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Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase. 2006

William L Jorgensen, and Juliana Ruiz-Caro, and Julian Tirado-Rives, and Aravind Basavapathruni, and Karen S Anderson, and Andrew D Hamilton
Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA. william.jorgensen@yale.edu

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.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009010 Monte Carlo Method In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993) Method, Monte Carlo
D009154 Mutation Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. Mutations
D015394 Molecular Structure The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds. Structure, Molecular,Molecular Structures,Structures, Molecular
D015658 HIV Infections Includes the spectrum of human immunodeficiency virus infections that range from asymptomatic seropositivity, thru AIDS-related complex (ARC), to acquired immunodeficiency syndrome (AIDS). HTLV-III Infections,HTLV-III-LAV Infections,T-Lymphotropic Virus Type III Infections, Human,HIV Coinfection,Coinfection, HIV,Coinfections, HIV,HIV Coinfections,HIV Infection,HTLV III Infections,HTLV III LAV Infections,HTLV-III Infection,HTLV-III-LAV Infection,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,T Lymphotropic Virus Type III Infections, Human
D017076 Computer-Aided Design The use of computers for designing and/or manufacturing of anything, including drugs, surgical procedures, orthotics, and prosthetics. CAD-CAM,Computer-Aided Manufacturing,Computer-Assisted Design,Computer-Assisted Manufacturing,Computer Aided Design,Computer Aided Manufacturing,Computer Assisted Design,Computer Assisted Manufacturing,Computer-Aided Designs,Computer-Assisted Designs,Design, Computer-Aided,Design, Computer-Assisted,Designs, Computer-Aided,Designs, Computer-Assisted,Manufacturing, Computer-Aided,Manufacturing, Computer-Assisted
D054303 HIV Reverse Transcriptase A reverse transcriptase encoded by the POL GENE of HIV. It is a heterodimer of 66 kDa and 51 kDa subunits that are derived from a common precursor protein. The heterodimer also includes an RNAse H activity (RIBONUCLEASE H, HUMAN IMMUNODEFICIENCY VIRUS) that plays an essential role the viral replication process. Reverse Transcriptase, HIV,Reverse Transcriptase, Human Immunodeficiency Virus,Transcriptase, HIV Reverse
D018894 Reverse Transcriptase Inhibitors Inhibitors of reverse transcriptase (RNA-DIRECTED DNA POLYMERASE), an enzyme that synthesizes DNA on an RNA template. Reverse Transcriptase Inhibitor,Inhibitors, Reverse Transcriptase,Inhibitor, Reverse Transcriptase,Transcriptase Inhibitor, Reverse
D024921 Drug Resistance, Multiple, Viral The ability of viruses to resist or to become tolerant to several structurally and functionally distinct drugs simultaneously. This resistance phenotype may be attributed to multiple gene mutation. Drug Resistance, Extensive, Viral,Drug Resistance, Extensively, Viral,Extensive Antiviral Drug Resistance,Extensively Antiviral Drug Resistance,Multidrug Resistance, Viral,Multiple Antiviral Drug Resistance,Resistance, Viral Multidrug,Viral Multidrug Resistance,Viral Multidrug Resistances

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