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Using machine learning and big data to explore the drug resistance landscape in HIV. PLoS Comput Biol 2021; 17:e1008873. [PMID: 34437532 PMCID: PMC8425536 DOI: 10.1371/journal.pcbi.1008873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/08/2021] [Accepted: 08/09/2021] [Indexed: 12/21/2022] Open
Abstract
Drug resistance mutations (DRMs) appear in HIV under treatment pressure. DRMs are commonly transmitted to naive patients. The standard approach to reveal new DRMs is to test for significant frequency differences of mutations between treated and naive patients. However, we then consider each mutation individually and cannot hope to study interactions between several mutations. Here, we aim to leverage the ever-growing quantity of high-quality sequence data and machine learning methods to study such interactions (i.e. epistasis), as well as try to find new DRMs. We trained classifiers to discriminate between Reverse Transcriptase Inhibitor (RTI)-experienced and RTI-naive samples on a large HIV-1 reverse transcriptase (RT) sequence dataset from the UK (n ≈ 55, 000), using all observed mutations as binary representation features. To assess the robustness of our findings, our classifiers were evaluated on independent data sets, both from the UK and Africa. Important representation features for each classifier were then extracted as potential DRMs. To find novel DRMs, we repeated this process by removing either features or samples associated to known DRMs. When keeping all known resistance signal, we detected sufficiently prevalent known DRMs, thus validating the approach. When removing features corresponding to known DRMs, our classifiers retained some prediction accuracy, and six new mutations significantly associated with resistance were identified. These six mutations have a low genetic barrier, are correlated to known DRMs, and are spatially close to either the RT active site or the regulatory binding pocket. When removing both known DRM features and sequences containing at least one known DRM, our classifiers lose all prediction accuracy. These results likely indicate that all mutations directly conferring resistance have been found, and that our newly discovered DRMs are accessory or compensatory mutations. Moreover, apart from the accessory nature of the relationships we found, we did not find any significant signal of further, more subtle epistasis combining several mutations which individually do not seem to confer any resistance. Almost all drugs to treat HIV target the Reverse Transcriptase (RT) and Drug resistance mutations (DRMs) appear in HIV under treatment pressure. Resistant strains can be transmitted and limit treatment options at the population level. Classically, multiple statistical testing is used to find DRMs, by comparing virus sequences of treated and naive populations. However, with this method, each mutation is considered individually and we cannot hope to reveal any interaction (epistasis) between them. Here, we used machine learning to discover new DRMs and study potential epistasis effects. We applied this approach to a very large UK dataset comprising ≈ 55, 000 RT sequences. Results robustness was checked on different UK and African datasets. Six new mutations associated to resistance were found. All six have a low genetic barrier and show high correlations with known DRMs. Moreover, all these mutations are close to either the active site or the regulatory binding pocket of RT. Thus, they are good candidates for further wet experiments to establish their role in drug resistance. Importantly, our results indicate that epistasis seems to be limited to the classical scheme where primary DRMs confer resistance and associated mutations modulate the strength of the resistance and/or compensate for the fitness cost induced by DRMs.
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Iwuji CC, Siedner MJ. Circulating resistance to first-line HIV drug regimens. Lancet HIV 2019; 7:e77-e78. [PMID: 31818715 DOI: 10.1016/s2352-3018(19)30374-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/10/2019] [Accepted: 10/23/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Collins C Iwuji
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Boston, MA, USA.
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Tarasova O, Poroikov V. HIV Resistance Prediction to Reverse Transcriptase Inhibitors: Focus on Open Data. Molecules 2018; 23:E956. [PMID: 29671808 PMCID: PMC6017644 DOI: 10.3390/molecules23040956] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/16/2022] Open
Abstract
Research and development of new antiretroviral agents are in great demand due to issues with safety and efficacy of the antiretroviral drugs. HIV reverse transcriptase (RT) is an important target for HIV treatment. RT inhibitors targeting early stages of the virus-host interaction are of great interest for researchers. There are a lot of clinical and biochemical data on relationships between the occurring of the single point mutations and their combinations in the pol gene of HIV and resistance of the particular variants of HIV to nucleoside and non-nucleoside reverse transcriptase inhibitors. The experimental data stored in the databases of HIV sequences can be used for development of methods that are able to predict HIV resistance based on amino acid or nucleotide sequences. The data on HIV sequences resistance can be further used for (1) development of new antiretroviral agents with high potential for HIV inhibition and elimination and (2) optimization of antiretroviral therapy. In our communication, we focus on the data on the RT sequences and HIV resistance, which are available on the Internet. The experimental methods, which are applied to produce the data on HIV-1 resistance, the known data on their concordance, are also discussed.
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Affiliation(s)
- Olga Tarasova
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya st., Moscow 119121, Russia.
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya st., Moscow 119121, Russia.
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Thirunavukarasu D, Udhaya V, Iqbal HS, Umaarasu T. Patterns of HIV-1 Drug-Resistance Mutations among Patients Failing First-Line Antiretroviral Treatment in South India. J Int Assoc Provid AIDS Care 2015; 15:261-8. [PMID: 26385878 DOI: 10.1177/2325957415603508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Although highly active antiretroviral therapy has improved the quality of life among HIV-infected people in India, the emergence of drug resistance along with the limited access and affordability to routine monitoring continues to be a challenge worldwide. METHODS The frequency and patterns of HIV-1 drug-resistance mutations among the first-line failing HIV-infected patients attending a hospital in Salem, Tamil Nadu, India, were genotypically analyzed using the online Stanford HIV Database. RESULTS Of the study patients followed up for 6 months, 23 patients failed first-line therapy and the mutation of I135R/T/V/X, L178 I/M, M184V/I, D67N, K70R, and K103N was most common. Phylogenetic analysis revealed that most of these patients belonged to HIV subtype C. CONCLUSION The study documents the frequency of nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor mutations that are prevalent in the first-line failing HIV-infected patients of South Indian region and adds up to the data for developing future algorithms to study the drug-resistance mutations of HIV subtype C. Thus, the results of the study call for the need for rational approach for selecting and for frequent viral monitoring to be performed to detect failure, followed by genotyping.
