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Potential Associations of Mutations within the HIV-1 Env and Gag Genes Conferring Protease Inhibitor (PI) Drug Resistance. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12040071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
An increasing number of patients in Africa are experiencing virological failure on a second-line antiretroviral protease inhibitor (PI)-containing regimen, even without resistance-associated mutations in the protease region, suggesting a potential role of other genes in PI resistance. Here, we investigated the prevalence of mutations associated with Lopinavir/Ritonavir (LPV/r) failure in the Envelope gene and the possible coevolution with mutations within the Gag-protease (gag-PR) region. Env and Gag-PR sequences generated from 24 HIV-1 subtype C infected patients failing an LPV/r inclusive treatment regimen and 344 subtype C drug-naïve isolates downloaded from the Los Alamos Database were analyzed. Fisher’s exact test was used to determine the differences in mutation frequency. Bayesian network probability was applied to determine the relationship between mutations occurring within the env and gag-PR regions and LPV/r treatment. Thirty-five mutations in the env region had significantly higher frequencies in LPV/r-treated patients. A combination of Env and Gag-PR mutations was associated with a potential pathway to LPV/r resistance. While Env mutations were not directly associated with LPV/r resistance, they may exert pressure through the Gag and minor PR mutation pathways. Further investigations using site-directed mutagenesis are needed to determine the impact of Env mutations alone and in combination with Gag-PR mutations on viral fitness and LPV/r efficacy.
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Sherry D, Worth R, Sayed Y. Elasticity-Associated Functionality and Inhibition of the HIV Protease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:79-108. [PMID: 34351572 DOI: 10.1007/5584_2021_655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV protease plays a critical role in the life cycle of the virus through the generation of mature and infectious virions. Detailed knowledge of the structure of the enzyme and its substrate has led to the development of protease inhibitors. However, the development of resistance to all currently available protease inhibitors has contributed greatly to the decreased success of antiretroviral therapy. When therapy failure occurs, multiple mutations are found within the protease sequence starting with primary mutations, which directly impact inhibitor binding, which can also negatively impact viral fitness and replicative capacity by decreasing the binding affinity of the natural substrates to the protease. As such, secondary mutations which are located outside of the active site region accumulate to compensate for the recurrently deleterious effects of primary mutations. However, the resistance mechanism of these secondary mutations is not well understood, but what is known is that these secondary mutations contribute to resistance in one of two ways, either through increasing the energetic penalty associated with bringing the protease into the closed conformation, or, through decreasing the stability of the protein/drug complex in a manner that increases the dissociation rate of the drug, leading to diminished inhibition. As a result, the elasticity of the enzyme-substrate complex has been implicated in the successful recognition and catalysis of the substrates which may be inferred to suggest that the elasticity of the enzyme/drug complex plays a role in resistance. A realistic representation of the dynamic nature of the protease may provide a more powerful tool in structure-based drug design algorithms.
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Affiliation(s)
- Dean Sherry
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roland Worth
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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Marin RC, Behl T, Negrut N, Bungau S. Management of Antiretroviral Therapy with Boosted Protease Inhibitors-Darunavir/Ritonavir or Darunavir/Cobicistat. Biomedicines 2021; 9:biomedicines9030313. [PMID: 33803812 PMCID: PMC8003312 DOI: 10.3390/biomedicines9030313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
A major challenge in the management of antiretroviral therapy (ART) is to improve the patient's adherence, reducing the burden caused by the high number of drugs that compose the treatment regimens for human immunodeficiency virus positive (HIV+) patients. Selection of the most appropriate treatment regimen is responsible for therapeutic success and aims to reduce viremia, increase the immune system response capacity, and reduce the incidence rate and intensity of adverse reactions. In general, protease inhibitor (PI) is one of the pillars of regimens, and darunavir (DRV), in particular, is frequently recommended, along with low doses of enzyme inhibitors as cobicistat (COBI) or ritonavir (RTV), by the international guidelines. The potential of clinically significant drug interactions in patients taking COBI or RTV is high due to the potent inhibitory effect on cytochrome CYP 450, which attracts significant changes in the pharmacokinetics of PIs. Regardless of the patient or type of virus, the combined regimens of DRV/COBI or DRV/RTV are available to clinicians, proving their effectiveness, with a major impact on HIV mortality/morbidity. This study presents current information on the pharmacokinetics, pharmacology, drug interactions, and adverse reactions of DRV; it not only compares the bioavailability, pharmacokinetic parameters, immunological and virological responses, but also the efficacy, advantages, and therapeutic disadvantages of DRV/COBI or DRV/RTV combinations.
