阅读说明：本技术 新缩肽类及其用途 (Novel depsipeptides and their use ) 是由 D·休斯 A·斯波林 A·J·皮普尔斯 L·L·玲 A·尼蒂 W·米利特 A·祖洛 K 于 2018-03-30 设计创作，主要内容包括：本发明一般性涉及新缩肽类、用于制备所述新缩肽类的方法、包含所述新缩肽类的药物组合物；以及使用所述新缩肽类治疗或抑制各种病症的方法。(The present invention relates generally to novel depsipeptides, processes for preparing said novel depsipeptides, pharmaceutical compositions comprising said novel depsipeptides; and methods of using the novel depsipeptides to treat or inhibit various disorders.)

1. An isolated compound of formula (I),

or an enantiomer, diastereomer, tautomer, or pharmaceutically acceptable salt thereof, wherein:

each stereocenter is denoted by "+" and may independently be in the R or S configuration;

R_1’、R_2’、R_3’、R_4’、R_5’and R_6’Each independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, substituted or unsubstituted aryl, -NR_bR_b’、-COR_c、-COOR_d、–CONR_eR_e’And an amino acid side chain;

wherein R is_a、R_a’、R_b、R_b’、R_c、R_d、R_eAnd R_e’Each independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, and substituted or unsubstituted aryl; and is

n is an integer of 1 to 5.

2. The isolated compound of claim 1, wherein n is an integer from 2 to 4.

3. The isolated compound of claim 1, wherein the isolated compound is a compound of formula (II),

or an enantiomer, diastereomer, tautomer, or pharmaceutically acceptable salt thereof, wherein:

each stereocenter is denoted by "+" and may independently be in the R or S configuration;

R₁、R₂、R₃、R₄、R₅、R₆、R₇and R₈Each independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, substituted or unsubstituted aryl, -NR_bR_b’、-COR_c、-COOR_d、–CONR_eR_e’And an amino acid side chain;

wherein R is_b、R_b’、R_c、R_d、R_e、R_e’、R_fAnd R_f’Each independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, and substituted or unsubstituted aryl.

4. The isolated compound of claim 3, wherein R₁Is benzyl.

5. The isolated compound of claim 4, wherein R_aAnd R_a’Are all hydrogen.

6. The isolated compound of any one of claims 3-5, wherein R₂Is a substituted or unsubstituted alkyl group.

7. The isolated compound of claim 6, wherein the substituted or unsubstituted alkyl is isobutyl.

8. The isolated compound of any one of claims 3-7, wherein R₃Is a substituted or unsubstituted alkyl group.

9. The isolated compound of claim 8, wherein the substituted or unsubstituted alkyl is amino-substituted butyl.

10. The isolated compound of any one of claims 3-9, wherein R₄Is a substituted or unsubstituted alkyl group.

11. The isolated compound of claim 10, wherein the substituted or unsubstituted alkyl is hydroxy-substituted methyl.

12. The isolated compound of any one of claims 3-11, wherein R₅is-CONR_eR_e’。

13. The isolated compound of claim 12, wherein R_eAnd R_e’Are all hydrogen.

14. The isolated compound of any one of claims 3-13, wherein R₆Is a substituted or unsubstituted alkyl group.

15. The isolated compound of claim 14, wherein the substituted or unsubstituted alkyl is methyl.

16. The isolated compound of any one of claims 3-15, wherein R₇Is a substituted or unsubstituted alkyl group.

17. The isolated compound of claim 16, wherein the substituted or unsubstituted alkyl is isobutyl.

18. The isolated compound of any one of claims 3-17, wherein R₈Is a substituted or unsubstituted alkyl group.

19. The isolated compound of claim 18, wherein the substituted or unsubstituted alkyl is isobutyl.

20. The isolated compound of any one of claims 1-19, wherein the isolated compound is a compound of formula (III):

21. the isolated compound of claim 1, wherein the isolated compound is selected from the group consisting of:

22. a culture medium comprising a compound of any one of claims 1-21.

23. The culture medium of claim 22, further comprising bacterial cells belonging to the class β -proteobacteria.

24. A bacterial lysate comprising the compound of any one of claims 1-21.

25. The bacterial lysate of claim 24, produced by bacterial cells belonging to the class β -proteobacteria.

26. The bacterial lysate of claim 25, wherein the bacterial cells are cultured bacterial cells.

27. A pharmaceutical composition comprising a compound of any one of claims 1-21 and a pharmaceutically acceptable excipient, carrier or diluent.

28. The pharmaceutical composition of claim 27, further comprising an agent selected from the group consisting of: antibiotics, antifungal agents, antiviral agents, antiprotozoal agents, anthelmintics, antineoplastic agents, immunomodulators, anti-hypercholesterolemic agents, and combinations thereof.

29. A method of producing the compound of any one of claims 1-21, comprising culturing a bacterial cell belonging to the class β -proteobacteria in a culture medium, wherein the culture medium comprises an assimilable carbon source, nitrogen source, and inorganic salts under aerobic conditions, thereby producing the compound.

30. The method of claim 29, further comprising isolating the compound.

31. A compound according to any one of claims 1 to 21, when manufactured according to a process of claim 29 or 30.

32. A method of treating a disorder in a subject in need thereof, the method comprising administering to the subject an effective amount of the compound of any one of claims 1-21, thereby treating the disorder in the subject.

33. The method of claim 32, wherein the subject is selected from the group consisting of an animal and a plant.

34. The method of claim 33, wherein the animal is a mammal.

35. The method of claim 34, wherein the mammal is a human or a livestock.

36. The method of any one of claims 32-35, wherein the disorder is caused by a pathogen selected from the group consisting of: bacteria, fungi, viruses, protozoa, helminths, parasites, and combinations thereof.

37. The method of claim 36, wherein the pathogen is a bacterium.

38. The method of claim 37, wherein the bacteria is a gram positive bacteria.

39. The method of claim 38, wherein the gram-positive bacterium belongs to a genus selected from the group consisting of: streptococcus (Streptococcus), Staphylococcus (Staphylococcus), enterococcus (Enterococcus), Corynebacterium (Corynebacterium), Listeria (Listeria), Bacillus (Bacillus), Erysipelothrix (Erysipelothrix), Mycobacterium (Mycobacterium), Clostridium (Clostridium) and Actinomycetes (Actinomycetes).

40. The method of claim 38, wherein the gram-positive bacterium is of a genus or species selected from the group consisting of: methicillin-sensitive and methicillin-resistant staphylococci (including Staphylococcus aureus (Staphylococcus aureus), Staphylococcus epidermidis (Staphylococcus epidermidis), Staphylococcus hemolyticus (Staphylococcus aureus), Staphylococcus hominis (Staphylococcus hominis), Staphylococcus saprophyticus (Staphylococcus saprophyticus), and Staphylococcus coagulase-negative), Staphylococcus aureus (Staphylococcus aureus) (GISA) with intermediate sensitivity in glycopeptides, Streptococcus mutans and penicillin-resistant streptococci (including Streptococcus pneumoniae (Streptococcus pneumoniae), Streptococcus pyogenes (Streptococcus pyogenicus), Streptococcus agalactiae (Streptococcus agalactiae), Streptococcus dysgalactiae (Streptococcus mutans), Streptococcus mutans (Streptococcus mutans Streptococcus bovis (Streptococcus mutans), Streptococcus mutans (Streptococcus mutans), Streptococcus agalactis (Streptococcus mutans C), Streptococcus constellae (Streptococcus mutans C), Streptococcus mutans group Streptococcus mutans, Streptococcus mutans C (Streptococcus mutans), Streptococcus mutans Streptococcus mutans group Streptococcus mutans, Streptococcus mutans C (Streptococcus mutans), Streptococcus mutans C (Streptococcus mutans), Streptococcus mutans, Streptococcus mutan, Group G streptococci and Green Streptococci (Viridansstreptococci)), enterococci (including vancomycin-sensitive and vancomycin-resistant strains such as Enterococcus faecalis (Enterococcus faecalis) and Enterococcus faecium (Enterococcus faecalis)), Clostridium difficile (Clostridium difficile), Clostridium clostridiforme (Clostridium clostridiforme), Clostridium avirulent (Clostridium innoccum), Clostridium capsular (Clostridium perfringens), Clostridium tetanium (Clostridium tetanium), Mycobacterium tuberculosis (Mycobacterium berculosis), Mycobacterium avium (Mycobacterium avium), Mycobacterium intracellulare (Mycobacterium lucellum), Mycobacterium guanidium (Mycobacterium kansui), Mycobacterium gordonii (Mycobacterium tuberculosis), Mycobacterium tuberculosis (Mycobacterium monomyceliophyte), Mycobacterium tuberculosis (Mycobacterium monomyceliophthora), Mycobacterium tuberculosis (Corynebacterium, Mycobacterium monomyceliophthora (Corynebacterium), Mycobacterium tuberculosis (, staphylococcus wowensis (Staphylococcus aureus) and Actinomyces schoenlei (Actinomyces israelli).

41. The method of claim 37, wherein the bacterium is Bacillus anthracis (Bacillus anthracensis).

42. The method of claim 37, wherein the bacteria is a gram-negative bacteria.

43. The method of claim 42, wherein the gram-negative bacterium belongs to a genus or species selected from the group consisting of: helicobacter pylori (Helicobacter pylori), Legionella pneumophila (Legionella pneumoniae), Neisseria gonorrhoeae), Neisseria meningitidis (Neisseria meningitidis), Campylobacter sporozoites (Campylobacter spontes), Haemophilus influenzae (Haemophilus influezae), Pseudomonas aeruginosa (Pseudomonas aeruginosa), Enterobacter aerogenes (Enterobacter prognostiens), Enterobacter cloacae (Enterobacter cloacae), Klebsiella pneumoniae (Klebsiella pneumoniae), Klebsiella oxytoca (Klebsiella oxytoca), Pasteurella multocida (Pasteurella Pasteurella), Salmonella Bacteroides sp (Salmonella typhimurium), Salmonella typhimurium (Salmonella typhimurium), salmonella arizona (Salmonella arizona), Salmonella bisarizona (Salmonella adiazolizonae), Salmonella hatoni (Salmonella houtenae), Salmonella bangolensis (Salmonella aborgo), Salmonella indonesia (Salmonella indica), Salmonella enteritidis (Salmonella enteritidis), Salmonella typhi (Salmonella typhi) and Citrobacter freundii (Citrobacter und).

44. The method of claim 36, wherein the pathogen is a virus.

45. The method of claim 44, wherein the virus is selected from the group consisting of: the family of Retroviridae (Retroviridae), the family of Picornaviridae (Picornaviridae), the family of caliciviridae (Calciviridae), the family of Togaviridae (Togaviridae), the family of flaviviridae (flaveridae), the family of Coronaviridae (Coronaviridae), the family of Rhabdoviridae (Rhabdoviridae), the family of Filoviridae (Filoviridae), the family of Paramyxoviridae (Paramyxoviridae), the family of Orthomyxoviridae (Orthomyxoviridae), the family of bunyaviridae (bunaviridae), the family of Arenaviridae (Arenaviridae), the family of Reoviridae (Reoviridae), the family of Birnaviridae (Birnaviridae), the family of Hepadnaviridae (Hepadnaviridae), the family of Parvoviridae (partoviridae), the family of Papovaviridae (povaciviridae), the family of picoviridae (poriviridae), the family of Herpesviridae (Herpesviridae), the family of adenoviruses (adnaviridae), and the family of iridae (Herpesviridae).

