Pendekatan Struktur Aktivitas dan Penambatan Molekul Senyawa 2-iminoethyl 2-(2-(1- hydroxypentan-2-yl) phenyl)acetate Hasil Isolasi Fungi Endofit Genus Fusarium sp pada Enzim β-ketoasil-ACP KasA Sintase dan Enzim Asam Mikolat Siklopropana Sintase

Rollando, Rollando

doi:10.21776/ub.pji.2017.003.02.2

Cited by 4 publications

(3 citation statements)

References 6 publications

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“…The alignment of the native ligand is assessed in terms of its resemblance to the pre-docking position of the native ligand, with the aim of validating the molecular docking methodology employed. The flexibility of ligands enables them to undergo structural alterations in order to attain a stable conformation upon binding to the receptor [17]. The root mean square deviation (RMSD) is a metric commonly employed in docking validation to assess the accuracy and reliability of a docking methodology.…”

Section: Resultsmentioning

confidence: 99%

In silico Exploration on The Potency of Basil (Ocimum basilicum) as an Anti-Aging Skin Agent

Amala,

Aziz,

Rohmah

et al. 2023

Bioactivities

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New and improved skin care products and procedures have been established by technological advances and scientific investigation. By increasing the skin's moisture, firmness, and elasticity, anti-aging skin care can enhance the skin's overall condition. The objective of this study was to examine the potential of basil's chemical compounds as an in silicoanti-aging agent. Exploration of online databases, scholarly articles from national and international journals, and analysis using docking software are selected as examples of data collection methods. Matrix metalloproteinase 1 (MMP1), with PDB code 966C, is one of the targeted proteins related to skin anti-aging. Ladanein, acacetin, luteolin, 5-hydroxy-7,4'-dimethoxyflavone and genkwanin are five basil compounds that are predicted to exhibit anti-aging agents based on the presence of the binding affinity score indicator and the similarity of the appropriate attachment sites compared to the native ligand used. The scores for the binding affinity of luteolin, ladanein, acacetin, 5-hydroxy-7,4'-dimethoxyflavone, and genkwanin are -10, -9.9, -9.9, -9.8, and -9.6 kcal/mol, respectively. At the attachment positions of five basil compounds, the interactions with ASN 180, LEU 181 and ALA 182 key amino acids, which are the attachment sites for the native ligands, were also formed.

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Section: Resultsmentioning

confidence: 99%

In silico Exploration on The Potency of Basil (Ocimum basilicum) as an Anti-Aging Skin Agent

Amala,

Aziz,

Rohmah

et al. 2023

Bioactivities

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show abstract

“…One of the factors that affect the value of ∆G is the hydrogen bond and hydrophobic bond formed between the ligand and the receptor. Ligands with more hydrogen bonds can hypothetically bind to the receptor more strongly and more easily (Rollando, 2018). At the same time, hydrophobic bonds are thought to contribute to stabilizing the ligand and receptor interactions.…”

Section: Discussionmentioning

confidence: 99%

In Silico, to Determine the Active Compounds of Black Tea and Turmeric in Increasing the Activity of the Enzyme Sod

Hasan

Safithri

Huda

et al. 2022

IJAR

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Damage to cells caused by stress can be reduced by the presence of antioxidants, one of which is Superoxide dismutase (SOD). The role of the active ingredients of black tea and turmeric will be studied using the in-silico method to identify the active compounds as components in SOD activation. The bioavailability and toxicity of the active compounds of black tea and turmeric were studied and followed by molecular docking and virtual games. The parameters studied are Gibbs's free energy (∆G) and binding site similarity (BSS). The results were analyzed using Gibbs's free energy (∆G) and binding site similarity (BSS) parameters. It was found that those that could increase the activity of Cu/Zn SOD enzymes were Epicatechin gallate (black tea) and curcumin (turmeric), with values of -9.5 and -7.4 Kcal/mol and the same BSS value of 81.8%. The control ligand used was beta amyrin. According to Lipinski's rules, Epicatechin gallate and curcumin compounds can be absorbed well and are safe for consumption. This study concludes that Epicatechin gallate, an active compound of black tea, and curcumin, an active compound of turmeric rhizome, have the best potential to increase the activity of Cu/Zn SOD enzymes based on the results of virtual screening and molecular docking. Epicatechin gallate and curcumin are predicted to be well absorbed by the body because they qualify Lipinski's rules and are not toxic and safe for consumption.

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“…The smallest average RMSD values at both the lower bound (LB) and the upper bound (UB) of wild-type receptor were employed for docking. According to Rollando [46], the docking method will be more effective if the RMSD value is less than 2.5 Å. Meanwhile, the ΔG with the most negative value was employed since it indicated a strong ligand affinity for the active region of the receptor [47].…”

Section: Molecular Docking and Mutant Structural Changesmentioning

confidence: 99%

Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production

et al. 2022

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Glucose oxidase (GOD) is an oxidoreductase enzyme that catalyzes the oxidation of glucose to gluconolactone and hydrogen peroxide. Then, gluconolactone will be hydrolyzed to gluconic acid. The wide application of gluconic acid in various industries has increased production demand. However, glucose concentrations higher than 40% (w/w) inhibited the conversion of glucose to gluconic acid due to a decrease in the oxygen solubility concentration at pH 6, 30℃, and 1 bar pressure. Therefore, decreasing the value of Km is predicted to reduce saturation and enhance gluconic acid production. This study aimed to analyze the interaction between the IPBCC.08.610 GOD mutant with β-D-Glucose in improving gluconic acid production by decreasing the Km value. Mutations were performed in silico using Chimera and then docked using AutoDock Vina. The mutations resulted in distinct ligand poses in the binding pocket, different -OH conformations of the ligands, and changes in the T554M/D578P mutant’s hydrophobicity index (554 mutated from threonine to methionine, and 578 mutated from aspartate to proline), and decreased ΔG and Km values in the H559D mutant (559 mutated from histidine to aspartate), D578P and T554M/D578P. This decrease might strengthen the ligand-receptor interaction, increasing gluconic acid production. The H559D was the best mutant to increase production based on the ΔG, Km value, and stability due to the addition of hydrogen bonds.

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Pendekatan Struktur Aktivitas dan Penambatan Molekul Senyawa 2-iminoethyl 2-(2-(1- hydroxypentan-2-yl) phenyl)acetate Hasil Isolasi Fungi Endofit Genus Fusarium sp pada Enzim β-ketoasil-ACP KasA Sintase dan Enzim Asam Mikolat Siklopropana Sintase

Cited by 4 publications

References 6 publications

In silico Exploration on The Potency of Basil (Ocimum basilicum) as an Anti-Aging Skin Agent

In silico Exploration on The Potency of Basil (Ocimum basilicum) as an Anti-Aging Skin Agent

In Silico, to Determine the Active Compounds of Black Tea and Turmeric in Increasing the Activity of the Enzyme Sod

Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production

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