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Reddy KK, Singh P, Singh SK. Blocking the interaction between HIV-1 integrase and human LEDGF/p75: mutational studies, virtual screening and molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2014; 10:526-36. [DOI: 10.1039/c3mb70418a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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152
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Morchikh M, Naughtin M, Di Nunzio F, Xavier J, Charneau P, Jacob Y, Lavigne M. TOX4 and NOVA1 proteins are partners of the LEDGF PWWP domain and affect HIV-1 replication. PLoS One 2013; 8:e81217. [PMID: 24312278 PMCID: PMC3842248 DOI: 10.1371/journal.pone.0081217] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/10/2013] [Indexed: 12/31/2022] Open
Abstract
PWWP domains are involved in the chromatin attachment of several proteins. They bind to both DNA and proteins and their interaction with specific histone methylation marks define them as a new class of histone code readers. The lens epithelium derived growth factor (LEDGF/p75) contains an N-terminal PWWP domain necessary for its interaction with chromatin but also a C-terminal domain which interacts with several proteins, such as lentiviral integrases. These two domains confer a chromatin-tethering function to LEDGF/p75 and in the case of lentiviral integrases, this tethering participates in the efficiency and site selectivity of integration. Although proteins interacting with LEDGF/p75 C-terminal domain have been extensively studied, no data exist about partners of its PWWP domain regulating its interaction with chromatin. In this study, we report the identification by yeast-two-hybrid of thirteen potential partners of the LEDGF PWWP domain. Five of these interactions were confirmed in mammalian cells, using both a protein complementation assay and co-immunoprecipitation approaches. Three of these partners interact with full length LEDGF/p75, they are specific for PWWP domains of the HDGF family and they require PWWP amino acids essential for the interaction with chromatin. Among them, the transcription activator TOX4 and the splicing cofactor NOVA1 were selected for a more extensive study. These two proteins or their PWWP interacting regions (PIR) colocalize with LEDGF/p75 in Hela cells and interact in vitro in the presence of DNA. Finally, single round VSV-G pseudotyped HIV-1 but not MLV infection is inhibited in cells overexpressing these two PIRs. The observed inhibition of infection can be attributed to a defect in the integration step. Our data suggest that a regulation of LEDGF interaction with chromatin by cellular partners of its PWWP domain could be involved in several processes linked to LEDGF tethering properties, such as lentiviral integration, DNA repair or transcriptional regulation.
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Affiliation(s)
- Mehdi Morchikh
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Monica Naughtin
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Francesca Di Nunzio
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Johan Xavier
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Charneau
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Yves Jacob
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Centre National de la Recherche Scientifique, Paris, France
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marc Lavigne
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- * E-mail:
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153
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Abstract
Integrase (IN) is required for lentivirus replication and is a proven drug target for the prevention of AIDS in HIV-1-infected patients. While clinical strand transfer inhibitors disarm the IN active site, allosteric inhibition of enzyme activity through the disruption of IN-IN protein interfaces holds great therapeutic potential. A promising class of allosteric IN inhibitors (ALLINIs), 2-(quinolin-3-yl) acetic acid derivatives, engage the IN catalytic core domain dimerisation interface at the binding site for the host integration co-factor LEDGF/p75. ALLINIs promote IN multimerisation and, independent of LEDGF/p75 protein, block the formation of the active IN-DNA complex, as well as inhibit the IN-LEDGF/p75 interaction in vitro. Yet, rather unexpectedly, the full inhibitory effect of these compounds is exerted during the late phase of HIV-1 replication. ALLINIs impair particle core maturation as well as reverse transcription and integration during the subsequent round of virus infection. Recapitulating the pleiotropic phenotypes observed with numerous IN mutant viruses, ALLINIs provide insight into underlying aspects of IN biology that extend beyond its catalytic activity. Therefore, in addition to the potential to expand our repertoire of HIV-1 antiretrovirals, ALLINIs afford important structural probes to dissect the multifaceted nature of the IN protein throughout the course of HIV-1 replication.
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154
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Le Rouzic E, Bonnard D, Chasset S, Bruneau JM, Chevreuil F, Le Strat F, Nguyen J, Beauvoir R, Amadori C, Brias J, Vomscheid S, Eiler S, Lévy N, Delelis O, Deprez E, Saïb A, Zamborlini A, Emiliani S, Ruff M, Ledoussal B, Moreau F, Benarous R. Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage. Retrovirology 2013; 10:144. [PMID: 24261564 PMCID: PMC4222603 DOI: 10.1186/1742-4690-10-144] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 11/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND LEDGF/p75 (LEDGF) is the main cellular cofactor of HIV-1 integrase (IN). It acts as a tethering factor for IN, and targets the integration of HIV in actively transcribed gene regions of chromatin. A recently developed class of IN allosteric inhibitors can inhibit the LEDGF-IN interaction. RESULTS We describe a new series of IN-LEDGF allosteric inhibitors, the most active of which is Mut101. We determined the crystal structure of Mut101 in complex with IN and showed that the compound binds to the LEDGF-binding pocket, promoting conformational changes of IN which explain at the atomic level the allosteric effect of the IN/LEDGF interaction inhibitor on IN functions. In vitro, Mut101 inhibited both IN-LEDGF interaction and IN strand transfer activity while enhancing IN-IN interaction. Time of addition experiments indicated that Mut101 behaved as an integration inhibitor. Mut101 was fully active on HIV-1 mutants resistant to INSTIs and other classes of anti-HIV drugs, indicative that this compound has a new mode of action. However, we found that Mut101 also displayed a more potent antiretroviral activity at a post-integration step. Infectivity of viral particles produced in presence of Mut101 was severely decreased. This latter effect also required the binding of the compound to the LEDGF-binding pocket. CONCLUSION Mut101 has dual anti-HIV-1 activity, at integration and post-integration steps of the viral replication cycle, by binding to a unique target on IN (the LEDGF-binding pocket). The post-integration block of HIV-1 replication in virus-producer cells is the mechanism by which Mut101 is most active as an antiretroviral. To explain this difference between Mut101 antiretroviral activity at integration and post-integration stages, we propose the following model: LEDGF is a nuclear, chromatin-bound protein that is absent in the cytoplasm. Therefore, LEDGF can outcompete compound binding to IN in the nucleus of target cells lowering its antiretroviral activity at integration, but not in the cytoplasm where post-integration production of infectious viral particles takes place.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sylvia Eiler
- IGBMC, Inserm, CNRS, Université de Strasbourg, Illkirch 67404, France
| | - Nicolas Lévy
- IGBMC, Inserm, CNRS, Université de Strasbourg, Illkirch 67404, France
| | | | | | - Ali Saïb
- CNRS UMR7212, Inserm U944, Université Paris Diderot, Conservatoire National des Arts et Métiers, Paris, France
| | - Alessia Zamborlini
- CNRS UMR7212, Inserm U944, Université Paris Diderot, Conservatoire National des Arts et Métiers, Paris, France
| | - Stéphane Emiliani
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes, Paris 75014, France
| | - Marc Ruff
- IGBMC, Inserm, CNRS, Université de Strasbourg, Illkirch 67404, France
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155
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Miri L, Bouvier G, Kettani A, Mikou A, Wakrim L, Nilges M, Malliavin TE. Stabilization of the integrase-DNA complex by Mg2+ions and prediction of key residues for binding HIV-1 integrase inhibitors. Proteins 2013; 82:466-78. [DOI: 10.1002/prot.24412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 07/18/2013] [Accepted: 08/14/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Lamia Miri
- Laboratoire de Virologie; Institut Pasteur du Maroc; Casablanca 20360 Morocco
- Unité de modélisation moléculaire et d'ingénierie des biomolécules, Laboratoire de recherche sur les lipoprotéines et l'athérosclérose; Unité Associée au CNRST-URAC34, Faculté des Sciences Ben M'Sik; Casablanca Morocco
| | - Guillaume Bouvier
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
| | - Anass Kettani
- Unité de modélisation moléculaire et d'ingénierie des biomolécules, Laboratoire de recherche sur les lipoprotéines et l'athérosclérose; Unité Associée au CNRST-URAC34, Faculté des Sciences Ben M'Sik; Casablanca Morocco
| | - Afaf Mikou
- Laboratoire de Catalyse et environnement; Faculté des Sciences Ain Chock; Casablanca Morocco
| | - Lahcen Wakrim
- Laboratoire de Virologie; Institut Pasteur du Maroc; Casablanca 20360 Morocco
| | - Michael Nilges
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
| | - Thérèse E. Malliavin
- Unité de Bioinformatique Structurale; UMR 3528 CNRS, Institut Pasteur; Paris 75724 France
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156
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DeAnda F, Hightower KE, Nolte RT, Hattori K, Yoshinaga T, Kawasuji T, Underwood MR. Dolutegravir interactions with HIV-1 integrase-DNA: structural rationale for drug resistance and dissociation kinetics. PLoS One 2013; 8:e77448. [PMID: 24146996 PMCID: PMC3797783 DOI: 10.1371/journal.pone.0077448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/10/2013] [Indexed: 01/12/2023] Open
Abstract
Signature HIV-1 integrase mutations associated with clinical raltegravir resistance involve 1 of 3 primary genetic pathways, Y143C/R, Q148H/K/R and N155H, the latter 2 of which confer cross-resistance to elvitegravir. In accord with clinical findings, in vitro drug resistance profiling studies with wild-type and site-directed integrase mutant viruses have shown significant fold increases in raltegravir and elvitegravir resistance for the specified viral mutants relative to wild-type HIV-1. Dolutegravir, in contrast, has demonstrated clinical efficacy in subjects failing raltegravir therapy due to integrase mutations at Y143, Q148 or N155, which is consistent with its distinct in vitro resistance profile as dolutegravir's antiviral activity against these viral mutants is equivalent to its activity against wild-type HIV-1. Kinetic studies of inhibitor dissociation from wild-type and mutant integrase-viral DNA complexes have shown that dolutegravir also has a distinct off-rate profile with dissociative half-lives substantially longer than those of raltegravir and elvitegravir, suggesting that dolutegravir's prolonged binding may be an important contributing factor to its distinct resistance profile. To provide a structural rationale for these observations, we constructed several molecular models of wild-type and clinically relevant mutant HIV-1 integrase enzymes in complex with viral DNA and dolutegravir, raltegravir or elvitegravir. Here, we discuss our structural models and the posited effects that the integrase mutations and the structural and electronic properties of the integrase inhibitors may have on the catalytic pocket and inhibitor binding and, consequently, on antiviral potency in vitro and in the clinic.