46. The method of claim 44, wherein the virus is selected from the group consisting of: influenza virus, human immunodeficiency virus and herpes simplex virus.

47. The method of claim 36, wherein the pathogen is a protozoan.

48. The method of claim 47, wherein the protozoa is selected from the group consisting of: trichomonas vaginalis (Trichomonas vaginalis), Giardia lamblia (Giardia lamblia), Entamoeba histolytica (Entamoeba histolytica), Balantis coli (Balattidium coli), Cryptosporidium microfine (Cryptosporidium parvum) and Isosporidium Belleville (Isosporidium belli), Trypanosoma cruzi (Trypansoma cruzi), Trypanosoma gambiae (Trypanosoma gambiense), Leishmania donovani (Leishmania donovani) and Freund's graciliate anamorpha (Naegria fool).

49. The method of claim 36, wherein the pathogen is a helminth.

50. The method of claim 49, wherein the helminth is selected from the group consisting of: schistosoma mansoni (Schistosoma mansoni), Schistosoma cercaria (Schistosoma cercariae), Schistosoma japonicum (Schistosoma japonicum), Schistosoma japonicum (Schistosoma mekongi), Schistosoma japonicum (Schistosoma hempri), human ascaris (Ascarimbucoides), Strongyloides stercoralis, Echinococcus granulosus (Echinococcus granulosus), Echinococcus polyacticola (Echinococcus multilocularis), Microcysticercus guanicus (Angiostrongylus cannensis), Ostertagineus atrophaeus (Angiostrongylus canthus lanensis), Ostertagia ridgelica (Angiostrongylus constatristictus), Sphaeformis brunaeus (Fangoniensis), Schistosoma fascicularis (Schistosoma), Schistosoma nervus fascicularis (Schistosoma), Schistosoma japonicum neria occidentalis), Schistosoma neria calis (Toxoides), Schistosoma neria californica neri), Schistosoma neraria and Schistosoma neria gibba (Toxoides), Schistosoma nervoides (Toxoides).

51. The method of claim 36, wherein the pathogen is a parasite.

52. The method of claim 51, wherein the parasite is selected from the group consisting of: plasmodium falciparum (Plasmodium falciparum), Plasmodium yoelii (Plasmodium yoelli), Sphaerotheca Brachycarpa (Hymenolepis na), Clonorchis sinensis (Clonorchis sinensis), Ardisia rosea (Loa Loa), Paragonimus westermani (Paragonimswestmann), Fasciola hepatica (Fasciola hepatica) and Toxoplasma gondii (Toxoplasma gondii).

53. The method of claim 51, wherein the pathogen is Plasmodium.

54. The method of claim 36, wherein the pathogen is a fungus.

55. The method of claim 54, wherein the fungus is selected from the group consisting of: cryptococcus neoformans (Cryptococcus neoformans), Histoplasma capsulatum (Histoplasma capsulatum), Coccidioides immitis (Coccidioides), Blastomyces dermatitidis (Blastomyces dermatitidis), Chlamydia trachomatis (Chlamydia trachomatis), Candida albicans (Candida albicans), Candida tropicalis (Candida tropicalis), Candida glabrata (Candida glabrata), Candida krusei (Candida krusei), Candida parapsilosis (Candida parapsilosis), Candida dubinanensis (Candida duculiginis), Candida viticola (Candida albicans), Epidermophytoides (Epidermophytophysum), Microsporum austenitalis (Microsporum aunidii), Microsporum canis (Microsporum canis), Microsporum (Microsporum Microsporum), Microsporum microsporhium, Microsporum caninum, Microsporum Microsporum, Microsporum canis (Microsporum), Microsporum Microsporum, Microsporum neospora canis, Microsporum Microsporum, Microsporum (Microsporum), microsporum dwarfis (Microsporum annum), Microsporum persicae (Microsporum persicum), Trichophyton angustifolia (Trichophyton ajelloi), Trichophyton mentagrophytes (Trichophyton mentagrophytes), Trichophyton equi (Trichophyton equi), Trichophyton glaucophytes (Trichophyton flaves), Trichophyton phototrophyton (Trichophyton glacias), Trichophyton glaucophytes (Trichophyton glaucophytes), Trichophyton Trichophyton (Trichophyton trichophytes), Trichophyton mentagrophytes (Trichophyton trichophytes), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton rubrum), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton, aspergillus flavus (Aspergillus flavus) and Aspergillus clavatus (Aspergillus clavatus).

56. A method of inhibiting the growth of an infectious agent, the method comprising contacting the infectious agent with the compound of any one of claims 1-21, thereby inhibiting the growth of the infectious agent.

57. The method of claim 56, wherein said infectious agent is cultured in vitro.

58. A method of inhibiting peptidoglycan synthesis in a bacterial cell, the method comprising contacting the bacterial cell with the compound of any one of claims 1-21, thereby inhibiting peptidoglycan synthesis in the bacterial cell.

Background

In modern medicine, the development and successful use of antimicrobial agents against disease-causing microorganisms is a great achievement. Antimicrobial agents save countless lives and reduce many of the complications of disease and infection. However, currently available antimicrobial agents are not as effective as they were once used.

Over time, many microorganisms have developed various ways to circumvent the antimicrobial effects of known antimicrobial agents, and in recent years, infections caused by microorganisms resistant to various antimicrobial agents have increased worldwide. With the increasing availability and convenience of global travel, the rapid spread of drug-resistant microorganisms throughout the world will become a serious problem. In the community, microbial resistance can be caused by the following reasons: hospitals acquire drug resistant pathogens (e.g., methicillin-resistant staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE)), develop drug resistance due to the use of antibiotics in the community (e.g., penicillin and quinolone resistant neisseria), acquire resistant pathogens due to travel (e.g., antibiotic resistant shigella), or subsequently transmit resistant pathogens to humans due to the use of antimicrobials in animals (e.g., antibiotic resistant salmonella). Antibiotic resistance in hospitals is often caused by overuse of antibiotics, and has become a serious problem due to MRSA, VRE, and multidrug resistant gram negative bacillus (MDR-GNB) (e.g., enterobacter, klebsiella, serratia, citrobacter, pseudomonas, and escherichia). In particular, catheter-related bloodstream infections and Skin and Soft Tissue Infections (SSTIs) caused by bacteria are becoming an increasingly serious problem.

Bacteria, viruses, fungi and parasites all develop resistance to known antimicrobial agents. Resistance is generally caused by three mechanisms: (i) changing the drug target such that the antimicrobial agent binds poorly, thereby reducing the effect of controlling infection; (ii) reduced drug access to the target due to impaired drug permeability or active drug efflux; and (iii) the drug is enzymatically inactivated by enzymes produced by the microorganism. Antimicrobial resistance provides a survival advantage to microorganisms and makes it more difficult to eliminate microbial infections from the body. Increased difficulty in combating microbial infections leads to an increased risk of infection occurring in hospitals and other settings. Diseases such as tuberculosis, malaria, gonorrhea and childhood ear infections are now more difficult to treat than just a few decades ago. Drug resistance is a significant problem in hospitals that receive critically ill patients who are nearly unable to fight infection without the aid of antibiotics. Unfortunately, the extensive use of antibiotics in these patients selects for changes in the microbes with drug resistance. These resistant bacteria are resistant to our strongest antibiotics and continue to plague susceptible hospital patients. It has been reported that 5 to 10% of patients admitted to hospitalization acquire infection during their hospitalization, and this risk steadily rises in the last decade.

In view of these problems, there is an urgent need for new antimicrobial agents that combat the problems of microbial infection and increasing resistance to drugs. Refocusing the discovery of antimicrobial drugs is critical, as pathogens are developing resistance to the drugs now available.

Despite the combination of efforts in combinatorial synthesis, high throughput screening, advanced medicinal chemistry, genomics and proteomics, and rational drug design, synthetic compounds have heretofore failed to replace natural antibiotics and produce a new broad spectrum of compound types. The problems with obtaining new synthetic antibiotics may be related in part to the fact that synthetic antibiotics are always pumped out by multidrug resistance pumps (MDRs) across the bacterial outer membrane barrier. The bacterial outer membrane is a barrier to amphiphilic compounds (substantially all drugs are amphiphilic compounds) and MDR drives out drugs across this barrier. Biological evolution has produced antibiotics that can largely bypass this dual barrier/eviction mechanism, but synthetic compounds almost always fail.

Disclosure of Invention

Thus, the present invention provides novel antimicrobial compounds that are resistant to microbial infections to overcome the growing problem of resistance. In some embodiments, the present invention provides an isolated compound of formula (I):

or an enantiomer, diastereomer, tautomer, or pharmaceutically acceptable salt thereof, wherein:

each stereocenter is denoted by "+" and may independently be in the R or S configuration;

each R_1’、R_2’、R_3’、R_4’、R_5’And R_6’Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstitutedAlkynyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, substituted or unsubstituted aryl, -NR_bR_b’、-COR_c、-COOR_d、–CONR_eR_e’And an amino acid side chain;

wherein each R_a、R_a’、R_b、R_b’、R_c、R_d、R_eAnd R_e’Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, and substituted or unsubstituted aryl;

x is-O-, -S-or-N-; and is

n is an integer of 1 to 5. In some embodiments, n is an integer from 2 to 4.

In a particular embodiment, X is-O-. In another specific embodiment, X is-N-. In yet another specific embodiment, X is-S-.

In some aspects, the isolated compound is a compound of formula (II):

or an enantiomer, diastereomer, tautomer, or pharmaceutically acceptable salt thereof, wherein

Each stereocenter is denoted by "+" and may independently be in the R or S configuration;

each R₁、R₂、R₃、R₄、R₅、R₆、R₇And R₈Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, substituted or unsubstituted aryl, -NR_bR_b’、-COR_c、-COOR_d、–CONR_eR_e’And an amino acid side chain;

wherein each R_b、R_b’、R_c、R_d、R_e、R_e’、R_fAnd R_f’Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, and substituted or unsubstituted aryl; and is

X is-O-, -S-or-N-.

In a particular embodiment, X is-O-. In another specific embodiment, X is-N-. In yet another specific embodiment, X is-S-.

In some aspects, R₁Is benzyl. In some aspects, R_aAnd R_a’Are all hydrogen. In some aspects, R₂Is a substituted or unsubstituted alkyl group. In a particular aspect, the substituted or unsubstituted alkyl is isobutyl.

In some embodiments, R₃Is a substituted or unsubstituted alkyl group, for example, an amino-substituted butyl group. In some embodiments, R₄Is a substituted or unsubstituted alkyl group, such as a hydroxy-substituted methyl group. In some aspects, R₅is-CONR_eR_e’. In a further aspect, R_eAnd R_e’Are all hydrogen. In some embodiments, R₆Is a substituted or unsubstituted alkyl group, such as methyl. In some aspects, R₇Is a substituted or unsubstituted alkyl group, such as isobutyl. In some aspects, R₈Is a substituted or unsubstituted alkyl group, such as isobutyl.

