Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
  • C07D471/12—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains three hetero rings
  • C07D471/18—Bridged systems
• • 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
  • A61K31/439—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 the ring forming part of a bridged ring system, e.g. quinuclidine
• • 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
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
  • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
  • C07D471/08—Bridged systems
• • 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

• antibacterial compounds which are useful for, among other uses, the treatment of bacterial infections.
• Such compounds are represented by Formula I,
• compositions comprising the compounds of Formula I.
• PBP3 Penicillin-Binding Protein 3
• PBPl PBPl inhibitors
• the disclosed PBP3 inhibitors also have substantial in vivo improvement over known PBP2 inhibitors. See e.g., the "in vivo profiling for P. aeruginosa PBP inhibitors" in the exemplification section as well as FIG. 1 and 2, where Example 40 of the subject application was compared with a PBP2 inhibitor (Comparator 1). The only structural difference between Example 40 and Comparator 1 is the replacement of an amino methyl for an N-methyl-amidoxime group. Yet, Comparator 1 was not active against a P.
• Example 40 of the subject application showed robust efficacy (more than 2 Log(CFU/g) reduction with an exposure of 57% Time above the MIC).
• FIG. 1 shows the in vivo efficacy of a PBP2 compound (Comparator 1) against a P. aeruginosa clinical isolate (ARC6347, AmpC+, PoxB+) in a neutropenic murine thigh model.
• FIG. 2 shows the in vivo efficacy of a PBP3 compound of the subject application (Example 40) against a P. aeruginosa clinical isolate (ARC6347, AmpC+, PoxB+) in a neutropenic murine thigh model.
• X is H, CN, C(0)NR 1 R 2 , NR l R 2 or (Ci-C 6 )alkyl optionally substituted with
• R 1 and R 2" are each independently hydrogen, cyano, C(0)NH 2 , NH 2 , OH, (Ci- C 6 )alkoxy, or (Ci-C 6 )alkyl optionally substituted with one or more R ;
• R 3 is hydrogen, C(0)(Ci-C 6 )alkyl, C(0)NR d R e , S0 2 NH 2 , S0 2 OH, or (Ci-C 6 )alkyl optionally substituted with one or more R ;
• R 4 , R 5 , and R 6 are each independently hydrogen, (Ci-C 6 )alkyl, or C(0)NR a R b , wherein said (Ci-C 6 )alkyl for R 4 , R 5 , and R 6 is optionally substituted with one or more R 7 , provided that at least one of R 4 and R 5 is not hydrogen and provided that R 4 and R 5 are not present when the corresponding nitrogen atom to which R 4 and R 5 are bound is connected to an adjacent ring atom via a double bond;
• R c is phenyl optionally substituted with one or more groups selected from
• R is hydrogen or (Ci-C 6 )alkyl
• a hyphen designates the point of attachment of that group to the variable to which it is defined.
• -NR d R e means that the point of attachment for this group occurs on the nitrogen atom.
• alkyl used alone or as part of a larger moiety, such as “alkoxy”, “haloalkyl”, and the like, means saturated straight-chain or branched monovalent
• an alkyl group typically has 1-6 carbon atoms, i.e., (Ci-C 6 )alkyl.
• a "(Ci-C 6 )alkyl” group means a radical having from 1 to 6 carbon atoms in a linear or branched arrangement.
• haloalkyl includes mono, poly, and perhaloalkyl groups where the halogens are independently selected from fluorine, chlorine, bromine, and iodine.
• Alkoxy means an alkyl radical attached through an oxygen linking atom, represented by -O-alkyl.
• (Ci-C4)alkoxy includes methoxy, ethoxy, propoxy, and butoxy.
• heteroaryl refers to a 5- to 12-membered aromatic radical containing 1-4 heteroatoms selected from N, O, and S. In some instances, nitrogen atoms in a heteroaryl may be quaternized.
• heteroaryl may be used interchangeably with the terms “heteroaryl ring", “heteroaryl group”, or “heteroaromatic”.
• a heteroaryl group may be mono- or bi-cyclic.
• Monocyclic heteroaryl includes, for example, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, etc.
• Bi-cyclic heteroaryls include groups in which a monocyclic heteroaryl ring is fused to one or more aryl or heteroaryl rings.
• Nonlimiting examples include indolyl, benzooxazolyl, benzooxodiazolyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, quinazolinyl, quinoxalinyl, pyrrolopyridinyl, pyrrolopyrimidinyl, pyrrolopyridinyl, thienopyridinyl, thienopyrimidinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl. It will be understood that when specified, optional substituents on a heteroaryl group may be present on any substitutable position and, include, e.g., the position at which the heteroaryl is attached.
• heterocyclyl means a 4- to 12-membered saturated or partially unsaturated heterocyclic ring containing 1 to 4 heteroatoms
• heterocycle independently selected from N, O, and S.
• heterocyclyl independently selected from N, O, and S.
• heterocyclyl ring refers to “heterocyclic ring”, “heterocyclic group”, “heterocyclic moiety”, and “heterocyclic radical”, are used interchangeably herein.
• a heterocyclyl ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure.
• a heterocyclyl group may be mono- or bicyclic.
