 Hz, 2H), 7.52 - 7.27 (m, 15H), 5.32 (s, 2H), 4.70 (d, J = 1 9.9 Hz, 4H).
Step e. Synthesis of N-Cbz-deca-Boc-(Compound 137)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-8 (0.429 g, 0.241 mmol), N-Cbz protected 3-((N-(1 '-(3'-carboxy-5-phenyl)phenylene)methylene)methyl)-5- phenylbenzoic acid (0.069 g, 0.121 mmol), DIPEA (0.128 mL, 0.736 mmol) in DMF (10 mL) by dropwise addition of HATU (0.094 g, 0.247 mmol in 3.0 mL of DMF). Yield 0.158 g, 37% yield. MS: [(M- 3Boc)+3H]/4 = 841 .2.
Step f. Synthesis of deca-Boc-(Compound 137)
N-Cbz-deca-Boc-(Compound 137) (0.1 58 g, 0.0431 mmol) was dissolved methanol (10 mL) and suspended with SiliaCat® Pd(0) (0.043 g; 0.009 mmol) under hydrogen atmosphere (~1 atm). When all the starting material was consumed by HPLC analysis, the mixture was filtered over a short Celite pad, and all the volitales were evaporated per vacuum techniques. HPLC analysis revealed the desired compound in high purity, and this material was used without further purification. Yield 0.151 g, 99% yield. MS: [(M-3Boc)+3H]/4 = 808.8.
Step g. Synthesis of Compound 137
Prepared in a similar fashion to "Step g. Synthesis Compound 109" from deca-Boc-(Compound 137) (0.074 g, 0.021 mmol), DCM (3 mL), and TFA (1 mL). Yield 0.017 g, 21 % yield as the undeca TFA salt. Main ions found by HRMS: (M+2H)/2 = 1264.7, (M+3H)/3 = 843.5, (M+4H)/4 = 632.8, (M+5H)/5 = 506.5.
Figure imgf000288_0001
Figure imgf000289_0001
Step a. Synthesis of Cbz-racemic-hexyl-Ser-D-Ser-lnt-1
A solution of D-Ser-lnt-1 (0.300 g, 0.261 mmol, described for Compound 135, step b), racemic Cbz-hexylserine (0.101 g, 0.313 mmol), DIEA (0.1 64 ml_, 0.940 mmol), and DMF (5 ml_), was treated with HATU (0.109 g, 0.287 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification.
Step b. Synthesis of hexyl-Ser-D-Ser-lnt-1
Crude Cbz-racemic-hexylSer-D-Ser-lnt-1 in DMF, was charged with 5% Pd/C (0.2g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 2h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.329 g, 97%. MS: [(M-1 Boc)+2H]/2 = 61 0.96, [(M-2Boc)+2H]/2 = 560.7, [(M-3Boc)+2H]/2 = 510.6
Step c. Synthesis of Cbz-Hexa-Boc-(Compound 138)
A solution of hexyl-Ser-D-Ser-lnt-10 (0.250 g, 0.189 mmol), Cbz-imino-diacetic acid (0.024 g, 0.090 mmol), DIEA(0.104 ml_, 0.596 mmol), and DMF (4 ml_), was treated with a solution of HATU (0.076 g, 0.199 mmol) in DMF (2 ml_) over 30 minutes, then stirred for 30 minutes. The crude reaction was taken-on to the next step without purification.
Step d. Synthesis of Hexa-Boc-(Compound 138)
Crude Cbz-Hexa-Boc-(Compound 138) in DMF, was charged with 5% Pd/C (0.125g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 3h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.177 g, 68%. MS: [(M-1 Boc)+2H]/2 = 61 0.96, [(M-2Boc)+3H]/3 = 846.9, [(M-3Boc)+3H]/3 = 813.3, [(M- 4Boc)+3H]/3 = 779.8,
Step e. Deprotection to Compound 138
Hexa-Boc-(Compound 138) (0.177 g, 0.065 mmol), was suspended in DCM (2 ml_) and treated with TFA (2 ml_), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.165 g, 90%. MS: (M+3H)/3 =712.8, (M+4H)/4 =535.0, (M+5H)/5 =428.2
Figure imgf000290_0001
The title compound was prepared from INT-35 and INT-13 in a similar manner as described for Compound 1 02. Yield: 32%, 2 steps. LC/MS [(M+3H)/3]+ = 752.4.
Figure imgf000290_0002
The title compounds were prepared from INT-36 and racemic trans-propane-1 ,2-dicarboxylic acid in an analogous procedure as described for Compound 102. Compound 140 is a mixture of cyclopropane diastereomers. Yield: 83%, 2 steps. LC/MS [(M+3H)/3]+ =778.0.
Figure imgf000291_0001
Step a. Synthesis of 1 ,4-bis(1 '-carboxymethylheptyl)piperazine
To a stirring mixture of (S)-methyl 2-aminooctanoate (1 .40 g, 8.08 mmol) and sodium triacetoxyborohydride (7.60 g, 40.40 mmol) in THF (40 mL), it was added a 40% aqueous solution of glyoxal (0.926 mL, 8.08 mmol). This mixture was quenched after 18 h by the addition of a saturated aqueous solution of sodium bicarbonate (100 mL). The obtained mixture was extracted with DCM (3 x 80 mL). The combined organic layers were dried with brine and solid sodium sulfate. Upon filtration, all the volatiles were evaporated. The desired product was isolated by normal phase liquid chromatography using an Isco CombiFlash liquid chromatograph eluted with 1 % to 100% hexanes and ethyl acetate. Yield 0.066 g, 2%. MS: (M+H)+ = 399.3. 1 H NMR (DMSO-d6) δ: 3.60 (s, 6H), 3.12 (t, J = 7.5 Hz, 2H), 2.83 - 2.57 (m, 8H), 1 .69 - 1 .37 (m, 4H), 1 .37 - 1 .02 (m, 16H), 0.85 (br t, J = 6.4 Hz, 6H).
Step b. Synthesis of deca-Boc-(Compound 141)
To a stirring solution of 1 ,4-bis(1 '-carboxymethylheptyl)piperazine (0.094 g, 0.236 mmol) in methanol (10 mL) and water (5 mL) was added sodium hydroxide (0.094 g, 2.358 mmol) and stirring was continued overnight at 40 °C. HPLC analysis revealed full conversion of the starting diester to a new peak. All the volatiles were evaporated. The residue was taken up in THF and a 1 .0 M solution of HCI (5 mL, 5.00 mmol) was added under stirring. After 10 minutes, all the volatiles were evaporated. The obtained crude 1 ,4-bis(1 '-carboxyheptyl)piperazine was used in the next step without any further purification assuming quantitative yield. MS: (M+H)+ = 371 .3. The said material was taken up in DMF (1 0 mL). Under stirring, INT-8 (0.775 g, 0.495 mmol), DIPEA (0.41 1 mL, 2.358 mmol) were added in the order, followed by dropwise addition of HATU (0.184 g, 0.483 mmol in 5.0 mL of DMF) over 30 minutes. After 1 .5 hour, all the volatiles were evaporated. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 50% to 100% methanol and water, using no modifier. Yield 0.394 g, 48% yield. MS: [(M-3Boc)+4H]/4= 791 .1 .
Step c. Synthesis of Compound 141
Prepared in a similar fashion to "Step g. Synthesis Compound 109" from deca-Boc-(Compound 141 ) (0.394 g, 0.1 14 mmol), DCM (6 mL), and TFA (3 mL). Yield 0.329 g, 75% yield as the dodeca TFA salt. LC-MS analysis of this compound revealed a mixture of diastereoisomers. MS: (M+4H)/4 = 615.8, (M+5H)/5 = 492.9. Examp
Figure imgf000292_0001
Step a. Synthesis of Cbz-L-Asn-lnt-1
A solution of lnt-1 (1 .500 g, 1 .41 mmol), Cbz-L-Asn (0.414 g, 1 .55 mmol), DIEA (0.812 mL, 4.66 mmol), and DMF (15 mL), was treated with HATU (0.590 g, 1 .55 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification.
Step b. Synthesis of L-Asn-lnt-1
Crude Cbz-L-Asn-lnt-1 in DMF, was charged with 5% Pd/C (0.6g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 3h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.317 g, 19%. MS: [(M-1 Boc)+2H]/2 = 535.5, [(M-2Boc)+2H]/2 = 488.6, [(M-3Boc)+2H]/2 = 438.6
Step c. Synthesis of Cbz-L-Thr-L-Asn-lnt-1
A solution of L-Asn-lnt-1 (0.317 g, 0.269 mmol), Cbz-L-Thr (0.075 g, 0.296 mmol), DIEA (0.1 55 mL, 0.889 mmol), and DMF (3 mL), was treated with HATU (0.1 13 g, 0.296 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification.
Step d. Synthesis of L-Thr-L-Asn-lnt-1
Crude Cbz-L-Thr-L-Asn-lnt-1 in DMF, was charged with 5% Pd/C (0.2g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 3h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 1 0% to 100% methanol and water, using no modifier. Yield 0.290 g, 99%. MS: [(M-1 Boc)+2H]/2 = 589.2, [(M-2Boc)+2H]/2 = 539.0, [(M-3Boc)+2H]/2 = 489.0 Step e. Synthesis of Cbz-L-aminooctanoic acid-L-Thr-L-Asn-lnt-1
A solution of L-Thr-L-Asn-lnt-1 (0.290 g, 0.228 mmol), Cbz-L-aminooctanoic acid (0.074 g, 0.252 mmol), DIEA (0.1 132 ml_, 0.755 mmol), and DMF (5 ml_), was treated with HATU (0.096 g, 0.252 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification
Step f. Synthesis of L-aminooctanoic acid-L-Thr-L-Asn-lnt-1
Crude Cbz-L-aminooctanoic acid-L-Thr-L-Asn-lnt-1 in DMF, was charged with 5% Pd/C (0.2g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 3h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.262 g, 81 %. MS: [(M-1 Boc)+2H]/2 = 659.6, [(M-2Boc)+2H]/2 = 609.3, [(M-3Boc)+2H]/2 = 559.6
Step g. Synthesis of hepta-Boc-(Compound 142)
A solution of L-aminooctanoic acid-L-Thr-L-Asn-lnt-1 (0.198 g, 0.140 mmol), Boc-imino-diacetic acid (0.0155 g, 0.066 mmol), DIEA(0.077 mL, 0.440 mmol), and DMF (3 mL), was treated with a solution of HATU (0.056 g, 0.147 mmol) in DMF (1 mL) over 30 minutes, then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.1 50 g, 71 %. MS: [(M-3Boc)+3H]/3 = 91 1 .8, [(M-4Boc)+3H]/3 = 878.4, [(M-5Boc)+3H]/3 = 845.5
Step h. Deprotection to Compound 142
Hepta-Boc-(Compound 142) (0.150 g, 0.049 mmol), was suspended in DCM (2 mL) and treated with TFA (2 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.129 g, 83%. MS: (M+3H)/3 =778.3, (M+4H)/4 =584.0, (M+5H)/5 =467.4
Example 180: Synthesis of Compound 143
Figure imgf000294_0001
Step a. Coupling of INT-13 with (2S,3R)-2-Z-amino-3-hydroxyhexanoic Acid
The title compound was prepared from INT-13 and (2S,3R)-2-Z-amino-3-hydroxyhexanoic acid as described by procedure INT-36. Yield: 83%, 2 steps. LC/MS [(M-Boc+2H)/2]+ = 640.4.
Step b. Coupling to INT-35
The title compound was prepared from the product of Step a. and INT-35 in an analogous procedure as described for Compound 102. Yield: 83%, 2 steps. LC/MS [(M+3H)/3]+ =839.0.
Figure imgf000295_0001
Step a. Synthesis of Cbz-aminohydroxybutanoic acid-D-Ser-lnt-12
A solution of lnt-12 (0.250 g, 21 8 mmol), (3R)-4-{[(benzyloxy)carbonyl]amino}-3-hydroxybutanoic acid (0.061 g, 0.240 mmol), DIEA(0.136 ml_, 0.783 mmol), and DMF (5 ml_), was treated with HATU (0.091 g, 0.239 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification.
Step b. Synthesis of Aminohydroxybutanoic acid-D-Ser-lnt-12
Crude Cbz-aminohydroxybutanoic acid-D-Ser-lnt-12 in DMF, was charged with 5% Pd/C (0.4g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 3h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.190 g, 100%. MS: [(M-1 Boc)+2H]/2 = 575.6, [(M-2Boc)+2H]/2 = 525.6, [(M-3Boc)+2H]/2 = 475.5
Step c. Synthesis of Hexa-Boc-(Compound 144)
A solution of aminohydroxybutanoic acid-D-Ser-lnt-12 (0.190 g, 0.152 mmol), Cbz-imino-diacetic acid (0.0192 g, 0.072 mmol), DIEA(0.087 mL, 0.501 mmol), and DMF (3 mL), was treated with a solution of HATU (0.061 g, 0.160 mmol) in DMF (1 mL) over 30 minutes, then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.1 02 g, 49%. MS: [(M-2Boc)+2H]/2 = 1266.6 Step d. Deprotection to Compound 144
Hexa-Boc-(Compound 144) (0.102 g, 0.037 mmol), was suspended in DCM (2 mL) and treated with TFA (2 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.097 g, 90%. MS: (M+3H)/3 =710.8, (M+4H)/4 =533.5, (M+5H)/5 =427.0
Figure imgf000296_0001
Step a. Coupling of Z-Asn to INT-13
Z-Asn-OH and INT-13 were coupled in an analogous procedure as described for INT-36. Yield: 85%, 2 steps. LC/MS [(M-Boc+2H)/2]+ = 633.0
Step b. Coupling with Fumaric Acid and Deprotection of the Boc Groups
Compound 145 was prepared from the product of Step a. and fumaric acid in an analogous procedure as described for Compound 102. Yield: 47%, 2 steps. LC/MS [(M+3H)/3]+ = 736.5.
Figure imgf000296_0002
Step a. Synthesis of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5-(trans-but-1- enyl))phenylene)methylene)methyl)-5-phenylbenzoic acid