In some embodiments, the isolated compound is a compound of formula (III):

in some embodiments, the isolated compound of the present invention is selected from the group consisting of:

in some aspects, the invention provides a medium comprising a compound of the invention as described above. In a further aspect, the medium further comprises bacterial cells belonging to the class β -proteobacteria.

In some embodiments, the present invention also provides a bacterial lysate comprising a compound of the present invention as described above. In a further aspect, the bacterial lysate is produced by bacterial cells belonging to the class β -proteobacteria. In some aspects, the bacterial cell is a cultured bacterial cell.

In some embodiments, the present invention also provides a pharmaceutical composition comprising a compound of the present invention as described above, and a pharmaceutically acceptable excipient, carrier or diluent. In some embodiments, the pharmaceutical composition further comprises an agent selected from the group consisting of: antibiotics, antifungal agents, antiviral agents, antiprotozoal agents, anthelmintics, antineoplastic agents, immunomodulators, anti-hypercholesterolemic agents, and combinations thereof.

In some embodiments, the invention also encompasses a method of producing a compound of the invention as described above by culturing a bacterial cell belonging to the class β -proteobacteria in a culture medium, wherein the culture medium comprises an assimilable carbon source, nitrogen source and inorganic salts under aerobic conditions, thereby producing the compound. In further embodiments, the method further comprises isolating the compound.

In some embodiments, the invention also provides a compound prepared according to the method described above, for example a compound of formula (I).

In some aspects, the invention also provides a method of treating a disorder in a subject in need thereof, comprising administering to the subject an effective amount of a compound of the invention as described above, thereby treating the disorder in the subject.

In some embodiments, the subject is selected from an animal and a plant. In a further aspect, the animal is a mammal. Such as humans or livestock.

In some aspects, the disorder is caused by a pathogen selected from the group consisting of: bacteria, fungi, viruses, protozoa, helminths, parasites, and combinations thereof.

In one aspect, the pathogen is a bacterium. In a further aspect, the bacterium is a gram-positive bacterium, for example a gram-positive bacterium belonging to a genus selected from the group consisting of: streptococcus (Streptococcus), Staphylococcus (Staphylococcus), enterococcus (Enterococcus), Corynebacterium (Corynebacterium), Listeria (Listeria), Bacillus (Bacillus), Erysipelothrix (Erysipelothrix), Mycobacterium (Mycobacterium), Clostridium (Clostridium) and Actinomycetes (Actinomycetes). In some aspects, the gram-positive bacterium belongs to a genus or species selected from: methicillin-sensitive and methicillin-resistant staphylococci (including Staphylococcus aureus (Staphylococcus aureus), Staphylococcus epidermidis (Staphylococcus epidermidis), Staphylococcus haemolyticus (Staphylococcus haemolyticus), Staphylococcus hominis (Staphylococcus hominis), Staphylococcus saprophyticus (Staphylococcus saprophyticus) and Staphylococcus coagulase-negative), Staphylococcus aureus (Staphylococcus aureus) (GISA) with intermediate sensitivity in glycopeptides, Streptococcus mutans (GISA), Streptococcus mutans and penicillin-resistant streptococci (including Streptococcus pneumoniae (Streptococcus pneumoniae), Streptococcus pyogenes (Streptococcus pyogenus), Streptococcus agalactiae (Streptococcus mutans), Streptococcus dysgalactiae (Streptococcus mutans), Streptococcus mutans (Streptococcus mutans Streptococcus bovis (Streptococcus mutans), Streptococcus mutans (Streptococcus mutans C), Streptococcus mutans (Streptococcus mutans C (Streptococcus mutans), Streptococcus mutans Streptococcus constellactis (Streptococcus mutans group C), Streptococcus mutans Streptococcus mutans (Streptococcus mutans), Streptococcus mutans C (Streptococcus mutans), Streptococcus mutans C (Streptococcus mutans), Streptococcus mutans, group G streptococci and Green Streptococci (Viridans streptococci)), enterococci (including vancomycin-sensitive and vancomycin-resistant strains such as Enterococcus faecalis (Enterococcus faecalis) and Enterococcus faecium (Enterococcus faecalis)), Clostridium difficile (Clostridium difficile), Clostridium clostridia (Clostridium clostridia), Clostridium avirulent (Clostridium incuum), Clostridium perfringens (Clostridium perfringens), Clostridium tetanium (Clostridium tetani), Clostridium tetani (Clostridium tetani), Mycobacterium tuberculosis (Mycobacterium tuberculosis), Mycobacterium avium (Mycobacterium avium), Mycobacterium intracellulare (Mycobacterium intracellulare), Mycobacterium gallinarum (Mycobacterium kansui), Mycobacterium gordonii (Mycobacterium tuberculosis), Mycobacterium tuberculosis (Corynebacterium), Bacillus subtilis), Bacillus megaterium (Corynebacterium glutamicum), Bacillus subtilis), Bacillus megaterium (Corynebacterium glutamicum), Bacillus gordonii (Corynebacterium), Bacillus subtilis (Corynebacterium glutamicum), Bacillus subtilis (Corynebacterium), Bacillus megaterium (Corynebacterium glutamicum), Bacillus subtilis (Corynebacterium glutamicum (Corynebacterium), Bacillus subtilis), Bacillus megaterium (Corynebacterium glutamicum (Corynebacterium), Bacillus subtilis (Corynebacterium), Bacillus subtilis), Bacillus megaterium (Corynebacterium glutamicum (Corynebacterium), Bacillus subtilis), Bacillus megaterium (Corynebacterium glutamicum (Corynebacterium), Bacillus subtilis (Corynebacterium glutamicum (Corynebacterium, erysipelothrix rhusiopathiae (Erysipelothrix), Staphylococcus wowensis (Staphylococcus aureus) and Actinomyces israelli (Actinomyces israelli).

In a particular embodiment, the bacterium is Bacillus anthracis (Bacillus anthracensis).

In some embodiments, the bacterium is a gram-negative bacterium, for example a gram-negative bacterium belonging to a genus or species selected from: helicobacter pylori (Helicobacter pylori), legionella pneumophila (Legionella), Neisseria gonorrhoeae), Neisseria meningitidis (Neisseria meningitidis), pathogenic Campylobacter sporozoites (Campylobacter spontes), Haemophilus influenzae (Haemophilus influezae), Pseudomonas aeruginosa (Pseudomonas aeruginosa), Enterobacter aerogenes (Enterobacter prognostiens), Enterobacter cloacae (Enterobacter cloacae), Klebsiella pneumoniae (Klebsiella pneumoniae), Klebsiella oxytoca (Klebsiella oxytoca), Pasteurella multocida (Paulospora lactis), Salmonella sporozoea (Salmonella sporozoensis), Salmonella typhimurium (Salmonella typhimurium), Salmonella typhimurii (Salmonella typhimurium), Salmonella typhimurium (Salmonella typhimurium), salmonella arizona (Salmonella arizona), Salmonella bisarizona (Salmonella diaparizona), Salmonella hatoni (Salmonella houtenae), Salmonella bangolensis (Salmonella bongori), Salmonella indiana (Salmonella indica), Salmonella Enteritidis (Salmonella Enteritidis), Salmonella typhi (Salmonella typhi) and Citrobacter freundii (Citrobacter reundii).

In some aspects, the pathogen is a virus, for example a virus selected from the group consisting of: the family of Retroviridae (Retroviridae), the family of Picornaviridae (Picornaviridae), the family of caliciviridae (Calciviridae), the family of Togaviridae (Togaviridae), the family of flaviviridae (flaveridae), the family of Coronaviridae (Coronaviridae), the family of Rhabdoviridae (Rhabdoviridae), the family of Filoviridae (Filoviridae), the family of Paramyxoviridae (Paramyxoviridae), the family of Orthomyxoviridae (Orthomyxoviridae), the family of bunyaviridae (bunaviridae), the family of Arenaviridae (Arenaviridae), the family of Reoviridae (Reoviridae), the family of Birnaviridae (Birnaviridae), the family of Hepadnaviridae (Hepadnaviridae), the family of Parvoviridae (partoviridae), the family of Papovaviridae (povaciviridae), the family of picoviridae (poriviridae), the family of Herpesviridae (Herpesviridae), the family of adenoviruses (adnaviridae), and the family of iridae (Herpesviridae). In further embodiments, the virus is selected from the group consisting of: influenza virus, human immunodeficiency virus and herpes simplex virus.

In some aspects, the pathogen is a protozoan, for example a protozoan selected from the group consisting of: trichomonas vaginalis (Trichomonas vaginalis), Giardia lamblia (Giardia lamblia), Entamoeba histolytica (Entamoeba histolytica), Pacific Chaetoceros colophonus (Ballantium coli), Cryptosporidium microfine (Cryptosporidium parvum) and Isosporidium Belleville (Isosporium belli), Trypanosoma cruzi (Trypanosoma cruzi), Trypanosoma gambiae (Trypanosoma gambiense), Leishmania donovani (Leishmania donovani) and Freund's graciliate-resistant Trypanosoma (Naegria fowl).

In some embodiments, the pathogen is a helminth, for example a helminth selected from the group consisting of: schistosoma mansoni (Schistosoma mansoni), Schistosoma cercaria (Schistosoma cercariae), Schistosoma japonicum (Schistosoma japonicum), Schistosoma japonicum (Schistosoma mekongi), Schistosoma japonicum (Schistosoma hempri), human Ascaris (Ascaris lucridoides), Strongyloides stercoralis, Echinococcus granulosus (Echinococcus grandis), Echinococcus multilocularis (Echinococcus multilocularis), Microcysticercus cantonensis (Angiostrongylus cannensis), Ostertagia carinatus (Angiostrongylus cantonensis), Ostertagia ridgericoides (Angiostrongylus constatristictus), Ostertagensis (Ostertagia punctatus), Ostertagia fasciata (Farlington), Schistosoma brunaeus wensis (Schistosoma), Schistosoma japonicum neria calis versicolor (Schistosoma), Schistosoma japonicum neria (Schistosoma), Schistosoma neria calis (Schistosoma), Schistosoma japonicum (Toxoma), Schistosoma neria occidentalis), Schistosoma neraria and Schistosoma (Toxoma), Schistosoma nervoides (Toxoma), Schistosoma nerogrisora spp).

In some aspects, the pathogen is a parasite, for example a parasite selected from the group consisting of: plasmodium falciparum (Plasmodium falciparum), Plasmodium yoelii (Plasmodium yoelli), Basidiomycetes (Hymenolepisana), Clonorchis sinensis (Clonorchis sinensis), Sirofilaria rosea (Loa Loa), Paragonimus westernani (Paragonimus westernmani), Fasciola hepatica (Fasciola hepatica) and Toxoplasma gondii (Toxoplasma grandiii). In a further aspect, the pathogen is plasmodium.