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Affiliation(s)
- Ruxandra-Cristina Marin
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India;
| | - Nicoleta Negrut
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
- Correspondence: ; Tel.: +40-726-776-588
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Soremekun OS, Omolabi KF, Adewumi AT, Soliman MES. Exploring the effect of ritonavir and TMC-310911 on SARS-CoV-2 and SARS-CoV main proteases: potential from a molecular perspective. Future Sci OA 2020; 7:FSO640. [PMID: 33432269 PMCID: PMC7651988 DOI: 10.2144/fsoa-2020-0079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/28/2020] [Indexed: 12/02/2022] Open
Abstract
AIM As coronavirus (CoV) disease 2019-associated pneumonia spreads globally, there has been an urgent need to combat the spread and develop vaccines. MATERIALS & METHODS We used an integrated computational algorithm to explore the binding mechanism of TMC-310911/ritonavir (RVT) with SARS-CoV-2 and SARS-CoV main proteases. RESULTS RVT and TMC-310911 had favorable interactions with the proteases, and these high interactions are facilitated by some significant residues such as Asn133, Gly195 and Gln192. Our study further implicated two important rings in the structure of RVT as a possible chemical culprit in its therapeutic activity. CONCLUSION Although there are conflicting clinical results on the therapeutic potency of RVT in the treatment of coronavirus disease 2019, our findings provided molecular insight into the binding mechanism of TMC-310911 and RVT with SARS-CoV-2 and SARS-CoV main proteases.
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Affiliation(s)
- Opeyemi S Soremekun
- Molecular Bio-computation & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, Kwa-Zulu Natal, South Africa
| | - Kehinde F Omolabi
- Molecular Bio-computation & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, Kwa-Zulu Natal, South Africa
| | - Adeniyi T Adewumi
- Molecular Bio-computation & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, Kwa-Zulu Natal, South Africa
| | - Mahmoud ES Soliman
- Molecular Bio-computation & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, Kwa-Zulu Natal, South Africa
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Olotu FA, Agoni C, Soremekun O, Soliman MES. The recent application of 3D-QSAR and docking studies to novel HIV-protease inhibitor drug discovery. Expert Opin Drug Discov 2020; 15:1095-1110. [PMID: 32692273 DOI: 10.1080/17460441.2020.1773428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Despite the availability of FDA approved inhibitors of HIV protease, numerous efforts are still ongoing to achieve 'near-perfect' drugs devoid of characteristic adverse side effects, toxicities, and mutational resistance. While experimental methods have been plagued with huge consumption of time and resources, there has been an incessant shift towards the use of computational simulations in HIV protease inhibitor drug discovery. AREAS COVERED Herein, the authors review the numerous applications of 3D-QSAR modeling methods over recent years relative to the design of new HIV protease inhibitors from a series of experimentally derived compounds. Also, the augmentative contributions of molecular docking are discussed. EXPERT OPINION Efforts to optimize 3D QSAR and molecular docking for HIV-1 drug discovery are ongoing, which could further incorporate inhibitor motions at the active site using molecular dynamics parameters. Also, highly predictive machine learning algorithms such as random forest, K-means, decision trees, linear regression, hierarchical clustering, and Bayesian classifiers could be employed.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Opeyemi Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
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Nascimento ALCS, Fernandes RP, Quijia C, Araujo VHS, Pereira J, Garcia JS, Trevisan MG, Chorilli M. Pharmacokinetic Parameters of HIV-1 Protease Inhibitors. ChemMedChem 2020; 15:1018-1029. [PMID: 32390304 DOI: 10.1002/cmdc.202000101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/29/2020] [Indexed: 12/15/2022]
Abstract
Since the beginning of the HIV epidemic, research has been carried out to control the virus. Understanding the mechanisms of replication has given access to the various classes of drugs that over time have transformed AIDS into a manageable chronic disease. The class of protease inhibitors (PIs) gained notice in anti-retroviral therapy, once it was found that peptidomimetic molecules act by blocking the active catalytic center of the aspartic protease, which is directly related to HIV maturation. However, mutations in enzymatic internal residues are the biggest issue for these drugs, because a small change in biochemical interaction can generate resistance. Low plasma concentrations of PIs favor viral natural selection; high concentrations can inhibit even partially resistant enzymes. Food-drug/drug-drug interactions can decrease the bioavailability of PIs and are related to many side effects. Therefore, this review summarizes the pharmacokinetic properties of current PIs, the changes when pharmacological boosters are used and also lists the major mutations to help understanding of how long the continuous treatment can ensure a low viral load in patients.
