Elsevier

Talanta

Volume 240, 1 April 2022, 123206
Talanta

Quantitative in silico analysis of SARS-CoV-2 S-RBD omicron mutant transmissibility

https://doi.org/10.1016/j.talanta.2022.123206Get rights and content

Highlights

  • Quantitative in silico analysis of Covid-19 variants was performed for analyzing their transmissibility.

  • The calculated binding affinity was related to their transmissibility.

  • The mutation to basic amino acids enhanced their transmissibility.

  • l Proposed treatment medicines did not work for blocking the S-RBD and SCE-2 binding. A further modification was proposed.

Abstract

Covid-19 variants transmissibility was quantitatively analyzed in silico to understand the reaction mechanisms and to find the reaction inhibitors. Especially, SARS-CoV-2 omicron mutant (omicron S-RBD) binding affinity with human angiotensin-converting enzyme-2 (ACE-2) was quantitatively analyzed using molecular interaction (MI) energy values (kcal.mol−1) between the S-RBD and ACE-2. The MI of their optimized complex structures demonstrated that omicron's MI value (749.8) was 1.4 times delta MI (538.1) and 2.7 times alfa MI (276.9). The omicron S-RBD demonstrated the most vital transmissible strength. The 14 currently proposed medical treatment compounds did not show as the inhibitors to block the omicron S-RBD and ACE-2 binding; instead, they adsorbed at the ACE-2 active site and may inhibit the ACE-2 activity. A modified candidate (Gallo catechin gallate) whose two phenolic hydroxy groups were replaced with two carboxy groups was repulsed from ACE-2, indicating that further modification of medical treatment candidates may produce an effective docking inhibitor.

Keywords

SARS-CoV-2 omicron valiant
ACE-2
Binding affinity
Quantitative in silico analysis
Molecular interaction energy
Docking inhibitor

Abbreviations

SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2
S-RBD
Spiked receptor-binding domain
ACE-2
Angiotensin-converting enzyme-2
MI
Molecular interaction
ES
Electrostatic
HB
Hydrogen bonding
VW
van der Waals
FS
Final (optimized) structure

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