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Affiliation(s)
- Felix DeAnda
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Kendra E. Hightower
- Biological Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Robert T. Nolte
- Chemical Sciences, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | | | | | - Takashi Kawasuji
- Chemistry Infectious Diseases, Shionogi & Co., Ltd., Osaka, Japan
| | - Mark R. Underwood
- Medicines Development Infectious Diseases, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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157
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Cavalluzzo C, Christ F, Voet A, Sharma A, Singh BK, Zhang KY, Lescrinier E, De Maeyer M, Debyser Z, Van der Eycken E. Identification of small peptides inhibiting the integrase-LEDGF/p75 interaction through targeting the cellular co-factor. J Pept Sci 2013; 19:651-8. [DOI: 10.1002/psc.2543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/27/2013] [Accepted: 07/02/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Claudia Cavalluzzo
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry; Katholieke Universiteit Leuven; Celestijnenlaan 200F B-3001 Leuven Belgium
- DestiNA Genomics Ltd; West Mains Road Edinburgh EH9 3JJ UK
| | - Frauke Christ
- Molecular Medicine; Katholieke Universiteit Leuven; Kapucijnenvoer 33 B-3000 Leuven Belgium
| | - Arnout Voet
- Laboratory for Biomolecular modeling; Katholieke Universiteit Leuven; Celestijnenlaan 200G B-3001 Leuven Belgium
- Zhang Initiative Research Unit; Advanced Science Institute; RIKEN 2-1 Hirosawa Wako 351-0198 Japan
| | - Ajendra Sharma
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry; Katholieke Universiteit Leuven; Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Brajendra Kumar Singh
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry; Katholieke Universiteit Leuven; Celestijnenlaan 200F B-3001 Leuven Belgium
- Bioorganic Laboratory, Department of Chemistry; University of Delhi; Delhi 110 007 India
| | - Kam Y.J. Zhang
- Zhang Initiative Research Unit; Advanced Science Institute; RIKEN 2-1 Hirosawa Wako 351-0198 Japan
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry; University of Leuven (KU Leuven); Minderbroedersstraat 10 B-3000 Leuven Belgium
| | - Marc De Maeyer
- Laboratory for Biomolecular modeling; Katholieke Universiteit Leuven; Celestijnenlaan 200G B-3001 Leuven Belgium
| | - Zeger Debyser
- Molecular Medicine; Katholieke Universiteit Leuven; Kapucijnenvoer 33 B-3000 Leuven Belgium
| | - Erik Van der Eycken
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry; Katholieke Universiteit Leuven; Celestijnenlaan 200F B-3001 Leuven Belgium
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158
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De Luca L, Morreale F, Christ F, Debyser Z, Ferro S, Gitto R. New scaffolds of natural origin as Integrase-LEDGF/p75 interaction inhibitors: virtual screening and activity assays. Eur J Med Chem 2013; 68:405-11. [PMID: 23994868 DOI: 10.1016/j.ejmech.2013.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 01/08/2023]
Abstract
The disruption of crucial interactions between HIV-1 Integrase and cellular cofactor LEDGF/p75 represents an emerging approach for the design and development of new antiretroviral agents. In this study we report the successful application of a structure-based virtual screening strategy for the discovery of natural hit structures able to inhibit Integrase-LEDGF/p75 interaction. The application of sequential filters (drug-likeness, 3D-pharmacophore mapping, docking, molecular dynamics simulations) yielded a hit list of compounds, out of which 9 were tested in the in vitro AlphaScreen assays and 8 exhibited a detectable inhibition of the interaction between the two proteins. The best inhibitors belong to different chemical classes and could be represent a good starting point for further optimization and structure-activity relationship studies.
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Affiliation(s)
- Laura De Luca
- Dipartimento di Scienze del Farmaco e Prodotti per la Salute, Università di Messina, Viale Annunziata, I-98168 Messina, Italy.
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159
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Computational design of a full-length model of HIV-1 integrase: modeling of new inhibitors and comparison of their calculated binding energies with those previously studied. J Mol Model 2013; 19:4349-68. [PMID: 23907552 DOI: 10.1007/s00894-013-1943-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 07/11/2013] [Indexed: 12/28/2022]
Abstract
A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was constructed based on the distinctly resolved X-ray crystal structures of its three domains, named N-terminal, catalytic core and C-terminal. Thirty-one already known inhibitors with varieties of structural differences as well as nine newly tested ones were docked into the catalytic core. The molecular dynamic (MD) and binding properties of these complexes were obtained by MD calculations. The binding energies calculated by molecular mechanic/Poisson Boltzmann solvation area were significantly correlationed with available IC50. Four inhibitors including two newly designed were also docked into the full-length model and their MD behaviors and binding properties were calculated. It was found that one of the newly designed compounds forms a better complex with HIV-1 IN compared to the rest including raltegravir. MD calculations were performed with AMBER suite of programs using ff99SB force field for the proteins and the general Amber force field for the ligands. In conclusion, the results have produced a promising standpoint not only in the construction of the full-length model but also in development of new drugs against it. However, the role of multimer formation and the involvement of DNAs, and their subsequent effect on the complexation and inhibition, are required to arrive at a conclusive decision.
