Analysis of Conocurvone, Ganoderic acid A and Oleuropein molecules against the main protease molecule of COVID-19 by in silico approaches: Molecular dynamics docking studies

Quynh Hoang Le; Bahareh Farasati Far; S Mohammad Sajadi; Bahar Saadaie Jahromi; Sogand Kaspour; Bilal Cakir; Zahra Abdelmalek; Mustafa Inc

doi:10.1016/j.enganabound.2023.02.043

Analysis of Conocurvone, Ganoderic acid A and Oleuropein molecules against the main protease molecule of COVID-19 by in silico approaches: Molecular dynamics docking studies

Eng Anal Bound Elem. 2023 May:150:583-598. doi: 10.1016/j.enganabound.2023.02.043. Epub 2023 Feb 27.

Authors

Quynh Hoang Le^{1

2}, Bahareh Farasati Far³, S Mohammad Sajadi⁴, Bahar Saadaie Jahromi⁵, Sogand Kaspour⁶, Bilal Cakir^{7

8}, Zahra Abdelmalek^{1

2}, Mustafa Inc^{9

10}

Affiliations

¹ Institute of Research and Development, Duy Tan University, Da Nang, Vietnam.
² School of Medicine and Pharmacy, Duy Tan University, Da Nang, Vietnam.
³ Department of Chemistry, Iran University of Science and Technology, Tehran, Iran.
⁴ Department of Nutrition, Cihan University-Erbil, Kurdistan Region, Iraq.
⁵ Biological Science Department, Western Michigan University, 1903W Michigan Avenue, Kalamazoo, MI 49008-5410, United States.
⁶ Department of Paramed, Tehran University of Medical Science, Tehran, Iran.
⁷ Halal Food R&D Center, İstanbul S. Zaim University (İZÜ), Halkalı, Küçükçekmece, İstanbul, Turkey.
⁸ İZÜ Food and Agricultural Research Center (GTUAM), Halkalı Campus,, Küçükçekmece, İstanbul 34303, Turkey.
⁹ Science Faculty, Department of Mathematics, Firat University, Elazig 23119, Turkey.
¹⁰ Department of Medical Research, China Medical University, Taichung 40402, Taiwan.

Abstract

Traditional medicines against COVID-19 have taken important outbreaks evidenced by multiple cases, controlled clinical research, and randomized clinical trials. Furthermore, the design and chemical synthesis of protease inhibitors, one of the latest therapeutic approaches for virus infection, is to search for enzyme inhibitors in herbal compounds to achieve a minimal amount of side-effect medications. Hence, the present study aimed to screen some naturally derived biomolecules with anti-microbial properties (anti-HIV, antimalarial, and anti-SARS) against COVID-19 by targeting coronavirus main protease via molecular docking and simulations. Docking was performed using SwissDock and Autodock4, while molecular dynamics simulations were performed by the GROMACS-2019 version. The results showed that Oleuropein, Ganoderic acid A, and conocurvone exhibit inhibitory actions against the new COVID-19 proteases. These molecules may disrupt the infection process since they were demonstrated to bind at the coronavirus major protease's active site, affording them potential leads for further research against COVID-19.

Keywords: Antiviral COVID-19; Conocurvone; Ganoderic acid A; In silico study; Molecular dynamics simulation; Oleuropein.