Study of Molecular Docking of Alkaloid Derivative Compounds from Stem Karamunting (Rhodomyrtus tomentosa)Against α-Glucosidase Enzymes

Mulyati, Budi; Panjaitan, Riong Seulina

doi:10.30598//ijcr.2020.9-bud

Cited by 5 publications

(4 citation statements)

References 9 publications

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“…Determining the grid box is one form of the parameter to specify the active side of the protein based on the box's location, which is determined based on the grid box size using the AutoDock Tool program (Version 1.5.6), where the results obtained in the form of x, y, and z coordinates and the size of the grid box are used as a reference or location where the docking process will occur on the target protein (Kelutur, 2022;Mulyati & Panjaitan, 2021).…”

Section: Grid Boxmentioning

confidence: 99%

Study of Anthocyanin Molecule Blocking as Anti-Hypertensive through the Pathway of the Renin-Angiotensin-Aldosterone System (RAAS)

Budiarto,

Wijianto,

2023

Indo. J. Chem. Res.

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Anthocyanins are flavonoid-derived compounds that can reduce blood pressure. This study aims to determine the affinity value of the compound to bind to Angiotensin Converting Enzyme (ACE) and bind to Angiotensin II type 1 Receptor (AT1R) and to determine the distance and shape of the bond that occurs. The results of anthocyanin-derived compounds Delphinidin, Petunidin, Malvidin, Cyanidin, Peonidin, and Pelargonidin have anti-hypertensive potential through the Renin Angiotensin Aldosterone (RAAS) pathway based on molecular docking calculations. The affinity value of each, against Angiotensin Converting Enzyme (ACE) -7.7; -7.8; -7.7; -7.7; -7.8, and -7.7, the best affinity value in anthocyanin-derived compounds is shown in the Malvidin test compound which has three types of hydrogen bonds at a distance of ± 2 Å (ASP377, TYR520, ASP415) and has 1 type of bond that is the same as the lisinopril control (TYR520). While the affinity value to Angiotensin Receptor (AT1R) is -7.7; -7.7; -7.8; -7.7; -7.8, and -7.6, respectively, the best affinity value is shown in the Malvidin test ligand compound of -7.8 kcal/mol which has four types of hydrogen bonds ± 2 Å distance (TYR92, SER105, ARG167, TRP84) and has one kind of bond in common with lisinopril control (TYR520).

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Section: Grid Boxmentioning

confidence: 99%

Study of Anthocyanin Molecule Blocking as Anti-Hypertensive through the Pathway of the Renin-Angiotensin-Aldosterone System (RAAS)

Budiarto,

Wijianto,

2023

Indo. J. Chem. Res.

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“…There are several alkaloid compounds in black cumin, such as Nigellicine, Nigellimine, Nigellidine and Decadienal. Alkaloid compounds have anti-microbial, anti-diabetic, anti-malarial, anti-diarrhoea, and suppression of Nf-κB gene expression [9], [30].…”

Section: Introductionmentioning

confidence: 99%

Molecular Docking Study of Nigella sativa Alkaloid Compounds as the Inhibitor of Papain-Like Protease SARS-CoV-2

Gholam,

Firdausy

2023

J. Trop. Pharm. Chem.

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SARS-CoV-2 causes about 66% of China’s Wuhan market workers to experience fever, dry cough, and fatigue. Black cumin (Nigella sativa) is a plant with many benefits to cure many illnesses like hypertension, headache, infection, and inflammation. This study aimed to investigate the inhibition by compounds belonging to the Alkaloid group from Black Cumin Seed to inhibit PLpro activity as a target for SARS-CoV-2. The study used five alkaloid compounds ((2E,4E)-Decadienal, (2E,4Z)-Decadienal, Nigellicine, Nigellidine, and Nigellimine) from the Black cumin seed and a PLpro SARS-CoV-2 receptor (PDB ID: 6WX4). The methods used are ligand and receptor preparation, grid box validation, molecular docking, 2D and 3D visualisation, and data analysis using Gibbs free energy, type of interaction, and contact of amino acid residues data. This study used YASARA structure and BIOVIA Discovery Studio. The results showed that Nigellidine has the highest Gibbs free energy with a -2.67 kcal/mol score, higher than VIR251. PLpro has a catalytic triad at Cys111, His272, and Asp286 residues, the compound that binds to the active site is Nigellicine found at amino acid Cys111 with Pi-Sulfur.

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“…Flavonoid compounds are extensively present in plants, demonstrating notable antioxidant activity. (Mulyati & Panjaitan, 2021). Natural antioxidants are sourced from plants, and they typically encompass phenolic secondary metabolites present in various plant components, including fruits, seeds, flowers, leaves, pollen, wood, and roots.…”

Section: Introductionmentioning

confidence: 99%

Microwave Assisted Hydrodistillation Essential Oil from Lime Peel Waste as Aromatherapy Candles

Mustam,

Azis,

Ramdani

et al. 2023

Indo. J. Chem. Res.

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Flavonoids belong to the extensive group of polyphenol compounds. They can function as antioxidants and antibacterials by denaturing bacterial cell proteins and damaging bacterial cells. One source of essential oils is lime peel, which is often discarded and goes unused. The distillation method utilizes microwaves, offering an alternative to conventional distillation techniques and resulting in enhanced effectiveness and efficiency. The Microwave Assisted Hydrodistillation (MAHD) method proves to be more energy-efficient, environmentally friendly, rapid, safe, and cost-effective. This study aims to assess the impact of the MAHD method on the quantity and quality of essential oils extracted from lime peels. Laboratory tests are conducted in accordance with Indonesian national standards. The overarching objective is to establish a process that transforms discarded lime peels into aromatherapy candles, contributing to respiratory health. The MAHD method is employed with a sample mass to distilled water solvent ratio of 1:1. The resulting essential oil undergoes analysis using the GC-MS method. According to the GC-MS test results, the compound with the highest percentage area is limonene at 98%. This is followed by trans-caryophyllene at 99% with a retention time of 12.422, and beta-selinene at 99% with a retention time of 13.191.

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Study of Molecular Docking of Alkaloid Derivative Compounds from Stem Karamunting (Rhodomyrtus tomentosa)Against α-Glucosidase Enzymes

Cited by 5 publications

References 9 publications

Study of Anthocyanin Molecule Blocking as Anti-Hypertensive through the Pathway of the Renin-Angiotensin-Aldosterone System (RAAS)

Study of Anthocyanin Molecule Blocking as Anti-Hypertensive through the Pathway of the Renin-Angiotensin-Aldosterone System (RAAS)

Molecular Docking Study of Nigella sativa Alkaloid Compounds as the Inhibitor of Papain-Like Protease SARS-CoV-2

Microwave Assisted Hydrodistillation Essential Oil from Lime Peel Waste as Aromatherapy Candles

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