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US-20260125371-A1 - METHOD FOR INHIBITING CLOSTRIDIOIDES DIFFICILE SPORE GERMINATION

US20260125371A1US 20260125371 A1US20260125371 A1US 20260125371A1US-20260125371-A1

Abstract

Oxadiazole antibiotics that exhibit bactericidal activity against C. difficile vegetative cells. We screened a library of 75 oxadiazoles against C. difficile ATCC 43255. The findings from this collection served as the basis for the syntheses of an additional 58 analogs, which were tested against the same strain. We discovered a potent (MIC 50 =0.5 μg/mL, MIC 90 =1 μg/mL for 101 C. difficile strains) and narrow-spectrum oxadiazole (3-(4-(cyclopentyloxy)phenyl)-5-(4-nitro-1H-imidazol-2-yl)-1,2,4-oxadiazole; compound 57) that is not active against common gut bacteria or other tested organisms, but is selectively bactericidal against C. difficile and targets cell-wall synthesis. Other similarly effective oxadiazole antibiotics of formula I and II are described herein, several of which inhibit or prevent C. difficile spore germination.

Inventors

  • Mayland Chang
  • Shahriar Mobashery
  • Yuanyuan QIAN

Assignees

  • UNIVERSITY OF NOTRE DAME DU LAC

Dates

Publication Date
20260507
Application Date
20231013

Claims (20)

  1. 1 . A compound of formula I or II: or a pharmaceutically acceptable salt thereof; wherein, Het is a 1,2,4-oxadiazole; R 1 is aminoalkyl or OH; R 2 is H or NH 2 ; R 3 is H, CF 3 , or 3-(trifluoromethyl)-3H-diazirine-3-yl; X is CH or N; Z 1 is nitro-imidazole, nitro-pyrazole, pyrrolidinone, 4-(aminoalkyl)phenyl, 4-hydroxylphenyl, or aminoalkyl; Z 2 is cyclopentyl or —(C 3 -C 4 or C 6 )cycloalkyl, branched or unbranched —(C 1 -C 6 )alkyl, or Ar wherein Ar is: wherein, R 4 is H, CH 2 (halo), or NO 2 ; R 5 is H or halo; and R 6 is H, halo, CF 3 , —C(═O)CH 3 , or —C≡CH; and R 7 is Ar or OAr; and provided Z 2 is not cyclopentyl when Z 1 is 4-(aminomethyl)phenyl or 4-hydroxylphenyl.
  2. 2 . The compound of claim 1 wherein Z 1 is 5-nitro-1H-imidazole-2-yl, —(CH 2 ) 4 NH 2 , 4-hydroxyphenyl, 4-(NH 2 CH 2 )phenyl, 4-(CH 3 NHCH 2 )phenyl, 4-nitro-1H-pyrazole-3-yl, or pyrrolidin-2-one-4-yl.
  3. 3 . The compound of claim 1 wherein Z 2 is cyclopentyl, cyclopropyl, cyclobutyl, or cyclohexyl.
  4. 4 . The compound of claim 1 wherein the compound is 57: or a pharmaceutically acceptable salt thereof.
  5. 5 . The compound of claim 1 wherein Z 2 is 4-(trifluoromethyl)phenyl, 4-fluorophenyl, 3,4-difluorophenyl, 4-iodophenyl, 3-iodophenyl, 2-nitrophenyl, 2-(bromomethyl)phenyl, phenyl, 4-acetophenyl, or 4-phenylethyne.
  6. 6 . The compound of claim 1 wherein formula I is represented by formula III: or a pharmaceutically acceptable salt thereof; wherein, R 1 is aminoalkyl or OH; R 2 is H or NH 2 ; R 3 is H, CF 3 , or 3-(trifluoromethyl)-3H-diazirine-3-yl; R 4 is H, —CH 2 (halo), or NO 2 ; R 5 is H or halo; R 6 is H, halo, CF 3 , —C(═O)CH 3 , or —C≡CH; and X is CH or N.
  7. 7 . The compound of claim 6 wherein R 1 is —CH 2 NH 2 , —CH 2 NHCH 3 , or —CH 2 CH 2 NH 2 .
  8. 8 . The compound of claim 6 wherein R 6 is CF 3 .
  9. 9 . The compound of claim 6 wherein R 2 and R 3 are H.
  10. 10 . The compound of claim 6 wherein R 4 and R 5 are H.
  11. 11 . The compound of claim 1 wherein formula II is represented by formula IV or V: or a pharmaceutically acceptable salt thereof; wherein, R 1 is —CH 2 NH 2 , —CH 2 NHCH 3 , or —CH 2 CH 2 NH 2 ; and R 7 is Ar or OAr, wherein Ar is: wherein, R 4 is H, CH 2 (halo), or NO 2 ; R 5 is H or halo; and R 6 is H, halo, CF 3 , —C(═O)CH 3 , or —C≡CH.
  12. 12 . The compound of claim 11 wherein R 1 is —CH 2 NH 2 .
  13. 13 . The compound of claim 11 wherein R 7 is 4-(trifluoromethyl)phenyl or oxy-4-(trifluoromethyl)phenyl.
  14. 14 . The compound of claim 1 wherein the compound is: or a pharmaceutically acceptable salt thereof.
  15. 15 . A method for treating a Clostridioides difficile infection (CDI) comprising administering to a subject having a CDI a therapeutically effective dose of a compound of claim 1 , wherein the compound inhibits growth of a Clostridioides difficile vegetative cell or germination of a Clostridioides difficile spore that is present in the CDI and the subject is thereby treated.
  16. 16 . The method of claim 15 wherein the Clostridioides difficile spore is in a vegetative state.
  17. 17 . The method of claim 15 wherein the compound selectively inhibits germination of a Clostridioides difficile spore by damaging the cell wall of the spore.
  18. 18 . The method of claim 15 wherein the compound is inactive toward inhibiting microbiome gut bacteria of the subject, or wherein the compound is inactive toward inhibiting Gram-negative bacteria.
  19. 19 . The method of claim 15 wherein the compound is administered, concurrently or sequentially, with an antibiotic capable of treating a CDI.
  20. 20 . The method of claim 15 wherein the compound is 3-(4-(cyclopentyloxy)phenyl)-5-(5-nitro-1H-imidazol-2-yl)-1,2,4-oxadiazole (57).

