Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2

Abstract

The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp . The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.

Inhibition of SARS-CoV-2 Replication by a Small Interfering RNA Targeting the Leader Sequence

“…Several other in silico studies predicted siRNAs targeting ORF1ab [48][49][50][51], S gene [49,[51][52][53], ORF3 [49,51], E gene [49], M gene [49,51] and N gene [51,53] of SARS-CoV-2. Two in vitro studies further demonstrated a robust downregulation of S, M and N on the mRNA or protein levels by siRNAs in overexpression cell culture models [54,55].…”

Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains

“…The proper interaction between siRNA duplex and RISC complex, as well as guide siRNA strand and target mRNA inside RISC complex, are required to trigger a sufficient antiviral response via RNAi-mediated viral gene silencing[18]. Hence for interaction pattern analysis, molecular docking was carried over between siRNA (guide strand) and argonaute protein.…”

“…RNA interference or RNAi, the biological mechanism by which double-stranded RNA (dsRNA) induces gene silencing by targeting complementary mRNA for degradation (Figure 1)[18], is a huge breakthrough in disease therapy and is changing the way scientists analyse transcriptional activity[19] and it is a prospective tool for the control of human viral infections. Small interfering RNA (siRNA) is a double-stranded RNA of around 21 base pairs long RNA duplex bearing overhangs of two nucleotides on the 3′ end[20].…”

Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract

“…These siRNAs could combine SARS-CoV-2 mRNA targets, inducing greater inhibition of viral replication and reduced off-target effects ( Table 1 ) [ 91 ]. In addition, bioinformatics-based methods were also used to design siRNA targeting SARS-CoV-2 RdRp as a therapeutic agent [ 101 ]. Chen et al identified nine potential siRNA targets in the SARS-CoV-2 genome [ 102 ].…”