US20220033383A1 - Functionalized peptides as antiviral agents - Google Patents

Functionalized peptides as antiviral agents Download PDF

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Publication number
US20220033383A1
US20220033383A1 US17/379,409 US202117379409A US2022033383A1 US 20220033383 A1 US20220033383 A1 US 20220033383A1 US 202117379409 A US202117379409 A US 202117379409A US 2022033383 A1 US2022033383 A1 US 2022033383A1
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optionally substituted
compound
pharmaceutically acceptable
alkyl
cycloalkyl
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Inventor
Joseph D. Panarese
Dexter Davis
Nathaniel Thomas Kenton
Samuel Bartlett
Sean M. Rafferty
Yat Sun Or
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Enanta Pharmaceuticals Inc
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Enanta Pharmaceuticals Inc
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Application filed by Enanta Pharmaceuticals Inc filed Critical Enanta Pharmaceuticals Inc
Priority to US17/379,409 priority Critical patent/US20220033383A1/en
Assigned to ENANTA PHARMACEUTICALS, INC. reassignment ENANTA PHARMACEUTICALS, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BARTLETT, SAMUEL, RAFFERTY, SEAN M., OR, YAT SUN, DAVIS, Dexter, KENTON, NATHANIEL THOMAS, PANARESE, JOSEPH D.
Priority to US17/506,981 priority patent/US20220041652A1/en
Priority to US17/522,176 priority patent/US11358953B2/en
Publication of US20220033383A1 publication Critical patent/US20220033383A1/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing three or more hetero rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/4025—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil not condensed and containing further heterocyclic rings, e.g. cromakalim
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/403—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil condensed with carbocyclic rings, e.g. carbazole
    • A—HUMAN NECESSITIES
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    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/403—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil condensed with carbocyclic rings, e.g. carbazole
    • A61K31/404—Indoles, e.g. pindolol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/403—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil condensed with carbocyclic rings, e.g. carbazole
    • A61K31/404—Indoles, e.g. pindolol
    • A61K31/4045—Indole-alkylamines; Amides thereof, e.g. serotonin, melatonin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/415—1,2-Diazoles
    • A61K31/4155—1,2-Diazoles non condensed and containing further heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445—Non condensed piperidines, e.g. piperocaine
    • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
    • A61K31/454—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • 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
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
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    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings
    • C—CHEMISTRY; METALLURGY
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    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
    • C07D405/14—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/02—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing at least one abnormal peptide link
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/02—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing at least one abnormal peptide link
    • C07K5/0202—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing at least one abnormal peptide link containing the structure -NH-X-X-C(=0)-, X being an optionally substituted carbon atom or a heteroatom, e.g. beta-amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/04—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing only normal peptide links
    • C07K5/06—Dipeptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/04—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing only normal peptide links
    • C07K5/06—Dipeptides
    • C07K5/06139—Dipeptides with the first amino acid being heterocyclic
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/04—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing only normal peptide links
    • C07K5/06—Dipeptides
    • C07K5/06139—Dipeptides with the first amino acid being heterocyclic
    • C07K5/06165—Dipeptides with the first amino acid being heterocyclic and Pro-amino acid; Derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/04—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing only normal peptide links
    • C07K5/08—Tripeptides
    • C07K5/0821—Tripeptides with the first amino acid being heterocyclic, e.g. His, Pro, Trp
    • C07K5/0823—Tripeptides with the first amino acid being heterocyclic, e.g. His, Pro, Trp and Pro-amino acid; Derivatives thereof

Definitions

  • the invention relates to compounds and methods of inhibiting coronavirus replication activity by contacting the 3C-Like protease (sometimes referred to as “3CLpro”, “Main protease”, or “Mpro”) with a therapeutically effective amount of a 3C-Like protease inhibitor.
  • the invention further relates to pharmaceutical compositions containing the coronavirus 3C-Like protease inhibitor in a mammal by administering effective amounts of such coronavirus 3C-Like protease inhibitor.
  • Coronaviruses are family of single-stranded, positive-strand RNA viruses with viral envelopes, classified within the Nidovirales order.
  • the coronavirus family comprises pathogens of many animal species, including humans, horses, cattle, pigs, birds, cats and monkeys, and have been known for more than 60 years.
  • Coronaviruses are common viruses that generally cause mild to moderate upper-respiratory tract illnesses in humans, and are named for the crown-like spikes on their envelope surface. There are four major sub-groups known as alpha, beta, gamma and delta coronaviruses, with the first coronaviruses identified in the mid-1960s.
  • coronaviruses known to infect humans include alpha coronaviruses 229E and NL63; and beta coronaviruses OC43, HKU1, SARS-CoV (the coronavirus that causes severe acute respiratory syndrome, or SARS), and MERS-CoV (the coronavirus that causes Middle East Respiratory Syndrome, or MERS).
  • SARS-CoV the coronavirus that causes severe acute respiratory syndrome, or SARS
  • MERS-CoV Middle East Respiratory Syndrome
  • human coronaviruses result in lower-respiratory tract illnesses, such as pneumonia, although this is more common in people with cardiopulmonary disease or compromised immune systems, or in the elderly. Transmission of the common human coronaviruses is not fully understood. However, it is likely that human coronaviruses spread from an infected person to others through the air by coughing and sneezing, and through close personal contact, such as touching or shaking hands. These viruses may also spread by touching contaminated objects or surfaces then touching the mouth, nose, or eyes.
  • Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses.
  • the genomic RNA of CoVs has a 5′-cap structure and 3′-poly-A tail, and contains at least 6 open reading frames (ORFs).
  • ORF 1a/b directly translates two polyproteins: pp1a and pp1ab.
  • These polyproteins are processed by a 3C-Like protease (3CLpro), also known as the main protease (Mpro), into 16 non-structural proteins.
  • 3CLpro also known as the main protease (Mpro)
  • Mpro main protease
  • These non-structural proteins engage in the production of subgenomic RNAs that encode four structural proteins, namely envelope, membrane, spike, and nucleocapsid proteins, among other accessory proteins.
  • 3C-Like protease has a critical role in the coronavirus life cycle.
  • 3CLpro is a cysteine protease involved in most cleavage events within the precursor polyprotein. Active 3CLpro is a homodimer containing two protomers and features a Cys-His dyad located in between domains I and II. 3CLpro is conserved among coronaviruses and several common features are shared among the substrates of 3CLpro in different coronaviruses. As there is no human homolog of 3CLpro, it is an ideal antiviral target. Although compounds have been reported to inhibit 3CLpro activity, they have not been approved as coronavirus therapies. (Refer to WO2018042343, WO2018023054, WO2005113580, and WO2006061714).
  • This invention describes the methods to prepare and methods for use of compounds that are believed to inhibit the coronavirus lifecycle. Compounds of this type might be used to treat coronavirus infections and decrease occurrence of disease complications such as organ failure or death.
  • the present invention relates to novel antiviral compounds, pharmaceutical compositions comprising such compounds, as well as methods to treat or prevent viral (particularly coronavirus) infection in a subject in need of such therapy with said compounds.
  • Compounds of the present invention inhibit the protein(s) encoded by a coronavirus or interfere with the life cycle of a coronavirus and are also useful as antiviral agents.
  • the present invention provides processes for the preparation of said compounds.
