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Identification of New Dna Gyrase Inhibitors Based on Bioactive Compounds From Streptomyces: Structure-Based Virtual Screening and Molecular Dynamics Simulations Approaches Publisher Pubmed



Kalhor H1 ; Sadeghi S2 ; Marashiyan M3 ; Kalhor R4 ; Aghaei Gharehbolagh S5 ; Akbari Eidgahi MR1 ; Rahimi H3
Authors
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Authors Affiliations
  1. 1. Department and Biotechnology Research Center, Semnan University of Medical Sciences, Semnan, Iran
  2. 2. Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
  3. 3. Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
  4. 4. Department of Biology, Qom Branch, Islamic Azad University, Qom, Iran
  5. 5. Department of Medical Mycology & Parasitology School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

Source: Journal of Biomolecular Structure and Dynamics Published:2020


Abstract

DNA gyrase enzyme has vital role in bacterial survival and can be considered as a potential drug target. Owing to the appearance of resistance to gyrase-targeted drugs, especially fluoroquinolone, screening new compounds which bind more efficiently to the mutant binding pocket is essential. Hence, in this work, using Smina Autodock and through structure-based virtual screening of StreptomeDB, several natural products were discovered based on the SimocyclinoneD8 (SD8) binding pocket of GyrA subunit of DNA gyrase. After evaluation of binding affinity, binding modes, critical interactions and physicochemical and pharmaceutical properties, three lead compounds were selected for further analysis. Afterward 60 ns molecular dynamics simulations were performed and binding free energies were calculated by the molecular mechanics/Poisson–Boltzmann surface area method. Also, interaction of the selected lead compounds with the mutated GyrA protein was evaluated. Results indicated that all of the selected compounds could bind to the both wild-type and mutated GyrA with the binding affinities remarkably higher than SimocyclinoneD8. Interestingly, we noticed that the selected compounds comprised angucycline moiety in their structure which could sufficiently interact with GyrA and block the DNA binding pocket of DNA gyrase, in silico. In conclusion, three DNA gyrase inhibitors were identified successfully which were highly capable of impeding DNA gyrase and can be considered as potential drug candidates for treatment of fluoroquinolone-resistant strains. Communicated by Ramaswamy H. Sarma. © 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group.
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