US-20260124203-A1 - CHEMICAL SYNTHETIC LETHALITY FOR ANTIMICROBIAL THERAPY

Abstract

The present disclosure provides a system for treating melioidosis, comprising a first antimicrobial agent comprising trimethoprim at a subinhibitory concentration and a second antimicrobial agent comprising a FolE2 enzyme inhibitor selected from dehydrocostus lactone, parthenolide, or β-lapachone, wherein the combination of the first antimicrobial agent and the second antimicrobial agent exhibits chemical synthetic lethality against Burkholderia pseudomallei while having minimal effect on commensal bacteria. The subinhibitory concentration of trimethoprim ranges between 5 μM and 30 μM. The FolE2 enzyme inhibitor acts as a mechanism-based inhibitor that covalently modifies a catalytic cysteine residue (Cys154) of the FolE2 enzyme. The combination exhibits greater than 90% growth suppression against Burkholderia pseudomallei . Methods for treating melioidosis and identifying antimicrobial drug targets using chemical synthetic lethality screening approaches are also provided.

Inventors

• Mohammad Seyedsayamdost
• Yifan Zhang
• Josephine Chandler
• Jennifer Klaus
• Katherine Davis
• Kirklin McWhorter
• Paul Rosen

Assignees

• THE TRUSTEES OF PRINCETON UNIVERSITY
• EMORY UNIVERSITY
• UNIVERSITY OF KANSAS

Dates

Publication Date

20260507

Application Date

20251105

Claims (20)