Prepared in a similar fashion to "Step d. Synthesis of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5- phenyl)phenylene)methylene)methyl)-5-phenylbenzoic acid" from previously described N-Cbz protected methyl 3-((N-(1 '-(3'-carboxymethyl-5-bromo)phenylene)methylene)methyl)-5-bromobenzoate (0.100 g, 0.165 mmol), 1 -butenylboronic acid (0.036 g, 0.363 mmol), sodium carbonate (0.105 g, 0.991 mmol) and bis(triphenylphosphine)palladium (II) dichloride (0.012 g, 0.016 mmol) in MeCN (4 mL) and water (4 mL). Yield 0.059 g, 68% yield. Ή NMR (Methanol-ck) δ: 7.82 (br s, 2H), 7.70 (br d, J = 17.2 Hz, 2H), 7.45 - 7.06 (m, 7H), 6.26 (br m, 4H), 5.25 (s, 2H), 4.57 (br s, 4H), 2.22 (br t, J = 7.3 Hz, 4H), 1 .09 (t, J = 7.4 Hz, 7H).
Step b. Synthesis of N-Cbz-deca-Boc-(Compound 146)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-8 (175 mg, 0.241 mmol), of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5-(trans-but-1 - enyl))phenylene)methylene)methyl)-5-phenylbenzoic acid (0.030 g, 0.059 mmol), DIPEA (0.1 19 mL, 0.682 mmol) in DMF (5 mL) by dropwise addition of HATU (0.045 g, 0.1 17 mmol in 1 .5 mL of DMF). Yield 0.1 16 g, 29% yield. MS: [(M-3Boc)+3H]/4 = 830.2.
Step c. Synthesis of deca-Boc-(Compound 146)
Prepared in a similar fashion to "Step f. Synthesis of deca-Boc-(Compound 137)" from N-Cbz- deca-Boc-(Compound 146) (18 mg, 0.005 mmol), SiliaCat® Pd(0) (0.005 g; 0.001 mmol), methanol (1 mL), DMF (0.1 mL) and hydrogen atmosphere (~1 atm). Yield 0.017 g, quantitative yield. MS: [(M- 3Boc)+3H]/4 = 797.7.
Step d. Synthesis of Compound 146
Prepared in a similar fashion to "Step f. Synthesis Compound 1 09" from deca-Boc-(Compound 146) (0.017 g, 0.005 mmol), DCM (2 mL), and TFA (1 mL). Yield 0.008 g, 43% yield as the undeca TFA salt. MS: (M+2H)/2 = 1244.8, (M+3H)/3 = 830.2, (M+4H)/4 = 622.9, (M+5H)/5 = 498.5.
Figure imgf000298_0001
Step a. Synthesis of Cbz-L-hydroxyproline-D-Ser-lnt-1
A solution of D-Ser-lnt-1 (INT-12) (0.500 g, 0.435 mmol, described for Compound 135, step b), (3S)-1 -[(benzyloxy)carbonyl]-3-hydroxy-L-proline (0.127 g, 0.479 mmol), DIEA(0.250 mL, 0.940 mmol), and DMF (10 mL), was treated with HATU (0.182 g, 0.479 mmol), then stirred for 30 minutes. The crude product solution was taken-on to the next step without purification
Step b. Synthesis of L-hydroxyproline-D-Ser-lnt-1
Crude Cbz-L-hydroxyproline-D-Ser-lnt-1 in DMF, was charged with 5% Pd/C (0.25g), vacuum flushed with hydrogen and stirred under a hydrogen atmosphere for 2h. The reaction was filtered through Celite, concentrated, and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.234 g, 51 %. MS: [(M-1 Boc)+2H]/2 = 581 .7, [(M-2Boc)+2H]/2 = 531 .6, [(M-3Boc)+2H]/2 = 481 .6
Step c. Synthesis of Hexa-Boc-(Compound 147)
A solution of aminohydroxybutanoic acid-D-Ser-lnt-1 (0.234g, 0.185 mmol), Cbz-imino-diacetic acid (0.024 g, 0.088 mmol), DIEA(0.1 07 mL, 0.501 mmol), and DMF (3 mL), was treated with a solution of
HATU (0.074 g, 0.195 mmol) in DMF (1 mL) over 30 minutes, then stirred for 30 minutes. The desired product was isolated by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 10% to 100% methanol and water, using no modifier. Yield 0.203 g, 79%. MS: [(M-3Boc)+2H]/2 = 818.8, [(M-4Boc)+2H]/2 = 785.7.
Step d. Deprotection to Compound 147
Hexa-Boc-(Compound 147) (0.203 g, 0.074 mmol), was suspended in DCM (2 mL) and treated with TFA (2 mL), while stirring at room temperature. After 5 minutes the reaction was concentrated and purified by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid
chromatograph eluted with 10% to 100% methanol and water, using TFA (0.1 %) as the modifier. Yield 0.089 g, 43%. MS: (M+3H)/3 =718.8, (M+4H)/4 =539.5
Example 185: Synthesis of Compound 148
Figure imgf000299_0001
Step a. Synthesis of (Z-B-3-Pyridyl-L-alanine)-Thr-DSer-cyclo[Dab-Dab(Boc)-DPhe-Leu- Dab(Boc)-Dab(Boc)-Thr]
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-13 (0.400 g, 0.320 mmol), Ζ-β-3-Pyridyl-L-alanine (0.096 g, 0. mmol), 2,4,6-trimethylpyridine (0.0 mL, 0.320 mmol) in DMF (5 mL) by dropwise addition of HATU (0.128 g, 0.336 mmol in 1 .5 mL of DMF). Yield 0.392 g, 80% yield. MS: [(M-1 Boc)+2H]/2 = 71 7.0, [(M-2Boc)+2H]/2 = 667.0.
Step b. Synthesis of (B-3-Pyridyl-L-alanine)-Thr-DSer-cyclo[Dab-Dab(Boc)-DPhe-Leu- Dab(Boc)-Dab(Boc)-Thr]
Prepared in a similar fashion to "Step f. Synthesis of deca-Boc-(Compound 137)" from (Ζ-β-3- Pyridyl-L-alanine)-Thr-DSer-cyclo[Dab-Dab(Boc)-DPhe-Leu-Dab(Boc)-Dab(Boc)-Thr] (0.392 g, 0.257 mmol), SiliaCat® Pd(0) (0.160 g; 0.032 mmol), methanol (6 mL) and hydrogen atmosphere (~1 atm). Yield 0.360 g, quantitative yield. MS: [(M-1 Boc)+2H]/2 = 650.0, [(M-2Boc)+2H]/2 = 599.9. Step c. Synthesis of (Z-(2S)-2-aminooctanoic acid)-(B-3-Pyridyl-L-alanine)-Thr-DSer- cyclo[Dab-Dab(Boc)-DPhe-Leu-Dab(Boc)-Dab(Boc)-Thr]
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from (β-3- Pyridyl-L-alanine)-Thr-DSer-cyclo[Dab-Dab(Boc)-DPhe-Leu-Dab(Boc)-Dab(Boc)-Thr] (0.360 g, 0.257 mmol), Z-(2S)-2-aminooctanoic acid (0.076 g, 0.257 mmol), 2,4,6-trimethylpyridine (0.105 mL, 0.798 mmol) in DMF (5 mL) by dropwise addition of HATU (0.103 g, 0.270 mmol in 1 .5 mL of DMF). Yield 0.321 g, 74% yield. MS LCMS: [(M-1 Boc)+2H]/2 = 787.2, [(M-2Boc)+2H]/2 = 737.4.
Step d. Synthesis of ((2S)-2-aminooctanoic acid)-(B-3-Pyridyl-L-alanine)-Thr-DSer- cyclo[Dab-Dab(Boc)-DPhe-Leu-Dab(Boc)-Dab(Boc)-Thr]
Prepared in a similar fashion to "Step f. Synthesis of deca-Boc-(Compound 137)" from (Z-(2S)-2- aminooctanoic acid)-( -3-Pyridyl-L-alanine)-Thr-DSer-cyclo[Dab-Dab(Boc)-DPhe-Leu-Dab(Boc)- Dab(Boc)-Thr] (0.321 g, 0.1 91 mmol), SiliaCat® Pd(0) (0.192 g; 0.038 mmol), methanol (4 mL) and hydrogen atmosphere (~1 atm). Yield 0.295 g, quantitative yield. MS: [(M-1 Boc)+2H]/2 = 650.2, [(M- 2Boc)+2H]/2 = 600.1 .
Step e. Synthesis of N-Z-hexa-Boc-(Compound 148)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from ((2S)-2- aminooctanoic acid)-( -3-Pyridyl-L-alanine)-Thr-DSer-cyclo[Dab-Dab(Boc)-DPhe-Leu-Dab(Boc)- Dab(Boc)-Thr] (0.321 g, 0.1 91 mmol), (2,2'-{[(benzyloxy)carbonyl]azanediyl}diacetic acid (0.026 g, 0.096 mmol), DIPEA (0.102 mL, 0.584 mmol) in DMF (5 mL) by dropwise addition of HATU (0.075 g, 0.196 mmol in 1 .5 mL of DMF). Yield 0.176 g, 55% yield. MS: [(M-3Boc)+3H]/4 = 753.3.
Step f. Synthesis of hexa-Boc-(Compound 148)
Prepared in a similar fashion to "Step f. Synthesis of deca-Boc-(Compound 137)" from N-Z-hexa-Boc- (Compound 148) (0.176 g, 0.053 mmol), SiliaCat® Pd(0) (0.053 g; 0.01 1 mmol), methanol (2 mL), DMF (0.2 mL) and hydrogen atmosphere (~1 atm). Yield 0.1 14 g, 68% yield. MS: [(M-3Boc)+3H]/4 = 719.8.
Step g. Synthesis of Compound 148
Prepared in a similar fashion to "Step f. Synthesis Compound 1 09" from hexa-Boc-(Compound 148) (0.015 g, 0.005 mmol), DCM (1 mL), and TFA (1 mL). Yield 0.006 g, 38% yield as the nona TFA salt. HRMS: (M+2H)/2 = 1288.7, (M+3H)/3 = 859.5, (M+4H)/4 = 644.9, (M+5H)/5 = 516.1 . of Compound 149
Figure imgf000301_0001
Figure imgf000301_0002
Step a. Synthesis of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5-(3'- ethylphenyl)phenylene)methylene)methyl)-5-(3'-ethylphenyl)benzoic acid
Prepared in a similar fashion to "Step d. Synthesis of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5- phenyl)phenylene)methylene)methyl)-5-phenylbenzoic acid" from previously described N-Cbz protected methyl 3-((N-(1 '-(3'-carboxymethyl-5-bromo)phenylene)methylene)methyl)-5-bromobenzoate (0.100 g, 0.165 mmol), 2-ethylphenylboronic acid (0.054 g, 0.363 mmol), sodium carbonate (0.105 g, 0.991 mmol) and bis(triphenylphosphine)palladium (II) dichloride (0.012 g, 0.016 mmol) in MeCN (4 mL) and water (4 mL). Yield 0.033 g, 32% yield. 1 H NMR (Methanol-ck) δ: 8.02 (br s, 2H), 7.84 (br d, J = 16.5 Hz, 2H), 7.66 - 7.12 (m, 15H), 5.27 (s, 2H), 4.71 (br s, 4H), 2.68 (q, J = 7.6 Hz, 4H), 1 .27 (t, J = 7.6 Hz, 8H).
Step b. Synthesis of N-Cbz-deca-Boc-(Compound 149)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-8 (0.082 g, 0.052 mmol), of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5-(3'- ethylphenyl)phenylene)methylene)methyl)-5-(3'-ethylphenyl)benzoic acid (0.01 7 g, 0.026 mmol), DIPEA (0.056 mL, 0.321 mmol) in DMF (5 mL) by dropwise addition of HATU (0.021 g, 0.052 mmol in 1 .5 mL of DMF). Yield 0.01 6 g, 10% yield. MS: [(M-3Boc)+3H]/4 = 855.3.
Step c. Synthesis of deca-Boc-(Compound 149)
Prepared in a similar fashion to "Step f. Synthesis of deca-Boc-(Compound 137)" from N-Cbz- deca-Boc-(Compound 149) (16 mg, 0.004 mmol), SiliaCat® Pd(0) (0.004 g; 0.001 mmol), methanol (1 mL), DMF (0.1 mL) and hydrogen atmosphere (~1 atm). Yield 0.012 g, quantitative yield. MS: [(M- 3Boc)+3H]/4 = 822.3.
Step d. Synthesis of Compound 149
Prepared in a similar fashion to "Step f. Synthesis Compound 1 09" from deca-Boc-(Compound 149) (0.012 g, 0.004 mmol), DCM (2 mL), and TFA (1 mL). Yield 0.016 g, 97% yield as the undeca TFA salt HRMS: (M+2H)/2 = 1292.2, (M+3H)/3 = 861 .8, (M+4H)/4 = 646.6, (M+5H)/5 = 517.5.
Figure imgf000302_0001
The title compound was prepared from INT-14 and INT-26 in an analogous procedure as described for Compound 102. Yield: 46%, 2 steps. MS [(M+4H)/4]+ = 612.7.
Example 188: Synthesis of Compound 151
Figure imgf000302_0002
Step a. Coupling of INT-8 and INT-16 and removal of the Cbz Group
The title compound was prepared from INT-8 and INT-16 in a similar fashion as described for the synthesis of INT-33. Yield: 78%, 2 steps. MS [(M-2Boc+4H)/4]+ = 813.4
Step b. Removal of the Boc groups
The compound from Step a (160 mg, 0.046 mmol) was stirred in a 1 /1 mixture of DCM/TFA (5 mL) and ambient temperature for 20 minutes. The solvent was evaporated and the compound was purified by reversed phase liquid chromatography (RPLC) using an Isco Combiflash liquid chromatograph eluted with 0 % to 75% acetonitrile and water using 0.1 % TFA modifier. Yield: 59 %. MS [(M+3H)/3]+ = 817.2.
Figure imgf000303_0001
Step a. Synthesis of dibenzyl 2,2'-({2-[(tert- butoxycarbonyl)amino]ethyl}azanediyl)diacetate
Benzyl bromo-acetate (4.6g, 20 mmol) was added into the solution of tert-butyl (2- aminoethyl)carbamate(1 .5g, 10mmol) and DIPEA (3.6 mL, 30mmol) in 60 mL DMF, the resulted solution was stirred at room temperature for overnight. The reaction solution was concentrated and purified by flash chromatography to provide products. MS [M+H]+ =457.2.
Step b. Synthesis of dibenzyl di-tert-butyl 2,2',2",2"'-(ethane-1 ,2-diyldinitrilo)tetraacetate
Dibenzyl 2,2'-({2-[(tert-butoxycarbonyl)amino]ethyl}azanediyl)diacetate (900 mg, 2mmol) was treated with TFA and stirred for half hour and then concentrated and dried under high vacuum used for next step without purification.
The De-Boc products from above were dissolved into 10 mL DMF, and then tert-butyl bromo- acetate (600 mg, 3 mmol) and triethylamine (0.7 mL, 5 mmol) were added the solution. The solution was stirred for overnight and concentrated, the residue was purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% acetonitrile and water, using 0.1 % trifluoroacetic acid as the modifier. Yield of oil product 850 mg, 85% yield. MS [M+H]+ =585.3 Step c. Synthesis of benzyl (10S,13S,16S,19R)-13-(2-aminoethyl)-6-[(4S,7S,10S,13R)-7-(2- aminoethyl)-4-hexyl-10-[(1 R)-1-hydroxyethyl]-13-(hydroxymethyl)-2,5,8,11 ,14-pentaoxo-14- {[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10, 13,16,19-heptaazacyclotricosan-21-yl]amino}- 3,6,9,12-tetraazatetradecan-1 -yl]-3-[2-(benzyloxy)-2-oxoethyl]-10-hexyl-16-[(1 R)-1 -hydroxyethyl]-19- (hydroxymethyl)-8,11 ,14,17,20-pentaoxo-20-{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1-hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo- 1 ,4,7, 10, 13,16,19-heptaazacyclotricosan-21-yl]amino}-3,6,9, 12,15, 18-hexaazaicosan-1-oate
