SARS-CoV-2 omicron RBD forms a weaker binding affinity to hACE2 compared to Delta RBD in in-silico studies.
Hoa Thanh LeLinh Hoang TranHuong Thi Thu PhungPublished in: Journal of biomolecular structure & dynamics (2023)
The COVID-19 pandemic sparked an unprecedented race in biotechnology in a search for effective therapies and a preventive vaccine. The continued appearance of SARS-CoV-2 variants of concern (VoCs) further swept the world. The entry of SARS-CoV-2 into cells is mediated by binding the receptor-binding domain (RBD) of the S protein to the cell-surface receptor, human angiotensin-converting enzyme 2 (hACE2). In this study, using a coarse-grained force field to parameterize the system, we employed steered-molecular dynamics (SMD) simulations to reveal the binding of SARS-CoV-2 Delta/Omicron RBD to hACE2. Our benchmarked results demonstrate a good correlation between computed rupture force and experimental binding free energy for known protein-protein systems. Moreover, our findings show that the Omicron RBD has a weaker binding affinity to hACE2, consistent with the respective experimental results. This indicates that our method can effectively be applied to other emerging SARS-CoV-2 strains.Communicated by Ramaswamy H. Sarma.
Keyphrases
- sars cov
- molecular dynamics
- binding protein
- respiratory syndrome coronavirus
- protein protein
- dna binding
- density functional theory
- oxidative stress
- escherichia coli
- angiotensin ii
- induced apoptosis
- molecular dynamics simulations
- genome wide
- computed tomography
- gene expression
- signaling pathway
- cell death
- optical coherence tomography
- copy number
- induced pluripotent stem cells
- mass spectrometry
- contrast enhanced
- cell proliferation