Preliminary Mapping of a Putative Inhibitor-Binding Pocket for Human Immunodeficiency Virus Type 1 Integrase Inhibitors

Lee, Deborah J; Robinson, William E.

doi:10.1128/aac.50.1.134-142.2006

Cited by 28 publications

(38 citation statements)

References 50 publications

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“…The virus with the greatest integration defect (3-fold) was Q148R. In vitro, Q148R has an altered dependence on magnesium (23), requiring 10-fold higher magnesium concentrations to effect maximal levels of strand transfer and inhibitor binding, and the overall strand transfer efficiency (k p / K m ) of Q148R was 15% of WT, similar to that reported for Q148A (46). However, although the k p for Q148R is only modestly reduced (63%) compared with the WT enzyme, Q148R has the largest elevation in the K m value for target DNA utilization of all the enzymes studied (4-fold).…”

Section: Discussionsupporting

confidence: 56%

Biochemical Analysis of HIV-1 Integrase Variants Resistant to Strand Transfer Inhibitors

Dicker

Terry

Lin

et al. 2008

Journal of Biological Chemistry

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In this study, eight different HIV-1 integrase proteins containing mutations observed in strand transfer inhibitor-resistant viruses were expressed, purified, and used for detailed enzymatic analyses. All the variants examined were impaired for strand transfer activity compared with the wild type enzyme, with relative catalytic efficiencies (k p /K m ) ranging from 0.6 to 50% of wild type. The origin of the reduced strand transfer efficiencies of the variant enzymes was predominantly because of poorer catalytic turnover (k p ) values. However, smaller secondorder effects were caused by up to 4-fold increases in K m values for target DNA utilization in some of the variants. All the variants were less efficient than the wild type enzyme in assembling on the viral long terminal repeat, as each variant required more protein than wild type to attain maximal activity. In addition, the variant integrases displayed up to 8-fold reductions in their catalytic efficiencies for 3-processing. The Q148R variant was the most defective enzyme. The molecular basis for resistance of these enzymes was shown to be due to lower affinity binding of the strand transfer inhibitor to the integrase complex, a consequence of faster dissociation rates. In the case of the Q148R variant, the origin of reduced compound affinity lies in alterations to the active site that reduce the binding of a catalytically essential magnesium ion. Finally, except for T66I, variant viruses harboring the resistance-inducing substitutions were defective for viral integration.

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Section: Discussionsupporting

confidence: 56%

Biochemical Analysis of HIV-1 Integrase Variants Resistant to Strand Transfer Inhibitors

Dicker

Terry

Lin

et al. 2008

Journal of Biological Chemistry

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“…Data from in vitro and clinical resistance studies on integrase inhibitors were collated from the scientific literature (Table 1) (1,4,7,8,11,13,19,22). The frequency of resistance-associated mutations was calculated for each subtype using the subtype PSSMs described above.…”

Section: Sequencesmentioning

confidence: 99%

Analysis of Natural Sequence Variation and Covariation in Human Immunodeficiency Virus Type 1 Integrase

Myers¹,

Pillay

2008

J Virol

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Human immunodeficiency virus type 1 (HIV-1) integrase inhibitors are in clinical trials, and raltegravir and elvitegravir are likely to be the first licensed drugs of this novel class of HIV antivirals. Understanding resistance to these inhibitors is important to maximize their efficacy. It has been shown that natural variation and covariation provide valuable insights into the development of resistance for established HIV inhibitors. Therefore, we have undertaken a study to fully characterize natural polymorphisms and amino acid covariation within an inhibitor-naïve sequence set spanning all defined HIV-1 subtypes. Inter-and intrasubtype variation was greatest in a 50-amino-acid segment of HIV-1 integrase incorporating the catalytic aspartic acid codon 116, suggesting that polymorphisms affect inhibitor binding and pathways to resistance. The critical mutations that determine the resistance pathways to raltegravir and elvitegravir (N155H, Q148K/R/H, and E92Q) were either rare or absent from the 1,165-sequence data set. However, 25 out of 41 mutations associated with integrase inhibitor resistance were present. These mutations were not subtype associated and were more prevalent in the subtypes that had been sampled frequently within the database. A novel modification of the Jaccard index was used to analyze amino acid covariation within HIV-1 integrase. A network of 10 covarying resistance-associated mutations was elucidated, along with a further 15 previously undescribed mutations that covaried with at least two of the resistance positions. The validation of covariation as a predictive tool will be dependent on monitoring the evolution of HIV-1 integrase under drug selection pressure.

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“…Therefore, it is important to understand the impact of RAL-selected resistance mutations on both the susceptibility and IN-mediated replication capacity (RC) of patient viruses, which provide additional information regarding treatment decisions and future drug discovery in this new class of antiretrovirals. Resistance to IN inhibitors involves the accumulation of mutations located primarily within the IN catalytic core domain (12,13,(17)(18)(19)26). Early IN inhibitor candidates that targeted the strand transfer step, like the diketo acids and naphthyridine carboxamides, were structurally distinct and gave rise to nonoverlapping patterns of resistance mutations in vitro (17).…”

mentioning

confidence: 99%

Loss of Raltegravir Susceptibility by Human Immunodeficiency Virus Type 1 Is Conferred via Multiple Nonoverlapping Genetic Pathways

Fransen¹,

Gupta²,

Danovich

et al. 2009

J Virol

158

206

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The human immunodeficiency virus type 1 (HIV-1) integrase mutations N155H and Q148R(H)(K) that reduce susceptibility to the integrase inhibitor raltegravir have been identified in patients failing treatment regimens containing raltegravir. Whether these resistance mutations occur individually or in combination within a single virus genome has not been defined, nor do we fully understand the impact of these primary mutations and other secondary mutations on raltegravir susceptibility and viral replication capacity. To address these important questions, we investigated the raltegravir susceptibility and replication capacity of viruses containing mutations at positions 155 and 148 separately or in combination with secondary mutations selected in subjects failing treatment regimens containing raltegravir. Clonal analysis demonstrated that N155H and Q148R(H)(K) occur independently, not in combination. Viruses containing a Q148R(H)(K) mutation generally displayed larger reductions in raltegravir susceptibility than viruses with an N155H mutation. Analysis of site-directed mutants indicated that E92Q in combination with N155H resulted in a higher level of resistance to raltegravir than N155H alone. Viruses containing a Q148R(H) mutation together with a G140S mutation were more resistant to raltegravir than viruses containing a Q148R(H) mutation alone; however, viruses containing G140S and Q148K were more susceptible to raltegravir than viruses containing a Q148K mutation alone. Both N155H and Q148R(H)(K) mutations reduced the replication capacity, while the addition of secondary mutations either improved or reduced the replication capacity depending on the primary mutation. This study demonstrates distinct genetic pathways to resistance in subjects failing raltegravir regimens and defines the effects of primary and secondary resistance mutations on raltegravir susceptibility and replication capacity.

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Preliminary Mapping of a Putative Inhibitor-Binding Pocket for Human Immunodeficiency Virus Type 1 Integrase Inhibitors

Cited by 28 publications

References 50 publications

Biochemical Analysis of HIV-1 Integrase Variants Resistant to Strand Transfer Inhibitors

Biochemical Analysis of HIV-1 Integrase Variants Resistant to Strand Transfer Inhibitors

Analysis of Natural Sequence Variation and Covariation in Human Immunodeficiency Virus Type 1 Integrase

Loss of Raltegravir Susceptibility by Human Immunodeficiency Virus Type 1 Is Conferred via Multiple Nonoverlapping Genetic Pathways

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