Exploring the Capability of Indonesia Natural Medicine Secondary Metabolite as Potential Inhibitors of SARS-CoV-2 Proteins to Prevent Virulence of COVID-19: In silico and Bioinformatic Approach

Bambang Cahyono; Nur Dina Amalina; Meiny Suzery; Damar Nur Wahyu Bima

doi:10.3889/oamjms.2021.5945

Authors

Bambang Cahyono Department of Chemistry, Faculty of Sciences and Mathematics, Diponegoro University, Semarang, Indonesia
Nur Dina Amalina Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Semarang State University, Semarang, Indonesia
Meiny Suzery Department of Chemistry, Faculty of Sciences and Mathematics, Diponegoro University, Semarang, IndonesiaDepartment of Chemistry, Faculty of Sciences and Mathematics, Diponegoro University, Semarang, Indonesia
Damar Nur Wahyu Bima Department of Chemistry, Faculty of Sciences and Mathematics, Diponegoro University, Semarang, Indonesia

DOI:

https://doi.org/10.3889/oamjms.2021.5945

Keywords:

Molecular docking, Bioinformatic, COVID-19, SARS-CoV2, Indonesia natural medicine

Abstract

BACKGROUND: SARS-CoV-2 was causing COVID-19 disease resulting in many deaths and being a significant concern in the world today. There is an emergent need to search for possible medications for COVID-19 treatment. The key point to halt SARS-CoV-2 infection through inhibition of the virus-receptor interaction and stimulates the immune system. Utilization of the bioinformatic and in silico molecular docking a number of available medications might be proven to be effective in inhibiting SARS-CoV-2 main drug targets including the SARS-CoV2 spike glycoprotein, the 3CL protease SARS-CoV-2 active target, PD-ACE2, 2019-nCoV PLpro, and NF-kβ.

AIM: This present study was conducted to identify the potential target and molecular mechanism of the major compound on Alpinia galanga extract and Citrus sinensis (L.) extract in circumventing COVID-19 using a bioinformatics approach and in silico molecular docking.

RESULTS: Direct protein target of all secondary metabolite and the gene list from PubMed “Severe acute respiratory syndrome coronavirus 2” generated 2 genes (CCL2 and VEGFA) as potential therapeutics target genes (PTTG). The molecular docking was conducted by the Protein-Ligand Ant System (PLANTS) software. The results show that hesperidin, naringenin, and galangin have lower docking score for all five-protein target receptor compared with chloroquine and remdesivir. The lower docking score suggests a high affinity to bind the protein. Moreover, these compounds have a strong affinity in their inhibitory capacity for viral infection.

CONCLUSION: In general, this study’s findings show that the compound of Alpinia galanga extract dan Citrus sinensis (L.) extract exhibit the best potential as an inhibitor to the development of the SARS-CoV-2 and inhibited cytokine storm through inactivation NF-kβ _pathway.

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