Defining the DNA Substrate Binding Sites on HIV-1 Integrase

Dolan, James R.; Chen, Aiping; Weber, Irene T.; Harrison, Robert W.; Leis, Jonathan

doi:10.1016/j.jmb.2008.10.083

Cited by 29 publications

(25 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, we suggest that Q148/N155 residues interact with the sterically and energetically more favorable terminal unpaired adenine, consistent with previous data showing post-3 0 -processing contact between Q148 and the 5 0 -AC overhang (Chiu and Davies, 2004;Esposito and Craigie, 1998) and the theoretical model of the IN-DNA complex (Dolan et al, 2009). By contrast, the Q148R mutant preferentially established specific interactions by binding the two bases of a pair, either A-T or G-C, simultaneously.…”

Section: Discussionsupporting

confidence: 91%

See 1 more Smart Citation

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Mouscadet

Arora

André

et al. 2009

J of Molecular Recognition

View full text Add to dashboard Cite

Virologic failure during treatment with raltegravir, the first effective drug targeting HIV integrase, is associated with two exclusive pathways involving either Q148H/R/K, G140S/A or N155H mutations. We carried out a detailed analysis of the molecular and structural effects of these mutations. We observed no topological change in the integrase core domain, with conservation of a newly identified Omega-shaped hairpin containing the Q148 residue, in particular. In contrast, the mutations greatly altered the specificity of DNA recognition by integrase. The native residues displayed a clear preference for adenine, whereas the mutant residues strongly favored pyrimidines. Raltegravir may bind to N155 and/or Q148 residues as an adenine bioisoster. This may account for the selected mutations impairing raltegravir binding while allowing alternative DNA recognition by integrase. This study opens up new opportunities for the design of integrase inhibitors active against raltegravir-resistant viruses.

show abstract

Section: Discussionsupporting

confidence: 91%

“…This result supports the validity of our model. A recent theoretical prediction for DNA substrate binding sites on HIV-1 IN indicated that amino acids 139-152 constitute a binding site that includes Q148, together with Q137, Q146, and N144 Dolan et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Mouscadet

Arora

André

et al. 2009

J of Molecular Recognition

View full text Add to dashboard Cite

show abstract

“…already been shown to be important for DNA binding and 3= processing (15,38), has more DNA interactions than are obvious from modeling. A more dramatic spatial and orientation shift of R262 relative to its wild-type position was observed in the inner integrase subunits (Fig.…”

Section: Isolation Of R263k Mutant Viruses With Dtgmentioning

confidence: 99%

Characterization of the R263K Mutation in HIV-1 Integrase That Confers Low-Level Resistance to the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir

Quashie

Mésplède

Han

et al. 2012

J Virol

214

306

View full text Add to dashboard Cite

Integrase (IN) strand transfer inhibitors (INSTIs) have been developed to inhibit the ability of HIV-1 integrase to irreversibly link the reverse-transcribed viral DNA to the host genome. INSTIs have proven their high efficiency in inhibiting viral replication in vitro and in patients. However, first-generation INSTIs have only a modest genetic barrier to resistance, allowing the virus to escape these powerful drugs through several resistance pathways. Second-generation INSTIs, such as dolutegravir (DTG, S/GSK1349572), have been reported to have a higher resistance barrier, and no novel drug resistance mutation has yet been described for this drug. Therefore, we performed in vitro selection experiments with DTG using viruses of subtypes B, C, and A/G and showed that the most common mutation to emerge was R263K. Further analysis by site-directed mutagenesis showed that R263K does confer low-level resistance to DTG and decreased integration in cell culture without altering reverse transcription. Biochemical cell-free assays performed with purified IN enzyme containing R263K confirmed the absence of major resistance against DTG and showed a slight decrease in 3= processing and strand transfer activities compared to the wild type. Structural modeling suggested and in vitro IN-DNA binding assays show that the R263K mutation affects IN-DNA interactions.T he high mutation rate of HIV-1 reverse transcriptase (RT) allows the virus to escape pressure through adaptive mutations that include drug resistance mutations that limit the effectiveness of antiretroviral drugs (5,31,66,69,70). The use of multiple drugs in combination can hamper this process by restraining viral replication, limiting the emergence of resistant strains. The addition of integrase inhibitors to the arsenal of drugs against HIV-1 is important since these inhibitors are active against viruses resistant to other drug classes (16,49,63).The HIV-1 integrase enzyme catalyzes two reactions. The first is 3= processing, which consists of cleavage of a dinucleotide at both 3= ends of the reverse-transcribed linear viral DNA and results in the exposure of reactive hydroxyl groups. The second step termed "strand transfer" is carried out through a nucleophilic attack by exposed 3= hydroxyl groups on host genomic DNA (26, 47). Even though 3= processing may be a suitable therapeutic target, the integrase inhibitors developed so far are integrase strand transfer inhibitors (INSTIs) that preferentially inhibit strand transfer while only modestly affecting 3= processing (18,24,26). Raltegravir (RAL) was the first INSTI to be approved for therapy in 2007 (64) and is safe and efficient in both treatment-naïve and treatment-experienced subjects (11,17,23,35,49,62,63). Elvitegravir (EVG) is another INSTI currently in advanced clinical trials (10,12,77).Although first-generation INSTIs strongly inhibit HIV-1 replication, they possess only a modest genetic barrier to resistance. Three main resistance pathways have been identified for RAL, involving initial mutations of the N1...

