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 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




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


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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How to Cite

Cahyono B, Amalina ND, Suzery M, Nur Wahyu Bima D. 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. Open Access Maced J Med Sci [Internet]. 2021 May 20 [cited 2023 Dec. 6];9(A):336-42. Available from: https://oamjms.eu/index.php/mjms/article/view/5945

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