Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus

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.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

“…While the concept that different enantiomers may have different biological activity is well-known, very recently Donald and co-authors observed that a single mutation (F98Y) in the methicillin-resistant Staphylococcus aureus flips the enantio-preference for cofactor binding and induces stereospecificity for binding of propargyl-linked antifolates as an antimicrobial drug . In this study, the bacterial enzyme target was found to evade inhibitor binding stereoselectively ( chiral evasion ).…”

Protocol for predicting drug-resistant protein mutations to an ERK2 inhibitor using RESISTOR

“…While the cut-off for resolution is still a matter of discussion in the scientific community, previous successful designs have used X-Ray diffraction resolutions ranging between 1.4 and 3.15 Å. 6 , 7 , 16 , 17 , 18 We have also had success with cryo-EM resolutions between 3.4 and 11.5 Å. For NMR structures, we recommend that the structure determination use RDCs; 2.…”

“…In cases where empirical structures are not available, it is possible to use docking, homology modeling, or other computational modeling techniques to generate structures. 1 , 6 , 7 , 17 , 20 For example, computational tools such as Modeller 21 or Alphafold 22 could be used to predict an initial protein structure, and docking tools such as AutoDock Vina 23 or those included in Maestro 19 could be used to dock the positive and negative design ligands. 1 , 3 With the recent explosion of available structural models, such as the Alphafold Protein Structure Database, 24 it may even be the case that a computationally predicted starting structure already exists.…”

Establishing a parallel compound screening method and identifying novel antimicrobial compounds targeting Staphylococcus aureus dihydrofolate reductase

“…SMX is a specific inhibitor of the dihydropteroate synthesis (DHPS) enzyme. It has been reported that the Phe98 group in DHFR is mutated to Tyr (F98Y) in many pathogenic S. aureus variants (Wang et al, 2022). Staphylococcus aureus with mutated DHFR developed resistance to the diaminopyrimidine (DAP) ring of TMP.…”

“…Therefore, identifying compounds different from TMP and those that are devoid of the DAP ring would help develop new therapeutic agents for patients infected with TMP-resistant S. aureus strains, as well as MRSA, VRSA, and caMRSA strains (Holland et al, 2014). Drug discovery targeting TMP-resistant S. aureus DHFR (TMP-resistant saDHFR) has attracted a great deal of attention (Huang et al, 2019;Keshipeddy et al, 2015;Reeve et al, 2019;Wang et al, 2022).…”