Cross-docking study on InhA inhibitors: a combination of Autodock Vina and PM6-DH2 simulations to retrieve bio-active conformations

2012 ◽  
Vol 10 (31) ◽  
pp. 6341 ◽  
Author(s):  
Jean-Luc Stigliani ◽  
Vania Bernardes-Génisson ◽  
Jean Bernadou ◽  
Geneviève Pratviel
Keyword(s):  
Docking Study ◽  
Autodock Vina ◽  
Cross Docking

scholarly journals Synthesis and Molecular Docking Studies of Coumarinyl Thiazole as Cell Division Protein Kinase 2 Inhibitor

2019 ◽  
Vol 31 (11) ◽  
pp. 2453-2456
Author(s):  
J. Brindha ◽  
T.F. Abbs Fen Reji
Keyword(s):  
Molecular Docking ◽  
Cell Division ◽  
Protein Kinase ◽  
Screening Tool ◽  
Docking Study ◽  
Docking Studies ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Molecular Docking Studies ◽  
Cell Division Protein

A series of 2-alkylamino-4-(3-coumarinyl)thiazoles were synthesized, characterized and evaluated their anticancer activity through molecular docking studies. Cell division protein kinase 2 (PDB code: 1KE9) is selected as a target and the compounds which obeys Lipinski rule of five is selected as a ligand. Molecular docking study is carried out using AutoDock Vina in PyRx virtual screening tool. This study revealed that all the compounds are active against the molecular target and compounds 5a and 5c have the highest docking score.

Computational study of the binding orientation and affinity of PPARγ agonists: inclusion of ligand-induced fit by cross-docking

RSC Advances ◽  
2016 ◽  
Vol 6 (69) ◽  
pp. 64756-64768 ◽  
Author(s):  
Camila Muñoz-Gutierrez ◽  
Francisco Adasme-Carreño ◽  
Eduardo Fuentes ◽  
Iván Palomo ◽  
Julio Caballero
Keyword(s):  
Computational Study ◽  
Protein Flexibility ◽  
Docking Study ◽  
Binding Energies ◽  
Induced Fit ◽  
Cross Docking ◽  
Pparγ Agonists ◽  
Differential Binding ◽  
Binding Orientation ◽  
Crystal Receptor

A cross-docking study for describing differential binding energies of PPARγ and agonists was successful after the inclusion of protein flexibility through the use of several crystal receptor conformations.

scholarly journals IDENTIFICATION OF NOVEL 5-STYRYL-1,2,4-OXADIAZOLE/TRIAZOLE DERIVATIVES AS THE POTENTIAL ANTI-ANDROGENS THROUGH MOLECULAR DOCKING STUDY

2016 ◽  
Vol 8 (10) ◽  
pp. 72 ◽  
Author(s):  
Paranjeet Kaur ◽  
Gopal L. Khatik
Keyword(s):  
Molecular Docking ◽  
Androgen Receptor ◽  
Binding Affinity ◽  
Docking Study ◽  
Molecular Structures ◽  
The Novel ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Triazole Derivatives ◽  
Better Than

<p class="Default"><strong>Objective: </strong>To identify the novel and simple bioactive antiandrogens, that can overcome to side effects as well as drug resistance.</p><p class="Default"><strong>Methods: </strong>The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes. The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by MM2 method and converted to pdb extension file which is readable at the ADT interface.</p><p class="Default"><strong>Results: </strong>Total ten compounds from both series were shown better binding affinity than <em>R</em>-bicalutamide including oxadiazole and triazole series. Among these pk42 and pk46 were studied in-depth which showed best binding affinity to the androgen receptor. The <em>cis</em>-isomers were found better than their <em>trans</em>-isomer.</p><p><strong>Conclusion: </strong>Novel 5-styryl-1,2,4-oxadiazole/triazole derivatives were studied through molecular modeling using Autodock Vina. The potent compounds which showed better binding affinity than <em>R</em>-bicalutamide like pk24 and 46 were further analyzed for their interactions. The conformational effect also found significant in binding to the androgen receptor.</p>

scholarly journals DOCKING STUDY OF METHYL HESPERIDIN AS NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR

2018 ◽  
Vol 10 (3) ◽  
pp. 85 ◽  
Author(s):  
Hafrizal Riza ◽  
Andhi Fahrurroji ◽  
Arif Wicaksono ◽  
Ahmad Kharis Nugroho ◽  
Sudibyo Martono
Keyword(s):  
Hydrogen Bond ◽  
Physicochemical Properties ◽  
Reverse Transcriptase ◽  
Van Der Waals ◽  
Docking Study ◽  
Transcriptase Inhibitor ◽  
Autodock Vina ◽  
Good Solubility ◽  
Reverse Transcriptase Inhibitor ◽  
Hiv 1