  • the present invention provides compounds represented by Formula (I), and pharmaceutically acceptable salts, N-oxides, esters and prodrugs thereof,
  • A is selected from:
  • L 1 is —C(R 11 R 12 )—;
  • L 2 is —C(R 11 R 12 )—;
  • n1 is 0, 1, 2, 3, or 4;
  • X is optionally substituted —C 1 -C 6 alkyl, —CN, —C(O)R 15 , —C(O)NR 13 R 14 , or —C(O)C(O)NR 13 R 14 ;
  • Each Q is —C(R 11 ′R 12 ′)—;
  • n2 is 0, 1, 2, 3 or 4; preferably n2 is not 0;
  • R 11 , R 11 ′, R 12 , and R 12 ′ is independently selected from:
  • Ru and R 12 are taken together with the carbon atom to which they are attached to form an optionally substituted 3- to 8-membered carbocyclic or heterocyclic ring;
  • n1 when n1 is not 0, two adjacent Ru groups are taken together with the carbon atoms to which they are attached to form an optionally substituted 3- to 8-membered carbocyclic or heterocyclic ring;
  • n1 is 2, 3 or 4, and the Ru groups on two non-adjacent carbon atoms are taken together with the carbon atoms to which they are attached to form an optionally substituted bridging moiety; in this embodiment,
  • R 13 and R 14 are each independently selected from:
  • R 16 is selected from:
  • R 13 and R 14 are each independently selected from hydrogen; optionally substituted —C 1 -C 6 alkyl; optionally substituted —C 3 -C 8 cycloalkyl; optionally substituted 3- to 8-membered heterocycloalkyl; optionally substituted aryl; optionally substituted heteroaryl; —C(O)R 15 ; —S(O) 2 R 16 ; and —NH 2 ; alternatively, R 13 and R 14 are taken together with the nitrogen atom to which they are attached to form an optionally substituted 3- to 8-membered heterocyclic ring; R 15 is selected from hydrogen; halogen; —OH; optionally substituted —C 1 -C 6 alkyl; optionally substituted —C 1 -C 6 alkoxy; optionally substituted —C 3 -C 8 cycloalkyl; optionally substituted 3- to 8-membered heterocycloalkyl; optionally substituted aryl; and
  • X is —CN
  • X is —C(O)CH 2 OC(O)R 21 , —C(O)CH 2 C(O) 2 R 21 , —C(O)CH 2 OR 21 , or —C(O)CH 2 R 22 ;
  • R 21 is hydrogen, optionally substituted —C 1 -C 6 alkyl, optionally substituted —C 3 -C 8 cycloalkyl, optionally substituted 3- to 8-membered heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl; and
  • R 22 is halogen, or —NR 13 R 14 .
  • X is —C(O)C(O)NHR 21 , and R 21 is as previously defined.
  • R 21 is optionally substituted benzyl, optionally substituted methyl, optionally substituted isopropyl, optionally substituted t-butyl, or optionally substituted cyclohexyl.
  • X is —C(O)Rai, and R 21 is previously defined.
  • X is —CHR 21 OC(O)R 21 , —CHR 21 C(O) 2 R 21 , —CHR 21 (OR 21 ), or —CH(OR 21 ) 2 , and R 21 is previously defined.
  • X is selected from —CN, —C(O)H,
  • X is —CN.
  • A is derived from one of the following by removal of a hydrogen atom and is optionally substituted:
  • A is selected from the following groups, and A is optionally substituted:
  • A has 0, 1 or 2 substituents.
  • the substituents are independently selected from fluoro, chloro, hydroxy, methoxy, fluoromethoxy, difluoromethoxy, and trifluoromethoxy.
  • A is —CH 2 R 23
  • R 23 is —NR 13 R 14 , optionally substituted —C 3 -C 12 cycloalkyl, optionally substituted 3- to 12-membered heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl.
  • A is —CR 23 R 24 R 25 , wherein R 24 is hydrogen, halogen, optionally substituted —C 1 -C 6 alkyl, optionally substituted —C 1 -C 6 alkoxy, optionally substituted —C 3 -C 12 cycloalkyl, optionally substituted 3- to 12-membered heterocycloalkyl, optionally substituted aryl, optionally substituted arylalkyl, optionally substituted heteroaryl, or optionally substituted heteroarylalkyl; R 25 is hydrogen or halogen; and R 23 is as previously defined.
  • A is —C(NR 13 R 14 )R 24 R 25 , wherein R 13 , R 14 , R 24 , and R 25 are as previously defined.
  • R 14 , R 15 , R 24 , and R 25 are as previously defined.
  • R 14 and R 25 are hydrogen and R 24 is C 1 -C 6 -alkyl, preferably t-butyl.
  • R 15 is preferably benzyl, C 1 -C 6 -alkyl, or C 3 -C 8 -cycloalkyl.
  • At least one Q is —CH 2 —. In certain embodiments of the compounds of Formula (I) all Qs are —CH 2 —.
  • the compound of Formula (I) is represented by one of Formulae (II-1) ⁇ (II-2), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (II-1a) ⁇ (II-2a), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (III-1) ⁇ (III-2), or a pharmaceutically acceptable salt thereof:
  • R 17 is halogen, —OR 16 , —SR 16 ; —NR 13 R 14 ; —OC(O)NR 13 R 14 ; optionally substituted —C 1 -C 6 alkyl; optionally substituted —C 3 -C 8 cycloalkyl; optionally substituted 3- to 8-membered heterocycloalkyl; optionally substituted aryl; or optionally substituted heteroaryl;
  • m1 is 0, 1, 2 or 3 and m2 is 0, 1, 2, 3, or 4.
  • m1 is 0 and m2 is 0.
  • the compound of Formula (I) is represented by one of Formulae (IV-1) ⁇ (IV-4), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (IV-1a) ⁇ (IV-4a), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (V-1) ⁇ (V-4), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (VI-1) ⁇ (VI-6), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (VI-1a) ⁇ (VI-8a), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (VII-1) (VII-6), or a pharmaceutically acceptable salt thereof:
  • the compound of Formula (I) is represented by one of Formulae (VII-1a) ⁇ (VII-6a), or a pharmaceutically acceptable salt thereof:
  • the present invention relates to compounds of Formulae (VI-1) ⁇ (VI-4), or Formulae (VII-1) ⁇ (VII-4), and pharmaceutically acceptable salts thereof, wherein
  • the present invention relates to compounds of Formulae (VI-5) ⁇ (VI-6), or Formulae (VII-5) ⁇ (VII-6), and pharmaceutically acceptable salts thereof,
  • the present invention relates to compounds of Formulae (VI-1) ⁇ (VI-6), or Formulae (VII-1) ⁇ (VII-6), and pharmaceutically acceptable salts thereof, wherein A is selected from the groups below:
  • A has 0, 1 or 2 substituents.
  • substituents are independently selected from fluoro, chloro, hydroxy, methoxy, fluoromethoxy, difluoromethoxy, and trifluoromethoxy.
  • the present invention relates to a compound of one of Formulae (VI-1) ⁇ (VI-6), and Formulae (VII-1) ⁇ (VII-6), or a pharmaceutically acceptable salt thereof, wherein A is —CH 2 R 23 , and R 23 is previously defined.
  • the present invention relates to a compound of one of Formulae (VI-1) ⁇ (VI-6), and Formulae (VII-1) (VII-6), or a pharmaceutically acceptable salt thereof, wherein X is —CN, —C(O)CH 2 OC(O)R 21 , —C(O)CH 2 C(O) 2 R 21 , —C(O)CH 2 OR 21 , —C(O)CH 2 R 22 , —C(O)C(O)NHR 21 , —C(O)R 21 , —CHR 21 OC(O)R 21 , —CHR 21 C(O) 2 R 21 , —CHR 21 (OR 21 ), or —CH(OR 21 ) 2 , and R 21 and R 22 are as previously defined.
  • the compound of Formula (I) is represented by one of Formulae (VIII-1) (VIII-12), or a pharmaceutically acceptable salt thereof:
  • R 31 is hydrogen, —F, —Cl, —OCH 3 , or —OCHF 2 ;
  • X is as previously defined.
  • X is —CN, —C(O)CH 2 OC(O)R 21 , —C(O)CH 2 C(O) 2 R 21 , —C(O)CH 2 OR 21 , —C(O)CH 2 R 22 , —C(O)C(O)NHR 21 , —C(O)R 21 , —CHR 21 OC(O)R 21 , —CHR 21 C(O) 2 R 21 , —CHR 21 (OR 21 ), or —CH(OR 21 ) 2 , and R 21 and R 22 are as previously defined.
  • the compound of Formula (I) is represented by one of Formulae (IX-1) ⁇ (IX-8), or a pharmaceutically acceptable salt thereof:
  • R 32 is hydrogen, —F, Cl, —CH 3 , —CF 3 or —OR;
  • R 33 is —Cl, —Br, —OR 21 , —NHR 21 , or —OC(O)R 21 ;
  • R 34 is R 21 , preferably, R 34 is optionally substituted —C 1 -C 6 alkyl, optionally substituted —C 3 -C 8 cycloalkyl, or optionally substituted 3- to 8-membered heterocycloalkyl, more preferably, R 34 is benzyl, cyclohexyl, isopropyl, t-butyl or optionally substituted methyl; and R 21 and A are as previously defined.
  • the compound of Formula (I) is represented by one of Formulae (IX-1) ⁇ (IX-8), or a pharmaceutically acceptable salt thereof, wherein R 32 , R 33 , and R 34 are as previously defined; A is selected from the groups below:
  • A has 0, 1 or 2 substituents.
