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Open Access 01-12-2023 | SARS-CoV-2 | Research

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

Authors: Rabia Nawaz, Muhammad Ali Arif, Zainab Ahmad, Ammara Ahad, Muhammad Shahid, Zohal Hassan, Ali Husnain, Ali Aslam, Muhammad Saad Raza, Uqba Mehmood, Muhammad Idrees

Published in: BMC Infectious Diseases | Issue 1/2023

Abstract

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.

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Title: An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes
Authors: Rabia Nawaz
Muhammad Ali Arif
Zainab Ahmad
Ammara Ahad
Muhammad Shahid
Zohal Hassan
Ali Husnain
Ali Aslam
Muhammad Saad Raza
Uqba Mehmood
Muhammad Idrees
Publication date: 01-12-2023
Publisher: BioMed Central
Keyword: SARS-CoV-2
Published in: BMC Infectious Diseases / Issue 1/2023
Electronic ISSN: 1471-2334
DOI: https://doi.org/10.1186/s12879-023-08870-0

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