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160
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Ferro S, De Luca L, Morreale F, Christ F, Debyser Z, Gitto R, Chimirri A. Synthesis and biological evaluation of novel antiviral agents as protein–protein interaction inhibitors. J Enzyme Inhib Med Chem 2013; 29:237-42. [DOI: 10.3109/14756366.2013.766609] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Stefania Ferro
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Laura De Luca
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Francesca Morreale
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Frauke Christ
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK
Leuven, FlandersBelgium
| | - Zeger Debyser
- Molecular Virology and Gene Therapy KU Leuven and IRC KULAK
Leuven, FlandersBelgium
| | - Rosaria Gitto
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
| | - Alba Chimirri
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina
MessinaItaly
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161
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BET proteins promote efficient murine leukemia virus integration at transcription start sites. Proc Natl Acad Sci U S A 2013; 110:12036-41. [PMID: 23818621 DOI: 10.1073/pnas.1307157110] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus, suggestive of targeting by binding to cellular factors. γ-Retroviral murine leukemia virus (MLV) DNA integration into the host genome is favored at transcription start sites, but the underlying mechanism for this preference is unknown. Here, we have identified bromodomain and extraterminal domain (BET) proteins (Brd2, -3, -4) as cellular-binding partners of MLV integrase. We show that purified recombinant Brd4(1-720) binds with high affinity to MLV integrase and stimulates correct concerted integration in vitro. JQ-1, a small molecule that selectively inhibits interactions of BET proteins with modified histone sites impaired MLV but not HIV-1 integration in infected cells. Comparison of the distribution of BET protein-binding sites analyzed using ChIP-Seq data and MLV-integration sites revealed significant positive correlations. Antagonism of BET proteins, via JQ-1 treatment or RNA interference, reduced MLV-integration frequencies at transcription start sites. These findings elucidate the importance of BET proteins for MLV integration efficiency and targeting and provide a route to developing safer MLV-based vectors for human gene therapy.
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162
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Long YQ, Huang SX, Zawahir Z, Xu ZL, Li H, Sanchez TW, Zhi Y, De Houwer S, Christ F, Debyser Z, Neamati N. Design of cell-permeable stapled peptides as HIV-1 integrase inhibitors. J Med Chem 2013; 56:5601-12. [PMID: 23758584 DOI: 10.1021/jm4006516] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
HIV-1 integrase (IN) catalyzes the integration of viral DNA into the host genome, involving several interactions with the viral and cellular proteins. We have previously identified peptide IN inhibitors derived from the α-helical regions along the dimeric interface of HIV-1 IN. Herein, we show that appropriate hydrocarbon stapling of these peptides to stabilize their helical structure remarkably improves the cell permeability, thus allowing inhibition of the HIV-1 replication in cell culture. Furthermore, the stabilized peptides inhibit the interaction of IN with the cellular cofactor LEDGF/p75. Cellular uptake of the stapled peptide was confirmed in four different cell lines using a fluorescein-labeled analogue. Given their enhanced potency and cell permeability, these stapled peptides can serve as not only lead IN inhibitors but also prototypical biochemical probes or "nanoneedles" for the elucidation of HIV-1 IN dimerization and host cofactor interactions within their native cellular environment.
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Affiliation(s)
- Ya-Qiu Long
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
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163
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Integrating the HIV-1 assembly/maturation pathway. Proc Natl Acad Sci U S A 2013; 110:8327-8. [DOI: 10.1073/pnas.1306620110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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164
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Qi X, Vargas E, Larsen L, Knapp W, Hatfield GW, Lathrop R, Sandmeyer S. Directed DNA shuffling of retrovirus and retrotransposon integrase protein domains. PLoS One 2013; 8:e63957. [PMID: 23691126 PMCID: PMC3656877 DOI: 10.1371/journal.pone.0063957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 04/11/2013] [Indexed: 12/15/2022] Open
Abstract
Chimeric proteins are used to study protein domain functions and to recombine protein domains for novel or optimal functions. We used a library of chimeric integrase proteins to study DNA integration specificity. The library was constructed using a directed shuffling method that we adapted from fusion PCR. This method easily and accurately shuffles multiple DNA gene sequences simultaneously at specific base-pair positions, such as protein domain boundaries. It produced all 27 properly-ordered combinations of the amino-terminal, catalytic core, and carboxyl-terminal domains of the integrase gene from human immunodeficiency virus, prototype foamy virus, and Saccharomyces cerevisiae retrotransposon Ty3. Retrotransposons can display dramatic position-specific integration specificity compared to retroviruses. The yeast retrotransposon Ty3 integrase interacts with RNA polymerase III transcription factors to target integration at the transcription initiation site. In vitro assays of the native and chimeric proteins showed that human immunodeficiency virus integrase was active with heterologous substrates, whereas prototype foamy virus and Ty3 integrases were not. This observation was consistent with a lower substrate specificity for human immunodeficiency virus integrase than for other retrovirus integrases. All eight chimeras containing the Ty3 integrase carboxyl-terminal domain, a candidate targeting domain, failed to target strand transfer in the presence of the targeting protein, suggesting that multiple domains of the Ty3 integrase cooperate in this function.
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Affiliation(s)
- Xiaojie Qi
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Edwin Vargas
- Department of Computer Science, School of Information and Computer Sciences, University of California Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
| | - Liza Larsen
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
| | - Whitney Knapp
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - G. Wesley Hatfield
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
- Department of Chemical Engineering and Materials Science, School of Engineering, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California, United States of America
- Department of Biomedical Engineering, School of Engineering, University of California Irvine, Irvine, California, United States of America
- CODA Genomics, Inc., Laguna Hills, California, United States of America
| | - Richard Lathrop
- Department of Computer Science, School of Information and Computer Sciences, University of California Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
- Department of Biomedical Engineering, School of Engineering, University of California Irvine, Irvine, California, United States of America
- CODA Genomics, Inc., Laguna Hills, California, United States of America
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
- Department of Chemical Engineering and Materials Science, School of Engineering, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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165
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Hu J, Wang Y. p53 and the PWWP domain containing effector proteins in chromatin damage repair. CELL & DEVELOPMENTAL BIOLOGY 2013; 2:112. [PMID: 25264544 PMCID: PMC4175562 DOI: 10.4172/2168-9296.1000112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In eukaryotic cells, DNA damage repair occurs on a template DNA that is organized with histones to form nucleosomes and chromatin structures. As such, chromatin plays an important role in DNA damage repair. In this review, we will use "chromatin damage repair" as a framework and highlight recent progress in understanding the role of chromatin, chromatin modifiers, chromatin binding effectors (e.g., the PWWP domain proteins), and the p53 tumor suppressor. We view chromatin as an active participant during DNA damage repair.
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Affiliation(s)
- Jing Hu
- Graduate Program in Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802 USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
| | - Yanming Wang
- Graduate Program in Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802 USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802 USA
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166
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Engelman A, Kessl JJ, Kvaratskhelia M. Allosteric inhibition of HIV-1 integrase activity. Curr Opin Chem Biol 2013; 17:339-45. [PMID: 23647983 DOI: 10.1016/j.cbpa.2013.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 04/03/2013] [Accepted: 04/09/2013] [Indexed: 01/28/2023]
Abstract
HIV-1 integrase is an important therapeutic target in the fight against HIV/AIDS. Integrase strand transfer inhibitors (INSTIs), which target the enzyme active site, have witnessed clinical success over the past 5 years, but the generation of drug resistance poses challenges to INSTI-based therapies moving forward. Integrase is a dynamic protein, and its ordered multimerization is critical to enzyme activity. The integrase tetramer, bound to viral DNA, interacts with host LEDGF/p75 protein to tether integration to active genes. Allosteric integrase inhibitors (ALLINIs) that compete with LEDGF/p75 for binding to integrase disrupt integrase assembly with viral DNA and allosterically inhibit enzyme function. ALLINIs display steep dose response curves and synergize with INSTIs ex vivo, highlighting this novel inhibitor class for clinical development.
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Affiliation(s)
- Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA 02215, USA.
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167
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Feng L, Sharma A, Slaughter A, Jena N, Koh Y, Shkriabai N, Larue RC, Patel PA, Mitsuya H, Kessl JJ, Engelman A, Fuchs JR, Kvaratskhelia M. The A128T resistance mutation reveals aberrant protein multimerization as the primary mechanism of action of allosteric HIV-1 integrase inhibitors. J Biol Chem 2013; 288:15813-20. [PMID: 23615903 DOI: 10.1074/jbc.m112.443390] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a very promising new class of anti-HIV-1 agents that exhibit a multimodal mechanism of action by allosterically modulating IN multimerization and interfering with IN-lens epithelium-derived growth factor (LEDGF)/p75 binding. Selection of viral strains under ALLINI pressure has revealed an A128T substitution in HIV-1 IN as a primary mechanism of resistance. Here, we elucidated the structural and mechanistic basis for this resistance. The A128T substitution did not affect the hydrogen bonding between ALLINI and IN that mimics the IN-LEDGF/p75 interaction but instead altered the positioning of the inhibitor at the IN dimer interface. Consequently, the A128T substitution had only a minor effect on the ALLINI IC50 values for IN-LEDGF/p75 binding. Instead, ALLINIs markedly altered the multimerization of IN by promoting aberrant higher order WT (but not A128T) IN oligomers. Accordingly, WT IN catalytic activities and HIV-1 replication were potently inhibited by ALLINIs, whereas the A128T substitution in IN resulted in significant resistance to the inhibitors both in vitro and in cell culture assays. The differential multimerization of WT and A128T INs induced by ALLINIs correlated with the differences in infectivity of HIV-1 progeny virions. We conclude that ALLINIs primarily target IN multimerization rather than IN-LEDGF/p75 binding. Our findings provide the structural foundations for developing improved ALLINIs with increased potency and decreased potential to select for drug resistance.
