Resistance to inhibitors of the human immunodeficiency virus type 1 integration

Hazuda, Daria J.

doi:10.1590/s1413-86702010000500016

Cited by 12 publications

(10 citation statements)

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“…In contrast to the viral DNAs recovered from untreated cells, a larger proportion of the viral DNAs recovered from RAL-treated cells were unintegrated circular forms. This is the expected result; RAL interferes with integration, and a larger fraction of the viral DNA is converted into the various circular forms (14). In contrast to what was seen with the proviruses recovered from untreated cells, we recovered both normal and aberrant proviruses from RAL-treated cells.…”

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confidence: 43%

“…The recent crystal structures of the prototype foamy virus (PFV) IN, in complexes with viral DNA and, in some cases, with viral DNA and inhibitors, sheds light on the mechanism of action of the INSTIs. PFV IN is structurally similar to HIV IN, especially in the region around the active site (7,(12)(13)(14)(15). RAL and the other known INSTIs have two essential components: a metal binding region that binds the two magnesium ions in the active site of HIV-1 IN, and a modified phenyl ring that displaces the nucleobase of the A at the 3′ end of the viral DNA and stacks on the penultimate C (Fig.…”

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confidence: 99%

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Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations

Varadarajan

McWilliams

Hughes

2013

Proc. Natl. Acad. Sci. U.S.A.

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Integration of the DNA copy of the HIV-1 genome into a host chromosome is required for viral replication and is thus an important target for antiviral therapy. The HIV-encoded enzyme integrase (IN) catalyzes two essential steps: 3′ processing of the viral DNA ends, followed by the strand transfer reaction, which inserts the viral DNA into host DNA. Raltegravir binds to IN and blocks the integration of the viral DNA. Using the Rous sarcoma virus-derived vector RCAS, we previously showed that mutations that cause one viral DNA end to be defective for IN-mediated integration led to abnormal integrations in which the provirus had one normal and one aberrant end, accompanied by rearrangements in the host genome. On the basis of these results, we expected that suboptimal concentrations of IN inhibitors, which could block one of the ends of viral integration, would lead to similar aberrant integrations. In contrast to the proviruses from untreated cells, which were all normal, ∼10-15% of the proviruses isolated after treatment with a suboptimal dose of raltegravir were aberrant. The aberrant integrations were similar to those seen in the RCAS experiments. Most of the aberrant proviruses had one normal end and one aberrant end and were accompanied by significant rearrangements in the host genome, including duplications, inversions, deletions and, occasionally, acquisition of sequences from other chromosomes. The rearrangements of the host DNA raise concerns that these aberrant integrations might have unintended consequences in HIV-1-infected patients who are not consistent in following a raltegravir-containing treatment regimen.strand transfer inhibitor | chromosomal rearrangements | integrase inhibitors H IV-1 integration is a two-step process: first, in the cytoplasm, an integrase (IN) dimer binds to each end of the newly synthesized linear viral DNA and removes two nucleotides from each of the 3′ ends, exposing the conserved CA dinucleotide. The preintegration complex (PIC) is translocated from the cytoplasm into the nucleus, where the viral DNA is integrated into the host genome. In the strand transfer (ST) reaction, the two exposed 3′ hydroxyl groups on the newly processed viral DNA ends attack phosphodiester bonds on the opposite strands of the target DNA at positions that lie across the major groove, 4-6 bp apart. This reaction is carried out by a tetramer of IN; each of the viral DNA ends is associated with an IN dimer. This transesterification reaction generates an intermediate in which the 3′ ends of the viral DNA are covalently joined to the host DNA and there are 4-to 6-bp gaps in the host DNA associated with both of the 5′ ends of the viral DNA. Cellular machinery repairs these gaps, creating a 4-to 6-bp duplication (the size of the duplication varies for different retroviruses) of the host DNA flanking the integrated viral DNA (1-4). HIV-1 integration generates a 5-bp duplication of the host DNA at the integration site (5, 6).Raltegravir (RAL) and all of the potent IN inhibitors thus far discovered bind to...

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Section: Resultsmentioning

confidence: 43%

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confidence: 99%

Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations

Varadarajan

McWilliams

Hughes

2013

Proc. Natl. Acad. Sci. U.S.A.

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“…These compounds have been shown to be highly potent bioavailable inhibitors of integrase strand transfer (8) but have demonstrated low-moderate genetic barriers to the development of drug resistance substitutions (DRMs) (9). There are three major pathways that are involved in resistance for RAL, commencing with substitutions at any of positions 155, 143, and 148 (9)(10)(11); EVG exhibits extensive cross-resistance with RAL due to substitutions at positions 155 and 148 (9,(12)(13)(14) and demonstrates other resistance pathways as well. This cross-resistance between RAL and EVG has necessitated the development of other INSTIs that possess higher barriers to resistance development as well as nonoverlapping resistance profiles.…”

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confidence: 99%

Biochemical Analysis of the Role of G118R-Linked Dolutegravir Drug Resistance Substitutions in HIV-1 Integrase

