Programme

P.5 -- Poster, VCTP-48

Date: Tuesday, 1 August 2023

Time: 08:30 - 10:00

SARS-CoV-2 Omicron Sub-variants Bind to Human Cells: Evidence from Molecular Dynamics Simulation

Hoang Linh Nguyen (1,2), Nguyen Quoc Thai (3), and Mai Suan Li (4)

(1) Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam (2) Faculty of Natural Sciences, Duy Tan University, Danang City 550000, Vietnam (3) Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam (4) Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668, Warsaw, Poland

The emergence of the variant of concern Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) aggravates the COVID-19 pandemic due to its very contagious ability. Studies observed that Omicron binds ACE2 more strongly than Wildtype. The prevalence of Omicron in new COVID-19 cases facilities the emergence of novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1 and CH.1.1 to hACE2 using all-atom molecular dynamics simulation and molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding energy to BA.1 lineage in which BA.2.75 and BA.2.75.2 subvariants bind ACE2 PD more strongly than others. The electrostatic force dominates over van der Waals in the interaction between these two proteins.

Presenter: Nguyen Hoang Linh