  • substituents are independently selected from fluoro, chloro, hydroxy, methoxy, fluoromethoxy, difluoromethoxy, and trifluoromethoxy.
  • the compound of Formula (I) is represented by one of Formulae (IX-1) ⁇ (IX-8), wherein A is —CH 2 R 23 ; R 23 , R 32 , R 33 , and R 34 are as previously defined.
  • the compound of Formula (I) is represented by Formula (X-a) or a pharmaceutically acceptable salt thereof, wherein A and X are as previously defined,
  • Representative compounds of the invention include, but are not limited to, compounds according to Formula (X-a), and pharmaceutically acceptable salts thereof, wherein A and X are delineated for each compound in Table 1.
  • the compound of Formula (I) is represented by Formula (X-b) or a pharmaceutically acceptable salt thereof, wherein A and X are as previously defined,
  • Representative compounds of the invention include, but are not limited to, compounds according to Formula (X-b), and pharmaceutically acceptable salts thereof, wherein A and X are delineated for each compound in Table 2.
  • the compound of Formula (I) is represented by Formula (X-c) or a pharmaceutically acceptable salt thereof, wherein A and X are previously defined,
  • Representative compounds of the invention include, but are not limited to, compounds according to Formula (X-c), and pharmaceutically acceptable salts thereof, wherein A and X are delineated for each compound in Table 3.
  • the compound of Formula (I) is represented by Formula (X-d) or a pharmaceutically acceptable salt thereof, wherein A and X are previously defined,
  • Representative compounds of the invention include, but are not limited to, compounds according to Formula (X-d), and pharmaceutically acceptable salts thereof, wherein A and X are delineated for each compound in Table 4.
  • the compound of Formula (I) is represented by Formula (X-e) or a pharmaceutically acceptable salt thereof, wherein A and X are previously defined,
  • Representative compounds of the invention include, but are not limited to, compounds according to Formula (X-e), and pharmaceutically acceptable salts thereof, wherein A and X are delineated for each compound in Table 5.
  • the compound of Formula (I) is represented by Formula (X-f) or a pharmaceutically acceptable salt thereof, wherein A and X are previously defined,
  • Representative compounds of the invention include, but are not limited to, compounds according to Formula (X-f), and pharmaceutically acceptable salts thereof, wherein A and X are delineated for each compound in Table 6.
  • the compound of Formula (I) is represented by one of Formulae (XI-1) ⁇ (XI-8), or a pharmaceutically acceptable salt thereof,
  • R 13 , R 14 , R 24 , R 25 , and X are as previously defined.
  • the compound of Formula (I) is represented by one of Formulae (XII-1) ⁇ (XII-4), or a pharmaceutically acceptable salt thereof,
  • R 14 , R 15 , R 24 , R 25 , and X are as previously defined.
  • the compound of Formula (I) is represented by one of Formulae (XIII-1) (XIII-4), or a pharmaceutically acceptable salt thereof,
  • R 15 , R 24 , and X are as previously defined.
  • X is —CN; and R 24 is optionally substituted —C 1 -C 6 alkyl, such as t-butyl.
  • the compounds of the present invention may contain one or more asymmetric carbon atoms and may exist in racemic, diastereoisomeric, and optically active forms. It will still be appreciated that certain compounds of the present invention may exist in different tautomeric forms. All tautomers are contemplated to be within the scope of the present invention.
  • the invention provides a method of treating or preventing a coronavirus infection in a subject, such as a human, in need thereof, comprising the step of administering to the subject a therapeutically effective amount of a compound of Formula (I) or a pharmaceutically acceptable salt thereof.
  • the coronavirus can be an alpha, beta, gamma or delta coronavirus.
  • the coronavirus is one which infects humans, such as coronavirus 229E, coronavirus NL63, coronavirus OC 43 , coronavirus HKU1, SARS-CoV-1, SARS-CoV-2, and MERS-CoV.
  • the coronavirus is SARS-CoV-1, SARS-CoV-2, or MERS-CoV.
  • the coronavirus is SARS-CoV-2.
  • Embodiments of the present invention provide administration of a compound to a healthy or virus-infected patient, either as a single agent or in combination with (1) another agent that is effective in treating or preventing coronavirus infections, (2) another agent that improves immune response and robustness, or (3) another agent that reduces inflammation and/or pain.
  • the compounds described herein, or salts, solvates or hydrates thereof, are believed to have activity in preventing, halting or reducing the effects of coronavirus by inhibiting the viral 3C or 3C-Like protease, thereby interfering with or preventing the polyprotein processing of the translated viral genome, in the host cell, rendering the virus unable to replicate.
  • this invention provides for a method of treating a respiratory disorder in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of Formula (I) or a pharmaceutically acceptable salt thereof.
  • respiratory disorders include, but are not limited to, an acute airway disease or a chronic airway disease. Examples of such respiratory disorders include acute asthma, lung disease secondary to environmental exposures, acute lung infection, and chronic lung infection.
  • the compounds of the present invention and any other pharmaceutically active agent(s) may be administered together or separately and, when administered separately, administration may occur simultaneously or sequentially, in any order.
  • the amounts of the compounds of the present invention and the other pharmaceutically active agent(s) and the relative timings of administration will be selected in order to achieve the desired combined therapeutic effect.
  • the administration in combination of a compound of the present invention and salts, solvates, or other pharmaceutically acceptable derivatives thereof with other treatment agents may be in combination by administration concomitantly in: (1) a unitary pharmaceutical composition including both compounds; or (2) separate pharmaceutical compositions each including one of the compounds.
  • administering the compound of the invention allows for administering of the additional therapeutic agent at a lower dose or frequency as compared to the administering of the at least one additional therapeutic agent alone that is required to achieve similar results in prophylactically treating a coronavirus infection in an individual in need thereof.
  • aryl refers to a mono- or polycyclic carbocyclic ring system comprising at least one aromatic ring, including, but not limited to, phenyl, naphthyl, tetrahydronaphthyl, indanyl, and indenyl.
  • a polycyclic aryl is a polycyclic ring system that comprises at least one aromatic ring.
  • Polycyclic aryls can comprise fused rings, covalently attached rings or a combination thereof.
  • heteroaryl refers to a mono- or polycyclic aromatic radical having one or more ring atom selected from S, O and N; and the remaining ring atoms are carbon, wherein any N or S contained within the ring may be optionally oxidized.
  • Heteroaryl includes, but is not limited to, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzoxazolyl, quinoxalinyl.
  • a polycyclic heteroaryl can comprise fused rings, covalently attached rings or a combination thereof.
  • aromatic groups can be substituted or unsubstituted.
  • alkyl refers to saturated, straight- or branched-chain hydrocarbon radicals.
  • C 1 -C 4 alkyl refers to saturated, straight- or branched-chain hydrocarbon radicals.
  • C 1 -C 4 alkyl refers to alkyl groups containing from one to four, one to six, one to eight, one to twelve, 2 to 4 and 3 to 6 carbon atoms respectively.
  • C 1 -C 8 alkyl radicals include, but are not limited to, methyl, ethyl, propyl, isopropyl, n-butyl, tert-butyl, neopentyl, n-hexyl, heptyl and octyl radicals.
  • alkenyl refers to straight- or branched-chain hydrocarbon radicals having at least one carbon-carbon double bond by the removal of a single hydrogen atom.
  • C 2 -C 8 alkenyl refers to alkenyl groups containing from two to eight, two to twelve, two to four, three to four or three to six carbon atoms respectively.
  • Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, 2-methyl-2-buten-2-yl, heptenyl, octenyl, and the like.
  • alkynyl refers to straight- or branched-chain hydrocarbon radicals having at least one carbon-carbon double bond by the removal of a single hydrogen atom.
  • C 2 -C 8 alkynyl refers to alkynyl groups containing from two to eight, two to twelve, two to four, three to four or three to six carbon atoms respectively.
  • Representative alkynyl groups include, but are not limited to, for example, ethynyl, 2-propynyl, 2-butynyl, heptynyl, octynyl, and the like.
  • cycloalkyl refers to a monocyclic or polycyclic saturated carbocyclic ring or a bi- or tri-cyclic group fused, bridged or spiro system, and the carbon atoms may be optionally oxo-substituted or optionally substituted with exocyclic olefinic double bond.