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Affiliation(s)
| | - Visvanathan Udhaya
- Department of Microbiology, Faculty of Medicine, Annamalai University, Chidambaram, Tamil Nadu, India
| | | | - Thirunavukarasu Umaarasu
- Department of Microbiology, Vivekanandha Dental College for Women, Tiruchengode, Tamil Nadu, India
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Impact of Y181C and/or H221Y mutation patterns of HIV-1 reverse transcriptase on phenotypic resistance to available non-nucleoside and nucleoside inhibitors in China. BMC Infect Dis 2014; 14:237. [PMID: 24885612 PMCID: PMC4024112 DOI: 10.1186/1471-2334-14-237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 04/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to investigate the role of K101Q, Y181C and H221Y emerging in HIV-1 reverse transcriptase with different mutations patterns in phenotypic susceptibility to currently available NNRTIs (nevirapine NVP, efavirenz EFV) and NRTIs (zidovudine AZT, lamivudine 3TC, stavudine d4T) in China. METHODS Phenotype testing of currently available NNRTIs (NVP, EFV) and NRTIs (AZT, 3TC, d4T) was performed on TZM-b1 cells using recombined virus strains. P ≤ 0.05 was defined significant considering the change of 50% inhibitory drug concentration (IC50) compared with the reference, while P ≤ 0.01 was considered to be statistically significant considering multiple comparisons. RESULTS Triple-mutation K101Q/Y181C/H221Y and double-mutation K101Q/Y181C resulted in significant increase in NVP resistance (1253.9-fold and 986.4-fold), while only K101Q/Y181C/H221Y brought a 5.00-fold significant increase in EFV resistance. Remarkably, K101Q/H221Y was hypersusceptible to EFV (FC = 0.04), but was significantly resistant to the three NRTIs. Then, the interaction analysis suggested the interaction was not significant to NVP (F = 0.77, P = 0.4061) but significant to EFV and other three NRTIs. CONCLUSION Copresence of mutations reported to be associated with NNRTIs confers significant increase to NVP resistance. Interestingly, some may increase the susceptibility to EFV. Certainly, the double mutation (K101Q/H221Y) also changes the susceptibility of viruses to NRTIs. Interaction between two different sites makes resistance more complex.
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Melikian GL, Rhee SY, Varghese V, Porter D, White K, Taylor J, Towner W, Troia P, Burack J, Dejesus E, Robbins GK, Razzeca K, Kagan R, Liu TF, Fessel WJ, Israelski D, Shafer RW. Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. J Antimicrob Chemother 2013; 69:12-20. [PMID: 23934770 DOI: 10.1093/jac/dkt316] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The introduction of two new non-nucleoside reverse transcriptase inhibitors (NNRTIs) in the past 5 years and the identification of novel NNRTI-associated mutations have made it necessary to reassess the extent of phenotypic NNRTI cross-resistance. METHODS We analysed a dataset containing 1975, 1967, 519 and 187 genotype-phenotype correlations for nevirapine, efavirenz, etravirine and rilpivirine, respectively. We used linear regression to estimate the effects of RT mutations on susceptibility to each of these NNRTIs. RESULTS Sixteen mutations at 10 positions were significantly associated with the greatest contribution to reduced phenotypic susceptibility (≥10-fold) to one or more NNRTIs, including: 14 mutations at six positions for nevirapine (K101P, K103N/S, V106A/M, Y181C/I/V, Y188C/L and G190A/E/Q/S); 10 mutations at six positions for efavirenz (L100I, K101P, K103N, V106M, Y188C/L and G190A/E/Q/S); 5 mutations at four positions for etravirine (K101P, Y181I/V, G190E and F227C); and 6 mutations at five positions for rilpivirine (L100I, K101P, Y181I/V, G190E and F227C). G190E, a mutation that causes high-level nevirapine and efavirenz resistance, also markedly reduced susceptibility to etravirine and rilpivirine. K101H, E138G, V179F and M230L mutations, associated with reduced susceptibility to etravirine and rilpivirine, were also associated with reduced susceptibility to nevirapine and/or efavirenz. CONCLUSIONS The identification of novel cross-resistance patterns among approved NNRTIs illustrates the need for a systematic approach for testing novel NNRTIs against clinical virus isolates with major NNRTI-resistance mutations and for testing older NNRTIs against virus isolates with mutations identified during the evaluation of a novel NNRTI.
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Wright DW, Sadiq SK, De Fabritiis G, Coveney PV. Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase. J Am Chem Soc 2012; 134:12885-8. [PMID: 22827470 DOI: 10.1021/ja301565k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the principal targets in human immunodeficiency virus type 1 (HIV-1) therapy is the reverse transcriptase (RT) enzyme. Non-nucleoside RT inhibitors (NNRTIs) are a class of highly specific drugs which bind to a pocket approximately 10 Å from the polymerase active site, inhibiting the enzyme allosterically. It is widely believed that NNRTIs function as "molecular wedges", disrupting the region between thumb and palm subdomains of the p66 subunit and locking the thumb in a wide-open conformation. Crystal structure data suggest that the binding of NNRTIs forces RT into a wide-open conformation in which the separation between the thumb and fingers subdomains is much higher than in the apo structure. Using ensemble molecular dynamics simulations (aggregate sampling ∼600 ns), we have captured RT bound to the NNRTI efavirenz in a closed conformation similar to that of the apo enzyme, suggesting the constraint of thumb motion is not as complete as previously believed. Rather, our investigation confirms that a conformational distribution across open and closed states must exist in the drug-bound enzyme and that allosteric modulation is effected via the alteration of the kinetic landscape of conformational transitions upon drug-binding. A more detailed understanding of the mechanism of NNRTI inhibition and the effect of binding upon domain motion could aid the design of more effective inhibitors and help identify novel allosteric sites.
