Bridge water mediates nevirapine binding to wild type and Y181C HIV-1 reverse transcriptase—Evidence from molecular dynamics simulations and MM-PBSA calculations

2009 ◽  
Vol 27 (8) ◽  
pp. 921-929 ◽  
Author(s):  
Witcha Treesuwan ◽  
Supa Hannongbua
Keyword(s):  
Molecular Dynamics ◽  
Reverse Transcriptase ◽  
Molecular Dynamics Simulations ◽  
Wild Type ◽  
Dynamics Simulations ◽  
Hiv 1

scholarly journals Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition

2014 ◽  
Author(s):  
Pedro J Silva ◽  
Carlos E. P. Bernardo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Reverse Transcriptase ◽  
Molecular Dynamics Simulations ◽  
Complex Interplay ◽  
Lead Compounds ◽  
High Affinity ◽  
Dynamics Simulations ◽  
Hiv 1

The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on the complex interplay of factors determining the ability of ligands to selectively target each mutant have been obtained.

scholarly journals Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition

2014 ◽  
Author(s):  
Pedro J Silva ◽  
Carlos E. P. Bernardo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Reverse Transcriptase ◽  
Molecular Dynamics Simulations ◽  
Complex Interplay ◽  
Lead Compounds ◽  
High Affinity ◽  
Dynamics Simulations ◽  
Hiv 1

The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on the complex interplay of factors determining the ability of ligands to selectively target each mutant have been obtained.

Insight into HIV-1 reverse transcriptase–aptamer interaction from molecular dynamics simulations

2014 ◽  
Vol 20 (8) ◽  
Author(s):  
Niran Aeksiri ◽  
Napat Songtawee ◽  
M. Paul Gleeson ◽  
Supa Hannongbua ◽  
Kiattawee Choowongkomon
Keyword(s):  
Molecular Dynamics ◽  
Reverse Transcriptase ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Insight Into ◽  
Hiv 1

scholarly journals Exploration of the cofactor specificity of wild-type phosphite dehydrogenase and its mutant using molecular dynamics simulations

RSC Advances ◽  
2021 ◽  
Vol 11 (24) ◽  
pp. 14527-14533
Author(s):  
Kunlu Liu ◽  
Min Wang ◽  
Yubo Zhou ◽  
Hongxiang Wang ◽  
Yudong Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wild Type ◽  
Cofactor Specificity ◽  
Phosphite Dehydrogenase ◽  
Dynamics Simulations

Phosphite dehydrogenase (Pdh) catalyzes the NAD-dependent oxidation of phosphite to phosphate with the formation of NADH.

Observation of “Ionic Lock” Formation in Molecular Dynamics Simulations of Wild-Type β1and β2Adrenergic Receptors

Biochemistry ◽  
2009 ◽  
Vol 48 (22) ◽  
pp. 4789-4797 ◽  
Author(s):  
Stefano Vanni ◽  
Marilisa Neri ◽  
Ivano Tavernelli ◽  
Ursula Rothlisberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wild Type ◽  
Dynamics Simulations
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