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A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2.
Genomics. 2021 01; 113(1 Pt 1):331-343.G

Abstract

An outbreak, caused by an RNA virus, SARS-CoV-2 named COVID-19 has become pandemic with a magnitude which is daunting to all public health institutions in the absence of specific antiviral treatment. Surface glycoprotein and nucleocapsid phosphoprotein are two important proteins of this virus facilitating its entry into host cell and genome replication. Small interfering RNA (siRNA) is a prospective tool of the RNA interference (RNAi) pathway for the control of human viral infections by suppressing viral gene expression through hybridization and neutralization of target complementary mRNA. So, in this study, the power of RNA interference technology was harnessed to develop siRNA molecules against specific target genes namely, nucleocapsid phosphoprotein gene and surface glycoprotein gene. Conserved sequence from 139 SARS-CoV-2 strains from around the globe was collected to construct 78 siRNA that can inactivate nucleocapsid phosphoprotein and surface glycoprotein genes. Finally, based on GC content, free energy of folding, free energy of binding, melting temperature, efficacy prediction and molecular docking analysis, 8 siRNA molecules were selected which are proposed to exert the best action. These predicted siRNAs should effectively silence the genes of SARS-CoV-2 during siRNA mediated treatment assisting in the response against SARS-CoV-2.

Authors+Show Affiliations

Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh.Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh.Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh.Department of Genetic Engineering and Biotechnology, University of Dhaka, Bangladesh.Department of Pharmacy, Brac University, 66 Mohakhali, Dhaka 1212, Bangladesh.WHO Collaborating Centre for eHealth, School of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales (UNSW), Sydney, Australia. Electronic address: m.moni@unsw.edu.au.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33321203

Citation

Chowdhury, Umar Faruq, et al. "A Computational Approach to Design Potential siRNA Molecules as a Prospective Tool for Silencing Nucleocapsid Phosphoprotein and Surface Glycoprotein Gene of SARS-CoV-2." Genomics, vol. 113, no. 1 Pt 1, 2021, pp. 331-343.
Chowdhury UF, Sharif Shohan MU, Hoque KI, et al. A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2. Genomics. 2021;113(1 Pt 1):331-343.
Chowdhury, U. F., Sharif Shohan, M. U., Hoque, K. I., Beg, M. A., Sharif Siam, M. K., & Moni, M. A. (2021). A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2. Genomics, 113(1 Pt 1), 331-343. https://doi.org/10.1016/j.ygeno.2020.12.021
Chowdhury UF, et al. A Computational Approach to Design Potential siRNA Molecules as a Prospective Tool for Silencing Nucleocapsid Phosphoprotein and Surface Glycoprotein Gene of SARS-CoV-2. Genomics. 2021;113(1 Pt 1):331-343. PubMed PMID: 33321203.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2. AU - Chowdhury,Umar Faruq, AU - Sharif Shohan,Mohammad Umer, AU - Hoque,Kazi Injamamul, AU - Beg,Mirza Ashikul, AU - Sharif Siam,Mohammad Kawsar, AU - Moni,Mohammad Ali, Y1 - 2020/12/13/ PY - 2020/04/18/received PY - 2020/11/18/revised PY - 2020/12/10/accepted PY - 2020/12/16/pubmed PY - 2021/1/29/medline PY - 2020/12/15/entrez KW - Nucleocapsid phosphoprotein KW - SARS-CoV-2 KW - Surface glycoprotein KW - siDirect KW - siRNA SP - 331 EP - 343 JF - Genomics JO - Genomics VL - 113 IS - 1 Pt 1 N2 - An outbreak, caused by an RNA virus, SARS-CoV-2 named COVID-19 has become pandemic with a magnitude which is daunting to all public health institutions in the absence of specific antiviral treatment. Surface glycoprotein and nucleocapsid phosphoprotein are two important proteins of this virus facilitating its entry into host cell and genome replication. Small interfering RNA (siRNA) is a prospective tool of the RNA interference (RNAi) pathway for the control of human viral infections by suppressing viral gene expression through hybridization and neutralization of target complementary mRNA. So, in this study, the power of RNA interference technology was harnessed to develop siRNA molecules against specific target genes namely, nucleocapsid phosphoprotein gene and surface glycoprotein gene. Conserved sequence from 139 SARS-CoV-2 strains from around the globe was collected to construct 78 siRNA that can inactivate nucleocapsid phosphoprotein and surface glycoprotein genes. Finally, based on GC content, free energy of folding, free energy of binding, melting temperature, efficacy prediction and molecular docking analysis, 8 siRNA molecules were selected which are proposed to exert the best action. These predicted siRNAs should effectively silence the genes of SARS-CoV-2 during siRNA mediated treatment assisting in the response against SARS-CoV-2. SN - 1089-8646 UR - https://www.unboundmedicine.com/medline/citation/33321203/A_computational_approach_to_design_potential_siRNA_molecules_as_a_prospective_tool_for_silencing_nucleocapsid_phosphoprotein_and_surface_glycoprotein_gene_of_SARS_CoV_2_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0888-7543(20)32067-X DB - PRIME DP - Unbound Medicine ER -