STEP-BY-STEP GUIDE TO MOLECULAR DOCKING USING PYRX 0.8: PREDICTING INTERACTIONS OF CHALCONE-AMIDE DERIVATIVES WITH SARS-COV-2 PLPRO

Nguyễn Duy Tuấn; Nguyễn Cường Quốc; Trần Quang Đệ; Trần Duy Khang

doi:10.34238/tnu-jst.10680

STEP-BY-STEP GUIDE TO MOLECULAR DOCKING USING PYRX 0.8: PREDICTING INTERACTIONS OF CHALCONE-AMIDE DERIVATIVES WITH SARS-COV-2 PLPRO

About this article

Received: 29/06/24 Revised: 16/10/24 Published: 17/10/24

Authors

1. Nguyen Duy Tuan , Nam Can Tho University
2. Nguyen Cuong Quoc, College of Natural Sciences - Can Tho University
3. Tran Quang De, College of Natural Sciences - Can Tho University
4. Tran Duy Khang, Nam Can Tho University

Abstract

Molecular docking plays a crucial role in drug discovery by predicting the binding modes and affinities of small molecules with target proteins. This paper provides a comprehensive tutorial on molecular docking using PyRx tools, an open-source software with a user-friendly interface compatible with various operating systems. Specifically tailored for the first time in Vietnamese, this tutorial elucidates the step-by-step process of preparing data, conducting docking simulations, and analyzing results within the PyRx environment. Subsequently, the methodology is applied to predict the interactions of chalcone compounds against SARS-CoV-2 PL^pro. Notably, the obtained results demonstrate a high correlation with RMSD values consistently below 1.5 Å, indicative of structural similarity with published crystallographic data. This manuscript highlighted the reliability of the PyRx-based molecular docking approach and its efficacy in virtual screening and drug discovery efforts. This was particularly valuable in identifying novel therapeutic agents against emerging viral threats, which demonstrated the potential to significantly advance antiviral research.

Keywords

Chalcone; Docking; PyRx; SARS-CoV-2; Crystallographic

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DOI: https://doi.org/10.34238/tnu-jst.10680

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