  • Preferred cycloalkyl groups include C 3 -C 12 cycloalkyl, C 3 -C 6 cycloalkyl, C 3 -C 8 cycloalkyl and C 4 -C 7 cycloalkyl.
  • C 3 -C 12 cycloalkyl examples include, but not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclopentyl, cyclooctyl, 4-methylene-cyclohexyl, bicyclo[2.2.1]heptyl, bicyclo[3.1.0]hexyl, spiro[2.5]octyl, 3-methylenebicyclo[3.2.1]octyl, spiro[4.4]nonanyl, and the like.
  • cycloalkenyl refers to monocyclic or polycyclic carbocyclic ring or a bi- or tri-cyclic group fused, bridged or spiro system having at least one carbon-carbon double bond and the carbon atoms may be optionally oxo-substituted or optionally substituted with exocyclic olefinic double bond.
  • Preferred cycloalkenyl groups include C 3 -C 12 cycloalkenyl, C 3 -C 8 cycloalkenyl or C 5 -C 7 cycloalkenyl groups.
  • C 3 -C 12 cycloalkenyl examples include, but not limited to, cyclopropenyl, cyclobutenyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl, bicyclo[2.2.1]hept-2-enyl, bicyclo[3.1.0]hex-2-enyl, spiro[2.5]oct-4-enyl, spiro[4.4]non-2-enyl, bicyclo[4.2.1]non-3-en-12-yl, and the like.
  • arylalkyl means a functional group wherein an alkylene chain is attached to an aryl group, e.g., —CH 2 CH 2 -phenyl.
  • substituted arylalkyl means an arylalkyl functional group in which the aryl group is substituted.
  • heteroarylalkyl means a functional group wherein an alkylene chain is attached to a heteroaryl group.
  • substituted heteroarylalkyl means a heteroarylalkyl functional group in which the heteroaryl group is substituted.
  • alkoxy employed alone or in combination with other terms means, unless otherwise stated, an alkyl group having the designated number of carbon atoms connected to the rest of the molecule via an oxygen atom, such as, for example, methoxy, ethoxy, 2-propoxy, 2-propoxy (isopropoxy) and the higher homologs and isomers.
  • Preferred alkoxy are (C 2 -C 3 ) alkoxy.
  • any alkyl, alkenyl, alkynyl, cycloalkyl, heterocyclic and cycloalkenyl moiety described herein can also be an aliphatic group or an alicyclic group.
  • An “aliphatic” group is a non-aromatic moiety comprised of any combination of carbon atoms, hydrogen atoms, halogen atoms, oxygen, nitrogen or other atoms, and optionally contains one or more units of unsaturation, e.g., double and/or triple bonds.
  • aliphatic groups are functional groups, such as alkyl, alkenyl, alkynyl, O, OH, NH, NH 2 , C(O), S(O) 2 , C(O)O, C(O)NH, OC(O)O, OC(O)NH, OC(O)NH 2 , S(O) 2 NH, S(O) 2 NH 2 , NHC(O)NH 2 , NHC(O)C(O)NH, NHS(O) 2 NH, NHS(O) 2 NH 2 , C(O)NHS(O) 2 , C(O)NHS(O) 2 NH or C(O)NHS(O) 2 NH 2 , and the like, groups comprising one or more functional groups, non-aromatic hydrocarbons (optionally substituted), and groups wherein one or more carbons of a non-aromatic hydrocarbon (optionally substituted) is replaced by a functional group.
  • groups comprising one or more functional groups, non-
  • Carbon atoms of an aliphatic group can be optionally oxo-substituted.
  • An aliphatic group may be straight chained, branched, cyclic, or a combination thereof and preferably contains between about 1 and about 24 carbon atoms, more typically between about 1 and about 12 carbon atoms.
  • aliphatic groups expressly include, for example, alkoxyalkyls, polyalkoxyalkyls, such as polyalkylene glycols, polyamines, and polyimines, for example. Aliphatic groups may be optionally substituted.
  • heterocyclic or “heterocycloalkyl” can be used interchangeably and referred to a non-aromatic ring or a bi- or tri-cyclic group fused, bridged or spiro system, where (i) each ring system contains at least one heteroatom independently selected from oxygen, sulfur and nitrogen, (ii) each ring system can be saturated or unsaturated (iii) the nitrogen and sulfur heteroatoms may optionally be oxidized, (iv) the nitrogen heteroatom may optionally be quaternized, (v) any of the above rings may be fused to an aromatic ring, and (vi) the remaining ring atoms are carbon atoms which may be optionally oxo-substituted or optionally substituted with exocyclic olefinic double bond.
  • heterocycloalkyl groups include, but are not limited to, 1,3-dioxolane, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, 2-azabicyclo[2.2.1]-heptyl, 8-azabicyclo[3.2.1]octyl, 5-azaspiro[2.5]octyl, 2-oxa-7-azaspiro[4.4]nonanyl, 7-oxooxepan-4-yl, and tetrahydrofuryl. Such heterocyclic groups may be further substituted. Heteroaryl or heterocyclic groups can be C-attached or N-attach
  • any alkyl, alkenyl, alkynyl, alicyclic, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heterocyclic, aliphatic moiety or the like, described herein can also be a divalent or multivalent group when used as a linkage to connect two or more groups or substituents, which can be at the same or different atom(s).
  • One of skill in the art can readily determine the valence of any such group from the context in which it occurs.
  • substituted refers to substitution by independent replacement of one, two, or three or more of the hydrogen atoms with substituents including, but not limited to, —F, —Cl, —Br, —I, —OH, C 1 -C 12 -alkyl; C 2 -C 12 -alkenyl, C 2 -C 12 -alkynyl, —C 3 -C 12 -cycloalkyl, protected hydroxy, —NO 2 , —N 3 , —CN, —NH 2 , protected amino, oxo, thioxo, —NH—C 2 -C 8 -alkenyl, —NH—C 2 -C 8 -alkynyl, —NH—C 3 -C 12 -cycloalkyl, —NH-aryl, —NH-heteroaryl, —NH— heterocycloalkyl, -dialkylamino, -diarylamin
  • the substituents are independently selected from halo, preferably C 1 and F; C 1 -C 4 -alkyl, preferably methyl and ethyl; halo-C 1 -C 4 -alkyl, such as fluoromethyl, difluoromethyl, and trifluoromethyl; C 2 -C 4 -alkenyl; halo-C 2 -C 4 -alkenyl; C 3 -C 6 -cycloalkyl, such as cyclopropyl; C 1 -C 4 -alkoxy, such as methoxy and ethoxy; halo-C 1 -C 4 -alkoxy, such as fluoromethoxy, difluoromethoxy, and trifluoromethoxy, —CN; —OH; NH 2 ; C 1 -C 4 -alkylamino; di(C 1 -C 4 -alkyl)amino; and NO 2 .
  • each substituent in a substituted moiety is additionally optionally substituted with one or more groups, each group being independently selected from C 1 -C 4 -alkyl; —CF 3 , —OCH 3 , —OCF 3 , —F, —Cl, —Br, —I, —OH, —NO 2 , —CN, and —NH 2 .
  • a substituted alkyl group is substituted with one or more halogen atoms, more preferably one or more fluorine or chlorine atoms.
  • halo or halogen alone or as part of another substituent, as used herein, refers to a fluorine, chlorine, bromine, or iodine atom.
  • the term “optionally substituted”, as used herein, means that the referenced group may be substituted or unsubstituted. In one embodiment, the referenced group is optionally substituted with zero substituents, i.e., the referenced group is unsubstituted. In another embodiment, the referenced group is optionally substituted with one or more additional group(s) individually and independently selected from groups described herein.
  • hydrox includes hydrogen and deuterium.
  • recitation of an atom includes other isotopes of that atom so long as the resulting compound is pharmaceutically acceptable.
  • hydroxy activating group refers to a labile chemical moiety which is known in the art to activate a hydroxyl group so that it will depart during synthetic procedures such as in a substitution or an elimination reaction.
  • hydroxyl activating group include, but not limited to, mesylate, tosylate, triflate, p-nitrobenzoate, phosphonate and the like.
  • activated hydroxyl refers to a hydroxy group activated with a hydroxyl activating group, as defined above, including mesylate, tosylate, triflate, p-nitrobenzoate, phosphonate groups, for example.
