Pharmacophore and Molecular Docking-Based Virtual Screening of B-Cell Lymphoma 2 (BCL 2) Inhibitor from Zinc Natural Database as Anti-Small Cell Lung Cancer

Muttaqin, Fauzan Zein; Kharisma, Dina; Asnawi, Aiyi; Kurniawan, Fransiska

doi:10.22270/jddt.v10i2.3923

Cited by 7 publications

(6 citation statements)

References 15 publications

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“…Visualization of docking poses and interacting were carried out by using the Discovery Studio Visualizer [24]. Preparation of macromolecule and ligands, as well as docking studies, were carried out using AutoDock 4.2 [25][26][27] and exploring ligand stability in protein crystal structures was carried out using Amber18 [28].…”

Section: Hardware and Softwarementioning

confidence: 99%

Molecular Docking and Molecular Dynamics Studies of Acalypha Indica L. Phytochemical Constituents With Caspase-3

et al. 2021

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Objective: This study investigated the structure-based molecular interactions between phytochemical constituents of Acalypha indica L. and caspase-3. Methods: Thirty-three phytochemical constituents of A. indica were screened against caspase-3. The X-ray crystal structure of human caspase-3 was retrieved from https://www.rcsb.org/structure/. The molecular interactions of the phytochemicals were studied using the AutoDock 4.2 software and followed by molecular dynamics (MD) simulations using the Amber18 software. Results: From this study, 25 screened phytochemicals were found to have a better binding mode than the native ligand. Moreover, the binding stability of the top four hits evaluated by MD indicated that the hydrogen bonds in MD were quite different from the molecular docking results due to the massive receptor and ligand movement in the MD simulations. However, with the exception of stigmasterol, all ligands were able to stabilize the protein. Conclusion: This study suggested that γ-sitosterol acetate, β-sitosterol acetate, and γ-sitosterol might be able to induce caspase-3, thereby activating apoptosis. These high-affinity compounds can bind to caspase-3 more efficiently and were able to stabilize the protein. Therefore, they have the potential to be used as lead compounds in the treatment of cancer.

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Section: Hardware and Softwarementioning

confidence: 99%

Molecular Docking and Molecular Dynamics Studies of Acalypha Indica L. Phytochemical Constituents With Caspase-3

et al. 2021

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“…The docking result was analyzed by observing the free binding energy of each ligand. The more negative free binding energy, the stronger the affinity of the ligand with the protein [22]. It means that ligands with smaller free binding energy than native ligands indicated that their affinity to the protein was better than the native ligand.…”

Section: Resultsmentioning

confidence: 99%

Potential Activity of Caryophyllene Derivatives as Xanthine Oxidase Inhibitor: An in silico Quantitative Structure-Activity Relationship Analysis

Setiawansyah

Gemantari²

2022

J. Food Pharm. Sci

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As the enzyme responsible for the uric acid formation, Xanthine oxidase was considered to be a therapeutic target for hyperuricemic treatment. This study was carried out to assess the potential of caryophyllene, and its derivates usually present in the natural product to inhibit Xanthine oxidase. The molecular docking using Autodock Tool and Biovia Discovery Studio was conducted to visualize the molecular interaction and to reveal the structure-activity relationship of those compounds. The results showed that the derivates of caryophyllene showed a higher affinity to Xanthine Oxide than Allopurinol. Among those all, caryophyllene oxide has the most stable bonding to xanthine oxide. Structure-activity relationship analysis showed that the chemical properties of the compound affected the affinity and molecular interaction to the enzyme as the target site in this study. The number of double bonds, substituents position, conformational structure related to steric hindrance, and the presence of lactone ring were assumed to influence the xanthine oxide inhibitory activity of caryophyllene derivates.

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“…In order to get the best compound, the screening results of target compounds obtained from the molecular docking were further analyzed by observing the values of the smallest binding energy. The test compounds which have lower binding energy values than native ligand indicated that the binding strength of those compounds to the receptor was better (Muttaqin et al, 2020). In addition, the analysis was also performed by observing the interactions that occur between ligands and amino acids residues in receptors.…”

Section: Molecular Docking-based Virtual Screeningmentioning

confidence: 99%

Molecular docking-based virtual screening of antidiabetic agents from Songga (Strychnos lucida R.Br.): an Indonesian native plant

Setiawansyah¹,

Reynaldi²,

Tjahjono³

et al. 2022

crbb

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This study was carried out to predict the compounds derived from Songga that have potential as antidiabetic and predict their mechanism of action on various pathways of glucose regulation in diabetes mellitus by molecular docking. Molecular docking-based virtual screening was done by using AutoDock Vina software assisted by AutoDockTools. The test compounds used for virtual screening were obtained from literature studies and were combined with Lipinski’s rule to select the compounds for the prediction of lead candidates that can be used in oral administration. The receptors used in this study were human aldose reductase, human maltase-glucoamylase, PPAR-gamma, pancreatic beta-cell SUR1, and human DPP-IV. The validation of the molecular docking method of five target receptors showed that RMSD values of human aldose reductase, human maltase-glucoamylase, PPAR-gamma, pancreatic beta-cell SUR1, and human DPP-IV were 0.6446 Å, 1.8668 Å, 0.2527 Å, 1.7452 Å, and 1.7439 Å, respectively. From the molecular docking-based virtual screening, we discovered that for each target protein, there were one to three optimal compounds that have the best interaction in our investigation. Those compounds were chlorogenic acid on human aldose reductase, phyllamycin A, chlorogenic acid, and brucine N-oxide on human maltase-glucoamylase, phyllamycin A on PPAR-gamma, strychnine N-oxide on pancreatic beta-cell SUR1 and strychnine on human DPP-IV with binding affinity value of -9.9 kcal/mol, -7.6 kcal/mol, -9.9 kcal/mol, -8.8 kcal/mol, and -6.2 kcal/mol, respectively. Several compounds are predicted to have potential to be developed as antidiabetic agents. However, further laboratory investigations like in vitro and in vivo assays need to be conducted.

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Pharmacophore and Molecular Docking-Based Virtual Screening of B-Cell Lymphoma 2 (BCL 2) Inhibitor from Zinc Natural Database as Anti-Small Cell Lung Cancer

Cited by 7 publications

References 15 publications

Molecular Docking and Molecular Dynamics Studies of Acalypha Indica L. Phytochemical Constituents With Caspase-3

Molecular Docking and Molecular Dynamics Studies of Acalypha Indica L. Phytochemical Constituents With Caspase-3

Potential Activity of Caryophyllene Derivatives as Xanthine Oxidase Inhibitor: An in silico Quantitative Structure-Activity Relationship Analysis

Molecular docking-based virtual screening of antidiabetic agents from Songga (Strychnos lucida R.Br.): an Indonesian native plant

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