In some embodiments, the pathogen is a fungus, for example a fungus selected from the group consisting of: cryptococcus neoformans (Cryptococcus neoformans), Histoplasma capsulatum (Histoplasma capsulatum), Coccidioides immitis, Blastomyces dermatitidis (Blastomyces dermatitidis), Chlamydia trachomatis (Chlamydia trachomatis), Candida albicans (Candida albicans), Candida tropicalis (Candida tropicalis), Candida glabrata (Candida glabrata), Candida krusei (Candida krusei), Candida parapsilosis (Candida parapsilosis), Candida dubinata (Candida duculiginensis), Candida vitis (Candida lucitaceae), Epidermophyton (Epidermophytococcus floccosum), Microsporum austenitalis (Microsporum audonii), Microsporum canis (Microsporum canis), Microsporum (Microsporum Microsporum), Microsporum microsporhium, Microsporum caninum, Microsporum carotoviridans (Microsporum), Microsporum Microsporum, Microsporum Microsporum, microsporum dwarfis (Microsporum annum), Microsporum persicae (Microsporum persicum), Trichophyton angustifolia (Trichophyton ajelloi), Trichophyton mentagrophytes (Trichophyton mentagrophytes), Trichophyton equi (Trichophyton equi), Trichophyton glaucophytes (Trichophyton flaves), Trichophyton phototrophyton (Trichophyton glacias), Trichophyton glaucophytes (Trichophyton glaucophytes), Trichophyton Trichophyton (Trichophyton trichophytes), Trichophyton mentagrophytes (Trichophyton trichophytes), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton rubrum), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton, aspergillus flavus (Aspergillus flavus) and Aspergillus clavatus (Aspergillus clavatus).

In some aspects, the invention also provides a method of inhibiting the growth of an infectious agent comprising contacting the infectious agent with a compound of the invention as described above. In some aspects, the infectious agent is cultured in vitro.

In some embodiments, the present invention also provides a method of inhibiting peptidoglycan synthesis in a bacterial cell comprising contacting the bacterial cell with a compound of the present invention as described above.

Drawings

FIG. 1 is a bar graph showing the average bacterial colony counts (in average log) in a thigh infection model of neutropenic mice infected with Staphylococcus aureus ATCC 33591 and treated with a compound of the invention and vancomycin₁₀CFU/g thigh).

Detailed Description

The present invention relates generally to novel depsipeptides, methods for preparing said novel depsipeptides, pharmaceutical compositions comprising said novel depsipeptides and methods of using said novel depsipeptides to treat or inhibit various disorders (e.g., bacterial infections). The present invention relates to novel antibiotics with broad activity against a number of bacterial pathogens, including strains resistant to other antibiotics, particularly gram-positive pathogens. The compounds disclosed herein have advantageous bioavailability and lower toxicity.

Definition of

For convenience, some terms used in the specification, examples, and appended claims are collected here. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Unless otherwise indicated, the initial definitions provided for a group or term herein apply to the group or term alone or as part of another group throughout the specification.

The articles "a" and "an" are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. For example, "an element" means one element or more than one element.

As used herein, the term "or" means the term "and/or," and is used interchangeably therewith, unless the context clearly indicates otherwise.

The term "substantially identical" as used herein means that two comparison objects have at least 90% of a common characteristic. In certain embodiments, the common characteristic of the two subjects is at least 95%. In certain other embodiments, the common characteristic of the two objects is at least 99%.

The term "isolated" as used herein refers to a compound of the present invention that is substantially free of other materials with which it is associated in its natural environment. For example, an isolated compound may be substantially free of contaminating material, such as cellular material or contaminating material from the cell from which the compound is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized. Substantially free of other materials typically means, for example, less than about 30%, or 20%, or 15%, or 10%, or 5%, or 2% (by dry weight) of impurities. In some embodiments, the isolated compound is substantially pure. In some embodiments, a preparation of a compound having less than about 10% (by dry weight) of contaminating substances or chemical precursors from cells is considered substantially pure. In other embodiments, a preparation of a compound having less than about 5%, about 4%, about 3%, about 2%, about 1% (by dry weight) of contaminating material or chemical precursor from a cell is considered substantially pure.

Unless otherwise indicated, any heteroatom having a valence that does not satisfy is considered to have a hydrogen atom sufficient to satisfy the valence.

The term "heating" includes, but is not limited to, warming by conventional heating (e.g., electrical heating, steam heating, gas heating, etc.) as well as microwave heating.

The term "pharmaceutically acceptable excipient, carrier or diluent" as used herein refers to a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting a subject agent from one organ or portion of the body to another organ or portion of the body. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.

The term "treating" with respect to a subject refers to ameliorating at least one symptom of a disorder in the subject. The treatment can be a cure of the disorder or condition, or an improvement in the disorder or condition.

Unless the context clearly dictates otherwise, the term "disorder" as used herein refers to, and is used interchangeably with, the term disease, condition or pathology.

The term "microorganism" as used herein refers to an organism, such as a bacterium, virus, protozoan or fungus, especially an organism that transmits a disease.

The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings, animals, and plants without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

Throughout the specification, groups and substituents thereof may be selected to provide stable moieties and compounds.

Compounds of the invention

In some embodiments, the present teachings relate to an isolated compound of formula (I):

or an enantiomer, diastereomer, tautomer, or pharmaceutically acceptable salt thereof, wherein:

each stereocenter is denoted by "+" and may independently be in the R or S configuration;

each R_1’、R_2’、R_3’、R_4’、R_5’And R_6’Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, substituted or unsubstituted aryl, -NR_bR_b’、-COR_c、-COOR_d、–CONR_eR_e’And an amino acid side chain;

wherein each R_a、R_a’、R_b、R_b’、R_c、R_d、R_eAnd R_e’Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, and substituted or unsubstituted aryl;

x is-O-, -S-or-N-; and is

n is an integer of 1 to 5.

In a particular embodiment, X is-O-. In another specific embodiment, X is-N-. In yet another specific embodiment, X is-S-.

In one embodiment, n is an integer from 1 to 2. In one embodiment, n is an integer from 2 to 3. In another embodiment, n is an integer from 3 to 4. In yet another embodiment, n is an integer from 4 to 5. In some embodiments, n is 1, 2, 3, 4, or 5.

In some embodiments, the amino acid side chain is a natural amino acid side chain. In other embodiments, the amino acid side chain is a non-natural amino acid side chain.

In some embodiments, R_aAnd R_a’Are all hydrogen.

In some embodiments, R_bAnd R_b’Are all hydrogen.

In some embodiments, R_eAnd R_e’Are all hydrogen.

In some embodiments, the present teachings relate to an isolated compound of formula (II):

or an enantiomer, diastereomer, tautomer, or pharmaceutically acceptable salt thereof, wherein:

each stereocenter is denoted by "+" and may independently be in the R or S configuration;

each R₁、R₂、R₃、R₄、R₅、R₆、R₇And R₈Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, substituted or unsubstituted aryl, -NR_bR_b’、-COR_c、-COOR_d、–CONR_eR_e’And an amino acid side chain;

wherein each R_b、R_b’、R_c、R_d、R_e、R_e’、R_fAnd R_f’Independently selected from: hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl, and substituted or unsubstituted aryl; and is

X is-O-, -S-or-N-.

In a particular embodiment, X is-O-. In another specific embodiment, X is-N-. In yet another specific embodiment, X is-S-.

In some examples, X is-O-and R_fAnd R_f’Are all hydrogen.

In some examples, R₁May be a benzyl group. In some examples, R₂And may be a substituted or unsubstituted alkyl group such as methyl, ethyl, propyl, isopropyl, butyl or isobutyl. In a particular embodiment, R₂Is an isobutyl group.

In some examples, R₃And may be substituted or unsubstituted alkyl, such as amino substituted butyl. In some examples, R₄And may be substituted or unsubstituted alkyl, such as hydroxy-substituted methyl. In some examples, R₅May be substituted or unsubstituted alkyl, e.g. methyl, ethyl, propyl, isopropyl, butyl or isobutyl, or-CONR_eR_e’. In one aspect, R₅Is methyl. In another aspect, R₅is-CONR_eR_e’And R is_eAnd R_e’Are all hydrogen.

In some aspectsIn the face of R₆And may be a substituted or unsubstituted alkyl group such as methyl, ethyl, propyl, isopropyl, butyl or isobutyl. In a particular embodiment, R₂Is methyl. In some examples, R₇And may be a substituted or unsubstituted alkyl group such as methyl, ethyl, propyl, isopropyl, butyl or isobutyl. In a particular embodiment, R₇Is an isobutyl group. In some examples, R₈And may be a substituted or unsubstituted alkyl group such as methyl, ethyl, propyl, isopropyl, butyl or isobutyl. In a particular embodiment, R₈Is an isobutyl group.

In some embodiments, R₁、R₂、R₃、R₄、R₅、R₆、R₇And R₈Each may independently be an amino acid side chain, such as a D-amino acid side chain or an L-amino acid side chain. The amino acid side chain can be a natural amino acid chain, such as an alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, or valine side chain. The amino acid side chain can also be a side chain of a non-natural amino acid, such as the side chain of any non-natural amino acid known in the art. Non-limiting examples of unnatural amino acid side chains include, for example, the unnatural amino acid side chains listed in the Sigma-Aldrich catalog, which is incorporated by reference herein in its entirety. In one embodiment, the unnatural amino acid side chain can be β -hydroxyglutamine.

For example, in some embodiments, R₁May be a phenylalanine (e.g., D-phenylalanine or L-phenylalanine) side chain. In some examples, R₂、R₇Or R₈May be a leucine (e.g., D-leucine or L-leucine) side chain. In some examples, R₃May be a lysine (e.g., D-lysine or L-lysine) side chain. In some examples, R₄Can be a serine (e.g., D-serine or L-serine) side chain. In some instances, it is desirable to have,R₆may be an alanine (e.g., D-alanine or L-alanine) side chain.

In some embodiments, R_bAnd R_b’Are all hydrogen. In some embodiments, R_eAnd R_e’Are all hydrogen. In some embodiments, R_fAnd R_f’Are all hydrogen.

The term "alkyl" refers to a straight or branched chain aliphatic group containing 1 to 12 carbon atoms (e.g., 1 to 6 carbon atoms for straight chain or 3 to 6 carbon atoms for branched chain). Exemplary "alkyl" groups include methyl, ethyl, propyl, isopropyl, n-butyl, t-butyl, isobutyl, pentyl, hexyl, isohexyl, heptyl, 4-dimethylpentyl, octyl, 2, 4-trimethylpentyl, nonyl, decyl, undecyl, dodecyl and the like.

The term "alkenyl" refers to a straight or branched chain hydrocarbon group containing 2 to 12 carbon atoms (e.g., 2 to 6 carbon atoms for straight chain or 3 to 6 carbon atoms for branched chain) and at least one carbon-carbon double bond. Exemplary "alkenyl" groups include ethenyl, propenyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl, and the like.

The term "alkynyl" refers to a straight or branched chain hydrocarbon group containing 2 to 12 carbon atoms (e.g., 2 to 6 carbon atoms for straight chain or 3 to 6 carbon atoms for branched chain) and at least one carbon-carbon triple bond. Exemplary such groups include ethynyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl, and the like.

The term "cycloalkyl" refers to a fully saturated cyclic hydrocarbon group containing 1 to 4 rings and 3 to 8 carbons per ring. Exemplary such groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, and the like. The term "cycloalkyl" also encompasses cycloalkyl groups that may further comprise oxygen, nitrogen, sulfur, or phosphorus atoms substituted for one or more carbons of the hydrocarbon backbone.