  • hydroxy protecting group refers to a labile chemical moiety which is known in the art to protect a hydroxyl group against undesired reactions during synthetic procedures. After said synthetic procedure(s) the hydroxy protecting group as described herein may be selectively removed. Hydroxy protecting groups as known in the art are described generally in T. H. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 3rd edition, John Wiley & Sons, New York (1999).
  • hydroxyl protecting groups include benzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, tert-butoxycarbonyl, isopropoxycarbonyl, diphenylmethoxycarbonyl, 2,2,2-trichloroethoxycarbonyl, allyloxycarbonyl, acetyl, formyl, chloroacetyl, trifluoroacetyl, methoxyacetyl, phenoxyacetyl, benzoyl, methyl, t-butyl, 2,2,2-trichloroethyl, 2-trimethylsilyl ethyl, allyl, benzyl, triphenyl-methyl (trityl), methoxymethyl, methylthiomethyl, benzyloxymethyl, 2-(trimethylsilyl)-ethoxymethyl, methanesulfonyl, trimethylsilyl, triisopropylsilyl, and the like.
  • protected hydroxy refers to a hydroxy group protected with a hydroxy protecting group, as defined above, including benzoyl, acetyl, trimethylsilyl, triethylsilyl, methoxymethyl groups, for example.
  • hydroxy prodrug group refers to a promoiety group which is known in the art to change the physicochemical, and hence the biological properties of a parent drug in a transient manner by covering or masking the hydroxy group. After said synthetic procedure(s), the hydroxy prodrug group as described herein must be capable of reverting back to hydroxy group in vivo. Hydroxy prodrug groups as known in the art are described generally in Kenneth B. Sloan, Prodrugs, Topical and Ocular Drug Delivery , (Drugs and the Pharmaceutical Sciences; Volume 53), Marcel Dekker, Inc., New York (1992).
  • amino protecting group refers to a labile chemical moiety which is known in the art to protect an amino group against undesired reactions during synthetic procedures. After said synthetic procedure(s) the amino protecting group as described herein may be selectively removed.
  • Amino protecting groups as known in the art are described generally in T. H. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 3rd edition, John Wiley & Sons, New York (1999). Examples of amino protecting groups include, but are not limited to, methoxycarbonyl, t-butoxycarbonyl, 12-fluorenyl-methoxycarbonyl, benzyloxycarbonyl, and the like.
  • protected amino refers to an amino group protected with an amino protecting group as defined above.
  • leaving group means a functional group or atom which can be displaced by another functional group or atom in a substitution reaction, such as a nucleophilic substitution reaction.
  • representative leaving groups include chloro, bromo and iodo groups; sulfonic ester groups, such as mesylate, tosylate, brosylate, nosylate and the like; and acyloxy groups, such as acetoxy, trifluoroacetoxy and the like.
  • aprotic solvent refers to a solvent that is relatively inert to proton activity, i.e., not acting as a proton-donor.
  • examples include, but are not limited to, hydrocarbons, such as hexane and toluene, for example, halogenated hydrocarbons, such as, for example, methylene chloride, ethylene chloride, chloroform, and the like, heterocyclic compounds, such as, for example, tetrahydrofuran and N-methylpyrrolidinone, and ethers such as diethyl ether, bis-methoxymethyl ether.
  • protic solvent refers to a solvent that tends to provide protons, such as an alcohol, for example, methanol, ethanol, propanol, isopropanol, butanol, t-butanol, and the like.
  • alcohol for example, methanol, ethanol, propanol, isopropanol, butanol, t-butanol, and the like.
  • solvents are well known to those skilled in the art, and it will be obvious to those skilled in the art that individual solvents or mixtures thereof may be preferred for specific compounds and reaction conditions, depending upon such factors as the solubility of reagents, reactivity of reagents and preferred temperature ranges, for example.
  • stable refers to compounds which possess stability sufficient to allow manufacture and which maintains the integrity of the compound for a sufficient period of time to be useful for the purposes detailed herein (e.g., therapeutic or prophylactic administration to a subject).
  • the synthesized compounds can be separated from a reaction mixture and further purified by a method such as column chromatography, high pressure liquid chromatography, or recrystallization.
  • a method such as column chromatography, high pressure liquid chromatography, or recrystallization.
  • further methods of synthesizing the compounds of the Formula herein will be evident to those of ordinary skill in the art. Additionally, the various synthetic steps may be performed in an alternate sequence or order to give the desired compounds.
  • Synthetic chemistry transformations and protecting group methodologies (protection and deprotection) useful in synthesizing the compounds described herein are known in the art and include, for example, those such as described in R. Larock, Comprehensive Organic Transformations, 2 nd Ed. Wiley-VCH (1999); T. W. Greene and P. G. M.
  • subject refers to an animal.
  • the animal is a mammal. More preferably, the mammal is a human.
  • a subject also refers to, for example, dogs, cats, horses, cows, pigs, guinea pigs, fish, birds and the like.
  • the compounds of this invention may be modified by appending appropriate functionalities to enhance selective biological properties.
  • modifications are known in the art and may include those which increase biological penetration into a given biological system (e.g., blood, lymphatic system, central nervous system), increase oral availability, increase solubility to allow administration by injection, alter metabolism and alter rate of excretion.
  • the compounds described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)-, or as (D)- or (L)- for amino acids.
  • the present invention is meant to include all such possible isomers, as well as their racemic and optically pure forms.
  • Optical isomers may be prepared from their respective optically active precursors by the procedures described above, or by resolving the racemic mixtures. The resolution can be carried out in the presence of a resolving agent, by chromatography or by repeated crystallization or by some combination of these techniques which are known to those skilled in the art.
  • any carbon-carbon double bond appearing herein is selected for convenience only and is not intended to designate a particular configuration unless the text so states; thus a carbon-carbon double bond or carbon-heteroatom double bond depicted arbitrarily herein as trans may be cis, trans, or a mixture of the two in any proportion.
  • Certain compounds of the present invention may also exist in different stable conformational forms which may be separable. Torsional asymmetry due to restricted rotation about an asymmetric single bond, for example because of steric hindrance or ring strain, may permit separation of different conformers.
  • the present invention includes each conformational isomer of these compounds and mixtures thereof.
  • the term “pharmaceutically acceptable salt,” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.
  • Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 66: 2-19 (1977).
  • the salts can be prepared in situ during the final isolation and purification of the compounds of the invention, or separately by reacting the free base function with a suitable organic acid.
  • nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
  • salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentane-propionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pam
  • alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate.
  • ester refers to esters which hydrolyze in vivo and include those that break down readily in the human body to leave the parent compound or a salt thereof.
  • Suitable ester groups include, for example, those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl moiety advantageously has not more than 6 carbon atoms.
  • esters include, but are not limited to, formates, acetates, propionates, butyrates, acrylates and ethylsuccinates.
  • compositions of the present invention comprise a therapeutically effective amount of a compound of the present invention formulated together with one or more pharmaceutically acceptable carriers or excipients.
  • the term “pharmaceutically acceptable carrier or excipient” means a non-toxic, inert solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type.
  • materials which can serve as pharmaceutically acceptable carriers are sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols such as propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid;
  • compositions of this invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir, preferably by oral administration or administration by injection.
  • the pharmaceutical compositions of this invention may contain any conventional non-toxic pharmaceutically-acceptable carriers, adjuvants or vehicles.
  • the pH of the formulation may be adjusted with pharmaceutically acceptable acids, bases or buffers to enhance the stability of the formulated compound or its delivery form.
  • parenteral as used herein includes subcutaneous, intracutaneous, intravenous, intramuscular, intraarticular, intra-arterial, intrasynovial, intrasternal, intrathecal, intralesional and intracranial injection or infusion techniques.
  • Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs.
  • the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
  • the oral compositions can also include adjuvants such as wetting agents, e
  • Injectable preparations for example, sterile injectable aqueous or oleaginous suspensions, may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol.
  • the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil can be employed including synthetic mono- or diglycerides.
  • fatty acids such as oleic acid are used in the preparation of injectable.
  • the injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
  • the rate of drug release can be controlled.
  • biodegradable polymers include poly(orthoesters) and poly(anhydrides).
  • Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissues.
  • compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
  • suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
  • Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules.
  • the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or: a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and g
  • compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
  • the solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.
  • Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches.
  • the active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required.
  • Ophthalmic formulation, ear drops, eye ointments, powders and solutions are also contemplated as being within the scope of this invention.