• Examples of monocyclic saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothienyl, terahydropyranyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, morpholinyl, dihydrofuranyl, dihydropyranyl, dihydropyridinyl, tetrahydropyridinyl, dihydropyrimidinyl, tetrahydropyrimidinyl, dihydrooxadizolyl, and dihydroisoxazolyl.
• Bi- cyclic heterocyclyl groups include, e.g., unsaturated heterocyclic radicals fused to another unsaturated heterocyclic radical, cycloalkyl, aryl, or heteroaryl ring, such as for example, benzodioxolyl, dihydrobenzodioxinyl, dihydrobenzofuranyl, and the like. It will be understood that when specified, optional substituents on a heterocyclyl group may be present on any substitutable position and, include, e.g., the position at which the heterocyclyl is attached. [0019] Certain of the disclosed compounds may exist in various stereoisomeric forms. Stereoisomers are compounds that differ only in their spatial arrangement. Enantiomers are pairs of stereoisomers whose mirror images are not superimpo sable, most commonly because they contain an asymmetrically substituted carbon atom that acts as a chiral center.
• Enantiomer means one of a pair of molecules that are mirror images of each other and are not superimposable. Diastereomers are stereoisomers that contain two or more
• Racemate or “racemic mixture” means a compound of equimolar quantities of two enantiomers, wherein such mixtures exhibit no optical activity, i.e., they do not rotate the plane of polarized light.
• Gaometric isomer means isomers that differ in the orientation of substituent atoms in relationship to e.g., a carbon-carbon double bond, to an oxime, to an oxime ether, to a cycloalkyl ring, or to a bridged bicyclic system. Atoms (other than H) on each side of a carbon-carbon double bond may be in an E (substituents are on opposite sides of the carbon- carbon double bond) or Z (substituents are oriented on the same side) configuration.
• R,” “S,” “S*,” “R*,” “E,” “Z,” “syn,” “anti,” “cis,” and “trans” indicate configurations relative to the core molecule.
• a wavy bond indicates that the structure encompasses one geometric isomer free of other geometric isomers, mixtures of geometric isomers, or mixtures of all geometric isomers.
• the geometrical isomer of the N-0 bond of the oxime is not named, the compound encompasses one geometric isomer free of other geometric isomers, mixtures of geometric isomers, or mixtures of all geometric isomers.
• the compounds of the herein may be prepared as individual enantiomers by either enantio-specific synthesis or resolved from an enantiomerically enriched mixture.
• Conventional resolution techniques include forming the salt of a free base of each isomer of an enantiomeric pair using an optically active acid (followed by fractional crystallization and regeneration of the free base), forming the salt of the acid form of each enantiomer of an enantiomeric pair using an optically active amine (followed by fractional crystallization and regeneration of the free acid), forming an ester or amide of each of the enantiomers of an enantiomeric pair using an optically pure acid, amine or alcohol (followed by
• the compounds can be prepared as individual enantiomers by separating a racemic mixture using conventional chiral chromatography techniques.
• the stereochemistry of a disclosed compound is named or depicted by structure
• the named or depicted stereoisomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by weight pure relative to all of the other stereoisomers.
• Percent by weight pure relative to all of the other stereoisomers is the ratio of the weight of one stereoisomer over the weight of the other stereoisomers.
• the depicted or named enantiomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by weight optically pure.
• Percent optical purity by weight is the ratio of the weight of the enantiomer over the weight of the enantiomer plus the weight of its optical isomer.
• stereochemistry of a disclosed compound is named or depicted by structure, and the named or depicted structure encompasses more than one stereoisomer (e.g., as in a diastereomeric pair), it is to be understood that one of the encompassed stereoisomers or any mixture of the encompassed stereoisomers are included. It is to be further understood that the stereoisomeric purity of the named or depicted stereoisomer is at least 60%, 70%, 80%, 90%, 99% or 99.9% by weight pure relative to all of the other stereoisomers.
• the stereoisomeric purity in this case is determined by dividing the total weight in the mixture of the stereoisomers encompassed by the name or structure by the total weight in the mixture of all of the stereoisomers.
• a disclosed compound is named or depicted by structure without indicating the stereochemistry and e.g. , the compound has more than one chiral center (e.g., at least two chiral centers), it is to be understood that the name or structure encompasses one stereoisomer free of other stereoisomers, mixtures of stereoisomers, or mixtures of stereoisomers in which one or more stereoisomers is enriched relative to the other stereoisomer(s).
• the name or structure may encompass one stereoisomer free of other diastereomers, mixtures of stereoisomers, or mixtures of stereoisomers in which one or more diastereomers is enriched relative to the other diastereomer(s).
• Example 40 means that the
• the compounds of the herein may be present in the form of pharmaceutically acceptable salts.
• the salts of the compounds of the invention refer to non-toxic "pharmaceutically acceptable salts.”
• Pharmaceutically acceptable salt forms include pharmaceutically acceptable acidic/anionic or basic/cationic salts.
• subject and “patient” may be used interchangeably, and means a mammal in need of treatment, e.g., companion animals (e.g., dogs, cats, and the like), farm animals (e.g., cows, pigs, horses, sheep, goats and the like) and laboratory animals (e.g., rats, mice, guinea pigs and the like).
