Influence of the T to S mutation at the STMK motif on antibiotic resistance of penicillin binding protein 1A: A comprehensive computational study

Behmard, Esmaeil and Ahmadi, Ali and Najafi, Ali (2019) Influence of the T to S mutation at the STMK motif on antibiotic resistance of penicillin binding protein 1A: A comprehensive computational study. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 87. pp. 185-191.

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Abstract

The emergence of antibiotic resistance has attracted the attention of scientists and scientific circles over the decades. beta-Lactam antibiotics resistance is a worldwide therapeutic challenge in bacterial infections, mediated through several mechanisms of which mutations in Penicillin Binding Proteins (PBPs) are an important issue, making critical therapeutic problems in the human population. Accordingly, investigating the dynamic structures of mutant variants could result in a profound understanding of such a specific resistance. Therefore, this work investigated structural properties sampled by all-atom molecular dynamics (MD) simulations, umbrella sampling, and binding free energy calculations for both a wild type and a cefotaxime-resistant T to S mutant of PBP1A. The T to S mutation significantly reduces the binding affinity of cefotaxime (a frequently clinically-administrated beta-lactam antibiotic) as the PBP1A inhibitor. In the conventional MD simulations presented here, more fluctuations of the mutant's active site cleft margins were detected. The cleft of the mutant protein also opened remarkably more than the wild-type's cleft and displayed more flexibility. Thus, our findings have shown that flexibility of cleft margins of the active site in the mutant PBP1A immediately results in the catalytic cleft opening. In addition, binding free energy calculation suggests that reducing hydrophobic contacts and increasing the polar contribution in the binding energy may play an important role in cefotaxime resistance. (C) 2018 Elsevier Inc. All rights reserved.

Item Type: Article
Uncontrolled Keywords: Penicillin binding protein 1A; beta-Lactam antibiotic; Antibiotic resistance; Umbrella sampling; MD simulations
Subjects: QV Pharmacology
Depositing User: Unnamed user with email eprints@fums.ac.ir
Date Deposited: 04 Jan 2020 08:35
Last Modified: 04 Jan 2020 08:35
URI: http://eprints.fums.ac.ir/id/eprint/2619

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