1
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Mușat MG, Nițulescu GM, Surleac M, Tsatsakis A, Spandidos DA, Margină D. HIV‑1 integrase inhibitors targeting various DDE transposases: Retroviral integration versus RAG‑mediated recombination (Review). Mol Med Rep 2019; 20:4749-4762. [PMID: 31702817 PMCID: PMC6854553 DOI: 10.3892/mmr.2019.10777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Transposases are ubiquitous mobile genetic elements responsible for genome development, driving rearrangements, such as insertions, deletions and translocations. Across species evolution, some transposases are tamed by their host and are made part of complex cellular systems. The proliferation of retroviruses is also dependent on transposase related enzymes termed integrases. Recombination‑activating gene protein (RAG)1 and metnase are just two examples of transposase domestication and together with retroviral integrases (INs), they belong to the DDE polynucleotidyl transferases superfamily. They share mechanistic and structural features linked to the RNase H‑like fold, harboring a DDE(D) metal dependent catalytic motif. Recent antiretroviral compounds target the catalytic domain of integrase, but they also have the potential of inhibiting other related enzymes. In this review, we report the activity of different classes of integrase inhibitors on various DDE transposases. Computational simulations are useful to predict the extent of off‑target activity and have been employed to study the interactions between RAG1 recombinase and compounds from three different pharmacologic classes. We demonstrate that strand‑transfer inhibitors display a higher affinity towards the RAG1 RNase H domain, as suggested by experimental data compared to allosteric inhibitors. While interference with RAG1 and 2 recombination is associated with a negative impact on immune function, the inhibition of metnase or HTLV‑1 integrase opens the way for the development of novel therapies for refractory cancers.
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Affiliation(s)
- Mihaela Georgiana Mușat
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - George Mihai Nițulescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Marius Surleac
- National Institute for Infectious Diseases ‘Matei Bals’, 021105 Bucharest, Romania
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Denisa Margină
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
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2
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Cancian M, Loreto ELS. A Mos1 transposase in vivo assay to screen new HIV-1 integrase inhibitors. Genetica 2018; 146:243-247. [PMID: 29352755 DOI: 10.1007/s10709-018-0007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 01/11/2018] [Indexed: 11/27/2022]
Abstract
The integrase and transposase enzymes of retrovirus and transposons, respectively, share the catalytic DDE domain. In vitro assays showed that inhibitors of HIV-1 integrase generally inhibit the mariner Mos1 transposase. Using a Drosophila strain in which the mobilisation of the mariner element can be quantified by mosaic eyes, we showed that flies maintained in medium containing 210 µM to 4 mM of raltegravir, or 1 or 2 mM of dolutegravir, which are HIV-1 integrase inhibitor used in AIDS treatment, have 23-33% less somatic mobilisation in mosaic eyes when treated with raltegravir and 28-32% when treated with dolutegravir. The gene expression of the mariner transposase gene, estimated by qPCR, is similar among treated and control flies. The results suggest that in vivo assays using Drosophila can be used as a primary screening of inhibitory drugs for transposase and retroviral integrase. The advantages of this assay are that it is easy, quick, cheap and is an in vivo test, meaning that the tested substance has to have been taken in by cells and has arrived at the target site, which is not the case when in vitro assays are applied.
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Affiliation(s)
- Mariana Cancian
- Curso Ciências Biológicas, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Elgion L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria, RS, 97105-900, Brazil.
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3
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Abstract
![]()
Bacteria
possess a remarkable ability to rapidly adapt and evolve
in response to antibiotics. Acquired antibiotic resistance can arise
by multiple mechanisms but commonly involves altering the target site
of the drug, enzymatically inactivating the drug, or preventing the
drug from accessing its target. These mechanisms involve new genetic
changes in the pathogen leading to heritable resistance. This recognition
underscores the importance of understanding how such
genetic changes can arise. Here, we review recent advances in our
understanding of the processes that contribute to the evolution of
antibiotic resistance, with a particular focus on hypermutation mediated
by the SOS pathway and horizontal gene transfer. We explore the molecular
mechanisms involved in acquired resistance and discuss their viability
as potential targets. We propose that additional studies into these
adaptive mechanisms not only can provide insights into evolution but
also can offer a strategy for potentiating our current antibiotic
arsenal.
