Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method

Suwipa Saen-oon; Mayuso Kuno; Supa Hannongbua

doi:10.1002/prot.20690

Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20690 ◽

2005 ◽

Vol 61 (4) ◽

pp. 859-869 ◽

Cited By ~ 37

Author(s):

Suwipa Saen-oon ◽

Mayuso Kuno ◽

Supa Hannongbua

Keyword(s):

Binding Energy ◽

Quantum Chemical Calculations ◽

Quantum Chemical ◽

Energy Analysis ◽

Complex Structures ◽

Wild Type ◽

Binding Energy Analysis ◽

Oniom Method ◽

Hiv 1

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Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors: Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design

Journal of Medicinal Chemistry ◽

10.1021/jm970535b ◽

1998 ◽

Vol 41 (6) ◽

pp. 836-852 ◽

Cited By ~ 82

Author(s):

Carlos Pérez ◽

Manuel Pastor ◽

Angel R. Ortiz ◽

Federico Gago

Keyword(s):

Binding Energy ◽

Drug Design ◽

Protease Inhibitors ◽

Solvent Effects ◽

Energy Analysis ◽

Comparative Binding ◽

Binding Energy Analysis ◽

Hiv 1

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Prediction of the Drug–Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00639 ◽

2021 ◽

Author(s):

Ariane Nunes-Alves ◽

Fabian Ormersbach ◽

Rebecca C. Wade

Keyword(s):

Binding Energy ◽

Drug Target ◽

Energy Analysis ◽

Binding Kinetics ◽

Comparative Binding ◽

Binding Energy Analysis ◽

Target Binding

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Comparative Binding Energy Analysis

3D QSAR in Drug Design - Three-Dimensional Quantitative Structure Activity Relationships ◽

10.1007/0-306-46857-3_2 ◽

2005 ◽

pp. 19-34 ◽

Cited By ~ 2

Author(s):

Rebecca C. Wade ◽

Angel R. Qrtiz ◽

Federico Gago

Keyword(s):

Binding Energy ◽

Energy Analysis ◽

Comparative Binding ◽

Binding Energy Analysis

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Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis

Journal of Medicinal Chemistry ◽

10.1021/jm00014a020 ◽

1995 ◽

Vol 38 (14) ◽

pp. 2681-2691 ◽

Cited By ~ 167

Author(s):

Angel R. Ortiz ◽

M. Teresa Pisabarro ◽

Federico Gago ◽

Rebecca C. Wade

Keyword(s):

Binding Energy ◽

Energy Analysis ◽

Drug Binding ◽

Binding Affinities ◽

Comparative Binding ◽

Binding Energy Analysis

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Methane Activation by (n=0, 1, 2; m= 1, 2): Reactivity Parameters, Electronic Properties and Binding Energy Analysis

ChemistrySelect ◽

10.1002/slct.201901166 ◽

2019 ◽

Vol 4 (27) ◽

pp. 7912-7921

Author(s):

Telles Cardoso Silva ◽

Maíra dos Santos Pires ◽

Alexandre Alves de Castro ◽

Lívia Clara Tavares Lacerda ◽

Marcus Vinícius Juliaci Rocha ◽

...

Keyword(s):

Binding Energy ◽

Electronic Properties ◽

Energy Analysis ◽

Methane Activation ◽

Binding Energy Analysis

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Binding energy analysis of solid hydrogen fluoride

Solid State Communications ◽

10.1016/0038-1098(86)90218-8 ◽

1986 ◽

Vol 58 (4) ◽

pp. 281-284 ◽

Cited By ~ 8

Author(s):

P. Otto ◽

E.O. Steinborn

Keyword(s):

Binding Energy ◽

Hydrogen Fluoride ◽

Energy Analysis ◽

Solid Hydrogen ◽

Binding Energy Analysis

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Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets

Journal of Medicinal Chemistry ◽

10.1021/jm060350h ◽

2006 ◽

Vol 49 (21) ◽

pp. 6241-6253 ◽

Cited By ~ 21

Author(s):

Marta Murcia ◽

Antonio Morreale ◽

Angel R. Ortiz

Keyword(s):

Binding Energy ◽

Energy Analysis ◽

3D Qsar ◽

Multiple Targets ◽

Multiple Receptors ◽

Qsar Models ◽

Comparative Binding ◽

Binding Energy Analysis

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A Study of the Binding Energies of Efavirenz to Wild-Type and K103N/Y181C HIV-1 Reverse Transcriptase Based on the ONIOM Method

ChemMedChem ◽

10.1002/cmdc.200700181 ◽

2008 ◽

Vol 3 (5) ◽

pp. 803-811 ◽

Cited By ~ 13

Author(s):

Pensri Srivab ◽

Supa Hannongbua

Keyword(s):

Reverse Transcriptase ◽

Binding Energies ◽

Wild Type ◽

Oniom Method ◽

Hiv 1

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Febrifugine analogues as Leishmania donovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2015.1135298 ◽

2016 ◽

Vol 35 (1) ◽

pp. 141-158 ◽

Cited By ~ 32

Author(s):

Rajan Kumar Pandey ◽

Bajarang Vasant Kumbhar ◽

Shubham Srivastava ◽

Ruchi Malik ◽

Shyam Sundar ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Binding Energy ◽

Leishmania Donovani ◽

Energy Analysis ◽

Dynamics Simulation ◽

Trypanothione Reductase ◽

Reductase Inhibitors ◽

Binding Energy Analysis

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Quantum Chemical Calculations on Binding Energy of Alkyl Substituted Crown Ethers with Sr2+

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.448-453.139 ◽

2013 ◽

Vol 448-453 ◽

pp. 139-144

Author(s):

Miao Li Hao ◽

Ying Ming Li ◽

Ying Zhang ◽

Xiao Rong Lan ◽

Yu Lei Guan ◽

...

Keyword(s):

Binding Energy ◽

Electron Density ◽

Quantum Chemical Calculations ◽

Crown Ethers ◽

Quantum Chemical ◽

Cavity Size ◽

Optimal Structures ◽

Alkyl Groups ◽

Strontium Ion

Structures of Dibenzo-18-crown-6(DB18C6), Di-methyl-dibenzo-18-crown-6(DMB18C6), Di-tert-butyl-dibenzo-18-crown-6(DTBB18C6), Di-tert-amyl-dibenzo-18-crown-6(DTAB1C6) and their complexes with strontium ion were optimized based upon DFT at B3LYP using 3-21G basis. The binding energy of crown ethers with Sr2+ was calculated according to the energy of optimal structures. The complex strength increased gradually from DB18C6 to DTAB18C6, which could be related to the changes of cavity size of crown ethers and electron density on the crown rings. Addition and extension of alkyl groups on DB18C6 could enhance the combination between crown and Sr2+.

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