• companion animals e.g., dogs, cats, and the like
• farm animals e.g., cows, pigs, horses, sheep, goats and the like
• laboratory animals e.g., rats, mice, guinea pigs and the like.
• the subject is a human in need of treatment.
• inhibitor includes a decrease in the baseline activity of a biological activity or process.
• treatment refers to reversing, alleviating, delaying the onset of, or inhibiting the progress of a disease or disorder, or one or more symptoms thereof, as described herein.
• treatment may be administered after one or more symptoms have developed, i.e., therapeutic treatment.
• treatment may be administered in the absence of symptoms.
• treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of exposure to a particular organism, or other susceptibility factors), i.e., prophylactic treatment. Treatment may also be continued after symptoms have resolved, for example to prevent or delay their recurrence.
• the term "effective amount” or “therapeutically effective amount” includes an amount of the compound described herein that will elicit a biological or medical response of a subject, for example, the reduction or inhibition of enzyme or protein activity related to a a bacterial infection, amelioration of symptoms of a bacterial infection, or the slowing or delaying of progression of a bacterial infection.
• the language “one or more” includes a pharmaceutically acceptable amount of the compound described herein that will elicit a biological or medical response of a subject, for example, the reduction or inhibition of enzyme or protein activity related to a a bacterial infection, amelioration of symptoms of a bacterial infection, or the slowing or delaying of progression of a bacterial infection.
• the language for example, the reduction or inhibition of enzyme or protein activity related to a a bacterial infection, amelioration of symptoms of a bacterial infection, or the slowing or delaying of progression of a bacterial infection.
• “effective amount” includes the amount of a compound described herein, that when administered to a subject, is effective to at least partially alleviate, inhibit, and/or ameliorate a bacterial infection or inhibit PBP3, and/or reduce or inhibit the bacterial growth, replication or bacterial load of a bacteria in a subject.
• compositions of this disclosure refers to a non-toxic carrier, adjuvant, or vehicle that does not destroy the pharmacological activity of the compound with which it is formulated.
• pharmaceutically acceptable carriers, adjuvants or vehicles that may be used in the compositions of this disclosure include, but are not limited to, organic or inorganic carriers, excipients or diluents suitable for pharmaceutical applications.
• the resent disclosure provides a compound of Formula I:
• said 4- to 6-membered cycloalkyl for R , R b , R d , and R e in the compound of Formula I is cyclohexyl and said 4- to 6-membered heterocyclyl for R g is piperazinyl, wherein the remaining variables are as described above for Formula I or the second embodiment.
• the compound of Formula I is of the Formula la:
• X is H, CN, C(0)NR 1 R 2 , NR ! R 2 or (Ci-C 6 )alkyl;
• R 1 and R 2" are each independently hydrogen, cyano, or (Ci-C 6 )alkyl optionally substituted with one or more R ;
• R 3 is hydrogen or (Ci ally substituted with one or more R 7
• R 4 , R 5 , and R 6 are each independently hydrogen, (Ci-C 6 )alkyl, or C(0)NR a R b , wherein said (Ci-C 6 )alkyl for R 4 , R 5 , and R 6 is optionally substituted with one or more R 7 , provided that at least one of R 4 and R 5 is not hydrogen and provided that R 4 and R 5 are not present when the corresponding nitrogen atom to which R 4 and R 5 are bound is connected to an adjacent ring atom via a double bond;
• R a , R b , R d , and R e are each independently hydrogen, (Ci-C 6 )alkyl, (Ci-C 6 )alkoxy, phenyl, 4- to 6-membered heterocyclyl or 5- to 6-membered heteroaryl, wherein each of said (Ci-C 6 )alkyl and (Ci-C 6 )alkoxy for R , R b , R d , and R e are optionally and independently substituted with one or more groups selected from NH 2 , NH(Ci-C 6 )alkyl, and N((Ci- C 6 )alkyl) 2 , and wherein each of said phenyl, 4- to 6-membered heterocyclyl, and 5- to 6- membered heteroaryl for R , R b , R d , and R e are optionally and independently substituted with one or more groups selected from (Ci-C 6 )alkyl, NH 2 , NH
• R c is phenyl optionally substituted with one or more groups selected from
• R is hydrogen or (Ci-C 6 )alkyl.
• R in any one of Formulae I, la, II, or III is hydrogen or (Ci-C6)alkyl optionally substituted with amino, wherein the remaining variables are as described above for Formula I or la.
• R in any one of Formulae I, la, II, or III is hydrogen, wherein the remaining variables are as described above for Formula I or la.
• R 1 in any one of Formulae I, la, II, or III is hydrogen and R is (Ci-C6)alkyl, wherein the remaining variables are as described above for Formula I or la or the seventh embodiment.
• R 1 in any one of Formulae I, la, II, or III is hydrogen and R is methyl, wherein the remaining variables are as described above for Formula I or la or the seventh embodiment.
• R 1 and R 2 in any one of Formulae I, la, II, or III are each (Ci-C6)alkyl, wherein the remaining variables are as described above for Formula I or la or the seventh embodiment.
• R 1 and R 2 in any one of Formulae I, la, II, or III are each methyl, wherein the variables are as described above for Formula I or la or the seventh embodiment.