(Compound 152)
Dibenzyl di-tert-butyl 2,2',2",2"'-(ethane-1 ,2-diyldinitrilo)tetraacetate (60 mg, 0.1 mmol) was treated with TFA and stirred for half hour and then concentrated and dried under high vacuum used for next step without purification.
The de-butylated products from above step, triethylamine (0.15 mL, 1 mmol) and INT-37 (330 mg, 0.2 mmol) in 10 mL DMF was added HATU (80 mg, 0.2mmol) in 1 mL DMF by syringe pump over 1 hour. Then the resulted solution was concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 5% to 100% methanol and water, using no modifier. Yield of product, 230 mg, 87% yield.
Step d. Removal of the Boc Groups
Per-Boc-(Compound 152) from previous step was treated in 2 mL DCM and 2 mL TFA at room temperature, the solution was stirred 1 0 min, then concentrated and purified by reverse phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% acetonitrile and water, using formic acid as the modifier. Yield 150 mg, 53% yield. MS: [(M+3H)/3]+= 940.2, [(M+4H)/4]+= 706.4 [(M+5H)/5]+=564.5 [(M+6H)/6]+=470.6.
Example 190. Synthesis of (10S,13S,16S,19R)-13-(2-aminoethyl)-6-[(4S,7S,10S,13R)-7-(2- aminoethyl)-4-hexyl-10-[(1 R)-1-hydroxyethyl]-13-(hydroxymethyl)-2,5,8,11 ,14-pentaoxo-14- {[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2-aminoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10, 13,16,19-heptaazacyclotricosan-21-yl]amino}- 3,6,9,12-tetraazatetradecan-1 -yl]-3-(carboxymethyl)-10-hexyl-16-[(1 R)-1 -hydroxyethyl]-19- (hydroxymethyl)-8,11 ,14,17,20-pentaoxo-20-{[(3S,6S,9S,12S,15R,18S,21 S)-6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1-hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo- 1 ,4,7, 10, 13,16,19-heptaazacyclotricosan-21-yl]amino}-3,6,9, 12,15, 18-hexaazaicosan-1-oic acid (Compound 153)
Figure imgf000305_0001
Compound 1 52 (28 mg, 0.01 mmol) was dissolved into 3 mL 5% H2O in MeOH, then 50 mg of 5% palladium on charcoal was added above solution, and the mixture was stirred at room temperature under the hydrogen atmosphere for 2hours. The palladium charcoal was removed by filtration, and the filtrate was concentrated to yield product 20 mg in 77% yield. MS: [(M+3H)/3]+=880.2, [(M+4H)/4]+=660.4, [(M+5H)/5]+=528.5, [(M+6H)/6]+=440.6.
Example 191 : Synthesis of Compound 155 through Compound 159 and Compound 171 through Compound 178
General Procedure: INT-10 was dissolved in DMF to obtain a 0.2 M stock solution. Next, stock solutions of the diacids listed in Table 14 were prepared aiming at a concentration of about 0.1 M. In a 96- well microtiter plate, the corresponding diacid (1 eq.), HATU (0.5 M stock solution, 2 eq.), DIPEA (5 eq.), and the solution of INT-10 (25 mg, 2.5 eq.) were consecutively added to each individual well. After completion of addition, the plate was sealed with the cap mat and left overnight. Next, the solvent was evaporated in a centrifugal evaporator under reduced pressure and cleavage cocktail (v/v 92.5% TFA, 5%H20, 2.5% TIS, 1 mL) was added to each well. After 3h, the cleavage cocktail was blown away with a stream of nitrogen. The crude peptides were analyzed and purified with RP-HPLC using TFA as modifier. Fractions were collected and lyophilized. The purity of the final products was analyzed by RP-HPLC. Table 14.
Figure imgf000306_0001
Figure imgf000307_0001
Figure imgf000308_0001
Step a. Synthesis of deca-Boc-(Compound 160)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-10 (0.200 g, 0.1 17 mmol), D-2,3-lsopropylidene tartaric acid (0.01 1 g, 0.058 mmol), DIPEA (0.125 mL, 0.71 5 mmol) in DMF (5 mL) by dropwise addition of HATU (0.091 g, 0.240 mmol in 1 .5 mL of DMF). Yield 0.044 g, 21 % yield. MS: [(M-3Boc)+3H]/4 = 81 6.7.
Step b. Synthesis Compound 160
Prepared in a similar fashion to "Step e. Synthesis Compound 166" from deca-Boc-(Compound 160) (0.044 g, 0.012 mmol), DCM (4 mL), triethylsilane (0.25 mL) and TFA (2 mL). Yield 0.030 g, 64% yield as the deca TFA salt. Ions found by LC-MS: (M+3H)/3 = 854.7, (M+4H)/4 = 641 .2, (M+5H)/5 = 513.2.
Example 193: Synthesis of Compound 161 - (2R,5S,8S,15S,18S,21 R)-8,15-dihexyl-5,18-bis[(1 R)-1- hydroxyethyl]-2,21-bis(hydroxymethyl)-4,7,10,13,16,19-hexaoxo-N~1 ~,N~22~- bis(3S,6S,9S,12S,15R,18S,21 S)[6,9,18-tris(2-am inoethyl)-15-benzyl-3-[(1 R)-1 -hydroxyethyl]-12-(2- methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-1 , 4,7,10,13,16,19-heptaazacyclotricosan-21 -yl]-
3,6,9, 11 ,14,17,20-heptaazadocosane-1 ,22-diamide
Figure imgf000308_0002
The title compound was prepared analogously to Compound 96 using INT-13 as the starting material. MS: [(M+3H)/3]+ = 755.8, [(M/4+4H)/4]+ =567.1 , [(M+5H)/5]+ =453.9. Example 194: Synthesis of Compound 162 - (2R,5S,8S,11S,18S,21 S,24S,27R)-8,21-bis(2- aminoethyl)-11 ,18-dihexyl-5,24-bis[(1 R)-1-hydroxyethyl]-2,27-bis(hydroxymethyl)-
4,7,10,13,16,19,22,25-octaoxo-N~1 ~,N~28~-bis(3S,6S,9S,12S,15R,18S,21 S)[6,9,18-tris(2- aminoethyl)-15-benzyl-3-[(1 R)-1-hydroxyethyl]-12-(2-methylpropyl)-2,5,8,11 ,14,17,20-heptaoxo-
1 , 4,7,10,13,16,19-heptaazacyclotricosan-21-yl]-3,6,9,12,14,17,20,23,26-nonaazaoctacosane-1 , 28- diamide
Figure imgf000309_0001
The title compound was prepared analogously to Compound 96 using INT-14 as the starting material. MS: [(M+3H)/3]+ = 822.5, [(M+4H)/4]+ =617.1 , [(M+5H)/5]+ =493.9.
Figure imgf000309_0002
Step a. Synthesis of deca-Boc-(Compound 163)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Comopund 1 09)" from INT-10 (0.200 g, 0.1 17 mmol), L-2,3-lsopropylidene tartaric acid (0.01 1 g, 0.058 mmol), DIPEA (0.125 mL, 0.71 5 mmol) in DMF (5 mL) by dropwise addition of HATU (0.091 g, 0.240 mmol in 1 .5 mL of DMF). Yield 0.1 18 g, 28% yield. MS: [(M-3Boc)+3H]/4 = 81 6.8.
Step b. Synthesis Compound 163
Prepared in a similar fashion to "Step e. Synthesis Compound 166" from deca-Boc-(Compound 163) (0.1 18 g, 0.033 mmol), DCM (4 mL), triethylsilane (0.25 mL) and TFA (2 mL). Yield 0.101 g, 81 % yield as the deca TFA salt. Ions found by LC-MS: (M+3H)/3 = 854.6, (M+4H)/4 = 641 .3, (M+5H)/5 = 513.2.
Figure imgf000310_0001
Step a. Synthesis of Gly-lnt-1
To a mixture of lnt-1 (1 .03 g, 1 mmol) and Z-Gly-OH (251 .1 mg, 1 .2 mmol) in anhydrous DMF (2 mL) was added HATU (456 mg, 1 .2 mmol). After the mixture was stirred for 10 minutes, it was added with DIPEA, and the reaction was continued for 30 minutes. It was then purified by RPLC (150 g, 20 to 85 % MeOH and water). The collected fractions were concentrated to a white solid (LCMS: [(M- 2Boc)/2]+ = 510). The material was re-dissolved in MeOH (20 mL) and added with Pd/C. The mixture was stirred under hydrogen for 3 hours. Pd/C was filtered, and the filtrate was concentrated by rotary evaporation and further dried under high vacuum. Yield 676 mg, 62.3 %. MS: [(M - Boc+2H)/2]+ = 493, [(M - 3Boc+2H)/2]+ = 393.
Step b. Synthesis of octa-Boc Compound 164 precursor
To a solution of step-a product (270.9 mg, 0.242 mmol) and Trans-cyclopentane-(Bis-norleu- YBocDab-Thr) linker (INT-18) (108.6 mg, 0.1 1 mmol) in anhydrous DMF (1 .5 mL) and DIPEA (65 mg, 0.5 mmol) was drop-wise added a solution of HATU (92 mg, 0.242 mmol) in DMF (0.5 mL) via syringe pump at a rate of 1 mL/hr. After the addition, the mixture was purified by RPLC (100 g, 20 to 95 % MeOH and water). Yield 264.2 mg, 75.3 %. MS: [(M - 3Boc+3H)/3]+ = 963.1 , [(M - 4Boc+3H)/3]+ = 930, [(M - 5Boc+3H)/3]+ = 896.6, [(M - 6Boc+3H)/3]+ = 863.9.
Figure imgf000311_0001
Step-b product was dissolved in 2 mL of TFA. The solution was stirred for 20 minutes. It was directly purified by HPLC (0 to 20 % acetonitrile and water, using 0.1 % TFA as modifier). Yield 149 mg, 54.5 %. MS:[(M+2H)/2]+ = 1 194.2, [(M+3H)/3]+ = 796.5, [(M+4H)/4]+ = 597.6, [(M+5H)/5]+ = 478.4, [(M+6H)/6]+ = 398.8.
Figure imgf000311_0002
The title compound was prepared analogously to Compound 1 64 using lnt-2 as starting material. MS: [(M+3H)/3]+ = 774.2, [(M+4H)/4]+ = 580.8, [(M+5H)/5]+ = 464.8, [(M+6H)/6]+ = 387.6, [(M+7H)/7]+ = 332.4.
Example 198: Synthesis of Compound 166
Figure imgf000312_0001
step d,e
1.INT-8,DIPEA,HATU DMF
2.TFA,Et3SiH,DCM
Figure imgf000312_0002
Step a. Synthesis of methyl 3-hydroxy-5-phenylbenzoate
A stirring mixture of 3-hydroxy-5-phenylbenzoic acid (0.508 g, 2.371 mmol) in methanol (30 mL) and sulfuric acid (0.300 mL, 98%) was heated at 75 in a sealed tube overnight. The reaction mixture was then added dropwise to a solution of sodium bicarbonate (1 .90 g in 20 mL) under vigorous stirring. When gas evolution ceased (bubbler monitoring), the mixture was reduced in volume (by about 25 mL) by rotatory evaporation. This concentrate was extracted with DCM (3 x 30 mL). The combined organics were dried with brine and solid magnesium sulfate. After filtration through a short Celite pad, the volatiles were evaporated. HPLC analysis revealed the desired compound in high purity, and this material was used without further purification. Yield 0.393 g, 73%. 1 H NMR (DMSO-afe) δ: 10.01 (s, 1 H), 7.63 (ddd, J = 4.4, 3.2, 1 .3 Hz, 3H), 7.53 - 7.44 (m, 2H), 7.43 - 7.33 (m, 2H), 7.28 (t, J = 2.0 Hz, 1 H), 3.86 (s, 3H)
Step b. Synthesis of 3-(methoxycarbonyl)-5-(phenyl)phenyl trifluoromethanesulfonate
To a 0°C stirring solution of methyl 3-hydroxy-5-phenylbenzoate (0.393 g, 1 .722 mmol) and 1 ,1 ,1 - trifluoro-N-phenyl-N-(trifluoromethanesulfonyl)methanesulfonamide (0.677 g, 1 .894 mmol) in N,N- dimethylformamide (5 mL) it was added triethylamine (0.360 mL, 2.583 mmol) and 4- dimethylaminopyridine (0.042 g, 0.344 mmol). The temperature was raised to ambient after 10 minutes and stirring was continued until complete disappearance of the phenolic starting material by LC-MS analysis. All the volatiles were removed per rotatory evaporation. The residue was taken up in ethyl acetate and washed with a saturated solution of ammonium chloride, then brine and finally treated with solid sodium sulfate. Upon filtration, all the volatiles were evaporated. The desired product was isolated by normal phase liquid chromatography using an Isco CombiFlash liquid chromatograph eluted with 1 % to 15% hexanes and ethyl acetate. Yield 0.585 g, 94% yield. 1 H NMR (DMSO-afe) δ: 8.29 (t, J = 1 .6 Hz, 1 H), 8.17 (t, J = 2.1 Hz, 1 H), 7.94 (dd, J = 2.5, 1 .4 Hz, 1 H), 7.84 - 7.75 (m, 2H), 7.60 - 7.43 (m, 3H), 3.93 (s, 3H). Step c. Synthesis of 3,5-bis(3'-carboxy-5'phenylphenylene)phenol
Prepared in a similar fashion to "Step d. Synthesis of N-Cbz protected 3-((N-(1 '-(3'-carboxy-5- phenyl)phenylene)methylene)methyl)-5-phenylbenzoic acid" from previously described 3- (methoxycarbonyl)-5-(phenyl)phenyl trifluoromethanesulfonate (0.470 g, 1 .304 mmol), 3,5-bis(4,4,5,5- tetramethyl-1 ,3,2-dioxaborolan-2-yl)phenol (0.226 g, 0.652 mmol, prepared accordingly to Chem
Commun, 2014, 50(89), 13683-13686), sodium carbonate (0.346 g, 3.261 mmol) and
bis(triphenylphosphine)palladium (II) dichloride (0.046 g, 0.065 mmol) in MeCN (5 mL) and water (5 mL). The desired product was isolated as a dodeca-TFA salt by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% methanol and water, using TFA as the modifier. Yield 0.074 g, 23% yield. Ή NMR (DMSO-afe) δ: 13.24 (br s, 2H), 9.82 (s, 1 H), 8.40 - 8.05 (m, 6H), 7.95 - 7.75 (m, 4H), 7.67 - 7.33 (m, 7H), 7.1 8 (d, J = 13.6 Hz, 2H)