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Affiliation(s)
- André L C S Nascimento
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Richard P Fernandes
- Araraquara Institute of Chemistry, São Paulo State University (UNESP), CP 355, 14801-970, Araraquara, SP, Brazil
| | - Christian Quijia
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
| | - Victor H S Araujo
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
| | - Juliana Pereira
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Jerusa S Garcia
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Marcello G Trevisan
- LACFar, Institute of Chemistry, Federal University of Alfenas, 37130-000, Alfenas, MG, Brazil
| | - Marlus Chorilli
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800-903, Araraquara, São Paulo, Brazil
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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8
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Baxter JD, Dunn D, White E, Sharma S, Geretti AM, Kozal MJ, Johnson MA, Jacoby S, Llibre JM, Lundgren J. Global HIV-1 transmitted drug resistance in the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial. HIV Med 2015; 16 Suppl 1:77-87. [PMID: 25711326 DOI: 10.1111/hiv.12236] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2014] [Indexed: 01/21/2023]
Abstract
OBJECTIVES HIV-1 transmitted drug resistance (TDR) in treatment-naïve individuals is a well-described phenomenon. Baseline genotypic resistance testing is considered standard of care in most developed areas of the world. The aim of this analysis was to characterize HIV-1 TDR and the use of resistance testing in START trial participants. METHODS In the Strategic Timing of AntiRetroviral Treatment (START) trial, baseline genotypic resistance testing results were collected at study entry and analysed centrally to determine the prevalence of TDR in the study population. Resistance was based on a modified 2009 World Health Organization definition to reflect newer resistance mutations. RESULTS Baseline resistance testing was available in 1946 study participants. Higher rates of testing occurred in Europe (86.7%), the USA (81.3%) and Australia (89.9%) as compared with Asia (22.2%), South America (1.8%) and Africa (0.1%). The overall prevalence of TDR was 10.1%, more commonly to nonnucleoside reverse transcriptase inhibitors (4.5%) and nucleoside reverse transcriptase inhibitors (4%) compared with protease inhibitors (2.8%). The most frequent TDR mutations observed were M41L, D67N/G/E, T215F/Y/I/S/C/D/E/V/N, 219Q/E/N/R, K103N/S, and G190A/S/E in reverse transcriptase, and M46I/L and L90M in protease. By country, the prevalence of TDR was highest in Australia (17.5%), France (16.7%), the USA (12.6%) and Spain (12.6%). No participant characteristics were identified as predictors of the presence of TDR. CONCLUSIONS START participants enrolled in resource-rich areas of the world were more likely to have baseline resistance testing. In Europe, the USA and Australia, TDR prevalence rates varied by country.
