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US-12622975-B2 - Peptide-conjugated prodrugs

US12622975B2US 12622975 B2US12622975 B2US 12622975B2US-12622975-B2

Abstract

The present disclosure relates to a conjugated prodrug comprising a peptide conjugated to an antibiotic molecules via a cleavable linker and pharmaceutical compositions thereof. Also disclosed are methods of enhancing the intracellular concentration of an antibiotic agent in a bacterium and methods of treating a patient for a bacterial infection.

Inventors

  • Bing Xu
  • Jiaqing Wang

Assignees

  • BRANDEIS UNIVERSITY

Dates

Publication Date
20260512
Application Date
20200918

Claims (14)

  1. 1 . A conjugated prodrug comprising: a peptide comprising two to four amino acids, which peptide is conjugated to an antibiotic molecule via a cleavable linker, wherein: (i) the peptide is selected from the group consisting of Gly-Gly, Gly-Gly-Gly, Gly-(D-Leu), Gly-(D-Ala), Gly-(D-Ser), Gly-Gly-Gly-Gly (SEQ ID NO: 1), Gly-Gly-(D-Phe), Gly-Gly-Phe, Gly-Phe-Gly, Gly-Gly-(D-Phe)-(D-Phe), Gly-Gly-Phe-Phe (SEQ ID NO: 3), Gly-Lys, and Gly-Asp; (ii) the antibiotic molecule is not an aminoglycoside; and (iii) wherein the cleavable linker forms an ester bond with the antibiotic molecule.
  2. 2 . The conjugated prodrug according to claim 1 , wherein the peptide is Gly-Gly-Gly-Gly (SEQ ID NO: 1), Gly-Gly-(D-Phe) (D-Phe), or Gly-Gly-Phe-Phe (SEQ ID NO: 3).
  3. 3 . The conjugated prodrug according to claim 1 , wherein the peptide is Gly-Gly, Gly-Gly-Gly, Gly-(D-Leu), Gly-(D-Ala), Gly-(D-Ser), Gly-Gly-(D-Phe), Gly-Gly-Phe, Gly-Phe-Gly, Gly-Lys, or Gly-Asp.
  4. 4 . The conjugated prodrug according to claim 1 , wherein the peptide is Gly-(D-Leu), Gly-(D-Ala), Gly-(L-Ser), Gly-Gly-(L-Phe), or Gly-Gly-(L-Phe)-(L-Phe).
  5. 5 . The conjugated prodrug according to claim 1 , wherein the peptide comprises a glycine residue covalently attached to the cleavable linker.
  6. 6 . The conjugated prodrug according to claim 1 , wherein the antibiotic molecule is selected from the group consisting of aminocoumarins, β-lactams, macrolides, ketolides, lincosamides, streptogramins, quinolones, rifamycins, tetracyclines, oxazolidinones, glycylcycline, amphenicals, and polymyxins.
  7. 7 . The conjugated prodrug according to claim 6 , wherein the antibiotic molecule is selected from the group consisting of chloramphenicol, N-(2-hydroxyacetyl)-ciprofloxacin, novobiocin, and benzylpenicillin (penicillin G).
  8. 8 . The conjugated prodrug according to claim 1 , wherein the antibiotic molecule is an efflux pump inhibitor.
  9. 9 . The conjugated prodrug according to claim 1 , wherein the cleavable linker is selected from the group consisting of: —C(O)—(CH 2 ) n —C(O)— where n is an integer from 1 to 14, —C(O)—(CH 2 ) m —CH═CH—C(O)— where m is an integer from 1 to 10, —C(O)—CH—CH—C(O)—, —C(O)-(1,2-cyclohexyl)-C(O)—, —C(O)—Ar—C(O)— where Ar is a phenyl group, naphthyl group, or multi-ring aromatic group, —C(O)—(CH 2 ) n —C(O)—(CH 2 ) q —C(O)—where n is an integer from 1 to 14 and q is from 1 to 10, —C(O)—(CH 2 ) m —CH═CH—C(O)—(CH 2 ) q —C(O)—where m is an integer from 1 to 14 and q is from 1 to 10, —C(O)—CH═CH—C(O)—(CH 2 ) q —C(O)—where q is an integer from 1 to 10, —C(O)-(1,2-cyclohexyl)-C(O)—(CH 2 ) q —C(O)—where q is an integer from 1 to 10, and —C(O)—Ar—C(O)—(CH 2 ) q —C(O)—where Ar is a phenyl group, naphthyl group, or multi-ring aromatic group and q is an integer from 1 to 10.
  10. 10 . The conjugated prodrug according to claim 1 , which is selected from the group consisting of: wherein n is an integer from 1 to 14, q is an integer from 1 to 10, and Z is the peptide.
  11. 11 . The conjugated prodrug according to claim 10 , wherein the peptide comprises a glycine residue covalently attached to the cleavable linker.
  12. 12 . The conjugated prodrug according to claim 1 , wherein the cleavable linker is —C(O)—(CH 2 ) n —C(O)—, where n is an integer from 1 to 14.
  13. 13 . A pharmaceutical composition comprising a pharmaceutically acceptable carrier and a conjugated prodrug according to claim 1 .
  14. 14 . A method of enhancing intracellular concentration of an antibiotic agent in a bacterium, the method comprising: contacting a bacterium with an effective amount of the conjugated prodrug according to claim 1 , whereby said conjugated prodrug is taken up by the bacterium and said linker is cleaved intracellularly to release the antibiotic agent from said prodrug, causing an increase in the intracellular concentration of the antibiotic agent.