The term "cycloalkenyl" refers to partially unsaturated cyclic hydrocarbon groups containing from 1 to 4 rings and from 3 to 8 carbons per ring. Exemplary such groups include cyclobutenyl, cyclopentenyl, cyclohexenyl, and the like.

The term "aryl" refers to a cyclic aromatic hydrocarbon group containing 1 to 5 aromatic rings, especially a monocyclic or bicyclic group such as phenyl, biphenyl, or naphthyl. When containing two or more aromatic rings (e.g., bicyclic or tricyclic), the aromatic rings of the aryl group can be joined at a single point (e.g., biphenyl) or fused (e.g., naphthyl, phenanthrenyl, etc.). The term "aryl" also refers to groups such as 5-and 6-membered monocyclic aromatic groups, which may contain 0 to 4 heteroatoms, such as pyrrole, furan, thiophene, thiazole, isothiazole, imidazole, triazole, tetrazole, pyrazole, oxazole, isoxazole, pyridine, pyrazine, pyridazine, and pyrimidine, and the like. Furthermore, the term "aryl" includes polycyclic aryl groups, such as tricyclic, bicyclic, e.g., naphthalene, benzoxazole, benzodioxazole, benzothiazole, benzimidazole, benzothiophene, methylenedioxyphenyl, quinoline, isoquinoline, naphthyridine, indole, benzofuran, purine, benzofuran, deazapurine, or indolizine. Those aryl groups having heteroatoms in the ring structure may also be referred to as "aryl heterocycles," heteroaryls, "or" aromatic heterocycles.

The alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl or aryl groups as described in the present teachings can be unsubstituted or substituted. The term "substituted" refers to an alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, or aryl group having at least one (e.g., 1, 2, 3, 4, or more) substituent substituted for a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents may include, for example, alkyl, alkenyl, alkynyl, acetyl, aryl, hydroxy, halo (e.g., -Br, -Cl, -I, OR-F), -OR, SR, NR₂COOH, COOR or COR, wherein R is hydrogen or alkyl containing 1 to 6 carbons.

In some examples, an isolated compound of the invention is a compound of formula (III):

wherein each stereocenter is denoted by an "+" and may independently be in the R or S configuration.

In some embodiments, the isolated compound is a compound having a structure as shown in table 1 below.

Table 1: compounds of the invention

In some embodiments, a compound of the invention (e.g., a compound of formula (III)) may be referred to as Novo 29. Novo29 is a depsipeptide having a molecular weight of 902 g/mole. Without wishing to be bound by theory, it is believed that Novo29 may be a peptidoglycan synthesis inhibitor that may exert its antibacterial properties by binding lipid II and lipid III.

In some embodiments, the compounds of the present invention do not exhibit gelation when added to serum up to 500 μ g/mL.

In some embodiments, it may also be used separately¹³C or²H replaces any carbon or hydrogen in the compounds of the invention (e.g., compounds of formula (I), formula (II), formula (III), or table 1).

The phrases "a compound of the invention", "a compound of formula (I)", "a compound of formula (II)", "a compound of formula (III)" or "a compound of table 1" as used herein are intended to include enantiomers, diastereomers, tautomers and pharmaceutically acceptable salts thereof. The depsipeptides of the invention and their salts may exist in their tautomeric form (for example, as amides or guanidines). All such tautomeric forms are included herein as part of the present invention. The compounds of the invention (e.g., compounds isolated from beta-proteobacteria) may also be referred to as "Novo 29". In some embodiments, the present teachings relate to mixtures of stereoisomers. In other embodiments, the present teachings are directed specifically to single stereoisomers of the compounds of the present invention.

In some embodiments, the compounds of the invention are isolated natural products of a bacterial species. For example, in some embodiments, the compounds of the invention are isolated natural products of β -proteobacteria that have not been previously cultured.

All stereoisomers of depsipeptides of the present invention (e.g., those which may exist due to asymmetric carbons on various substituents) include enantiomeric forms and diastereomeric forms and are included within the scope of the invention. In one embodiment, the compounds of the present invention are mixtures. Alternatively, however, the compounds of the present invention are single stereoisomers that are substantially free of other stereoisomers (e.g., pure or substantially pure optical isomers with a particular activity). In some embodiments, the present invention relates to single stereoisomers wherein less than about 10% (by dry weight) of the other isomer is present. In some embodiments, the present invention relates to single stereoisomers wherein less than about 5% (by dry weight) of the other isomer is present. In some embodiments, the present invention relates to single stereoisomers wherein less than about 2% (by dry weight) of the other isomer is present. In some embodiments, the present invention relates to single stereoisomers wherein less than about 1% (by dry weight) of the other isomer is present. In some embodiments, the present invention relates to a single stereoisomer of the other isomer that is present from about 5% (by dry weight) to about 10% (by dry weight). In some embodiments, the present invention relates to a single stereoisomer of the other isomer being present from about 1% (by dry weight) to about 5% (by dry weight). In some embodiments, the present invention relates to a single stereoisomer of the other isomer being present from about 1% (by dry weight) to about 10% (by dry weight). In some embodiments, the present invention relates to a single stereoisomer of the other isomer that is present from about 5% (by dry weight) to about 10% (by dry weight). Less than 2% of unrelated compounds (dry basis). In other embodiments, the present teachings relate to mixtures of stereoisomers. The chiral center of the compounds of the invention may have the S or R configuration as defined by the IUPAC 1974 recommended nomenclature. The stereoisomeric forms may be resolved by physical methods such as fractional crystallization, separation or crystallization of diastereomeric derivatives or separation by chiral column chromatography. The individual optical isomers may be obtained from a mixture of stereoisomers by any suitable method, including but not limited to conventional methods such as salt formation with an optically active acid followed by crystallization.

The depsipeptide compounds of the invention may be prepared, for example, by isolating and purifying to obtain a composition comprising an amount equal to or greater than 90% (by dry weight), which is then used or formulated as described herein. The depsipeptide compounds of the invention may be prepared, for example, by isolating and purifying to obtain a composition comprising an amount equal to or greater than 95% (by dry weight), which is then used or formulated as described herein. The depsipeptide compounds of the invention may be prepared, for example, by isolating and purifying to obtain a composition comprising an amount of from about 90% (by dry weight) to about 95% (by dry weight), which is then used or formulated as described herein. The depsipeptide compounds of the invention may be prepared, for example, by isolating and purifying to obtain a composition comprising an amount of from about 85% (by dry weight) to about 95% (by dry weight), which is then used or formulated as described herein. The depsipeptide compounds of the invention may be prepared, for example, by isolating and purifying to obtain a composition comprising an amount of from about 95% (by dry weight) to about 99% (by dry weight), which is then used or formulated as described herein.

All configurational isomers of the compounds of the present invention are included, as mixtures, in pure or substantially pure form.

In another embodiment, the present invention relates to a pharmaceutical composition comprising a compound described in the present teachings and a pharmaceutically acceptable excipient, carrier or diluent. In certain embodiments, the composition further comprises an agent selected from the group consisting of: antibiotics, antifungal agents, antiviral agents, antiprotozoal agents, anthelmintics, antineoplastic agents, immunomodulators, anti-hypercholesterolemic agents, and combinations thereof.

The depsipeptides of the invention may form salts, which are also within the scope of the invention. Unless otherwise indicated, reference to a compound of the invention herein is to be understood as including reference to a salt thereof. The term "salt" as used herein denotes an acidic salt formed with an inorganic and/or organic acid. Pharmaceutically acceptable (i.e., non-toxic, physiologically acceptable) salts are preferred, but other salts may also be used, for example, in isolation or purification steps used in the preparation process. For example, a salt of a compound of the invention can be formed by reacting a compound of the invention with an amount of acid (e.g., an equivalent amount of acid) in a medium (e.g., a medium in which the salt precipitates) or in an aqueous or aqueous and organic medium, followed by lyophilization.

Depsipeptides of the present invention containing basic moieties such as, but not limited to, amines can be salified with various organic and inorganic acids. Exemplary acid addition salts include acetates (e.g., those formed with acetic acid or trihaloacetic acids such as trifluoroacetic acid), adipates, alginates, ascorbates, aspartates, benzoates, benzenesulfonates, bisulfates, borates, butyrates, citrates, camphorates, camphorsulfonates, cyclopentanepropionates, digluconates, dodecylsulfates, ethanesulfonates, fumarates, glucoheptanoates, glycerophosphates, hemisulfates, heptanoates, hexanoates, hydrochlorides, hydrobromides, hydroiodides, hydroxyethanesulfonates (e.g., 2-hydroxyethanesulfonates), lactates, maleates, methanesulfonates, naphthalenesulfonates (e.g., 2-naphthalenesulfonates), nicotinates, nitrates, oxalates, pectinates, persulfates, phenylpropionates (e.g., 3-phenylpropionates), Phosphates, picrates, pivalates, propionates, salicylates, succinates, sulfates (e.g., those formed with sulfuric acid), sulfonates, tartrates, thiocyanates, tosylates such as p-toluenesulfonate (tosilate), undecanoates, and the like.

Process for preparing the Compounds of the invention

The present teachings also relate to methods for producing a compound of the invention (e.g., a compound of formula (I), formula (II), formula (III), or table 1, as described above).

The method comprises culturing (cultivating) or culturing (culturing) a β -proteobacteria in a medium containing assimilable carbon, nitrogen and inorganic salts under aerobic conditions and capable of producing measurable amounts of the compounds of the invention.

In certain embodiments, the methods further comprise isolating and/or purifying a compound of the invention. The compounds of the invention can be isolated by centrifuging the fermentation broth (e.g., at 10,000rpm for 20 minutes) and isolating and/or purifying the compounds of the invention, e.g., by reverse phase chromatography.

In some embodiments, the methods further comprise isolating and/or purifying a compound of the invention to at least about 75% purity (by dry weight), e.g., to at least about 80% purity (by dry weight), at least about 85% purity (by dry weight), at least about 90% purity (by dry weight), at least about 95% purity (by dry weight), at least about 97% purity (by dry weight), or at least about 99% purity (by dry weight).

In yet another embodiment, the invention relates to a compound of the invention prepared according to the methods described herein.

In some embodiments, the invention also provides a culture medium comprising a compound of the invention, e.g., a compound of formula (I), formula (II), formula (III), or a compound of table 1. The medium may be a medium suitable for culturing bacterial cells (e.g., bacterial cells belonging to the class β -proteobacteria).

In some embodiments, the invention also provides a cell lysate (e.g., a bacterial cell lysate) comprising a compound of the invention, e.g., a compound of formula (I), formula (II), formula (III), or a compound of table 1. The bacterial cell lysate can be prepared using bacterial cells (e.g., cultured bacterial cells belonging to the class β -proteobacteria).

Alternatively, the compounds of the present invention, for example, compounds of formula (I), formula (II), formula (III), or the compounds of Table 1, may be synthesized using synthetic methods known in the art.

Methods of treatment using compounds of the invention

The invention also provides methods of inhibiting the growth of a pathogen. The method comprises contacting the pathogen with an effective amount of one or more depsipeptide compounds of the invention, thereby inhibiting the growth of the pathogen compared to the growth of the pathogen in the absence of treatment with the compound. In certain embodiments, the method reduces the growth of a pathogen compared to the growth of the pathogen in the absence of treatment with the compound. In other cases, the treatment results in killing of the pathogen. Non-limiting examples of pathogens include, but are not limited to, bacteria, fungi, viruses, protozoa, helminths, parasites, and combinations thereof. These methods may be performed in vivo or in vitro.