Objective: This study aims to analyze the methyl hesperidin physicochemical properties related to solubility and permeability, and the affinity of methyl hesperidin against reverse transcriptase HIV-1 activity as a competitive substrate.Methods: This research was conducted using the computerized method, ChemOffice 15.0, to predict ligand physicochemical properties related to solubility and permeability, and Autodock Vina with Autodock Tools program to analyze ligand-receptor affinity.Results: The analysis result of physicochemical properties of hesperidin and methyl hesperidin is respectively 300,27 g/Mol, 1,78, and 314,29 g/Mol, 2,04. The docking result shows that the binding energy of hesperidin, methyl hesperidin and zidovudine with receptor are respectively-8,0,-8,8 and-9,3 kcal/Mol. The type of interactions between receptor and hesperidin is van der Waals and phi-phi staked, methyl hesperidin are van der Waals, hydrogen bond, phi-sigma, and phi-phi stacked, and zidovudine is an attractive charge, hydrogen bond, and phi-sigma.Conclusion: Methyl hesperidin has good solubility and permeability, and has affinity with the receptor, a substrate of reverse transcriptase HIV-1. 

scholarly journals Study of Molecular Docking of Chalcone Analoque Compound as Inhibitors for Liver Cancer Cells HepG2

2018 ◽  
Vol 7 (2) ◽  
pp. 147-158
Author(s):  
Neni Frimayanti ◽  
Enda Mora ◽  
Rizki Anugrah
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Liver Cancer ◽  
Docking Study ◽  
Positive Control ◽  
Crystallographic Structure ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Liver Cancer Cells

Molecular docking study using chalcone analogue compounds with proteins target from modeling crystallographic structure of Tyrosine kinase enzymes with code 1T46 was carried out with the aid of a computer using the AutoDock Vina program. The aim this study to determine the activity of 5 chalcone analogue compounds obtained from previous studies and 3 chalcone analogues which were modified as inhibitors of liver cancer using 5-fluorouracil as a positive control. Based on the docking results, it has been carried out and shown those compounds 1, 2, and 3 have the potential as the active inhibitors againts HepG2 liver cancer with a successive affinity of -10.1 kcal/mol, -9.7 kcal/mol, and - 9.6 kcal/mol, respectively. For the modified chalcone analogue compounds, compound 8 has the best results with an affinity value of -8.3 kcal/mol and this compound also has six amino acid residues which are the same as 5-flourouracyl (i.e. positive control).

scholarly journals Docking Study of Naringin Binding with COVID-19 Main Protease Enzyme

2020 ◽  
Vol 29 (2) ◽  
pp. 231-238
Author(s):  
Narmin H. Amin Huseen
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Hydroxyl Groups ◽  
Human Pathogen ◽  
Autodock Vina ◽  
Protease Enzyme ◽  
Main Protease ◽  
Novel Scaffold ◽  
3Cl Protease ◽  
Pi Interactions

The Coronavirus Disease (COVID-19) has recently emerged as a human pathogen caused by SARS-CoV-2 virus was first reported from Wuhan, China, on 31 December 2019. Upon study, it has been used molecular docking to binding affinity between COVID-19 protease enzyme and flavonoids with evaluations based on docking scores calculated by AutoDock Vina. Results showed that naringin suppressed COVID-19 protease, as it has the highest binding value than other flavonoids including quercetin, hesperetin, garcina and naringenin. An important finding in this study is that naringin with neighboring poly hydroxyl groups can serve as inhibitors of COVID-19 protease bind to the S pocket of protein, it is shown that residues His163, Glu166, Asn142, His41and PHe181 participate in the hydrogen bonding and pi-pi interactions, the same as happened with decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors.In other hand, some of the known protease inhibitors and anti-influenza drugs docked with COVID-19 protease, it has low binding value than naringin

scholarly journals Toluene Dioxygenase-Catalyzed cis-Dihydroxylation of Quinolines: A Molecular Docking Study and Chemoenzymatic Synthesis of Quinoline Arene Oxides

2021 ◽  
Vol 8 ◽  
Author(s):  
Derek R. Boyd ◽  
Narain D. Sharma ◽  
Pui L. Loke ◽  
Jonathan G. Carroll ◽  
Paul J. Stevenson ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Docking Studies ◽  
Chemoenzymatic Synthesis ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Toluene Dioxygenase ◽  
Arene Oxide ◽  
Carbocyclic Rings ◽  
Derivatives Of

Molecular docking studies of quinoline and 2-chloroquinoline substrates at the active site of toluene dioxygenase (TDO), were conducted using Autodock Vina, to identify novel edge-to-face interactions and to rationalize the observed stereoselective cis-dihydroxylation of carbocyclic rings and formation of isolable cis-dihydrodiol metabolites. These in silico docking results of quinoline and pyridine substrates, with TDO, also provided support for the postulated cis-dihydroxylation of electron-deficient pyridyl rings, to give transient cis-dihydrodiol intermediates and the derived hydroxyquinolines. 2-Chloroquinoline cis-dihydrodiol metabolites were used as precursors in the chemoenzymatic synthesis of enantiopure arene oxide and arene dioxide derivatives of quinoline, in the context of its possible mammalian metabolism and carcinogenicity.

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