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Affiliation(s)
- David W Wright
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, U.K
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Hachiya A, Marchand B, Kirby KA, Michailidis E, Tu X, Palczewski K, Ong YT, Li Z, Griffin DT, Schuckmann MM, Tanuma J, Oka S, Singh K, Kodama EN, Sarafianos SG. HIV-1 reverse transcriptase (RT) polymorphism 172K suppresses the effect of clinically relevant drug resistance mutations to both nucleoside and non-nucleoside RT inhibitors. J Biol Chem 2012; 287:29988-99. [PMID: 22761416 DOI: 10.1074/jbc.m112.351551] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polymorphisms have poorly understood effects on drug susceptibility and may affect the outcome of HIV treatment. We have discovered that an HIV-1 reverse transcriptase (RT) polymorphism (RT(172K)) is present in clinical samples and in widely used laboratory strains (BH10), and it profoundly affects HIV-1 susceptibility to both nucleoside (NRTIs) and non-nucleoside RT inhibitors (NNRTIs) when combined with certain mutations. Polymorphism 172K significantly suppressed zidovudine resistance caused by excision (e.g. thymidine-associated mutations) and not by discrimination mechanism mutations (e.g. Q151M complex). Moreover, it attenuated resistance to nevirapine or efavirenz imparted by NNRTI mutations. Although 172K favored RT-DNA binding at an excisable pre-translocation conformation, it decreased excision by thymidine-associated mutation-containing RT. 172K affected DNA handling and decreased RT processivity without significantly affecting the k(cat)/K(m) values for dNTP. Surface plasmon resonance experiments revealed that RT(172K) decreased DNA binding by increasing the dissociation rate. Hence, the increased zidovudine susceptibility of RT(172K) results from its increased dissociation from the chain-terminated DNA and reduced primer unblocking. We solved a high resolution (2.15 Å) crystal structure of RT mutated at 172 and compared crystal structures of RT(172R) and RT(172K) bound to NNRTIs or DNA/dNTP. Our structural analyses highlight differences in the interactions between α-helix E (where 172 resides) and the active site β9-strand that involve the YMDD loop and the NNRTI binding pocket. Such changes may increase dissociation of DNA, thus suppressing excision-based NRTI resistance and also offset the effect of NNRTI resistance mutations thereby restoring NNRTI binding.
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Affiliation(s)
- Atsuko Hachiya
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
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Van der Borght K, Van Craenenbroeck E, Lecocq P, Van Houtte M, Van Kerckhove B, Bacheler L, Verbeke G, van Vlijmen H. Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations. BMC Bioinformatics 2011; 12:386. [PMID: 21966893 PMCID: PMC3223907 DOI: 10.1186/1471-2105-12-386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 10/03/2011] [Indexed: 12/03/2022] Open
Abstract
Background Linear regression models are used to quantitatively predict drug resistance, the phenotype, from the HIV-1 viral genotype. As new antiretroviral drugs become available, new resistance pathways emerge and the number of resistance associated mutations continues to increase. To accurately identify which drug options are left, the main goal of the modeling has been to maximize predictivity and not interpretability. However, we originally selected linear regression as the preferred method for its transparency as opposed to other techniques such as neural networks. Here, we apply a method to lower the complexity of these phenotype prediction models using a 3-fold cross-validated selection of mutations. Results Compared to standard stepwise regression we were able to reduce the number of mutations in the reverse transcriptase (RT) inhibitor models as well as the number of interaction terms accounting for synergistic and antagonistic effects. This reduction in complexity was most significant for the non-nucleoside reverse transcriptase inhibitor (NNRTI) models, while maintaining prediction accuracy and retaining virtually all known resistance associated mutations as first order terms in the models. Furthermore, for etravirine (ETR) a better performance was seen on two years of unseen data. By analyzing the phenotype prediction models we identified a list of forty novel NNRTI mutations, putatively associated with resistance. The resistance association of novel variants at known NNRTI resistance positions: 100, 101, 181, 190, 221 and of mutations at positions not previously linked with NNRTI resistance: 102, 139, 219, 241, 376 and 382 was confirmed by phenotyping site-directed mutants. Conclusions We successfully identified and validated novel NNRTI resistance associated mutations by developing parsimonious resistance prediction models in which repeated cross-validation within the stepwise regression was applied. Our model selection technique is computationally feasible for large data sets and provides an approach to the continued identification of resistance-causing mutations.
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Abstract
Combination antiretroviral therapy for HIV-1 infection has resulted in profound reductions in viremia and is associated with marked improvements in morbidity and mortality. Therapy is not curative, however, and prolonged therapy is complicated by drug toxicity and the emergence of drug resistance. Management of clinical drug resistance requires in depth evaluation, and includes extensive history, physical examination and laboratory studies. Appropriate use of resistance testing provides valuable information useful in constructing regimens for treatment-experienced individuals with viremia during therapy. This review outlines the emergence of drug resistance in vivo, and describes clinical evaluation and therapeutic options of the individual with rebound viremia during therapy.
