1
|
Wang S, Reeve SM, Holt GT, Ojewole AA, Frenkel MS, Gainza P, Keshipeddy S, Fowler VG, Wright DL, Donald BR. Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus. PLoS Comput Biol 2022; 18:e1009855. [PMID: 35143481 PMCID: PMC8865654 DOI: 10.1371/journal.pcbi.1009855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/23/2022] [Accepted: 01/21/2022] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers resistance to the clinically important antifolate trimethoprim (TMP). Propargyl-linked antifolates (PLAs), next generation DHFR inhibitors, are much more resilient than TMP against this F98Y variant, yet this F98Y substitution still reduces efficacy of these agents. Surprisingly, differences in the enantiomeric configuration at the stereogenic center of PLAs influence the isomeric state of the NADPH cofactor. To understand the molecular basis of F98Y-mediated resistance and how PLAs' inhibition drives NADPH isomeric states, we used protein design algorithms in the osprey protein design software suite to analyze a comprehensive suite of structural, biophysical, biochemical, and computational data. Here, we present a model showing how F98Y SaDHFR exploits a different anomeric configuration of NADPH to evade certain PLAs' inhibition, while other PLAs remain unaffected by this resistance mechanism.
Collapse
Affiliation(s)
- Siyu Wang
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Stephanie M. Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Graham T. Holt
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Adegoke A. Ojewole
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Marcel S. Frenkel
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Pablo Gainza
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Vance G. Fowler
- Division of Infections Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, United States of America
| | - Bruce R. Donald
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
2
|
Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Eur J Med Chem 2019; 183:111673. [PMID: 31536894 DOI: 10.1016/j.ejmech.2019.111673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 02/08/2023]
Abstract
Cryptosporidiosis is a human gastrointestinal disease caused by protozoans of the genus Cryptosporidium, which can be fatal in immunocompromised individuals. The essential enzyme, thymidylate synthase (TS), is responsible for de novo synthesis of deoxythymidine monophosphate. The TS active site is relatively conserved between Cryptosporidium and human enzymes. In previous work, we identified compound 1, (2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidin-methyl-phenyl-l-glutamic acid), as a promising selective Cryptosporidium hominis TS (ChTS) inhibitor. In the present study, we explore the structure-activity relationship around 1 glutamate moiety by synthesizing and biochemically evaluating the inhibitory activity of analogues against ChTS and human TS (hTS). X-Ray crystal structures were obtained for compounds bound to both ChTS and hTS. We establish the importance of the 2-phenylacetic acid moiety methylene linker in optimally positioning compounds 23, 24, and 25 within the active site. Moreover, through the comparison of structural data for 5, 14, 15, and 23 bound in both ChTS and hTS identified that active site rigidity is a driving force in determining inhibitor selectivity.
Collapse
|