Genetic Barrier to the Development of Resistance to Integrase Inhibitors in HIV-1 Subtypes CRF01_AE and B

ABSTRACT TMC125 is a potent new investigational nonnucleoside reverse transcriptase inhibitor (NNRTI) that is active against human immunodeficiency virus type 1 (HIV-1) with resistance to currently licensed NNRTIs. Sequential passage experiments with both wild-type virus and NNRTI-resistant virus were performed to identify mutations selected by TMC125 in vitro. In addition to “classic” selection experiments at a low multiplicity of infection (MOI) with increasing concentrations of inhibitors, experiments at a high MOI with fixed concentrations of inhibitors were performed to ensure a standardized comparison between TMC125 and current NNRTIs. Both low- and high-MOI experiments demonstrated that the development of resistance to TMC125 required multiple mutations which frequently conferred cross-resistance to efavirenz and nevirapine. In high-MOI experiments, 1 μM TMC125 completely inhibited the breakthrough of resistant virus from wild-type and NNRTI-resistant HIV-1, in contrast to efavirenz and nevirapine. Furthermore, breakthrough of virus from site-directed mutant (SDM) SDM-K103N/Y181C occurred at the same time or later with TMC125 as breakthrough from wild-type HIV-1 with efavirenz or nevirapine. The selection experiments identified mutations selected by TMC125 that included known NNRTI-associated mutations L100I, Y181C, G190E, M230L, and Y318F and the novel mutations V179I and V179F. Testing the antiviral activity of TMC125 against a panel of SDMs indicated that the impact of these individual mutations on resistance was highly dependent upon the presence and identity of coexisting mutations. These results demonstrate that TMC125 has a unique profile of activity against NNRTI-resistant virus and possesses a high genetic barrier to the development of resistance in vitro.

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Cross-Resistance Profile Determination of Two Second-Generation HIV-1 Integrase Inhibitors Using a Panel of Recombinant Viruses Derived from Raltegravir-Treated Clinical Isolates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01733-09 ◽

2010 ◽

Vol 55 (1) ◽

pp. 321-325 ◽

Cited By ~ 35

Author(s):

L. Van Wesenbeeck ◽

E. Rondelez ◽

M. Feyaerts ◽

A. Verheyen ◽

K. Van der Borght ◽

...

Keyword(s):

Second Generation ◽

Treated Patient ◽

Integrase Inhibitor ◽

Cross Resistance ◽

Integrase Inhibitors ◽

Genetic Barrier ◽

Resistance Profile ◽

Recombinant Viruses ◽

Treatment Naïve ◽

Hiv 1

ABSTRACTThe integrase inhibitor raltegravir (RAL) is currently used for the treatment of both treatment-naïve and treatment-experienced HIV-1-infected patients. Elvitegravir (EVG) is in late phases of clinical development. Since significant cross-resistance between RAL and EVG is observed, there is a need for second-generation integrase inhibitors (INIs) with a higher genetic barrier and limited cross-resistance to RAL/EVG. A panel of HIV-1 integrase recombinants, derived from plasma samples from raltegravir-treated patients (baseline and follow-up samples), were used to study the cross-resistance profile of two second-generation integrase inhibitors, MK-2048 and compound G. Samples with Q148H/R mutations had elevated fold change values with all compounds tested. Although samples with the Y143R/C mutation had reduced susceptibility to RAL, they remained susceptible to MK-2048 and compound G. Samples with the N155H mutation had no reduced susceptibility to compound G. In conclusion, our results allowed ranking of the INIs on the basis of the antiviral activities using recombinant virus stocks from RAL-treated patient viruses. The order according to decreasing susceptibility is compound G, MK-2048, and EVG.

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Genetic barrier to the development of resistance to rilpivirine and etravirine between HIV-1 subtypes CRF02_AG and B

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkt251 ◽

2013 ◽

Vol 68 (11) ◽

pp. 2515-2520 ◽

Cited By ~ 4

Author(s):

D. B. Fofana ◽

C. Soulie ◽

A. I. Maiga ◽

S. Fourati ◽

I. Malet ◽

...

