Novel Specific SARS-CoV-2 miRNAs Targeting Human Genes Involved in COVID-19 Infection and Their Regulation by Bemcentinib and Zavegepant: A Promising Evidence for RNA-Based Repurposing Therapeutic Strategy

Abstract

The 2019 coronavirus pandemic prompted extensive research into the molecular composition of the virus. The SARS-CoV-2 virus contains small noncoding RNAs (sNCR, miRNAs) targeting crucial host genes. This study identified 24 potential precursor and mature Viral-miRNAs (V-miRNAs) in the SARS-CoV-2 genome with favorable thermodynamic energies associated with 1883 human genes, 334 of which are involved in the COVID-19 infection. Out of 24, 14 predicted mature SARS-CoV-2 V-miRNAs target 28 host genes of the 334 genes involved in COVID-19 based on their robust molecular hybridization (thermodynamic stability, canonical base pairing, minimal noncanonical base pairs, loops, and bulges). Eight of the 14 mature V-miRNAs showed sequence conservancy with other organisms based on predicted 3D structures. Gene ontology enrichment analysis revealed these 28 host genes are involved in 42 biological processes, 4 cellular components, and 10 molecular processes. Further, the 14 predicted mature V-miRNAs were screened against FDA-approved (COVID-19 drug dataset) to identify the top best-hit compounds, which include Bemcentinib and Zavegepant. These two drugs show strong binding affinities ([Formula: see text]9.2 to −12.4 kcal/mol) with 13 and 12 predicted mature V-miRNAs, respectively. Furthermore, molecular docking of V-miRs-host AGO protein interactions suggested strong binding affinities and extensive hydrogen bonding interactions between V-miRNAs and the host AGO protein (involved in miRNA biogenesis and mRNA regulation). These findings suggest a potential regulatory role of Bemcentinib and Zavegepant through strong binding interaction with various V-miRNAs and in modulating host gene expression through their interactions with the AGO protein.