Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin Resistant <i>Staphylococcus aureus</i>

Reeve, Stephanie M.; Si, Debjani; Krucinska, J.; Yan, Yongzhao; Viswanathan, Kishore; Wang, Siyu; Holt, Graham T.; Frenkel, Marcel S.; Ojewole, Adegoke; Estrada, Alexavier; Agabiti, Sherry S; Alverson, Jeremy B.; Gibson, Nathan D.; Priestley, Nigel D.; Wiemer, Andrew J.; Donald, Bruce Randall; Wright, Dennis L.

doi:10.1021/acsinfecdis.9b00222

Cited by 24 publications

(17 citation statements)

References 42 publications

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“…However, the hTopo IIα DNA binding/cleavage domain is still able to oscillate between the closed and pre-open states in presence of etoposide, despite the fact that the G-segment base pairs remain annealed (see supplemental analysis in the Supplementary information). This conformational oscillation has also been observed in different bacterial DNA gyrase complexes bound to antibiotics 28 , 29 (Fig. 3 , Supplementary Figs.…”

Section: Resultssupporting

confidence: 68%

Structural basis for allosteric regulation of Human Topoisomerase IIα

et al. 2021

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The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, structural information on this large dimeric assembly is limited to the catalytic domains, hindering the exploration of allosteric mechanism governing the enzyme activities and the contribution of its non-conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human Topo IIα nucleoprotein complex in different conformations solved at subnanometer resolutions (3.6–7.4 Å). Our data unveils the molecular determinants that fine tune the allosteric connections between the ATPase domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA-binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in modulating the enzyme’s activities and opens perspective for the analysis of post-translational modifications.

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Section: Resultssupporting

confidence: 68%

Structural basis for allosteric regulation of Human Topoisomerase IIα

et al. 2021

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“…The use of computational drug design and protein design algorithms provided new insight, informed hypotheses in biology, and made contributions to biochemistry. The data and models we present here have already been useful in medicinal chemistry campaigns for F98Y resilient inhibitors [ 33 ], which suggests that they will have significant value for the scientific community.…”

Section: Discussionmentioning

confidence: 99%

“…The osprey -produced ensembles of conformations predicted the detailed molecular contacts around the enzyme active sites, providing a structural basis for the mechanism of F98Y-mediated resistance and SaDHFR’s chiral evasion. Moreover, our methodology and structural models of resistance mechanism have already been demonstrated to be helpful in a prospective empirical study on developing novel and resilient inhibitors towards drug candidates [ 33 ].…”

Section: Introductionmentioning

confidence: 99%

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus

et al. 2022

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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.

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“…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).…”

Section: Introductionmentioning

confidence: 99%

“…Based on the three-dimensional structure of the target protein, chemical compounds that bind to the pocket structure of the target were searched using proteincompound docking tools. In silico SBDS was performed using docking simulation tools such as GOLD (Scarpino et al, 2018), DOCK (Kinjo et al, 2013), GLIDE (Reddy et al, 2020), FRED (Gentile et al, 2020), AutoDock Vina (Trott and Olson, 2010), and Hex (Uciechowska-Kaczmarzyk et al, 2019. Multistep in silico SBDS, which consists of two or more docking simulation tools, has been used as a more effective way to identify active compounds (Taira et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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

Nakashima¹,

Takeuchi²,

Kawamoto³

et al. 2022

j app pharm sci

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The emergence of drug-resistant Staphylococcus aureus strains, such as methicillin-resistant S. aureus and vancomycinresistant S. aureus, and their spread not only inside hospitals but also outside hospitals has become a major problem worldwide. In this study, we investigated novel antimicrobial compounds targeting trimethoprim-resistant S. aureus dihydrofolate reductase (TMP-resistant saDHFR). A novel screening method, called the parallel compound screening (PCS) method, was established to analyze a common population of compounds that showed top scores using two docking tools, GOLD and AutoDock Vina. Using 154,118 compounds in the structural library, we conducted a threestep in silico structure-based drug screening, including PCS, and identified nine candidate compounds targeting TMP-resistant saDHFR. The growth inhibitory effects of the candidate compounds on bacteria were examined on Staphylococcus epidermidis, a model microbial strain of S. aureus. Among the candidate compounds, two compounds showed strong growth inhibition against S. epidermidis. The IC 50 values of the two compounds (6.34 and 56.94 µM) were determined. Molecular dynamics simulations predicted the direct and stable interactions between the active compounds and TMP-resistant saDHFR. The data regarding these active compounds from this study are expected to contribute to the development of new antibacterial agents against drug-resistant strains of S. aureus.

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Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin Resistant Staphylococcus aureus

Abstract: The spread of plasmid borne resistance enzymes in clinical Staphylococcus aureus isolates is rendering trimethoprim and iclaprim, both inhibitors of dihydrofolate reductase (DHFR), ineffective. Continued exploitation of these targets will require compounds that can broadly inhibit *

Cited by 24 publications

References 42 publications

Structural basis for allosteric regulation of Human Topoisomerase IIα

Structural basis for allosteric regulation of Human Topoisomerase IIα

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus

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

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