Keyword(s):

Genetic Barrier ◽

Development Of Resistance ◽

Hiv 1

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An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00539-19 ◽

2019 ◽

Vol 63 (8) ◽

Cited By ~ 2

Author(s):

Kristof Theys ◽

Pieter J. K. Libin ◽

Kristel Van Laethem ◽

Ana B. Abecasis

Keyword(s):

Sequence Data ◽

Evolutionary Model ◽

Integrase Inhibitors ◽

Genetic Barrier ◽

Viral Pathogens ◽

Model Based ◽

Subtype B ◽

Genetic Potential ◽

The Impact ◽

Hiv 1

ABSTRACT Viral pathogens causing global disease burdens are often characterized by high rates of evolutionary changes. The extensive viral diversity at baseline can shorten the time to escape from therapeutic or immune selective pressure and alter mutational pathways. The impact of genotypic background on the barrier to resistance can be difficult to capture, particularly for agents in experimental stages or that are recently approved or expanded into new patient populations. We developed an evolutionary model-based counting method to quickly quantify the population genetic potential to resistance and assess population differences. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequence data and corresponding knowledge gap. A large sequence data set encompassing most prevailing HIV-1 subtypes and resistance-associated mutations of currently approved integrase inhibitors was investigated. A complex interplay between codon predominance, polymorphisms, and associated evolutionary costs resulted in a subtype-dependent varied genetic potential for 15 resistance mutations against integrase inhibitors. While we confirm the lower genetic barrier of subtype B for G140S, we convincingly discard a similar effect previously suggested for G140C. A supplementary analysis for HIV-1 reverse transcriptase inhibitors identified a lower genetic barrier for K65R in subtype C through differential codon usage not reported before. To aid evolutionary interpretations of genomic differences for antiviral strategies, we advanced existing counting methods with increased sensitivity to identify subtype dependencies of resistance emergence. Future applications include novel HIV-1 drug classes or vaccines, as well as other viral pathogens.

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An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors

10.1101/647297 ◽

2019 ◽

Author(s):

Kristof Theys ◽

Pieter Libin ◽

Kristel Van Laethem ◽

Ana B Abecasis

Keyword(s):

Drug Resistance ◽

Antiviral Treatment ◽

Integrase Inhibitors ◽

Resistance Mutations ◽

Genetic Barrier ◽

Viral Pathogens ◽

Subtype B ◽

Genetic Potential ◽

The Impact ◽

Hiv 1

AbstractViral pathogens causing global disease burdens are often characterised by high rates of evolutionary changes, facilitating escape from therapeutic or immune selective pressure. Extensive viral diversity at baseline can shorten the time to resistance emergence and alter mutational pathways, but the impact of genotypic background on the genetic barrier can be difficult to capture, in particular for antivirals in experimental stages, recently approved or expanded into new settings. We developed an evolutionary-based counting method to quantify the population genetic potential to resistance and assess differences between populations. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequences and corresponding knowledge gap on drug resistance. A large sequence dataset encompassing most prevailing subtypes and resistance mutations of first- and second-generation inhibitors were investigated. A varying genetic potential for resistance across HIV-1 subtypes was detected for 15 mutations at 12 positions, with notably 140S in subtype B, while 140C was discarded to vary across subtypes. An additional analysis for HIV-1 reverse transcriptase inhibitors identified a higher potential for 65R in subtype C, on the basis of a differential codon usage not reported before. The evolutionary interpretation of genomic differences for antiviral treatment remains challenging. Our framework advances existing counting methods with an increased sensitivity that identified novel subtype dependencies as well as rejected previous statements. Future applications include novel HIV-1 drug classes as well as other viral pathogens.

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Human DDX3 protein is a valuable target to develop broad spectrum antiviral agents

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1522987113 ◽

2016 ◽

Vol 113 (19) ◽

pp. 5388-5393 ◽

Cited By ~ 50

Author(s):

Annalaura Brai ◽

Roberta Fazi ◽

Cristina Tintori ◽

Claudio Zamperini ◽

Francesca Bugli ◽

...

Keyword(s):

Broad Spectrum ◽

Antiviral Agents ◽

Antiviral Agent ◽

Host Factor ◽

Human Pathogens ◽

Genetic Barrier ◽

Dna And Rna ◽

Development Of Resistance ◽

Emerging Viral Diseases ◽

Hiv 1

Targeting a host factor essential for the replication of different viruses but not for the cells offers a higher genetic barrier to the development of resistance, may simplify therapy regimens for coinfections, and facilitates management of emerging viral diseases. DEAD-box polypeptide 3 (DDX3) is a human host factor required for the replication of several DNA and RNA viruses, including some of the most challenging human pathogens currently circulating, such as HIV-1, Hepatitis C virus, Dengue virus, and West Nile virus. Herein, we showed for the first time, to our knowledge, that the inhibition of DDX3 by a small molecule could be successfully exploited for the development of a broad spectrum antiviral agent. In addition to the multiple antiviral activities, hit compound 16d retained full activity against drug-resistant HIV-1 strains in the absence of cellular toxicity. Pharmacokinetics and toxicity studies in rats confirmed a good safety profile and bioavailability of 16d. Thus, DDX3 is here validated as a valuable therapeutic target.