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4
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Wolkowicz U, Morris ER, Robson M, Trubitsyna M, Richardson JM. Structural basis of Mos1 transposase inhibition by the anti-retroviral drug Raltegravir. ACS Chem Biol 2014; 9:743-51. [PMID: 24397848 PMCID: PMC3977574 DOI: 10.1021/cb400791u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/07/2014] [Indexed: 11/28/2022]
Abstract
DNA transposases catalyze the movement of transposons around genomes by a cut-and-paste mechanism related to retroviral integration. Transposases and retroviral integrases share a common RNaseH-like domain with a catalytic DDE/D triad that coordinates the divalent cations required for DNA cleavage and integration. The anti-retroviral drugs Raltegravir and Elvitegravir inhibit integrases by displacing viral DNA ends from the catalytic metal ions. We demonstrate that Raltegravir, but not Elvitegravir, binds to Mos1 transposase in the presence of Mg(2+) or Mn(2+), without the requirement for transposon DNA, and inhibits transposon cleavage and DNA integration in biochemical assays. Crystal structures at 1.7 Å resolution show Raltegravir, in common with integrases, coordinating two Mg(2+) or Mn(2+) ions in the Mos1 active site. However, in the absence of transposon ends, the drug adopts an unusual, compact binding mode distinct from that observed in the active site of the prototype foamy virus integrase.
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Affiliation(s)
- Urszula
M. Wolkowicz
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Elizabeth R. Morris
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Michael Robson
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Maryia Trubitsyna
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
| | - Julia M. Richardson
- School of Biological Sciences, University
of Edinburgh, Mayfield
Road, Edinburgh EH9 3JR, United Kingdom
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5
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Balaraju T, Kumar A, Bal C, Chattopadhyay D, Jena N, Bal NC, Sharon A. Aromatic interaction profile to understand the molecular basis of raltegravir resistance. Struct Chem 2012. [DOI: 10.1007/s11224-012-0181-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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7
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Liao C, Nicklaus MC. Tautomerism and magnesium chelation of HIV-1 integrase inhibitors: a theoretical study. ChemMedChem 2010; 5:1053-66. [PMID: 20533499 DOI: 10.1002/cmdc.201000039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The tautomerism and corresponding transition states of four authentic HIV-1 integrase (IN) inhibitor prototype structures, alpha,gamma-diketo acid, alpha,gamma-diketotriazole, dihydroxypyrimidine carboxamide and 4-quinolone-3-carboxylic acid, were investigated at the B3LYP/6-311++G(d,p) level in vacuum and in aqueous solvent models. To study the possible chelating modes of these tautomers with two magnesium ions--a process important for inhibition--we modeled an assembly of three formic acids, four water molecules and two Mg(2+) ions as a template mimicking the binding site of IN. The DFT calculation results show that deprotonated enolized or phenolic hydroxy groups of specific tautomers in water lead to the most stable complexes, with the two magnesium ions separated by a distance of approximately 3.70 to 3.74 A, and with each magnesium ion at the center of an octahedron. The drug candidate GS-9137 (Gilead), based on the 4-quinolone-3-carboxylic acid scaffold, and its analogues form similar but different chelating modes. When one water molecule in the complex is replaced by a methanol molecule, which mimics the terminal 3'-OH of viral DNA, a good chelating complex is retained. This supports the hypothesis that, in the binding site of IN after 3'-processing, the terminal 3'-OH of viral DNA interacts with one Mg(2+) by chelation.
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Affiliation(s)
- Chenzhong Liao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles St, Frederick, MD 21702, USA
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8
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Abstract
PURPOSE OF REVIEW Most of the studies investigating inhibition of human immunodeficiency virus integration have focused on blocking the enzymatic functions of HIV integrase, with the predominant judgment that integration inhibitors need to block at least one of the integrase-catalyzed reactions. Recent studies, however, have highlighted the importance of other proteins and their contacts with integrase in the preintegration complex, and their involvement in chromosomal integration of the viral DNA. RECENT FINDINGS Promising results of clinical trials for two new integrase inhibitors were announced recently, providing the proof of the concept for using HIV-1 integrase inhibitors as antiretroviral therapy. Two strategies are currently employed for the development of novel inhibitors of HIV integrase: synthesis of hybrid molecules comprising core structures of two or more known inhibitors, and three-dimensional pharmacophore searches based on previously discovered compounds. By highlighting the role of the cellular cofactor LEDGF/p75 in HIV integration, novel approaches are indicated that aim to develop compounds altering contact between HIV integrase and integration cofactors. SUMMARY By the discovery of novel inhibitors and targets for HIV integration, coupled with recent studies in characterizing preintegration complex formation, new insight is provided for the rational design of anti-HIV integration inhibitors.
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Abstract
Tn5 was one of the first transposons to be identified ( 10 ). As a result of Tn5's early discovery and its simple macromolecular requirements for transposition, the Tn5 system has been a very productive tool for studying the molecular mechanism of DNA transposition. These studies are of broad value because they offer insights into DNA transposition in general, because DNA transposition is a useful model with which to understand other types of protein-DNA interactions such as retroviral DNA integration and the DNA cleavage events involved in immunoglobulin gene formation, and because Tn5-derived tools are useful adjuncts in genetic experimentation.
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Affiliation(s)
- William S Reznikoff
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts 02543, USA.