Description

RELATED APPLICATIONS This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 63/415,872, filed Oct. 13, 2022, which is incorporated herein by reference. BACKGROUND OF THE INVENTION Infections caused by Clostridioides difficile (previously known as Clostridium difficile) are an urgent public health threat that resulted in 202,600 hospitalizations and 11,500 deaths in the United States in 2019. C. difficile is a Gram-positive anaerobic opportunistic bacterium, which colonizes the gut in patients who have used broad-spectrum antibiotics that disrupt the gut microflora. Damage to the gut epithelium from toxins produced by C. difficile results in inflammation and diarrhea. C. difficile infection (CDI) produces spores that can remain dormant for days/months and are not affected by antibiotics. Bile acids in the host gastrointestinal tract initiate germination of the spores, converting them into active vegetative cells, starting the cycles of re-infection. Recurrent CDI occurs in about 25% of patients. The current antibiotics for treatment of CDI are vancomycin (VAN), fidaxomicin (FDX), and metronidazole (MTZ), with the first two used as first-line treatments. FDX has a narrower spectrum of activity compared to VAN and MTZ, and this likely explains its lower 15% recurrence of infection, compared to 24% for VAN and 27% for MTZ. Antibiotics with narrow-spectrum activity that selectively target C. difficile would provide significant advantage to current treatments, as gut microflora dysbiosis that contributes to recurrence of CDI would be avoided. Accordingly, new antibiotics are needed to reduce C. difficile vegetative cells, as well as inhibit toxins and spores, and at the same time would not encourage microbial resistance or affect the host microbiota. In addition, the antibiotic should not cause adverse events in the host. It is extremely challenging for an antibiotic to meet all these criteria, therefore new antibiotics for treating CDIs are urgently needed. SUMMARY We previously reported (ACS Med. Chem. Lett. 2020, 11, 322) on the 1,2,4-oxadiazole class of antibacterials active against methicillin-resistant Staphylococcus aureus (MRSA). The oxadiazoles were discovered by in silico screening of 1.2 million compounds against penicillin-binding protein (PBP)2a, an essential enzyme whose catalytic activity confers resistance to β-lactam antibiotics. The lead oxadiazole (compound 1, ND-421) exhibits a minimal-inhibitory concentration (MIC) against MRSA of 2 μg/mL and is efficacious in mouse models of MRSA infection. We evaluated the activity of 1 against C. difficile ATCC 43255 strain and found a MIC of 4 μg/mL (Proc. Natl. Acad. Sci. USA. 2023, 120, e2304110120) and also reported on the discovery of oxadiazole 2, with a MIC of 2 μg/mL against C. difficile ATCC 43255. We screened our existing library of 75 oxadiazoles, against C. difficile ATCC 43255 to develop preliminary structure-activity relationships (SAR) for this series. Building on the observed SAR for this study, we synthesized an additional 58 analogs for in vitro evaluation. As a result, we discovered a potent (MIC=0.25 μg/mL against C. difficile ATCC 43255) and narrow-spectrum oxadiazole (compound 57) that is not active against representative gut bacteria or other Gram-positive and Gram-negative bacteria. Compound 57 is bactericidal against vegetative C. difficile and targets cell-wall synthesis. Accordingly, this disclosure provides a compound of formula I or II: or a pharmaceutically acceptable salt thereof; wherein, Het is a 1,2,4-oxadiazole;R1 is aminoalkyl or OH; located ortho, meta, or para to Het;R2 is H, CF3, NH2, or 3-(trifluoromethyl)-3H-diazirine-3-yl;R3 is H, CF3, NH2, or 3-(trifluoromethyl)-3H-diazirine-3-yl;X is CH or N;Z1 is an imidazole, pyrazole, pyrrolidinone, phenyl, or an aminoalkyl, each optionally substituted (for example, nitro-imidazole, nitro-pyrazole, (aminoalkyl)phenyl, or hydroxylphenyl);Z2 is cyclopentyl or —(C3-C6)cycloalkyl, branched or unbranched —(C1-C6)alkyl, or Ar; andR7 is Ar or OAr; wherein Ar is: wherein R4, R5, and R6 are each independently H, halo (e.g., F or Cl), CH2(halo), CF3, —C(═O)CH3, —C≡CH or NO2;further, wherein the variables of formulas I and II, and their sub-formulas III, IV, and V, can also be the substituents as illustrated for the corresponding variable for any compound of Charts 1, 2, and 3, hereinbelow, or a select subset thereof;optionally, provided Z2 is not cyclopentyl when Z1 is 4-(aminomethyl)phenyl or 4-hydroxylphenyl, and/or optionally excluding any compound described by U.S. Pat. No. 11,168,062 (Chang et al.). Additionally, a method is disclosed for treating a Clostridioides difficile infection (CDI) comprising administering to a subject having a CDI a therapeutically effective dose of a compound described herein, wherein the compound inhibits germination of a Clostridioides difficile spore that is present in the CDI and the subject is thereby t