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In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors

Journal of Virology ◽

10.1128/jvi.00967-10 ◽

2010 ◽

Vol 84 (22) ◽

pp. 11961-11969 ◽

Cited By ~ 65

Author(s):

Yasuhiro Koh ◽

Masayuki Amano ◽

Tomomi Towata ◽

Matthew Danish ◽

Sofiya Leshchenko-Yashchuk ◽

...

Keyword(s):

Homologous Recombination ◽

In Vitro Selection ◽

Multiple Drug ◽

Drug Resistant ◽

Genetic Barrier ◽

Development Of Resistance ◽

Multiple Drug Resistant ◽

Moderately Resistant ◽

Hiv 1

ABSTRACT We attempted to select HIV-1 variants resistant to darunavir (DRV), which potently inhibits the enzymatic activity and dimerization of protease and has a high genetic barrier to HIV-1 development of resistance to DRV. We conducted selection using a mixture of 8 highly multi-protease inhibitor (PI)-resistant, DRV-susceptible clinical HIV-1 variants (HIV-1MIX) containing 9 to 14 PI resistance-associated amino acid substitutions in protease. HIV-1MIX became highly resistant to DRV, with a 50% effective concentration (EC50) ∼333-fold greater than that against HIV-1NL4-3. HIV-1MIX at passage 51 (HIV-1MIXP51 ) replicated well in the presence of 5 μM DRV and contained 14 mutations. HIV-1MIXP51 was highly resistant to amprenavir, indinavir, nelfinavir, ritonavir, lopinavir, and atazanavir and moderately resistant to saquinavir and tipranavir. HIV-1MIXP51 had a resemblance with HIV-1C of the HIV-1MIX population, and selection using HIV-1C was also performed; however, its DRV resistance acquisition was substantially delayed. The H219Q and I223V substitutions in Gag, lacking in HIV-1CP51 , likely contributed to conferring a replication advantage on HIV-1MIXP51 by reducing intravirion cyclophilin A content. HIV-1MIXP51 apparently acquired the substitutions from another HIV-1 strain(s) of HIV-1MIX through possible homologous recombination. The present data suggest that the use of multiple drug-resistant HIV-1 isolates is of utility in selecting drug-resistant variants and that DRV would not easily permit HIV-1 to develop significant resistance; however, HIV-1 can develop high levels of DRV resistance when a variety of PI-resistant HIV-1 strains are generated, as seen in patients experiencing sequential PI failure, and ensuing homologous recombination takes place. HIV-1MIXP51 should be useful in elucidating the mechanisms of HIV-1 resistance to DRV and related agents.

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Pharmacotherapy Update: Treatment of HIV Infection with Darunavir

Clinical Medicine Insights Therapeutics ◽

10.4137/cmt.s1101 ◽

2010 ◽

Vol 2 ◽

pp. CMT.S1101

Author(s):

A. Viganò ◽

V. Manfredini ◽

C. Mameli ◽

V. Giacomet ◽

G.V. Zuccotti

Keyword(s):

Protease Inhibitor ◽

Pharmacokinetic Profile ◽

Hepatic Function ◽

Genetic Barrier ◽

Development Of Resistance ◽

Drug Concentrations ◽

Function Impairment ◽

Age Range ◽

Hiv 1 ◽

Antiretroviral Activity

Darunavir is an oral peptidomimetic HIV-1 protease inhibitor with antiretroviral activity against wild type HIV strains and HIV strains with protease inhibitor mutations. Ritonavir-boosted darunavir is rapidly absorbed and it has a higher bioavailability than unboosted darunavir. In HIV infected adults, the pharmacokinetic profile of darunavir showed that the drug concentrations are similar in the age range between 18 to 65 years and unaffected by the presence of moderate renal or hepatic function impairment. Darunavir chemical structure provides a strong interaction between the drug and HIV-1 protease and accounts for its potent antiretroviral activity and high genetic barrier to the development of resistance. The efficacy, safety and tolerability of darunavir have been widely demonstrated in HIV-infected treatment-experienced and naïve adult patients and it's use has been labelled in this population. Recently, upon the approval of the Food and Drug Administration, a 75 mg darunavir's tablet formulation has been licensed for the treatment of HIV-infected children and adolescents in the age range between 6 to 17 years.

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