Step d. Synthesis of deca-Boc-(Compound 166)
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-8 (0.100 g, 0.064 mmol), 3,5-bis(3'-carboxy-5'phenylphenylene)phenol (0.016 g, 0.032 mmol), DIPEA (0.079 mL, 0.454 mmol) in DMF (3 mL) by dropwise addition of HATU (0.026 g, 0.067 mmol in 1 .5 mL of DMF). Yield 0.076 g, 33% yield. MS: [(M-3Boc)+3H]/4 = 820.0.
Step e. Synthesis Compound 166
A solution of deca-Boc-(Compound 166) (0.076 g, 0.021 mmol), dissolved in DCM (4 mL) and triethylsilane (0.250 mL), was treated with TFA (2 mL), while stirring at room temperature. After 30 minutes, all the volatiles were evaporated per vacuum techniques. The desired product was isolated as the deca-TFA salt by reversed phase liquid chromatography (RPLC) using an Isco CombiFlash liquid chromatograph eluted with 0% to 100% methanol and water, using TFA as the modifier. Yield 0.066 g, 84% yield. Main ions found by HRMS: (M+2H)/2 = 1289.2, (M+3H)/3 = 859.8, (M+4H)/4 = 645.1 , (M+5H)/5 = 51 6.3.
Figure imgf000313_0001
Figure imgf000314_0001
Step a. Coupling of homo-Ser to INT-1
A solution of HATU (182.06 mg, 0.49 mmol) in DMF (1 .0 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-1 (578.0 mg, 0.12 mmol), (2S)-4-hydroxy-2- [(phenylmethoxy)carbonylamino]butanoic acid (125.02 mg, 0.48 mmol) and diisopropylethylamine (144.69 mg, 1 .12 mmol) in DMF (5.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-30-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the desired compound (1 1 7.56 mg, 75%). LC/MS [(M-2Boc)+2H]/2 549.8.
Step b. Removal of the Cbz group
A solution of the product from Step a. in methanol (5 mL) was charged with 5% Pd/C and stirred in under H2 balloon for 16 hours. After the reaction was completed, the reaction mixture was filtered through a pad of Celite®, washed with MeOH then concentrated under reduced pressure. The residue was purified by reverse phase liquid chromatography (5-30-80% of methanol in Dl water without TFA as modifier) to yield the title compound as free base white solid (487.6 mg, 93%). LC/MS [(M-2Boc)+2H]/2 482.0.
Step c. Coupling of Cbz-Thr
A solution of HATU (156.89 mg, 0.41 mmol) in DMF (0.9 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of the product from Step b. (0.40 mg, 0.34 mmol), Z-L-Thr-OH (104.49 mg, 0.41 mmol) and diisopropylethylamine (133.21 mg, 1 .03 mmol) in DMF (4.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5- 25-85% of methanol in Dl water) to yield the title compound as free base (450.1 mg, 84%). LC/MS [(M- 2Boc)+2H]/2 600.8.
Step d. Removal of the Cbz protecting group
The product from Step c. (405.1 mg, 0.29 mmol) was dissolved in MeOH (1 0 mL), and 5% Pd/C (61 .65 mg, 0.029 mmol) was added. Under H2 gas balloon, the reaction mixture was stirred at room temperature overnight. It was then filtered through a pad of Celite® and washed with MeOH then concentrated under reduced pressure. The residue was purified by reversed phase liquid chromatography (5-20-80% in methanol and Dl water) to yield the title compound as a free base white solid (381 .7 mg, 93%). LC/MS [(M-2Boc)+2H]/2 532.8. Step e. Coupling of protected L-Dab
A solution of HATU (122.58 mg, 0.32mmol) in DMF (0.9 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of the product from Step d. (381 .7 mg, 0.29 mmol), Z-L-Dab-OH (1 13.6 mg, 0.32 mmol) and diisopropylethylamine (1 04.08 mg, 0.81 mmol) in DMF (5.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5- 20-85% of methanol in Dl water) to yield the title compound as free base (313.0 mg, 67%). LC/MS [(M- 2Boc)+2H]/2 699.9.
Step f. Removal of the Cbz group
To a solution of the product from Step e. in MeOH (2 mL) was added SiCatPd(O) and H2 balloon. The reaction was stirred at room temperature overnight. After the reaction was completed, the reaction mixture was filtered through a pad of Celite®, and washed with MeOH then concentrated under reduced pressure. The residue was purified by reverse phased liquid chromatography (5-20-85% of methanol and Dl water without TFA as a modifier) to yield the title compound as a free base (171 .80 mg, 58%). LC/MS [(M-2Boc)+2H]/2 633.9.
Step g. Synthesis of Compound 168
A solution of HATU (31 .15 mg, 0.082mmol) in DMF (0.5 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of the amine product from Step f. (125.30 mg, 0.082 mmol), INT-26 (15.30 mg, 0.039 mmol) and diisopropylethylamine (30.23 mg, 0.23 mmol) in DMF (3.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5- 30-100% of methanol in Dl water) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid
chromatography (0-40% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (12.1 mg, 9%). LC/MS (M+4H)/4 620.3, (M+5H)/5 496.5 and (M+6H)/6 414.2.
Example 200: Synthesis of Compound 170
Figure imgf000315_0001
Step a. Synthesis of dimethyl 2,3-O-methylene-L-tartaric acid
Prepared in a similar fashion to "Step d. Synthesis of N,N-1 ,3-Phenylene bis-(2-aminooctanoic acid)" from dimethyl 2,3-O-methylene-L-tartrate (1 .158 g, 6.090 mmol, prepared accordingly to PCT Int. AppL, 2007139749), NaOH (0.499 g, 12.48 mmol), MeOH (7 mL) , and water (1 mL). Yield 0.590 g, 60% yield, and the material used in the next step without further purification. 1 H NMR (Methanol-dt) δ: 5.18 (s, 2H), 4.74 (s, 2H).
Step b. Synthesis of tartaric linker-3
Prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from (S)-methyl 2-aminooctanoate (0.676 g, 3.720 mmol), 2,3-O-methylene-L-tartaric acid, (0.300 g, 1 .851 mmol), 2,4,6- trimethylpyridine (1 .492 mL, 1 1 .29 mmol) in DMF (1 0 mL) by dropwise addition of HATU (1 .422 g, 3.734 mmol in 1 0 mL of DMF). Yield 0.694 g, 90% yield. MS: (M+H)+ = 421 .3 - 417.2.
Step c. Synthesis of deca-Boc-(Compound 170)
The intermediate diacid was prepared in similar fashion to "Step d. Synthesis of N,N-1 ,3- Phenylene bis-(2-aminooctanoic acid)" from tartaric linker-3 (0.694 g, 1 .666 mmol), LiOH (0.084 g, 3.499 mmol), THF (5 mL), and water (5 mL). Yield was considered quantitative and the material used in the next step without further purification. Deca-Boc-(Compound 170) was prepared in a similar fashion to "Step e. Synthesis of deca-Boc-(Compound 1 09)" from INT-8 (0.200 g, 0.128 mmol), the herein above described intermediated diacid (0.025 g, 0.064 mmol), DIPEA (0.057 mL, 0.326 mmol) in DMF (5 mL) by dropwise addition of HATU (0.050 g, 0.131 mmol in 1 .5 mL of DMF). Yield 0.176 g, 79% yield. MS: [(M- 3Boc)+3H]/4 = 795.5
Step d. Synthesis Compound 170
Prepared in a similar fashion to "Step e. Synthesis Compound 166" from deca-Boc-(Compound 170) (0.176 g, 0.050 mmol), DCM (4 mL), triethylsilane (0.25 mL) and TFA (2 mL). Yield 0.122 g, 67% yield as the deca TFA salt. Ions found by LC-MS: (M+4H)/4 = 620.3, (M+5H)/5 = 496.4.
Example 201. Synthesis of INT-38
Figure imgf000316_0001
Step a. Coupling of cis-Cyclohexane 1 ,2-Dicarboxylic Acid
A solution of HATU (4.87 g, 12.82 mmol) in DMF (20.5 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of c/'s-cyclohexane-1 ,2-dicarboxylic acid (1 .00 g, 5.82 mmol), L-Norleu- OMe-hydrochloride (2.33 g, 12.82 mmol), and diisopropylethylamine (4.53 g, 35.02 mmol) in DMF (8.3 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-50% of acetonitrile in Dl water with 0.1 % TFA as modifier) to yield the diester (1 .29 g, 52%). LC/MS [M+H] 427.3.
Step b. Hydrolysis of the Methyl Ester
To a solution of the product from Step a. in THF:MeOH:H20 (1 :1 :2, 30 mL) was added LiOH (217.3 mg, 9.07 mmol). The reaction mixture was stirred at room temperature for 3 hours. After the reaction was completed. The reaction mixture was quenched with acetic acid to pH4 then concentrated under reduced pressure. The residue was purified by reverse phase liquid chromatography (Isco, 0-50% ACN/H2O with 0.1 % TFA; P came at 38%) to yield the title compound as a white solid (1 .22 g, 100%). LC/MS [M+H] 399.2.
Figure imgf000317_0001
A solution of HATU (41 .98 mg, 0.1 1 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-38 (20.10 mg, 0.05 mmol), INT-8 (172.67 mg, 0.1 1 mmol) and diisopropylethylamine (38.89 mg, 0.30 mmol) in DMF (2.0 mL). The reaction mixture was stirred for an additional hour then applied directly to reverse phase liquid chromatography (5-30-100% of methanol in Dl water) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in
TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reverse phase liquid chromatography (0-30% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (14.6 mg, 8%). LC/MS [(M+4)/4]+ = 622.8, [(M+5)/5]+ = 498.25, [(M+6)/6]+ = 415.55.
Example 203. Preparation of INT-39
Figure imgf000317_0002
Step a. Coupling of Cyclopentane 1 ,2-Dicarboxylic Acid
To a solution of racemic trans-cyclopentane-1 ,2-dicarboxylic acid (0.70 g, 4.44 mmol), methyl (2S)-2-aminopentanoate (1 .28 g, 9.77 mmol), and diisopropylethylamine (3.44 g, 26.66 mmol) in DMF (12.6 mL) was added a solution of HATU (3.72 g, 9.77 mmol) in DMF (21 mL) via a syringe pump at a rate of 2.5 mL/hr. After the addition, the reaction mixture was stirred for an additional of 1 h at room temperature. The volume of solvent was reduced under reduced pressure then applied directly to reversed phase liquid chromatography (5-35% acetonitrile and water with 0.1 % TFA as modifier) to yield two diastereomers: a more polar diastereomer (a) (490 mg, 29%) and a less polar diastereomer (b) (550 mg, 38%). LC/MS [M+H] = 385.0. Note: the isomers were taken forward separately in subsequent synthesis.
Step b. Hydrolysis of Methyl Ester
A solution of the more polar isomer from Step a. (330. Omg, 0.86 mmol) and LiOH (61 .67 mg, 2.68 mmol) was stirred in MeOH :THF:H20 (1 :1 :2, 30 mL) at room temperature overnight. After the reaction was completed, it was quenched with AcOH to pH 3 then concentrated under reduced pressure. The residue was redissolved in MeOH and absorbed in Celite® then purified by reversed phase liquid chromatography (0-30% of acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound as a white solid (176.5 mg, 58%). LC/MS (M+H) = 357.0.
Example 204. Preparation of Compound 180
Figure imgf000318_0001
A solution of HATU (35.21 mg, 0.093 mmol) in DMF (0.4 mL) was added via a syringe pump at a rate of 2.5 mL/hr into a solution of INT-39 (15.0 mg, 0.042 mmol), INT-8 (134.32 mg, 0.093 mmol) and diisopropylethylamine (32.61 mg, 0.25 mmol) in DMF (1 .0 mL). The reaction mixture was stirred for an additional hour then applied directly to reversed phase liquid chromatography (5-25-100% of methanol in Dl water with 0.1 % TFA as modifier) to yield the Boc-protected intermediate. The Boc-protected intermediate was stirred in TFA:DCM (1 :1 , 4 mL) at room temperature for 20 minutes. After the reaction was completed, the reaction mixture was concentrated and purified by reversed phase liquid
chromatography (0-30% acetonitrile and water with 0.1 % TFA as modifier) to yield the title compound (45.5 mg, 32%). LC/MS [(M+4H)/4]+ 605.9, [(M+5H)/5]+ 484.9, [(M+6H)/6]+ 404.2.
Other Embodiments
While the disclosure has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the disclosure following, in general, the principles of the disclosure and including such departures from the present disclosure come within known or customary practice within the art to which the disclosure pertains and may be applied to the essential features hereinbefore set forth. All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

