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Targeting SARS-CoV-2 endoribonuclease: a structure-based virtual screening supported by in vitro analysis
Ibrahim M Ibrahim1, Abdo A Elfiky1, Mohamed M Fathy1
1Biophysics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt.
Scientific Reports
|August 3, 2022
Summary
Researchers identified a potential COVID-19 drug candidate by screening over 800,000 compounds. The compound ZINC000104379474 effectively targets the virus
Area of Science:
- Computational chemistry and drug discovery.
- Virology and molecular biology.
Background:
- COVID-19's non-structural protein 15 (NSP15) endoribonuclease is crucial for viral RNA processing and evading host defenses.
- Targeting viral proteins is a key strategy for developing antiviral therapies.
Purpose of the Study:
- To identify novel compounds that inhibit the COVID-19 life cycle by targeting the NSP15 endoribonuclease.
- To employ a structure-based virtual screening approach for efficient compound discovery.
Main Methods:
- Screened 823,821 compounds from five databases using deep learning and hierarchical structure-based virtual screening.
- Utilized extra precision and induced fit docking protocols to assess binding affinity.
- Performed molecular dynamic simulations with MM-GBSA for binding energy calculations.
- Evaluated therapeutic effect in vitro using VERO-E6 cell line.
Main Results:
- Identified ZINC000104379474 from the ZINC15 database with a binding affinity of -7.68 kcal/Mol.
- Determined half-maximal cytotoxic concentration (CC50) of 0.9 mg/ml and inhibitory concentration 50 (IC50) of 0.01 mg/ml in VERO-E6 cells.
- Calculated a high selectivity index of 90, indicating a favorable therapeutic window.
Conclusions:
- ZINC000104379474 is a promising hit compound for targeting COVID-19.
- Further in vivo investigations are warranted to evaluate its potential as a drug candidate.