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Affiliation(s)
- Lei Feng
- Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
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Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation. Proc Natl Acad Sci U S A 2013; 110:8690-5. [PMID: 23610442 DOI: 10.1073/pnas.1300703110] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Integration is essential for HIV-1 replication, and the viral integrase (IN) protein is an important therapeutic target. Allosteric IN inhibitors (ALLINIs) that engage the IN dimer interface at the binding site for the host protein lens epithelium-derived growth factor (LEDGF)/transcriptional coactivator p75 are an emerging class of small molecule antagonists. Consistent with the inhibition of a multivalent drug target, ALLINIs display steep antiviral dose-response curves ex vivo. ALLINIs multimerize IN protein and concordantly block its assembly with viral DNA in vitro, indicating that the disruption of two integration-associated functions, IN catalysis and the IN-LEDGF/p75 interaction, determines the multimode mechanism of ALLINI action. We now demonstrate that ALLINI potency is unexpectedly accounted for during the late phase of HIV-1 replication. The compounds promote virion IN multimerization and, reminiscent of class II IN mutations, block the formation of the electron-dense viral core and inhibit reverse transcription and integration in subsequently infected target cells. Mature virions are recalcitrant to ALLINI treatment, and compound potency during virus production is independent of the level of LEDGF/p75 expression. We conclude that cooperative multimerization of IN by ALLINIs together with the inability for LEDGF/p75 to effectively engage the virus during its egress from cells underscores the multimodal mechanism of ALLINI action. Our results highlight the versatile nature of allosteric inhibitors to primarily inhibit viral replication at a step that is distinct from the catalytic requirement for the target enzyme. The vulnerability of IN to small molecules during the late phase of HIV-1 replication unveils a pharmacological Achilles' heel for exploitation in clinical ALLINI development.
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169
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Maillot B, Lévy N, Eiler S, Crucifix C, Granger F, Richert L, Didier P, Godet J, Pradeau-Aubreton K, Emiliani S, Nazabal A, Lesbats P, Parissi V, Mely Y, Moras D, Schultz P, Ruff M. Structural and functional role of INI1 and LEDGF in the HIV-1 preintegration complex. PLoS One 2013; 8:e60734. [PMID: 23593299 PMCID: PMC3623958 DOI: 10.1371/journal.pone.0060734] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/01/2013] [Indexed: 02/07/2023] Open
Abstract
Integration of the HIV-1 cDNA into the human genome is catalyzed by the viral integrase (IN) protein. Several studies have shown the importance of cellular cofactors that interact with integrase and affect viral integration and infectivity. In this study, we produced a stable complex between HIV-1 integrase, viral U5 DNA, the cellular cofactor LEDGF/p75 and the integrase binding domain of INI1 (INI1-IBD), a subunit of the SWI/SNF chromatin remodeling factor. The stoichiometry of the IN/LEDGF/INI1-IBD/DNA complex components was found to be 4/2/2/2 by mass spectrometry and Fluorescence Correlation Spectroscopy. Functional assays showed that INI1-IBD inhibits the 3′ processing reaction but does not interfere with specific viral DNA binding. Integration assays demonstrate that INI1-IBD decreases the amount of integration events but inhibits by-product formation such as donor/donor or linear full site integration molecules. Cryo-electron microscopy locates INI1-IBD within the cellular DNA binding site of the IN/LEDGF complex, constraining the highly flexible integrase in a stable conformation. Taken together, our results suggest that INI1 could stabilize the PIC in the host cell, by maintaining integrase in a stable constrained conformation which prevents non-specific interactions and auto integration on the route to its integration site within nucleosomes, while LEDGF organizes and stabilizes an active integrase tetramer suitable for specific vDNA integration. Moreover, our results provide the basis for a novel type of integrase inhibitor (conformational inhibitor) representing a potential new strategy for use in human therapy.
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Affiliation(s)
- Benoit Maillot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Nicolas Lévy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Corinne Crucifix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Florence Granger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Pascal Didier
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Karine Pradeau-Aubreton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Stéphane Emiliani
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), INSERM (U567), Paris, France
| | | | - Paul Lesbats
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS (UMR5234), Université de Bordeaux 2, Bordeaux, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS (UMR5234), Université de Bordeaux 2, Bordeaux, France
| | - Yves Mely
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, UDS, Faculté de Pharmacie, Illkirch, France
| | - Dino Moras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale intégrative, Université de Strasbourg, U596 INSERM, UMR7104 CNRS, Illkirch, France
- * E-mail:
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170
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Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res 2013; 41:3924-36. [PMID: 23396443 PMCID: PMC3616739 DOI: 10.1093/nar/gkt074] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/27/2012] [Accepted: 01/18/2013] [Indexed: 01/19/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin.
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Affiliation(s)
- Jocelyn O. Eidahl
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Brandon L. Crowe
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Justin A. North
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher J. McKee
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nikoloz Shkriabai
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lei Feng
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew Plumb
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert L. Graham
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert J. Gorelick
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sonja Hess
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael G. Poirier
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark P. Foster
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mamuka Kvaratskhelia
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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171
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Johnson BC, Métifiot M, Ferris A, Pommier Y, Hughes SH. A homology model of HIV-1 integrase and analysis of mutations designed to test the model. J Mol Biol 2013; 425:2133-46. [PMID: 23542006 DOI: 10.1016/j.jmb.2013.03.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 01/26/2023]
Abstract
Although there are structures of the different domains of human immunodeficiency virus type 1 (HIV-1) integrase (IN), there is no structure of the entire protein. The recently determined crystal structures of the prototype foamy virus (PFV) IN tetramer, in complexes with viral DNA, led to the generation of models of full-length HIV-1 IN. These models were generated, in part, by superimposing the structures of the domains of HIV-1 IN onto the structure of full-length PFV IN. We developed a model for HIV-1 IN-based solely on its sequence alignment with PFV IN-that differs in several ways from the previous models. Specifically, in our model, the junction between the catalytic core domain and C-terminal domain adopts a helix-loop-helix motif that is similar to the corresponding segment of PFV IN and differs from the crystal structures of these two HIV-1 IN domains. The alignment of residues in the C-terminal domain also differs from the previous models. Our model can be used to explain the phenotype of previously published HIV-1 IN mutants. We made additional mutants, and the behavior of these new mutants provides additional support for the model.
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Affiliation(s)
- Barry C Johnson
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA.
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172
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173
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Sanchez TW, Debnath B, Christ F, Otake H, Debyser Z, Neamati N. Discovery of novel inhibitors of LEDGF/p75-IN protein-protein interactions. Bioorg Med Chem 2013; 21:957-63. [PMID: 23306052 PMCID: PMC6188659 DOI: 10.1016/j.bmc.2012.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/25/2012] [Accepted: 12/03/2012] [Indexed: 11/30/2022]
Abstract
Human lens epithelium-derived growth factor (LEDGF)/p75 plays an important role in the HIV life cycle by stimulating integrase (IN)-led viral DNA integration into cellular chromosomes. Mechanistic studies show the majority of IN inhibitors chelate magnesium ions in the catalytic active site, a region topologically distant from the LEDGF/p75 binding site. Compounds disrupting the formation of LEDGF/p75 and IN complexes serve as a novel mechanistic approach different from current antiretroviral therapies. We previously built pharmacophore models mimicking LEDGF/p75 residues and identified four classes of LEDGF/p75-IN inhibitors. Substructure and similarity searches yielded additional LEDGF/p75-IN inhibitors containing an acylhydrazone moiety. The most potent of the acylhydrazones inhibited LEDGF/p75-IN interaction with an IC(50) value of 400nM. We explored structure-activity relationships (SAR) and identified new acylhydrazones, hydrazines, and diazenes as lead molecules for further optimization. Two lead LEDGF/p75-IN inhibitors showed antiviral activity.
