1
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Eilers G, Gupta K, Allen A, Montermoso S, Murali H, Sharp R, Hwang Y, Bushman FD, Van Duyne G. Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization. PLoS Pathog 2023; 19:e1011097. [PMID: 36867659 PMCID: PMC10016701 DOI: 10.1371/journal.ppat.1011097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/15/2023] [Accepted: 01/03/2023] [Indexed: 03/04/2023] Open
Abstract
HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.
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Affiliation(s)
- Grant Eilers
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Audrey Allen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Saira Montermoso
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hemma Murali
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert Sharp
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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2
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Rocha S, Hendrix J, Borrenberghs D, Debyser Z, Hofkens J. Imaging the Replication of Single Viruses: Lessons Learned from HIV and Future Challenges To Overcome. ACS NANO 2020; 14:10775-10783. [PMID: 32820634 DOI: 10.1021/acsnano.0c06369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The molecular composition of viral particles indicates that a single virion is capable of initiating an infection. However, the majority of viruses that come into contact with cells fails to infect them. Understanding what makes one viral particle more successful than others requires visualizing the infection process directly in living cells, one virion at a time. In this Perspective, we explain how single-virus imaging using fluorescence microscopy can provide answers to unsolved questions in virology. We discuss fluorescent labeling of virus particles, resolution at the subviral and molecular levels, tracking in living cells, and imaging of interactions between viral and host proteins. We end this Perspective with a set of remaining questions in understanding the life cycle of retroviruses and how imaging a single virus can help researchers address these questions. Although we use examples from the HIV field, these methods are of value for the study of other viruses as well.
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Affiliation(s)
- Susana Rocha
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, B-3001 Heverlee, Flanders, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, B-3001 Heverlee, Flanders, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, B-3590 Diepenbeek, Flanders, Belgium
| | - Doortje Borrenberghs
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, B-3001 Heverlee, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3001 Heverlee, Flanders, Belgium
| | - Johan Hofkens
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, B-3001 Heverlee, Flanders, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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3
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A Conformational Escape Reaction of HIV-1 against an Allosteric Integrase Inhibitor. J Virol 2020; 94:JVI.00486-20. [PMID: 32611758 DOI: 10.1128/jvi.00486-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/23/2020] [Indexed: 01/01/2023] Open
Abstract
HIV-1 often acquires drug-resistant mutations in spite of the benefits of antiretroviral therapy (ART). HIV-1 integrase (IN) is essential for the concerted integration of HIV-1 DNA into the host genome. IN further contributes to HIV-1 RNA binding, which is required for HIV-1 maturation. Non-catalytic-site integrase inhibitors (NCINIs) have been developed as allosteric IN inhibitors, which perform anti-HIV-1 activity by a multimodal mode of action such as inhibition of the IN-lens epithelium-derived growth factor (LEDGF)/p75 interaction in the early stage and disruption of functional IN multimerization in the late stage of HIV-1 replication. Here, we show that IN undergoes an adaptable conformational change to escape from NCINIs. We observed that NCINI-resistant HIV-1 variants have accumulated 4 amino acid mutations by passage 26 (P26) in the IN-encoding region. We employed high-performance liquid chromatography (HPLC), thermal stability assays, and X-ray crystallographic analysis to show that some amino acid mutations affect the stability and/or dimerization interface of the IN catalytic core domains (CCDs), potentially resulting in the severely decreased multimerization of full-length IN proteins (IN undermultimerization). This undermultimerized IN via NCINI-related mutations was stabilized by HIV-1 RNA and restored to the same level as that of wild-type HIV-1 in viral particles. Recombinant HIV-1 clones with IN undermultimerization propagated similarly to wild-type HIV-1. Our study revealed that HIV-1 can eventually counteract NCINI-induced IN overmultimerization by IN undermultimerization as one of the escape mechanisms. Our findings provide information on the understanding of IN multimerization with or without HIV-1 RNA and may influence the development of anti-HIV-1 strategies.IMPORTANCE Understanding the mechanism of HIV-1 resistance to anti-HIV-1 drugs could lead to the development of novel drugs with increased efficiency, resulting in more effective ART. ART composed of more potent and long-acting anti-HIV-1 drugs can greatly improve drug adherence and also provide HIV-1 prevention such as preexposure prophylaxis. NCINIs with a multimodal mode of action exert potent anti-HIV-1 effects through IN overmultimerization during HIV-1 maturation. However, HIV-1 can acquire some mutations that cause IN undermultimerization to alleviate NCINI-induced IN overmultimerization. This undermultimerized IN was efficiently stabilized by HIV-1 RNA and restored to the same level as that of wild-type HIV-1. Our findings revealed that HIV-1 eventually acquires such a conformational escape reaction to overcome the unique NCINI actions. The investigation into drug-resistant mutations associated with HIV-1 protein multimerization may facilitate the elucidation of its molecular mechanism and functional multimerization, allowing us to develop more potent anti-HIV-1 drugs and unique treatment strategies.
