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Computational drug screening against the SARS-CoV-2 Saudi Arabia isolates through a multiple-sequence alignment
Pooi Ling Mok1,2,3, Avin Ee-Hwan Koh2, Aisha Farhana1
1Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, P.O. Box 2014, Sakaka, Al-Jawf Province, Saudi Arabia.
Saudi Journal of Biological Sciences
|February 8, 2021
Summary
Researchers screened existing drugs for COVID-19 treatment using genomic data from Saudi Arabia. Tanshinones showed high binding affinity to a key SARS-CoV-2 protein, suggesting potential as drug candidates for COVID-19.
Area of Science:
- Virology
- Drug Discovery
- Genomics
Background:
- The COVID-19 pandemic, caused by SARS-CoV-2, lacks specific antiviral treatments.
- Drug repurposing offers an economical and efficient strategy for identifying potential therapeutics.
- Genomic surveillance of viral isolates is crucial for understanding regional variations and guiding drug development.
Purpose of the Study:
- To conduct a preliminary screening of commercially available drugs against SARS-CoV-2 isolates from Saudi Arabia.
- To identify potential drug candidates by analyzing viral genomic sequences and drug-binding affinities.
- To leverage computational approaches for accelerating the drug discovery process for COVID-19.
Main Methods:
- Multiple-sequence alignment of 164 SARS-CoV-2 genomic sequences from Saudi Arabia isolates.
- Phylogenetic analysis using MEGA X software to assess sequence similarity (approx. 98%).
- Genomic annotation with VIGOR4 and drug screening via ZINC database mining based on viral gene expression.
Main Results:
- Identified SARS-CoV replicase polyprotein 1a as the highest sequence similarity target (79.91%).
- Discovered tanshinones exhibiting high binding affinities to the identified viral target.
- Generated a list of 29 orthologs with purchasable drug information, with other matches ranging from 27-52%.
Conclusions:
- Tanshinones represent promising candidates for further investigation as potential SARS-CoV-2 therapeutics.
- This study provides a valuable foundation for drug discovery efforts against COVID-19.
- Computational screening of existing drugs accelerates the identification of effective treatments for emerging infectious diseases.
