Computational investigation of remdesivir, favipiravir, ribavirin, and their phosphate derivatives against Nipah virus RNA-dependent RNA polymerase

法维皮拉维 病毒学 利巴韦林 RNA依赖性RNA聚合酶 RNA聚合酶 聚合酶 病毒 核糖核酸 化学 2019年冠状病毒病(COVID-19) 生物 医学 基因 丙型肝炎病毒 生物化学 疾病 病理 传染病(医学专业)
作者
Vishal S. Patil,Sanjay Deshpande,Darasaguppe R. Harish,Pukar Khanal,Jameel M. Abduljalil,Subarna Roy
出处
期刊:Molecular Simulation [Taylor & Francis]
卷期号:: 1-13
标识
DOI:10.1080/08927022.2024.2387797
摘要

Outbreaks of human Nipah virus (NiV) cases have recently been reported in several countries. With a mortality rate of around 80% and no known therapy, there is an urgent need to test existing antivirals repurposed for it. Due to its central role in virus replication, the RNA-dependent RNA polymerase (RdRp) of NiV-L protein is a potential target for such antiviral therapies. In this study, Favipiravir, Remdesivir, Ribavirin, and their metabolites, including monophosphate (MP), diphosphate (DP), and triphosphate (TP), were virtually screened against RdRp. Using molecular dynamics (MD) simulations, lead hits from the docking study were examined for conformational changes. Additional analyses, including MM-PBSA, residual decomposition energy, and principal component analysis, were performed on the MD trajectory. Remdesivir-TP, Favipiravir-TP, and Ribavirin-TP exhibited the lowest binding energies of –7.8, −7.4, and −6.9 kcal/mol, respectively, and displayed an affinity for pocket 1, forming interactions with active site residues Asp726 and Asn727. During the 100 ns MD simulation, Remdesivir-TP demonstrated a more stable binding mode compared to Favipiravir-TP and Ribavirin-TP. The relative binding energies were −94.709 kJ/mol, −68.882 kJ/mol, and −46.98 kJ/mol for Remdesivir-TP, Favipiravir-TP, and Ribavirin-TP, respectively. This research anticipates Remdesivir-TP to be a potential candidate for an antiviral drug against NiV infection.

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