Molecular Docking and Molecular Dynamics Simulation-Based Identification of Natural Inhibitors against Druggable Human Papilloma Virus Type 16 Target

Hidayatullah, Arief; Putra, Wira Eka; Sustiprijatno, Sustiprijatno; Widiastuti, Diana; Salma, Wa Ode; Heikal, Muhammad Fikri

doi:10.48048/tis.2023.4891

Cited by 5 publications

(3 citation statements)

References 57 publications

(77 reference statements)

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“…Together, these findings suggest that both compounds might potentially develop into anti-diabetic drug candidates. In view of the fact that the greater the negative value of the binding value, the stronger the binding that occurs between the ligand and the target protein (Putra 2018;Uzzaman et al 2019;Hidayatullah et al 2023). xx Several physicochemical properties of the proteinligand bond complex were obtained.…”

Section: Resultsmentioning

confidence: 99%

Computational study demonstrated anti-diabetic potencies of Diosgenin and Multiflorenol as peroxisome proliferator-activated receptor gamma agonist

Wira Eka,

Sustiprijatno,

Hidayatullah

et al. 2024

Nova Biotechnol. Chim.

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The prevalence of diabetes mellitus continues to rise on a global basis, making this entity one of the most pressing issues facing public health nowadays. Generally, diabetes mellitus is characterized by increased blood sugar levels caused by insulin secretion or action abnormalities. Natural products have become more popular in treating various types of diseases, including diabetes mellitus, due to their minimal adverse effects. Promoting the peroxisome proliferator-activated receptor γ (PPARG) activation is an anti-diabetic strategy due to its biological function for adipocyte storage, mobilization, differentiation, and insulin sensitivity. This study aims to evaluate diosgenin and multiflorenol in silico as anti-diabetic drug candidates by targeting PPARG. Several analyses, such as molecular docking, protein target prediction, biological function prediction, protein-protein interaction, and pharmacokinetics analyses were carried out in this study. Computational prediction showed PPARG have involved in several activities, such as fat cell differentiation, fatty acid oxidation, fatty acid transport, and cellular response to fatty acid. The binding affinity score revealed that diosgenin and multiflorenol have a higher value than the control drug. Other characteristics, such as chemical interaction, amino acid residues, and physicochemical properties, demonstrated supportive drug development outcomes. Therefore, based on our findings, we suggested that diosgenin and multiflorenol, both of which target PPARG, would hold promise as potential candidates for an anti-diabetic drug.

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Section: Resultsmentioning

confidence: 99%

Computational study demonstrated anti-diabetic potencies of Diosgenin and Multiflorenol as peroxisome proliferator-activated receptor gamma agonist

Wira Eka,

Sustiprijatno,

Hidayatullah

et al. 2024

Nova Biotechnol. Chim.

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“…Using the previously described method, a molecular docked analysis was carried out in study on 2 substances with the highest RT values, namely 2,3,4,5,6-pentaphenylbenzazocine and Thraustochytroside A and alpha-glucosidase as protein targets (Hidayatullah et al, 2022(Hidayatullah et al, , 2023. The 2D structures of Thraustochytroside A (CID.…”

Section: Molecular Docking Biological Activity and Admet (Absorption ...mentioning

confidence: 99%

Antidiabetic Activity of Averrhoa bilimbi L. Fruit Extracts and the Identification of Active Compounds Using LC-MS and In silico Methods

