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Mbhele N, Gordon M. Structural effects of HIV-1 subtype C integrase mutations on the activity of integrase strand transfer inhibitors in South African patients. J Biomol Struct Dyn 2022; 40:12546-12556. [PMID: 34488561 DOI: 10.1080/07391102.2021.1972840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
HIV-1 integrase enzyme is responsible for the integration of viral DNA into the host genomic DNA. Integrase strand transfer inhibitors (INSTIs) are highly potent antiretroviral agents that inhibit this process, and are internationally approved for the treatment of both naïve and treated HIV-1 patients. However, their long-term efficacy is threatened by development of drug resistance strains resulting in resistance mutations. This work aimed to examine the effect of INSTI resistance-associated mutations (RAMs) and polymorphisms on the structure of HIV-1 subtype C (HIV-1C) integrase. Genetic analysis was performed on seven HIV-1C infected individuals with virologic failure after at least 6 months of INSTI-based antiretroviral therapy, presenting at the King Edward VIII hospital in Durban, South Africa. These were compared with sequences from 41 INSTI-naïve isolates. Integrase structures of selected isolates were modeled on the SWISS model online server. Molecular docking and dynamics simulations were also conducted using AutoDock-Vina and AMBER 18 force fields, respectively. Only one INSTI-treated isolate (14.28%) harboured major mutations (G140A + Q148R) as well as the E157Q minor mutation. Interestingly, S119T and V151I were only found in patients failing raltegravir (an INSTI drug). Molecular modeling and docking showed that RAMs and polymorphisms associated with INSTI-based therapy affect protein stability and this is supported by their weakened hydrogen-bond interactions compared to the wild-type. To the best of our knowledge, this is the first study to identify a double mutant in the 140's loop region from South African HIV-1C isolates and study its effects on Raltegravir, Elvitegravir, and Dolutegravir binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nokuzola Mbhele
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Michelle Gordon
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
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Nilavar NM, Paranjape AM, Raghavan SC. Biochemical activity of RAGs is impeded by Dolutegravir, an HIV integrase inhibitor. Cell Death Discov 2020; 6:50. [PMID: 32566255 PMCID: PMC7293277 DOI: 10.1038/s41420-020-0281-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/26/2020] [Accepted: 04/22/2020] [Indexed: 02/03/2023] Open
Abstract
HIV is a retrovirus that infects CD4+ T lymphocytes in human beings and causes immunodeficiency. In the recent years, various therapies have been developed against HIV, including targeting the HIV specific protein, integrase, responsible for integration of HIV cDNA into host DNA. Although, integrase is specific to HIV, it has functional and structural similarity with RAG1, one of the partner proteins associated with V(D)J recombination, a process by which immune diversity is generated in humans. Currently, there are three HIV integrase inhibitors: Elvitegravir, Dolutegravir, and Raltegravir, in the market which have been approved by the FDA (USA). All three drugs are used in anti-retroviral therapy (ART). Previously, we showed that amongst the HIV inhibitors, Elvitegravir could significantly decrease B cell maturation in vivo and inhibit the physiological activities of RAGs in vitro, unlike Raltegravir. In the present study, we address the effect of second-generation integrase inhibitor, Dolutegravir on RAG activities. Binding and nicking studies showed that, Dolutegravir could decrease the binding efficiency of RAG1 domains and cleavage on DNA substrates, but not as considerably as Elvitegravir. Thus, we show that although the integrase inhibitors such as Elvitegravir show an affinity towards RAG1, the newer molecules may have lesser side-effects.