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The rare HIV-1 gp41 mutations 43T and 50V elevate enfuvirtide resistance levels of common enfuvirtide resistance mutations that did not impact susceptibility to sifuvirtide. Antiviral Res 2010; 86:253-60. [DOI: 10.1016/j.antiviral.2010.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2010] [Revised: 02/26/2010] [Accepted: 03/02/2010] [Indexed: 12/22/2022]
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Wang J, Liang H, Bacheler L, Wu H, Deriziotis K, Demeter LM, Dykes C. The non-nucleoside reverse transcriptase inhibitor efavirenz stimulates replication of human immunodeficiency virus type 1 harboring certain non-nucleoside resistance mutations. Virology 2010; 402:228-37. [PMID: 20399480 DOI: 10.1016/j.virol.2010.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 02/20/2010] [Accepted: 03/11/2010] [Indexed: 11/19/2022]
Abstract
We measured the effects of non-nucleoside reverse transcriptase (RT) inhibitor-resistant mutations K101E+G190S, on replication fitness and EFV-resistance of HIV(NL4-3). K101E+G190S reduced fitness in the absence of EFV and increased EFV resistance, compared to either single mutant. Unexpectedly, K101E+G190S also replicated more efficiently in the presence of EFV than in its absence. Addition of the nucleoside resistance mutations L74V or M41L+T215Y to K101E+G190S improved fitness and abolished EFV-dependent stimulation of replication. D10, a clinical RT backbone containing M41L+T215Y and K101E+G190S, also demonstrated EFV-dependent stimulation that was dependent on the presence of K101E. These studies demonstrate that non-nucleoside reverse transcriptase inhibitors can stimulate replication of NNRTI-resistant HIV-1 and that nucleoside-resistant mutants can abolish this stimulation. The ability of EFV to stimulate NNRTI-resistant mutants may contribute to the selection of HIV-1 mutants in vivo. These studies have important implications regarding the treatment of HIV-1 with combination nucleoside and non-nucleoside therapies.
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Affiliation(s)
- J Wang
- Department of Medicine, 601 Elmwood Ave., University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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Kanizsai S, Ghidán A, Ujhelyi E, Bánhegyi D, Nagy K. Monitoring of drug resistance in therapy-naïve HIV infected patients and detection of African HIV subtypes in Hungary. Acta Microbiol Immunol Hung 2010; 57:55-68. [PMID: 20350879 DOI: 10.1556/amicr.57.2010.1.5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations in the HIV-1 pol gene associated with resistance to antiretroviral drugs in therapy-naïve Hungarian individuals transmitted as primary infection by their foreign sexual partners originated from African, Asian and other European countries had been analyzed. Drug resistance genotyping of HIV RT and PR genes were performed where mutations of 72 codons - among them 64 specific resistance codons representing 6 nucleoside reverse transcriptase inhibitor (NRTIs), 2 non-nucleoside reverse transcriptase inhibitor (NNRTIs) and 6 proteinase inhibitor (PRIs) drugs - had been analyzed by Truegene HIV-1 Genotyping kit and OpenGene Sequencing System. Viral variants harboring resistance mutations in the po l gene were detected in 14% of the subjects. The highest rate of resistance to a single class of inhibitors was detected towards PR inhibitors (12%), followed by NRTI (8%) and NNRTI (5%). On the contrary, 25% of viruses transmitted by homosexual activity contained mutations led to resistance to NNRT. Viruses from 11 percent of cases were resistant to 2 classes of inhibitors, and 7 percent to three classes of inhibitors. Based upon sequence data non-B subtypes and CRFs were detected in more than 71% of cases. HIV-1 C (10.7%), HIV-F1 (7.2%) and HIV-1 G (3.6%) were detected as the more frequent subtypes. Among the HIV-1 recombinant viruses CRF02_AG variants were found more frequently (28.5%) followed by CRF06_cpx (17.8%) indicating penetration of non-B subtypes and recombinant African variants into Hungary, which raises serious clinical and public health consequences.
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Affiliation(s)
- Szilvia Kanizsai
- Semmelweis University Institute of Medical Microbiology Budapest Hungary
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Non-nucleoside reverse transcriptase inhibitors (NNRTIs), their discovery, development, and use in the treatment of HIV-1 infection: A review of the last 20 years (1989–2009). Antiviral Res 2010; 85:75-90. [DOI: 10.1016/j.antiviral.2009.09.008] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 09/08/2009] [Accepted: 09/12/2009] [Indexed: 11/20/2022]
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Antiviral activity of MK-4965, a novel nonnucleoside reverse transcriptase inhibitor. Antimicrob Agents Chemother 2009; 53:2424-31. [PMID: 19289522 DOI: 10.1128/aac.01559-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are the mainstays of therapy for the treatment of human immunodeficiency virus type 1 (HIV-1) infections. However, the effectiveness of NNRTIs can be hampered by the development of resistance mutations which confer cross-resistance to drugs in the same class. Extensive efforts have been made to identify new NNRTIs that can suppress the replication of the prevalent NNRTI-resistant viruses. MK-4965 is a novel NNRTI that possesses both diaryl ether and indazole moieties. The compound displays potency at subnanomolar concentrations against wild-type (WT), K103N, and Y181C reverse transcriptase (RT) in biochemical assays. MK-4965 is also highly potent against the WT virus and two most prevalent NNRTI-resistant viruses (viruses that harbor the K103N or the Y181C mutation), against which it had 95% effective concentrations (EC(95)s) of <30 nM in the presence of 10% fetal bovine serum. The antiviral EC(95) of MK-4965 was reduced approximately four- to sixfold when it was tested in 50% human serum. Moreover, MK-4965 was evaluated with a panel of 15 viruses with NNRTI resistance-associated mutations and showed a superior mutant profile to that of efavirenz but not to that of etravirine. MK-4965 was similarly effective against various HIV-1 subtypes and viruses containing nucleoside reverse transcriptase inhibitor or protease inhibitor resistance-conferring mutations. A two-drug combination study showed that the antiviral activity of MK-4965 was nonantagonistic with each of the 18 FDA-licensed drugs tested vice versa in the present study. Taken together, these in vitro data show that MK-4965 possesses the desired properties for further development as a new NNRTI for the treatment of HIV-1 infection.
