Studi In Silico Aktivitas Analog Senyawa Zizyphine dari Bidara Arab (Zizyphus spina-christi) sebagai Antivirus SARS-CoV-2 terhadap Reseptor 3CLpro

Fakih, Taufik Muhammad; Jannati, Firda Aulia; Meilani, Annisa; Ramadhan, Dwi Syah Fitra; Darusman, Fitrianti

doi:10.20961/alchemy.18.1.52188.70-79

Cited by 3 publications

(4 citation statements)

References 29 publications

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“…Docking results stored in (*.dlg) format were analyzed using AutoDock Tools for parameters including binding energy and inhibition constants (Ki), then ligand and amino acid interactions were visualized. The binding energy value and Ki are parameters of the conformational stability of the investigated compounds in terms of affinity towards VEGFR-2 receptor 15 . The binding energy value was obtained through the interaction of the ligand with a receptor, which showed the suitability between the shape and size of the ligand and the binding site on receptor 16 .…”

Section: Figure 1 Rmsd Resultsmentioning

confidence: 99%

Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity

Maharani,

Adelina,

Aini

et al. 2024

Valensi

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Liver cancer is a serious health concern characterized by abnormal cell growth, but currently, available treatment options are limited, suggesting the need for a new therapeutic method. Therefore, this research aimed to investigate the potential of chemical compounds obtained from the cangkring plant (Erythrina fusca) as anti-liver cancer agents targeting Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2). The investigation was conducted in silico through molecular docking and dynamic method. Molecular docking was performed using AutoDock Tools, followed by visualization with Biovia Discovery Studio. Additionally, molecular dynamics simulation was conducted using GROMACS software and visualized with Grace. A total of 36 chemical compounds from E. fusca were used as ligands for molecular docking. The results showed that Isobavachalcone (ISB) was the most effective test compound with a binding energy of -11.45 kcal/mol, compared to the positive control Sorafenib with a value of - 11.51 kcal/mol. In this context, hydrogen bonding, as well as hydrophobic, electrostatic, and unfavorable molecular interactions were identified. Moreover, molecular dynamics simulation provided RMSD, RMSF, Radius of Gyration (Rg), and hydrogen bond parameters. Analysis of these parameters further confirmed the superior stability of ISB in binding to VEGFR-2, suggesting the potential to suppress angiogenesis by blocking the receptor.

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Section: Figure 1 Rmsd Resultsmentioning

confidence: 99%

Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity

Maharani,

Adelina,

Aini

et al. 2024

Valensi

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“…The outcomes of these interactions were visually represented in a 2D format. The use of the Biovia Discovery Studio software followed the procedure of Fakih et al [19].…”

Section: Molecular Docking Results Analysismentioning

confidence: 99%

In vitro and In silico Studies of Kayu Raja (Cassia fistula L.) Leaves Extract as Potential Antifungal Agent Against Candida albicans

Christian,

Kasiyati,

Yuliani

et al. 2023

J. Kim. Sains Apl.

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Candida albicans is one of the most common fungal species causing opportunistic infections, such as candidiasis. Candida albicans has the ability to produce and secrete hydrolytic enzymes, namely secrete aspartate protease (SAP). SAP3 is a virulence factor for mucosal or disseminated infections. Cassia fistula leaves have bioactive compounds that can be used as antimicrobial agents, such as hyperoside, delphin, epicatechin, isoquercitrin, and astragalin. This study aims to determine the potential of bioactive compounds in Cassia fistula L. as an antifungal by in silico method molecular docking and Minimum Inhibitory Concentration (MIC) analysis with FE-SEM test for microscopical visual results. The results showed that the delphin compound had the best binding energy of -7.73 and an inhibition constant of 2.17 M, almost equivalent to ketoconazole as a positive control. MIC test of ethanol and ethyl acetate extracts of Cassia fistula leaves resulted in 100 ppm in the ethanol extract and 50 ppm in the ethyl acetate fraction. This result was supported by FE-SEM results, which showed that the ethanol extract at 100 ppm could damage the structure of Candida albicans colony.

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“…Semakin banyak ikatan hydrogen yang terbentuk menandakan bahwa bioaktivitas senyawa tersebut semakin tinggi. Ikatan hydrogen ikatan yang paling kuat karena dapat terbentuk meskipun jarak antara ligan dan reseptor jauh [5,9,10,14].…”

Section: Molekular Dockingunclassified

“…Senyawa-senyawa diduga dapat menghambat enzim Lanosterol 14-alpha demethylase pada C.albicans. Senyawa-senyawa tersebut bersifat agonis, Senyawa fitokimia dianggap sebagai agonis apabila memiliki interaksi ikatan pada kedua tempat ikatan tersebut [9,[14][15][16].…”

Section: Molekular Dockingunclassified

Kajian in Silico Daun Sungkai (Peronema canescens) dalam Menghambat Enzim lanosterol 14-α demethylase Jamur Candida albicans

Istiqomah

Fatikasari

2023

IJPE

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Candida albicans (C. albicans) is a fungus that causes candidiasis. C. albicans has the enzyme Lanosterol 14- α demethylase. Lanosterol 14-α-demethylase has bioactivity in converting lanosterol to ergosterol, a special sterol found in fungal membranes, which mediates membrane permeability and fluidity. One way to treat candidiasis is to use traditional medicinal plants. Sungkai (Peronema canescens) can be used as an anti-fungal medicine. Drug development efforts can be done using the In silico method. Objectives of this study was to determine the interaction between terpenoid, flavonoid, and phenol compounds in Sungkai leaves against Lanosterol 14-α demethylase in Candida albicans. The research design used was a pre-experimental one-shot case study. Toxtree software was used to test the toxicity of compounds. Test for compound potency using the Pass Online webserver. Docking molecular using PyRx software. Visualization of docking results using Discovery Studio 2019 Software. Physicochemical test of compounds using Lipinski Test. The results showed that the compounds that had a low risk of toxicity were butanoic, catechol, guaiacol, hydroquinone, isopropanol, methanoic acid, palmitic acid, and phytol. Compounds that have anti-fungal activity based on Pharma-expert analysis are butanoic acid, genkwanin, guaiacol, hydroquinone, isopropanol, palmitic acid, and phytol. Compounds that have hydrogen bonds and binding affinity value 10 and RMSD value 2 are butanoic acid, catechol, genkwanin, guaiacol, hydroquinone, isopropanol, methanoic acid, palmitic acid, and quinic acid compounds. These compounds are thought to inhibit the Lanosterol 14-alpha demethylase enzyme in C. albicans. Compounds that comply with Lipinski's rules are anthocyanin and genkwanin compounds. The groups of compounds found in Sungkai leaves that have antifungal activity are the terpenoids, flavonoids, and phenols.

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Studi In Silico Aktivitas Analog Senyawa Zizyphine dari Bidara Arab (Zizyphus spina-christi) sebagai Antivirus SARS-CoV-2 terhadap Reseptor 3CLpro

Cited by 3 publications

References 29 publications

Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity

Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity

In vitro and In silico Studies of Kayu Raja (Cassia fistula L.) Leaves Extract as Potential Antifungal Agent Against Candida albicans

Kajian in Silico Daun Sungkai (Peronema canescens) dalam Menghambat Enzim lanosterol 14-α demethylase Jamur Candida albicans

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