Inhibition of Spike Protein of SARS-CoV2 from (Merremia mammosa (Lour) Hall. F.) Bioactive Compounds: Molecular Docking and ADMET Study

Abstract

Spike protein is a receptor protein that has e role in the entry step of SARS-CoV2. This protein will bind to the ACE2 receptor in the human body and activate TMPRSS2. Inhibition of this protein will prevent the binding of the virus to host cells to spread the infection. This study aims to identify the activity of bioactive compounds of Merremia mammosa (Lour) tuber obtained from LC-MS/MS QTOF analysis of a previous study against the Spike protein of SARS-CoV2 using molecular docking and ADMET analysis. Molecular docking was conducted using SARS-CoV2 spike protein (PDB id. 6M0J) using Maestro Schrodinger software. Results showed that from 206 compounds there are 8 compounds of Merremia mammosa (Lour) that have lower predictive binding energies than standard drugs arbidol, hydroxychloroquine, and chloroquine. Result: 206 compounds of Merremia mammosa (Lour) tuber were successfully docked, there were 8 compounds that have docking scores more negative than standard drugs. It indicates that 8 compounds are more active than the positive controls. ADMET study revealed all of those potential ligands had the possibility to be developed as drugs. Conclusion: Molecular docking simulations were successfully utilized to identify the potential compounds from Merremia mammosa (Lour) tuber with the activity as an inhibitor for spike protein of SARS-CoV2. Further in vitro assay and purification are needed for future research.

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“…Merremia mammosa Hall was found to have action in suppressing the spike protein of SARS-CoV2 with the PDB id. 6M0J protein, as determined by an in silico investigation of the chemical analysis using LC-MS/MS QTOF [11]. The cytotoxic test with Vero E6 cells (host of the SARS-CoV2 virus) from the ethanol extract of bidara upas using the MTT method showed that the maximum non-toxic concentration (MNTC) is 500 µg/mL, as determined as the maximum concentration of the extract at which the cells developed normally, therefore the viral inhibition assay used 500 µg/mL as highest concentration [18,19].…”

“…In this study, the results of the plaque test showed that the higher the concentration given, the % inhibition increased, which means that the cell death zone was getting bigger. This activity is because Merremia mammosa Hall contains Gemixanthone A which provides inhibiting activities to SARS-COV2 Spike Protein [11]. Agil et al [29], examined the rhizome of the bidara upas used for research as an antituberculosis drug by the Madurese community.…”

“…This plant contains various secondary metabolite compounds that can be used as medicine. In Indonesia and Malaysia, this plant is used to treat various respiratory and digestive disorders, wounds caused by snake bites or burns, and diabetes [10,11]. In addition, the active compounds in the bidara upas extract can actually overcome typhoid fever caused by the bacterium Salmonella typhimurium, that upas bidara also has antibacterial activity against Staphylococcus aureus and Escherichia coli [12,13].…”

Studi In Silico Senyawa Flavonoid dalam Mengambat RNA-dependent RNA polymerase (RdRp) sebagai Antivirus COVID-19

“…Penelitian terbaru yang dilakukan oleh Purwitasari dkk., (2023) menjelaskan bahwa senyawa flavonoid menunjukkan aktivitas penghambatan yang baik terhadap protein spike SARS-COV-2 [19]. Diantara senyawa flavonoid yang terkenal memiliki berbagai manfaat farmakologi seperti antiinflamasi, antiosteoporosis, neurodegeneratif adalah Genistein, Daidzein, Glycitein, Formonoetin, dan Biochanin A [20,21].…”