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Affiliation(s)
- Tino Wilson Sanchez
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
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174
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Christ F, Debyser Z. The LEDGF/p75 integrase interaction, a novel target for anti-HIV therapy. Virology 2013; 435:102-9. [PMID: 23217620 DOI: 10.1016/j.virol.2012.09.033] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 01/12/2023]
Abstract
To accomplish their viral life cycle, lentiviruses such as HIV highjack host proteins, the so-called cellular co-factors of replication. Lens Epithelium-derived Growth factor (LEDGF/p75), a transcriptional co-activator, is a co-factor of HIV-integrase (IN) and is required for the tethering and correct integration of the viral genome into the host chromatin. Due to its important role in HIV-replication the LEDGF/p75-IN interaction is an attractive antiviral novel target for the treatment of HIV/AIDS. Intensive drug discovery efforts over the past years have validated the LEDGF/p75-IN interaction as a drugable target for antiviral therapy and have resulted in the design and synthesis of LEDGINs, small molecule inhibitors binding to the dimer interface of HIV-integrase and inhibiting viral replication with a dual mechanism of action: potent inhibition of the LEDGF/p75-IN protein-protein interaction and allosteric inhibition of the catalytic function. Furthermore they inhibit both early and late steps of the replication cycle which increases their potential for further clinical development. In this review we will highlight the research validating the LEDGF/p75-IN interaction as a target for anti-HIV drug discovery and the recent advances in the design and development of LEDGINs.
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Affiliation(s)
- Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Belgium.
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175
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Gérard A, Soler N, Ségéral E, Belshan M, Emiliani S. Identification of low molecular weight nuclear complexes containing integrase during the early stages of HIV-1 infection. Retrovirology 2013; 10:13. [PMID: 23369367 PMCID: PMC3571920 DOI: 10.1186/1742-4690-10-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 01/03/2013] [Indexed: 12/18/2022] Open
Abstract
Background HIV-1 replication requires integration of its reverse transcribed viral cDNA into a host cell chromosome. The DNA cutting and joining reactions associated to this key step are catalyzed by the viral protein integrase (IN). In infected cells, IN binds the viral cDNA, together with viral and cellular proteins, to form large nucleoprotein complexes. However, the dynamics of IN complexes formation is still poorly understood. Results Here, we characterized IN complexes during the early stages of T-lymphocyte infection. We found that following viral entry into the host cell, IN was rapidly targeted to proteasome-mediated degradation. Interactions between IN and cellular cofactors LEDGF/p75 and TNPO3 were detected as early as 6 h post-infection. Size exclusion chromatography of infected cell extracts revealed distinct IN complexes in vivo. While at 2 h post-infection the majority of IN eluted within a high molecular weight complex competent for integration (IN complex I), IN was also detected in a low molecular weight complex devoid of full-length viral cDNA (IN complex II, ~440 KDa). At 6 h post-infection the relative proportion of IN complex II increased. Inhibition of reverse transcription or integration did not alter the elution profile of IN complex II in infected cells. However, in cells depleted for LEDGF/p75 IN complex II shifted to a lower molecular weight complex (IN complex III, ~150 KDa) containing multimers of IN. Notably, cell fractionation experiments indicated that both IN complex II and III were exclusively nuclear. Finally, IN complex II was not detected in cells infected with a virus harboring a mutated IN defective for LEDGF/p75 interaction and tetramerization. Conclusions Our findings indicate that, shortly after viral entry, a significant portion of DNA–free IN that is distinct from active pre-integration complexes accumulates in the nucleus.
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176
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Gabizon R, Faust O, Benyamini H, Nir S, Loyter A, Friedler A. Structure–activity relationship studies using peptide arrays: the example of HIV-1 Rev–integrase interaction. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20225e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used peptide arrays to perform structure–activity relationship studies on anti-HIV peptides derived from HIV-1 integrase.
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Affiliation(s)
- Ronen Gabizon
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Ofrah Faust
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Hadar Benyamini
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Sivan Nir
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Abraham Loyter
- Department of Biological Chemistry
- The Alexander Silberman Institute of Life Sciences
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
| | - Assaf Friedler
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
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177
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Métifiot M, Marchand C, Pommier Y. HIV integrase inhibitors: 20-year landmark and challenges. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 67:75-105. [PMID: 23885999 DOI: 10.1016/b978-0-12-405880-4.00003-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the discovery of HIV as the cause for AIDS 30 years ago, major progress has been made, including the discovery of drugs that now control the disease. Here, we review the integrase (IN) inhibitors from the discovery of the first compounds 20 years ago to the approval of two highly effective IN strand transfer inhibitors (INSTIs), raltegravir (Isentress) and elvitegravir (Stribild), and the promising clinical activity of dolutegravir. After summarizing the molecular mechanism of action of the INSTIs as interfacial inhibitors, we discuss the remaining challenges. Those include: overcoming resistance to clinical INSTIs, long-term safety of INSTIs, cost of therapy, place of the INSTIs in prophylactic treatments, and the development of new classes of inhibitors (the LEDGINs) targeting IN outside its catalytic site. We also discuss the role of chromatin and host DNA repair factor for the completion of integration.
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Affiliation(s)
- Mathieu Métifiot
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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178
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Huang HJ, Jian YR, Chen CYC. Traditional Chinese medicine application in HIV: an in silico study. J Biomol Struct Dyn 2012; 32:1-12. [PMID: 23252879 DOI: 10.1080/07391102.2012.745168] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Viral infection by human immunodeficiency virus (HIV) requires integration of viral DNA with host DNA which involves the binding of HIV integrase (IN) with its co-factor lens epithelium-derived growth factor (LEDGF/p75). Since disrupted binding of IN with LEDGF/p75 inhibits proliferation of HIV, inhibition or denaturation of IN is a possible method for inhibiting HIV replication. D77 is a known drug with demonstrated inhibition against HIV by binding to IN. Herein, we utilized D77 as a control to screen for traditional Chinese medicine (TCM) compounds that exhibit similar atomic-level characteristics. 9-Hydroxy-(10E)-octadecenoic acid and Beauveriolide I were found to have higher Dock Scores to IN than D77 through virtual screening. Multiple linear regression (R2 = 0.9790) and support vector machine (R2 = 0.9114) models consistently predicted potential bioactivity of the TCM candidates against IN. The 40 ns molecular dynamics simulation showed that the TCM compounds fulfilled the drug-like criteria of forming stable complexes with IN. Atomic-level investigations revealed that 9-hydroxy-(10E)-octadecenoic acid bound to an important residue A:Lys173, and Beauveriolide I formed stable interactions with the core LEDGF binding site and with Asn256 of the IN binding site on LEDGF. The TCM candidates also initiated loss of α-helices that could affect the functionality of IN. Taken together, the ability of 9-hydroxy-(10E)-octadecenoic acid and Beauveriolide I to (1) form stable interactions affecting IN-LEDGF binding and (2) have predicted bioactivity against IN suggests that the TCM candidates might be potential starting structures for developing compounds that may disrupt IN-LEDGF binding. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:40.