Claims

What is claimed is:
1 . A compound described by formula (I):
M2-U-M1
(I)
wherein M1 comprises a first cyclic heptapeptide comprising a linking nitrogen and M2 comprises a second cyclic heptapeptide comprising a linking nitrogen;
L' is a linker covalently attached to the linking nitrogen in each of M1 and M2, or a
pharmaceutically acceptable salt thereof;
wherein L' is not
Figure imgf000320_0001
wherein L" is a remainder of L'; and
each of R'L and RL is, independently, C1 -C1 0 alkyl.
2. The compound of claim 1 , wherein L' is described by:
— A2— L— A1— \
wherein L is a remainder of L';
A1 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M1 or is absent; and A2 is a 1 -5 amino acid peptide covalently attached to the linking nitrogen in M2 or is absent.
3. The compound of claim 1 or 2, wherein the compound is described by formula (II):
Figure imgf000320_0002
(II)
wherein L is a remainder of L':
each of each of R1 , R12, R'1 , and R'12 is, independently, a lipophilic moiety, a polar moiety, or H; each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is, independently, optionally substituted C1 -C5 alkamino, a polar moiety, a positively charged moiety, or H;
each of R15 and R'15 is, independently, a lipophilic moiety or a polar moiety;
each of R2, R3, R4, R5, R6, R7, R8, R9, R10, R'2, R'3, R'4, R'5, R'6, R'7, R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5- C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl ; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring;
each of a', b', c', a, b, and c is, independently, 0 or 1 ;
each of N1 , N2, N3, N4, N'1 , N'2, N'3, and N'4 is a nitrogen atom,
each of C1 , C2, C3, C'1 , C'2, and C'3 is a carbon atom,
or a pharmaceutically acceptable salt thereof.
4. The compound of claim 3, wherein the compound comprises at least one optionally substituted 5-8 membered ring formed by joining (i) R2, R3, and C1 ; (ii) R3, R4, N1 , and C1 ; (iii) R5, R6, and C2; (iv) R6, R7, N2, and C2; (v) R8, R9, and C3; (vi) R9, R10, N3, and C3; (vii) R'2, R'3, and C'1 ; (viii) R'3, R'4, N'1 , and C'1 ; (ix) R'5, R'6, and C'2; (x) R'6, R'7, N'2, and C'2; (xi) R'8, R'9, and C'3; or (xii) R'9, R'10, N'3, and C'3.
5. The compound of any one of claims 1 -4, wherein the compound is described by formula (III)
Figure imgf000321_0001
(III)
wherein L is a remainder of L';
or a pharmaceutically acceptable salt thereof.
6. The compound of any one of claims 3-5, wherein
each of R1 , R12, R'1 , and R'12 is, independently, a lipophilic moiety;
each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is, independently, optionally substituted C1 -C5 alkamino, a polar moiety, or a positively charged moiety; and/or
each of R15 and R'15 is, independently, a polar moiety.
7. The compound of any one of claims 3-6, wherein each of R1 , R12, R'1 , and R'12 is a lipophilic moiety.
8. The compound of claim 7, wherein each lipophilic moiety is, independently, optionally substituted C1 - C20 alkyi, optionally substituted C5-C1 5 aryl, optionally substituted C6-C35 alkaryl, or optionally substituted C3-C15 heteroaryl.
9. The compound of claim 7 or 8, wherein each lipophilic moiety is, independently, C1 -C8 alkyi, methyl substituted C2-C4 alkyi, (C1 -C10)alkylene(C6)aryl, phenyl substituted (C1 -C10)alkylene(C6)aryl, or alkyi substituted C4-C9 heteroaryl.
10. The compound of any one of claims 7-9, wherein each lipophilic moiety is, independently, benzyl, isobutyl, sec-butyl, isopropyl, n-propyl, methyl, biphenylmethyl, n-octyl, or methyl substituted indolyl.
1 1 . The compound of any one of claims 3-10, wherein each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is independently optionally substituted C1 -C5 alkamino.
12. The compound of claim 1 1 , wherein each of R1 1 , R13, R14, R'1 1 , R'13, and R'14 is CH2CH2NH2.
13. The compound of any one of claims 3-12, wherein each of R15 and R'15 is a polar moiety.
14. The compound of claim 13, wherein each polar moiety comprises a hydroxyl group, a carboxylic acid group, an ester group, or an amide group.
15. The compound of claim 13 or 14, wherein each polar moiety is hydroxyl substituted C1 -C4 alkyi.
16. The compound of any one of claims 13-15, wherein each polar moiety is CHCH3OH.
17. The compound of claim 3, wherein the compound is described by formula (IV):
Figure imgf000322_0001
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2,
or a pharmaceutically acceptable salt thereof.
18. The compound of claim 17, wherein the compound is described by formula (IV-1 ):
Figure imgf000323_0001
(IV-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
19. The compound of claim 17, wherein the compound is described by formula (IV-2):
Figure imgf000323_0002
(IV-2)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2, or a pharmaceutically acceptable salt thereof.
20. The compound of claim 3, wherein the compound is described by formula (V):
Figure imgf000323_0003
(V) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3- C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl,
or a pharmaceutically acceptable salt thereof.
21 . The compound of claim 20, wherein the compound is described by formula (V-1 ):
Figure imgf000324_0001
(V-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
22. The compound of claim 21 , wherein the compound is described by formula (V-2):
Figure imgf000324_0002
(V-2)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
23. The compound of claim 20, wherein the compound is described by formula (V-3):
Figure imgf000325_0001
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
24. The compound of claim 23, wherein the compound is described by formula (V-4):
Figure imgf000325_0002
(V-4)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
25. The compound of claim 24, wherein the compound is described by formula (V-5):
Figure imgf000325_0003
(V-5)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
26. The compound of claim 3, wherein the compound is described by formula (VI):
Figure imgf000326_0001
(VI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R8, R'2, R'6, and R'8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl,
or a pharmaceutically acceptable salt thereof.
27. The compound of claim 26, wherein the compound is described by formula (VI-1 ):
Figure imgf000326_0002
(VI-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof. The compound of claim 27, wherein the compound is described by formula (VI-2)
Figure imgf000327_0001
(VI-2)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
29. The compound of claim 26, wherein the compound is described by formula (VI-3):
Figure imgf000327_0002
(VI-3)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
30. The compound of claim 29, wherein the compound is described by formula (VI-4):
Figure imgf000327_0003
(VI-4)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
31 . The compound of claim 26, wherein the compound is described by formula (VI-5):
Figure imgf000328_0001
(VI-5)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
32. The compound of claim 31 , wherein the compound is described by formula (VI-6):
Figure imgf000328_0002
(VI-6)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
The compound of claim 32, wherein the compound is described by formula (VI-7):
Figure imgf000328_0003
(VI-7)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
34. The compound of claim 3, wherein the compound is described by formula (VII):
Figure imgf000329_0001
(VII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R8, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl,
or a pharmaceutically acceptable salt thereof.
35. The compound of claim 3, wherein the compound is described by formula (VIII):
Figure imgf000329_0002
(VIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R8, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl, or a pharmaceutically acceptable salt thereof.
36. The compound of claim 3, wherein the compound is described by formula (IX):
Figure imgf000330_0001
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyi, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl,
or a pharmaceutically acceptable salt thereof.
37. The compound of claim 3, wherein the compound is described by formula (X):
Figure imgf000330_0002
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2 and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyi, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted heteroalkyi, optionally substituted C3-C20 heterocycloalkyi, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl,
or a pharmaceutically acceptable salt thereof.
38. The compound of claim 37, wherein the compound is described by formula (X-1 ):
Figure imgf000331_0001
(X-1 )
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
39. The compound of any one of claims 24, 26, and 34-37, wherein each of R2 and R'2 is optionally substituted C1 -C5 alkamino.
40. The compound of claim 39, wherein each of R2 and R'2 is CH2NH2 or CH2CH2NH2.
41 . The compound of any one of claims 24, 26, and 34-37, wherein each of R2 and R'2 is a polar moiety.
42. The compound of claim 41 , wherein each polar moiety comprises a hydroxyl group, a carboxylic acid group, an ester group, or an amide group.
43. The compound of claim 41 or 42, wherein each polar moiety is hydroxyl substituted C1 -C4 alkyl.
44. The compound of claim 43, wherein each polar moiety is CHCH3OH or CH2OH.
45. The compound of any one of claims 24, 26, and 34-36, wherein R6 is a polar moiety.
46. The compound of any one of claims 24, 26, and 34, wherein R'6 is a polar moiety.
47. The compound of claim 45 or 46, wherein the polar moiety comprises a hydroxyl group, a carboxylic acid group, an ester group, or an amide group.
48. The compound of any one of claims 45-47, wherein the polar moiety is hydroxyl substituted C1 -C4 alkyl.
49. The compound of claim 48, wherein the polar moiety is CHCH3OH or CH2OH.
50. The compound of any one of claims 26, 34, and 35, wherein R8 is optionally substituted C1 -C5 alkamino.
51 . The compound of claim 26, wherein R'8 is optionally substituted C1 -C5 alkamino.
52. The compound of claim 50 or 51 , wherein the optionally substituted C1 -C5 alkamino is CH2NH2 or
53. The compound of claim 3, wherein the compound is described by formula (XI):
Figure imgf000332_0001
(XI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2,
or a pharmaceutically acceptable salt thereof.
54. The compound of any one of claims 1 -53, wherein L', L", or L comprises one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, optionally substituted C3-C15 heteroarylene, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino, wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C1 5 heteroaryl.
55. The compound of any one of claims 1 -54, wherein the backbone of L', L", or L comprises no more than 100 atoms.
56. The compound of claims 55, wherein the backbone of L', L", or L consists of one or more optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, optionally substituted C3-C15 heteroarylene, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino, wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C1 5 heteroaryl.
57. The compound of any one of claims 2-53, wherein L is a bond.
58. The compound of any one of claims 2-53, wherein L is capable of forming an amide, a carbamate, a sulfonyl, or a urea linkage.
59. The compound of any one of claims 2-56, wherein L is described by formula (L-1 ):
l1-(V1)f-(U1 )g-(V2)h-(U2)i-(V3)j-(U3)k-(V4)|-(U4)m-(V5)n-l2
(L-1 )
wherein I1 is a bond attached to A2 or M2 if A2 is absent;
I2 is a bond attached to A1 or M1 if A1 is absent;
each of U1 , U2, U3, and U4 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C1 5 heteroarylene;
each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino; wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C1 5 heteroaryl; and
each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
The compound of claim 59, wherein L is
Figure imgf000334_0001
61 . The compound of claim 59, wherein each of U1 , U2, U3, and U4 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, or optionally substituted C2-C20 heteroalkynylene;
each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino;
wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C1 5 heteroaryl; and
each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 . The compound of claim 61 , wherein L is
Figure imgf000335_0001
Figure imgf000336_0001
wherein d is an integer from 1 to 5.
63. The compound of claim 59, wherein each of U1 , U2, U3, and U4 is, independently, optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene, or optionally substituted C3-C15 heteroarylene;
each of V1 , V2, V3, V4, and V5 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino;
wherein R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C5-C1 5 heteroaryl; and
each of f, g, h, i, j, k, I, m, and n is, independently, 0 or 1 .
64. The compound of claim 63, wherein L is
Figure imgf000336_0002
Figure imgf000337_0001
A compound of formula (XII):
Figure imgf000337_0002
(XII)
wherein:
each A1 and A2 is an independently selected amino acid;
L is a linker that, when m is 1 , 2, 3, 4, or 5, is bound to a nitrogen atom in any A1 and a nitrogen atom in any A2;
each m is independently 0, 1 , 2, 3, 4, or 5; and
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
or a pharmaceutically acceptable salt thereof.
66. The compound of claim 65, wherein Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of a natural amino acid, or a pharmaceutically acceptable salt thereof.
67. The compound of claim 65, wherein at least one of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
68. The compound of claim 65, wherein at least two of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
69. The compound of claim 65, wherein at least three of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
70. The compound of claim 65, wherein at least four of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
71 . The compound of claim 65, wherein at least five of Q1 , Q2, Q3, Q4, Q5 and Q6 are independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
72. The compound of claim 65, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of a non-natural amino acid, or a pharmaceutically acceptable salt thereof.
73. The compound of claim 65, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
74. The compound of claim 65, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
75. The compound of claim 65, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2- aminoethyl, or a pharmaceutically acceptable salt thereof.
76. The compound of claim 65, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000338_0001
Figure imgf000339_0001
or a p armaceut ca y accepta e sa t t ereo .
77. The compound of any one of claims 65-76, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently selected from 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
78. The compound of any one of claims 65-77, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
79. The compound of any one of claims 65-78, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000340_0001
or a pharmaceutically acceptable salt thereof.
80. The compound of claim 65, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3 or 4; and
the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000340_0002
or a pharmaceutically acceptable salt thereof.
81 . The compound of any one of claims 65-76, wherein each m is 0, or a pharmaceutically acceptable salt thereof. A compound of formula (XIII):
Figure imgf000341_0001
(XIII)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
R1 is hydrogen, Ci-Cio alkyi, or -CH2C(0)NR2R3;
R2 is hydrogen or C1 C10 alkyi;
R3 is hydrogen or C1 C10 alkyi; and
each d is independently 1 to 10;
or a pharmaceutically acceptable salt thereof.
83. The compound of claim 82, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
84. The compound of claim 82, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyi, C3-C9 cycloalkyi C1 -C4 alkyi, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, C6-C10 aryl, and C6- C35 alkaryl, or a pharmaceutically acceptable salt thereof.
85. The compound of claim 82, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2- aminoethyl, or a pharmaceutically acceptable salt thereof.
86. The compound of claim 82, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000341_0002
Figure imgf000342_0001
or a p armaceut ca y accepta e sa t t ereo .
87. The compound of any one of claims 82-86, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
88. The compound of any one of claims 82-87, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
89. The compound of any one of claims 82-88, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000343_0001
or a pharmaceutically acceptable salt thereof.
90. The compound of claim 82, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
R1 is hydrogen;
each m is independently 1 , 2, 3 or 4; and
the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000343_0002
or a pharmaceutically acceptable salt thereof. A compound of formula (XIV):
Figure imgf000344_0001
(XIV)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and
each d is independently 1 to 10;
or a pharmaceutically acceptable salt thereof.
92. The compound of claim 91 , wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
93. The compound of claim 91 , wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
94. The compound of claim 91 , wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2- aminoethyl, or a pharmaceutically acceptable salt thereof.
95. The compound of claim 91 , wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000344_0002
Figure imgf000345_0001
or a p armaceut ca y accepta e sa t t ereo .
96. The compound of any one of claims 91 -95, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3, 4, or 5; and
d is an integer from 1 to 5;
or a pharmaceutically acceptable salt thereof.
97. The compound of any one of claims 91 -96, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
98. The compound of any one of claims 91 -97, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000346_0001
or a pharmaceutically acceptable salt thereof.
99. The compound of claim 91 , wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3 or 4;
d is an integer from 1 to 5; and
the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000346_0002
or a pharmaceutically acceptable salt thereof.
100. The compound of claim 99, wherein m is 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
101 . The compound of claim 100, wherein m is 2, or a pharmaceutically acceptable salt thereof.
102. The compound of claim 100, wherein m is 3, or a pharmaceutically acceptable salt thereof,
103. The compound of claim 100, wherein m is 4, or a pharmaceutically acceptable salt thereof,
104. The compound of any one of claims 91 -103, wherein d is 1 , 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
105. A compound of formula (XV):
Figure imgf000347_0001
(XV)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; X is O or is absent;
each Y is independently -CH2- or -C(O)-; and
each Z is independently N or CH;
or a pharmaceutically acceptable salt thereof.
106. The compound of claim 105, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
107. The compound of claim 105, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
108. The compound of claim 105, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
109. The compound of claim 105, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000348_0001
1 10. The compound of any one of claims 105-109, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methyl hex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
1 1 1 . The compound of any one of claims 105-1 10, wherein X is absent, or a pharmaceutically acceptable salt thereof.
1 12. The compound of claim 1 1 1 , wherein Y is -CH2-, or a pharmaceutically acceptable salt thereof.
1 13. The compound of claim 1 1 1 , wherein Y is -C(O)-, or a pharmaceutically acceptable salt thereof.
