An in-silico approach to identify the potential hot spots in SARS-CoV-2 spike RBD to block the interaction with ACE2 receptor.

ABSTRACT

A novel acute viral pneumonia induced by SARS-CoV-2 exploded at the end of 2019, causing a severe medical and economic crisis. For developing specific pharmacotherapy against SARS-CoV-2, an in silico virtual screening was developed for the available in-house molecules. The conserved domain analysis was performed to identify the highly conserved and exposed amino acid regions in the SARS-CoV-2-S RBD sites. The Protein-Protein interaction analyses demonstrated the higher affinity between the SARS-CoV-2-S and ACE2 due to varieties of significant interactions between them. The computational alanine scanning mutation study has recognized the highly stabilized amino acids in the SARS-CoV-2-S RBD/ACE2 complex. The cumulative sequence investigations have inferred that Lys417, Phe486, Asn487, Tyr489, and Gln493 are perhaps the iconic target amino acids to develop a drug molecule or vaccine against SARS-CoV-2 infection. Most of the selected compounds include luteolin, zhebeirine, 3-dehydroverticine, embelin, andrographolide, ophiopogonin D, crocin-1, sprengerinin A, B, C, peimine, etc. were exhibited distinguish drug actions through the strong hydrogen bonding with the hot spots of the RBD. Besides, the 100 ns molecular dynamics simulation and free energy binding analysis showed the significant efficacy of luteolin to inhibit the infection of SARS-CoV-2. HighlightsHighly conserved and exposed amino acids in the SARS-CoV-2-S-RBD sites has been identifiedComputational alanine scanning mutation study has recognized the highly stabilized hot spots in the SARS-CoV-2-S RBD/ACE2 complex.Virtual screening has been executed to identify the drug actions in the RBD regionMost of the selected natural products were involved in the distinctive strong interactions with hot spots of RBD to inhibit the infection of SARS-CoV-2.[Formula see text] Communicated by Ramaswamy H. Sarma.