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Hachiya A, Shimane K, Sarafianos SG, Kodama EN, Sakagami Y, Negishi F, Koizumi H, Gatanaga H, Matsuoka M, Takiguchi M, Oka S. Clinical relevance of substitutions in the connection subdomain and RNase H domain of HIV-1 reverse transcriptase from a cohort of antiretroviral treatment-naïve patients. Antiviral Res 2009; 82:115-21. [PMID: 19428602 DOI: 10.1016/j.antiviral.2009.02.189] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/27/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022]
Abstract
Some mutations in the connection subdomain of the polymerase domain and in the RNase H domain of HIV-1 reverse transcriptase (RT) have been shown to contribute to resistance to RT inhibitors. However, the clinical relevance of such mutations is not well understood. To address this point we determined the prevalence of such mutations in a cohort of antiretroviral treatment-naïve patients (n=123) and assessed whether these substitutions are associated with drug resistance in vitro and in vivo. We report here significant differences in the prevalence of substitutions among subtype B, and non-subtype B HIV isolates. Specifically, the E312Q, G333E, G335D, V365I, A371V and A376S substitutions were present in 2-6% of subtype B, whereas the G335D and A371V substitutions were commonly observed in 69% and 75% of non-B HIV-1 isolates. We observed a significant decline in the viral loads of patients that were infected with HIV-1 carrying these substitutions and were subsequently treated with triple drug regimens, even in the case where zidovudine (AZT) was included in such regimens. We show here that, generally, such single substitutions at the connection subdomain or RNase H domain have no influence on drug susceptibility in vitro by themselves. Instead, they generally enhance AZT resistance in the presence of excision-enhancing mutations (EEMs, also known as thymidine analogue-associated mutations, TAMs). However, N348I, A376S and Q509L did confer varying amounts of nevirapine resistance by themselves, even in the absence of EEMs. Our studies indicate that several connection subdomain and RNase H domain substitutions typically act as pre-therapy polymorphisms.
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Affiliation(s)
- Atsuko Hachiya
- AIDS Clinical Center, International Medical Center of Japan, Japan
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Abstract
BACKGROUND Efavirenz is a potent, safe and tolerable non-nucleoside reverse transcriptase inhibitor (NNRTI) recommended as initial therapy. Recently, several new antiretroviral drugs, including second generation NNRTIs, protease-inhibitors, an integrase-inhibitor and a CCR5 inhibitor, have become or will be shortly available. OBJECTIVE This article will review relevant efficacy and safety data of efavirenz compared to these novel agents or certain common alternate drugs currently used as initial therapy in treatment-naive patients. METHODS Published articles and conference presentations pertaining to efavirenz and/or the newer antiretroviral agents were evaluated. RESULTS/CONCLUSIONS Efavirenz will continue to be preferred initial therapy for now. If longer-term studies of integrase inhibitors and second-generation NNRTIs confirm initial findings, they will eventually supplant efavirenz as preferred first-line agents.
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Affiliation(s)
- Brookie M Best
- University of California, Division of Pharmacology and Drug Discovery, San Diego, La Jolla, CA 92093-0719, USA.
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Juhász E, Ghidán A, Kemény B, Nagy K. Emergence of antiretroviral drug resistance in therapy-naive HIV infected patients in Hungary. Acta Microbiol Immunol Hung 2008; 55:383-94. [PMID: 19130746 DOI: 10.1556/amicr.55.2008.4.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations in the HIV-1 genes associated with resistance to antiretroviral drugs were detected also in primary HIV infected individuals who did not receive antiretroviral treatment. Drug resistance genotyping of HIV pol gene was done by in situ DNA hybridization using a Line Probe Assay and by direct sequencing. Viral variants harbouring resistance mutations such as: M41, T69R, K70R, M184V, T215Y in the pol gene were detected in 14% of the subjects. HIV mutants resistant to NRT inhibitors were found in 10 and 20% of patients infected before and after the year 2000, respectively. Multiple drug resistant viruses (2-3 drug classes) were present in 3.5% of the mainly recently infected patients. In protease gene only minor resistant mutations were found such as L101 and A71V. These findings indicate the evolution of drug resistance showing a correlation with the time of introduction of combination therapy in our country, where more than 70% of HIV infections were by homo/bisexual transmission. This confirms the transmission of drug-resistant HIV shown by genotype testing during primary infection in therapy-naive patients and initiates serious clinical and public health consequences.
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Affiliation(s)
- Emese Juhász
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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19
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McGovern BH, Abu Dayyeh BK, Chung RT. Avoiding therapeutic pitfalls: the rational use of specifically targeted agents against hepatitis C infection. Hepatology 2008; 48:1700-12. [PMID: 18972443 DOI: 10.1002/hep.22563] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of specifically targeted antiviral agents against hepatitis C is a major therapeutic advance that promises to markedly improve treatment response rates in patients with chronic infection. However, rapid emergence of drug resistance has already been described, the consequences of which are not yet understood. Although there are important differences between hepatitis C (HCV) and human immunodeficiency virus (HIV) infection, the judicious use of candidate agents against HCV should be guided by principles that have been established in the HIV therapeutic arena. In this review, we attempt to draw useful parallels between the development of antiretroviral therapy for HIV and preliminary data on antiviral agents for hepatitis C virus infection. Applying concepts learned in HIV therapeutics will hopefully lead to a prudent and cautious path in HCV treatment paradigms, particularly with respect to drug resistance.
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Affiliation(s)
- Barbara H McGovern
- Division of Infectious Diseases, Lemuel Shattuck Hospital, Jamaica Plain, MA, USA.
