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ORIGINAL RESEARCH article

Front. Bioinform.
Sec. Integrative Bioinformatics
Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1411935
This article is part of the Research Topic Omics Technologies and Bioinformatic Tools in Probiotic Research View all articles

Predictive Identification and Design of Potent Inhibitors Targeting Resistance-Inducing Candidate Genes from E. Coli Whole Genome Sequences

Provisionally accepted
Abdullahi T. Aborode Abdullahi T. Aborode 1Neeraj Kumar Neeraj Kumar 2Christopher Olowosoke Christopher Olowosoke 3Tope A. Ibisanmi Tope A. Ibisanmi 3Islamiyyah Ayoade Islamiyyah Ayoade 3Haruna I. Umar Haruna I. Umar 3Abdullahi T. Jamiu Abdullahi T. Jamiu 4Basit Bolarinwa Basit Bolarinwa 5Zainab Olapade Zainab Olapade 6Abidemi R. Idowu Abidemi R. Idowu 7Ibrahim O. Adelakun Ibrahim O. Adelakun 8Isreal Onifade Isreal Onifade 9Benjamin Akangbe Benjamin Akangbe 10Modesta Abacheng Modesta Abacheng 10Odion O. Ikhimiukor Odion O. Ikhimiukor 8Aeshah A. Awaji Aeshah A. Awaji 11Ridwan O. Adesola Ridwan O. Adesola 12*
  • 1 Mississippi State University, Starkville, Mississippi, United States
  • 2 Bhupal Nobles University, Udaipur, Rajasthan, India
  • 3 Federal University of Technology, Akure, Ondo, Nigeria
  • 4 University of the Free State, Bloemfontein, Free State, South Africa
  • 5 The Maurice and Gabriela Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Tel Aviv, Israel
  • 6 Lamar University, Beaumont, Texas, United States
  • 7 University of Louisville, Louisville, Colorado, United States
  • 8 State of New York, New York, United States
  • 9 University at Albany, Albany, New York, United States
  • 10 Georgia State University, Atlanta, Georgia, United States
  • 11 Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia
  • 12 Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria

The final, formatted version of the article will be published soon.

    The work aims to utilize predictive modelling in drug discovery to unravel potential candidate genes from E. coli that are implicated in antimicrobial resistance and subsequently target gidB, MacB and KatG with some plant compounds from plants with reported antibacterial potentials. The resistance genes and plasmid were identified from Ten whole-genome sequence data sets of E. coli, forty-two plant compounds were selected with their 3D structures retrieved and optimized for docking, 3D crystals structures of KatG, MacB, and gidB were retrieved and prepared for molecular docking, molecular dynamics simulations, and ADMET profiling. Hesperidin showed the least binding energy (kcal/mol) against KatG (-9.3), MacB (-10.7), and gidB (-6.7). good pharmacokinetics profile and structure-dynamics integrity with their respective protein complexes was observed. While these findings suggest hesperidin as a potential inhibitor against MacB, gidB and KatG in E. coli, validation through urgent in vitro and in vivo experiments is important going forward. This research holds promise for providing an alternative avenue to address existing antimicrobial resistance associated with E. coli's MacB, gidB, and KatG.

    Keywords: E. coli, Resistance, antimicrobial, inhibitors, Genes, whole genome sequences

    Received: 03 Apr 2024; Accepted: 12 Jun 2024.

    Copyright: © 2024 Aborode, Kumar, Olowosoke, Ibisanmi, Ayoade, Umar, Jamiu, Bolarinwa, Olapade, Idowu, Adelakun, Onifade, Akangbe, Abacheng, Ikhimiukor, Awaji and Adesola. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Ridwan O. Adesola, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.