The antibacterial activity of the depsipeptides of the invention against specific bacteria can be assessed by in vitro assays such as monitoring the zone of inhibition and the Minimum Inhibitory Concentration (MIC) assay. The antifungal activity of the depsipeptides of the invention can be determined, for example, by tracking the viability of the fungal pathogens of interest, such as Candida albicans and Aspergillus species, for example as described in Santi et al, A new triazine, voriconazole (UK-109,496), blocks sterol biosynthesis in Candida albicans and Candida krusei, antibiotic. Agents Chemotherol., 1997, 11 months; 41(11) 2492 and 2496, the entire contents of which are incorporated herein by reference. The antiviral properties of the depsipeptides of the invention can be determined, for example, by Monitoring the inhibition of influenza neuraminidase or by measuring the viability of the virus, as described in Tisdale M, Monitoring of viral infection, new strains with the depth of infection of influenza NAinhibitors, Rev.Med.Virol, 2000 Jan-Feb; 10(1) 45-55, the entire contents of which are incorporated herein by reference. The anti-protozoal activity of the depsipeptides of the invention can be determined by tracking the viability of protozoan parasites such as Trichomonas vaginalis (Trichomonas vaginalis) and Giardia lamblia (Giardia lamblia),such as in Katiyar et al, antibiotic activities of benzimidazoles and coatelationswith beta-tubulin sequence, antibiotic. Agents Chemother, 9.1994; 38(9) 2086-2090, which is incorporated herein by reference in its entirety. The anthelmintic activity of the depsipeptides of the invention can be determined, for example, by following the effect of said compounds on the viability of nematodes such as Schistosoma mansoni, Schistosoma cercaria and Caenorhabditis elegans, for example inP, et al, Traditional herbal remamellaries used for the treatment of the respiratory tract in Zimbabwe, J.Ethnopharmacol, month 4 of 1994; 42(2) 125-32, the entire contents of which are incorporated herein by reference.

In other embodiments, the invention relates to methods of treating a disorder (e.g., a pathogen infection) in a subject in need thereof by administering to the subject an effective amount of one or more depsipeptide compounds described herein. In certain embodiments, the disorder is caused by a pathogen, such as, but not limited to, a bacterium, a fungus, a virus, a protozoan, a helminth, a parasite, or a combination thereof.

In some embodiments, the disorder is caused by bacteria. The depsipeptides described herein are useful against gram-positive and gram-negative bacteria. In particular, the condition may be caused by gram-positive bacteria. Alternatively, the condition may be caused by gram-negative bacteria. Non-limiting examples of gram-positive bacteria include bacteria belonging to a genus selected from the group consisting of: streptococcus (Streptococcus), Staphylococcus (Staphylococcus), enterococcus (Enterococcus), Corynebacterium (Corynebacterium), Listeria (Listeria), Bacillus (Bacillus), Erysipelothrix (Erysipelothrix) and Actinomycetes (Actinomycetes). In some embodiments, the compounds of the present invention are used to treat an infection caused by one or more of: helicobacter pylori (helicobacter pylori), Legionella pneumophila (Leginella pneumoniae), Mycobacterium tuberculosis (Mycobacterium tuberculosis), Mycobacterium avium (Mycobacterium avium), Mycobacterium intracellulare (Mycobacterium intracellulare), Mycobacterium kansasii (Mycobacterium kansaii), Mycobacterium gordonii (Mycobacterium gordonae), Mycobacterium sporozoite, Staphylococcus aureus (Staphylococcus aureus), Staphylococcus epidermidis (Staphylococcus epidermidis), Neisseria gonorrhoeae (Neisseria gonorrhoeae), Neisseria meningitidis (Neisseria meningitidis), Listeria monocytogenes (Listeria monocytogenes), Streptococcus pyogenes (Streptococcus pneumoniae), Streptococcus faecalis (Streptococcus faecalis), Streptococcus curare (Streptococcus faecalis), Streptococcus faecalis (Streptococcus faecalis group B), Streptococcus faecalis (Streptococcus faecalis group, Streptococcus), Streptococcus faecalis (Streptococcus faecalis group B), Streptococcus faecalis (Streptococcus), Streptococcus faecalis group B (Streptococcus), Streptococcus faecalis group B), Streptococcus (Streptococcus faecalis group B), Streptococcus group B, Pseudomonas aeruginosa (Pseudomonas aeruginosa), Bacillus anthracis (Bacillus ankara), Bacillus subtilis (Bacillus subtilis), Escherichia coli (Escherichia coli), Corynebacterium diphtheriae (Corynebacterium diphtheriae), Corynebacterium jejuni (Corynebacterium jeikeium), Corynebacterium glutamicum (Corynebacterium sporogenes), Escherichia coli (Erysipelothrix rhuspathioides), Clostridium perfringens (Clostridium perfringens), Clostridium tetani (Clostridium tei), Clostridium difficile (Clostridium difficile), Enterobacter sp (Enterobacteriaceae), Klebsiella pneumoniae (Klebsiella pneumoniae), Clostridium polybundea (Pasteurella), Bacillus multocida (Bacillus multocida), Bacillus subtilis, Streptomyces monotitaceae, Bacillus subtilis (Corynebacterium parvum), Bacillus subtilis (Clostridium sporogenes), Bacillus subtilis (Corynebacterium parvum), Bacillus subtilis (Bacillus subtilis), Bacillus subtilis (Bacillus subtilis), Bacillus subtilis, and Bacillus subtilis (Bacillus subtilis). In particular embodiments, the compounds described herein are used to treat methicillin-resistant staphylococcus aureus (MRSA) or vancomycin-resistant enterococci (VRE) infections. In the united states, MRSA causes approximately 19,000 deaths per year. Although most of these deaths are attributed to hospital-acquired MRSA (HA-MRSA), community-acquired MRSA (CA-MRSA) are actually more virulent and known to be potentially fatal to previously healthy individuals. The virulence of CA-MRSA is due in part to the expression of phenol soluble regulatory proteins or PSM peptides. Thus, compounds of the invention may be used in combination with agents that modulate the expression and/or activity of virulence factors such as, but not limited to, PSM peptides, in the treatment of CA-MRSA. In certain embodiments, the depsipeptides of the present invention are useful in the treatment of spirochetes, such as borrelia burgdorferi (Borelia burgdorferi), Treponema pallidum (Treponema pallidium), and Treponema tenue (Treponema pertenue).

In a particular embodiment, the gram-positive bacteria may be selected from the genera Staphylococcus (Staphylococcus) (including, for example, s.aureus spp., s.epidermidis spp., s.wannerri spp., and s.haemolyticus spp.); streptococcus (Streptococcus) (including, for example, s.viridans spp., s.pneumoconiae spp., s.agalactiae spp., and s.pyogenes spp.); bacillus (Bacillus) (including, for example, b.antrhrasis spp. and b.subtilis, spp.); clostridium (Clostridium) (including, for example, c.difficile spp.); propionibacterium (Propionibacterium) (including, for example, p.acnes spp.); enterococcus (Enterococcus) (including, e.g., e.faecium spp., vancomycin-resistant e.faecium spp., and vancomycin-resistant e.faecium spp.); and mycobacteria (Mycobacterium) (including, for example, m.smegmatis spp. and m.tuboculosis spp.). The compounds described herein are useful for treating conditions caused by these bacteria. Examples of such conditions include acute bacterial skin and skin structure infections, clostridium difficile (c.difficile) associated diarrhea, anthrax, sepsis, botulism, urinary tract infections, bacteremia, bacterial endocarditis, diverticulitis, meningitis, pneumonia and tuberculosis.

In a particular embodiment, the gram-negative bacteria are selected from the genera Haemophilus (haempohilus) (including, for example, h.influenzae spp.); klebsiella (Klebsiella) (including, for example, k. pneumoniae spp.); pseudomonas (Pseudomonas) (including, for example, p. aeruginosa spp.); escherichia coli (Escherichia) (including e.g., e.coli spp.); yersinia (Yersinia) (including, e.g., y.pestis spp.); neisseria (Neisseria) (including, for example, n.gonorrhoeae spp.); bacteroides (Bacteriodes) (including, for example, b.fragilis spp.); proteobacteria (Proteus) (including, for example, p.mirabilis spp. and p.vulgarisspp.); enterobacter (Enterobacter) (including, for example, e.cloacae spp. and e.aerogenes spp.); serratia (Serratia) (including, e.g., s. marcescens spp.); acinetobacter (including, e.g., a. baumann spi.); and Moraxella (Moraxella) (including, for example, m. In a particular embodiment, the gram-negative bacterium is Haemophilus (haempohilus) and in particular Haemophilus influenzae (h.influenzae); or Moraxella (Moraxella) and in particular m. The compounds described herein are useful for treating conditions caused by these bacteria. Examples of such conditions include influenza, bacteremia, pneumonia, acute bacterial meningitis, gonorrhea, urinary tract infections, respiratory tract infections, catheter-related bacteremia, wound infections, otitis media, bronchitis, sinusitis and laryngitis.

In other embodiments, the depsipeptide compounds described herein can be used to treat viral disorders. Non-limiting examples of infectious viruses that can cause a condition treated by a compound of the invention include: retroviridae (e.g., human immunodeficiency viruses such as HIV-1 (also known as HTLV-III, LAV or HTLV-III/LAV) or HIV-III; and other isolates such as HIV-LP); picornaviridae (Picornaviridae) (e.g., poliovirus, hepatitis A virus; enterovirus, human coxsackievirus, rhinovirus, echovirus); caliciviridae (Calciviridae) (e.g., strains that cause gastroenteritis); togaviridae (Togaviridae) (e.g., equine encephalitis virus, rubella virus); flaviviridae (Flaviridae) (e.g., dengue virus, encephalitis virus, yellow fever virus); coronaviridae (Coronaviridae) (e.g., coronavirus, Severe Acute Respiratory Syndrome (SARS) virus); rhabdoviridae (Rhabboviridae) (e.g., vesicular stomatitis virus, rabies virus); filoviridae (Filoviridae) (e.g., ebola virus); paramyxoviridae (Paramyxoviridae) (e.g., parainfluenza virus, mumps virus, measles virus, respiratory syncytial virus); orthomyxoviridae (Orthomyxoviridae) (e.g., influenza virus); bunyaviridae (bunaviridae) (e.g., hantavirus, bunyavirus, phlebovirus, and norovirus); arenaviridae (Arenaviridae) (hemorrhagic fever virus); reoviridae (Reoviridae) (e.g., reovirus, circovirus, and rotavirus); binuclear glyconucleoviridae (birnaveridae); hepadnaviridae (Hepadnaviridae) (e.g., hepatitis b virus); parvoviridae (Parvoviridae) (parvovirus); papovaviridae (Papovaviridae) (papilloma virus, polyoma virus); adenoviridae (adenoviruses) (most adenoviruses); herpesviridae (Herpesviridae) (e.g., Herpes Simplex Virus (HSV)1 and 2, varicella zoster virus, Cytomegalovirus (CMV), herpes virus); poxviridae (Poxviridae) (e.g., variola virus, vaccinia virus, poxvirus); and Iridoviridae (Iridoviridae) (e.g., african swine fever virus); and unclassified viruses (e.g., causative agents of spongiform encephalopathies, causative agents of hepatitis delta (thought to be a defective adjunct to hepatitis b virus), causative agents of non-a, non-b hepatitis (class 1: enterally transmitted; class 2: parenterally transmitted, i.e., hepatitis c); Norwalk and related viruses and astrovirus). In particular embodiments, the compounds of the present invention are useful for the treatment of influenza virus, human immunodeficiency virus, and herpes simplex virus.