• the compound of Formula I or la is of the Formula IV or V:
• R 6 in any one of Formulae I, la, II, III, IV, or V is hydrogen, -C(0)NR R b , or (Ci-C 6 )alkyl optionally substituted with OR c , wherein the remaining variables are as described above for Formula I or la or the seventh, eighth, or ninth embodiment.
• R in any one of Formulae I, la, II, III, IV, or V is hydrogen;
• R b is 5- to 6-membered heteroaryl optionally substituted with one or more (Ci- C 6 )alkyl, or (Ci-C 6 )alkyl optionally substituted with -OR c ;
• R in any one of Formulae I, la, II, III, IV, or V is hydrogen and R b is pyrazolyl optionally substituted with one or more (Ci-C 6 )alkyl, wherein the remaining variables are as described above for Formula I or la or the seventh, eighth, ninth, or eleventh embodiment.
• the compound of Formula I or la is of the Formula
• R 4 in any one of Formulae I, la, II, III, IV, V, or VI is C(0)NR a R b or (Ci-C 6 )alkyl optionally substituted with NH 2 ; R a is hydrogen; and R b is (Q- C 6 )alkyl optionally substituted with NH 2 , wherein the remaining variables are as described above for Formula I or la or the eighth or ninth embodiment.
• R 4 in any one of Formulae I, la, II, III, IV, V, or VI is (Ci-C 6 )alkyl, wherein the remaining variables are as described above for Formula I or la or the eighth or ninth embodiment.
• R 4 in any one of Formulae I, la, II, III, IV, V, or VI is methyl, wherein the remaining variables are as described above for Formula I or la or the eighth or ninth embodiment.
• the compound of Formula I or la is of the Formula
• R 5 in any one of Formulae I, la, II, III, IV, VI, or VII is C(0)NR a R b or (Ci-C 6 )alkyl optionally substituted with NH 2 ; R a is hydrogen; and R b is (Q- C 6 )alkyl optionally substituted with NH 2 , wherein the remaining variables are as described above for Formula I or la or the eighth or ninth embodiment.
• R 5 in any one of Formulae I, la, II, III, IV, VI, or VII is (Ci-C 6 )alkyl, wherein the remaining variables are as described above for Formula I or la or the eighth or ninth embodiment.
• R 5 in any one of Formulae I, la, II, III, IV, VI, or VII is methyl, wherein the remaining variables are as described above for Formula I or la or the eighth or ninth embodiment.
• Gram-negative bacteria include, but are not limited, to Haemophilus influenzae, Acinetobacter baumannii,
• Burkholderia spp. Citrobacter spp., Escherichia coli, Enterobacter spp., Pseudomonas aeruginosa, Klebsiella spp., Stenotrophomonas maltophila, Francisella tularensis, Yersinia spp., Salmonella spp., Shigella spp., Legionella spp. and Neisseria gonorrhoeae.
• Atypical bacteria include, but are not limited to, Mycoplasma pneumoniae, Chlamydophila
• the bacteria are resistant to one or more antibacterials other than the compounds described herein.
• the language “resistance” and “antibacterial resistance” refers to bacteria that are able to survive exposure to one or more antibacterials.
• the compounds described herein can be used to treat bacterial infections caused by Gram-negative bacteria or resistant Gram-negative bacteria. In another aspect, the compounds described herein can be used to treat bacterial infections caused by
• the compounds described herein can be used to treat bacterial infections caused by P. aeruginosa, A. baumannii, or Enterobacteriaceae, as well as antibacterial-resistant forms. In yet a further aspect, the compounds described herein can be used to treat bacterial infections caused by P. aeruginosa, as well as antibacterial-resistant forms.
• resistance mechanisms in Gram-negative bacteria include, but are not limited to, extended- spectrum ⁇ - lactamase expression, metallo-P-lactamase expression, carbapenemase expression, DNA gyrase mutation, porin mutation, efflux system overexpression, lipopolysaccharide modification, and 16S rRNA methylase expression.
• the bacterial infection treated by the present compounds is caused by a Gram-negative bacteria.
• the bacterial infection treated by the present compounds is caused by P. aeruginosa, A. baumannii, E. coli, or K. pneumoniae and other Enterobacteriaceae.
• the bacterial infection treated by the present compounds is caused by P. aeruginosa.
• the bacterial infection treated by the present compounds is caused by an antibacterial-resistant Gram-negative bacteria.
• the bacterial infection treated by the present compounds is caused by an antibacterial-resistant strain of P. aeruginosa.
• the bacterial infection treated by the present compounds is caused by Enterobacteriaceae.
• the bacterial infection treated by the present compounds is caused by E. coli, K. pneumoniae, or Acinetobacter spp. In yet another aspect, the bacterial infection treated by the present compounds is caused by a pathogen selected from Burkholderia spp., B. anthracis, Y. pestis, and F. tularensis.
• Bacterial infections treated by the present compounds include, but are not limited to, respiratory (e.g., pneumonia), blood stream (e.g., bacteremia), heart (e.g., endocarditis), CNS (e.g., meningitis, brain abscess), ear (e.g., otitis externa), eye (e.g., bacterial keratitis, endophthalmitis), GI tract (diarrhea, enteritis, enterocolitis), urinary tract, skin,
• respiratory e.g., pneumonia
• blood stream e.g., bacteremia
• CNS e.g., meningitis, brain abscess
• ear e.g., otitis externa
• eye e.g., bacterial keratitis, endophthalmitis
• GI tract diarrhea, enteritis, enterocolitis
• the compounds described herein inhibit penicillin-binding protein 3 (PBP3).