1. 1 . A system for treating melioidosis, comprising: a first antimicrobial agent comprising trimethoprim at a subinhibitory concentration; and a second antimicrobial agent comprising a FolE2 enzyme inhibitor selected from dehydrocostus lactone, parthenolide, or β-lapachone; wherein the combination of the first antimicrobial agent and the second antimicrobial agent exhibits chemical synthetic lethality against Burkholderia pseudomallei while having minimal effect on commensal bacteria.
2. 2 . The system of claim 1 , wherein the subinhibitory concentration of trimethoprim is between 5 μM and 30 μM.
3. 3 . The system of claim 2 , wherein the subinhibitory concentration of trimethoprim is between 5 μM and 30 μM.
4. 4 . The system of claim 1 , wherein the FolE2 enzyme inhibitor is dehydrocostus lactone.
5. 5 . The system of claim 4 , wherein the dehydrocostus lactone has an IC 50 value of between 1.7 μM and 2.5 μM in the presence of trimethoprim.
6. 6 . The system of claim 1 , wherein the FolE2 enzyme inhibitor is β-lapachone.
7. 7 . The system of claim 6 , wherein the β-lapachone has an IC 50 value of between 3.2 μM and 6.4 μM in the presence of trimethoprim.
8. 8 . The system of claim 1 , wherein the FolE2 enzyme inhibitor is parthenolide.
9. 9 . The system of claim 1 , wherein the combination exhibits greater than 90% growth suppression against Burkholderia pseudomallei.
10. 10 . The system of claim 1 , wherein the FolE2 enzyme inhibitor acts as a mechanism-based inhibitor that covalently modifies a catalytic cysteine residue of the FolE2 enzyme.
11. 11 . The system of claim 10 , wherein the catalytic cysteine residue is Cys154.
12. 12 . A method for treating melioidosis in a subject, comprising: administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising trimethoprim at a subinhibitory concentration and a FolE2 enzyme inhibitor; wherein the FolE2 enzyme inhibitor is selected from dehydrocostus lactone, parthenolide, or β-lapachone; and wherein the combination exhibits chemical synthetic lethality against Burkholderia pseudomallei.
13. 13 . The method of claim 12 , wherein the subinhibitory concentration of trimethoprim is between 5 μM and 30 μM.
14. 14 . The method of claim 13 , wherein the subinhibitory concentration of trimethoprim is about 20 μM.
15. 15 . The method of claim 12 , wherein the FolE2 enzyme inhibitor is dehydrocostus lactone having an IC 50 value of between 1.7 μM and 2.5 μM in the presence of trimethoprim.
16. 16 . The method of claim 12 , wherein the FolE2 enzyme inhibitor acts as a mechanism-based inhibitor that covalently modifies a catalytic cysteine residue of the FolE2 enzyme.
17. 17 . The method of claim 16 , wherein the catalytic cysteine residue is Cys154.
18. 18 . The method of claim 12 , wherein the combination exhibits greater than 90% growth suppression against Burkholderia pseudomallei while having minimal effect on commensal bacteria selected from Bacteroides fragilis, Bifidobacterium longum, Clostridium sporogenes , and Parabacteroides distasonis.
19. 19 . A method for identifying antimicrobial drug targets, comprising: screening a library of compounds for growth inhibition of a target bacterial pathogen in the presence of a subinhibitory concentration of a known antibiotic; identifying compounds that exhibit no growth inhibition individually but cause growth inhibition when combined with the subinhibitory concentration of the known antibiotic; determining the molecular target of the identified compounds; and validating the molecular target as a conditionally essential enzyme that becomes essential in the presence of the subinhibitory concentration of the known antibiotic.
20. 20 . The method of claim 19 , wherein the library of compounds comprises natural products and FDA-approved small-molecule drugs.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application No. 63/716,570, titled Combatting Melioidosis with Chemical Synthetic Lethality, filed Nov. 5, 2024, which is hereby incorporated by reference in its entirety. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT This invention was made with government support under Grant Nos. GM133572, GM147557, and GM140034 awarded by the National Institutes of Health and DE-AC02-06CH11357 awarded by the Department of Energy. The government has certain rights in the invention. TECHNICAL FIELD The present disclosure relates to antimicrobial therapy methods, and more particularly to chemical synthetic lethality approaches for treating bacterial infections by combining subinhibitory concentrations of known antibiotics with enzyme inhibitors to selectively target pathogenic bacteria while sparing commensal microorganisms. BACKGROUND Antimicrobial resistance represents a growing global health challenge that threatens the effectiveness of existing antibiotic therapies. The emergence of resistant bacterial strains has outpaced the development of new antimicrobial agents, creating an urgent need for novel therapeutic approaches. Traditional antibiotic discovery methods have increasingly yielded diminishing returns, with many pharmaceutical companies reducing their investment in antimicrobial research due to economic and scientific challenges. Conventional antimicrobial therapy typically relies on single-agent treatments that target widely distributed bacterial pathways or structures. While this approach has proven effective against many pathogens, it often results in broad-spectrum activity that can disrupt beneficial microbial communities, particularly in the gastrointestinal tract. Such disruption of the microbiome can lead to secondary infections, antibiotic-associated diarrhea, and other adverse effects that complicate patient care. The concept of synthetic lethality, originally developed in genetics, describes a phenomenon where the simultaneous disruption of two genes results in cell death, while disruption of either gene alone is tolerated. This principle has been successfully applied in cancer therapy, where combinations of targeted agents can selectively kill cancer cells while sparing normal cells. However, the application of synthetic lethality principles to antimicrobial therapy remains largely unexplored. Many bacterial pathogens possess large genomes that encode extensive metabolic capabilities and redundant pathways, making them particularly challenging to treat with conventional single-agent therapies. These organisms can often compensate for the inhibition of one pathway by upregulating alternative metabolic routes, leading to treatment failure or the development of resistance. The metabolic flexibility of such pathogens suggests that combination approaches targeting multiple pathways simultaneously may be more effective. Current combination antimicrobial therapies, such as trimethoprim-sulfamethoxazole, typically employ two agents at therapeutic concentrations to achieve synergistic effects or prevent resistance development. However, these combinations often retain the broad-spectrum activity of their individual components, continuing to impact commensal bacteria and potentially causing collateral damage to the host microbiome. The identification of conditionally essential genes and pathways in bacterial pathogens offers new opportunities for selective antimicrobial targeting. These pathways may be dispensable under normal growth conditions but become essential when bacteria are subjected to specific stresses or metabolic perturbations. Such conditional essentiality could provide a basis for developing more selective antimicrobial strategies that exploit the unique metabolic requirements of pathogens under stress conditions. SUMMARY This summary is provided to introduce a selection of concepts in a simplified form that are further described below in the detailed description. This summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used as an aid in determining the scope of the claimed subject matter. According to an aspect of the present disclosure, a system for treating melioidosis is provided. The system comprises a first antimicrobial agent comprising trimethoprim at a subinhibitory concentration and a second antimicrobial agent comprising a FolE2 enzyme inhibitor selected from dehydrocostus lactone, parthenolide, or β-lapachone. The combination of the first antimicrobial agent and the second antimicrobial agent exhibits chemical synthetic lethality against Burkholderia pseudomallei while having minimal effect on commensal bacteria. This combination approach provides selective antimicrobial activity by exploiting the metabolic vulnerabilities of pathogenic bacteria under stress conditions while preserving beneficial micro