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Desimmie BA, Weydert C, Schrijvers R, Vets S, Demeulemeester J, Proost P, Paron I, De Rijck J, Mast J, Bannert N, Gijsbers R, Christ F, Debyser Z. Correction to: HIV-1 IN/Pol recruits LEDGF/p75 into viral particles. Retrovirology 2020; 17:23. [PMID: 32727480 PMCID: PMC7388445 DOI: 10.1186/s12977-020-00531-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Belete Ayele Desimmie
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium.,Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Caroline Weydert
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Rik Schrijvers
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Sofie Vets
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Jonas Demeulemeester
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Paul Proost
- KU Leuven, Laboratory of Molecular Immunology, Rega Institute, Louvain, Flanders, Belgium
| | - Igor Paron
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Jan De Rijck
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Jan Mast
- Veterinary and Agrochemical Research Centre CODA-CERVA, Brussels, Belgium
| | - Norbert Bannert
- Robert Koch Institute, Centre for HIV and Retrovirology, Berlin, Germany
| | - Rik Gijsbers
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Frauke Christ
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium
| | - Zeger Debyser
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Louvain, Flanders, Belgium.
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Ortiz-Hernandez GL, Sanchez-Hernandez ES, Casiano CA. Twenty years of research on the DFS70/LEDGF autoantibody-autoantigen system: many lessons learned but still many questions. AUTOIMMUNITY HIGHLIGHTS 2020; 11:3. [PMID: 32127038 PMCID: PMC7065333 DOI: 10.1186/s13317-020-0126-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/14/2020] [Indexed: 12/24/2022]
Abstract
The discovery and initial characterization 20 years ago of antinuclear autoantibodies (ANAs) presenting a dense fine speckled (DFS) nuclear pattern with strong staining of mitotic chromosomes, detected by indirect immunofluorescence assay in HEp-2 cells (HEp-2 IIFA test), has transformed our view on ANAs. Traditionally, ANAs have been considered as reporters of abnormal immunological events associated with the onset and progression of systemic autoimmune rheumatic diseases (SARD), also called ANA-associated rheumatic diseases (AARD), as well as clinical biomarkers for the differential diagnosis of these diseases. However, based on our current knowledge, it is not apparent that autoantibodies presenting the DFS IIF pattern fall into these categories. These antibodies invariably target a chromatin-associated protein designated as dense fine speckled protein of 70 kD (DFS70), also known as lens epithelium-derived growth factor protein of 75 kD (LEDGF/p75) and PC4 and SFRS1 Interacting protein 1 (PSIP1). This multi-functional protein, hereafter referred to as DFS70/LEDGF, plays important roles in the formation of transcription complexes in active chromatin, transcriptional activation of specific genes, regulation of mRNA splicing, DNA repair, and cellular survival against stress. Due to its multiple functions, it has emerged as a key protein contributing to several human pathologies, including acquired immunodeficiency syndrome (AIDS), leukemia, cancer, ocular diseases, and Rett syndrome. Unlike other ANAs, "monospecific" anti-DFS70/LEDGF autoantibodies (only detectable ANA in serum) are not associated with SARD and have been detected in healthy individuals and some patients with non-SARD inflammatory conditions. These observations have led to the hypotheses that these antibodies could be considered as negative biomarkers of SARD and might even play a protective or beneficial role. In spite of 20 years of research on this autoantibody-autoantigen system, its biological and clinical significance still remains enigmatic. Here we review the current state of knowledge of this system, focusing on the lessons learned and posing emerging questions that await further scrutiny as we continue our quest to unravel its significance and potential clinical and therapeutic utility.