• PBP3 penicillin-binding protein 3
• the present disclosure provides a method of inhibiting bacterial PBP3, comprising administering to a subject in need thereof one or more of the compounds described herein, or a pharmaceutically acceptable salt thereof.
• the compounds described herein inhibit penicillin-binding protein 1 (e.g., PBPla and/or PBPlb).
• the present disclosure provides a method of inhibiting bacterial PBPl, comprising administering to a subject in need thereof one or more of the compounds described herein, or a pharmaceutically acceptable salt thereof.
• the present disclosure provides a method of inhibiting bacterial PBPl (e.g., PBPla and/or PBPlb) and bacterial PBP3, comprising administering to a subject in need thereof one or more of the compounds described herein, or a pharmaceutically acceptable salt thereof.
• bacterial PBPl e.g., PBPla and/or PBPlb
• bacterial PBP3 e.g., PBPla and/or PBPlb
• the compounds described herein are not specific inhibitors of penicillinbinding protein 2 (PBP2).
• compositions comprising a compound described herein; and a pharmaceutically acceptable carrier. These compositions can be used to treat one or more of the bacterial infections described above, as well as inhibit PBP3.
• compositions described herein may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir.
• parenteral as used herein includes subcutaneous, intravenous, intramuscular, intra-articular, intra- synovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques.
• Liquid dosage forms, injectable preparations, solid dispersion forms, and dosage forms for topical or transdermal administration of a compound are included herein.
• the amount of provided compounds that may be combined with carrier materials to produce a composition in a single dosage form will vary depending upon the patient to be treated and the particular mode of administration.
• a specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, the judgment of the treating physician, and the severity of the particular disease being treated.
• the amount of a provided compound in the composition will also depend upon the particular compound in the composition.
• Aqueous saturated sodium bicarbonate solution was added to the combined organic layers until pH >7.
• the aqueous phase was separated and acidified by adding citric acid solution (10%). It was then extracted with ethyl acetate (4 x 500 mL).
• the material was purified on a short silica pad, eluting with hexanes (100 mL), followed by ethyl acetate/hexanes (1: 1, 100 mL), ethyl acetate (100 mL) and acetone (200 mL).
• Example 6 and 7 were synthesized by following a similar synthetic sequence as shown for Example 4.
• the other examples in Table 1 were synthesized in a manner similar to Scheme 1 using similar reactions easily known to a person skilled in the art. All compounds were isolated as trans racemic.
• Example 43 was synthesized by following similar reaction conditions as in
• Example 42 Taking (4R,8S)-8-((Z)-N'-(((2-aminoethyl)carbamoyl)oxy)-N- methylcarbamimidoyl)-l-methyl-6-oxo-4,8-dihydro-lH-4,7-methanopyrazolo[3,4- e][l,3]diazepin-5(6H)-yl hydrogen sulfate (Example 18, 8.3 mg, 0.0192 mmol) as the substrate, to afford (4R,8S)-8-((Z)-N-carbamoyl-N-methyl-N'-(((2- ureidoethyl)carbamoyl)oxy)carbamimidoyl)-l-methyl-6-oxo-4,8-dihydro-lH-4,7- methanopyrazolo[3,4-e][l,3]diazepin-5(6H)-yl hydrogen
• Example 44 was synthesized by following similar reaction conditions as shown for Example 42. Taking (4R,8S)-8-((Z)-N'-(((2-aminoethyl)carbamoyl)oxy)-N- methylcarbamimidoyl)-l-methyl-6-oxo-4,8-dihydro-lH-4,7-methanopyrazolo[3,4- e][l,3]diazepin-5(6H)-yl hydrogen sulfate (Example 18, 8 mg, 0.0185 mmol) as the substrate, and acetyl chloride ( 0.001 mL, 0.0185 mmol) as reagent to afford (4R,8S)-8-((Z)- N'-(((2-acetamidoethyl)carbamoyl)oxy)-N-methylcarbamimidoyl)-l-methyl-6-oxo-4,8- dihydro-lH-4,
• TMSCN (35.7 g, 360.7 mmol) was added to the solution of N-(benzyloxy)-N-(l- (2-((tert-butyldimethylsilyl)oxy)ethyl)-4,5-dihydro-lH-pyrazolo[3,4-c]pyridin-4-yl)-4- nitrobenzenesulfonamide (Int-40).
• the reaction mixture was stirred for overnight at room temperature. It was diluted with saturated aqueous sodium bicarbonate solution (500 mL) and extracted with DCM (2 x 500 mL). The organic extracts were combined, dried over anhydrous sodium sulfate, and concentrated under vacuum.
• Acetyl chloride (148 g, 1896 mmol) was added dropwise. The resulting reaction mixture was stirred for 1 hour at room temperature, and then 2 hours at 55 °C. It was cooled to room temperature. The pH value of the reaction mixture was adjusted to 9 with saturated aqueous sodium bicarbonate solution and extracted with ethyl acetate (3 x 50 mL).
