Molecular Docking and Molecular Dynamic Studies of Stilbene Derivative Compounds as Sirtuin-3 (Sirt3) Histone Deacetylase Inhibitor on Melanoma Skin Cancer and Their Toxicities Prediction

Muttaqin, Fauzan Zein

doi:10.36465/jop.v2i2.489

Cited by 20 publications

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“…That means that energy describes the spontaneity and stability of the bond (Purnomo et al, 2015).. The low inhibitory constant indicates that the barrier between the ligand and protein is small, so it is easy to bind to the receptor (Arrasyid et al, 2020;Muttaqin, 2019). The high surface interaction indicates a high probability of the active compound interacting with the target protein.…”

Section: Resultsmentioning

confidence: 99%

Activity of Phenolic Compounds in Figs (Ficus carica L.) as Antihyperlipidemic through in Silico Study

Shofi

2022

jobe

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<p>Figs (Ficus carica L.) belongs to family Moraceae which contains a lot of phenolic compounds that have an antihyperlipidemic effect. However, the phenolic compounds of figs have not been intensively studied. The purpose of this study was to determine the activity of phenolic compounds in figs as antihyperlipidemic in inhibiting the work of the HMG-CoA reductase enzyme. This research uses an experimental technique with the in silico method. The in-silico method was performed to predict the physicochemical, pharmacokinetic, toxicity, and molecular docking properties by comparing the phenolic compounds in figs and Pravastatin with the HMG-CoA reductase receptor. Rutaretin, Pimpinellin dan Seselin has the highest affinity values, met the physicochemical, pharmacokinetic, and toxicity parameters compared to Psoralen, 8-Methoxypsoralen, Angelicin, Bergapten and Pravastatin control compounds. The presence of this binding enzyme was able to inhibit the work activity of HMG-CoA reductase with amino acid residues Cys526, Gln814, Ile536, Leu811, Ile762, Pro813, Ala763, Ala556, Val538, Pro535, Tyr533, Met534, Gly765, Tyr517, Val522, Cys527. These results suggest that phenolic compounds Rutaretin, Pimpinellin, and Seselin in figs could be an antihyperlipidemic on inhibiting the action of HMG-CoA reductase enzyme.</p>

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Section: Resultsmentioning

confidence: 99%

Activity of Phenolic Compounds in Figs (Ficus carica L.) as Antihyperlipidemic through in Silico Study

Shofi

2022

jobe

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“…This result is consistent with the hydrogen bonding interaction with the standard ligand vildagliptin on the amino acid residue Tyr547 (Figure 3). An interaction occurs at the same amino acid residue so that 2-Phenylchromenylium Anthocyanin is predicted to have similar biological activity to vildagliptin (Muttaqin, 2019). Hydrogen bonding contributes to the affinity of a molecule for the target protein, thereby forming electrostatic interaction (hydrogen donor and acceptor) (Murray, 2003;Bissantz et al, 2010).…”

Section: Resultsmentioning

confidence: 99%

Molecular Docking of Compounds in Moringa oleifera Lam with Dipeptidyl Peptidase-4 Receptors as Antidiabetic Candidates

Rendi

Maranata

Chaerunisa

et al. 2021

JFIKI

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Background: Diabetes mellitus (DM) type 2 is a metabolic disorder that needs special attention because it can damage several organs if the severity increases. One of the treatments for diabetes mellitus (DM) type 2 is by inhibiting Dipeptidyl peptidase 4 (DPP-IV) with vildagliptin to prolong the hypoglycemic effect of GLP-1 and GIP. Objective: In the search for candidate compounds as new antidiabetic compounds, an in silico test with molecular docking was carried out to predict the antidiabetic activity of 10 Moringa oleifera Lam (MO) plant compounds at the DPP-IV receptor (PDB ID: 6B1E). Method: The study was conducted using the molecular docking method. Result: Validation of the vildagliptin DPP-IV ligand obtained free energy values of -9.27 kcal/mol and RMSD 1.49 Å (RMSD < 2 Å), then tested with 10 test compounds obtained 8 test compounds that have the potential to be antidiabetic. Conclusion: Serpentine compounds have better potential as an antidiabetic drug than other target compounds because they have the closest Gibbs energy (∆G) value to the natural ligand of Vidaglibtin, which is -7.90 kcal/mol. This value is still lower than the free energy of vildagliptin, which is -9.37 kcal/mol. Therefore further testing is needed to ensure the potential of the compound as a candidate for antidiabetic drugs.

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“…Ini berarti bahwa energi menggambarkan spontanitas dan stabilitas ikatan (Purnomo et al, 2015). Konstanta penghambatan yang rendah menunjukkan bahwa penghalang antara ligan dan protein kecil, sehingga mudah berikatan dengan reseptor (Arrasyid et al, 2020;Muttaqin, 2019). Interaksi permukaan yang tinggi menunjukkan kemungkinan besar senyawa aktif berinteraksi dengan protein target.…”

Section: Hasil Dan Pembahasanunclassified

Analysis of a-spinasterol Compounds in Trembesi Seeds (Samanea saman (jacq.) Merr) Against Inhibition of 3C-like Protease SARS-CoV-2 Through In Silico Test

Shofi

2022

Jurnal Sintesis

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Coronavirus Disease 2019 or known as COVID-19 is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In the virus, there is 3C-like Protease which is a non-structural protein in SARS-CoV-2. These proteins are responsible for the process of translation and viral replication. alpha -spinasterol is a sterol compound in trembesi seeds (Samanea saman (jacq.) Merr) which functions to increase immunity. The purpose of this study was to determine the potential of the alpha-spinasterol compound in trembesi seeds (Samanea saman (jacq.) Merr) as an inhibitor of the 3C-like Protease SARS-CoV-2 with PDB ID: 6M2N using the in silico test. The type of research in this research is computer-based experimental research using in silico tests or molecular docking. The working procedure in this study is molecular docking by comparing the alpha-spinasterol compound in trembesi seeds (Samanea saman (jacq.) Merr) and the comparison compound lopinavir with a protein target of 3C-like Protease SARS-CoV-2 and predicting its physicochemical properties. The results of the in silico test showed that the free bond energy was -8.4 kcal/mol and smaller than the comparison compound lopinavir (-8.2 kcal/mol). The amino acid residues in alpha-spinasterol are Asn203, Gly109, Pro108, Gln107, Gln110, Pro293, and Leu202 which have similar acid residues to lopinavir on compound binding to the 3CL-like Protease from SARS-CoV-2. Meanwhile, based on the Lipinski Rule of Five law, the alpha spinasterol compound still meets the requirements if it will be used as a new drug compound so that alternative drugs can be used to replace lopinavir

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Molecular Docking and Molecular Dynamic Studies of Stilbene Derivative Compounds as Sirtuin-3 (Sirt3) Histone Deacetylase Inhibitor on Melanoma Skin Cancer and Their Toxicities Prediction

Cited by 20 publications

References 0 publications

Activity of Phenolic Compounds in Figs (Ficus carica L.) as Antihyperlipidemic through in Silico Study

Activity of Phenolic Compounds in Figs (Ficus carica L.) as Antihyperlipidemic through in Silico Study

Molecular Docking of Compounds in Moringa oleifera Lam with Dipeptidyl Peptidase-4 Receptors as Antidiabetic Candidates

Analysis of a-spinasterol Compounds in Trembesi Seeds (Samanea saman (jacq.) Merr) Against Inhibition of 3C-like Protease SARS-CoV-2 Through In Silico Test

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