1
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Richetta C, Tu NQ, Delelis O. Different Pathways Conferring Integrase Strand-Transfer Inhibitors Resistance. Viruses 2022; 14:v14122591. [PMID: 36560595 PMCID: PMC9785060 DOI: 10.3390/v14122591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Integrase Strand Transfer Inhibitors (INSTIs) are currently used as the most effective therapy in the treatment of human immunodeficiency virus (HIV) infections. Raltegravir (RAL) and Elvitegravir (EVG), the first generation of INSTIs used successfully in clinical treatment, are susceptible to the emergence of viral resistance and have a high rate of cross-resistance. To counteract these resistant mutants, second-generation INSTI drugs have been developed: Dolutegravir (DTG), Cabotegravir (CAB), and Bictegravir (BIC). However, HIV is also able to develop resistance mechanisms against the second-generation of INSTIs. This review describes the mode of action of INSTIs and then summarizes and evaluates some typical resistance mutations, such as substitution and insertion mutations. The role of unintegrated viral DNA is also discussed as a new pathway involved in conferring resistance to INSTIs. This allows us to have a more detailed understanding of HIV resistance to these inhibitors, which may contribute to the development of new INSTIs in the future.
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2
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Urvashi, Senthil Kumar JB, Das P, Tandon V. Development of Azaindole-Based Frameworks as Potential Antiviral Agents and Their Future Perspectives. J Med Chem 2022; 65:6454-6495. [PMID: 35477274 PMCID: PMC9063994 DOI: 10.1021/acs.jmedchem.2c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Indexed: 11/29/2022]
Abstract
The azaindole (AI) framework continues to play a significant role in the design of new antiviral agents. Modulating the position and isosteric replacement of the nitrogen atom of AI analogs notably influences the intrinsic physicochemical properties of lead compounds. The intra- and intermolecular interactions of AI derivatives with host receptors or viral proteins can also be fine tuned by carefully placing the nitrogen atom in the heterocyclic core. This wide-ranging perspective article focuses on AIs that have considerable utility in drug discovery programs against RNA viruses. The inhibition of influenza A, human immunodeficiency, respiratory syncytial, neurotropic alpha, dengue, ebola, and hepatitis C viruses by AI analogs is extensively reviewed to assess their plausible future potential in antiviral drug discovery. The binding interaction of AIs with the target protein is examined to derive a structural basis for designing new antiviral agents.
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Affiliation(s)
- Urvashi
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
- Department of Chemistry, University of
Delhi, New Delhi 110007, India
| | - J. B. Senthil Kumar
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
| | - Parthasarathi Das
- Department of Chemistry, Indian Institute
of Technology (ISM), Dhanbad 826004, India
| | - Vibha Tandon
- Drug Discovery Laboratory, Special Centre for
Molecular Medicine, Jawaharlal Nehru University, New Delhi 110
067, India
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3
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Dilly S, Roman LJ, Bogliotti N, Xie J, Deprez E, Slama-Schwok A. Design of Light-Sensitive Triggers for Endothelial NO-Synthase Activation. Antioxidants (Basel) 2020; 9:antiox9020089. [PMID: 31972975 PMCID: PMC7070953 DOI: 10.3390/antiox9020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 12/11/2022] Open
Abstract
A specific light trigger for activating endothelial Nitric Oxide-Synthase (eNOS) in real time would be of unique value to decipher cellular events associated with eNOS activation or to generate on demand cytotoxic levels of NO at specific sites for cancer research. We previously developed novel tools called nanotriggers (NT), which recognized constitutive NO-synthase, eNOS or neuronal NOS (nNOS), mainly via their 2’ phosphate group which is also present in NADPH in its binding site. Laser excitation of NT1 bound to eNOS triggered recombinant NOS activity and released NO. We recently generated new NTs carrying a 2’ or 3’ carboxylate group or two 2’ and 3’ carboxylate moieties replacing the 2’ phosphate group of NADPH. Among these new NT, only the 3’ carboxylate derivative released NO from endothelial cells upon laser activation. Here, Molecular Dynamics (MD) simulations showed that the 3’ carboxylate NT formed a folded structure with a hydrophobic hub, inducing a good stacking on FAD that likely drove efficient activation of nNOS. This NT also carried an additional small charged group which increased binding to e/nNOS; fluorescence measurements determined a 20-fold improved affinity upon binding to nNOS as compared to NT1 affinity. To gain in specificity for eNOS, we augmented a previous NT with a “hook” targeting variable residues in the NADPH site of eNOS. We discuss the potential of exploiting the chemical diversity within the NADPH site of eNOS for reversal of endothelial dysfunction in cells and for controlled generation of cytotoxic NO-derived species in cancer tissues.