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Affiliation(s)
- Hung-Jin Huang
- a Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources , China Medical University , Taichung , 40402 , Taiwan
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179
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Hu G, Li X, Li Y, Sun X, Liu G, Li W, Huang J, Shen X, Tang Y. Inhibitors of HIV-1 Integrase-Human LEDGF/p75 Interaction Identified from Natural Products via Virtual Screening. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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180
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De Luca L, Morreale F, Chimirri A. Insight into the Fundamental Interactions between LEDGF Binding Site Inhibitors and Integrase Combining Docking and Molecular Dynamics Simulations. J Chem Inf Model 2012. [DOI: 10.1021/ci300361e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura De Luca
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Francesca Morreale
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
| | - Alba Chimirri
- Dipartimento
di Scienze del Farmaco e Prodotti per
la Salute, Università di Messina, Viale Annunziata, I-98168
Messina, Italy
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181
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Wielens J, Headey SJ, Rhodes DI, Mulder RJ, Dolezal O, Deadman JJ, Newman J, Chalmers DK, Parker MW, Peat TS, Scanlon MJ. Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? ACTA ACUST UNITED AC 2012; 18:147-59. [PMID: 23139382 DOI: 10.1177/1087057112465979] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment screening is becoming widely accepted as a technique to identify hit compounds for the development of novel lead compounds. In neighboring laboratories, we have recently, and independently, performed a fragment screening campaign on the HIV-1 integrase core domain (IN) using similar commercially purchased fragment libraries. The two campaigns used different screening methods for the preliminary identification of fragment hits; one used saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR), and the other used surface plasmon resonance (SPR) spectroscopy. Both initial screens were followed by X-ray crystallography. Using the STD-NMR/X-ray approach, 15 IN/fragment complexes were identified, whereas the SPR/X-ray approach found 6 complexes. In this article, we compare the approaches that were taken by each group and the results obtained, and we look at what factors could potentially influence the final results. We find that despite using different approaches with little overlap of initial hits, both approaches identified binding sites on IN that provided a basis for fragment-based lead discovery and further lead development. Comparison of hits identified in the two studies highlights a key role for both the conditions under which fragment binding is measured and the criteria selected to classify hits.
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182
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Hu G, Li X, Zhang X, Li Y, Ma L, Yang LM, Liu G, Li W, Huang J, Shen X, Hu L, Zheng YT, Tang Y. Discovery of inhibitors to block interactions of HIV-1 integrase with human LEDGF/p75 via structure-based virtual screening and bioassays. J Med Chem 2012; 55:10108-17. [PMID: 23046280 DOI: 10.1021/jm301226a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study aims to identify inhibitors that bind at the interface of HIV-1 integrase (IN) and human LEDGF/p75, which represents a novel target for anti-HIV therapy. To date, only a few such inhibitors have been reported. Here structure-based virtual screening was performed to search for the inhibitors from an in-house library of natural products and their derivatives. Among the 38 compounds selected by our strategy, 18 hits were discovered. The two most potent inhibitors showed IC(50) values at 0.32 and 0.26 μM, respectively. Three compounds were subsequently selected for anti-HIV assays, among which (E)-3-(2-chlorophenyl)-1-(2,4-dihydroxyphenyl)prop-2-en-1-one (NPD170) showed the highest antiviral activity (EC(50) = 1.81 μM). The antiviral mechanism of these compounds was further explored, and the results validated that the compounds interrupted the binding of transfected IN to endogenous LEDGF/p75. These findings could be helpful for anti-HIV drug discovery.
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Affiliation(s)
- Guoping Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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183
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Krishnan L, Engelman A. Retroviral integrase proteins and HIV-1 DNA integration. J Biol Chem 2012; 287:40858-66. [PMID: 23043109 DOI: 10.1074/jbc.r112.397760] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Retroviral integrases catalyze two reactions, 3'-processing of viral DNA ends, followed by integration of the processed ends into chromosomal DNA. X-ray crystal structures of integrase-DNA complexes from prototype foamy virus, a member of the Spumavirus genus of Retroviridae, have revealed the structural basis of integration and how clinically relevant integrase strand transfer inhibitors work. Underscoring the translational potential of targeting virus-host interactions, small molecules that bind at the host factor lens epithelium-derived growth factor/p75-binding site on HIV-1 integrase promote dimerization and inhibit integrase-viral DNA assembly and catalysis. Here, we review recent advances in our knowledge of HIV-1 DNA integration, as well as future research directions.
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Affiliation(s)
- Lavanya Krishnan
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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184
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Wang H, Jurado KA, Wu X, Shun MC, Li X, Ferris AL, Smith SJ, Patel PA, Fuchs JR, Cherepanov P, Kvaratskhelia M, Hughes SH, Engelman A. HRP2 determines the efficiency and specificity of HIV-1 integration in LEDGF/p75 knockout cells but does not contribute to the antiviral activity of a potent LEDGF/p75-binding site integrase inhibitor. Nucleic Acids Res 2012; 40:11518-30. [PMID: 23042676 PMCID: PMC3526291 DOI: 10.1093/nar/gks913] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The binding of integrase (IN) to lens epithelium-derived growth factor (LEDGF)/p75 in large part determines the efficiency and specificity of HIV-1 integration. However, a significant residual preference for integration into active genes persists in Psip1 (the gene that encodes for LEDGF/p75) knockout (KO) cells. One other cellular protein, HRP2, harbors both the PWWP and IN-binding domains that are important for LEDGF/p75 co-factor function. To assess the role of HRP2 in HIV-1 integration, cells generated from Hdgfrp2 (the gene that encodes for HRP2) and Psip1/Hdgfrp2 KO mice were infected alongside matched control cells. HRP2 depleted cells supported normal infection, while disruption of Hdgfrp2 in Psip1 KO cells yielded additional defects in the efficiency and specificity of integration. These deficits were largely restored by ectopic expression of either LEDGF/p75 or HRP2. The double-KO cells nevertheless supported residual integration into genes, indicating that IN and/or other host factors contribute to integration specificity in the absence of LEDGF/p75 and HRP2. Psip1 KO significantly increased the potency of an allosteric inhibitor that binds the LEDGF/p75 binding site on IN, a result that was not significantly altered by Hdgfrp2 disruption. These findings help to rule out the host factor-IN interactions as the primary antiviral targets of LEDGF/p75-binding site IN inhibitors.
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Affiliation(s)
- Hao Wang
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
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185
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Abstract
Integrase (IN) is a clinically validated target for the treatment of human immunodeficiency virus infections and raltegravir exhibits remarkable clinical activity. The next most advanced IN inhibitor is elvitegravir. However, mutant viruses lead to treatment failure and mutations within the IN coding sequence appear to confer cross-resistance. The characterization of those mutations is critical for the development of second generation IN inhibitors to overcome resistance. This review focuses on IN resistance based on structural and biochemical data, and on the role of the IN flexible loop i.e., between residues G140-G149 in drug action and resistance.
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Affiliation(s)
| | | | | | - Yves Pommier
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-301-496-5944; Fax: +1-301-402-0752
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186
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Cellular cofactors of lentiviral integrase: from target validation to drug discovery. Mol Biol Int 2012; 2012:863405. [PMID: 22928108 PMCID: PMC3420096 DOI: 10.1155/2012/863405] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/03/2012] [Accepted: 06/27/2012] [Indexed: 01/30/2023] Open
Abstract
To accomplish their life cycle, lentiviruses make use of host proteins, the so-called cellular cofactors. Interactions between host cell and viral proteins during early stages of lentiviral infection provide attractive new antiviral targets. The insertion of lentiviral cDNA in a host cell chromosome is a step of no return in the replication cycle, after which the host cell becomes a permanent carrier of the viral genome and a producer of lentiviral progeny. Integration is carried out by integrase (IN), an enzyme playing also an important role during nuclear import. Plenty of cellular cofactors of HIV-1 IN have been proposed. To date, the lens epithelium-derived growth factor (LEDGF/p75) is the best studied cofactor of HIV-1 IN. Moreover, small molecules that block the LEDGF/p75-IN interaction have recently been developed for the treatment of HIV infection. The nuclear import factor transportin-SR2 (TRN-SR2) has been proposed as another interactor of HIV IN-mediating nuclear import of the virus. Using both proteins as examples, we will describe approaches to be taken to identify and validate novel cofactors as new antiviral targets. Finally, we will highlight recent advances in the design and the development of small-molecule inhibitors binding to the LEDGF/p75-binding pocket in IN (LEDGINs).