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10
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Ferro S, De Luca L, Barreca ML, Iraci N, De Grazia S, Christ F, Witvrouw M, Debyser Z, Chimirri A. Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1H-Benzylindole Derivatives through Fluorine Substitutions. J Med Chem 2008; 52:569-73. [DOI: 10.1021/jm8009266] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefania Ferro
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Laura De Luca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Nunzio Iraci
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Sara De Grazia
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Frauke Christ
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Myriam Witvrouw
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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11
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Pasquini S, Mugnaini C, Tintori C, Botta M, Trejos A, Arvela RK, Larhed M, Witvrouw M, Michiels M, Christ F, Debyser Z, Corelli F. Investigations on the 4-Quinolone-3-carboxylic Acid Motif. 1. Synthesis and Structure−Activity Relationship of a Class of Human Immunodeficiency Virus type 1 Integrase Inhibitors. J Med Chem 2008; 51:5125-9. [DOI: 10.1021/jm8003784] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Serena Pasquini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Claudia Mugnaini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Cristina Tintori
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Alejandro Trejos
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Riina K. Arvela
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Mats Larhed
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Myriam Witvrouw
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Martine Michiels
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Frauke Christ
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Federico Corelli
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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12
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Dayam R, Gundla R, Al-Mawsawi LQ, Neamati N. HIV-1 integrase inhibitors: 2005-2006 update. Med Res Rev 2008; 28:118-54. [PMID: 17979144 DOI: 10.1002/med.20116] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) catalyzes the integration of proviral DNA into the host genome, an essential step for viral replication. Inhibition of IN catalytic activity provides an attractive strategy for antiretroviral drug design. Currently two IN inhibitors, MK-0518 and GS-9137, are in advanced stages of human clinical trials. The IN inhibitors in clinical evaluation demonstrate excellent antiretroviral efficacy alone or in combination regimens as compared to previously used clinical antiretroviral agents in naive and treatment-experienced HIV-1 infected patients. However, the emergence of viral strains resistant to clinically studied IN inhibitors and the dynamic nature of the HIV-1 genome demand a continued effort toward the discovery of novel inhibitors to keep a therapeutic advantage over the virus. Continued efforts in the field have resulted in the discovery of compounds from diverse chemical classes. In this review, we provide a comprehensive report of all IN inhibitors discovered in the years 2005 and 2006.
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Affiliation(s)
- Raveendra Dayam
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, USA
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13
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Barreca ML, Ortuso F, Iraci N, De Luca L, Alcaro S, Chimirri A. Tn5 transposase as a useful platform to simulate HIV-1 integrase inhibitor binding mode. Biochem Biophys Res Commun 2007; 363:554-60. [PMID: 17889829 DOI: 10.1016/j.bbrc.2007.08.199] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 08/30/2007] [Indexed: 11/22/2022]
Abstract
The targeting of HIV-1 integrase (IN) for the design of novel antiviral compounds has until now proceeded slowly, mainly due to the lack of three-dimensional structures reporting detail interactions between IN and its DNA substrates as well as the complete enzyme with its three domains. Recently, we have proposed that Tn5 transposase (Tnp) can be used as a useful surrogate model for IN in attempt to address the potential binding modes of Integrase Strand Transfer Inhibitors. In order to strengthen our hypothesis, molecular dynamics simulations of IN inhibitors bound to Tn5 Tnp active site are now reported. A comparison of the obtained results with well documented specific mutations associated with resistance to HIV-1 IN inhibitors confirmed that Tn5 Tnp can provide a valuable platform for the structure-based discovery of new ligands.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina,Viale Annunziata, I-98168 Messina, Italy.
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14
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Abstract
Considerable progress has been made in recent years in the field of drug development against HIV. Many different kinds of natural products, including coumarins, have been found to be active in anti-HIV models and are thus undergoing further investigation. This review demonstrates the variety of coumarins with unique mechanisms of action in the different stages of HIV replication. The discovery and development of coumarins as anti-HIV agents has expanded in the past two decades. Most of the studies have been focused on the inhibitory activity of reverse transcriptase, but anti-integrase and antiprotease activities were also described. The objective of this review is to evaluate data on coumarins’ potent activity with respect to the inhibition of HIV-reverse transcriptase, HIV-integrase or HIV-protease. Recent requirements for potential anti-HIV agents increasingly require adequate definition of the mechanism of action as well as definition of toxic effects and this also applies to natural as well as synthetic coumarins. Structural modification is a powerful tool to increase the potential of bioactive principles. By applying scientific expertise and modern scientific technology, new single compounds will assuredly be developed as potent anti-HIV candidates for world-class new drug development.