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Affiliation(s)
- Sébastien Dilly
- UMR CNRS 8200, Gustave Roussy Cancer Research Center, Université Paris-Saclay, 94607 Villejuif, France;
| | - Linda J. Roman
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA;
| | - Nicolas Bogliotti
- PPSM, CNRS UMR8531, ENS Paris-Saclay, Université Paris-Saclay, IDA FR3242, F-94235 Cachan, France; (N.B.); (J.X.)
| | - Juan Xie
- PPSM, CNRS UMR8531, ENS Paris-Saclay, Université Paris-Saclay, IDA FR3242, F-94235 Cachan, France; (N.B.); (J.X.)
| | - Eric Deprez
- LBPA, CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-94235 Cachan, France;
| | - Anny Slama-Schwok
- UMR CNRS 8200, Gustave Roussy Cancer Research Center, Université Paris-Saclay, 94607 Villejuif, France;
- Centre de Recherche Saint Antoine INSERM UMR S-938, Sorbonne Université, 75006 Paris, France
- Correspondence:
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4
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Veras Ribeiro Filho H, Tambones IL, Mariano Gonçalves Dias M, Bernardi Videira N, Bruder M, Amorim Amato A, Migliorini Figueira AC. Modulation of nuclear receptor function: Targeting the protein-DNA interface. Mol Cell Endocrinol 2019; 484:1-14. [PMID: 30703486 DOI: 10.1016/j.mce.2019.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/02/2023]
Abstract
Nuclear receptors (NRs) are a superfamily of ligand-dependent transcription factors that modulate several biological processes. Traditionally, modulation of NRs has been focused on the development of ligands that recognize and bind to the ligand binding domain (LBD), resulting in activation or repression of transcription through the recruitment of coregulators. However, for more severe diseases, such as breast and prostate cancer, the conventional treatment addressing LBD modulation is not always successful, due to tumor resistance. To overcome these challenges and aiming to modulate NR activity by inhibiting the NR-DNA interaction, new studies focus on the development of molecules targeting alternative sites and domains on NRs. Here, we discuss two different approaches for this alternative NR modulation: one targeting the NR DNA binding domain (DBD); and the other targeting the DNA sites recognized by NRs. Our aim is to present the challenges and perspectives for developing specific inhibitors for each purpose, alongside with already reported examples.
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Affiliation(s)
- Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Biosciences and Technology of Bioactive Products, Institute of Biology, State University of Campinas (Unicamp), Campinas, 13083-970, Brazil
| | - Izabella Luisa Tambones
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Biosciences and Technology of Bioactive Products, Institute of Biology, State University of Campinas (Unicamp), Campinas, 13083-970, Brazil
| | - Marieli Mariano Gonçalves Dias
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Molecular and Functional Biology, Institute of Biology, State University of Campinas (Unicamp), Campinas, SP, 13083-970, Brazil
| | - Natalia Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Angélica Amorim Amato
- Laboratory of Molecular Pharmacology, Department of Pharmaceutical Science, University of Brasilia (UnB), Brasília, DF, 70910-900, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil.
