Allosteric inhibition of tRNA synthetase Gln4 by N-pyrimidinyl-β-thiophenylacrylamides exerts highly selective antifungal activity

Emily Puumala; David Sychantha; Elizabeth Lach; Shawn Reeves; Sunna Nabeela; Meea Fogal; AkshatKumar Nigam; Jarrod W Johnson; Alán Aspuru-Guzik; Rebecca S Shapiro; Priya Uppuluri; Subha Kalyaanamoorthy; Jakob Magolan; Luke Whitesell; Nicole Robbins; Gerard D Wright; Leah E Cowen

doi:10.1016/j.chembiol.2024.01.010

Allosteric inhibition of tRNA synthetase Gln4 by N-pyrimidinyl-β-thiophenylacrylamides exerts highly selective antifungal activity

Cell Chem Biol. 2024 Apr 18;31(4):760-775.e17. doi: 10.1016/j.chembiol.2024.01.010. Epub 2024 Feb 22.

Authors

Emily Puumala¹, David Sychantha², Elizabeth Lach², Shawn Reeves³, Sunna Nabeela⁴, Meea Fogal⁵, AkshatKumar Nigam⁶, Jarrod W Johnson², Alán Aspuru-Guzik⁷, Rebecca S Shapiro⁵, Priya Uppuluri⁸, Subha Kalyaanamoorthy³, Jakob Magolan², Luke Whitesell¹, Nicole Robbins¹, Gerard D Wright², Leah E Cowen⁹

Affiliations

¹ Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
² M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
³ Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
⁴ Division of Infectious Diseases, The Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA.
⁵ Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
⁶ Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
⁷ Chemical Physics Theory Group, Department of Chemistry, University of Toronto Toronto, ON M5S 3H6, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada; Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4, Canada; Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada; Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada; Acceleration Consortium, University of Toronto, Toronto, ON M5S 3H6, Canada.
⁸ Division of Infectious Diseases, The Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA.
⁹ Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: leah.cowen@utoronto.ca.

PMID: 38402621
PMCID: PMC11031294 (available on 2025-04-18)
DOI: 10.1016/j.chembiol.2024.01.010

Abstract

Candida species are among the most prevalent causes of systemic fungal infections, which account for ∼1.5 million annual fatalities. Here, we build on a compound screen that identified the molecule N-pyrimidinyl-β-thiophenylacrylamide (NP-BTA), which strongly inhibits Candida albicans growth. NP-BTA was hypothesized to target C. albicans glutaminyl-tRNA synthetase, Gln4. Here, we confirmed through in vitro amino-acylation assays NP-BTA is a potent inhibitor of Gln4, and we defined how NP-BTA arrests Gln4's transferase activity using co-crystallography. This analysis also uncovered Met496 as a critical residue for the compound's species-selective target engagement and potency. Structure-activity relationship (SAR) studies demonstrated the NP-BTA scaffold is subject to oxidative and non-oxidative metabolism, making it unsuitable for systemic administration. In a mouse dermatomycosis model, however, topical application of the compound provided significant therapeutic benefit. This work expands the repertoire of antifungal protein synthesis target mechanisms and provides a path to develop Gln4 inhibitors.

Keywords: Candida; Gln4; antifungal; fungal pathogens; glutaminyl-tRNA synthetase; translation inhibitor.

MeSH terms

Amino Acyl-tRNA Synthetases* / genetics
Animals
Antifungal Agents* / pharmacology
Candida albicans
Mice
Structure-Activity Relationship

Substances

Antifungal Agents
Amino Acyl-tRNA Synthetases

Grants and funding

R01 AI127375/AI/NIAID NIH HHS/United States