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Affiliation(s)
- Greisha L Ortiz-Hernandez
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA.,Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, USA
| | - Evelyn S Sanchez-Hernandez
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA.,Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, USA
| | - Carlos A Casiano
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA. .,Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, USA. .,Department of Medicine/Division of Rheumatology, Loma Linda University School of Medicine, Loma Linda, USA.
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6
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Sadowski I, Hashemi FB. Strategies to eradicate HIV from infected patients: elimination of latent provirus reservoirs. Cell Mol Life Sci 2019; 76:3583-3600. [PMID: 31129856 PMCID: PMC6697715 DOI: 10.1007/s00018-019-03156-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
Abstract
35 years since identification of HIV as the causative agent of AIDS, and 35 million deaths associated with this disease, significant effort is now directed towards the development of potential cures. Current anti-retroviral (ART) therapies for HIV/AIDS can suppress virus replication to undetectable levels, and infected individuals can live symptom free so long as treatment is maintained. However, removal of therapy allows rapid re-emergence of virus from a highly stable reservoir of latently infected cells that exist as a barrier to elimination of the infection with current ART. Prospects of a cure for HIV infection are significantly encouraged by two serendipitous cases where individuals have entered remission following stem cell transplantation from compatible HIV-resistant donors. However, development of a routine cure that could become available to millions of infected individuals will require a means of specifically purging cells harboring latent HIV, preventing replication of latent provirus, or destruction of provirus genomes by gene editing. Elimination of latently infected cells will require a means of exposing this population, which may involve identification of a natural specific biomarker or therapeutic intervention to force their exposure by reactivation of virus expression. Accordingly, the proposed "Shock and Kill" strategy involves treatment with latency-reversing agents (LRA) to induce HIV provirus expression thus exposing these cells to killing by cellular immunity or apoptosis. Current efforts to enable this strategy are directed at developing improved combinations of LRA to produce broad and robust induction of HIV provirus and enhancing the elimination of cells where replication has been reactivated by targeted immune modulation. Alternative strategies may involve preventing re-emergence virus from latently infected cells by "Lock and Block" intervention, where transcription of provirus is inhibited to prevent virus spread or disruption of the HIV provirus genome by genome editing.
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Affiliation(s)
- Ivan Sadowski
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
| | - Farhad B Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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7
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Mahler M, Andrade LE, Casiano CA, Malyavantham K, Fritzler MJ. Anti-DFS70 antibodies: an update on our current understanding and their clinical usefulness. Expert Rev Clin Immunol 2019; 15:241-250. [DOI: 10.1080/1744666x.2019.1562903] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Michael Mahler
- Research & Development, Inova Diagnostics, San Diego, CA, USA
| | - Luis E. Andrade
- Rheumatology Division, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Immunology Division, Fleury Laboratories, São Paulo, Brazil
| | - Carlos A. Casiano
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Department of Medicine, Division of Rheumatology, Loma Linda University School of Medicine, Loma Linda, CA, USA
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8
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Weydert C, van Heertum B, Dirix L, De Houwer S, De Wit F, Mast J, Husson SJ, Busschots K, König R, Gijsbers R, De Rijck J, Debyser Z. Y-box-binding protein 1 supports the early and late steps of HIV replication. PLoS One 2018; 13:e0200080. [PMID: 29995936 PMCID: PMC6040738 DOI: 10.1371/journal.pone.0200080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 06/19/2018] [Indexed: 12/31/2022] Open
Abstract
The human immunodeficiency virus (HIV) depends on cellular proteins, so-called cofactors, to complete its replication cycle. In search for new therapeutic targets we identified the DNA and RNA binding protein Y-box-binding Protein 1 (YB-1) as a cofactor supporting early and late steps of HIV replication. YB-1 depletion resulted in a 10-fold decrease in HIV-1 replication in different cell lines. Dissection of the replication defects revealed that knockdown of YB-1 is associated with a 2- to 5-fold decrease in virion production due to interference with the viral RNA metabolism. Using single-round virus infection experiments we demonstrated that early HIV-1 replication also depends on the cellular YB-1 levels. More precisely, using quantitative PCR and an in vivo nuclear import assay with fluorescently labeled viral particles, we showed that YB-1 knockdown leads to a block between reverse transcription and nuclear import of HIV-1. Interaction studies revealed that YB-1 associates with integrase, although a direct interaction with HIV integrase could not be unambiguously proven. In conclusion, our results indicate that YB-1 affects multiple stages of HIV replication. Future research on the interaction between YB-1 and the virus will reveal whether this protein qualifies as a new antiviral target.
