scholarly journals Conformational Landscape of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Non-Nucleoside Inhibitor Binding Pocket: Lessons for Inhibitor Design from a Cluster Analysis of Many Crystal Structures

2009 ◽  
Vol 52 (20) ◽  
pp. 6413-6420 ◽  
Author(s):  
Kristina A. Paris ◽  
Omar Haq ◽  
Anthony K. Felts ◽  
Kalyan Das ◽  
Eddy Arnold ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Cluster Analysis ◽  
Reverse Transcriptase ◽  
Crystal Structures ◽  
Human Immunodeficiency Virus Type ◽  
Binding Pocket ◽  
Inhibitor Binding ◽  
Immunodeficiency Virus ◽  
Conformational Landscape

scholarly journals Influence of naturally occurring insertions in the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase on polymerase fidelity and mutation frequencies in vitro

2006 ◽  
Vol 87 (2) ◽  
pp. 419-428 ◽  
Author(s):  
Kenneth Curr ◽  
Snehlata Tripathi ◽  
Johan Lennerstrand ◽  
Brendan A. Larder ◽  
Vinayaka R. Prasad
Keyword(s):  
Human Immunodeficiency Virus ◽  
Reverse Transcriptase ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Nucleoside Analogue ◽  
Binding Pocket ◽  
Resistance Mutations ◽  
Immunodeficiency Virus

The fingers subdomain of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is a hotspot for nucleoside analogue resistance mutations. Some multi-nucleoside analogue-resistant variants contain a T69S substitution along with dipeptide insertions between residues 69 and 70. This set of mutations usually co-exists with classic zidovudine-resistance mutations (e.g. M41L and T215Y) or an A62V mutation and confers resistance to multiple nucleoside analogue inhibitors. As insertions lie in the vicinity of the dNTP-binding pocket, their influence on RT fidelity was investigated. Commonly occurring insertion mutations were selected, i.e. T69S-AG, T69S-SG and T69S-SS alone, in combination with 3′-azido-2′,3′-deoxythymidine-resistance mutations M41L, L210W, R211K, L214F, T215Y (LAGAZ and LSGAZ) or with an alternate set where A62V substitution replaces M41L (VAGAZ, VSGAZ and VSSAZ). Using a lacZα gapped duplex substrate, the forward mutation frequencies of recombinant wild-type and mutant RTs bearing each of the above sets of mutations were measured. All of the mutants displayed significant decreases in mutation frequencies. Whereas the dipeptide insertions alone showed the least decrease (4·0- to 7·5-fold), the VAG series showed an intermediate reduction (5·0- to 11·4-fold) and the LAG set showed the largest reduction in mutation frequencies (15·3- and 16·3-fold for LAGAZ and LSGAZ, respectively). Single dNTP exclusion assays for mutants LSGAZ and LAGAZ confirmed their large reduction in misincorporation efficiencies. The increased in vitro fidelity was not due to excision of the incorrect nucleotide via ATP-dependent removal. There was also no direct correlation between increased fidelity and template–primer affinity, suggesting a change in the active site that is conducive to better discrimination during dNTP insertion.

scholarly journals Drug Resistance Mutations in the Nucleotide Binding Pocket of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Differentially Affect the Phosphorolysis-Dependent Primer Unblocking Activity in the Presence of Stavudine and Zidovudine and Its Inhibition by Efavirenz

2005 ◽  
Vol 49 (1) ◽  
pp. 342-349 ◽  
Author(s):  
Emmanuele Crespan ◽  
Giada A. Locatelli ◽  
Reynel Cancio ◽  
Ulrich Hübscher ◽  
Silvio Spadari ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Nucleotide Binding ◽  
Binding Pocket ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) derivatives with D113E, Y115F, F116Y, Q151E/N, and M184V mutations were studied for their phosphorolysis-mediated resistance to the nucleoside RT inhibitors (NRTIs) zidovudine and stavudine and for their inhibition by the nonnucleoside analogs (NNRTIs) efavirenz and nevirapine. The results presented here indicate that these single amino acid substitutions within the nucleotide binding pocket of the viral RT can independently affect different enzymatic properties, such as catalytic efficiency, drug binding, and phosphorolytic activity. Moreover, small local alterations of the physicochemical properties of the microenvironment around the active site can have profound effects on some NRTIs while hardly affecting other ones. In conclusion, even though different mutations within the nucleotide binding pocket of HIV-1 RT can result in a common phenotype (i.e., drug resistance), the molecular mechanisms underlying this phenotype can be very different. Moreover, the same mutation can give rise to different phenotypes depending on the nature of the substrates and/or inhibitors.

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