Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H17/00—Compounds containing heterocyclic radicals directly attached to hetero atoms of saccharide radicals
  • C07H17/04—Heterocyclic radicals containing only oxygen as ring hetero atoms
  • C07H17/08—Hetero rings containing eight or more ring members, e.g. erythromycins
• • 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
• • 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
• • 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
• • 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
• • 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
  • A61K31/42—Oxazoles
  • A61K31/424—Oxazoles condensed with heterocyclic ring systems, e.g. clavulanic acid
• • 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
  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
  • A61K31/7048—Compounds having saccharide radicals and heterocyclic rings having oxygen as a ring hetero atom, e.g. leucoglucosan, hesperidin, erythromycin, nystatin, digitoxin or digoxin
• • 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
• • 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
  • A61P31/10—Antimycotics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P33/00—Antiparasitic agents
  • A61P33/02—Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P33/00—Antiparasitic agents
  • A61P33/02—Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
  • A61P33/04—Amoebicides
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D498/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D498/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms
  • C07D498/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D498/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms
  • C07D498/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
  • C07D498/04—Ortho-condensed systems

Definitions

• the invention described herein pertains to a novel macrolide antibacterial agent of formula (I), as defined below, and pharmaceutically acceptable salts, solvates, and hydrates thereof.
• the new macrolide antibacterial agent is active against a number of bacterial species, including resistant species.
• Macrolide antibiotics characterized by a large lactone ring to which are attached one or more deoxy sugars, usually cladinose and desosamine, are antimicrobial drugs that are active against aerobic and anaerobic gram positive cocci and are prescribed for the treatment of respiratory tract and soft tissue infections.
• the macrolides which belong to the polyketide class of natural products, function by reversibly binding to the 23S rRNA component of the 50S subunit of the bacterial ribosome, blocking protein synthesis and preventing bacterial growth and reproduction.
• the macrolide antibiotics bind to the large ribosomal subunit and inhibit protein synthesis by blocking the path of the nascent peptide in the exit tunnel (Gaynor, M., and A. S.
• the binding site of macrolides in the ribosome includes the 23S rRNA residues A2058, A2059, A2062, A2503, G2505, and C2611 [or U2611] (using here and throughout the E. coli numbering, see Tu, D., G. Blaha, P. B. Moore, and T. A. Steitz. 2005 . Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance . Cell 121:257-270). It is to be understood that the corresponding nucleic acid residues in ribosomes of other organisms are described herein by reference to the E. coli nucleic acids.
• Ketolides-telithromycin an example of a new class of antibacterial agents. Clin. Microbiol. Infect. 6:661-669). Ketolides show improved activity against strains with inducible erm genes and are believed to exhibit a tighter binding to the ribosome compared with macrolides of the previous generations (Poehlsgaard, J., and S. Douthwaite. 2003. Macrolide antibiotic interaction and resistance on the bacterial ribosome. Curr. Opin. Investig. Drugs 4: 140-148; Poehlsgaard, J., P. Pfister, E. C. Bottger, and S. Douthwaite. 2005.
• ketolides the 3-O-cladinose is replaced by a keto function (hence the name of the class); a cyclic carbamate is fused at the CI 1-C12 position; and an extended side chain, such as an alkyl side chain bearing a an aryl or heteroaryl group, which may be substituted, is attached at the CI 1-N atom (11-N) of the carbamate, as in the ketolide telithromycin, or at another position of the lactone ring, such as the 6-0- position as in cethromycin.
• the macrolide-ketolide antibiotic binding site is formed by structures in domains II and V of 23S ribosomal RNA. Mol. Microbiol. 31:623-632; Xiong, L., S. Shah, P. Mauvais, and A. S. Mankin. 1999. A ketolide resistance mutation in domain II of 23S rRNA reveals proximity of hairpin 35 to the peptidyl transferase centre. Mol. Microbiol. 31:633-639 46).
• telithromycin the first ketolide introduced into medical practice in 2001, showed excellent activity against many strains of Gram positive pathogens, the safety issues that became apparent upon the wider use of the drug have curbed its clinical use
• CEM-101 is similar to that of telithromycin except for the presence of a fluorine atom at C2 of the lactone and the differing aromatic groups on the 11-N side chain (which in CEM-101 is a
• CEM-101 In microbiological tests involving a number of clinical pathogens, CEM-101 is characterized by lower minimal inhibitory concentration (MIC) values compared with telithromycin and exhibits enhanced activity against resistant organisms, including
• telithromycin-intermediate and telithromycin-resistant organisms (McGhee, P., C. Clark, K. M. Kosowska-Shick, K. Nagai, B. Dewasse, L. Beachel, and P. C. Appelbaum. 2010. In vitro activity of CEM-101 against Streptococcus pneumoniae and Streptococcus pyogenes with defined macrolide resistance mechanisms. Antimicrob. Agents. Chemother. 54:230-238).