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Affiliation(s)
- Namrata M. Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Amita M. Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2017; 7:2165. [PMID: 28123383 PMCID: PMC5225119 DOI: 10.3389/fmicb.2016.02165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2016. [PMID: 28123383 DOI: 10.3389/fmicb.2016.02165/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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Billamboz M, Suchaud V, Bailly F, Lion C, Demeulemeester J, Calmels C, Andréola ML, Christ F, Debyser Z, Cotelle P. 4-Substituted 2-Hydroxyisoquinoline-1,3(2H,4H)-diones as a Novel Class of HIV-1 Integrase Inhibitors. ACS Med Chem Lett 2013; 4:606-11. [PMID: 24900718 DOI: 10.1021/ml400009t] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/17/2013] [Indexed: 12/25/2022] Open
Abstract
A series of 2-hydroxy-1,3-dioxoisoquinoline-4-carboxamides featuring an N-hydroxyimide chelating functionality was evaluated for their inhibitory properties against human immunodeficiency virus type 1 integrase (HIV-1 IN). Several derivatives displayed low nanomolar IC50 values comparable to that of the clinically used raltegravir. A marked effect of one compound on both primary IN-catalyzed reactions, strand transfer (ST), and 3' processing (3'-P), emphasizes a novel IN inhibition mechanism establishing it as a potential new generation IN inhibitor. Substitution of the 2-hydroxyisoquinoline-1,3-dione scaffold at position 4 by carboxamido chains was beneficial for antiviral activity since reproducible low micromolar anti-HIV activities were obtained for the first time within this scaffold.
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Affiliation(s)
- Muriel Billamboz
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Virginie Suchaud
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Fabrice Bailly
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Cedric Lion
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Jonas Demeulemeester
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Christina Calmels
- UMR 5234 CNRS, Université Bordeaux Segalen, 146 Rue Léo Saignat, F-33076 Bordeaux, France
| | - Marie-Line Andréola
- UMR 5234 CNRS, Université Bordeaux Segalen, 146 Rue Léo Saignat, F-33076 Bordeaux, France
| | - Frauke Christ
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Philippe Cotelle
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
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de Melo EB, Ferreira MMC. Four-dimensional structure-activity relationship model to predict HIV-1 integrase strand transfer inhibition using LQTA-QSAR methodology. J Chem Inf Model 2012; 52:1722-32. [PMID: 22657398 DOI: 10.1021/ci300039a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite highly active antiretroviral therapy (HAART) implementation, there is a continuous need to search for new anti-HIV agents. HIV-1 integrase (HIV-1 IN) is a recently validated biological target for AIDS therapy. In this work, a four-dimensional quantitative structure-activity relationship (4D-QSAR) study using the new methodology named LQTA-QSAR approach with a training set of 85 HIV-1 IN strand transfer inhibitors (INSTI), containing the β-diketo acid (DKA) substructure, was carried out. The GROMACS molecular dynamic package was used to obtain a conformational ensemble profile (CEP) and LQTA-QSAR was employed to calculate Coulomb and Lennard-Jones potentials and to generate the field descriptors. The partial least-squares (PLS) regression model using 14 field descriptors and 8 latent variables (LV) yielded satisfactory statistics (R2= 0.897, SEC = 0.270, and F = 72.827), good performance in internal (QLOO2 = 0.842 and SEV = 0.314) and external prediction (Rpred2 = 0.839, SEP = 0.384, AREpred = 4.942%, k = 0.981, k′ = 1.016, and |R02 – R0′2 = 0.0257). The QSAR model was shown to be robust (leave-N-out cross validation; average QLNO2 = 0.834) and was not built by chance (y-randomization test; R2 intercept = 0.109; Q2 intercept = -0.398). Fair chemical interpretation of the model could be traced, including descriptors related to interaction with the metallic cofactors and the hydrophobic loop. The model obtained has a good potential for aid in the design of new INSTI, and it is a successful example of application of LQTA-QSAR as an useful tool to be used in computer-aided drug design (CADD).
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Affiliation(s)
- Eduardo B de Melo
- Theoretical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Parana State University-Unioeste, 2069 Universitaria St, Cascavel, PR 85819-110, Brazil
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Jiang F, Chen W, Yi K, Wu Z, Si Y, Han W, Zhao Y. The evaluation of catechins that contain a galloyl moiety as potential HIV-1 integrase inhibitors. Clin Immunol 2010; 137:347-56. [DOI: 10.1016/j.clim.2010.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 07/12/2010] [Accepted: 08/11/2010] [Indexed: 10/19/2022]
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