• the reaction mixture was stirred for 1 hour at room temperature, and diluted with EtOAc (200 mL). It was washed with brine (200 mL). The aqueous layer was extracted with EtOAc (100 mL) and the organic layers combined. The organic extract was washed with brine (5 x 100 mL), dried over anhydrous sodium sulfate, and concentrated under vacuum.
• reaction mixture was partitioned between water (200 mL) and EtOAc (200 mL).
• EtOAc 200 mL
• the oraganic layer was separated, washed with water (100 mL), brine (100 mL), dried over anhydrous sodium sulfate, and concentrated to give the crude product.
• lnt-59 was synthesized by following similar reaction conditions as shown for Int- 55 (Scheme 9, steplO), using (4R,8S,Z)-l-(2-azidoethyl)-5-(benzyloxy)-N'-((tert- butyldimethylsilyl)oxy)-N-methyl-6-oxo-4,5,6,8-tetrahydro-lH-4,7-methanopyrazolo[3,4- e][l,3]diazepine-8-carboximidamide (lnt-54, 89 mg, 0.17 mmol) as substrate, and no Boc 2 0 was added, to afford (4R,8S,Z)-l-(2-aminoethyl)-5-(benzyloxy)-N'-((tert- butyldimethylsilyl)oxy)-N-methyl-6-oxo-4,5,6,8-tetrahydro-lH-4,7-me
• Int-62 was synthesized by following similar reaction conditions as shown for Int-
• Example 48 was synthesized by following similar reaction conditions as shown for Int-16 (Scheme 1, stepl6), using (4R,8S)-l-(2-acetamidoethyl)-8-((Z)-N'-((tert- butyldimethylsilyl)oxy)-N-methylcarbamimidoyl)-6-oxo-4,8-dihydro-lH-4,7- methanopyrazolo[3,4-e][l,3]diazepin-5(6H)-yl hydrogen sulfate (Int-62, 57 mg, 0.107 mmol) as substrate, and afford (4R,8S)-l-(2-acetamidoethyl)-8-((Z)-N'-hydroxy-N- methylcarbamimidoyl)-6-oxo-4,8-dihydro-lH-4,7-methanopyrazolo[3,4-e][l,3]dia
• reaction mixture was warmed to room temperature and stirred for 15 minutes then diluted with ethyl acetate (50 mL) and washed with saturated ammonium chloride (20 mL) and brine (20 mL). The organics were dried over anhydrous sodium sulfate, filtered and
• reaction mixture was stirred for 15 minutes at 0 °C then neutralized with IN HC1.
• the THF was removed and the aqueous was frozen and lyophilized to afford a white solid.
• the solid was dissolved in water to give a cloudy solution.
• the pH was adjusted to -3-4 and the product was extracted with ethyl acetate (2 x 100 mL).
• reaction mixture was stirred for 5 minutes. To the solution was added methylamine (0.05 mL, 1.31 mmol) dropwise. The reaction mixture was then allowed to warm to room temperature and stir for 1.5 hours. The reaction mixture was diluted with DCM and washed once with saturated ammonium chloride. The organics were dried over magnesium sulfate, filtered and concentrated.
• reaction mixture was flushed with nitrogen and methanol was added (1 mL). The reaction mixture was degassed. More Pd/C (9.82 mg, 0.01 mmol) was added and the reaction mixture was degassed and placed under hydrogen balloon again. The reaction mixture was stirred for -40 minutes then flushed with nitrogen and filtered to remove the catalyst.
• reaction mixture was stirred for 30 minutes. More trifluoroacetic acid (0.14 mL, 1.84 mmol) was added and the reaction mixture was warmed to room temperature for 15 minutes. The reaction mixture was concentrated with DCM several times to remove excess TFA. The resulting oil was dried under vacuum.
• Chlorotrimethylsilane (4.5 g, 41.42 mmol) was added dropwise with stirring at -30 °C in 5 minutes. The solution was stirred at -20 °C for 30 minutes. To the mixture was added n-BuLi (45 mL, 112.3 mmol) dropwise with stirring at -50° C in 10 minutes. The solution was stirred at -50 °C for 2 hours. Then C0 2 was purged into the reaction at -50 °C in 20 minutes. The resulting solution was stirred for 20 minutes at room temperature. The reaction was then quenched by the addition of water (1000 mL). The pH value of the solution was adjusted to 3 with hydrogen chloride (1 mol/L).
• reaction mixture was stirred at room temperature for 2 hours. Still only starting material. 0.2 eq lithium hydroxide added every hour until 1 eq more added. The reaction mixture was kept in freezer overnight. In the morning there is still only 50% product. Another 0.2 eq LiOH added and after 30 minutes the reaction is -70-80% complete. Continue stirring at room temperature for 1 hour. The reaction mixture was cooled to 0 °C, acidified to ⁇ pH 4 with 0.5N HC1 and extracted with ethyl acetate 4 times. The aqueous was further acidified to ⁇ pH 2 and extracted four times with ethyl acetate.
• reaction mixture was stirred for 15 minutes at room temperature then diluted with ethyl acetate and washed with saturated sodium bicarbonate solution and brine/water (1: 1). Aqueous alyer was extracted twice with ethyl acetate. The organics were pooled, dried over anhydrous magnesium sulfate, filtered and concentrated.