Quashie

Mésplède

Han

et al. 2013

Antimicrob Agents Chemother

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Drug resistance mutations (DRMs) have been reported for all currently approved anti-HIV drugs, including the latest integrase strand transfer inhibitors (INSTIs). We previously used the new INSTI dolutegravir (DTG) to select a G118R integrase resistance substitution in tissue culture and also showed that secondary substitutions emerged at positions H51Y and E138K. Now, we have characterized the impact of the G118R substitution, alone or in combination with either H51Y or E138K, on 3= processing and integrase strand transfer activity. The results show that G118R primarily impacted the strand transfer step of integration by diminishing the ability of integrase-long terminal repeat (LTR) complexes to bind target DNA. The addition of H51Y and E138K to G118R partially restored strand transfer activity by modulating the formation of integrase-LTR complexes through increasing LTR DNA affinity and total DNA binding, respectively. This unique mechanism, in which one function of HIV integrase partially compensates for the defect in another function, has not been previously reported. The G118R substitution resulted in low-level resistance to DTG, raltegravir (RAL), and elvitegravir (EVG). The addition of either of H51Y or E138K to G118R did not enhance resistance to DTG, RAL, or EVG. Homology modeling provided insight into the mechanism of resistance conferred by G118R as well as the effects of H51Y or E138K on enzyme activity. The G118R substitution therefore represents a potential avenue for resistance to DTG, similar to that previously described for the R263K substitution. For both pathways, secondary substitutions can lead to either diminished integrase activity and/or increased INSTI susceptibility. The HIV integrase (IN) enzyme catalyzes the insertion of viral DNA into host DNA, a process known as integration (1). In a reaction termed 3= processing, integrase recognizes and cleaves off a dinucleotide GT downstream of a conserved dinucleotide CA signal, located within the last 15 bp of the long terminal repeats (LTR) that flank the viral DNA, and this effectively creates new 3= hydroxyl ends (2). The second step in integration, termed strand transfer, is the integrase-mediated insertion of the processed viral DNA into host DNA by a 5-bp staggered cleavage of target DNA. The exposed 3= hydroxyl groups on the viral insert interact with exposed 5= phosphates on the host DNA. Integration, which occurs primarily in highly expressed genes (3), causes the host machinery to transcribe viral genes and leads to successful propagation of viral particles. Integration is essential for productive infection and the establishment of viral persistence; therefore, integration was an early choice for the development of inhibitory compounds (4).The development of in vitro microtiter plate-based biochemical assays for the measurement of the various biochemical activities of integrase facilitated compound screening and identification of viable integrase inhibitors (5). The first specific integrase inhibitors, identified in 2000 (5), posses...

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“…INSTIs inhibit the strand transfer step of integration that is critical in the replication cycle of retroviruses (11)(12)(13)(14). Mutations that confer resistance to both RAL and EVG have been observed in treatment-naive individuals following treatment failure and major resistance pathways have been iden-tified that involve substitutions at any of positions E92 (EVG), Y143 (RAL), Q148 (both drugs), and N155 (both drugs) (11,(15)(16)(17)(18)(19)(20). After an initial loss of viral replicative fitness, secondary mutations at multiple positions may compensate for this deficit, while simultaneously increasing the overall levels of drug resistance.…”

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Effect of HIV-1 Integrase Resistance Mutations When Introduced into SIVmac239 on Susceptibility to Integrase Strand Transfer Inhibitors

Hassounah

Mésplède

Quashie

et al. 2014

J Virol

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Studies on the in vitro susceptibility of SIV to integrase strand transfer inhibitors (INSTIs) have been rare. In order to determine the susceptibility of SIVmac239 to INSTIs and characterize the genetic pathways that might lead to drug resistance, we inserted various integrase (IN) mutations that had been selected with HIV under drug pressure with raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG) into the IN gene of SIV. We evaluated the effects of these mutations on SIV susceptibility to INSTIs and on viral infectivity. Sequence alignments of SIVmac239 IN with various HIV-1 isolates showed a high degree of homology and conservation of each of the catalytic triad and the key residues involved in drug resistance. Each of the G118R, Y143R, Q148R, R263K, and G140S/Q148R mutations, when introduced into SIV, impaired infectiousness and replication fitness compared to wild-type virus. Using TZM-bl cells, we demonstrated that the Q148R and N155H mutational pathways conferred resistance to EVG (36-and 62-fold, respectively), whereas R263K also displayed moderate resistance to EVG (12-fold). In contrast, Y143R, Q148R, and N155H all yielded low levels of resistance to RAL. The combination of G140S/Q148R conferred highlevel resistance to both RAL and EVG (>300-and 286-fold, respectively). DTG remained fully effective against all site-directed mutants except G118R and R263K. Thus, HIV INSTI mutations, when inserted into SIV, resulted in a similar phenotype. These findings suggest that SIV and HIV may share similar resistance pathways profiles and that SIVmac239 could be a useful nonhuman primate model for studies of HIV resistance to INSTIs. IMPORTANCEThe goal of our project was to establish whether drug resistance against integrase inhibitors in SIV are likely to be the same as those responsible for drug resistance in HIV. Our data answer this question in the affirmative and show that SIV can probably serve as a good animal model for studies of INSTIs and as an early indicator for possible emergent mutations that may cause treatment failure. An SIV-primate model remains an invaluable tool for investigating questions related to the potential role of INSTIs in HIV therapy, transmission, and pathogenesis, and the present study will facilitate each of the above.

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Resistance to inhibitors of the human immunodeficiency virus type 1 integration

Abstract: This review will summarize the role of integrase in HIV-1 infection, the mechanism of integrase inhibitors and resistance with an emphasis on raltegravir (RAL), the fi rst integrase inhibitor licensed to treat HIV-1 infection.

Cited by 12 publications

References 33 publications

Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations

Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations

Biochemical Analysis of the Role of G118R-Linked Dolutegravir Drug Resistance Substitutions in HIV-1 Integrase

Effect of HIV-1 Integrase Resistance Mutations When Introduced into SIVmac239 on Susceptibility to Integrase Strand Transfer Inhibitors

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