• CEM-101 shows significantly enhanced accumulation in the macrophages.
• ketolides may be designed with high activity against pathogenic bacteria and against resistant strains of bacteria, including strains resistant to other ketolides like telithromycin.
• A is a moiety capable of forming one or more of the hydrogen bond interactions with one or more of A752, G748, and G748;
• L is a linking chain consisting of one or more divalent radicals selected from the group consisting of amino, O, and S, and alkylene, heteroalkylene, cycloalkylene,
• heterocycloalkylene alkenylene, heteroalkenylene, cycloalkenylene, heterocycloalkenylene, arylene, and heteroarylene, each of which is optionally substituted, provided that L does not include an 0-0 or O-S;
• Q is a 3-keto- or 2-fluoro-3-keto macrolactone capable of binding in the major macrolide site in the upper part of a bacterial ribosomal exit tunnel.
• R2 is H or F
• R6 is H or (l-6C)alkyl
• A-L- is other than 4-[4-(3-aminophenyl)[l,2,3]triazol-l-yl]butyl or 4-[4-(6-aminopyridin-2-yl)[l,2,3]triazol-l-yl]butyl bonded to the 11-N of Q.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein (a) A is a moiety capable of forming one or more of the hydrogen bond interactions with one or more of 04' of A752 (as a donor), 06 of G748 (as a donor), and Nl of G748 (as an acceptor).
• A is a moiety capable of forming one or more of the hydrogen bond interactions with one or more of 04' of A752 (as a donor), 06 of G748 (as a donor), and Nl of G748 (as an acceptor).
• the 3-keto group of Q is capable of forming a hydrogen bond interaction with U2609.
• the aminosaccharide of Q is capable of forming a hydrogen bond interaction with A2059.
• aminosaccharide of Q is capable of forming a hydrogen bond interaction with G2505.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein the compound exhibits any combination of (a), (b), (c), and (d).
• hydrogen bond forming capability of A may be determined using any conventional method.
• hydrogen bond forming capability of A may be determined by computer modeling the compound in the E. coli 23S ribosomal site; or by co-crystallizing the compound in the E. coli 23S ribosomal site.
• the hydrogen bond forming capability of the 3- keto group of Q may be determined using any conventional method.
• the compound protects U2609 from modification by CMCT, such as protecting against modification to a greater extent than does telithromycin, in RNA footprinting.
• the hydrogen bond forming capability of the aminosaccharide of Q may be determined using any conventional method.
• the compound protects G2505 from modification by kethoxal, such as protecting against modification to a greater extent than does erythromycin, clarithromycin, azithromycin, and/or telithromycin, in RNA footprinting.
• the compound blocks methylation of A2059 by DMS,such as blocking methylation to a greater extent than does erythromycin, clarithromycin, azithromycin, and/or telithromycin, in RNA footprinting.
• the bacteria may be a resistant strain.
• exemplary resistant strains include but are not limited to erythromycin resistant strains, clarithromycin resistant strains, azithromycin resistant strains, telithromycin resistant strains, mefA resistant strains, and ermB resistant strains.
• Embodiments of the invention include those described by the following enumerated clauses: 1A.
• A is a hydrogen bond forming group
• L is a bivalent linking group comprising one or more units selected from the group consisting of optionally substituted methylene, O, S, optionally substituted NH, sulfonyl, vinylene, and cyclic units selected from the group consisting of divalent monocyclic and bicyclic carbocyclic and aromatic rings, and monocyclic and bicyclic heterocyclic and heteroaromatic rings, where the monocyclic and bicyclic heterocyclic and heteroaromatic rings contain 1 to 4 hetero atoms each independently selected from oxygen, sulfur and nitrogen, and where the cyclic units contain 5 to 10 ring atoms whichare optionally substituted; providing that L does not include-O-0- or -0-S-;
• R2 is H or F
• R5 is an amino saccharide residue
• R6 is H or (l-6C)alkyl
• A is capable of forming a hydrogen bond interaction in a bacterial ribosome selected from the group consisting of hydrogen bond donation to 04' of A752, hydrogen bond donation to 06 of G748, and hydrogen bond acceptance from Nl of G748; or
• amino saccharide of Q is capable of forming a hydrogen bond interaction with A2059; or aminosaccharide of Q is capable of forming a hydrogen bond interaction with G2505; or
• A-L- is other than 4-[4-(3-aminophenyl)[l,2,3]triazol-l-yl]butyl or 4- [4- (6-aminopyridin-2-yl) [ 1 ,2,3] triazol- 1 -yl]butyl .