In some embodiments, depsipeptides of the present invention may be useful in the treatment of conditions caused by fungi. Non-limiting examples of fungi that can be inhibited by the compounds of the present invention include, but are not limited to, Cryptococcus neoformans (Cryptococcus neoformans), Histoplasma capsulatum (Histoplasma capsulatum), Coccidioides immitis (Coccidioides), Blastomyces dermatitidis (Blastomyces dermatitidis), Chlamydia trachomatis (Chlamydirachycarachitis), Candida albicans (Candida albicans), Candida tropicalis (Candida tropicalis), Candida glabrata (Candida glabrata), Candida krusei (Candida parapsilosis), Candida dubia (Candida duiniensis), Candida vitis (Candida luciata), Candida vitis (Candida albicans), Microsporum (Microsporum floccosum), Microsporum floccosum (Microsporum), Microsporum floccosum, Microsporum (Microsporum), Microsporum floccosum (Microsporum), Microsporum canis, Microsporum Microsporum gallinarum (Microsporum gallinae), Microsporum gypseum (Microsporum gypseum), Microsporum dwarum (Microsporum annuum), Microsporum persicinum (Microsporum persicum), Trichophyton angularis (Trichophyton ajelloi), Trichophyton mentagrophytes (Trichophyton mentarum), Trichophyton equinus (Trichophyton equinum), Trichophyton xanthum (Trichophyton flaves), Trichophyton phototrophyton (Trichophyton glareophyceae), Trichophyton Trichophyton (Trichophyton mentarini), Trichophyton mentagrophytes (Trichophyton Trichophyton var. rubrum), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton rubrum (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton rubrum), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton (Trichophyton Trichophyton), Trichophyton Trichophyton strain (Trichophyton Trichophyton, Trichophyton tricho, Trichophyton violaceum (Trichophyton violacea), Trichophyton rubrum (Trichophyton yaoudei), Aspergillus fumigatus (Aspergillus fumigatus), Aspergillus flavus (Aspergillus flavus), and Aspergillus clavatus (Aspergillus clavus).

In other embodiments, the depsipeptides described herein may be used to treat conditions caused by protozoans. Non-limiting examples of protozoa that may be inhibited by the compounds of the present invention include, but are not limited to, Trichomonas vaginalis (Trichomonas vaginalis), Giardia lamblia (Giardia lamblia), Entamoeba histolytica (Entamoeba histolytica), Balantidian (Balanicdium coli), Cryptosporidium microfine (Cryptosporidium parvum) and Isospora bellina (Isospora belli), Trypanosoma cruzi (Trypanosoma cruzi), Trypanosoma gambiae (Trypanosoma gambiense), Leishmania donovani (Leishmania donovani) and Trypanosoma fornica (Naegleria fowleri).

In certain embodiments, the depsipeptides described herein may be used to treat conditions caused by helminths. Non-limiting examples of helminths that can be inhibited by the compounds of the present invention include, but are not limited to: schistosoma mansoni (Schistosoma japonicum), Schistosoma cercaria (Schistosoma cercariae), Schistosoma japonicum (Schistosoma japonicum), Schistosoma meibomensis (Schistosoma mekongi), Schistosoma japonicum (Schistosoma japonicum), human roundworm (Ascaris lucbricides), Strongyloides stercoralis (Strongyloides stercoralis), Echinococcus granulosus (Echinococcus grandilosus), Echinococcus polyactinus (Echinococcus multilocularis), Ostertagineus guanoides (Angiostrongylus cantonensis), Ostreoschus ridgensis (Angiostrongylcoccus), Kaempferia bruguinii (Fasciola bungiensis), philippine nematodes (Capilaria philippinensis), Paragonimus westernani (Paragonimus westernani), ancylostomus duodenalis (Ancylostoma dudodenale), Ancylostoma americanum (Necator americanus), trichinella spiralis (Trichinella spiralis), Wuchereria marcescens (Wuchereria banrofti), Trichosis malayi (Brugia malayi) and Trichosis striatellus (Brugia timori), Toxocara canis (Toxocara canis), Toxocara felis (Toxocara cati), Toxocara bovis (Toxocara vitulum), Cryptorhabditis elegans (Caenorhabditis elegans) and Isopyralis (Anisakis).

In some embodiments, depsipeptides compounds described herein can be used to treat conditions caused by parasites. Non-limiting examples of parasites that may be inhibited by the compounds of the invention include, but are not limited to, Plasmodium falciparum (Plasmodium falciparum), Plasmodium yoellii (Plasmodium yoelli), Thelephora brevicornus (Hymenolepis nana), Clonorchis sinensis (Clonorchis sinensis), Roxathrix reana (Loa Loa), Paragonimus proliferatum (Paragonimswestermani), Fasciola hepatica (Fasciola hepatica), and Toxosma gondii (Toxosma gondii). In a particular embodiment, the parasite is plasmodium.

In other embodiments, depsipeptide compounds can be used to inhibit the growth of an infectious agent as compared to the growth of an infectious agent in the absence of treatment with the compound. Non-limiting examples of infectious agents include, but are not limited to, bacteria, fungi, viruses, protozoa, helminths, parasites, and combinations thereof. Depsipeptides can be used for inhibiting infectious agents in vivo or in vitro.

Pharmaceutical compositions comprising the compounds of the invention

The invention also provides pharmaceutical compositions comprising at least one depsipeptide compound of the invention and a pharmaceutically acceptable carrier, e.g., a carrier in which the depsipeptide compound of the invention is soluble. These depsipeptide compositions are suitable for administration to a subject (e.g., a mammal such as a human). The pharmaceutical composition may be used for the treatment of a disorder. Non-limiting examples of such disorders are provided above, and include infection by a pathogen (e.g., a bacterium).

In one embodiment, the depsipeptide compound is administered in a pharmaceutically acceptable carrier. Any suitable carrier known in the art may be used. Carriers that effectively dissolve the compounds of the present invention are preferred. Carriers include, but are not limited to, solids, liquids, or mixtures of solids and liquids. The carrier may take the form of capsules, tablets, pills, powders, lozenges, suspensions, emulsions or syrups. Carriers may include substances that act as flavoring agents, lubricants, solubilizers, suspending agents, binders, stabilizers, tablet disintegrating agents, and encapsulating materials. The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

Non-limiting examples of materials that can serve as pharmaceutically acceptable carriers include: (1) sugars such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth gum; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols such as glycerol, sorbitol, mannitol and polyethylene glycol; (12) esters such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline, (18) ringer's solution, (19) ethanol; (20) phosphate buffer; and (21) other non-toxic compatible substances used in pharmaceutical formulations.

The dosage forms may conveniently be presented in unit dosage form and may be prepared by any of the methods well known in the pharmaceutical arts. The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form will vary depending upon the subject to be treated, the particular mode of administration, the particular condition being treated, and the like. The amount of active ingredient that can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect. Typically, the amount is from about 1% to about 99% active ingredient, preferably from about 5% to about 70%, most preferably from about 10% to about 30%, by weight.

Methods of preparing these formulations or compositions include the step of bringing into association a compound of the invention with a carrier and, optionally, one or more accessory ingredients. Typically, the formulation is prepared by: the depsipeptides of the invention are intimately associated with liquid carriers or with immediately comminuted solid carriers or both, and the product is then, if necessary, shaped.

In solid dosage forms for oral administration (e.g., capsules, tablets, pills, lozenges, powders, granules, etc.), the active ingredient is mixed with one or more additional ingredients such as sodium citrate or dicalcium phosphate and/or any of the following: fillers or extenders such as, but not limited to, starch, lactose, sucrose, glucose, mannitol, and/or silicic acid; binders such as, but not limited to, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidone, sucrose, and/or acacia; humectants such as, but not limited to, glycerin; disintegrating agents such as, but not limited to, agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; dissolution retarders such as, but not limited to, paraffin; absorption enhancers such as, but not limited to, quaternary ammonium compounds; wetting agents such as, but not limited to, cetyl alcohol and glycerol monostearate; adsorbents such as, but not limited to, kaolin and bentonite; lubricants such as, but not limited to, talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; and a colorant. In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using excipients such as lactose or milk sugar (milk sugar) as well as high molecular weight polyethylene glycols and the like.

In powders, the carrier is a finely divided solid which is mixed with an effective amount of the finely divided medicament. Powders and sprays can contain, in addition to a compound of the invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder or mixtures of these substances. Sprays can additionally contain conventional propellants, for example chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, for example butane and propane.

Tablets for systemic oral administration may include one or more excipients as known in the art, for example calcium carbonate, sodium carbonate, sugars (e.g., lactose, sucrose, mannitol, sorbitol), cellulose (e.g., methylcellulose, sodium carboxymethylcellulose), gums (e.g., acacia, tragacanth), and one or more disintegrants (e.g., corn starch or alginic acid), binders (e.g., gelatin, collagen or acacia), lubricants (e.g., magnesium stearate, stearic acid or talc), inert diluents, preservatives, disintegrants (e.g., sodium starch glycolate), surfactants and/or dispersing agents. Tablets may be prepared by compression or molding, optionally with one or more accessory ingredients.

In solutions, suspensions, emulsions or syrups, an effective amount of the depsipeptide compound is dissolved or suspended in a carrier, such as sterile water or an organic solvent, such as aqueous propylene glycol. Other compositions may be prepared by dispersing the compound in an aqueous solution of starch or sodium carboxymethyl cellulose or in a suitable oil as known in the art. 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, but not limited to, ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1, 3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and sorbitan fatty acid esters, and mixtures thereof.

Besides inert diluents, the oral compositions can also contain adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.

Suspensions, in addition to containing the active compound, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

Formulations of pharmaceutical compositions for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more compounds of the present invention with one or more suitable non-irritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which may be solid at room temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the agent. Formulations suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.

Dosage forms for topical or transdermal administration of the compounds of the present invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, drops, patches and inhalants. The active depsipeptide compound may be mixed under sterile conditions with a pharmaceutically acceptable carrier and any preservatives, buffers, or propellants which may be required.

The ointments, pastes, creams and gels may contain, in addition to the active ingredient, 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.

Transdermal patches have the added advantage of providing controlled delivery of the compounds of the present invention to the body. Such dosage forms may be prepared by dissolving or dispersing the agent in a suitable medium. Absorption enhancers may also be used to increase the flux of the agent across the skin. Such flux rates can be controlled by providing a rate controlling membrane or dispersing the depsipeptide compound in a polymer matrix or gel.