1 14. The compound of any one of claims 105-109, wherein X is O, or a pharmaceutically acceptable salt thereof.
1 15. The compound of any one of claims 105-1 14, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
1 16. The compound of any one of claims 105-1 15, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000349_0001
or a pharmaceutically acceptable salt thereof.
1 17. The compound of claim 105, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3 or 4; and
the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000350_0002
or a pharmaceutically acceptable salt thereof.
1 18. The compound of claim 1 17, wherein Y is -CH2- and X is O, or a pharmaceutically acceptable salt thereof.
1 19. The compound of claim 1 17, wherein Y is -C(O)-, X is absent, and Z is CH, or a pharmaceutically acceptable salt thereof.
120. The compound of claim 1 17, wherein Y is -C(O)-, X is absent, and Z is N, or a pharmaceutically acceptable salt thereof.
121 . The compound of any one of claims 105-120, wherein:
each A1 and A2 is independently threonine or 2,4-diaminobutyric acid; and
m is 2 or 3;
or a pharmaceutically acceptable salt thereof.
122. A compound of formula (XVI):
Figure imgf000350_0001
(XVI)
wherein: each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
X is -CR1 R2-, -C(R1)=C(R2)-, -CH2OCH2-, -C(O)-, or is absent;
each Y is independently -C(O)-, -S(O)-, -S(0)2-, or is absent;
R1 is hydrogen, C1 -C10 alkyl, -N(R3R4), or -OH;
R2 is hydrogen, C1 -C10 alkyl, or -OH;
R3 and R4 are independently hydrogen or C1 -C10 alkyl; and
d is an integer from 1 to 10;
or a pharmaceutically acceptable salt thereof.
123. The compound of claim 122, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
124. The compound of claim 122, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
125. The compound of claim 122, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
126. The compound of claim 122, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000351_0001
Figure imgf000352_0001
or a p armaceut ca y accepta e sa t t ereo .
127. The compound of any one of claims 122-126, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
128. The compound of any one of claims 122-127, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
129. The compound of any one of claims 122-128, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000352_0002
Figure imgf000353_0001
or a pharmaceutically acceptable salt thereof.
130. The compound of claim 122, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3 or 4; and
the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000353_0002
or a pharmaceutically acceptable salt thereof.
131 . The compound of claim 130, wherein:
Y is -C(O)-;
X is -CR1 R2-, -CR1=CR2-;
R1 is hydrogen or -NR3R4;
R3 and R4 are hydrogen; and
d is 1 , 2, or 3;
or a pharmaceutically acceptable salt thereof.
132. The compound of claim 130, wherein: X is -CH2-; and d is 1 , 2, or 3;
or a pharmaceutically acceptable salt thereof.
133. The compound of claim 130, wherein Y is absent, X is -C(O)- and d is 1 , or a pharmaceutically acceptable salt thereof.
134. The compound of any one of claims 122-133, wherein each A1 and A2 is independently threonine, 3- hydroxyalaline, 2,4-diaminobutyric acid, 3-hydroxyproline, 2-amino-4-(dimethylamino)butyric acid, and 2- aminooctanoic acid, or a pharmaceutically acceptable salt thereof.
A compound of formula (XVII):
Figure imgf000354_0001
(XVII)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; each Y is independently -CH2-, -C(O)-, -S(O)-, or -S(0)2-;
or a pharmaceutically acceptable salt thereof.
136. The compound of claim 135, wherein the compound is of the formula (XVII-1 ):
Figure imgf000355_0001
(XVII-1 )
armaceutically acceptable salt thereof.
Figure imgf000355_0002
138. The compound of claim 135, wherein the compound is of the formula (XVII-3):
Figure imgf000356_0001
(XVII-3)
or a pharmaceutically acceptable salt thereof.
139. The compound of any one of claims 135-138, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
140. The compound of any one of claims 135-138, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
141 . The compound of claim 140, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
142. The compound of claim 141 , wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000356_0002
Figure imgf000357_0001
or a p armaceut ca y accepta e sa t t ereo .
143. The compound of any one of claims 135-142, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
144. The compound of any one of claims 135-143, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
145. The compound of any one of claims 135-144, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000358_0001
or a pharmaceutically acceptable salt thereof.
146. The compound of any one of claims 135-138, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3 or 4; and
the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000358_0002
or a pharmaceutically acceptable salt thereof.
147. The compound of claim 146, wherein Y is -C(O)-, and m is 2, 3 or 4, or a pharmaceutically acceptable salt thereof.
148. The compound of any one of claims 138-147, wherein each A1 and A2 is independently threonine or 2,4-diaminobutyric acid, or a pharmaceutically acceptable salt thereof.
149. A compound of formula (XVIII):
Figure imgf000359_0001
(XVIII)
wherein:
each A1 and A2 is an independently selected amino acid;
e is an integer from 1 to 5;
f is an integer from 1 to 5;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and
R1 is hydrogen, C1 -C10 alkyl, -C(0)OR2, -C(0)-(CH2OCH2)d-heterocyclic, and -C(0)R2;
R2 is C1 -C10 alkyl, benzyl, -CH2(biphenyl), -(CH2CH20)g-R3;
R3 is -(CH2)iNR4R5 and -(CH2)i-(C2-C8 alkynyl);
R4 is hydrogen or C1 -C10 alkyl;
R5 is hydrogen or C1 -C10 alkyl; and
d is an integer from 1 to 10;
g is an integer from 1 to 10; and
i is an integer from 1 to 5;
or a pharmaceutically acceptable salt thereof.
150. The compound of claim 149, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
151 . The compound of claim 149, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
152. The compound of claim 151 , wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
153. The compound of claim 152, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000360_0001
154. The compound of any one of claims 149-153, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
155. The compound of any one of claims 149-154, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
156. The compound of any one of claims 149-155, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000361_0001
or a pharmaceutically acceptable salt thereof.
157. The compound of any one of claims 149-156, wherein e and f are 1 , or a pharmaceutically acceptable salt thereof.
158. The compound of any one of claims 149-157, wherein R1 is hydrogen, or a pharmaceutically acceptable salt thereof.
159. The compound of any one of claims 149-158, wherein R1 is -CO2R2, or a pharmaceutically acceptable salt thereof.
160. The compound of any one of claims 149-158, wherein R1 is -C(0)R2, or a pharmaceutically acceptable salt thereof.
161 . The compound of any one of claims 149-160, wherein each A1 and A2 is independently threonine, 2,4-diaminobutyric acid, 2-aminooctanoic acid, 4-methylpentanoic acid, 5-methylhexanoic acid, 2- aminodecanoic acid, O-allyl serine, tryptophan, and 3-(4,4'-biphenyl)alanine, or a pharmaceutically acceptable salt thereof.
162. A compound of formula (XIX):
Figure imgf000362_0001
(XIX)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
R1 and R2 are independently hydrogen, C1 -C10 alkyl, or -C(0)OR3;
R3 is hydrogen C1 -C10 alkyl, or benzyl ; and
d is an integer from 1 to 4;
or a pharmaceutically acceptable salt thereof.
163. The compound of claim 162, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
164. The compound of claim 162, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
165. The compound of claim 162, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
166. The compound of claim 165, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000362_0002
Figure imgf000363_0001
or a p armaceut ca y accepta e sa t t ereo .
167. The compound of any one of claims 162-166, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
168. The compound of any one of claims 162-167, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
169. The compound of any one of claims 162-168, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000364_0002
or a pharmaceutically acceptable salt thereof.
170. The compound of any one of claims 162-169, wherein d is 1 or 2, R1 is hydrogen, and R2 is hydrogen, or a pharmaceutically acceptable salt thereof.
171 . The compound of any one of claims 162-170, wherein d is 1 , or a pharmaceutically acceptable salt thereof.
172. The compound of any one of claims 162-170, wherein d is 2, or a pharmaceutically acceptable salt thereof.
173. The compound of anyone of claims 162-172, wherein each A1 and A2 is independently 2,4- daminobutyric acid, threonine, or 4-aminoproline, or a pharmaceutically acceptable salt thereof.
A compound of formula (XX):
Figure imgf000364_0001
(XX)
wherein:
each A1 and A2 is an independently selected amino acid; each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
R1 is hydrogen or C1 -C10 alkyl; and
d and d' are, independently, an integer from 1 to 5;
or a pharmaceutically acceptable salt thereof.
175. The compound of claim 174, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
176. The compound of claim 174, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
177. The compound of claim 176, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
178. The compound of claim 177, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000365_0001
Figure imgf000366_0001
or a pharmaceutically acceptable salt thereof.
179. The compound of any one of claims 174-178, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
180. The compound of any one of claims 174-178, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
181 . The compound of any one of claims 174-180, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000366_0002
or a pharmaceutically acceptable salt thereof.
182. The compound of any one of claims 174-181 , wherein d is 1 , 2, or 3, or a pharmaceutically acceptable salt thereof.
183. The compound of any one of claims 174-182, wherein d is 1 , or a pharmaceutically acceptable salt thereof.
184. The compound of any one of claims 174-183, wherein R1 is hydrogen, or a pharmaceutically acceptable salt thereof.
185. The compound of any one of claims 174-184, wherein each A1 and A2 is independently 2,4- diaminobutyric acid or threonine, or a pharmaceutically acceptable salt thereof.
186. A compound of formula (XXI):
Figure imgf000367_0001
(XXI)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5; and
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
187. The compound of claim 186, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
188. The compound of claim 186, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
189. The compound of claim 188, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
190. The compound of claim 189, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000368_0001
191 . The compound of any one of claims 186-190, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
192. The compound of any one of claims 186-191 , wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
193. The compound of any one of claims 186-192, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000369_0002
or a pharmaceutically acceptable salt thereof.
194. A compound according any one of claims 186-193, wherein each A1 and A2 is independently 2,4- diaminobutyric acid or threonine, or a pharmaceutically acceptable salt thereof.
195. A compound of formula (XXII):
Figure imgf000369_0001
(XXII) wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5; and
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; or a pharmaceutically acceptable salt thereof.
196. The compound of claim 195, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
197. The compound of claim 195, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
198. The compound of claim 197, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
199. The compound of claim 198, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000370_0001
Figure imgf000371_0001
or a pharmaceutically acceptable salt thereof.
200. The compound of any one of claims 195-199, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
201 . The compound of any one of claims 195-200, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
202. The compound of any one of claims 195-201 , wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000371_0002
or a pharmaceutically acceptable salt thereof.
203. A compound of formula (XXIII):
Figure imgf000372_0001
(XXIII)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5; and
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
or a pharmaceutically acceptable salt thereof.
204. The compound of claim 203, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
205. The compound of claim 203, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
206. The compound of claim 205, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
207. The compound of claim 203, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000372_0002
Figure imgf000373_0001
or a pharmaceutically acceptable salt thereof.
208. The compound of any one of claims 203-207, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine; and
each m is independently 1 , 2, 3, 4, or 5;
or a pharmaceutically acceptable salt thereof.
209. The compound of any one of claims 203-208, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
210. The compound of any one of claims 203-209, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000374_0002
or a pharmaceutically acceptable salt thereof.
A compound of formula (XXIV):
Figure imgf000374_0001
(XXIV)
wherein:
each A1 and A2 is an independently selected amino acid;
R1 is hydrogen or C1 -C10 alkyl;
each m is independently 0, 1 , 2, 3, 4, or 5;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid; and
d is an integer from 1 to 6;
or a pharmaceutically acceptable salt thereof.
212. The compound of claim 21 1 , wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
213. The compound of claim 21 1 , wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
214. The compound of claim 213, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
215. The compound of claim 214, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000375_0001
216. The compound of any one of claims 21 1 -215, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3, 4, or 5;
d is an integer from 1 to 2; and
or a pharmaceutically acceptable salt thereof.
217. The compound of any one of claims 21 1 -216, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
218. The compound of any one of claims 21 1 -217, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000376_0001
or a pharmaceutically acceptable salt thereof.
219. The compound of any one of claims 21 1 -218, wherein d is 1 , 2, or 3, or a pharmaceutically acceptable salt thereof.
220. The compound of any one of claims 21 1 -219, wherein d is 3, or a pharmaceutically acceptable salt thereof.
221 . The compound of any one of claims 21 1 -220, wherein each A1 and A2 is independently 2,4- diaminobutyric acid, threonine, or 2-aminooctanoic acid, or a pharmaceutically acceptable salt thereof.
222. A compound of formula (XXV):
Figure imgf000377_0001
(XXV)
wherein:
each A1 and A2 is an independently selected amino acid;
each m is independently 0, 1 , 2, 3, 4, or 5;
d and d' are, independently, 0, 1 , or 2;
Q1 , Q2, Q3, Q4, Q5 and Q6 are each independently selected from the side chain of an amino acid;
R1 is hydrogen, C1 -C10 alkyl, -(CH2)d-R2 or -C(0)(CH2)d-R2;
d is an integer from 1 to 10;
R2 is aryl, C1 -C10 alkyl, -NR3R4, or -OR4; and
R3 and R4 are independently hydrogen or C1 -C10 alkyl;
or a pharmaceutically acceptable salt thereof.
223. The compound of claim 222, wherein each Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from the side chain of serine, threonine, cysteine, glycine, proline, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan, or a pharmaceutically acceptable salt thereof.
224. The compound of claim 222, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from C1 -C4 alkyl, C1 -C2 hydroxyalkyi, C1 -C5 alkamino, and C6-C35 alkaryl, or a pharmaceutically acceptable salt thereof.
225. The compound of claim 224, wherein each of Q1 , Q2, Q3, Q4, Q5 and Q6 is independently selected from 2-methyl-1 -propyl, 2-propyl, 1 -hydroxyethyl, butyl, benzyl, hydroxymethyl, propyl, 2-butyl, methyl, and 2-aminoethyl, or a pharmaceutically acceptable salt thereof.
226. The compound of claim 225, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000377_0002
Figure imgf000378_0001
or a p armaceut ca y accepta e sa t t ereo .
227. The compound of any one of claims 222-226, wherein:
each A1 and A2 is independently selected from glycine, arginine, asparagine, glutamine, 3-(2H- tetrazol-5-yl)alanine, 3-aminoalanine, piperazine-2-carboxylic acid, 2,4-diaminobutyric acid, 3- hydroxyproline, threonine, 2-amino-4-phenylbutyric acid, 3-(2-naphthyl)alanine, 2-piperazinecarboxylic acid, 2-aminooctanoic acid, serine, 2-aminohexanoic acid, 4-amino-4-piperidinyl carboxylic acid, methionine, methionine sulfoxide, methionine sulfone, S-methylcysteine, S-ethylcysteine, S- propylhomocysteine, cyclopropylalanine, 3-fluoroalanine, 2-amino-5-methylhexanoic acid, 2-amino-5- methylhex-4-enoic acid, alpha-t-butylglycine, alpha-neopentylglycine, 3-aminoproline, 4-aminoproline, 2- amino-4-(dimethylamino)butyric acid, phenylalanine, 3-(4,4'-biphenyl)alanine, tryptophan, 2- aminopentanoic acid, alanine, 4-methylpentanoic acid, 5-methylhexanoic acid, 2-aminoheptanoic acid, 2- aminononanoic acid, 2-aminodecanoic acid, and O-allyl serine;
each m is independently 1 , 2, 3, 4, or 5; or a pharmaceutically acceptable salt thereof.
228. The compound of any one of claims 222-227, wherein each m is independently 2, 3, or 4, or a pharmaceutically acceptable salt thereof.
229. The compound of any one of claims 222-228, wherein the combination of Q1 , Q2, Q3, Q4, Q5 and Q6 is selected from one of
Figure imgf000379_0002
or a pharmaceutically acceptable salt thereof.
230. The compound of claim 3, wherein the compound is described by formula (XXVI):
Figure imgf000379_0001
(XXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R3, R4, R5, R6, R7, R8, R9, R10, R'2, R'3, R'4, R'5, R'6, R'7, R'8, R'9, and R'10 is, independently, a lipophilic moiety, a positively charged moiety, a polar moiety, H, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5- C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl ; or two R groups on the same or adjacent atoms join to form an optionally substituted 5-8 membered ring;
each of a', b', c', a, b, and c is, independently, 0 or 1 ;
each of N1 , N2, N3, N4, N'1 , N'2, N'3, and N'4 is a nitrogen atom ;
each of C1 , C2, C3, C'1 , C'2, and C'3 is a carbon atom; L is a linker comprising at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C15 heteroarylene;
or a pharmaceutically acceptable salt thereof.
231 . The compound of claim 230, wherein the compound comprises at least one optionally substituted 5- 8 membered ring formed by joining (i) R2, R3, and C1 ; (ii) R3, R4, N1 , and C1 ; (iii) R5, R6, and C2; (iv) R6, R7, N2, and C2; (v) R8, R9, and C3; (vi) R9, R10, N3, and C3; (vii) R'2, R'3, and C'1 ; (viii) R'3, R'4, N'1 , and C'1 ; (ix) R'5, R'6, and C'2; (x) R'6, R'7, N'2, and C'2; (xi) R'8, R'9, and C'3; or (xii) R'9, R'10, N'3, and C'3.
232. The compound of claim 230 or 231 , wherein L is described by formula (L-2):
l1-(V1)f-(U1 )g-(V2)h-(U2)i-(V3)j-(U3)-(V4)k-(U4)|-(V5)m-(U5)n-(V6)o-l2
(L-2)
wherein I1 is a bond attached to N'1 , N'2, N'3, or N'4;
I2 is a bond attached to N1 , N2, N3, or N4;
U3 comprises at least one optionally substituted C3-C20 cycloalkylene, optionally substituted C3- C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C1 5 arylene, or optionally substituted C3-C1 5 heteroarylene;