show abstract

“…Elegant knockdown studies have demonstrated the importance of LEDGF/p75 in integration targeting and integrase stability (27,48,50,62,77). Additional studies have explored the link between chromosomal DNA structure and integration, suggesting that nucleosome-bound DNA may be more susceptible to integration due to conformational changes (16,25,63,64,79).…”

Section: Quiescent Cd4mentioning

confidence: 99%

Human Immunodeficiency Virus Integration Efficiency and Site Selection in Quiescent CD4 ⁺ T Cells

Vatakis

Kim

et al. 2009

J Virol

View full text Add to dashboard Cite

Until very recently, quiescent CD4؉ T cells were thought to be resistant to human immunodeficiency virus (HIV) infection. Subsequent studies, attempting to fully elucidate the mechanisms of resistance, showed that quiescent cells could become infected by HIV at low efficiency and form a latently infected population. In this study, we set out to identify the sites of viral integration and to assess the efficiency of the overall integration process in quiescent cells. Based on our results, HIV integration in quiescent CD4؉ T cells occurs in sites similar to those of their prestimulated counterparts. While site selections are similar, the integration process in quiescent cells is plagued by the formation of high levels of incorrectly processed viral ends and abortive two-long-terminal-repeat circles. Quiescent CD4ϩ T cells have been shown to be resistant to human immunodeficiency virus (HIV) infection, and the resistance is characterized by incomplete reverse transcription (82,83). However, the permissiveness of other nondividing cell types, such as resting T cells and macrophages, raised further questions regarding the nature of the block (10,26,56,65,67,(69)(70)(71). Later studies further elucidated which subsets of resting cells were refractory to infection. Truly quiescent cells in the G 0/1a phase were resistant to infection, while cells in the G 1b phase, characterized by high levels of RNA synthesis but not DNA synthesis, were susceptible to infection (43). These combined studies suggested that certain nondividing cells could support a productive infection. Subsequent studies were aimed at further examining the different steps of the viral life cycle in quiescent cells, as well as identifying potential cellular factors or the lack thereof that may block infection. One potential block to infection was hypothesized to be the lack of raw materials such as nucleotides. Treatment of quiescent cells with nucleosides resulted in increased reverse transcription but did not lead to a productive infection following stimulation of the cells (42, 61), suggesting that other factors may contribute to the resistance to productive infection. Recent studies examined the presence or absence of cellular factors responsible for the block in quiescent CD4 ϩ T cells. Both Murr1 and APOBEC3G have been shown to influence the viral life cycle in quiescent CD4 ϩ T cells (18, 29). However neither factor fully explains the lack of rescue of productive infection if quiescent cells are stimulated subsequent to infection.A more detailed examination of the viral life cycle in quiescent CD4 ϩ T cells can shed more light on the nature of the block presented by quiescent CD4 ϩ T cells. A series of recent studies looking at the different stages of the HIV life cycle in quiescent cells have further supported data from our earlier work (82, 83). More specifically, it has been shown that reverse transcription is inefficient in quiescent cells, generating fulllength viral transcripts that are very labile (half-life of 1 day) but are integration co...

show abstract

Defining the DNA Substrate Binding Sites on HIV-1 Integrase

Cited by 29 publications

References 70 publications

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Characterization of the R263K Mutation in HIV-1 Integrase That Confers Low-Level Resistance to the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir

Human Immunodeficiency Virus Integration Efficiency and Site Selection in Quiescent CD4 ⁺ T Cells

Contact Info

Product

Resources

About

Defining the DNA Substrate Binding Sites on HIV-1 Integrase

Cited by 29 publications

References 70 publications

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Characterization of the R263K Mutation in HIV-1 Integrase That Confers Low-Level Resistance to the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir

Human Immunodeficiency Virus Integration Efficiency and Site Selection in Quiescent CD4 + T Cells

Contact Info

Product

Resources

About

Human Immunodeficiency Virus Integration Efficiency and Site Selection in Quiescent CD4 ⁺ T Cells