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187
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Christ F, Shaw S, Demeulemeester J, Desimmie BA, Marchand A, Butler S, Smets W, Chaltin P, Westby M, Debyser Z, Pickford C. Small-molecule inhibitors of the LEDGF/p75 binding site of integrase block HIV replication and modulate integrase multimerization. Antimicrob Agents Chemother 2012; 56:4365-74. [PMID: 22664975 PMCID: PMC3421592 DOI: 10.1128/aac.00717-12] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/30/2012] [Indexed: 02/02/2023] Open
Abstract
Targeting the HIV integrase (HIV IN) is a clinically validated approach for designing novel anti-HIV therapies. We have previously described the discovery of a novel class of integration inhibitors, 2-(quinolin-3-yl)acetic acid derivatives, blocking HIV replication at a low micromolar concentration through binding in the LEDGF/p75 binding pocket of HIV integrase, hence referred to as LEDGINs. Here we report the detailed characterization of their mode of action. The design of novel and more potent analogues with nanomolar activity enabled full virological evaluation and a profound mechanistic study. As allosteric inhibitors, LEDGINs bind to the LEDGF/p75 binding pocket in integrase, thereby blocking the interaction with LEDGF/p75 and interfering indirectly with the catalytic activity of integrase. Detailed mechanism-of-action studies reveal that the allosteric mode of inhibition is likely caused by an effect on HIV-1 integrase oligomerization. The multimodal inhibition by LEDGINs results in a block in HIV integration and in a replication deficiency of progeny virus. The allosteric nature of LEDGINs leads to synergy in combination with the clinically approved active site HIV IN strand transfer inhibitor (INSTI) raltegravir, and cross-resistance profiling proves the distinct mode of action of LEDGINs and INSTIs. The allosteric nature of inhibition and compatibility with INSTIs underline an interest in further (clinical) development of LEDGINs.
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Affiliation(s)
- Frauke Christ
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
| | | | - Jonas Demeulemeester
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
| | - Belete A. Desimmie
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
| | | | | | - Wim Smets
- CISTIM, CISTIM Leuven Vzw, Leuven, Belgium
| | - Patrick Chaltin
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
- CISTIM, CISTIM Leuven Vzw, Leuven, Belgium
| | | | - Zeger Debyser
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
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188
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Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev Mol Med 2012; 14:e16. [PMID: 22831787 DOI: 10.1017/erm.2012.10] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions (PPIs) control the assembly of multi-protein complexes and, thus, these contacts have enormous potential as drug targets. However, the field has produced a mix of both exciting success stories and frustrating challenges. Here, we review known examples and explore how the physical features of a PPI, such as its affinity, hotspots, off-rates, buried surface area and topology, might influence the chances of success in finding inhibitors. This analysis suggests that concise, tight binding PPIs are most amenable to inhibition. However, it is also clear that emerging technical methods are expanding the repertoire of 'druggable' protein contacts and increasing the odds against difficult targets. In particular, natural product-like compound libraries, high throughput screens specifically designed for PPIs and approaches that favour discovery of allosteric inhibitors appear to be attractive routes. The first group of PPI inhibitors has entered clinical trials, further motivating the need to understand the challenges and opportunities in pursuing these types of targets.
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189
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Phage display-directed discovery of LEDGF/p75 binding cyclic peptide inhibitors of HIV replication. Mol Ther 2012; 20:2064-75. [PMID: 22828501 DOI: 10.1038/mt.2012.132] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The interaction between the human immunodeficiency virus (HIV) integrase (IN) and its cellular cofactor lens epithelium-derived growth factor (LEDGF/p75) is crucial for HIV replication. While recently discovered LEDGINs inhibit HIV-1 replication by occupying the LEDGF/p75 pocket in IN, it remained to be demonstrated whether LEDGF/p75 by itself can be targeted. By phage display we identified cyclic peptides (CPs) as the first LEDGF/p75 ligands that inhibit the LEDGF/p75-IN interaction. The CPs inhibit HIV replication in different cell lines without overt toxicity. In accord with the role of LEDGF/p75 in HIV integration and its inhibition by LEDGINs, CP64, and CP65 block HIV replication primarily by inhibiting the integration step. The CPs retained activity against HIV strains resistant to raltegravir or LEDGINs. Saturation transfer difference (STD) NMR showed residues in CP64 that strongly interact with LEDGF/p75 but not with HIV IN. Mutational analysis identified tryptophan as an important residue responsible for the activity of the peptides. Serial passaging of virus in the presence of CPs did not yield resistant strains. Our work provides proof-of-concept for direct targeting of LEDGF/p75 as novel therapeutic strategy and the CPs thereby serve as scaffold for future development of new HIV therapeutics.
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190
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Maes M, Loyter A, Friedler A. Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions. FEBS J 2012; 279:2795-809. [PMID: 22742518 DOI: 10.1111/j.1742-4658.2012.08680.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 integrase (IN) is one of the key enzymes in the viral replication cycle. It mediates the integration of viral cDNA into the host cell genome. IN activity requires interactions with several viral and cellular proteins, as well as IN oligomerization. Inhibition of IN is an important target for the development of anti-HIV therapies, but there is currently only one anti-HIV drug used in the clinic that targets IN. Several other small-molecule anti-IN drug leads are either undergoing clinical trials or in earlier stages of development. These molecules specifically inhibit one of the IN-mediated reactions necessary for successful integration. However, small-molecule inhibitors of protein-protein interactions are difficult to develop. In this review, we focus on peptides that inhibit IN. Peptides have advantages over small-molecule inhibitors of protein-protein interactions: they can mimic the structures of the binding domains within proteins, and are large enough to competitively inhibit protein-protein interactions. The development of peptides that bind IN and inhibit its protein-protein interactions will increase our understanding of the IN mode of action, and lead to the development of new drug leads, such as small molecules derived from these peptides, for better anti-HIV therapy.
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Affiliation(s)
- Michal Maes
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
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191
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Peat TS, Rhodes DI, Vandegraaff N, Le G, Smith JA, Clark LJ, Jones ED, Coates JAV, Thienthong N, Newman J, Dolezal O, Mulder R, Ryan JH, Savage GP, Francis CL, Deadman JJ. Small molecule inhibitors of the LEDGF site of human immunodeficiency virus integrase identified by fragment screening and structure based design. PLoS One 2012; 7:e40147. [PMID: 22808106 PMCID: PMC3393750 DOI: 10.1371/journal.pone.0040147] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/01/2012] [Indexed: 11/24/2022] Open
Abstract
A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.
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Affiliation(s)
- Thomas S Peat
- CSIRO Materials, Science and Engineering, Parkville, Victoria, Australia.
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192
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Abstract
Retroviruses are distinguished from other viruses by two characteristic steps in the viral replication cycle. The first is reverse transcription, which results in the production of a double-stranded DNA copy of the viral RNA genome, and the second is integration, which results in covalent attachment of the DNA copy to host cell DNA. The initial catalytic steps of the integration reaction are performed by the virus-encoded integrase (IN) protein. The chemistry of the IN-mediated DNA breaking and joining steps is well worked out, and structures of IN-DNA complexes have now clarified how the overall complex assembles. Methods developed during these studies were adapted for identification of IN inhibitors, which received FDA approval for use in patients in 2007. At the chromosomal level, HIV integration is strongly favored in active transcription units, which may promote efficient viral gene expression after integration. HIV IN binds to the cellular factor LEDGF/p75, which promotes efficient infection and tethers IN to favored target sites. The HIV integration machinery must also interact with many additional host factors during infection, including nuclear trafficking and pore proteins during nuclear entry, histones during initial target capture, and DNA repair proteins during completion of the DNA joining steps. Models for some of the molecular mechanisms involved have been proposed, but important details remain to be clarified.
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Affiliation(s)
- Robert Craigie
- Molecular Virology Section, NIDDK, National Institutes of Health, Bethesda, Maryland, USA.
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193
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Abstract
Integration of viral DNA into cellular DNA is an essential step in the replication cycle of HIV and other retroviruses. The first antiviral drugs that target integrase, the viral enzyme that catalyzes DNA integration, have recently been approved and more are in the pipeline. These drugs bind to an intermediate in DNA integration called the intasome, in which a pair of viral DNA ends are synapsed by a tetramer of integrase, rather than free integrase enzyme. We discuss the biochemical mechanism of integration, which is now quite well understood, and recent progress towards obtaining atomic-resolution structures of HIV intasomes in complex with inhibitors. Such structures are ultimately required to understand the detailed mechanism of inhibition and the mechanisms by which mutations in integrase confer resistance. The path from early biochemical studies to therapeutic inhibitors of integrase highlights the value of basic science in fighting human diseases.
