Target-Specific Machine Learning Scoring Function Improved Structure-Based Virtual Screening Performance for SARS-CoV-2 Drugs Development

• Published in: International journal of molecular sciences 2022-10, Vol.23 (19), p.11003
• Main Authors: Tahir ul Qamar, Muhammad, Zhu, Xi-Tong, Chen, Ling-Ling, Alhussain, Laila, Alshiekheid, Maha A., Theyab, Abdulrahman, Algahtani, Mohammad
• Format: Article
• Language: English
• Subjects: Algorithms; Coronaviruses; COVID-19; Drug development; Drug discovery; Drug screening; Enzymes; Factor analysis; Fingerprints; Genomes; Learning algorithms; Ligands; Machine learning; Molecular dynamics; Proteins; R&D; Research & development; RNA polymerase; Severe acute respiratory syndrome coronavirus 2; Structure-function relationships
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms231911003

Leveraging machine learning has been shown to improve the accuracy of structure-based virtual screening. Furthermore, a tremendous amount of empirical data is publicly available, which further enhances the performance of the machine learning approach. In this proof-of-concept study, the 3CLpro enzyme of SARS-CoV-2 was used. Structure-based virtual screening relies heavily on scoring functions. It is widely accepted that target-specific scoring functions may perform more effectively than universal scoring functions in real-world drug research and development processes. It would be beneficial to drug discovery to develop a method that can effectively build target-specific scoring functions. In the current study, the bindingDB database was used to retrieve experimental data. Smina was utilized to generate protein-ligand complexes for the extraction of InteractionFingerPrint (IFP) and SimpleInteractionFingerPrint SIFP fingerprints via the open drug discovery tool (oddt). The present study found that randomforestClassifier and randomforestRegressor performed well when used with the above fingerprints along the Molecular ACCess System (MACCS), Extended Connectivity Fingerprint (ECFP4), and ECFP6. It was found that the area under the precision-recall curve was 0.80, which is considered a satisfactory level of accuracy. In addition, our enrichment factor analysis indicated that our trained scoring function ranked molecules correctly compared to smina’s generic scoring function. Further molecular dynamics simulations indicated that the top-ranked molecules identified by our developed scoring function were highly stable in the active site, supporting the validity of our developed process. This research may provide a template for developing target-specific scoring functions against specific enzyme targets.