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20
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Anderson JA, Jiang H, Ding X, Petch L, Journigan T, Fiscus SA, Haubrich R, Katzenstein D, Swanstrom R, Gulick RM. Genotypic susceptibility scores and HIV type 1 RNA responses in treatment-experienced subjects with HIV type 1 infection. AIDS Res Hum Retroviruses 2008; 24:685-94. [PMID: 18462083 DOI: 10.1089/aid.2007.0127] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study compared the role of genotypic susceptibility scores (GSS) as a predictor of virologic response in a group (n = 234) of HIV-infected, protease inhibitor (PI)-experienced subjects. Two scoring methods [discrete genotypic susceptibility score (dGSS) and continuous genotypic susceptibility score (cGSS)] were developed. Each drug in the subject's regimen was given a binary susceptibility score using Stanford inferred drug resistance scores to calculate the dGSS. In contrast to the dGSS, the cGSS model was designed to reflect partial susceptibility to a drug. Both GSS were independent predictors of week 16 virologic response. We also compared the GSS to a phenotypic susceptibility score (PSS) model on a subset of subjects that had both GSS and PSS performed, and found that both models were predictive of virologic response. Genotypic analyses at enrollment showed that subjects who were virologic nonresponders at week 16 revealed enrichment of several mutated codons associated with nucleoside reverse transcriptase inhibitors (NRTI) (codons 67, 69, 70, 118, 215, and 219) or PI resistance (codons 10, 24, 71, 73, and 88) compared to subjects who were virologic responders. Regression analyses revealed that protease mutations at codons 24 and 90 were most predictive of poor virologic response, whereas mutations at 82 were associated with enhanced virologic response. Certain NNRTI-associated mutations, such as K103N, were rapidly selected in the absence of NRTIs. These data indicate that GSS may be a useful tool in selecting drug regimens in HIV-1-infected subjects to maximize virologic response and improve treatment outcomes.
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Affiliation(s)
- Jeffrey A. Anderson
- UNC Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27759
| | - Hongyu Jiang
- Harvard School of Public Health, Boston, Massachusetts 02115
| | - Xiao Ding
- Harvard School of Public Health, Boston, Massachusetts 02115
| | - Leslie Petch
- UNC Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27759
| | - Terri Journigan
- UNC Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27759
| | - Susan A. Fiscus
- UNC Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27759
| | | | | | - Ronald Swanstrom
- UNC Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27759
| | - Roy M. Gulick
- Weill Medical College of Cornell University, New York, New York 10021
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21
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Sluis-Cremer N, Tachedjian G. Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors. Virus Res 2008; 134:147-56. [PMID: 18372072 DOI: 10.1016/j.virusres.2008.01.002] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 01/04/2008] [Accepted: 01/04/2008] [Indexed: 11/18/2022]
Abstract
The non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are a therapeutic class of compounds that are routinely used, in combination with other antiretroviral drugs, to treat HIV-1 infection. NNRTIs primarily block HIV-1 replication by preventing RT from completing reverse transcription of the viral single-stranded RNA genome into DNA. However, some NNRTIs, such as efavirenz, have been shown to inhibit the late stages of HIV-1 replication by interfering with HIV-1 Gag-Pol polyprotein processing, while others, such as the pyrimidinediones, have been shown to inhibit both HIV-1 RT-mediated reverse transcription and HIV-1/HIV-2 viral entry. Accordingly, in this review we describe the multiple mechanisms by which NNRTIs inhibit HIV-1 reverse transcription (and in some cases HIV-2 reverse transcription) and other key steps involved in HIV-1/HIV-2 replication.
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Affiliation(s)
- Nicolas Sluis-Cremer
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, S817 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA.
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22
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Demeter LM, DeGruttola V, Lustgarten S, Bettendorf D, Fischl M, Eshleman S, Spreen W, Nguyen BY, Koval CE, Eron JJ, Hammer S, Squires K. Association of efavirenz hypersusceptibility with virologic response in ACTG 368, a randomized trial of abacavir (ABC) in combination with efavirenz (EFV) and indinavir (IDV) in HIV-infected subjects with prior nucleoside analog experience. HIV CLINICAL TRIALS 2008; 9:11-25. [PMID: 18215978 DOI: 10.1310/hct0901-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PURPOSE To evaluate the association of efavirenz hypersusceptibility (EFV-HS) with clinical outcome in a double-blind, placebo-controlled, randomized trial of EFV plus indinavir (EFV+IDV) vs. EFV+IDV plus abacavir (ABC) in 283 nucleoside-experienced HIV-infected patients. METHOD AND RESULTS Rates of virologic failure were similar in the 2 arms at week 16 (p = .509). Treatment discontinuations were more common in the ABC arm (p = .001). Using logistic regression, there was no association between virologic failure and either baseline ABC resistance or regimen sensitivity score. Using 3 different genotypic scoring systems, EFV-HS was significantly associated with reduced virologic failure at week 16, independent of treatment assignment. In some patients on the nucleoside-sparing arm, the nucleoside-resistance mutation L74V was selected for in combination with the uncommonly occurring EFV-resistance mutations K103N+L100I; L74V was not detected as a minority variant, using clonal sequence analysis, when the nucleoside-sparing regimen was initiated. CONCLUSION Premature treatment discontinuations in the ABC arm and the presence of EFV-HS HIV variants in this patient population likely made it difficult to detect a benefit of adding ABC to EFV+IDV. In addition, L74V, when combined with K103N+L100I, may confer a selective advantage to the virus that is independent of its effects on nucleoside resistance.
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Affiliation(s)
- Lisa M Demeter
- University of Rochester, Rochester, New York 14642, USA.
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23
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Martinez-Cajas JL, Wainberg MA. Antiretroviral therapy : optimal sequencing of therapy to avoid resistance. Drugs 2008; 68:43-72. [PMID: 18081372 DOI: 10.2165/00003495-200868010-00004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the second decade of highly active antiretroviral therapy, drug regimens offer more potent, less toxic and more durable choices. However, strategies addressing convenient sequential use of active antiretroviral combinations are rarely presented in the literature. Studies have seldom directly addressed this issue, despite it being a matter of daily use in clinical practice. This is, in part, because of the complexity of HIV-1 resistance information as well as the complexity of designing these types of studies. Nevertheless, several principles can effectively assist the planning of antiretroviral drug sequencing. The introduction of tenofovir disoproxil fumarate, abacavir and emtricitabine into current nucleoside backbone options, with each of them selecting for an individual pattern of resistance mutations, now permits sequencing in the context of previously popular thymidine analogues (zidovudine and stavudine). Similarly, newer ritonavir-boosted protease inhibitors could potentially be sequenced in a manner that uses the least cross-resistance prone protease inhibitor at the start of therapy, while leaving the most cross-resistance prone drugs for later, as long as there is rationale to employ such a compound because of its utility against commonly observed drug-resistant forms of HIV-1.