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Affiliation(s)
- Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Bethesda, MD 20892-0560, USA, Tel.: +1 301 496 4081, ,
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194
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Identification of old drugs as potential inhibitors of HIV-1 integrase – human LEDGF/p75 interaction via molecular docking. J Mol Model 2012; 18:4995-5003. [DOI: 10.1007/s00894-012-1494-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 06/05/2012] [Indexed: 01/03/2023]
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195
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Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet 2012; 8:e1002717. [PMID: 22615581 PMCID: PMC3355077 DOI: 10.1371/journal.pgen.1002717] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 04/02/2012] [Indexed: 12/25/2022] Open
Abstract
Increasing evidence suggests that chromatin modifications have important roles in modulating constitutive or alternative splicing. Here we demonstrate that the PWWP domain of the chromatin-associated protein Psip1/Ledgf can specifically recognize tri-methylated H3K36 and that, like this histone modification, the Psip1 short (p52) isoform is enriched at active genes. We show that the p52, but not the long (p75), isoform of Psip1 co-localizes and interacts with Srsf1 and other proteins involved in mRNA processing. The level of H3K36me3 associated Srsf1 is reduced in Psip1 mutant cells and alternative splicing of specific genes is affected. Moreover, we show altered Srsf1 distribution around the alternatively spliced exons of these genes in Psip1 null cells. We propose that Psip1/p52, through its binding to both chromatin and splicing factors, might act to modulate splicing.
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Affiliation(s)
- Madapura M. Pradeepa
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Heidi G. Sutherland
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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196
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Tsiang M, Jones GS, Niedziela-Majka A, Kan E, Lansdon EB, Huang W, Hung M, Samuel D, Novikov N, Xu Y, Mitchell M, Guo H, Babaoglu K, Liu X, Geleziunas R, Sakowicz R. New class of HIV-1 integrase (IN) inhibitors with a dual mode of action. J Biol Chem 2012; 287:21189-203. [PMID: 22535962 DOI: 10.1074/jbc.m112.347534] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
tert-Butoxy-(4-phenyl-quinolin-3-yl)-acetic acids (tBPQA) are a new class of HIV-1 integrase (IN) inhibitors that are structurally distinct from IN strand transfer inhibitors but analogous to LEDGINs. LEDGINs are a class of potent antiviral compounds that interacts with the lens epithelium-derived growth factor (LEDGF) binding pocket on IN and were identified through competition binding against LEDGF. LEDGF tethers IN to the host chromatin and enables targeted integration of viral DNA. The prevailing understanding of the antiviral mechanism of LEDGINs is that they inhibit LEDGF binding to IN, which prevents targeted integration of HIV-1. We showed that in addition to the properties already known for LEDGINs, the binding of tBPQAs to the IN dimer interface inhibits IN enzymatic activity in a LEDGF-independent manner. Using the analysis of two long terminal repeat junctions in HIV-infected cells, we showed that the inhibition by tBPQAs occurs at or prior to the viral DNA 3'-processing step. Biochemical studies revealed that this inhibition operates by compound-induced conformational changes in the IN dimer that prevent proper assembly of IN onto viral DNA. For the first time, tBPQAs were demonstrated to be allosteric inhibitors of HIV-1 IN displaying a dual mode of action: inhibition of IN-viral DNA assembly and inhibition of IN-LEDGF interaction.
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Affiliation(s)
- Manuel Tsiang
- Gilead Sciences, Inc, Foster City, California 94404, USA.
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197
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Qi X, Sandmeyer S. In vitro targeting of strand transfer by the Ty3 retroelement integrase. J Biol Chem 2012; 287:18589-95. [PMID: 22493285 DOI: 10.1074/jbc.m111.326025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The Saccharomyces cerevisiae long terminal repeat retrotransposon Ty3 integrates within one or two nucleotides of the transcription initiation sites of genes transcribed by RNA polymerase III. In this study the minimal components required to re-constitute position-specific strand transfer by Ty3 integrase are defined. Ty3 integrase targeted by a synthetic fusion of RNA polymerase III transcription factor IIIB subunits, Brf1 and TBP, mediated position-specific strand transfer of duplex oligonucleotides representing the ends of the Ty3 cDNA. These results further delimit the TFIIIB domains targeted by the Ty3 element and show that IN is the Ty3 component sufficient in vitro to target integration. These results underscore the commonality of protein interactions that mediate transcription and retrotransposon targeting. Surprisingly, in the presence of MnCl(2), strand transfer was TFIIIB-independent and targeted sequences resembling the Ty3 terminal inverted repeat.
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Affiliation(s)
- Xiaojie Qi
- Department of Biological Chemistry, University of California-Irvine, Irvine, California 92697, USA
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198
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Hayouka Z, Levin A, Hurevich M, Shalev DE, Loyter A, Gilon C, Friedler A. A comparative study of backbone versus side chain peptide cyclization: application for HIV-1 integrase inhibitors. Bioorg Med Chem 2012; 20:3317-22. [PMID: 22507205 DOI: 10.1016/j.bmc.2012.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/18/2012] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
Abstract
Peptide cyclization is an important tool for overcoming the limitations of linear peptides as drugs. Backbone cyclization (BC) has advantages over side chain (SC) cyclization because it combines N-alkylation for extra peptide stability. However, the appropriate building blocks for BC are not yet commercially available. This problem can be overcome by preparing SC cyclic peptide analogs of the most active BC peptide using commercially available building blocks. We have recently developed BC peptides that inhibit the HIV-1 integrase enzyme (IN) activity and HIV-1 replication in infected cells. Here we used this system as a model for systematically comparing the BC and SC cyclization modes using biophysical, biochemical and structural methods. The most potent SC cyclic peptide was active almost as the BC peptide and inhibited IN activity in vitro and blocked IN activity in cells even after 6 days. We conclude that both cyclization types have their respective advantages: The BC peptide is more active and stable, probably due to the N-alkylation, while SC cyclic peptides are easier to synthesize. Due to the high costs and efforts involved in preparing BC peptides, SC may be a more approachable method in many cases. We suggest that both methods are interchangeable.
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Affiliation(s)
- Zvi Hayouka
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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199
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Kessl JJ, Jena N, Koh Y, Taskent-Sezgin H, Slaughter A, Feng L, de Silva S, Wu L, Le Grice SFJ, Engelman A, Fuchs JR, Kvaratskhelia M. Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors. J Biol Chem 2012; 287:16801-11. [PMID: 22437836 DOI: 10.1074/jbc.m112.354373] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The multifunctional HIV-1 enzyme integrase interacts with viral DNA and its key cellular cofactor LEDGF to effectively integrate the reverse transcript into a host cell chromosome. These interactions are crucial for HIV-1 replication and present attractive targets for antiviral therapy. Recently, 2-(quinolin-3-yl) acetic acid derivatives were reported to selectively inhibit the integrase-LEDGF interaction in vitro and impair HIV-1 replication in infected cells. Here, we show that this class of compounds impairs both integrase-LEDGF binding and LEDGF-independent integrase catalytic activities with similar IC(50) values, defining them as bona fide allosteric inhibitors of integrase function. Furthermore, we show that 2-(quinolin-3-yl) acetic acid derivatives block the formation of the stable synaptic complex between integrase and viral DNA by allosterically stabilizing an inactive multimeric form of integrase. In addition, these compounds inhibit LEDGF binding to the stable synaptic complex. This multimode mechanism of action concordantly results in cooperative inhibition of the concerted integration of viral DNA ends in vitro and HIV-1 replication in cell culture. Our findings, coupled with the fact that high cooperativity of antiviral inhibitors correlates with their increased instantaneous inhibitory potential, an important clinical parameter, argue strongly that improved 2-(quinolin-3-yl) acetic acid derivatives could exhibit desirable clinical properties.
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Affiliation(s)
- Jacques J Kessl
- Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
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200
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Abstract
Three-dimensional molecular structures can provide detailed information on biological mechanisms and, for cases in which the molecular function affects human health, can significantly aid in the development of therapeutic interventions. For almost 25 years, key components of the lentivirus HIV-1, including the envelope glycoproteins, the capsid and the replication enzymes reverse transcriptase, integrase and protease, have been scrutinized to near atomic-scale resolution. Moreover, structural analyses of the interactions between viral and host cell components have yielded key insights into the mechanisms of viral entry, chromosomal integration, transcription and egress from cells. Here, we review recent advances in HIV-1 structural biology, focusing on the molecular mechanisms of viral replication and on the development of new therapeutics.
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