Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach

• Authors: Swetha Pulakuntla, REVA University; Kiran Bharat Lokhande, Dr. D. Y. Patil Vidyapeeth; Pannuru Padmavathi, DR Biosciences, Research & Development Unit; Meena Pal, ICMR-National Institute of Cancer Prevention and Research; Kakumani Venkateswara Swamy, MIT Art, Design and Technology University; Jayashree Sadasivam, REVA University; Shri Abhiav Singh, Indian Council of Medical Research; Sree Latha Aramgam, REVA University; Vaddi Damodara Reddy, REVA University
• Journal Title: VirusDisease
• Volume: Volume 32, Number 4
• Publisher: Indian Virological Society | 2021-12-01, Pages 690-702
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.1007/s13337-021-00720-4
• Subjects: Biology, Molecular; Chemistry, Biochemistry
• Keywords: SARS-CoV-2; simulation approach; Mutational analysis

Abstract

The novel SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) is spreading, as the causative pathogen of coronavirus disease-19 (COVID-19). It has infected more than 1.65 billion people all over the world since it was discovered and reported 3.43 million deaths by mid of May 2021. SARS-CoV-2 enters the host cell by binding to viral surface glycoprotein (S protein) with human ACE2 (angiotensin-converting enzyme2). Spike protein (contains S1 and S2 sub-domains) molecular interaction with the host cells is considered as a major step in the viral entry and disease initiation and progression and this identifies spike protein as a promising therapeutic target against antiviral drugs. Currently, there are no efficient antiviral drugs for the prevention of COVID-19 infection. In this study, we have analyzed global 8719 spike protein sequences from patients infected with SAR-CoV-2. These SAR-CoV-2 genome sequences were downloaded from the GISAID database. By using an open reading frame (ORF) tool we have identified the spike protein sequence. With these, all spike protein amino acid sequences are subjected to multiple sequence alignment (MSA) with Wuhan strain spike protein sequence as a query sequence, and it shows all SAR-CoV strain spike proteins are 99.8% identical. In the mutational analysis, we found 639 mutations in the spike protein sequence of SARS-CoV-2 and identified/highlighted 20 common mutations L5F, T22I, T29I, H49Y, L54F, V90F, S98F, S221L, S254F, V367F, A520S, T572I, D614G, H655Y, P809S, A879S, D936Y, A1020S, A1078S, and H1101Y. Further, we have analyzed the crystal structure of the 2019-nCoV chimeric receptor-binding complex with ACE2 (PDB ID: 6VW1) as a major target protein. The spike receptor binding protein (RBD) used as target region for our studies with FDA-approved drugs for repurposing, and identified few anti-SARS-CoV2 potential drugs (Silmitasertib, AC-55541, Merimepodib, XL413, AZ3451) based on their docking score and binding mode calculations expected to strongly bind to motifs of ACE2 receptor and may show impart relief in COVID-19 patients.