Preprint Article Version 2 Preserved in Portico This version is not peer-reviewed

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Version 1 : Received: 6 April 2020 / Approved: 7 April 2020 / Online: 7 April 2020 (12:08:57 CEST)
Version 2 : Received: 8 April 2020 / Approved: 9 April 2020 / Online: 9 April 2020 (12:39:54 CEST)
Version 3 : Received: 30 June 2020 / Approved: 1 July 2020 / Online: 1 July 2020 (08:37:49 CEST)

How to cite: Tallei, T.E.; Tumilaar, S.G.; Niode, N.J.; Fatimawali, F.; Kepel, B.J.; Idroes, R.; Effendi, Y. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Preprints 2020, 2020040102 (doi: 10.20944/preprints202004.0102.v2). Tallei, T.E.; Tumilaar, S.G.; Niode, N.J.; Fatimawali, F.; Kepel, B.J.; Idroes, R.; Effendi, Y. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Preprints 2020, 2020040102 (doi: 10.20944/preprints202004.0102.v2).

Abstract

Background: Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the cause of COVID-19. The search for plant-based antivirals against the SARS-CoV-2 is promising, as several plants have been shown to possess antiviral activities against betacoronaviruses (beta-CoVs) Objective: The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit Main Protease (Mpro) (PDB code: 6LU7) and Spike (S) Glycoprotein (PDB code: 6VXX) of SARS-CoV-2. Methods: Evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. For each compound that was docked, a rule of five was calculated to determine whether a compound with certain pharmacological or biological activities might have chemical and physical properties that would make it an active drug orally in humans. Determination of the docking score was done by selecting the conformation of the ligand that has the lowest binding free energy (best pose). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. Results: The results showed that hesperidine, cannabinoids, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and cannabinoids had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Conclusion: Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19.

Subject Areas

Medicinal plants; Mpro; 3CLpro; spike (S) glycoprotein; COVID-19; SARS-CoV-2

Comments (1)

Comment 1
Received: 9 April 2020
Commenter: Trina Tallei
Commenter's Conflict of Interests: Author
Comment: There were some typing errors that have been corrected, also some duplication that have been removed. This sentences: which is also one of the main proteases of SARSCoV-2 (Qamar et al., 2020; Wu et al., 2020). The function of this main protease together with Mpro is to form a viral replication complex. has been removed since it is not relevant
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