In silico investigation of ACE2 and the main protease of SARS-CoV-2 with phytochemicals from Myristica fragrans (Houtt.) for the discovery of a novel COVID-19 drug

Tassanee Ongtanasup; Smith Wanmasae; Siriwan Srisang; Chawan Manaspon; Soiphet Net-Anong; Komgrit Eawsakul

doi:10.1016/j.sjbs.2022.103389

In silico investigation of ACE2 and the main protease of SARS-CoV-2 with phytochemicals from Myristica fragrans (Houtt.) for the discovery of a novel COVID-19 drug

Saudi J Biol Sci. 2022 Sep;29(9):103389. doi: 10.1016/j.sjbs.2022.103389. Epub 2022 Jul 25.

Authors

Tassanee Ongtanasup^{1

2}, Smith Wanmasae³, Siriwan Srisang⁴, Chawan Manaspon⁵, Soiphet Net-Anong¹, Komgrit Eawsakul^{1

2}

Affiliations

¹ School of Medicine, Walailak University, Nakhon Si Thammarat 80160, Thailand.
² Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat 80160, Thailand.
³ School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand.
⁴ Energy Engineering Division, Department of Engineering, King Mongkut's Institute of Technology Ladkrabang, Prince of Chumphon Campus, Chumphon 86160, Thailand.
⁵ Biomedical Engineering Institute, Chiang Mai University, Chiang Mai 50200, Thailand.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), is a new coronavirus strain that was first reported in December 2019 in Wuhan, China. A specific treatment for COVID-19 has yet to be identified. Potential therapeutic targets include SARS-CoV-2 main protease (Mpro) and the SARS-CoV-2 spike-ACE2 interaction. Molecular docking, molecular dynamics (MD), solvent screening for the extraction of the specified compounds, and prediction of the drug properties of certain molecules were the methods used in this study to investigate compounds from the medicinal plant Myristica fragrans, which is one of twelve herbs in Prasachandaeng remedy (PSD). ArgusLab, AutoDock Vina, and AutoDock were used to perform docking tasks. The examined ligands were compared with panduratin A as a standard (Kanjanasirirat et al., 2020), which is a promising medicinal plant molecule for the treatment of COVID-19. Molecular docking revealed that malabaricones B and C and licarins A, B and C bound to SARS-CoV-2/ACE2 and SARS-CoV-2 Mpro with low binding energies compared to that of the standard ligand. Furthermore, appropriate solvent usage is important. Acetone was selected by COSMOquick software for compound extraction in this investigation because it can extract large amounts of all five of the abovementioned M. fragrans compounds. Furthermore, the drug-like properties of these compounds were studied utilizing the Lipinski, Veber, and Ghose criteria. The results revealed that these M. fragrans compounds have potential as effective medicines to combat the COVID-19 pandemic. However, to assess the therapeutic potential of these ligands, additional research is needed, which will use our findings as a foundation.

Keywords: Molecular Dynamics; Molecular docking; Myristica fragrans (houtt.); Pharmacokinetics; SAR-CoV-2 main protease; SARs-CoV-2 spike-ACE-2.