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Publications

Journal Article Epublish

PubMed: 39987216 DOI: 10.1038/s41598-025-89548-2

The Omicron variant BA.2.86.1 of SARS- CoV-2 demonstrates an altered interaction network and dynamic features to enhance the interaction with the hACE2.

Sci Rep 15(1):6482

Authors: Taimur Khan, Muhammad Shahab, Ahmad M Alharbi, Muhammad Waqas, Zakirullah, Guojun Zheng

Affiliations

  • State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
  • Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.
  • Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, 2100, Pakistan.
  • College of Life Sciences and Technology, Beijing University of Technology, Beijing, 100029, China.
  • State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.

Abstract

The SARS-CoV-2 variant BA.2.86 (Omicron) has emerged with unique mutations that may increase its transmission and infectivity. This study investigates how these mutations alter the interaction network and dynamic properties of the Omicron receptor-binding domain (RBD) compared to the wild-type virus, focusing on its binding affinity to the human ACE2 (hACE2) receptor. Protein-protein docking and all-atom molecular dynamics simulations were used to analyze structural and dynamic differences. Despite the structural similarity, the Omicron variant exhibits a distinct interaction network with new residues such as Lys353 and Arg498 that significantly enhance its binding capacity. The dynamic analysis reveals increased flexibility in the RBD, particularly in loop regions crucial for hACE2 interaction. Mutations significantly alter the secondary structure, leading to greater flexibility and conformational adaptability compared to the wild type. Binding free energy calculations confirm that the Omicron RBD has a higher binding affinity (- 70.47 kcal/mol) to hACE2 than the wild-type RBD (- 61.38 kcal/mol). These results suggest that the altered interaction network and enhanced dynamics of the Omicron variant contribute to its increased infectivity, providing insights for the development of targeted therapeutics and vaccines.

MeSH

Sars-Cov-2, Severe Acute Respiratory Syndrome-Related Coronavirus, Mutation