Molecular Docking of Cymbopogon Nardus (L.) Rendle Compounds as a Protease Inhibitor of Sars-Cov-2

RIFALDI, FAJRI; Mumpuni, Esti; Kumala, Shirly; Yantih, Novi; AULENA, DESI NADYA; Nafisa, Safira

doi:10.22159/ijap.2022.v14s3.24

Cited by 2 publications

(2 citation statements)

References 6 publications

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“…Furthermore, the complex of compound caryophyllene oxide-SARS-CoV-2 glycoprotein was taken for visualization and further analysis. The visualization of this complex was served the information of specific location of interaction [15]. It is essential to define the ability of small molecules to induce the function of protein.…”

Section: Resultsmentioning

confidence: 99%

Identification of Potential Activity of Volatile Compounds Derived From Pogostemon Cablin Benth as Antiviral of Sars-Cov-2

Ongko¹,

Hardjo²

2023

Int J App Pharm

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Objective: Coronavirus disease-19 (COVID-19) is global pandemic which caused by SARS-CoV-2 infection. Mechanism of infection is initiated by attachment between viral glycoprotein with ACE2 receptor in human cells. Furthermore, Indonesia had a massive diversity of plants with a high potency of drugs, such as Pogostemon cablin Benth. In brief, it contained of various volatile compounds with many therapeutic properties. Therefore, this research aimed to identify the ability of volatile compounds from Pogostemon cablin Benth as a potential inhibitor of SARS-CoV-2 spike glycoprotein. Methods: SMILE notation of 22 volatile compounds of Pogostemon cablin Benth were collected from PubChem and the 3D structure of SARS-CoV-2 glycoprotein (PDB ID: 6VXX) was obtained from PDB database. Simulation of interaction between volatile compound and glycoprotein was conducted by using Pyrx molecular docking. Moreover, the complex of compounds-glycoprotein was depicted by using Chimera and the amino acid residue was analysed by using LigPlot. Selected potential compounds were identified for biological activity prediction, drug-likeness, and toxicity analysis. Results: Analysis showed that among those volatile compounds, only caryophyllene oxide (-6.3 kcal/mol) naturally bind specific into RBD site as compared to the control. Furthermore, it had comparable hydrogen and hydrophobic interactions with glycoprotein. Further analysis showed it has strong potential biological function for antiviral with low toxicity. Conclusion: Caryophyllene oxide is considered as promising candidate compounds that inhibited viral infection through SARS-CoV-2 glycoprotein.

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Section: Resultsmentioning

confidence: 99%

Identification of Potential Activity of Volatile Compounds Derived From Pogostemon Cablin Benth as Antiviral of Sars-Cov-2

Ongko¹,

Hardjo²

2023

Int J App Pharm

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“…The complex binding affinity was calculated using the MMGBSA method [15]. The 2D structure of asiatic acid was generated using the ChemDraw 2D Ultra 12.0 program, and the energy was minimized using MM2 by ChemDraw 3D software, and then the structure was saved in the pdb format [32,33].…”

Section: Molecular Dynamic Simulation Of Asiatic Acidmentioning

confidence: 99%

Stability Analysis of the Asiatic Acid-COX-2 Complex Using 100 ns Molecular Dynamic Simulations and Its Selectivity against COX-2 as a Potential Anti-Inflammatory Candidate

et al. 2023

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Asiatic acid, a triterpenoid compound, has been shown to have anti-inflammatory activity through the inhibition of the formation of cyclooxygenase-2 (COX-2) in vitro and in vivo. This study was conducted to determine the binding stability and the inhibitory potential of asiatic acid as an anti-inflammatory candidate. The study involved in vitro testing utilizing a colorimetric kit as well as in silico testing for the pharmacophore modeling and molecular dynamic (MD) simulation of asiatic acid against COX-2 (PDB ID: 3NT1). The MD simulations showed a stable binding of asiatic acid to COX-2 and an RMSD range of 1–1.5 Å with fluctuations at the residues of Phe41, Leu42, Ile45, Arg44, Asp367, Val550, Glu366, His246, and Gly227. The total binding energy of the asiatic acid–COX-2 complex is −7.371 kcal/mol. The anti-inflammatory activity of the asiatic acid inhibition of COX-2 was detected at IC50 values of 120.17 µM. Based on pharmacophore modeling, we discovered that carboxylate and hydroxyl are the two main functional groups that act as hydrogen bond donors and acceptors interacting with the COX-2 enzyme. From the results, it is evident that asiatic acid is a potential anti-inflammatory candidate with high inhibitory activity in relation to the COX-2 enzyme.

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Molecular Docking of Cymbopogon Nardus (L.) Rendle Compounds as a Protease Inhibitor of Sars-Cov-2

Cited by 2 publications

References 6 publications

Identification of Potential Activity of Volatile Compounds Derived From Pogostemon Cablin Benth as Antiviral of Sars-Cov-2

Identification of Potential Activity of Volatile Compounds Derived From Pogostemon Cablin Benth as Antiviral of Sars-Cov-2

Stability Analysis of the Asiatic Acid-COX-2 Complex Using 100 ns Molecular Dynamic Simulations and Its Selectivity against COX-2 as a Potential Anti-Inflammatory Candidate

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