Table 4 Comparative analysis of in silico pipelines from the previous antiviral siRNA studies and their in vitro implementation results
Targeted viruses and their genomic region | In silico siRNA designed pipeline | Total designed siRNAs | In vitro implementation and results | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sequence retrieval from repositories & databases | Multiple Sequence Alignment | Consensus sequence generation | Phylogenetic analysis | siRNA prediction using siDirect 2.0 | Binary validation using siRNApred | i-Score and s-Biopredsi scores calculation | Thermo-dynamic stability | Secondary structures prediction & MFE calculation using RNAStructure | Tertiary structure Prediction using RNA Composer | Molprobity validation | Off-target minimization | |||
Receptor-binding domain (RBD-S) of SARS-CoV-2 [26] | ✓a | ✘ | ✘ | ✘ | ✓ | ✘ | ✘ | ✘ | ✘ | ✘ | ✘ | ✘ | 4 | No cytotoxicity for tested siRNAs was found in Vero E6 cells based on experimental evaluation and analysis of generated results. Following strict selection and scoring criteria, a better antiviral efficiency was observed in 1 out of 4 siRNAs based on q-real-time PCR Ct value. |
ORF1ab of MERS-CoV [25] | ✓a | ✓ | ✘ | ✘ | ✘ | ✘ | ✓ | ✘ | ✘ | ✘ | ✘ | ✘ | 7 | siRNAs showed no cytotoxic effects at various concentrations in Vero cells (ATCC CCL-81). On the basis of real-time PCR results, two of the designed siRNAs were found to inhibit viral replication more efficiently as compared to the other five. |
5′ UTR of Zika virus [23] | ✓a | ✓ | ✓ | ✓ | ✓ | ✘ | ✘ | ✘ | ✓ | ✓ | ✓ | ✓ | 1 | Significant reduction in cycle thresholds was observed in C6/36 cells upon transfection with 1 and 2 μg of designed siRNA after being infected with Zika virus at an MOI of 0.001 for 1 hour (p < 0.05). |
5′ NTR of Hepatitis C virus [19] | ✓b | ✓ | ✓ | ✘ | ✘ | ✘ | ✓ | ✘ | ✘ | ✘ | ✘ | ✓ | 2 | Both of the designed siRNAs (HCV353 and HCV258) demonstrated efficient inhibition of HCV replication mechanism at low concentrations. Moreover, both siRNAs suppressed the replication of HCV genotype 4 isolates derived from infected Huh-7 cells efficiently. Also the long-term treatment of HCV replicon cells did not result in the emergence of escape mutant viruses. |