  • the ointments, pastes, creams and gels may contain, in addition to an active compound of this invention, excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
  • excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
  • Powders and sprays can contain, in addition to the compounds of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances.
  • Sprays can additionally contain customary propellants such as chlorofluorohydrocarbons.
  • Transdermal patches have the added advantage of providing controlled delivery of a compound to the body.
  • dosage forms can be made by dissolving or dispensing the compound in the proper medium.
  • Absorption enhancers can also be used to increase the flux of the compound across the skin.
  • the rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
  • a therapeutic composition of the invention is formulated and administered to the patient in solid or liquid particulate form by direct administration e.g., inhalation into the respiratory system.
  • Solid or liquid particulate forms of the active compound prepared for practicing the present invention include particles of respirable size: that is, particles of a size sufficiently small to pass through the mouth and larynx upon inhalation and into the bronchi and alveoli of the lungs.
  • Delivery of aerosolized therapeutics, particularly aerosolized antibiotics is known in the art (see, for example U.S. Pat. No. 5,767,068 to Van Devanter et al., U.S. Pat. No. 5,508,269 to Smith et al., and WO 98/43650 by Montgomery, all of which are incorporated herein by reference).
  • the compounds of the present invention may be used in combination with one or more antiviral therapeutic agents or anti-inflammatory agents useful in the prevention or treatment of viral diseases or associated pathophysiology.
  • antiviral therapeutic agents or anti-inflammatory agents useful in the prevention or treatment of viral diseases or associated pathophysiology.
  • the compounds of the present invention and their salts, solvates, or other pharmaceutically acceptable derivatives thereof may be employed alone or in combination with other antiviral or anti-inflammatory therapeutic agents.
  • the compounds herein and pharmaceutically acceptable salts thereof may be used in combination with one or more other agents which may be useful in the prevention or treatment of respiratory disease, inflammatory disease, autoimmune disease, for example; anti-histamines, corticosteroids, (e.g., fluticasone propionate, fluticasone furoate, beclomethasone dipropionate, budesonide, ciclesonide, mometasone furoate, triamcinolone, flunisolide), NSAIDs, Ieukotriene modulators (e.g., montelukast, zafirlukast.pranlukast), tryptase inhibitors, IKK2 inhibitors, p38 inhibitors, Syk inhibitors, protease inhibitors such as elastase inhibitors, integrin antagonists (e.g., beta-2 integrin antagonists), adenosine A2a agonists, mediator release inhibitors such as sodium chromoglycate
  • antigen non-specific immunotherapies e.g. interferon or other cytokines/chemokines, chemokine receptor modulators such as CCR3, CCR4 or CXCR2 antagonists, other cytokine/chemokine agonists or antagonists, TLR agonists and similar agents
  • suitable anti-infective agents including antibiotic agents, antifungal agents, antheimintic agents, antimalarial agents, antiprotozoal agents, antitubercuiosis agents, and antiviral agents, including those listed at https://www.drugs.com/drug-class/anti-infectives.html.
  • combination therapy is typically preferred over alternation therapy because it induces multiple simultaneous stresses on the virus.
  • An inhibitory amount or dose of the compounds of the present invention may range from about 0.01 mg/Kg to about 500 mg/Kg, alternatively from about 1 to about 50 mg/Kg. Inhibitory amounts or doses will also vary depending on route of administration, as well as the possibility of co-usage with other agents.
  • viral infections are treated or prevented in a patient such as a human or another animal by administering to the patient a therapeutically effective amount of a compound of the invention, in such amounts and for such time as is necessary to achieve the desired result.
  • a “therapeutically effective amount” of a compound of the invention is meant an amount of the compound which confers a therapeutic effect on the treated subject, at a reasonable benefit/risk ratio applicable to any medical treatment.
  • the therapeutic effect may be objective (i.e., measurable by some test or marker) or subjective (i.e., subject gives an indication of or feels an effect).
  • An effective amount of the compound described above may range from about 0.1 mg/Kg to about 500 mg/Kg, preferably from about 1 to about 50 mg/Kg. Effective doses will also vary depending on route of administration, as well as the possibility of co-usage with other agents. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment.
  • the specific therapeutically effective dose level for any particular patient will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or contemporaneously with the specific compound employed; and like factors well known in the medical arts.
  • the total daily dose of the compounds of this invention administered to a human or other animal in single or in divided doses can be in amounts, for example, from 0.01 to 50 mg/kg body weight or more usually from 0.1 to 25 mg/kg body weight.
  • Single dose compositions may contain such amounts or submultiples thereof to make up the daily dose.
  • treatment regimens according to the present invention comprise administration to a patient in need of such treatment from about 10 mg to about 1000 mg of the compound(s) of this invention per day in single or multiple doses.
  • the compounds of the present invention described herein can, for example, be administered by injection, intravenously, intra-arterial, subdermally, intraperitoneally, intramuscularly, or subcutaneously; or orally, buccally, nasally, transmucosally, topically, in an ophthalmic preparation, or by inhalation, with a dosage ranging from about 0.1 to about 500 mg/kg of body weight, alternatively dosages between 1 mg and 1000 mg/dose, every 4 to 120 hours, or according to the requirements of the particular drug.
  • the methods herein contemplate administration of an effective amount of compound or compound composition to achieve the desired or stated effect.
  • the pharmaceutical compositions of this invention will be administered from about 1 to about 6 times per day or alternatively, as a continuous infusion.
  • Such administration can be used as a chronic or acute therapy.
  • the amount of active ingredient that may be combined with pharmaceutically excipients or carriers to produce a single dosage form will vary depending upon the host treated and the particular mode of administration.
  • a typical preparation will contain from about 5% to about 95% active compound (w/w).
  • such preparations may contain from about 20% to about 80% active compound.
  • a maintenance dose of a compound, composition or combination of this invention may be administered, if necessary. Subsequently, the dosage or frequency of administration, or both, may be reduced, as a function of the symptoms, to a level at which the improved condition is retained when the symptoms have been alleviated to the desired level. Patients may, however, require intermittent treatment on a long-term basis upon any recurrence of disease symptoms.
  • compositions of this invention comprise a combination of a compound of the Formula described herein and one or more additional therapeutic or prophylactic agents
  • both the compound and the additional agent should be present at dosage levels of between about 1 to 100%, and more preferably between about 5 to 95% of the dosage normally administered in a monotherapy regimen.
  • the additional agents may be administered separately, as part of a multiple dose regimen, from the compounds of this invention. Alternatively, those agents may be part of a single dosage form, mixed together with the compounds of this invention in a single composition.
  • additional therapeutic or prophylactic agents include but are not limited to, immune therapies (eg. interferon), therapeutic vaccines, antifibrotic agents, anti-inflammatory agents such as corticosteroids or NSAIDs, bronchodilators such as beta-2 adrenergic agonists and xanthines (e.g. theophylline), mucolytic agents, anti-muscarinics, anti-leukotrienes, inhibitors of cell adhesion (e.g. ICAM antagonists), anti-oxidants (e.g. N-acetylcysteine), cytokine agonists, cytokine antagonists, lung surfactants and/or antimicrobial and anti-viral agents (e.g. ribavirin and amantidine).
  • the compositions according to the invention may also be used in combination with gene replacement therapy.
  • Intermediate 1 (R 1 defined as H, optionally substituted alkyl, optionally substituted aryl, or optionally substituted heterocyclic; J defined as an amino protecting group) can be reacted in a carbon-carbon bond forming reaction with nitrile 2 (X defined as halogen, OMs, OAc, OTf, OTs, or OTf), typically mediated by a base (denoted as [Base]) including, but not limited to: LDA, LiHMDS or LiTMP.
  • Base denoted as [Base]
  • Intermediate 3 can be reduced (denoted as [Reduction]), typically mediated by a reducing agent including, but not limited to: LiBH 4 or NaBH 4 .
  • Lactam 4 can be reacted in a deprotection step (denoted as [Deprotection]), typically mediated by an acidic reagent including, but not limited to: TFA or HCl to produce compound 5.
  • lactam 4 can be reacted in a deprotection step (denoted as [Deprotection]), mediated by a reducing agent including, but not limited to hydrogen over palladium on carbon to produce compound 5.
  • Ester 3 can be reacted in a hydrolysis reaction (denoted as [Hydrolysis]), typically mediated by an acidic reagent including, but not limited to: TFA or HCl to produce acid 4.