• A when the compound is co-crystallized in the E. coli 23S ribosomal site, A is a moiety capable of forming one or more of the hydrogen bond interactions of the group consisting of hydrogen bond donation to 04' of A752, hydrogen bond donation to 06 of G748, and hydrogen acceptance from Nl of G748; or
• RNA footprinting of S. aureus N315 ribosomes blocks methylation of A2059 with DMS to a greater extent than does telithromycin, or
• RNA footprinting of S. aureus N315 ribosomes protects G2505 from modification with kethoxal to a greater extent than does telithromycin, or
• L is a linking chain comprising one or more units selected from the group consisting of optionally substituted methylene, O, S, optionally substituted NH, vinylene, and a divalent monocyclic or bicyclic carbocyclic or aromatic or monocyclic or bicyclic heterocyclic or hetero aromatic ring containing 1 to 4 hetero atoms selected from O, S and N which ring contains 5 to 10 ring atoms and may bear one or more substituents, provided L does not include an -O-O- or -O-S- portion; Q is
• R2 is H or F
• R5 is an aminosaccaride residue
• R6 is H or (l-6C)alkyl
• A-L- is other than 4-[4-(3-aminophenyl)[l,2,3]triazol-l-yl]butyl or 4-[4-(6-aminopyridin-2-yl)[l,2,3]triazol-l-yl]butyl bonded to the 11-N of Q.
• amino saccharide of Q is capable of forming a hydrogen bond interaction with A2059;
• the aminosaccharide of Q is capable of forming a hydrogen bond interaction with G2505. 5.
• heterocyclic ring is monocyclic or bicyclic heteroaromatic ring containing 1 to 4 hetero atoms selected from O, S and N which ring may bear one or more substituents.
• each of a, b and c is independently 0 or 1, provided at least one of a, b and c is 1;
• X is CH 2 R a R b , O, S or NR C ;
• Y is an monocyclic or bicyclic aromatic or a monocyclic or bicyclic heteroaromatic ring containing 1 to 4 hetero atoms selected from O, S and N which ring may bear one or more substituents;
• Z is -(CH2) m - in which m is 1, 2, 3 or 4, one or more methylene units may bear one or two methyl groups, and a methylene unit may be replaced by O, S or NR ⁇ ; and
• each of R a , R b , R c and R d is independently H or CH3
• A-X-Y- is 4-(indol-3-ylmethyl)[l,2,3]triazol-l-yl.
• a pharmaceutical composition comprising an agent of formula (I), as described in any of the preceding clauses 1A-43 and further comprising at least one
• a method of treatment of a bacterial infection, a protozoal infection, or a disorder related to a bacterial infection or protozoal infection comprising the step of administering to a subject in need thereof a therapeutically effective amount of an agent of formula (I), as described in any of the preceding clauses 1A-43.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone where the lactone ring forms positive hydrophobic interactions with the walls of the tunnel.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein A-L- is arylalkyl, and the arylalkyl arm is oriented down the tunnel and makes contact with a base pair formed by A752 and U2609 of the 23S rRNA.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein A-L has a low atomic displacement parameter (ADP).
• ADP atomic displacement parameter
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone that includes a fluoro group capable of a positive interaction with the glycosidic bond (atom Nl) of C2611.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone that includes a fluoro group capable of a positive interaction with the glycosidic bond (atom Nl) of C2611 of a ribosome present in a resistant bacteria, such as a ribosome monomethylated or dimethylated at A2058 and/or A2059.
• the foregoing positive interactions are positive interactions with a ribosome present in a resistant bacteria, such as a ribosome monomethylated or dimethylated at A2058 and/or A2059.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine protects A2058 and A2059 in domain V of 23S rRNA from modification with DMS.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine protects A752 from DMS modification.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine protects A2059 in domain V of 23S rRNA in an erm resistant and/or erm modified bacteria from modification with DMS.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine substantially protects A2059 in domain V of 23S rRNA in an erm resistant and/or erm modified bacteria from modification with DMS.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine protects G2505 from kethoxal modification.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine substantially protects G2505 from kethoxal modification.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine protects U2609 from modification with CMCT.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein Q is a macrolactone substituted with a desosamine, where the desosamine substantially protects U2609 from modification with CMCT.