Widiastuti,

Sinaga,

Warnasih

et al. 2024

Indonesian J Pharm

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Patients with diabetes mellitus require drugs that do not cause side effects in long-term use. In this era, many people use herbal medicine to treat diabetes mellitus. One species we can use as herbal medicine is Averrhoa bilimbi L., a plant whose fruit is known as belimbing wuluh and is used because it has value as an alternative medicine. This study aims to determine the antidiabetic activity of the active fraction of Averrhoa bilimbi L. fruit in vitro and in silico and to obtain the active compounds contained in the fruit fraction of starfruit (A. bilimbi L.) using Liquid Chromatography Mass Spectrometer (LC-MS). Sixteen organic compounds were identified using LC-MS analysis of the n-hexane fraction, which had the highest IC50 (7.03 μg/mL) antidiabetic activity compared to ethyl acetate (102.77 μg/mL) and n-butanol (181.65 μg/mL). In silico molecular docking, analysis was performed for all identified compounds to support the antidiabetic characteristics further. Computational predictions in this investigation revealed that two A. bilimbi fruit compounds with the greatest RT value, namely 2,3,4,5,6-pentaphenylbenzazocine (-16.0 kcal/mol) and Thraustochytroside A (-6.2 kcal/mol), exhibited higher binding affinity values than miglitol (-5.4 kcal /mol). This indicates that both compounds have promising futures as α-glucosidase inhibitor alternatives for treating diabetic disorders.

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“…In this study, a molecular docking analysis was conducted on 2 compounds with the greatest RT values, namely tautomycetin and lithocholic acid, and α-glucosidase as protein targets, using the prior procedure [10,11]. Tautomycetin (CID: 6439037) and lithocholic acid (CID: 9903) 2D structures were retrieved from the PubChem database (https://pubchem.ncbi.nih.gov/).…”

Section: Molecular Docking Biological Activity and Admet (Absorption ...mentioning

confidence: 99%

Identification of Active Compounds from Averrhoa bilimbi L. (Belimbing Wuluh) Flower using LC-MS and Antidiabetic Activity Test using in vitro and in silico Approaches

Widiastuti

Sinaga²,

Warnasih

et al. 2023

Trends Sci

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Averrhoa bilimbi L., (Belimbing wuluh), is traditionally used for various antidiabetic, anti-larvicidal, antioxidant, hypoallergenic, antibacterial, antifungal, and anti-inflammatory treatments. This study evaluated 3 extracts (n-hexane, ethyl acetate, and n-butanol) isolated from starfruit flowers for antidiabetic effects using in vitro and in silico methods. Ethyl acetate extract showed the highest activity, followed by n-hexane and n-butanol extracts in inhibiting α-glucosidase. Each extract has an IC50 value of 89.84, 52.88, and 114.86 µg/mL. The active compounds contained in the ethyl acetate extract were determined using LC-MS, and the compounds with the highest retention time were identified as tautomycetin (8.585) and lithocholic acid (8.993). Tautomycetin and lithocholic acid showed promising results in the in silico test. The computational predictions showed that tautomycetin (−6.2 kcal/mol) and lithocholic acid (−10.0 kcal/mol) have better binding affinity values than miglitol (−5.4 kcal/mol). This is the first time the antidiabetic test of starfruit flower extract has been carried out. HIGHLIGHTS Averrhoa bilimbi L well-known as belimbing wuluh. is a highly nutritious plant and an endemic and tropical species mainly used as a traditional medicine to treat several diseases. Its fruit is food with economic value in Indonesia Extracts of ethyl acetate from the flower showed the highest antidiabetic activity with IC50 52.88 μg/mL In the phytochemical determination from Averrhoa bilimbi L flower using Liquid Chromatography Mass Spectrometer (LC-MS), several compounds were suspected of having antidiabetic activity, namely the compound lithocholic acid, and tautomycetin Lithocholic acid and tautomycetin have been tested for their bioactivity as antidiabetic with in vitro and in vivo methods GRAPHICAL ABSTRACT

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Molecular Docking and Molecular Dynamics Simulation-Based Identification of Natural Inhibitors against Druggable Human Papilloma Virus Type 16 Target

Cited by 5 publications

References 57 publications

Computational study demonstrated anti-diabetic potencies of Diosgenin and Multiflorenol as peroxisome proliferator-activated receptor gamma agonist

Computational study demonstrated anti-diabetic potencies of Diosgenin and Multiflorenol as peroxisome proliferator-activated receptor gamma agonist

Antidiabetic Activity of Averrhoa bilimbi L. Fruit Extracts and the Identification of Active Compounds Using LC-MS and In silico Methods

Identification of Active Compounds from Averrhoa bilimbi L. (Belimbing Wuluh) Flower using LC-MS and Antidiabetic Activity Test using in vitro and in silico Approaches

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