Drug Repositioning for SARS-CoV-2 Helicase

Drug ReposER tool, a web server that uses a modified version of the SPRITE search engine to identify similar amino acid arrangements to known drug binding interfaces for potential drug repositioning, was used to predict/identify drugs that could interact with the SARS-CoV-2 helicase based on the presence of amino acid arrangements matching binding sites of drugs in previously annotated protein structures^{28 (link)}. The tool predicts the binding of drugs with query protein based on RMSD. We used RMSD of 3.0 Å or less as the threshold, and structures of drugs exhibiting RMSD 3.0 Å and under were retrieved from PubChem Database in 3D SDF format. The 3D geometrical structures of drugs were then minimized by the Merck Molecular Force Field 94 (MMFF94S) force field using SZYBKI software^{29 ,30 (link)}. Before docking analysis, SDF structures were converted to PDBQT format using the OpenBabel tool, and polar hydrogens were added to the drug structures during conversion^{31 (link)}.

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Abidi S.H., Almansour N.M., Amerzhanov D., Allemailem K.S., Rafaqat W., Ibrahim M.A., la Fleur P., Lukac M, & Ali S. (2021). Repurposing potential of posaconazole and grazoprevir as inhibitors of SARS-CoV-2 helicase. Scientific Reports, 11, 10290.

Publication 2021

MMFF94S

Amino acid Binding sites Drug Helicase Hydrogens Molecular force Protein Sars cov 2

Corresponding Organization :

Other organizations : Aga Khan University, University of Hafr Al-Batin, Nazarbayev University, Qassim University, Minia University

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Variable analysis

independent variables

Amino acid arrangements matching binding sites of drugs in previously annotated protein structures

dependent variables

Binding of drugs with query protein based on RMSD

control variables

RMSD of 3.0 Å or less as the threshold for drug binding prediction
Minimization of 3D geometrical structures of drugs using the Merck Molecular Force Field 94 (MMFF94S) force field
Conversion of SDF structures to PDBQT format and addition of polar hydrogens to the drug structures

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

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