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Affiliation(s)
- Jorge L Martinez-Cajas
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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24
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Menéndez-Arias L. Mechanisms of resistance to nucleoside analogue inhibitors of HIV-1 reverse transcriptase. Virus Res 2008; 134:124-46. [PMID: 18272247 DOI: 10.1016/j.virusres.2007.12.015] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 10/22/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) inhibitors can be classified into nucleoside and nonnucleoside RT inhibitors. Nucleoside RT inhibitors are converted to active triphosphate analogues and incorporated into the DNA in RT-catalyzed reactions. They act as chain terminators blocking DNA synthesis, since they lack the 3'-OH group required for the phosphodiester bond formation. Unfortunately, available therapies do not completely suppress viral replication, and the emergence of drug-resistant HIV variants is facilitated by the high adaptation capacity of the virus. Mutations in the RT-coding region selected during treatment with nucleoside analogues confer resistance through different mechanisms: (i) altering discrimination between nucleoside RT inhibitors and natural substrates (dNTPs) (e.g. Q151M, M184V, etc.), or (ii) increasing the RT's phosphorolytic activity (e.g. M41L, T215Y and other thymidine analogue resistance mutations), which in the presence of a pyrophosphate donor (usually ATP) allow the removal of chain-terminating inhibitors from the 3' end of the primer. Both mechanisms are implicated in multi-drug resistance. The excision reaction can be modulated by mutations conferring resistance to nucleoside or nonnucleoside RT inhibitors, and by amino acid substitutions that interfere with the proper binding of the template-primer, including mutations that affect RNase H activity. New developments in the field should contribute towards improving the efficacy of current therapies.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
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25
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Wainberg MA, Martinez-Cajas JL, Brenner BG. Strategies for the optimal sequencing of antiretroviral drugs toward overcoming and preventing drug resistance. ACTA ACUST UNITED AC 2007. [DOI: 10.2217/17469600.1.3.291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Drug regimens now offer more potent, less toxic and more durable choices in the treatment of HIV disease than ever before. This has led to a need to consider the convenient, sequential use of active antiretroviral combinations. Ritonavir-boosted protease inhibitors (PIs) can now be potentially sequenced in a manner that uses the least cross-resistance-prone PI at the start of therapy while leaving the most cross-resistance-prone drug for later, if the latter retains activity against commonly observed drug-resistant forms. Similarly, such new drugs as tenofovir, abacavir and emtricitabine, which make up current nucleoside backbone options, can be potentially sequenced, since each of them selects for an individual pattern of resistance mutations that are generally distinct from those selected by previously popular thymidine analogs such as zidovudine and stavudine.
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Affiliation(s)
- Mark A Wainberg
- McGill University AIDS Center, Jewish General Hospital, 3755 Cote-Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
| | - Jorge L Martinez-Cajas
- McGill University AIDS Center, Jewish General Hospital, 3755 Cote-Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
| | - Bluma G Brenner
- McGill University AIDS Center, Jewish General Hospital, 3755 Cote-Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
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26
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Ceccherini-Silberstein F, Svicher V, Sing T, Artese A, Santoro MM, Forbici F, Bertoli A, Alcaro S, Palamara G, d'Arminio Monforte A, Balzarini J, Antinori A, Lengauer T, Perno CF. Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitors. J Virol 2007; 81:11507-19. [PMID: 17686836 PMCID: PMC2045529 DOI: 10.1128/jvi.00303-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y, K223E/Q, and L228H/R) in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase which are involved in the regulation of resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs). These mutations are strongly associated with NNRTI failure and strongly correlate with the classical NNRTI resistance mutations in a data set of 1,904 HIV-1 B-subtype pol sequences from 758 drug-naïve patients, 592 nucleoside reverse transcriptase inhibitor (NRTI)-treated but NNRTI-naïve patients, and 554 patients treated with both NRTIs and NNRTIs. In particular, L74V and H221Y, positively correlated with Y181C, were associated with an increase in Y181C-mediated resistance to nevirapine, while I135M/T mutations, positively correlated with K103N, were associated with an increase in K103N-mediated resistance to efavirenz. In addition, the presence of the I135T polymorphism in NNRTI-naïve patients significantly correlated with the appearance of K103N in cases of NNRTI failure, suggesting that I135T may represent a crucial determinant of NNRTI resistance evolution. Molecular dynamics simulations show that I135T can contribute to the stabilization of the K103N-induced closure of the NNRTI binding pocket by reducing the distance and increasing the number of hydrogen bonds between 103N and 188Y. H221Y also showed negative correlations with type 2 thymidine analogue mutations (TAM2s); its copresence with the TAM2s was associated with a higher level of zidovudine susceptibility. Our study reinforces the complexity of NNRTI resistance and the significant interplay between NRTI- and NNRTI-selected mutations. Mutations beyond those currently known to confer resistance should be considered for a better prediction of clinical response to reverse transcriptase inhibitors and for the development of more efficient new-generation NNRTIs.
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27
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Vermeiren H, Van Craenenbroeck E, Alen P, Bacheler L, Picchio G, Lecocq P. Prediction of HIV-1 drug susceptibility phenotype from the viral genotype using linear regression modeling. J Virol Methods 2007; 145:47-55. [PMID: 17574687 DOI: 10.1016/j.jviromet.2007.05.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 05/02/2007] [Accepted: 05/03/2007] [Indexed: 11/30/2022]
Abstract
Linear regression modeling on a database of HIV-1 genotypes and phenotypes was applied to predict the HIV-1 resistance phenotype from the viral genotype. In this approach, the phenotypic measurement is estimated as the weighted sum of the effects of individual mutations. Higher order interaction terms (mutation pairs) were included to account for synergistic and antagonistic effects between mutations. The most significant mutations and interactions identified by the linear regression models for 17 approved antiretroviral drugs are reported. Although linear regression modeling is a statistical data-driven technique focused on obtaining the best possible prediction, many of these mutations are also known resistance-associated mutations, indicating that the statistical models largely reflect well characterized biological phenomena. The performance of the models in predicting in vitro susceptibility phenotype and virologic response in treated patients is described. In addition to a high concordance with in vitro measured fold change, which was the primary aim of model design, the models per drug show good predictivity of therapy response for regimens including that drug, even in the absence of other clinically relevant factors such as background regimen.