  • ester 3 can be reacted in a hydrolysis reaction (denoted as [Hydrolysis]), typically mediated by a basic reagent including, but not limited to: NaOH, LiOH, or Me 3 SnOH to produce acid 4.
  • ester 3 can be reacted in a hydrolysis reaction (denoted as [Hydrolysis]), typically mediated by a reducing agent including, but not limited to hydrogen over palladium on carbon to produce acid 4.
  • a reagent or group of reagents (denoted as [Oxidant]) including, but not limited to: SO 3 -pyridine, DMP, or Ac 2 O/DMSO to produce aldehyde 3.
  • This intermediate can undergo an oxidation reaction, denoted as [Oxidation] that is mediated by a reagent including, but not limited to: sulfur trioxide pyridine complex (Py-SO 3 ), DMSO, oxalyl chloride, and/or acetic anhydride, to produce keto-amide 4.
  • a reagent including, but not limited to: sulfur trioxide pyridine complex (Py-SO 3 ), DMSO, oxalyl chloride, and/or acetic anhydride, to produce keto-amide 4.
  • Mass spectra were run on LC-MS systems using electrospray ionization. These were Agilent 1290 Infinity II systems with an Agilent 6120 Quadrupole detector. Spectra were obtained using a ZORBAX Eclipse XDB-C 18 column (4.6 ⁇ 30 mm, 1.8 micron). Spectra were obtained at 298K using a mobile phase of 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B). Spectra were obtained with the following solvent gradient: 5% (B) from 0-1.5 min, 5-95% (B) from 1.5-4.5 min, and 95% (B) from 4.5-6 min. The solvent flowrate was 1.2 mL/min. Compounds were detected at 210 nm and 254 nm wavelengths. [M+H] + refers to mono-isotopic molecular weights.
  • Compounds were purified via reverse-phase high-performance liquid chromatography (RPHPLC) using a Gilson GX-281 automated liquid handling system. Compounds were purified on a Phenomenex Kinetex EVO C18 column (250 ⁇ 21.2 mm, 5 micron), unless otherwise specified. Compounds were purified at 298K using a mobile phase of water (A) and acetonitrile (B) using gradient elution between 0% and 100% (B), unless otherwise specified. The solvent flowrate was 20 mL/min and compounds were detected at 254 nm wavelength.
  • RPHPLC reverse-phase high-performance liquid chromatography
  • NPLC normal-phase liquid chromatography
  • Teledyne ISCO Combiflash purification system a Teledyne ISCO Combiflash purification system.
  • Compounds were purified on a REDISEP silica gel cartridge.
  • Compounds were purified at 298K and detected at 254 nm wavelength.
  • Step 1 A suspension of 4-methoxy-1H-indole-2-carboxylic acid (3.6 g) in DCM (94 mL) was cooled to 0° C. Then tert-butyl (1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylate oxalate (6.81 g) was added, followed by DMAP (0.690 g). Then EDC (7.22 g) was added and the reaction was allowed to stir at 0° C. for 30 minutes, then overnight at r.t. The mixture was then washed with water (1 ⁇ 30 mL), and the organic layer was dried over Na 2 SO 4 , filtered, and concentrated. The crude product was used directly in the next step.
  • Step 2 Trifluoroacetic acid (32.6 mL) was added to a solution of methyl (1S,3aR,6aS)-2-(4-methoxy-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxylate (7.24 g) in DCM (106 mL) at room temperature. The resulting solution was stirred at room temperature for 2 h, then concentrated.
  • Step 3 A vial was charged with (S)-3-((S)-2-amino-4-chloro-3-oxobutyl)pyrrolidin-2-one hydrochloride (150 mg), DMF (3 mL), HATU (239 mg), and (1S,3aR,6aS)-2-(4-methoxy-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxylic acid (212 mg) then cooled to 0° C. Then, Hunig's base (261 mg) was added. The reaction mixture was stirred for 75 minutes, then diluted with ethyl acetate, washed three times with sat.
  • Step 1 A vial was charged with 2,6-dichlorobenzoic acid (62 mg), cesium fluoride (91 mg), and (1S,3aR,6aS)-N—((S)-4-chloro-3-oxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)-2-(4-methoxy-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxamide (140 mg). The vial was purged with nitrogen gas, then DMF (2 mL) was added. The reaction mixture was heated at 65° C. for one hour.
  • Step 2 Into a 3-L 4-necked round-bottom flask purged and maintained with an inert atmosphere of nitrogen, was placed tert-butyl N-[(1S)-1-carbamoyl-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]carbamate (150.00 g, 552.859 mmol, 1.00 equiv), dichloroacetonitrile (607.81 g, 5528.590 mmol, 10.00 equiv) in ACN (900 mL) and water (900 mL).
  • Step 3 Trifluoroacetic acid (790 ⁇ L) was added to a solution of tert-butyl ((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)carbamate (20 mg, 0.079 mmol) and DCM (0.790 mL) at 22° C. After 15 min, the resulting solution was concentrated directly in vacuo. The residue was redissolved in methanol (2 mL) and concentrated in vacuo, then redissolved in ethyl acetate (2 mL) and concentrated once more.
  • Step 4 4-(difluoromethoxy)-1H-indole-2-carboxylic acid (3.5 g, 15.41 mmol) was suspended in 25 mL DCM and 4.5 mL THF. Oxalyl chloride (1.618 mL, 18.49 mmol) was then added dropwise at 22° C., followed by DMF (3 drops). After 15 minutes, the mixture had become homogenous and TLC analysis (MeOH-quenched aliquot) showed full conversion. The resulting solution was concentrated directly to afford crude 4-(difluoromethoxy)-1H-indole-2-carbonyl chloride as a red oil, which was used immediately without further purification.
  • Step 5 Ethyl (1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylate hydrochloride (9.57 g, 43.6 mmol), was suspended in EtOH (87 mL), then aqueous 5 N sodium hydroxide (37 mL, 185 mmol) was added at 22° C. with vigorous stirring. After 1 h, the ethanol was distilled in vacuo to afford ⁇ 40 mL of a viscous aqueous solution containing sodium (1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylate, which was used directly.
  • Step 6 Crude 4-(difluoromethoxy)-1H-indole-2-carbonyl chloride (2.161 g, 8.8 mmol) was dissolved in THF (5 mL) at 22° C. The aqueous solution of sodium (1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylate (16 mL) was then poured in at 22° C. with vigorous stirring. After 1 h of stirring 1 N HCl was added until the pH of the solution was about 1. The resulting aqueous suspension was extracted twice with DCM, then the pooled organic fractions were dried over MgSO 4 , filtered and concentrated.
  • Step 7 HATU (69.6 mg, 0.183 mmol) was added to a solution of (1S,3aR,6aS)-2-(4-(difluoromethoxy)-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxylic acid (57.8 mg, 0.159 mmol), (S)-2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanenitrile 2,2,2-trifluoroacetate (32.6 mg, 0.122 mmol), DMF (0.407 mL), and Et3N (150 ⁇ l, 1.08 mmol) at 22° C.
  • Step 1 Methyl (S)-2-amino-3-((S)-2-oxopyrrolidin-3-yl)propanoate hydrochloride (0.880 g, 3.95 mmol) and (1S,3aR,6aS)-2-(4-(difluoromethoxy)-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxylic acid (1.01 g, 2.77 mmol) were dissolved in a mixture of DMF and DCM (1:1 v/v, 26 mL), and the resulting solution was cooled to 0° C. under a nitrogen atmosphere.
  • HATU (1.126 g, 2.96 mmol) then was added in one portion. After 3 min of stirring, added Hunig's base (1.656 mL, 9.48 mmol) dropwise. After stirring for 30 min at 0° C., precooled 1 N HCl (15 mL) was added, followed by water (40 mL). The resulting mixture was extracted with DCM twice. The pooled organic fractions were twice washed with saturated aqueous NaHCO 3 , then brine, then dried over MgSO 4 and concentrated.
  • Step 2 Methyl (S)-2-((1S,3aR,6aS)-2-(4-(difluoromethoxy)-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxamido)-3-((S)-2-oxopyrrolidin-3-yl)propanoate (1.42 g, 2.67 mmol) was dissolved in THF (26.7 mL) and cooled to 0° C. with stirring under a nitrogen atmosphere. Lithium borohydride (2 M in THF, 6.67 mL, 13.33 mmol) was then added dropwise over 4-5 min.
