RNAi-mediated siRNA sequences to combat the COVID-19 pandemic with the inhibition of SARS-CoV2

Virus-specific Dicer-substrate siRNA swarms inhibit SARS-CoV-2 infection in TMPRSS2-expressing Vero E6 cells

After 4 years of the COVID-19 pandemic, SARS-CoV-2 continues to circulate with epidemic waves caused by evolving new variants. Although the rapid development of vaccines and approved antiviral drugs has reduced virus transmission and mitigated the symptoms of infection, the continuous emergence of new variants and the lack of simple-use (non-hospitalized, easy timing, local delivery, direct acting, and host-targeting) treatment modalities have limited the effectiveness of COVID-19 vaccines and drugs. Therefore, novel therapeutic approaches against SARS-CoV-2 infection are still urgently needed. As a positive-sense single-stranded RNA virus, SARS-CoV-2 is highly susceptible to RNA interference (RNAi). Accordingly, small interfering (si)RNAs targeting different regions of SARS-CoV-2 genome can effectively block the expression and replication of the virus. However, the rapid emergence of new SARS-CoV-2 variants with different genomic mutations has led to the problem of viral escape from the targets of RNAi strategy, which has increased the potential of off-target effects by siRNA and decreased the efficacy of long-term use of siRNA treatment. In our study, we enzymatically generated a set of Dicer-substrate (D)siRNA swarms containing DsiRNAs targeting single or multiple conserved sequences of SARS-CoV-2 genome by using in vitro transcription, replication and Dicer digestion system. Pre-transfection of these DsiRNA swarms into Vero E6-TMPRSS2 cells inhibited the replication of several SARS-CoV-2 variants, including the recent Omicron subvariants BQ.1.1 and XBB.1.5. This in vitro investigation of novel DsiRNA swarms provides solid evidence for the feasibility of this new RNAi strategy in the prevention and treatment of SARS-CoV-2 infection.

An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

BACKGROUND

The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV) in host Golgi apparatus. These vesicles provide anchorage to viral replicative complexes, thus assist replication inside the host cell. While the accessory genes coded by ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, 9b, 9c, and 10 contribute in cell entry, immunoevasion, and pathological progression.

METHODS

This in silico study is focused on designing sequence specific siRNA molecules as a tool for silencing the non-structural and accessory genes of the virus. The gene sequences of NSP3, 4, and 6 along with ORF3a, 6, 7a, 8, and 10 were retrieved for conservation, phylogenetic, and sequence logo analyses. siRNA candidates were predicted using siDirect 2.0 targeting these genes. The GC content, melting temperatures, and various validation scores were calculated. Secondary structures of the guide strands and siRNA-target duplexes were predicted. Finally, tertiary structures were predicted and subjected to structural validations.

RESULTS

This study revealed that NSP3, 4, and 6 and accessory genes ORF3a, 6, 7a, 8, and 10 have high levels of conservation across globally circulating SARS-CoV-2 strains. A total of 71 siRNA molecules were predicted against the selected genes. Following rigorous screening including binary validations and minimum free energies, final siRNAs with high therapeutic potential were identified, including 7, 2, and 1 against NSP3, NSP4, and NSP6, as well as 3, 1, 2, and 1 targeting ORF3a, ORF7a, ORF8, and ORF10, respectively.

CONCLUSION

Our novel in silico pipeline integrates effective methods from previous studies to predict and validate siRNA molecules, having the potential to inhibit viral replication pathway in vitro. In total, this study identified 17 highly specific siRNA molecules targeting NSP3, 4, and 6 and accessory genes ORF3a, 7a, 8, and 10 of SARS-CoV-2, which might be used as an additional antiviral treatment option especially in the cases of life-threatening urgencies.

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

Nucleic acid technologies with designed intracellular delivery systems are some of the most promising therapies of the future. Small interfering (si)RNAs inhibit gene expression and protein synthesis and may complement current vaccines with faster design and production. Although successful delivery remains an issue, delivery peptides may help to fill this gap. Here, we address this issue by applying bioinformatic approaches to design new putative cell delivery peptides and siRNAs for COVID-19 variants and other related viral diseases. Of the 29,880 RNA sequences analyzed, 62 were identified in silico as able to target the virus mRNA sequence, and from the 9,984 peptide sequences analyzed, 10 were selected as delivery peptides. From the latter, we further performed in vitro studies of the two best-ranked peptides and compared them with the broadly used TAT delivery peptide. One of them, seq5, displayed better internalization results with about double intensity signal compared to TAT after a 1 h incubation time in GFP-HeLa cells. This peptide has, thus, the features of a delivery peptide and could be used for cargo intracellular delivery.

A Comprehensive In Silico Study of New Metabolites from Heteroxenia fuscescens with SARS-CoV-2 Inhibitory Activity

Chemical investigation of the total extract of the Egyptian soft coral Heteroxenia fuscescens, led to the isolation of eight compounds, including two new metabolites, sesquiterpene fusceterpene A (1) and a sterol fuscesterol A (4), along with six known compounds. The structures of 1–8 were elucidated via intensive studies of their 1D, 2D-NMR, and HR-MS analyses, as well as a comparison of their spectral data with those mentioned in the literature. Subsequent comprehensive in-silico-based investigations against almost all viral proteins, including those of the new variants, e.g., Omicron, revealed the most probable target for these isolated compounds, which was found to be M^pro. Additionally, the dynamic modes of interaction of the putatively active compounds were highlighted, depending on 50-ns-long MDS. In conclusion, the structural information provided in the current investigation highlights the antiviral potential of H. fuscescens metabolites with 3β,5α,6β-trihydroxy steroids with different nuclei against SARS-CoV-2, including newly widespread variants.

Interaction of panduratin A and derivatives with the SARS-CoV-2 main protease (mpro): a molecular docking study

Panduratin A (Pa-A) is a prenylated cyclohexenyl chalcone isolated from the rhizomes of the medicinal and culinary plant Boesenbergia rotunda (L.) Mansf., commonly called fingerroots. Both an ethanolic plant extract and Pa-A have shown a marked antiviral activity against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic disease. Pa-A functions as a protease inhibitor inhibiting infection of human cells by the virus. We have modeled the interaction of Pa-A, and 26 panduratin analogues with the main protease (M^pro) of SARS-CoV-2 using molecular docking. The natural product 4-hydroxypanduratin showed a higher M^pro binding capacity than Pa-A and isopanduratin A. The interaction with M^Pro of all known panduratin derivatives (Pa-A to Pa-Y) have been compared, together with more than 60 reference products. Three compounds emerged as potential robust M^Pro binders: Pa-R, Pa-V, Pa-S, with a binding capacity significantly higher than 4-OH-Pa-A and Pa-A. The empirical energy of interaction (ΔE) calculated with the best compound in the panduratin series, Pa-R bound to M^pro, surpassed that measured with the top reference protease inhibitors such a ruprintrivir, lufotrelvir, and glecaprevir. Structure-binding relationships are discussed. Compounds with a flavanone moiety (PA-R/S) are the best binders, better than those with a chromene unit (Pa-F/G). The extended molecules (such as Pa-V) exhibit good M^pro binding, but the dimeric compound Pa-Y is too long and protrudes outside the binding cavity. The work provides novel ideas to guide the design of new molecules interacting with M^pro.Communicated by Ramaswamy H. Sarma.