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Affiliation(s)
- J D Baxter
- Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA
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Non-infectious in-cell HIV-1 protease assay utilizing translocalization of a fluorescent reporter protein and apoptosis induction. Arch Pharm Res 2015; 38:2201-7. [DOI: 10.1007/s12272-015-0651-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
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10
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Tseng A, Seet J, Phillips EJ. The evolution of three decades of antiretroviral therapy: challenges, triumphs and the promise of the future. Br J Clin Pharmacol 2015; 79:182-94. [PMID: 24730660 PMCID: PMC4309625 DOI: 10.1111/bcp.12403] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/02/2014] [Indexed: 12/22/2022] Open
Abstract
The evolution of human immunodeficiency virus (HIV) treatment has improved our understanding and management of complex pharmacological issues that have driven improved outcomes and quality of life of the HIV-infected patient. These issues include adherence, long- and short-term toxicities, pharmacoenhancement, pharmacogenomics, therapeutic drug monitoring, differential penetration of drugs into sanctuary sites, such as the central nervous system, genital tract and small bowel, and drug-drug and drug-food interactions related to cytochrome P450 drug-metabolizing enzymes, uridine diphosphate glucuronyltransferases and drug transporters, to name a few. There is future promise, as an increased understanding of the immunopathogenesis of HIV and global public health initiatives are driving novel treatment approaches with goals to prevent, control and, ultimately, eradicate HIV.
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Affiliation(s)
- Alice Tseng
- University Health NetworkToronto, Ontario, Canada
- Leslie Dan Faculty of Pharmacy, University of TorontoToronto, Ontario, Canada
| | - Jason Seet
- Sir Charles Gairdner HospitalNedlands, WA, Australia
| | - Elizabeth J Phillips
- Vanderbilt University School of MedicineNashville, TN, USA
- Institute for Immunology & Infectious Diseases, Murdoch UniversityMurdoch, WA, Australia
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Abstract
The latest HIV-1 protease inhibitor (PI) darunavir (Prezista™) has a high genetic barrier to resistance development and is active against wild-type HIV and HIV strains no longer susceptible to some older PIs. Ritonavir-boosted darunavir, as a component of antiretroviral therapy (ART), is indicated for the treatment of HIV-1 infection in adult and paediatric patients (aged ≥3 years), with or without treatment experience (details vary depending on region of approval). Several open-label or partially-blinded trials have evaluated the efficacy of ritonavir-boosted darunavir ART regimens for up to 192 weeks in these settings. In treatment-naïve adults, once-daily boosted darunavir was no less effective in establishing virological suppression than once- or twice-daily boosted lopinavir, yet was more effective at maintaining suppression long term. Moreover, treatment-experienced adults with no darunavir resistance-associated mutations (RAMs) had no less effective viral load suppression with once-daily than with twice-daily boosted darunavir. In treatment-experienced adults, including some with multiple major PI RAMs, twice-daily boosted darunavir was more effective than twice-daily boosted lopinavir or boosted control PIs in reducing viral load, and provided virological benefit as part of a salvage regimen in those with few remaining treatment options. Boosted darunavir also reduced viral load when administered once-daily in treatment-naïve adolescents or twice-daily in treatment-experienced children and adolescents. Boosted darunavir is generally well tolerated, with gastrointestinal disturbances and lipid abnormalities among the most common tolerability issues. It has a lipid profile more favourable than that of boosted lopinavir in terms of total cholesterol and triglyceride changes and, when administered once daily, its lipid effects are generally similar to those of boosted atazanavir. Thus, boosted darunavir is a useful option for the ART regimens of adult and paediatric patients with HIV-1 infection.
