Computers in Biology and Medicine 138 (2021) 104929 Available online 9 October 2021 0010-4825/© 2021 Elsevier Ltd. All rights reserved. Structural probing of HapR to identify potent phytochemicals to control Vibrio cholera through integrated computational approaches Muhammad Tahir ul Qamar a, 1 , Sajjad Ahmad b, 1 , Abbas Khan c, 1 , Muhammad Usman Mirza d , Sarfraz Ahmad e , Asma Abro f , Ling-Ling Chen a, * , Ahmad Almatroudi g , Dong-Qing Wei c, h, i, ** a College of Life Science and Technology, Guangxi University, Nanning, PR China b Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan c Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China d Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada e Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia f Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology Engineering and Management Sciences, Quetta, Pakistan g Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia h Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, PR China i State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China A R T I C L E INFO Keywords: Vibrio cholera HapR Medicinal plants Molecular docking Molecular dynamics simulations ABSTRACT Cholera is a severe small intestine bacterial disease caused by consumption of water and food contaminated with Vibrio cholera. The disease causes watery diarrhea leading to severe dehydration and even death if left untreated. In the past few decades, V. cholerae has emerged as multidrug-resistant enteric pathogen due to its rapid ability to adapt in detrimental environmental conditions. This research study aimed to design inhibitors of a master virulence gene expression regulator, HapR. HapR is critical in regulating the expression of several set of V. cholera virulence genes, quorum-sensing circuits and bioflm formation. A blind docking strategy was employed to infer the natural binding tendency of diverse phytochemicals extracted from medicinal plants by exposing the whole HapR structure to the screening library. Scoring function criteria was applied to prioritize molecules with strong binding affnity (binding energy < 11 kcal/mol) and as such two compounds: Strych- nogucine A and Gallufavanone were fltered. Both the compounds were found favourably binding to the conserved dimerization interface of HapR. One rare binding conformation of Strychnogucine A was noticed docked at the elongated cavity formed by α1, α4 and α6 (binding energy of 12.5 kcal/mol). The binding sta- bility of both top leads at dimer interface and elongated cavity was further estimated using long run of molecular dynamics simulations, followed by MMGB/PBSA binding free energy calculations to defne the dominance of different binding energies. In a nutshell, this study presents computational evidence on antibacterial potential of phytochemicals capable of directly targeting bacterial virulence and highlight their great capacity to be utilized in the future experimental studies to stop the evolution of antibiotic resistance evolution. 1. Introduction Cholera is a commonly occurring deadly disease caused by the gram- negative bacterium Vibrio cholerae. The expression of various virulence factors such as cholera toxin, toxin co-regulated pilus and a critical colonization factor, play key role in enabling the bacterium to cause the disease [1,2]. A transcriptional cascade is responsible for the expression of these factors that starts at the tcpPH promoter [3–5]. AphA and AphB * Corresponding author. ** Corresponding author. Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China. E-mail addresses: llchen@gxu.edu.cn (L.-L. Chen), dqwei@sjtu.edu.cn (D.-Q. Wei). 1 These authors contributed equally in this study. Contents lists available at ScienceDirect Computers in Biology and Medicine journal homepage: www.elsevier.com/locate/compbiomed https://doi.org/10.1016/j.compbiomed.2021.104929 Received 19 August 2021; Received in revised form 6 October 2021; Accepted 6 October 2021