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Affiliation(s)
- Caroline Weydert
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Bart van Heertum
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Lieve Dirix
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Belgium
| | - Stéphanie De Houwer
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Flore De Wit
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan Mast
- Veterinary and Agrochemical Research Centre, VAR-CODA-CERVA, Brussels, Belgium
| | - Steven J. Husson
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, 3000 Leuven, Belgium
- Systemic Physiological & Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, 2000 Antwerp, Belgium
| | - Katrien Busschots
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Rik Gijsbers
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan De Rijck
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- * E-mail:
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9
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Engelman AN, Singh PK. Cellular and molecular mechanisms of HIV-1 integration targeting. Cell Mol Life Sci 2018; 75:2491-2507. [PMID: 29417178 PMCID: PMC6004233 DOI: 10.1007/s00018-018-2772-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/21/2022]
Abstract
Integration is central to HIV-1 replication and helps mold the reservoir of cells that persists in AIDS patients. HIV-1 interacts with specific cellular factors to target integration to interior regions of transcriptionally active genes within gene-dense regions of chromatin. The viral capsid interacts with several proteins that are additionally implicated in virus nuclear import, including cleavage and polyadenylation specificity factor 6, to suppress integration into heterochromatin. The viral integrase protein interacts with transcriptional co-activator lens epithelium-derived growth factor p75 to principally position integration within gene bodies. The integrase additionally senses target DNA distortion and nucleotide sequence to help fine-tune the specific phosphodiester bonds that are cleaved at integration sites. Research into virus-host interactions that underlie HIV-1 integration targeting has aided the development of a novel class of integrase inhibitors and may help to improve the safety of viral-based gene therapy vectors.
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Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, A-111, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, A-111, 25 Shattuck Street, Boston, MA, 02115, USA
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10
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Patent Highlights October-November 2016. Pharm Pat Anal 2017; 6:53-60. [PMID: 28248128 DOI: 10.4155/ppa-2017-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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11
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Borrenberghs D, Dirix L, De Wit F, Rocha S, Blokken J, De Houwer S, Gijsbers R, Christ F, Hofkens J, Hendrix J, Debyser Z. Dynamic Oligomerization of Integrase Orchestrates HIV Nuclear Entry. Sci Rep 2016; 6:36485. [PMID: 27830755 PMCID: PMC5103197 DOI: 10.1038/srep36485] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 11/16/2022] Open
Abstract
Nuclear entry is a selective, dynamic process granting the HIV-1 pre-integration complex (PIC) access to the chromatin. Classical analysis of nuclear entry of heterogeneous viral particles only yields averaged information. We now have employed single-virus fluorescence methods to follow the fate of single viral pre-integration complexes (PICs) during infection by visualizing HIV-1 integrase (IN). Nuclear entry is associated with a reduction in the number of IN molecules in the complexes while the interaction with LEDGF/p75 enhances IN oligomerization in the nucleus. Addition of LEDGINs, small molecule inhibitors of the IN-LEDGF/p75 interaction, during virus production, prematurely stabilizes a higher-order IN multimeric state, resulting in stable IN multimers resistant to a reduction in IN content and defective for nuclear entry. This suggests that a stringent size restriction determines nuclear pore entry. Taken together, this work demonstrates the power of single-virus imaging providing crucial insights in HIV replication and enabling mechanism-of-action studies.
