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

Israel E. Ebhohimen1, Ojei H. Onyijen2, Vaishali Arora3, Vanisha Arora4, Victoria T. Adeleke5, Moses Okpeku6*
1Department of Chemical Sciences, Samuel Adegboyega University, Ogwa, Edo State, Nigeria
2Department of Mathematical and Physical Sciences, Samuel Adegboyega University, Ogwa, Edo State, Nigeria
3Department of Botany, University of Delhi, India
4Department of Botany, Osmania University, Hyderabad, India
5Department of Chemical Engineering, Mangosuthu University of Technology, Umlazi, South Africa
6Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa


Corresponding Author: [email protected]; Tel: +27641286372
Recieved Date: 06 April 2022; Accepted Date: 19 August 2022; Published Date: 03 September
Citation: Ebhohimen IE, Onyijen OH, Arora V, Arora V, Adeleke VT, Okpeku M. Mutation Pattern in the Receptor Binding Motif of SARS-Cov-2 Variants and the Effect on Molecular Interactions in Docked Ligand Complexes. Trop J Nat Prod Res. 2022; 6(8):1262-1267. http://www.doi.org/10.26538/tjnpr/v6i8.17
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© 2022 Ebhohimen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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ABSTRACT

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.

Keywords:
SARS-Cov-2 spike glycoprotein, receptor binding motif, Covid-19, Molecular dynamics simulation
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ISSN: 2616-0684 (Print)
ISSN: 2616-0692 (Online)
DOI: 10.26538/tjnpr
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