each of U1 , U2, U4, and U5 is, independently, optionally substituted C1 -C20 alkylene, optionally substituted C1 -C20 heteroalkylene, optionally substituted C2-C20 alkenylene, optionally substituted C2- C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene;
each of V1 , V2, V3, V4, V5, and V6 is, independently, O, S, NR', P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino;
R' is H, optionally substituted C1 -C20 alkyl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C1 5 aryl, or optionally substituted C5-C15 heteroaryl; and each of f, g, h, i, j, k, I, m, n, and o is, independently, 0 or 1 .
233. The compound of any one of claims 230-232, wherein the compound is described by formula (XXVII)
Figure imgf000381_0001
(XXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R8, R'2, R'6, and R'8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3- C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
234. The compound of any one of claims 230-232, wherein the compound is described by formula (XXVIII):
Figure imgf000381_0002
(XXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R8, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3- C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl; or a pharmaceutically acceptable salt thereof.
235. The compound of any one of claims 230-232, wherein the compound is described by formula (XXIX):
Figure imgf000382_0001
(XXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R8, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3- C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
236. The compound of any one of claims 230-232, wherein the compound is described by formula (XXX):
Figure imgf000382_0002
(XXX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, and R8 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
237. The compound of any one of claims 230-232, wherein the compound is described by formula (XXXI):
Figure imgf000383_0001
(XXXI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, R'2, and R'6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyi, optionally substituted C3- C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
238. The compound of any one of claims 230-232, wherein the compound is described by formula (XXXII):
Figure imgf000383_0002
(XXXII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2, R6, and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
239. The compound of any one of claims 230-232, wherein the compound is described by formula (XXXIII):
Figure imgf000384_0001
(XXXIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
each of R2 and R6 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
240. The compound of any one of claims 230-232, wherein the compound is described by formula (XXXIV):
Figure imgf000384_0002
(XXXIV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; each of R2 and R'2 is, independently, a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4-C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C1 5 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
241 . The compound of any one of claims 230-232, wherein the compound is described by formula (XXXV):
Figure imgf000385_0001
(XXXV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
R2 is a positively charged moiety, a polar moiety, optionally substituted C1 -C5 alkamino, optionally substituted C1 -C20 alkyl, optionally substituted C3-C20 cycloalkyi, optionally substituted C4- C20 cycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C5-C15 aryl, optionally substituted C1 -C20 heteroalkyl, optionally substituted C3-C20 heterocycloalkyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C3-C15 heteroaryl, optionally substituted C6-C35 alkaryl, or optionally substituted C6-C35 heteroalkaryl;
or a pharmaceutically acceptable salt thereof.
242. The compound of any one of claims 230-232, wherein the compound is described by formula (XXXVI):
Figure imgf000385_0002
(XXXVI) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2;
or a pharmaceutically acceptable salt thereof.
243. The compound of claim any one of claims 230-242, wherein L comprises at least one optionally substituted C3 cycloalkylene or at least one optionally substituted C3 heterocycloalkylene.
244. The compound of claim 243, wherein the compound is described by formula (XXXVM):
Figure imgf000386_0001
(XXXVM)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
245. The compound of claim 244, wherein the compound is described by formula (XXXVMI):
Figure imgf000386_0002
(XXXVIII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C3 cycloalkylene or an optionally substituted C3 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof. L is
Figure imgf000386_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
247. The compound of claim 230-242, wherein L comprises at least one optionally substituted C5 cycloalkylene or at least one optionally substituted C5 heterocycloalkylene.
248. The compound of claim 247, wherein the compound is described by formula (XXXIX):
Figure imgf000387_0001
(XXXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
249. The compound of claim 247, wherein the compound is described by formula (XXXX):
Figure imgf000387_0002
(XXXX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
Figure imgf000388_0001
(XXXXI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
251 . The compound of claim 247, wherein the compound is described by formula (XXXXII):
Figure imgf000388_0002
(XXXXII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
252. The compound of claim 247, wherein the compound is described by formula (XXXXMI):
Figure imgf000388_0003
(XXXXMI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and L comprises an optionally substituted C5 cycloalkylene or an optionally substituted C5 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
253. The compound of any one of claims 247-252, wherein L comprises at least one optionally substituted pyrrolidine.
254. The compound of claim 253, wherein the pyrrolidine is substituted with an alkyne functional group.
255. The compound of claim 254, wherein L is
Figure imgf000389_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
256. The compound of claim 253, wherein the pyrrolidine is substituted with an azide functional group.
257. The compound of claim 256, wherein L is
Figure imgf000389_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
258. The compound of claim 253, wherein the pyrrolidine is substituted with a fluorophore.
259. The compound of claim 258, wherein the fluorophore is fluorescein, rhodamine, coumarin, or a derivative thereof.
260. The compound of claim 258 or 259, wherein L is
Figure imgf000390_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
261 . The compound of claim 253, wherein the pyrrolidine is substituted with a sulfone functional group.
262. The compound of claim 261 , wherein L is
Figure imgf000390_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
263. The compound of claim 253, wherein the pyrrolidine is substituted with an amine functional group.
Figure imgf000390_0003
Figure imgf000391_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
265. The compound of any one of claims 247-252, wherein L comprises at least one optionally substituted 1 ,3-dioxolane.
266. The compound of claim 265, wherein L is
Figure imgf000391_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
267. The compound of any one of claims 247-252, wherein L is
Figure imgf000391_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
268. The compound of any one of claims 230-242, wherein L comprises at least one optionally substituted C6 cycloalkylene or at least one optionally substituted C6 heterocycloalkylene.
269. The compound of claim 268, wherein the compound is described by formula (XXXXIV):
Figure imgf000391_0004
(XXXXIV) wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C6 cycloalkylene or an optionally substituted C6 heterocycloalkylene,
or a pharmaceutically acceptable salt thereof.
270. The compound of claim 268 or 269, wherein L is
Figure imgf000392_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
271 . The compound of any one of claims 230-242, wherein L comprises at least one optionally substituted C6 arylene or at least one optionally substituted C6 heteroarylene.
272. The compound of claim 271 , wherein the compound is described by formula (XXXXV):
Figure imgf000392_0002
(XXXXV)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
273. The compound of claim 271 , wherein the compound is described by formula (XXXXVI):
Figure imgf000392_0003
(XXXXVI)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C6 arylene or an optionally substituted C6 heteroarylene, or a pharmaceutically acceptable salt thereof.
274. The compound of claim 271 , wherein the compound is described by formula (XXXXVII):
Figure imgf000393_0001
(XXXXVII)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C6 arylene,
or a pharmaceutically acceptable salt thereof.
275. The compound of any one of claims 271 -274, wherein L is
Figure imgf000393_0002
Figure imgf000394_0001
wherein each q is, independently, an integer from 1 to 1 1 , inclusive
276. The compound of any one of claims 230-242, wherein L comprises at least two optionally substituted C6 arylene.
277. The compound of claim 276, wherein the compound is described by formula (XXXXVIM):
Figure imgf000394_0002
(XXXXVIM)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises at least two optionally substituted C6 arylene,
or a pharmaceutically acceptable salt thereof.
278. The compound of claim 276 or 277, wherein L is
Figure imgf000394_0003
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
279. The compound of any one of claims 230-242, wherein L comprises at least one optionally substituted C5 arylene or at least one optionally substituted C5 heteroarylene.
280. The compound of claim 279, wherein the compound is described by formula (XXXXIX):
Figure imgf000395_0001
(XXXXIX)
wherein each of R'1 and R1 is, independently, benzyl or CH2CH(CH3)2; and
L comprises an optionally substituted C5 arylene or an optionally substituted C5 heteroarylene, or a pharmaceutically acceptable salt thereof. 280, wherein L is
Figure imgf000395_0002
wherein each q is, independently, an integer from 1 to 1 1 , inclusive.
282. A compound selected from any one of compounds 1 -1 80, or a pharmaceutically acceptable salt thereof.
283. A pharmaceutical composition comprising a compound of any of claims 1 -282, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.
284. The pharmaceutical composition of claim 283, further comprising an antibacterial agent.
285. The pharmaceutical composition of claim 284, wherein the antibacterial agent is selected from the group consisting of linezolid, tedizolid, posizolid, radezolid, retapamulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem, imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime, cefpodoxime, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, dalbavancin, oritavancin, clindamycin, lincomycin, daptomycin, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, spiramycin, aztreonam, furazolidone, nitrofurantoin, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin g, penicillin v, piperacillin, penicillin g, temocillin, ticarcillin, amoxicillin clavulanate, ampicillin/sulbactam, piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, temafloxacin, mafenide, sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (tmp-smx), sulfonamidochrysoidine, eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, clofazimine, dapsone, capreomycin, cycloserine, ethambutol(bs), ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, streptomycin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, trimethoprim, prodrugs thereof, and pharmaceutically acceptable salts thereof.
286. The pharmaceutical composition of claim 285, wherein a prodrug of tedizolid is tedizolid phosphate.
287. The pharmaceutical composition of claim 285, wherein the antibacterial agent is linezolid or tedizolid phosphate.
288. A method of protecting against or treating a bacterial infection in a subject, comprising administering to the subject a compound of any one of claims 1 -282.
289. The method of claim 288, further comprising administering to the subject an antibacterial agent.
290. A method of protecting against or treating a bacterial infection in a subject, comprising administering to the subject (1 ) a compound of any one of claims 1 -282 and (2) an antibacterial agent.
291 . The method of any one of claims 288-290, wherein the bacterial infection is caused by Gram- negative bacteria.
292. The method of any one of claims 288-291 , wherein the bacterial infection is caused by a resistant strain of bacteria.
293. The method of claim 292, wherein the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, the mcr-3 gene, and/or a chromosomal mutation conferring polymyxin resistance.
294. The method of claim 293, wherein the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, or the mcr-3 gene.
295. The method of claim 293, wherein the resistant strain of bacteria possesses a chromosomal mutation conferring polymyxin resistance.
296. The method of any one of claims 292-295, wherein the resistant strain of bacteria is a resistant strain of E. coli.
297. A method of protecting against or treating sepsis in a subject, comprising administering to the subject a compound of any one of claims 1 -282.
298. A method of preventing lipopolysaccharides (LPS) in Gram-negative bacteria from activating an immune system in a subject, comprsing administering to the subject a compound of any one of claims 1 - 282.
299. The method of claim 298, wherein the method prevents LPS from activating a macrophage.
300. The method of claim 298 or 299, wherein the method prevents LPS-induced nitroic oxide (NO) production from a macrophage.
301 . The method of any one of claims 298-300, wherein the Gram-negative bacteria is a resistant strain of Gram-negative bacteria.
302. The method of claim 301 , wherein the resistant strain of Gram-negative bacteria possesses the mcr- 1 gene, the mcr-2 gene, the mcr-3 gene, and/or a chromosomal mutation conferring polymyxin resistance.
303. The method of claim 302 wherein the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, or the mcr-3 gene.
304. The method of claim 302, wherein the resistant strain of bacteria possesses a chromosomal mutation conferring polymyxin resistance.
305. The method of any one of claims 301 -304, wherein the resistant strain of bacteria is a resistant strain of E. coli.
306. The method of any one of claims 297-305, further comprising administering to the subject an antibacterial agent.
307. The method of any one of claims 289, 290, and 306, wherein the compound and the antibacterial agent are administered substantially simultaneously.
308. The method of any one of claims 289, 290, and 306, wherein the compound and the antibacterial agent are administered separately.
309. The method of claim 308, wherein the compound is administered first, followed by administering of the antibacterial agent alone.
310. The method of claim 308, wherein the antibacterial agent is administered first, followed by administering of the compound alone.
31 1 . The method of any one of claims 289, 290, and 306, wherein the compound and the antibacterial agent are administered substantially simultaneously, followed by administering of the compound or the antibacterial agent alone.
312. The method of any one of claims 289, 290, and 306, wherein the compound or the antibacterial agent is administered first, followed by administering of the compound and the antibacterial agent substantially simultaneously.
313. The method of any one of claims 289, 290, and 306-312, wherein administering the compound and the antibacterial agent together lowers the MIC of each of the compound and the antibacterial agent relative to the MIC of each of the compound and the antibacterial agent when each is used alone.
314. The method of any one of claims 288-313, wherein the compound and/or the antibacterial agent is administered intramuscularly, intravenously, intradermal^, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally, locally, by inhalation, by injection, or by infusion.
315. A method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria, comprising contacting the bacteria or a site susceptible to bacterial growth with a compound of any of claims 1 -282.
316. The method of claim 315, further comprising contacting the bacteria or the site susceptible to bacterial growth with an antibacterial agent.
317. A method of preventing, stabilizing, or inhibiting the growth of bacteria, or killing bacteria, comprising contacting the bacteria or a site susceptible to bacterial growth with (1 ) a compound of any of claims 1 -282 and (2) an antibacterial agent.
318. The method of any one of claims 289, 290, 306, 315, and 31 6, wherein the antibacterial agent is selected from the group consisting of linezolid, tedizolid, posizolid, radezolid, retapamulin, valnemulin, tiamulin, azamulin, lefamulin, plazomicin, amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, spectinomycin, geldanamycin, herbimycin, rifaximin, loracarbef, ertapenem, doripenem, imipenem/cilastatin, meropenem, cefadroxil, cefazolin, cefalotin, cefalexin, cefaclor, cefamandole, cefoxitin, cefprozil, cefuroxime, cefixime, cefdinir, cefditoren, cefoperazone, cefotaxime, cefpodoxime, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, cefepime, ceftaroline fosamil, ceftobiprole, teicoplanin, vancomycin, telavancin, dalbavancin, oritavancin, clindamycin, lincomycin, daptomycin, solithromycin, azithromycin, clarithromycin, dirithromycin, erythromycin, roxithromycin, troleandomycin, telithromycin, spiramycin, aztreonam, furazolidone, nitrofurantoin, amoxicillin, ampicillin, azlocillin, carbenicillin, cloxacillin, dicloxacillin, flucloxacillin, mezlocillin, methicillin, nafcillin, oxacillin, penicillin g, penicillin v, piperacillin, penicillin g, temocillin, ticarcillin, amoxicillin clavulanate,
ampicillin/sulbactam, piperacillin/tazobactam, ticarcillin/clavulanate, bacitracin, ciprofloxacin, enoxacin, gatifloxacin, gemifloxacin, levofloxacin, lomefloxacin, moxifloxacin, nalidixic acid, norfloxacin, ofloxacin, trovafloxacin, grepafloxacin, sparfloxacin, temafloxacin, mafenide, sulfacetamide, sulfadiazine, silver sulfadiazine, sulfadimethoxine, sulfamethizole, sulfamethoxazole, sulfanamide, sulfasalazine, sulfisoxazole, trimethoprim-sulfamethoxazole (tmp-smx), sulfonamidochrysoidine, eravacycline, demeclocycline, doxycycline, minocycline, oxytetracycline, tetracycline, clofazimine, dapsone, capreomycin, cycloserine, ethambutol(bs), ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, streptomycin, arsphenamine, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin/dalfopristin, thiamphenicol, tigecycline, tinidazole, and
trimethoprim.
319. The method of claim 318, wherein a prodrug of tedizolid is tedizolid phosphate.
320. The method of claim 319, wherein the antibacterial agent is linezolid or tedizolid phosphate.
321 . The method of any one of claims 315-320, wherein the bacteria is Gram-negative bacteria.
322. The method of any one of claims 315-321 , wherein the bacteria is a resistant strain of bacteria.
323. The method of claim 322, wherein the resistant strain of bacteria possesses the mcr- 1 gene, the mcr-2 gene, the mcr-3 gene, and/or a chromosomal mutation conferring polymyxin resistance.
324. The method of claim 322 or 323, wherein the resistant strain of bacteria is a resistant strain of E. coli.
PCT/US2017/037924 2016-06-17 2017-06-16 Compositions and methods for the treatment of bacterial infections WO2017218922A2 (en)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201662351537P 2016-06-17 2016-06-17
US62/351,537 2016-06-17
US201662397045P 2016-09-20 2016-09-20
US62/397,045 2016-09-20
US201662434268P 2016-12-14 2016-12-14
US62/434,268 2016-12-14