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Affiliation(s)
- Doortje Borrenberghs
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.,Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Lieve Dirix
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.,Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Flore De Wit
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Jolien Blokken
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Stéphanie De Houwer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
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12
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Cermakova K, Weydert C, Christ F, De Rijck J, Debyser Z. Lessons Learned: HIV Points the Way Towards Precision Treatment of Mixed-Lineage Leukemia. Trends Pharmacol Sci 2016; 37:660-671. [PMID: 27290878 DOI: 10.1016/j.tips.2016.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/27/2022]
Abstract
Protein-protein interactions are involved in most if not all pathogenic and pathophysiological processes and represent attractive therapeutic targets. Extensive biological and clinical research efforts have led to the identification and validation of several cellular hubs that are crucially involved in disease pathogenesis. An interesting example of such a hub is the lens epithelium-derived growth factor (LEDGF/p75), a protein that tethers multiple unrelated proteins and protein complexes to the chromatin. Its chromatin-tethering ability is linked to at least two unrelated diseases-HIV infection and MLL-rearranged acute leukemia. In this review we discuss recent progress in our understanding of the interaction of LEDGF/p75 with its binding partners and focus on the first steps towards therapies targeting protein-protein interactions of LEDGF/p75.
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Affiliation(s)
- Katerina Cermakova
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium; Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic (ASCR), v.v.i, Laboratory of Structural Biology, Prague, Czech Republic
| | - Caroline Weydert
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Frauke Christ
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Jan De Rijck
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Zeger Debyser
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium.
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13
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Feng L, Dharmarajan V, Serrao E, Hoyte A, Larue RC, Slaughter A, Sharma A, Plumb MR, Kessl JJ, Fuchs JR, Bushman FD, Engelman AN, Griffin PR, Kvaratskhelia M. The Competitive Interplay between Allosteric HIV-1 Integrase Inhibitor BI/D and LEDGF/p75 during the Early Stage of HIV-1 Replication Adversely Affects Inhibitor Potency. ACS Chem Biol 2016; 11:1313-21. [PMID: 26910179 DOI: 10.1021/acschembio.6b00167] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Allosteric HIV-1 integrase inhibitors (ALLINIs) have recently emerged as a promising class of antiretroviral agents and are currently in clinical trials. In infected cells, ALLINIs potently inhibit viral replication by impairing virus particle maturation but surprisingly exhibit a reduced EC50 for inhibiting HIV-1 integration in target cells. To better understand the reduced antiviral activity of ALLINIs during the early stage of HIV-1 replication, we investigated the competitive interplay between a potent representative ALLINI, BI/D, and LEDGF/p75 with HIV-1 integrase. While the principal binding sites of BI/D and LEDGF/p75 overlap at the integrase catalytic core domain dimer interface, we show that the inhibitor and the cellular cofactor induce markedly different multimerization patterns of full-length integrase. LEDGF/p75 stabilizes an integrase tetramer through the additional interactions with the integrase N-terminal domain, whereas BI/D induces protein-protein interactions in C-terminal segments that lead to aberrant, higher-order integrase multimerization. We demonstrate that LEDGF/p75 binds HIV-1 integrase with significantly higher affinity than BI/D and that the cellular protein is able to reverse the inhibitor induced aberrant, higher-order integrase multimerization in a dose-dependent manner in vitro. Consistent with these observations, alterations of the cellular levels of LEDGF/p75 markedly affected BI/D EC50 values during the early steps of HIV-1 replication. Furthermore, genome-wide sequencing of HIV-1 integration sites in infected cells demonstrate that LEDGF/p75-dependent integration site selection is adversely affected by BI/D treatment. Taken together, our studies elucidate structural and mechanistic details of the interplay between LEDGF/p75 and BI/D during the early stage of HIV-1 replication.