• methods for determining the capability of the compounds described herein to have positive interactions with and/or protections of ribosomal functional groups of E. coli as described herein including computational methods, computer modeling, computational docking, energy minimization, X-ray crystallography, atomic displacement parameter (ADP) refinement, RNA footprinting, RNA binding assessments, and the like, may be predictive of the same, similar, equivalent, and/or corresponding interactions with pathogenic bacteria, including but not limited to S. aureus, S. pyogenes, S. penuomiae, and the like, as well as resistant pathogenic bacterial strains, including but not limited to telithromycin resistant S. aureus, MRSA, and the like.
• positive interactions are interactions that are lower energy states for the compound and/or the ribosome.
• positive interactions are those that are not sterically crowded, such as interactions that are at least about 0.5 A or at least about 1 A separated in space.
• positive interactions are those that are close enough to provide an energetic benefit, such as interactions that are about 5 A or less, about 4.5 A or less, about 4 A or less, about 3.5 A or less, about 3 A or less, about 2.5 A or less, about 1.5 A or less, or about 1 A or less, while at the same time at least about 0.5 A separated in space.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein in competition binding experiments, the compounds are capable of displacing erythromycin bound to a ribosome.
• compounds of formula (I) are described herein, and pharmaceutically acceptable salts, hydrates, solvates, and prodrugs thereof, wherein in competition binding experiments, the compounds are capable of displacing telithromycin bound to a ribosome.
• the IC50 of such displacement is about 1 ⁇ or less, about 500 nM or less, about 250 nM or less, about 200 nM or less, about 150 nM or less, or about 100 nM or less.
• CEM-101 is not included in the invention described herein. It is also to be understood that telithromycin is not included in the invention described herein because it does not form a hydrogen bond with any of A752, G748, or G748.
• compositions comprising a therapeutically effective amount of one or more of compounds described herein are described.
• the compositions optionally include one or more diluents, excipients, or carriers, and combinations thereof.
• methods for treating a patient with a bacterial infection include the step of administering a therapeutically effective amount of one or more compounds and/or one or more compositions described herein to the patient.
• telithromycin determinations include those from studies of the binding of telithromycin (Berisio, R., J. Harms, F. Schluenzen, R. Zarivach, H. A. Hansen, P. Fucini, and A. Yonath. 2003. Structural insight into the antibiotic action of telithromycin against resistant mutants. J. Bacteriol. 185:4276-4279; Tu, D., G. Blaha, P. B. Moore, and T. A. Steitz. 2005. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 121:257-270), and particularly the determination wherein the E. coli 23S ribosomal site is defined by the X-ray coordinates of the complex of CEM-101 with the E. coli 23S ribosome described herein.
• docking refers to positioning the compound at/in the 23S ribosome, and may optionally include minimization calculations, such that once positioned there are no negative interactions which preclude docking.
• the side chain may be capable of a stacking interaction with the A753/U2609 base pair and the 2-fluoro group, if present, is capable of an interaction with C2610 or C2611.
• the moiety A when the molecule is docked in the 23S ribosome, the moiety A is capable of forming one or more of the hydrogen bond interactions of the group consisting of hydrogen bond donation to 04' of A752, hydrogen bond donation to 06 of G748, and hydrogen acceptance from Nl of G748.
• a in the compounds is capable of forming one or more of the hydrogen bond interactions with one or more of A752, G748, and G748, and Q is a macrolactone substituted with a desosamine, where the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft
• the compounds may be characterized by a calculated energy minima corresponding to a conformation where both A and the desosamine are positioned for each of the positive interactions, respectively.
• the compounds may be characterized by a calculated energy minima corresponding to a conformation where both A and the fluoro group are positioned for each of the positive interactions, respectively.
• a in the compounds is capable of forming one or more of the hydrogen bond interactions with one or more of A752, G748, and G748, and Q is macrolactone that includes a fluoro group capable of a positive interaction with the glycosidic bond (atom Nl) of C2611, and Q is a macrolactone substituted with a desosamine, where the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft
• the compounds may be characterized by a calculated energy minima corresponding to a conformation where A, the fluoro group, and the desosamine are positioned for each of the positive interactions, respectively.
• the group A-L- is arylalkyl
• the arylalkyl arm is oriented down the tunnel and makes contact with a base pair formed by A752 and U2609 of the 23S rRNA
• the compounds may be characterized by a calculated energy minimum corresponding to a conformation where A-L- is also positioned for the positive interaction.