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Affiliation(s)
- Irena Kostova
- Department of Chemistry, Faculty of Pharmacy, 2 Dunav Str, Sofia 1000, Medical University, Bulgaria
| | - Jan Mojzis
- Department of Pharmacology, Medical Faculty, P.J. Safarik University, Tr. SNP 1 040 11 Kosice, Slovak Republic
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15
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Cox AG, Nair V. Novel HIV integrase inhibitors with anti-HIV activity: insights into integrase inhibition from docking studies. Antivir Chem Chemother 2007; 17:343-53. [PMID: 17249248 DOI: 10.1177/095632020601700604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mechanism of integrase is generally accepted to be dependant on the presence of two divalent metal ions in the active site. However, the only available crystal structures of HIV-1 integrase contain either one or no metal ions, hampering structure-based design studies of integrase inhibitors. For this reason, a two-metal ion model of integrase was constructed. This model was used for computational docking studies with novel diketoacid integrase inhibitors containing pyrimidine nucleobase scaffolds. The docking protocol allowed for some steric contact between the ligand and protein during docking simulations, which implicitly accounted for potential conformational changes in the protein as a result of binding viral DNA or the ligand. The results suggest that the aromatic rings in these diketo acids bind to regions close to the viral DNA and may interfere with mobility of a vital catalytic loop. The docking data also suggest that the ligand can be prevented from adopting a favourable conformation by changes in the relative orientation of its diketo side-chain and aromatic rings. The docked pose of each of the active compounds coordinated both of the metal ions present in the active site of integrase through the diketo acid functionality of these compounds. This result is more consistent with theoretical data on inhibitor mechanism, and thus recommends this docking approach over rigid use of one-metal ion models derived from current crystal structures of integrase.
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Affiliation(s)
- Arthur G Cox
- The Center for Drug Discovery and Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, GA, USA
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16
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Abstract
HIV-1 integrase, which catalyzes the joining of viral DNA to the host cell DNA, has attracted considerable attention as a target for the design and screening of novel anti-HIV drugs as it is essential for virus replication and the establishment of persistent infection. Progress in the identification of different classes of compounds that block integrase activity has been summarized recently in several excellent reviews. Here, we present a brief overview of integrase inhibition, highlighting some of the unusual properties of this protein and important considerations in searching for potential new inhibitors and their evaluation.
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Affiliation(s)
- Joseph Ramcharan
- Locus Pharmaceuticals Inc., 4 Valley Square, 512 East Township Line Road, Blue Bell, PA 19422, USA
| | - Anna Marie Skalka
- Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, PA 19111, USA
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Whitfield CR, Wardle SJ, Haniford DB. Formation, characterization and partial purification of a Tn5 strand transfer complex. J Mol Biol 2006; 364:290-301. [PMID: 17014865 DOI: 10.1016/j.jmb.2006.09.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/07/2006] [Accepted: 09/11/2006] [Indexed: 10/24/2022]
Abstract
DNA transposition reactions typically involve a strand transfer step wherein the transposon ends are covalently joined by the transposase protein to a short target site. There is very little known about the transposase-DNA interactions that direct this process, and thus our overall understanding of the dynamics of DNA transposition reactions is limited. Tn5 presents an attractive system for defining such interactions because it has been possible to solve the structure of at least one Tn5 transposition intermediate: a transpososome formed with pre-cleaved ends. However, insertion specificity in the Tn5 system is low and this has hampered progress in generating target-containing transpososomes that are homogeneous in structure (i.e. where a single target site is engaged) and therefore suitable for biochemical and structural analysis. We have developed a system where the Tn5 transpososome integrates almost exclusively into a single target site within a short DNA fragment. The key to establishing this high degree of insertion specificity was to use a target DNA with tandem repeats of a previously characterized Tn5 insertion hotspot. The target DNA requirements to form this strand transfer complex are evaluated. In addition, we show that target DNAs missing single phosphate groups at specific positions are better substrates for strand transfer complex formation relative to the corresponding unmodified DNA fragments. Moreover, utilization of missing phosphate substrates can increase the degree of target site selection. A method for concentrating and partially purifying the Tn5 strand transfer complex is described.
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Affiliation(s)
- Crystal R Whitfield
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
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Barreca ML, De Luca L, Iraci N, Chimirri A. Binding Mode Prediction of Strand Transfer HIV-1 Integrase Inhibitors Using Tn5 Transposase as a Plausible Surrogate Model for HIV-1 Integrase. J Med Chem 2006; 49:3994-7. [PMID: 16789757 DOI: 10.1021/jm060323r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The crystal structure of Tn5 transposase-DNA complex was used in docking experiments to predict binding modes of HIV-1 integrase strand transfer inhibitors (INSTIs). In fact, the identification of HIV-1 integrase inhibitors from an in vitro screen using Tn5 transposase as the target has been recently reported. Our results suggest the utility of this protein as a useful surrogate model for IN and also for in silico screening, in the search for new potential INSTIs.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy.
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