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Affiliation(s)
- Lei Feng
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Venkatasubramanian Dharmarajan
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
| | - Erik Serrao
- Department
of Cancer Immunology and Virology, Dana-Farber Cancer Institute and
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Ashley Hoyte
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross C. Larue
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alison Slaughter
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amit Sharma
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Matthew R. Plumb
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jacques J. Kessl
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry and Pharmacognosy,
College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Frederic D. Bushman
- Perelman School of Medicine, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alan N. Engelman
- Department
of Cancer Immunology and Virology, Dana-Farber Cancer Institute and
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Patrick R. Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Kumar A, Darcis G, Van Lint C, Herbein G. Epigenetic control of HIV-1 post integration latency: implications for therapy. Clin Epigenetics 2015; 7:103. [PMID: 26405463 PMCID: PMC4581042 DOI: 10.1186/s13148-015-0137-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/17/2015] [Indexed: 12/31/2022] Open
Abstract
With the development of effective combined anti-retroviral therapy (cART), there is significant reduction in deaths associated with human immunodeficiency virus type 1 (HIV-1) infection. However, the complete cure of HIV-1 infection is difficult to achieve without the elimination of latent reservoirs which exist in the infected individuals even under cART regimen. These latent reservoirs established during early infection have long life span, include resting CD4+ T cells, macrophages, central nervous system (CNS) resident macrophage/microglia, and gut-associated lymphoid tissue/macrophages, and can actively produce virus upon interruption of the cART. Several epigenetic and non-epigenetic mechanisms have been implicated in the regulation of viral latency. Epigenetic mechanisms such as histone post translational modifications (e.g., acetylation and methylation) and DNA methylation of the proviral DNA and microRNAs are involved in the establishment of HIV-1 latency. The better understanding of epigenetic mechanisms modulating HIV-1 latency could give clues for the complete eradication of these latent reservoirs. Several latency-reversing agents (LRA) have been found effective in reactivating HIV-1 reservoirs in vitro, ex vivo, and in vivo. Some of these agents target epigenetic modifications to elicit viral expression in order to kill latently infected cells through viral cytopathic effect or host immune response. These therapeutic approaches aimed at achieving a sterilizing cure (elimination of HIV-1 from the human body). In the present review, we will discuss our current understanding of HIV-1 epigenomics and how this information can be moved from the laboratory bench to the patient’s bedside.
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Affiliation(s)
- Amit Kumar
- Department of Virology, Pathogens & Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Hôpital Saint-Jacques, 2 place Saint-Jacques, F-25030 Besançon cedex, France
| | - Gilles Darcis
- Service of Molecular Virology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles (ULB), 12 Rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Institute of Molecular Biology and Medicine, Université Libre de Bruxelles (ULB), 12 Rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Georges Herbein
- Department of Virology, Pathogens & Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Hôpital Saint-Jacques, 2 place Saint-Jacques, F-25030 Besançon cedex, France
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15
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Grandgenett DP, Pandey KK, Bera S, Aihara H. Multifunctional facets of retrovirus integrase. World J Biol Chem 2015; 6:83-94. [PMID: 26322168 PMCID: PMC4549773 DOI: 10.4331/wjbc.v6.i3.83] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/01/2015] [Accepted: 07/27/2015] [Indexed: 02/05/2023] Open
Abstract
The retrovirus integrase (IN) is responsible for integration of the reverse transcribed linear cDNA into the host DNA genome. First, IN cleaves a dinucleotide from the 3’ OH blunt ends of the viral DNA exposing the highly conserved CA sequence in the recessed ends. IN utilizes the 3’ OH ends to catalyze the concerted integration of the two ends into opposite strands of the cellular DNA producing 4 to 6 bp staggered insertions, depending on the retrovirus species. The staggered ends are repaired by host cell machinery that results in a permanent copy of the viral DNA in the cellular genome. Besides integration, IN performs other functions in the replication cycle of several studied retroviruses. The proper organization of IN within the viral internal core is essential for the correct maturation of the virus. IN plays a major role in reverse transcription by interacting directly with the reverse transcriptase and by binding to the viral capsid protein and a cellular protein. Recruitment of several other host proteins into the viral particle are also promoted by IN. IN assists with the nuclear transport of the preintegration complex across the nuclear membrane. With several retroviruses, IN specifically interacts with different host protein factors that guide the preintegration complex to preferentially integrate the viral genome into specific regions of the host chromosomal target. Human gene therapy using retrovirus vectors is directly affected by the interactions of IN with these host factors. Inhibitors directed against the human immunodeficiency virus (HIV) IN bind within the active site of IN containing viral DNA ends thus preventing integration and subsequent HIV/AIDS.
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16
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Optimization of rhodanine scaffold for the development of protein–protein interaction inhibitors. Bioorg Med Chem 2015; 23:3208-14. [DOI: 10.1016/j.bmc.2015.04.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 11/21/2022]
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