Biological activity of kencur (Kaempferia galanga L.) against SARS-CoV-2 main protease

Abstract

COVID-19 is a syndrome affecting pulmonary function but rather in serious conditions leads to death. Kencur (Kaempferia galanga L.) is a type of rhizome plant in Indonesia that is used as an herbal medicine called Jamu because it is believed to be able to cure various types of diseases. One of which is for anti-virus. The goal of this study was to see how effective the compounds in kencur are against COVID-19 with a molecular docking strategy. Kencur biological activities were obtained from the library and the design of the Acute Respiratory Syndrome Main protease (Mpro) has been gained from the protein data bank website. In addition, the biological activities in kencur were examined utilizing Lipinski's five-point concept was used to evaluate their substance molecular characteristics. Molecular docking analysis was performed with the PyRx Virtual Screening Tool software. The PyRx program was used for molecular docking simulation. While, the Discovery Studio Visualizer program was used to visualize the interaction between SARS-CoV-2 (Mpro) and the pharmacologically active metabolites in kencur. The docking evaluation on three antiviral substances revealed that Quercetin had the lowest binding energy when bound with Mpro and thus had the greatest potential as a viral inhibitor.

In Silico Screening of Bioactive Compounds from Syzygium cumini L. and Moringa oleifera L. Against SARS-CoV-2 via Tetra Inhibitors

“…35 SARS-CoV-2 helicase is involved in RNA replication. 11,12 Some helicase segments of SARS-CoV-2 variants show similarities to the 5' RNA NSP13 site, indicating that the part has great potential as a docked part in the development of anti-SARS-CoV-2. 12,36 Myricetin and ellagic acid have a variety bonds, including hydrogen bonds, pi-sigma, pi-alkyl, and vdw interactions.…”

“…11,12 Some helicase segments of SARS-CoV-2 variants show similarities to the 5' RNA NSP13 site, indicating that the part has great potential as a docked part in the development of anti-SARS-CoV-2. 12,36 Myricetin and ellagic acid have a variety bonds, including hydrogen bonds, pi-sigma, pi-alkyl, and vdw interactions. The presence of pi-anion bonds in ellagic acid aids the stability interaction with helicase so that the binding affinity is more negative.…”

“…9,10 Viral RNA helixes are involved in RNA replication. 11,12 Furthermore, viral RNA undergoes translations producing pp1a and pp1ab proteins which are then folded by proteolytic enzymes such as Mpro. 13,14 RdRp binds to RNA genome (negative-sense) to form genome and subgenome RNA (positive sense) via replication and transcription.…”

Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach

“…7,8 SARS-CoV-2 has a genome length of 29.903 bp and ssRNA as genetic material. 9 This virus has 4 structural proteins: envelope protein (E), membrane glycoprotein (M), nucleocapsid phosphoprotein (N), and spike glycoprotein (S). 10 In addition, there are two proteases that play an important role in this viral infection such as transmembrane protease serine 2 (TMPRSS2) and papain-like protease (PLpro).…”

In Silico Screening of Bioactive Compounds from Garcinia mangostana L. Against SARS-CoV-2 via Tetra Inhibitors

“…5,6 SARS-CoV-2 infection in human cells occurs mediated by receptor binding of the spike domain in the terminal C domain (SARS-CoV-2-CTD) with angiotensin-converting enzyme 2 (ACE-2). 7,8 Viral RNA helicase plays a role in the replication and folding of RNA in the target cell. 9 Furthermore, viral RNA is translated into pp1a and pp1ab proteins then folded by proteolytic enzymes such as Mpro into nonstructural proteins (nsps).…”