• the calculated conformations may be obtained from any conventional software program.
• additional conformations may be calculated for the compounds when the initial conformations do not include a distance between a particular hydrogen-bonding group or the fluoro group and each required binding site of about 5 to 0.5 A.
• the compounds are characterized by high potency against pathogenic cells, such as bacteria.
• the compounds are characterized by high potency against bacteria that are resistant to one or more other compounds.
• Illustrative resistant bacteria include, but are not limited to mefA resistant
• A is a phenyl, indenyl, naphthyl, furanyl, thiophenyl, pyrrolyl, oxadiazolyl, thiadiazolyl, imidazolyl, pyrazolyl, 1,2,4-oxadiazolyl, 1,2,4-thiadiazolyl, 1,3,4-oxadiazolyl; 1,3,4-thiadiazolyl, 1,2,3-triazolyl, 1,2,4-triazolyl, tetrazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, benzofuranyl, benzothiophenyl, indolyl, indazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazolyl; benzoxazolyl; benzisothiazolyl, quinolinyl, isoquinolinyl or quinazolin
• an optionally substituted methylene may bear one or two methyl groups; an optionally substituted NH may bear a methyl group; a divalent monocyclic or bicyclic carbocyclic or aromatic or monocyclic or bicyclic heterocyclic or heteroaromatic ring may be a cyclopropanediyl, cyclopentanediyl, cyclohexanediyl, cycloheptanediyl, phenylene, indanediyl, indenediyl, naphthalenediyl,
• a divalent monocyclic or bicyclic aromatic or monocyclic or bicyclic heteroaromatic ring may be a phenylene, indanediyl, indenediyl, naphthalenediyl, tetrahydronaphthalenediyl, furandiyl, thiophenediyl, pyrrolediyl, oxazolediyl, thiazolediyl, imidazolediyl, pyrazolediyl, 1,2,4-oxadiazolediyl, 1,2,4-thiadiazolediyl,
• benzoxazolediyl benzisothiazolediyl, quinolinediyl, isoquinolinediyl or quinazolinediyl; and a ring may bear one or more hydroxy, fluoro, chloro or methyl substituents.
• A-X-Y- is selected from the following group of radicals, where Z is covalentl connected at (*):
• (l-6C)alkyl is methyl, ethyl, propyl, butyl, pentyl or hexyl, any of which may be branched. In another embodiment (l-6C)alkyl is methyl.
• compositions comprising an agent of formula (I), as described in any of the descriptions herein and further comprising at least one pharmaceutically acceptable carrier or excipient.
• compositions may include one or more carriers, diluents, and/or excipients.
• the compounds described herein, or compositions containing them may be formulated in any conventional dosage forms appropriate for the methods described herein, and include one or more carriers, diluents, and/or excipients therefor.
• compositions may be administered by a wide variety of conventional routes for the methods described herein, and in a wide variety of dosage formats, utilizing known procedures.
• Capsules and tablets are embodiments commonly used for oral administration of antibiotics. See generally, Remington: The Science and Practice of Pharmacy, (21 st ed., 2005).
• a method of treatment of a bacterial infection, a protozoal infection, or a disorder related to a bacterial infection or protozoal infection comprising the step of administering to a subject in need thereof a therapeutically effective amount of an agent of formula (I), as described herein.
• Illustrative dosing schedules include administration of a loading dose on day 1 of 800 mg, followed by a dose of 400 mg/day on each of days 2-5, or, alternatively a loading dose on day 1 of 400 mg, followed by a dose of 200 mg/day on each of days 2-5.
• an agent of formula (I), as described herein for the treatment of a bacterial infection, a protozoal infection, or a disorder related to a bacterial infection or protozoal infection.
• an agent of formula (I), as described herein for the manufacture of a medicament for the treatment of a bacterial infection, a protozoal infection, or a disorder related to a bacterial infection or protozoal infection.
• method or use described above is one wherein the subject is a mammal, a fish, a bird or a reptile.
• a method or use wherein the subject is a mammal.
• a method or use wherein the subject is a human.
• therapeutically effective amount refers to that amount of active compound or pharmaceutical agent that elicits the biological or medicinal response in a tissue system, animal or human that is being sought by a researcher, veterinarian, medical doctor or other clinician, which includes alleviation of the symptoms of the disease or disorder being treated.
• the therapeutically effective amount is that which may treat or alleviate the disease or symptoms of the disease at a reasonable benefit/risk ratio applicable to any medical treatment.