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Affiliation(s)
- H Vermeiren
- Virco BVBA, Gen De Wittelaan L 11B 4, 2800 Mechelen, Belgium
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28
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Abstract
Efavirenz is a non-nucleoside reverse transcriptase inhibitor that in most treatment guidelines is recommended to be taken combined with two nucleoside analogue reverse transcriptase inhibitors, as a preferred first-line regimen for the treatment of HIV-1 infection. The antiretroviral efficacy of efavirenz-based combination regimens is good, as has been demonstrated in many clinical trials. Efavirenz has a long plasma half-life, which allows for once-daily dosing, but, as a consequence of this and the low genetic barrier, it is also prone to select for viral resistance when adherence to therapy is suboptimal. The most frequently encountered side effects are neuropsychiatric symptoms. These side effects are usually transient, but have been shown to persist for up to 2 years after initiation of therapy in some patients. This review outlines important and recent pharmacological and clinical data, which explain why efavirenz became a component of preferred treatment regimens today.
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29
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Nebbia G, Sabin CA, Dunn DT, Geretti AM. Emergence of the H208Y mutation in the reverse transcriptase (RT) of HIV-1 in association with nucleoside RT inhibitor therapy. J Antimicrob Chemother 2007; 59:1013-6. [PMID: 17356061 DOI: 10.1093/jac/dkm067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The aim of the study was to determine whether mutations at RT codon 208 are associated with nucleoside RT inhibitor (NRTI) exposure, NRTI resistance patterns and HIV-1 subtype. METHODS Six thousand three hundred and fifty two genotypic resistance tests linked to a clinical database were analysed. RESULTS The prevalence of mutations at codon 208 was 6/2347 (0.3%) in treatment-naive and 165/4005 (4.1%) in treatment-experienced persons. H208Y was the most common mutation in both groups (0.2% and 3.8%, respectively) and occurred in 4.5% of treatment-experienced persons with Subtype B, 1.7% of those with Subtype C and 0.7% of those with other non-B subtypes (P=0.001). The association with subtypes was independent of treatment experience. H208Y showed a strong association with NRTI experience, which persisted after adjusting for subtype [odds ratio (OR) 19.34; 95% confidence interval (CI) 7.87-47.54; P=0.0001]. The prevalence of H208Y was highest in genotypes harbouring M184V and the thymidine analogue mutations (TAMs) M41L, D67N, L210W and T215Y. The median number of TAMs was 4 and 0 in genotypes with and without H208Y, respectively (P=0.0001). The prevalence of H208Y declined over time, being highest in 1998 (9.9%) and lowest in 2003 (0.9%) (P=0.0001). CONCLUSIONS There is a strong association between H208Y and NRTI experience, particularly in persons with Subtype B harbouring multiple NRTI resistance mutations. These findings indicate an accessory role for H208Y in NRTI resistance.
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Affiliation(s)
- G Nebbia
- Department of Virology, Royal Free and University College Medical School, Rowland Hill Street, NW3 2PF London, UK
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30
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Interactions between non-nucleoside reverse transcriptase inhibitor and nucleoside reverse transcriptase inhibitor mutations: phenotypes and mechanisms. Curr Opin HIV AIDS 2007; 2:88-93. [PMID: 19372872 DOI: 10.1097/coh.0b013e328055505c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Antiretroviral regimens that combine nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors have consistently been the most effective regimens for the initial treatment of HIV-1 infection. Such combinations have been manufactured in several fixed-dose combinations and are the most commonly used treatments worldwide. The success of these regimens may partly be a result of the synergistic manner in which the two classes of compounds inhibit the HIV-1 reverse transcriptase enzyme. RECENT FINDINGS Multiple synergistic effects have been described in the mechanisms and pathways of drug resistance. This review outlines what is currently known about the interactions between nucleoside reverse transcriptase inhibitor and non-nucleoside reverse transcriptase inhibitor resistance. SUMMARY These synergistic interactions are likely to be the driving force behind the potency and durability of the nucleoside reverse transcriptase inhibitor/non-nucleoside reverse transcriptase inhibitor combinations used in clinical practice.
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Abstract
PURPOSE OF REVIEW HIV knowledge is based on subtype B, common in resource-rich settings, whereas globally non-B subtypes predominate. Inter-subtype pol diversity encompasses multiple genotypic differences among HIV variants, the consequence of which is unknown. This review summarizes publications from the past year relevant to the impact of HIV diversity on drug resistance evolution and its potential clinical implications. RECENT FINDINGS The benefit of antiretroviral therapy in non-B infected patients is ongoing, though subtype heterogeneity in rates of disease progression is observed. Pol inter-subtype diversity is high, and known subtype B drug resistance mutations occur in non-B subtypes. New mutations and subtype-specific mutation rates are identified, however, unexplained drug susceptibilities are seen, and additional insight is offered on structural pathogenic mechanisms of resistance in non-B subtypes. These differences may affect genotypic interpretation and our ability to apply drug resistance to patient care. SUMMARY Current evidence suggests good treatment response and comparable drug resistance evolution in HIV-1 B and non-B infected patients, with increasingly emerging differences. Impact of inter-subtype diversity on drug susceptibility and on evolution of drug resistance should continue to be a major research focus to increase our understanding and ability to improve global patient care.
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Affiliation(s)
- Rami Kantor
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island 02906, USA.
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