Literature DB >> 16263277

Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase.

William L Jorgensen1, Juliana Ruiz-Caro, Julian Tirado-Rives, Aravind Basavapathruni, Karen S Anderson, Andrew D Hamilton.   

Abstract

Design principles are delineated for non-nucleoside inhibitors for HIV-1 reverse transcriptase (NNRTIs). Simultaneous optimization of binding affinity for wild-type RT, tolerance for viral mutations, and physical properties is pursued. Automated lead generation with the growing program BOMB, Monte Carlo simulations with free-energy perturbation theory for lead optimization, and property analysis with QikProp are featured. An initial 30 microM lead has been optimized rapidly to the 10 nM level.

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Year:  2005        PMID： 16263277     DOI： 10.1016/j.bmcl.2005.10.038

Source DB:  PubMed          Journal:  Bioorg Med Chem Lett        ISSN： 0960-894X            Impact factor:   2.823


  37 in total

1.  The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic.

Authors:  Vigneshwaran Namasivayam; Murugesan Vanangamudi; Victor G Kramer; Sonali Kurup; Peng Zhan; Xinyong Liu; Jacob Kongsted; Siddappa N Byrareddy
Journal:  J Med Chem       Date:  2018-12-27       Impact factor: 7.446

2.  Designing the molecular future.

Authors:  Gisbert Schneider
Journal:  J Comput Aided Mol Des       Date:  2011-11-30       Impact factor: 3.686

Review 3.  Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations.

Authors:  Julien Michel; Jonathan W Essex
Journal:  J Comput Aided Mol Des       Date:  2010-05-28       Impact factor: 3.686

Review 4.  Identification of HIV inhibitors guided by free energy perturbation calculations.

Authors:  Orlando Acevedo; Zandrea Ambrose; Patrick T Flaherty; Hadega Aamer; Prashi Jain; Somisetti V Sambasivarao
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

5.  The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA.

Authors:  Andreas Schüller; Marcel Suhartono; Uli Fechner; Yusuf Tanrikulu; Sven Breitung; Ute Scheffer; Michael W Göbel; Gisbert Schneider
Journal:  J Comput Aided Mol Des       Date:  2007-12-07       Impact factor: 3.686

6.  From docking false-positive to active anti-HIV agent.

Authors:  Gabriela Barreiro; Joseph T Kim; Cristiano R W Guimarães; Christopher M Bailey; Robert A Domaoal; Ligong Wang; Karen S Anderson; William L Jorgensen
Journal:  J Med Chem       Date:  2007-10-06       Impact factor: 7.446

7.  Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring.

Authors:  Gabriela Barreiro; Cristiano R W Guimarães; Ivan Tubert-Brohman; Theresa M Lyons; Julian Tirado-Rives; William L Jorgensen
Journal:  J Chem Inf Model       Date:  2007-10-20       Impact factor: 4.956

Review 8.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

9.  Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria.

Authors:  William L Jorgensen; Laura L Thomas
Journal:  J Chem Theory Comput       Date:  2008-05-09       Impact factor: 6.006

10.  Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization.

Authors:  Julien Michel; Julian Tirado-Rives; William L Jorgensen
Journal:  J Am Chem Soc       Date:  2009-10-28       Impact factor: 15.419
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