• the total daily usage of the compounds and compositions described herein may 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; activity of the specific compound employed; the specific composition employed; the age, body weight, general health, gender 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 coincidentally with the specific compound employed; and like factors well known to the researcher, veterinarian, medical doctor or other clinician of ordinary skill.
• A-L- is: 4-[4-(3-aminophenyl)-[l,2,3]triazol-l-yl]butyl, 4-[4-(4-pentylphenyl)-[l,2,3]triazol-l-yl]butyl, 4-[4-(2-pyridinyl)-[l,2,3]triazol-l-yl]butyl, 4-[4-(6-aminopyridin-2-yl)-[l,2,3]triazol-l-yl]butyl, 4-[4-(3-aminophenylmethyl)- [l,2,3]triazol-l-yl]butyl, 4-[4-(2-pyridinylmethyl)-[l,2,3]triazol-l-yl]butyl,
• Antibiotics were dissolved in 100% ethanol at a concentration of 10 mM, and serial dilutions were made in water to obtain the needed concentrations for competition binding studies and cell-free transcription -translation assays.
• the antibiotics were diluted in ethanol for ribosome probing experiments.
• Ribosomes were prepared from E. coli, strain MRE 600, S. aureus strain ATCC 29212, or S. aureus strain N315 by standard protocols (Spedding , G. 1990. Isolation and analysis of ribosomes from prokaryotes, eukaryotes , and organelles , p. 1-29 . In G. Spedding (ed.), Ribosomes and protein synthesis , a practical approach. Oxford University Press, Oxford, United Kingdom; Adams, P. D., P. V. Afonine, G. Bunkoczi, V. B. Chen, I. W. Davis, N.
• EXAMPLE Competition binding studies. Binding of erythromycin to E. coli and S. aureus ribosomes and competition experiments were done by size-exclusion
• ribosomes 100 nM were preincubated with 100 nM [ 14 C] erythromycin (48.8 mCi/mmol; PerkinElmer) in 160 ⁇ . of buffer A at 37 °C for 15 min, then at 20 °C for 10 min. Competing antibiotics were added at varying
• Binding data were analyzed using Prism software (GraphPad). Cell free transcription-translation assays.
• the E. coli transcription-translation (TnT) S30 extract system for circular DNA was used to evaluate the effect of antibiotics on bacterial protein synthesis.
• Experiments were carried out in 96- well conical bottom plates in a final volume of 10 ⁇ L ⁇ S30 extract (3 ⁇ ) was dispensed into wells of the plate, combined with 1 ⁇ L ⁇ of water or antibiotic solution, and preincubated at 25 °C for 5 min. The reactions were initiated by adding 6 ⁇ L ⁇ of translation mix containing 1 ⁇ L ⁇ of pBEST/wcTM DNA (0.7 ⁇ g), 1 of 1 mM amino acid mixture, and 4 ⁇ L ⁇ of S30 premix.
• the rabbit reticulocyte cell-free translation system (Promega, Cat. No. L4540) was used to assay the effect of the drugs on activity of the eukaryotic ribosome. Experiments were carried out in 96-well conical bottom plates in a final volume of 10 ⁇ ⁇ . Rabbit reticulocyte lysate (7 ⁇ ) was mixed with 1 ⁇ L ⁇ of water or antibiotics and preincubated at 25 °C for 5 min. Polyadenylated luciferase mRNA (Promega, Cat. No. L4561) was denatured before use by incubating the RNA at 65 °C for 3 min and then placed on ice.
• Translation mix (2 ⁇ > was mixed with the rabbit reticulocyte lysate to start the reaction.
• the translation mix contained 0.3 ⁇ ⁇ of denatured luciferase mRNA (0.3 ⁇ g), 0.2 ⁇ L ⁇ of 1 mM amino acid mixture, 0.2 ⁇ , of ribonuclease inhibitor (8U, Roche, Cat. No. 03 335 399001), 0.4 ⁇ , of 2.5 M potassium chloride, and 0.9 ⁇ ⁇ of water. Reactions were incubated at 30 °C for 30 min and then placed on ice. In another 96-well plate, 150 ⁇ ⁇ of Bright-Glo dilution reagent (Promega, Cat. No.
• E266A was dispensed and mixed with 1.5 ⁇ ⁇ of the translation reactions; 30 ⁇ ⁇ of the resulting solution was mixed with 30 ⁇ ⁇ of Bright-Glo luciferase assay reagent (Promega, Cat. No. E2610) in a 96-well white-wall plate. Luminescence was measured on a TopCount Scintillation and Luminescence Counter (PerkinElmer).
