HIGHER BINDING AFFINITIES OF HOPEA PHYTOCOMPOUNDS TO THE SARS-COV-2 MAIN PROTEASE THAN KNOWN ANTIVIRALS: MOLECULAR DOCKING AND DYNAMIC SIMULATION STUDY

• Published in: Journal of Engineering Science and Technology
• Main Author: Rozani N.H.A.; Jusoh S.A.; Majid F.A.A.; Mokhtar N.A.; Khairudin N.B.A.; Tap F.M.
• Format: Article
• Language: English
• Published: Taylor's University 2024
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85204101167&partnerID=40&md5=3b1651293b4db9dbb493d34f860427ba

The COVID-19 pandemic has caused catastrophic worldwide, resulting in over 6.9 million reported deaths as of June 2023. While approved vaccines have significantly reduced fatalities, infections persist due to emerging SARS-CoV-2 variants. The emerging variants challenge vaccine effectiveness, prompting caution and a need for potent COVID-19 treatments. This research employed molecular docking and dynamic simulations to investigate the properties of phytochemicals from the Hopea plants. The results unveiled notably stronger binding affinities of compounds, hopeahainol C, alpha-viniferin, and balanocarpol (-12.1, -10.7, and -10.5 kcal/mol), towards the active site of the main protease, compared to FDA-approved antivirals (-8.8 to -7.3 kcal/mol). Moreover, these compounds remained stable in the active site during 200 ns molecular dynamics (MD) simulations. The most consistent hydrogen bonds were observed between the compounds and THR26, ASP187, GLN192, GLU166, including the catalytic dyad, HIS41 and CYS145. Additionally, MMGBSA analysis determined that hopeahainol C exhibited the highest affinity for the main protease’s active site, compared to alpha-viniferin and balanocarpol, with binding free energies of -25.60, -16.88, and - 16.69 kcal/mol, respectively. This work suggests these compounds can be potential inhibitors of SARS-CoV-2, which can be further enhanced for the development of an efficient therapeutic for COVID-19. © School of Engineering, Taylor’s University.