Prediction of Putative Potential Sirnas for Inhibiting SARS-CoV-2 Strains, Including Variants of Concern and Interest

Abstract

Aim: To predict siRNAs as a therapeutic intervention for highly infectious new variants of SARS-CoV-2. Methods: Conserved coding sequence regions of 11 SARS-CoV-2 proteins were used to construct siRNAs through sampling of metadata comprising 214,256 sequences. Results: Predicted siRNAs S1: 5′-UCAUUGAGAAAUGUUUACGCA-3′ and S2: 5′-AAAGACAUCAGCAUACUCCUG-3′ against RdRp of SARS-CoV-2 satisfied all the stringent filtering processes and showed good binding characteristics. The designed siRNAs are expected to inhibit viral replication and transcription of various coronavirus strains encompassing variants of concern and interest. Conclusion: The predicted siRNAs are expected to be potent against SARS-CoV-2, and following in vitro and in vivo validations may be considered as potential therapeutic measures.

Designing Cell Delivery Peptides and SARS-CoV-2-Targeting Small Interfering RNAs: A Comprehensive Bioinformatics Study with Generative Adversarial Network-Based Peptide Design and In Vitro Assays

“…It is important to note that a general first step of siRNA sequence generation without filtering enables researchers to apply their own designed filters to select those sequences that would better fit their needs. Other studies have used bioinformatics methods to design siRNA sequences targeting SARS-CoV-2 genome, with similar filtering steps, but most of them relied on the selection of genes of interest and design of siRNAs targeting only those. − While this approach may deliver more specific results right away, it may lead to the loss of interesting siRNA candidates. Nevertheless, Ambike et al .…”

RNA Interference Approach Is a Good Strategy against SARS-CoV-2

“…Moreover, siRNA-based therapies have been developed and implemented for anticancer, antiviral, and antibacterial infections and genetic disease purposes [ 26 ]. Recent studies, including this study, have demonstrated that the siRNA approach can be a highly effective strategy against SASR-CoV-2 infection and reduces viral loads via replication suppression [ 28 , 29 , 30 ]. Although siRNA targeting RdRp and the SP is predicted to be a good candidate against SARS-CoV-2, these prediction studies are limited because they have no evidence for viral infection studies [ 28 , 29 ].…”

Most frequently harboured missense variants of hACE2 across different populations exhibit varying patterns of binding interaction with spike glycoproteins of emerging SARS-CoV-2 of different lineages

“…SARS-CoV and MERS-CoV have been repurposed for SARS-CoV-2 infection. Moreover, with advanced computer-aided drug design, many specific therapeutic components in the forms of small molecules, monoclonal antibodies, siRNA and miRNA have been proposed since the emergence of the novel coronavirus [ [6] , [7] , [8] ]. In this short period of time, several vaccines have been produced with considerable efficacy and many are currently in clinical trial [ [9] , [10] , [11] , [12] ].…”