• CMCT Modification reaction
• Ribosome crystals were grown and handled as described (Zhang, W., J. A. Dunkle, and J. H. Cate. 2009. Structures of the ribosome in intermediate states of ratcheting. Science 325: 1014- 1017), except that cryoprotection buffer was supplemented with 50 ⁇ CEM- 101. The crystals were soaked in cryoprotection buffer plus CEM-101 for 12 to 24 h, then flash frozen with liquid nitrogen. X-Ray diffraction data were collected at beamline 12.3.1 of the
• Fo-Fc maps were calculated using PHENIX, and coordinates for CEM-101 were placed into this unbiased difference density using the software Coot (Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. Biol. Crystallogr. 60:2126-2132). Individual atomic displacement parameter values for the comparison between CEM-101 and telithromcyin were calculated using
• EXAMPLE Affinity of CEM-101 to wild- type ribosomes from E. coli and S. aureus. Binding of CEM-101 to wild- type ribosomes from Gram-negative and Gram-positive bacteria was initially analyzed by competition with [ ⁇ C] erythromycin. For that, the binding of radiolabeled erythromycin to the preparations of E. coli and S. aureus 70S ribosomes was first analyzed. In saturation binding experiments, [ ⁇ C] erythromycin readily bound to ribosomes from both bacteria, exhibiting Kd of 66 + 11 nM and 11 + 1 nM for the E. coli and S. aureus ribosomes, respectively (data not shown).
• CEM-101 readily displaced erythromycin from both types of ribosomes with IC50 of 155 + 8 nM for the E. coli ribosome, and 117 + 3 nM for the S. aureus ribosome resulting in CEM-101 Kd of 62 + 3 nM (E. coli) and 12 + 1 nM (S. aureus) (Table 1).
• the affinity of radiolabeled [ 14 C]CEM-101 for S. aureus wild-type ribosomes was measured by saturation binding experiments. A Kd of 50 + 13 nM obtained with this approach was similar to that obtained by competition with erythromycin.
• CEM-101 interacts with the ribosomal site that either coincides or overlaps with that of erythromycin and demonstrated that the drug binds to ribosomes of Gram-positive and Gram-negative bacteria with affinities similar to those of other macrolides.
• EXAMPLE Inhibition of bacterial protein synthesis by CEM-101. The effect of CEM-101 upon bacterial protein synthesis was assayed in an E. coli cell-free transcription- translation system. CEM-101 inhibited the synthesis of firefly luciferase (Lux) with an IC50 of 1.1 ⁇ , comparable to inhibition afforded by azithromycin (IC50 0.3 ⁇ ) and telithromycin (IC50 0.5 ⁇ ).
• CEM-101 exhibits selective and efficient inhibition of bacterial translation.
• telithromycin was previously studied by X-ray crystallography (Berisio, R., J. Harms, F. Schluenzen, R. Zarivach, H. A. Hansen, P. Fucini, and A. Yonath. 2003. Structural insight into the antibiotic action of telithromycin against resistant mutants. J. Bacterid. 185:4276-4279; Tu, D., G. Blaha, P. B. Moore, and T. A. Steitz. 2005. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 121:257-270).
• the aminophenyltriazole head of the side chain of CEM-101 makes a similar stacking interaction with the A752-U2609 base pair as the pyridinylimidazole moiety of telithromycin; it is located at a distance of 3.5 A from the A752 and U2609 bases and oriented parallel to them.
• ketolides complexed with the E. coli ribosome likely more accurately reflect interactions of the drugs with the ribosome of pathogenic bacteria.
• the atomic displacement parameter (ADP) refinement for the CEM-101 atoms shows that the extended arm of CEM-101 exhibits a significantly lower ADP value compared with the side chain of telithromycin, whereas the average ADP values for all the other antibiotic atoms are very similar in both cases.
• a distinctive feature of CEM-101 compared to telithromycin and several other ketolides is the presence of a fluorine atom at the C2 position of the lactone ring.
• the fluorine atom is positioned at a distance of 2.7 A from the glycosidic bond (atom Nl) of C2611 and thus, can potentially contribute to the drug binding.
• Streptococcus pneumoniae 12 0.5 0.5 4 4 Pen R , Tel 1 *, Mac R
• CEM-Des-F a derivative of CEM-101 lacking fluorine atom; Tel, telithromycin; Azt, azithromycin.
• MIC50 and MIC90 values correspond to the concentration of antibiotic ⁇ g/mL) that inhibited 50% (MIC50) or 90% (MIC90) of the strains tested.