• the reaction mixture was stirred at room temperature for 30 minutes. See a mixture of starting material, mono and bis TBS protected. More tert- butyldimethylsilyl trifluoromethanesulfonate (0.03 mL, 0.12 mmol) and 2,6-lutidine (0.01 mL, 0.12 mmol) added. After 1 hour the major product is bis TBS protected. More tert- butyldimethylsilyl trifluoromethanesulfonate (0.03 mL, 0.12 mmol) and 2,6-lutidine (0.01 mL, 0.12 mmol) added again. After another hour the reaction mixture was diluted with dichloromethane and washed with saturated ammonium chloride solution.
• TBA salt of (4R,8S)-l-(2-amino-2-oxoethyl)-8-((Z)- N'-hydroxy-N-methylcarbamimidoyl)-6-oxo-4,8-dihydro-lH-4,7-methanopyrazolo[3,4- e][l,3]diazepin-5(6H)-yl sulfate TBA salt as a white solid (11.9 mg, 70%).
• Int-94 was synthesized by following similar reaction conditions as shown for Int- 14 (Scheme 1, stepl4), using tert-butyl (2-(azidomethyl)thiazol-4-yl)carbamate (Int-93, 501 mg, 01.96 mmo) as substrate, and EtOH as solvent, to afford tert-butyl (2- (aminomethyl)thiazol-4-yl)carbamate (380 mg, 84%) as a white solid. MS: 230 ES+
• Int-100 was synthesized by following similar reaction conditions as shown for Int-11 (Scheme 1, step 11), using (E)-5-(allyloxy)- l-methyl-6-oxo-4,5,6,8-tetrahydro-lH- 4,7-methanopyrazolo[3,4-e][l,3]diazepine-8-carbaldehyde oxime (Int-99, 614 mg, 2.21 mmol) as substrate, to afford (4R,8S,Z)-5-(allyloxy)-N-hydroxy-l-methyl-6-oxo-4, 5,6,8- tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepine-8-carbimidoyl chloride (690 mg, 99%) as a white solid. MS: 312 ES+ (C 12 H 14 CIN 5 O 3 ).
• Int-101 was synthesized by following similar reaction conditions as shown for Int-12 (Scheme 1, step 12), using (4R,8S,Z)-5-(allyloxy)-N-hydroxy-l-methyl-6-oxo-4,5,6,8- tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepine-8-carbimidoyl chloride (Int-100, 470 mg, 1.51 mmol), and tert-butyl (2-(aminomethyl)thiazol-4-yl)carbamate (Int-94, 380 mg, 1.66 mmol) as substrates, to afford tert-butyl (2-(((4R,8S,Z)-5-(allyloxy)-N'-hydroxy-l- methyl-6-oxo-4,5,6,8-tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,
• Int-102 was synthesized by following similar reaction conditions as shown for Int-13 (Scheme 1, step 13), using tert-butyl (2-(((4R,8S,Z)-5-(allyloxy)-N'-hydroxy-l- methyl-6-oxo-4,5,6,8-tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepine-8- carboximidamido)methyl)thiazol-4-yl)carbamate (Int-101, 58 mg, 0.11 mmol) as substrates, to afford tert-butyl (2-((Z)-3-((4R,8S)-5-(allyloxy)-l-methyl-6-oxo-4,5,6,8-tetrahydro-lH- 4,7-methanopyrazolo[3,4-e][l,3]diazepin-8-yl)-6,6,7,7-tetra
• Int-104 was synthesized by following similar reaction conditions as shown for Int-16 (Scheme 1, step 16), using (4R,8S)-8-((Z)-N-((4-((tert-butoxycarbonyl)amino)thiazol- 2-yl)methyl)-N'-hydroxycarbamimidoyl)-l-methyl-6-oxo-4,8-dihydro-lH-4,7- methanopyrazolo[3,4-e][l,3]diazepin-5(6H)-yl hydrogen sulfate (Int-103, 54 mg, 0.082 mmol) as substrates, to afford (4R,8S)-8-((Z)-N-((4-((tert-butoxycarbonyl)amino)thiazol-2- yl)methyl)-N'-hydroxycarbamimidoyl)-l-methyl-6-oxo-4,8-dihydro-lH-4,7- me
• Int-107 was synthesized by following similar reaction conditions as shown for Int-103 (Scheme 15, step 7), using tert-butyl (Z)-3-((4R,8S)-5-(allyloxy)-l-methyl-6-oxo- 4,5,6,8-tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepin-8-yl)-l-(4-((tert- butoxycarbonyl)amino)thiazol-2-yl)-8,8-dimethyl-6-oxo-5-oxa-2,4,7-triazanon-3-en-9-oate (Int-105, 18 mg, 0.03 mmol) as the substrate, to afford tert-butyl (Z)-l-(4-((tert- butoxycarbonyl)amino)thiazol-2-yl)-8,8-dimethyl-3-((4R,8S)
• Example 52 was synthesized by following similar reaction conditions as shown for Example 51 (Scheme 15, step 9), using tert-butyl (Z)-l-(4-((tert- butoxycarbonyl)amino)thiazol-2-yl)-8,8-dimethyl-3-((4R,8S)-l-methyl-6-oxo-5-(sulfooxy)- 4,5,6,8-tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepin-8-yl)-6-oxo-5-oxa-2,4,7- triazanon-3-en-9-oate (Int-107, 15 mg, 0.02 mmol) as the substrate, to afford (Z)-l-(4- aminothiazol-2-yl)-8,8-dimethyl-3-((4R,8S)-l-methyl-6-oxo-5-(sulfooxy)-4,5,6,8