Description

This application is a national stage application under 35 U.S.C. § 371 of International Application No. PCT/US2020/051410, filed Sep. 18, 2020, which claims the priority benefit of U.S. Provisional Patent Application No. 62/902,371, filed Sep. 18, 2019, which is hereby incorporated by reference in its entirety. This invention was made with government support under grant number R21 AI130560 awarded by the National Institutes of Health, and grant number DMR-1420382 awarded by the National Science Foundation. The government has certain rights in the invention. FIELD The present invention relates to conjugated prodrugs that include a peptide conjugated to an antibiotic molecule via a cleavable linker and methods of use thereof. The invention also describes pharmaceutical compositions that include a pharmaceutically acceptable carrier and the conjugated prodrug. BACKGROUND Resulting from a large amount of antibiotics used for human and animal treatment, multidrug resistance (MDR) in bacteria remains a serious threat in public health (Neu, H. C., “The Crisis in Antibiotic Resistance,” Science 257(5073):1064-1073 (1992); Ghafourian et al., “Extended Spectrum Beta-Lactamases: Definition, Classification and Epidemiology. Curr. Issues Mol. Biol. 17(1):11-22 (2014); Carattoli, A., “Plasmids and the Spread of Resistance,” Int. J. Med. Microbiol. 303(6-7):298-304 (2013); Butler et al., “Antibiotics in the Clinical Pipeline at the End of 2015,” J. Antibiot. 70:3-24 (2017); and World Health Organization, WHO list of critically important antimicrobials for human medicine (WHO CIA list). No. WHO/NMH/FOS/FZD/19.1. World Health Organization: 2019). Drugs recently developed to thwart emerging antibiotic resistances, such as linezolid and the latest β-lactams, to vancomycin, have already lost effectiveness against some bacterial strains (Appelbaum, P. C., “2012 and Beyond: Potential for the Start of a Second Pre-Antibiotic Era?,” J. Antimicrob. Chemother. 67(9):2062-2068 (2012); Arias & Murray, “Emergence and Management of Drug-Resistant Enterococcal Infections,” Expert Rev. Anti-infect. Ther. 6(5):637-655 (2008); and Yong et al., “Characterization of a New Metallo-β-Lactamase Gene, blaNDM-1, and a Novel Erythromycin Esterase Gene Carried on a Unique Genetic Structure in Klebsiella pneumoniae Sequence Type 14 from India,” Antimicrob. Agents Chemother. 53(12):5046-5054 (2009)). An even more serious threat may be the emergence of MDR Gram-negative bacteria that are resistant to essentially all of the available agents (Livermore, D., “The Need for New Antibiotics,” Clin. Microbiol. Infect. 10:1-9 (2004)). Even more discouraging, the development of alternatives to the existing strategies for killing pathogenic bacteria has slowed dramatically over the past decades and failed to keep pace with the outbreak of resistance. Moreover, newer, successfully developed alternatives are strictly reserved to treat only the most serious infections. These factors have contributed to a limited antibiotic supply in the clinical pipeline (Butler et al., “Antibiotics in the Clinical Pipeline at the End of 2015,” J. Antibiot. 70:3-24 (2017) and Blaskovich, M. A., “The Diminished Antimicrobial Pipeline,” Microbiol. Aust. 40(2):92-96 (2019)). Thus, there is an urgent need for developing new antimicrobial approaches against MDR bacterial pathogens. Different strategies being used to discover and develop novel drugs to fight bacteria, mainly include (1) drug derivatives, which enhance the efficacy and safety of existing antibacterial agents via the modification of the drugs (Walsh et al., “Prospects for New Antibiotics: A Molecule-Centered Perspective,” J. Antibiot. 67(1):7-22 (2014)) or increase specificity, e.g., efflux pump inhibitors (Goemaere et al., “New Peptide Deformylase Inhibitors and Cooperative Interaction: A Combination to Improve Antibacterial Activity,” J. Antimicrob. Chemother. 67(6):1392-1400 (2012)); (2) discovery of new antibacterial agents, which involves the development of new tools to discover genomic or target-based antibiotics via previously unexplored mechanisms (Walsh & Wencewicz, “Prospects for New Antibiotics: A Molecule-Centered Perspective,” J. Antibiot. 67(1):7-22 (2014)), and classical or whole-cell antibacterial assay to find antibiotics produced by microorganism of different sources (Singh et al., “Screening Strategies for Discovery of Antibacterial Natural Products,” Expert Rev. Anti-infect. Ther. 9(8):589-613 (2011)); (3) bacteriophages or enzybiotics, which utilize bacteriophages or phage-lytic enzymes (Pastagia et al., “Lysins: The Arrival of Pathogen-Directed Anti-Infectives,” J. Med. Microbiol. 62(10):1506-1516 (2013) and Bragg et al., “Bacteriophages as Potential Treatment Option for Antibiotic Resistant Bacteria,” Adv. Exp. Med. Biol. 807:97-110 (2014)); (4) ecology/evolutionary biology approaches, which target the ecology and evolution of antibiotic resistance (Mosqueda et al., “Characterization of Plasmids Carr