Mutation Pattern in the Receptor Binding Motif of SARS-Cov-2 Variants and the Effect on Molecular Interactions in Docked Ligand Complexes


  • Israel E. Ebhohimen Department of Chemical Sciences, Samuel Adegboyega University, Ogwa, Edo State, Nigeria
  • Ojei H. Onyijen Department of Mathematical and Physical Sciences, Samuel Adegboyega University, Ogwa, Edo State, Nigeria
  • Vaishali Arora Department of Botany, University of Delhi, India
  • Vanisha Arora Department of Botany, Osmania University, Hyderabad, India
  • Victoria T. Adeleke Department of Chemical Engineering, Mangosuthu University of Technology, Umlazi, South Africa
  • Moses Okpeku Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa


SARS-Cov-2 spike glycoprotein, receptor binding motif,, Covid-19,, Molecular dynamics simulation


The spike glycoprotein of SARS-Cov-2 is a therapeutic target for Covid-19 and mutations in the Receptor Binding Motif (RBM) may alter the binding properties of ligands proposed to inhibit viral entry. This study aimed to identify the existence of a mutation pattern in the RBMs of SARS-Cov-2 variants and study the effect on ligand binding interactions. RBM sequences were obtained using NCBI BLASTP and subjected to multiple and pairwise sequence alignment analysis. Hypothetical generations were drawn from the phylogenetic tree. The  effect  of mutation on ligand binding was studied by docking zafirlukast on selected RBMs. Molecular dynamics simulations were conducted to explain molecular interactions. The sequences at the same phylogenetic level showed higher similarity with the observed differences defined by the crystallized chain length. 6XDG_E, a leaf node sequence was 76% similar to 7NXA_E, a branch from the root, and had the highest mutation. Differences in sequence similarity across successive generations were based on mutations and crystallized chain length and the amino acid substitution is not predictable. Different bond types and binding affinities were observed as well as varying Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Region of Gyration (RoG) values for the RBMs in different variants. The RMSD, RMSF, and RoG did not differ significantly in the bound and free states of RBM from specific variants suggesting that the observed differences are attributable to amino acid substitutions. This information is crucial for drug development intended to block SARS-Cov-2 entry.


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How to Cite

E. Ebhohimen, I., H. Onyijen, O., Arora, V., Arora, V., T. Adeleke, V., & Okpeku, M. (2022). Mutation Pattern in the Receptor Binding Motif of SARS-Cov-2 Variants and the Effect on Molecular Interactions in Docked Ligand Complexes: Tropical Journal of Natural Product Research (TJNPR), 6(8), 1262–1267. Retrieved from