The depsipeptide compound is administered in an amount effective for the patient in need of such treatment. The phrase "effective amount" as used herein refers to an amount of a compound of the present invention or a composition comprising a compound of the present invention that is effective to produce some desired effect in an animal. It will be appreciated that when a pharmaceutical agent is used to achieve a therapeutic effect, the actual dosage comprising an "effective amount" will vary depending on conditions including, but not limited to, the particular condition being treated, the severity of the disease, the size and health of the patient, the route of administration. Suitable dosages can be readily determined by the skilled medical practitioner using methods well known in the medical arts. In some embodiments, the effective amount is an amount effective to treat the disorder in a subject in need thereof. Moreover, one skilled in the art will appreciate that the effective amount of a depsipeptide compound may be decreased or increased by fine-tuning (fine-tuning) and/or by administering more than one depsipeptide compound, or by administering the depsipeptide compound with a second agent (e.g., an antibiotic, antifungal, antiviral, NSAIDS, DMARDS, steroid, etc.). An effective amount can be determined empirically, for example, by starting at a relatively low amount and progressing with a concurrent assessment of beneficial effects (e.g., symptom relief). The actual effective amount will be determined by dose/response assays using standard methods in the art (Johnson et al, diabetes.42:1179, (1993)). As known to those skilled in the art, an effective amount will depend on the bioavailability, bioactivity, and biodegradability of the depsipeptide compound.

In some embodiments, an effective amount is an amount capable of reducing symptoms of a disorder in a subject. Thus, the amount may vary with the subject being treated. For example, an effective amount of a depsipeptide compound may comprise from about 1 μ g/kg body weight to about 100mg/kg body weight. In one embodiment, an effective amount of a compound comprises about 1 μ g/kg body weight to about 50mg/kg body weight. In a further embodiment, an effective amount of a compound comprises from about 10 μ g/kg body weight to about 10mg/kg body weight. When one or more depsipeptide compounds or agents are combined with a carrier, they can be present in an amount of about 1% to about 99% by weight, with the balance consisting of a pharmaceutically acceptable carrier. In some embodiments, the effective amount is between about 1mg and about 10g per dose, for example between about 10mg and about 1g per dose. Values and ranges intermediate to the ranges set forth above are intended to be included in the present teachings.

Administration of the depsipeptide compound may be hourly, daily, weekly, monthly, yearly, or a single administration. Further, the duration of administration may be from one day to one year or more. In some embodiments, administration refers to administration once per day over a period of time (e.g., about 1 week, 2 weeks, 3 weeks, 1 month, 3 months, 6 months, or 1 year). In some embodiments, administration refers to administration once per week over a period of time (e.g., about 1 month, 3 months, 6 months, 1 year, or longer).

The invention also provides kits comprising at least one depsipeptide compound of the invention. The kit may contain at least one container and may further comprise instructions directing the use of these materials. In another embodiment, the kit may comprise reagents for treating the condition under consideration, with or without such above-mentioned substances that may be present to determine whether the subject has an inflammatory disease.

Administration of the pharmaceutical compositions of the invention

The method of administration of the formulations of the invention comprising the depsipeptides of the invention described herein may be any of a variety of methods well known in the art. These methods include local administration or systemic administration. Exemplary routes of administration include oral, parenteral, transdermal, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal (e.g., nebulizer, inhaler, aerosol dispenser), intraocular (e.g., for treating conjunctivitis), otic (e.g., for treating ear infections), colorectal, rectal, intravaginal, and any combination thereof. Furthermore, it may be desirable to introduce the pharmaceutical compositions of the present invention into the central nervous system by any suitable route, including intraventricular and intrathecal injection. Intraventricular injections may be assisted by an intraventricular catheter, for example, connected to a reservoir such as an Ommaya reservoir. The method of introduction may also be provided by a refillable or biodegradable device (e.g., a reservoir). In addition, administration may be achieved by a coating device, implant, stent, or prosthesis. The compounds of the present invention may also be used to coat catheters in any situation where the catheter is inserted into the body.

In another embodiment, the subject depsipeptides may be administered as part of a combination therapy with other drugs. Combination therapy refers to any form of administration that combines two or more different therapeutic compounds such that a second compound is administered while the previously administered therapeutic compound is still effective in vivo (e.g., both compounds are effective in the patient at the same time, which may include a synergistic effect of both compounds). For example, different therapeutic compounds may be administered simultaneously or sequentially in the same formulation or in separate formulations. Thus, an individual receiving such treatment may have a combined effect of different therapeutic compounds.

For example, depsipeptides may be used in combination with other known antibiotics. The depsipeptide compounds of the invention may be administered sequentially or substantially simultaneously. Altering antibiotics can help reduce the ability of pathogens to develop resistance to drugs. Non-limiting examples of antibiotics include penicillins (e.g., natural penicillins, penicillinase-resistant penicillins, anti-pseudomonas penicillins, aminopenicillins), tetracyclines, macrolides (e.g., erythromycin), lincosamides (e.g., clindamycin), streptogramins (e.g., Synercid), aminoglycosides, and sulfonamides. In some embodiments, the depsipeptide compounds of the invention are used in combination with compounds that target virulence factors (such as, but not limited to, phenol soluble regulatory proteins). In some embodiments, the depsipeptide compounds of the invention are used in combination with compounds that target pathogen efflux pumps.

Kits and articles of manufacture comprising pharmaceutical compositions of the compounds of the invention

Kits comprising a compound of the invention or a pharmaceutically acceptable salt thereof and instructions for use are also within the scope of the invention. The term "kit" as used herein refers to a packaged product containing ingredients for treating a disease caused by a pathogen, which is used to administer a pharmaceutical composition comprising a compound of the present invention, or a pharmaceutically acceptable salt thereof. The kit preferably comprises a box or container containing the kit components. The box or container is labeled with a label or protocol approved by the U.S. food and drug administration. The box or container contains the composition of the invention, preferably contained in a plastic, polyethylene, polypropylene, ethylene or propylene container. The container may be a capped tube or bottle or a bottle containing a dropper suitable for drop-wise application of a solution containing a compound of the invention (e.g., into the ear or eye of a subject). The kit may further comprise instructions for administering a pharmaceutical composition comprising a compound of the invention or a pharmaceutically acceptable salt thereof. In a particular embodiment, the kit may comprise (a) a pharmaceutical composition comprising a compound of the present invention, or a pharmaceutically acceptable salt thereof, wherein the pharmaceutical composition is in a container; and (b) instructions describing a method of using the pharmaceutical composition.

The kit can additionally contain one or more additional agents such as antibiotics, antifungal agents, antiviral agents, antiprotozoal agents, anthelmintics, antineoplastic agents, immunomodulators, anti-hypercholesterolemic agents and combinations thereof. The kit will typically include a label identifying the intended use of the kit contents. The term label includes any written or recorded material provided on or with the kit or otherwise accompanying the kit.

The invention also provides a pharmaceutical package or kit comprising one or more containers holding a liquid formulation of a pharmaceutical composition comprising a compound of the invention, or a pharmaceutically acceptable salt thereof. In another embodiment, the container containing the liquid formulation of the present invention is a prefilled syringe. In a particular embodiment, the formulation of the present invention is formulated as a sterile liquid in a single dose vial. For example, the formulation may be provided in a 3cc ISP type I borosilicate amber vial (West Pharmaceutical Services-part number 6800-0675) with a target volume of 1.2 mL. Optionally, associated with such containers may be a notice prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of the manufacture, use or sale of the human product.

Any prefilled syringe known to those skilled in the art may be used in conjunction with the liquid formulations of the present invention. Prefilled syringes that can be used are described in, for example, but not limited to, PCT publications WO05032627, WO08094984, WO9945985, WO03077976, US patent US6792743, US5607400, US5893842, US7081107, US7041087, US5989227, US6807797, US6142976, US5899889, US patent publications US20070161961a1, US20050075611a1, US20070092487a1, US20040267194a1, US20060129108a 1. The prefilled syringe can be made of various materials. In one embodiment, the prefilled syringe is a glass syringe. In another embodiment, the prefilled syringe is a plastic syringe. One skilled in the art will appreciate that the nature and/or quality of the materials used to produce the syringe may affect the stability of the compound formulation stored in the syringe. For example, it is understood that silicon-based lubricants deposited on the interior surfaces of the syringe chamber may affect particle formation in the compound formulation. In another embodiment, the prefilled syringe contains a silicone-based lubricant. In another embodiment, the prefilled syringe comprises a baked silicone. In another embodiment, the prefilled syringe is free of silicone-based lubricants. It will also be appreciated by those skilled in the art that the immersion of small amounts of contaminating elements into the formulation from the syringe barrel, syringe needle cover, plunger or stopper may also affect the stability of the formulation. For example, it is understood that tungsten introduced during the manufacturing process may adversely affect the stability of the formulation. In another embodiment, the prefilled syringe may contain tungsten at a level greater than 500 ppb. In another embodiment, the prefilled syringe is a low tungsten syringe. In another embodiment, the prefilled syringe may contain tungsten at a level between about 500ppb to about 10ppb, between about 400ppb to about 10ppb, between about 300ppb to about 10ppb, between about 200ppb to about 10ppb, between about 100ppb to about 10ppb, between about 50ppb to about 10ppb, between about 25ppb to about 10 ppb.

The invention also encompasses a packaged and labeled pharmaceutical product. The article of manufacture comprises a suitable unit dosage form in a suitable vial or container (e.g., a glass vial), a prefilled syringe or other container that is sealed. In one embodiment, the unit dosage form is provided as a sterile, particle-free solution comprising a pharmaceutical composition containing a compound of the present invention, or a pharmaceutically acceptable salt thereof, suitable for parenteral administration. In another embodiment, the unit dosage form is provided as a sterile lyophilized powder comprising a pharmaceutical composition comprising a compound of the present invention, or a pharmaceutically acceptable salt thereof, suitable for reconstitution.

In one embodiment, the unit dosage form is suitable for intravenous, intramuscular, intranasal, oral, topical, or subcutaneous delivery. Thus, the present invention encompasses sterile solutions suitable for each delivery route. The invention also encompasses sterile lyophilized powders suitable for reconstitution.

As with any pharmaceutical product, packaging materials and containers are designed to preserve the stability of the product during storage and transport. In addition, the products of the invention include instructions for use and other informational material advising a physician, technician, or patient how to properly prevent or treat the disease or condition in question, and how and for how often to administer the drug. In other words, the article of manufacture includes guidance means to indicate or suggest a dosing regimen, including but not limited to actual dosages, monitoring procedures, and other monitoring information.

In particular, the present invention provides an article of manufacture comprising packaging materials such as boxes, bottles, tubes, vials, containers, prefilled syringes, nebulizers, inhalers, intravenous (i.v.) bags, envelopes, and the like; and a unit dosage form comprising at least one compound of the invention in a packaging material, wherein the compound comprises a liquid formulation comprising an antibiotic. The packaging material comprises instructional means which indicate how the compound can be used to prevent, treat and/or manage one or more symptoms associated with the disease or condition.

The invention is further illustrated by the following examples, which should not be construed as limiting in any way. Throughout this application, various patents, patent applications, and publications are referenced. The disclosures of these patents, patent applications, and publications are incorporated herein by reference in their entirety. In the event of any inconsistency between the patents, patent applications, and publications and the present disclosure, the present disclosure controls.