Publications (3)

Publication Number Publication Date
WO2017218922A2 true WO2017218922A2 (en) 2017-12-21
WO2017218922A3 WO2017218922A3 (en) 2018-01-25
WO2017218922A8 WO2017218922A8 (en) 2018-03-01

Family

ID=60664378

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2017/037924 WO2017218922A2 (en) 2016-06-17 2017-06-16 Compositions and methods for the treatment of bacterial infections

Country Status (1)

Country Link
WO (1) WO2017218922A2 (en)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN108329225A (en) * 2018-01-24 2018-07-27 北京大学 It is a kind of to dibenzoyl dimer derivate and its synthetic method and application
WO2020014469A1 (en) * 2018-07-11 2020-01-16 Cidara Therapeutics, Inc. Compositions and methods for the treatment of bacterial infectons
CN111060606A (en) * 2018-09-29 2020-04-24 湖南九典制药股份有限公司 Method for detecting dirithromycin related substances
WO2020150275A1 (en) * 2019-01-14 2020-07-23 New York University Cyclic peptide dimers
CN111909047A (en) * 2020-08-20 2020-11-10 苏州亚科科技股份有限公司 Preparation process of N- (2-acetamido) -2-iminodiacetic acid
US11352315B2 (en) * 2017-04-05 2022-06-07 Curza Global, Llc Compositions and methods comprising a triaryl polyamine

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6380356B1 (en) * 1999-12-07 2002-04-30 Advanced Medicine, Inc. Multivalent polymyxin antibiotics
US7807637B2 (en) * 2006-08-11 2010-10-05 Northern Antibiotics Oy Polymyxin derivatives and uses thereof
NZ593892A (en) * 2008-12-23 2013-11-29 Biosource Pharm Inc Antibiotic compositions for the treatment of gram negative infections

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11352315B2 (en) * 2017-04-05 2022-06-07 Curza Global, Llc Compositions and methods comprising a triaryl polyamine
CN108329225A (en) * 2018-01-24 2018-07-27 北京大学 It is a kind of to dibenzoyl dimer derivate and its synthetic method and application
CN108329225B (en) * 2018-01-24 2021-03-09 北京大学 P-dibenzoyl dimer derivative and synthetic method and application thereof
WO2020014469A1 (en) * 2018-07-11 2020-01-16 Cidara Therapeutics, Inc. Compositions and methods for the treatment of bacterial infectons
CN111060606A (en) * 2018-09-29 2020-04-24 湖南九典制药股份有限公司 Method for detecting dirithromycin related substances
WO2020150275A1 (en) * 2019-01-14 2020-07-23 New York University Cyclic peptide dimers
CN111909047A (en) * 2020-08-20 2020-11-10 苏州亚科科技股份有限公司 Preparation process of N- (2-acetamido) -2-iminodiacetic acid
CN111909047B (en) * 2020-08-20 2023-01-31 苏州亚科科技股份有限公司 Preparation process of 2- [ (2-amino-2-oxyethyl) - (carboxymethyl) amino ] acetic acid

Also Published As

Publication number Publication date
WO2017218922A3 (en) 2018-01-25
WO2017218922A8 (en) 2018-03-01

Similar Documents

Publication Publication Date Title
WO2017218922A2 (en) Compositions and methods for the treatment of bacterial infections
AU2016302940B2 (en) Prodrugs of glutamine analogs
WO2018006063A1 (en) Compositions and methods for the treatment of bacterial infections
Socha et al. Diversity-oriented synthesis of cyclic acyldepsipeptides leads to the discovery of a potent antibacterial agent
US20230190950A1 (en) Compositions and methods for the treatment of bacterial infections
US11639343B2 (en) Compounds targeting and degrading BCR-ABL protein and its antitumor application
US20200140489A1 (en) Peptide-Based Quorum Sensing Inhibitors for the Attenuation of Virulence in Staphylococcus Aureus
WO2013106646A2 (en) Compounds and methods for the inhibition of vcb e3 ubiquitin ligase
CZ290445B6 (en) Urethanes and ureas, processes of their preparation and pharmaceutical preparations based thereon
WO2015035102A2 (en) Compositions and methods for the treatment of fungal infections
WO2017151587A1 (en) Aza-peptide aldehydes and ketones
WO2015164289A1 (en) Compositions and methods for the treatment of fungal infections
WO2018187574A1 (en) Compositions and methods for the treatment of fungal infections
WO2020014501A1 (en) Compositions and methods for the treatment of bacterial infections
WO2019148194A2 (en) Peptidyl inhibitors of calcineurin-nfat interaction
US20090264345A1 (en) Macrocyclic peptides and methods for making and using them
JP5221146B2 (en) Peptide compound
WO2019126341A2 (en) Compositions and methods for the treatment of bacterial infections
WO2019126353A2 (en) Compositions and methods for the treatment of bacterial infections
US10421778B2 (en) Isoform-selective lysine deacetylase inhibitors
OA12164A (en) Protease inhibitors and their pharmaceutical uses.
CA2368733C (en) Phenylalanine derivatives
EP0538383A1 (en) Inhibitors of aspartic proteases
WO2020014469A1 (en) Compositions and methods for the treatment of bacterial infectons
CA3134518A1 (en) Arginine gingipain inhibitors

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 17814191

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 17814191

Country of ref document: EP

Kind code of ref document: A2