  • Step 3 (1S,3aR,6aS)-2-(4-(difluoromethoxy)-1H-indole-2-carbonyl)-N—((S)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)octahydrocyclopenta[c]pyrrole-1-carboxamide (0.958 g, 1.899 mmol) was dissolved in DCM (12.66 mL), then cooled to 0° C. under a nitrogen atmosphere. Dess-Martin periodinane (1.127 g, 2.66 mmol) was then added in one portion.
  • Step 1 A flask was charged with dimethyl (tert-butoxycarbonyl)-L-glutamate (6.5 g) and THF (70 mL). The flask was cooled to ⁇ 78° C. under a nitrogen atmosphere. Then LiHMDS (52 mL, 1 M in THF) was added over 5 min. After 1 h, 3-bromopropanenitrile (3 mL) was added dropwise. After 90 minutes, the reaction mixture was warmed to ⁇ 55° C., then quenched with aq. NH 4 C 1 . The reaction mixture was allowed to reach rt, then diluted with 20 mL water. The product was extracted with MTBE then concentrated. An additional 30 mL of MTBE was added, by which a precipitate formed. This was filtered off and the filtrate was concentrated to provide an orange oil that was used directly in the next step.
  • Step 2 A flask was charged with cobalt(II) chloride hexahydrate (2.8 g). Then a solution of product from Step 1 in THF (20 mL) was transferred to this flask with MeOH washings (140 mL). The flask was cooled to 0° C., then sodium borohydride (3.6 g) was added ovr 20 min. The reaction was allowed to reach rt and stirred for 24 h. Then, most of the volatiles were removed under reduced pressure. EtOAc (100 mL) and 1 M HCl (40 mL) were added. The product was extracted with EtOAc, and the combined organic layers were washed with 1 M HCl, brine, then concentrated.
  • Step 3 A flask was charged with methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-yl)propanoate (421 mg) and then 4 M ammonia in MeOH (2.8 mL) was added. The reaction mixture was stirred for 72 h, then heated to 65° C. for 1.5 h. The volatiles were removed, and the residue was purified on silica gel to provide tert-butyl ((S)-1-amino-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)carbamate (237 mg).
  • Step 4 A vial was charged with tert-butyl ((S)-1-cyano-2-((S)-2-oxopiperidin-3-yl)ethyl)carbamate (88 mg) and DCM (1 mL). Then, TFA (2 mL) was added. After 1 h, the volatiles were removed and the product, (S)-2-amino-3-((S)-2-oxopiperidin-3-yl)propanenitrile 2,2,2-trifluoroacetate, was used without further purification.
  • Step 5 A vial was charged with (1S,3aR,6aS)-2-(4-methoxy-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxylic acid (50 mg), (S)-2-amino-3-((S)-2-oxopiperidin-3-yl)propanenitrile 2,2,2-trifluoroacetate (20 mg), DMF (1 mL), and DIPEA (0.1 mL). Then HATU (40 mg) was added.
  • Step 1 A vial was charged with (1S,3aR,6aS)-2-(4-(difluoromethoxy)-1H-indole-2-carbonyl)-N—((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)octahydrocyclopenta[c]pyrrole-1-carboxamide (58 mg) and DCM (1 mL). The flask was cooled to 0° C. under a nitrogen atmosphere. Then acetic acid (0.3 mL) was added as a solution in DCM (1 mL).
  • Step 2 A vial was charged with (1S,3aR,6aS)-N-((2S)-4-(cyclohexylamino)-3-hydroxy-4-oxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)-2-(4-(difluoromethoxy)-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxamide (39 mg), DCM (1 mL), and Hunig's base (0.033 mL) at 0° C. Py-503 (30 mg) was added as a solution in DMSO (1 mL).
  • Step 1 A vial was charged with (1S,3aR,6aS)-N—((S)-4-chloro-3-oxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)-2-(4-methoxy-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxamide (99 mg), cesium fluoride (67 mg), 2-oxo-2-phenylacetic acid (38 mg), and DMF (2 mL). The flask was heated to 65° C. for 75 min. After cooling to room temperature, the reaction mixture was partitioned between ethyl acetate and water.
  • Step 2 A vial was charged with (S)-3-((1S,3aR,6aS)-2-(4-methoxy-1H-indole-2-carbonyl)octahydrocyclopenta[c]pyrrole-1-carboxamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butyl 2-oxo-2-phenylacetate (121 mg) and MeOH (3 mL). Then, potassium carbonate (27 mg) was added. After 1 h, 1 M aq. HCl was added (0.5 mL). The reaction mixture was filtered and concentrated.
  • Step 1 A vial was charged with Boc-L-tert-leucine (1.55 g), DCM (20 mL), and DMF (5 mL). The vial was cooled to 0° C. then HATU (2.2 g) was added. Then Hunig's base (1.8 g) was added. The yellow suspension was stirred for 2 min then methyl (1R,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylate hydrochloride was added. Then Hunig's base (1.8 g) was added and the reaction was allowed to reach room temperature. After 2 h, the reaction mixture was diluted with ethyl acetate and partitioned with water.
  • Step 2 A vial was charged with methyl (1R,2S,5S)-3-((S)-2-((tert-butoxycarbonyl)amino)-3,3-dimethylbutanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylate (300 mg) and MeOH (4 mL). The vial was cooled to 0° C. then 2.5 M aq. LiOH (2 mL) was added. After 3.5 h, the reaction mixture was concentrated. Then, 4 M HCl in dioxanes (5.5 mL) was added and the reaction mixture was stirred for 1 h.
  • Step 3 A vial was charged with (1R,2S,5S)-3-((S)-2-amino-3,3-dimethylbutanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylic acid (304 mg), triethylamine (0.42 mL), and MeCN (6 mL). The vial was stirred at 0° C., then cyclopentanecarbonyl chloride (147 mg) was added dropwise under a nitrogen atmosphere. After 1 h, DCM (25 mL) was added. The reaction mixture was partitioned with water (25 mL) and stirred at room temperature. After 10 min, the organic layer was removed.
  • Step 4 A vial was charged with (1R,2S,5S)-3-((S)-2-(cyclopentanecarboxamido)-3,3-dimethylbutanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylic acid (130 mg) and DMF (5 mL). DIEA (139 mg) was then added. HATU (274 mg) was then added at room temperature and the reaction mixture was stirred for 10 min. Then, tert-butyl ((S)-1-cyano-2-((S)-2-oxopyrrolidin-3-yl)ethyl)carbamate (155 mg) was added.
  • SARS-CoV-2 3C-like (3CL) protease fluorescence assay FRET: Recombinant SARS-CoV-2 3CL-protease was expressed and purified. TAMRA-SITSAVLQSGFRKMK-Dabcyl-OH peptide 3CLpro substrate was synthesized. Black, low volume, round-bottom, 384 well microplates were used.
  • test compound 0.85 ⁇ L of test compound was dissolved in DMSO then incubated with SARS-CoV-2 3CL-protease (10 nM) in 10 ⁇ L assay buffer (50 mM HEPES [pH 7.5], 1 mM DTT, 0.01% BSA, 0.01% Triton-X 100) for 30 min at RT.
  • 10 ⁇ L of 3CL-protease substrate (40 ⁇ M) in assay buffer was added and the assays were monitored continuously for 1 h in an Envision multimode plate reader operating in fluorescence kinetics mode with excitation at 540 nm and emission at 580 nm at RT. No compound (DMSO only) and no enzyme controls were routinely included in each plate. All experiments were run in duplicate.
  • SARS-CoV-2 3CL-protease enzyme activity was measured as initial velocity of the linear phase (RFU/s) and normalized to controlled samples DMSO (100% activity) and no enzyme (0% activity) to determine percent residual activity at various concentrations of test compounds (0-10 ⁇ M). Data were fitted to normalized activity (variable slope) versus concentration fit in GraphPad Prism 7 to determine IC 50 . All experiments were run in duplicate, and IC 50 ranges are reported as follows: A ⁇ 0.1 ⁇ M; B 0.1-1 ⁇ M; C>1 ⁇ M.

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US11912714B2 (en) 2021-11-12 2024-02-27 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
US12145941B2 (en) 2021-12-08 2024-11-19 Enanta Pharmaceuticals, Inc. Heterocyclic antiviral agents
US11993600B2 (en) 2021-12-08 2024-05-28 Enanta Pharmaceuticals, Inc. Saturated spirocyclics as antiviral agents
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