• EXAMPLE Interactions of CEM-101 with wild-type E. coli and S. aureus ribosomes in solution. Because the binding of the drug to the ribosome in the crystalline state may differ from that in solution and because biochemical, genetic, and crystallographic evidence indicates that the same compound may exhibit different interactions with the ribosomes of different species (Bottger, E. C. 2006. The ribosome as a drug target. Trends Biotechnol. 24: 145-147), the question of whether the crystallographic structure of CEM-101 bound to the E.
• coli ribosome accurately reflects the drug's interactions with ribosomes of Gram-positive pathogens was explored by expanding the structural studies of CEM-101 binding by probing its interactions with the E. coli and S. aureus ribosomes using RNA footprinting (Moazed, D., and H. F. Noller. 1987. Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie 69:879-884). Also included in this study was a C3-cladinose cousin of CEM- 101, CEM-103, which lacks the C2-linked fluorine atom.
• CEM-101 and CEM-103 protect A2058 and A2059 in domain V of 23S rRNA from modification with DMS. As can be inferred from the crystallographic structure, these protections are afforded by C5 desosamine sugar, which closely approaches the cleft formed by A2058 and A2059 residues. Furthermore, in excellent agreement with crystallographic structures of CEM-101 (and telithromycin) complexed with the E. coli ribosome, CEM-101, as well as telithromycin and CEM-103, strongly protects A752 from DMS modification both in E. coli and in S. aureus ribosomes.
• erythromycin which lacks the extended side chain, fails to protect A752 from DMS modification.
• the interaction of the CEM-101 side chain with the A752-U2609 base pair seen in the crystalline state appears to accurately reflect binding of the drug to the ribosome in solution.
• the lack of a C2 fluorine or the presence of a C3 cladinose in CEM-103 does not bring about any difference in the footprinting pattern, confirming that these moieties of the drug do not make contacts with rRNA residues accessible for DMS modification.
• the footprinting pattern of CEM-101 in the ribosome of E. coli is indistinguishable from that in the ribosome of S. aureus, indicating that the high-resolution structure of CEM-101 complexed to the E. coli ribosome described herein likely accurately reflects binding of the drug to the ribosomes of Gram-positive pathogens.
• EXAMPLE Interaction of CEM-101 with S. aureus ribosomes dimethylated at A2058 by Erm-methyltransferase. Erm-methyltransferase modifies A2058 in 23S rRNA by consecutively adding two methyl groups to the exocyclic amino group of the adenine base.
• aureus ribosome, footprinting studies were extended by including two more modifying reagents, kethoxal, which modifies guanosines, and l-cyclohexyl-3-(2-morpholinoethyl)- carbodiimide metho-p-toluene sulfonate (CMCT), which modifies uridines (Merryman, C, and H. F. Noller. 1998. Footprinting and modification-interference analysis of binding sites on RNA, p. 237-253. In C. W. J. Smith (ed.), RNA:Protein Interactions, A Practical Approach. Oxford University Press, Oxford).
• Kethoxal probing showed that CEM-101 and CEM-103 partially protected G2505 from kethoxal modification and fully protected U2609 from modification with CMCT. Telithromycin afforded a notably weaker protection at both positions. Erythromycin did not protect either of the two positions, consistent with the fact that dimethylation of A2058 is known to prevent erythromycin binding (Weisblum, B. 1995.
• the new macrolide agents can be prepared using methods which are analogous to methods known in the art for the preparation of macrocyles and the substituents or by methods described herein.
• the following examples further illustrate specific embodiments of the invention; however, the following illustrative examples should not be interpreted in any way to limit the invention. Abbreviations used in the examples include the following: DCM, dichloromethane; DMAP,
• Mass analysis of the crude 2 showed the desired product peak as the major peak (Mw of 821) along with a very minor peak with molecular weight of 861 which was attributed to an over-reacted side-product.
• ⁇ H-NMR of the crude 2 showed the desired structure of 2 along with the contamination of the possible 2-methoxypropan-2-ol and pyridine. This crude product was used for the next step reaction without further purification.
• Mass analysis of the purified product showed the desired product peak (Mw of 956) as the major component along with a minor peak with Mw of 970 which was attributed to the C-l 1 hydroxy methylated impurity carried over from the prior step.
• 1H-NMR analysis of the purified product showed the desired structure of clarithromycin dibenzoate.
• the compound may be prepared from the azide of Preparation 2, above, using methods analogous to those described for the preparation of CEM-101.
• the compound may be prepared from the azide of Preparation 3, above, using methods analogous to those described for the preparation of CEM-101.

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