Journal article
Structure-based virtual screening, in silico docking, ADME properties prediction and molecular dynamics studies for the identification of potential inhibitors against SARS-CoV-2 M-pro
Molecular diversity, v 26(3), pp 1645-1661
01 Jun 2022
PMID: 34480682
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
COVID-19 is a viral pandemic caused by SARS-CoV-2. Due to its highly contagious nature, millions of people are getting affected worldwide knocking down the delicate global socio-economic equilibrium. According to the World Health Organization, COVID-19 has affected over 186 million people with a mortality of around 4 million as of July 09, 2021. Currently, there are few therapeutic options available for COVID-19 control. The rapid mutations in SARS-CoV-2 genome and development of new virulent strains with increased infection and mortality among COVID-19 patients, there is a great need to discover more potential drugs for SARS-CoV-2 on a priority basis. One of the key viral enzymes responsible for the replication and maturation of SARS-CoV-2 is M-pro protein. In the current study, structure-based virtual screening was used to identify four potential ligands against SARS-CoV-2 M-pro from a set of 8,722 ASINEX library compounds. These four compounds were evaluated using ADME filter to check their ADME profile and druggability, and all the four compounds were found to be within the current pharmacological acceptable range. They were individually docked to SARS-CoV-2 M-pro protein to assess their molecular interactions. Further, molecular dynamics (MD) simulations was carried out on protein-ligand complex using Desmond at 100 ns to explore their binding conformational stability. Based on RMSD, RMSF and hydrogen bond interactions, it was found that the stability of protein-ligand complex was maintained throughout the entire 100 ns simulations for all the four compounds. Some of the key ligand amino acid residues participated in stabilizing the protein-ligand interactions includes GLN 189, SER 10, GLU 166, ASN 142 with PHE 66 and TRP 132 of SARS-CoV-2 M-pro. Further optimization of these compounds could lead to promising drug candidates for SARS-CoV-2 M-pro target.
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Details
- Title
- Structure-based virtual screening, in silico docking, ADME properties prediction and molecular dynamics studies for the identification of potential inhibitors against SARS-CoV-2 M-pro
- Creators
- Anbuselvam Mohan - Department of BiotechnologyNicole Rendine - Drexel UniversityMohammed Kassim Sudheer Mohammed - Government Arts College, CoimbatoreAnbuselvam Jeeva - Bharathidasan UniversityHai-Feng Ji - Drexel UniversityVenkateswara Rao Talluri - Varsha Bioscience and Technology (India)
- Publication Details
- Molecular diversity, v 26(3), pp 1645-1661
- Publisher
- Springer Nature
- Number of pages
- 17
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemistry
- Web of Science ID
- WOS:000692433600001
- Scopus ID
- 2-s2.0-85114183579
- Other Identifier
- 991019330626204721
UN Sustainable Development Goals (SDGs)
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Chemistry, Applied
- Chemistry, Medicinal
- Chemistry, Multidisciplinary