Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations.
Kundan SolankiSajjan RajpootAshutosh KumarKam Y J ZhangTomokazu OhishiNik HiraniKhandu WadhonkarPramod PatidarQiuwei PanMubashir Baig MirzaPublished in: Future virology (2022)
Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.
Keyphrases
- sars cov
- wild type
- binding protein
- respiratory syndrome coronavirus
- dna binding
- angiotensin ii
- angiotensin converting enzyme
- protein protein
- molecular dynamics
- molecular dynamics simulations
- gene expression
- small molecule
- transcription factor
- escherichia coli
- mass spectrometry
- staphylococcus aureus
- pseudomonas aeruginosa
- coronavirus disease
- genome wide