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Joshi A, Véron JB, Unge J, Rosenquist Å, Wallberg H, Samuelsson B, Hallberg A, Larhed M. Design and Synthesis of P1–P3 Macrocyclic Tertiary-Alcohol-Comprising HIV-1 Protease Inhibitors. J Med Chem 2013; 56:8999-9007. [DOI: 10.1021/jm400811d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Advait Joshi
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Jean-Baptiste Véron
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Johan Unge
- MAX IV-laboratory, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden
| | | | - Hans Wallberg
- Medivir AB, P.O. Box 1086, SE-141
22 Huddinge, Sweden
| | | | - Anders Hallberg
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Mats Larhed
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
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Alteri C, Artese A, Beheydt G, Santoro MM, Costa G, Parrotta L, Bertoli A, Gori C, Orchi N, Girardi E, Antinori A, Alcaro S, d'Arminio Monforte A, Theys K, Vandamme AM, Ceccherini-Silberstein F, Svicher V, Perno CF. Structural modifications induced by specific HIV-1 protease-compensatory mutations have an impact on the virological response to a first-line lopinavir/ritonavir-containing regimen. J Antimicrob Chemother 2013; 68:2205-9. [DOI: 10.1093/jac/dkt173] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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McKinnon JE, Delgado R, Pulido F, Shao W, Arribas JR, Mellors JW. Single genome sequencing of HIV-1 gag and protease resistance mutations at virologic failure during the OK04 trial of simplified versus standard maintenance therapy. Antivir Ther 2012; 16:725-32. [PMID: 21817194 DOI: 10.3851/imp1812] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Ritonavir-boosted lopinavir (LPV/RTV) alone has been evaluated as simplified maintenance therapy for HIV-1 infection, but there are concerns about greater potential for emergence of protease inhibitor (PI) resistance. The OK04 trial evaluated maintenance therapy with LPV/RTV alone versus standard therapy (ST) with two NRTIs plus LPV/RTV in 205 patients, of whom 15 had virological rebound by week 48 (11 versus 4 patients, respectively). We developed a single genome sequencing (SGS) assay of HIV-1 gag and protease to assess the emergence of low frequency drug-resistant variants during virological rebound. METHODS Plasma samples from 15 subjects at virological rebound were analysed by SGS of HIV-1 gag and protease genes. A total of 45 SGS sequences were planned per sample, providing 90% power to detect variants comprising >5% of the virus population. RESULTS Overall, 521 single sequences obtained from 13 patients (range 4-48 sequences/patient) revealed similar frequencies of major protease resistance mutations in samples from the LPV/RTV alone (3/11) and ST (3/4) arms (P=0.10), with a median number of minor protease resistance mutations of 3.0 versus 3.5, respectively (P=0.23). Median number of gag PI resistance mutations were similar between the LPV/RTV alone and ST arms at cleavage sites (3.0 versus 2.5; P=0.83), non-cleavage sites (21 versus 16.5; P=0.71) and the transframe protein-p6 pol region cleavage sites (4.0 versus 3.0; P=0.6). CONCLUSIONS Although more subjects with simplified maintenance therapy with LPV/RTV alone had virological rebound compared to the ST arm, this was not associated with more frequent emergence of variants encoding PI resistance mutations in gag or protease detected by SGS.
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Affiliation(s)
- John E McKinnon
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA.
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Doherty KM, Nakka P, King BM, Rhee SY, Holmes SP, Shafer RW, Radhakrishnan ML. A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics 2011; 12:477. [PMID: 22172090 PMCID: PMC3305535 DOI: 10.1186/1471-2105-12-477] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 12/15/2011] [Indexed: 12/19/2022] Open
Abstract
Background Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to arise within the population. Understanding the phenotypic and genotypic patterns responsible for multi-PI resistance is necessary for developing PIs that are active against clinically-relevant PI-resistant HIV-1 variants. Results In this work, we use globally optimal integer programming-based clustering techniques to elucidate multi-PI phenotypic resistance patterns using a data set of 398 HIV-1 protease sequences that have each been phenotyped for susceptibility toward the nine clinically-approved HIV-1 PIs. We validate the information content of the clusters by evaluating their ability to predict the level of decreased susceptibility to each of the available PIs using a cross validation procedure. We demonstrate the finding that as a result of phenotypic cross resistance, the considered clinical HIV-1 protease isolates are confined to ~6% or less of the clinically-relevant phenotypic space. Clustering and feature selection methods are used to find representative sequences and mutations for major resistance phenotypes to elucidate their genotypic signatures. We show that phenotypic similarity does not imply genotypic similarity, that different PI-resistance mutation patterns can give rise to HIV-1 isolates with similar phenotypic profiles. Conclusion Rather than characterizing HIV-1 susceptibility toward each PI individually, our study offers a unique perspective on the phenomenon of PI class resistance by uncovering major multidrug-resistant phenotypic patterns and their often diverse genotypic determinants, providing a methodology that can be applied to understand clinically-relevant phenotypic patterns to aid in the design of novel inhibitors that target other rapidly evolving molecular targets as well.