• Int-108 was synthesized by following similar reaction conditions as shown for Int-107 (Scheme 16, step 2), using tert-butyl (2-((3-((4R,8S)-5-(allyloxy)-l-methyl-6-oxo- 4,5,6,8-tetrahydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepin-8-yl)-5-oxo-l,2,4-oxadiazol- 4(5H)-yl)methyl)thiazol-4-yl)carbamate (lnt-106, 27 mg, 0.05 mmol) as the substrate, to afford (4R,8S)-8-(4-((4-((tert-butoxycarbonyl)amino)thiazol-2-yl)methyl)-5-oxo-4,5-dihydro- l,2,4-oxadiazol-3-yl)-l-methyl-6-oxo-4
• Example 53 was synthesized by following similar reaction conditions as shown for Example 52 (Scheme 16, step 3), using (4R,8S)-8-(4-((4-((tert- butoxycarbonyl)amino)thiazol-2-yl)methyl)-5-oxo-4,5-dihydro-l,2,4-oxadiazol-3-yl)-l- methyl-6-oxo-4,8-dihydro-lH-4,7-methanopyrazolo[3,4-e][l,3]diazepin-5(6H)-yl hydrogen sulfate (Int-108, 13 mg, 0.02 mmol) as the substrate, to afford (4R,8S)-8-(4-((4- aminothiazol-2-yl)methyl)-5-oxo-4,5-dihydro-l,2,4-oxadiazol-3-yl)-l-methyl-6-oxo-4,8- dihydro-lH-4,7-
• reaction mixture was stirred at 0 °C for 30 minutes. Saturated ammonium chloride solution was added. The mixture was then extracted with ethyl acetate. The organic layer was separated, washed with water, brine and dried over anhydrous sodium sulfate and
• reaction mixture was stirred at room temperature for 20 minutes. Saturated ammonium chloride solution and DCM were added to the reaction mixture. The organic layer was separated, washed with water, brine and dried over anhydrous sodium sulfate, and concentrated to give the crude product.
• Example 63 was synthesized by following similar reaction conditions as shown for Example 62. Using Te/t-butyl 2-((((Z)-((4R,8S)-5-(benzyloxy)- l-methyl-6-oxo-4,5,6,8- tetrahydro- lH-4,7-methanopyrazolo[3,4-e][l,3]diazepin-8- yl)(methylamino)methylene)amino)oxy)-2-methylpropanoate (Int-123) as substrate in Scheme 24, stepl .
• Example 65 was synthesized by following similar reaction conditions as shown for Example 64 using 3-((4R,8S)-5-(benzyloxy)- l-methyl-6-oxo-4,5,6,8-tetrahydro- lH-4,7- methanopyrazolo[3,4-e][l,3]diazepin-8-yl)-4,6,6-trimethyl-4H- l,2,4-oxadiazin-5(6H)-one (Int-124) as substrate in Scheme 25, stepl .
• reaction was warmed up to room temperature and stirred at room temperature for 30 minutes.
• the reaction was diluted with DCM.
• Organic layer was separated, washed with water, brine, dried over anhydrous magnesium sulfate, and concentrated to give the crude product.
• the reaction was heated at 60 °C for 8 hours.
• the reaction mixture was cooled to room temperature.
• Saturated ammonium chloride solution and Ethyl acetate were added to the reaction mixture.
• the organic layer was separated, washed with water, brine, dried over anhydrous magnesium sulfate, and concentrated to give the crude product.
• the reaction was heated at 80 °C for 20 minutes and cooled to room temperature. Ethyl acetate and water were added to the reaction mixture. The organic layer was separated, washed with water, brine, dried over anhydrous sodium sulfate, and concentrated to give the crude product.
• reaction mixture was stirred for 5 minutes. To the solution was added methylamine (0.36 mL, 0.72 mmol, 2N in THF) dropwise. The reaction mixture was then allowed to warm to room temperature and stir for 2 hours. The reaction mixture was diluted with DCM and washed once with saturated ammonium chloride solution. The organics were dried over magnesium sulfate, filtered and concentrated.
• aeruginosa were measured using the BOCILLIN FL penicillin fluorescence anisotropy assay method (Anal. Biochem. 463, 15-22 (2014)).
• the BOCILLIN FL (Thermo-Fisher Scientific, Waltham, MA) concentration was 30 nM in each case.
• the PBP concentrations were 60 nM for P. aeruginosa PBPla and PBP3, and 300 nM for P. aeruginosa PBP2.
• the assay buffer was 0.1 M sodium phosphate with 0.01% Triton X-100.
• the pH was 7.0 for all the PBPs with the exception of P. aeruginosa PBP2, for which the pH was 6.2.
• Serial 2-fold dilutions of compounds were employed, with concentrations ranging from 328 to 0.02 ⁇ for the P. aeruginosa PBPs. Results are shown below in Table 5.
• Table 5 Table 5

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