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Flor-Parra F, Pérez-Pulido AJ, Pachón J, Pérez-Romero P. The HIV type 1 protease L10I minor mutation decreases replication capacity and confers resistance to protease inhibitors. AIDS Res Hum Retroviruses 2011; 27:65-70. [PMID: 21142921 DOI: 10.1089/aid.2010.0072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effect of minor mutations in PR on treatment outcome has not been well established. We characterized the HIV protease minor mutations, L10I, compared to the minor mutation, L63P, and the major mutation D30N and their impact on viral fitness and resistance to protease inhibitors. Mutations were introduced individually and in combination by site-directed mutagenesis into the provirus pNL4.3ren and constructs used for replication capacity (RC) and resistance assays. A structure prediction of the protease carrying the L10I mutation was determined. The prevalence of the minor mutation L10I had a pattern similar to that found for major mutations D30N, with a low prevalence (4.9%) in naive patients and significantly higher prevalence in treated patients. Furthermore, viruses carrying the major mutation D30N or the minor mutation L10I showed a significant decrease in RC (p-value <0.05), whereas viruses carrying the minor mutation L63P had RC similar to wild-type virus. In addition, the L10I mutation conferred resistance to saquinavir, which was supported by the higher prevalence in the cohort of the L10I mutation among patients with SQV resistance. The molecular modeling suggests that L10I may affect the conformation of Leu-23, a critical residue in the substrate binding site. In conclusion, the L10I mutation impairs RC and confers resistance to SQV, similarly to other major mutations, which may be related with changes in the conformation in the protease binding site. The presence of this mutation in the genotype of HIV from patients should be taken into consideration when designing new optimize treatments.
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Affiliation(s)
- Fernando Flor-Parra
- Institute of Biomedicine of Sevilla, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Spain
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Enhanced Susceptibility of Human Immunodeficiency Virus Type 1 to Tipranavir in Treatment-Experienced Patients. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2010. [DOI: 10.1097/ipc.0b013e3181f0c036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Discovery of a highly synergistic anthelmintic combination that shows mutual hypersusceptibility. Proc Natl Acad Sci U S A 2010; 107:5955-60. [PMID: 20231450 DOI: 10.1073/pnas.0912327107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The soil-transmitted helminths or nematodes (hookworms, whipworms, and Ascaris) are roundworms that infect more than 1 billion of the poorest peoples and are leading causes of morbidity worldwide. Few anthelmintics are available for treatment, and only one is commonly used in mass drug administrations. New anthelmintics are urgently needed, and crystal (Cry) proteins made by Bacillus thuringiensis are promising new candidates. Combination drug therapies are considered the ideal treatment for infectious diseases. Surprisingly, little work has been done to define the characteristics of anthelmintic combinations. Here, by means of quantitative assays with wild-type and mutants of the roundworm Caenorhabditis elegans, we establish a paradigm for studying anthelmintic combinations using Cry proteins and nicotinic acetylcholine receptor (nAChR) agonists, e.g., tribendimidine and levamisole. We find that nAChR agonists and Cry proteins, like Cry5B and Cry21A, mutually display what is known in the HIV field as hypersusceptibility--when the nematodes become resistant to either class, they become hypersensitive to the other class. Furthermore, we find that when Cry5B and nAChR agonists are combined, their activities are strongly synergistic, producing combination index values as good or better than seen with antitumor, anti-HIV, and insecticide combinations. Our study provides a powerful means by which anthelmintic combination therapies can be examined and demonstrate that the combination of nAChR agonists and Cry proteins has excellent properties and is predicted to give improved cure rates while being recalcitrant to the development of parasite resistance.
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Abstract
PURPOSE OF REVIEW To provide a regulatory perspective on developing new HIV protease inhibitors. The present review highlights the risks and benefits of certain design aspects for studies in treatment-naïve and treatment-experienced patients, including timing of studies, study design options, choice of control arms, and duration of treatment. RECENT FINDINGS The present review highlights published studies to illustrate the need for new therapies and highlights potential historical data to help design future HIV clinical trials better. SUMMARY New antiretroviral agents for patients with multidrug resistance, including safer, more convenient therapies without significant drug-drug interactions, are still needed for all patients. The goals of therapy have evolved and the expectation for treatment regimens is that the majority of patients, including treatment-experienced patients, will achieve undetectable HIV RNA. New study designs, particularly for treatment-experienced patients, are needed to help identify potential risks and benefits of new treatments.
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