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5
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Ciubotaru M, Musat MG, Surleac M, Ionita E, Petrescu AJ, Abele E, Abele R. The Design of New HIV-IN Tethered Bifunctional Inhibitors Using Multiple Microdomain Targeted Docking. Curr Med Chem 2018; 26:2574-2600. [PMID: 29623824 DOI: 10.2174/0929867325666180406114405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/17/2022]
Abstract
Currently, used antiretroviral HIV therapy drugs exclusively target critical groups in the enzymes essential for the viral life cycle. Increased mutagenesis of their genes changes these viral enzymes, which once mutated can evade therapeutic targeting, effects which confer drug resistance. To circumvent this, our review addresses a strategy to design and derive HIV-Integrase (HIV-IN) inhibitors which simultaneously target two IN functional domains, rendering it inactive even if the enzyme accumulates many mutations. First we review the enzymatic role of IN to insert the copied viral DNA into a chromosome of the host T lymphocyte, highlighting its main functional and structural features to be subjected to inhibitory action. From a functional and structural perspective we present all classes of HIV-IN inhibitors with their most representative candidates. For each chosen compound we also explain its mechanism of IN inhibition. We use the recently resolved cryo EM IN tetramer intasome DNA complex onto which we dock various reference IN inhibitory chemical scaffolds such as to target adjacent functional IN domains. Pairing compounds with complementary activity, which dock in the vicinity of a IN structural microdomain, we design bifunctional new drugs which may not only be more resilient to IN mutations but also may be more potent inhibitors than their original counterparts. In the end of our review we propose synthesis pathways to link such paired compounds with enhanced synergistic IN inhibitory effects.
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Affiliation(s)
- Mihai Ciubotaru
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Mihaela Georgiana Musat
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Biochemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Marius Surleac
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Elena Ionita
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Andrei Jose Petrescu
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Edgars Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Ramona Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
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6
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Probing Resistance Mutations in Retroviral Integrases by Direct Measurement of Dolutegravir Fluorescence. Sci Rep 2017; 7:14067. [PMID: 29070877 PMCID: PMC5656594 DOI: 10.1038/s41598-017-14564-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022] Open
Abstract
FDA-approved integrase strand transfer inhibitors (raltegravir, elvitegravir and dolutegravir) efficiently inhibit HIV-1 replication. Here, we present fluorescence properties of these inhibitors. Dolutegravir displays an excitation mode particularly dependent on Mg2+ chelation, allowing to directly probe its Mg2+-dependent binding to the prototype foamy virus (PFV) integrase. Dolutegravir-binding studied by both its fluorescence anisotropy and subsequent emission enhancement, strictly requires a preformed integrase/DNA complex, the ten terminal base pairs from the 3′-end of the DNA reactive strand being crucial to optimize dolutegravir-binding in the context of the ternary complex. From the protein side, mutation of any catalytic residue fully abolishes dolutegravir-binding. We also compared dolutegravir-binding to PFV F190Y, G187R and S217K mutants, corresponding to HIV-1 F121Y, G118R and G140S/Q148K mutations that confer low-to-high resistance levels against raltegravir/dolutegravir. The dolutegravir-binding properties derived from fluorescence-based binding assays and drug susceptibilities in terms of catalytic activity, are well correlated. Indeed, dolutegravir-binding to wild-type and F190Y integrases are comparable while strongly compromised with G187R and S217K. Accordingly, the two latter mutants are highly resistant to dolutegravir while F190Y shows only moderate or no resistance. Intrinsic fluorescence properties of dolutegravir are thus particularly suitable for a thorough characterization of both DNA-binding properties of integrase and resistance mutations.
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7
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2017; 7:2165. [PMID: 28123383 PMCID: PMC5225119 DOI: 10.3389/fmicb.2016.02165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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8
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Abstract
To complete its life cycle, HIV-1 enters the nucleus of the host cell as reverse-transcribed viral DNA. The nucleus is a complex environment, in which chromatin is organized to support different structural and functional aspects of cell physiology. As such, it represents a challenge for an incoming viral genome, which needs to be integrated into cellular DNA to ensure productive infection. Integration of the viral genome into host DNA depends on the enzymatic activity of HIV-1 integrase and involves different cellular factors that influence the selection of integration sites. The selection of integration site has functional consequences for viral transcription, which usually follows the integration event. However, in resting CD4+ T cells, the viral genome can be silenced for long periods of time, which leads to the generation of a latent reservoir of quiescent integrated HIV-1 DNA. Integration represents the only nuclear event in the viral life cycle that can be pharmacologically targeted with current therapies, and the aspects that connect HIV-1 nuclear entry to HIV-1 integration and viral transcription are only beginning to be elucidated.
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9
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Mechanistic insight into cadmium-induced inactivation of the Bloom protein. Sci Rep 2016; 6:26225. [PMID: 27194376 PMCID: PMC4872126 DOI: 10.1038/srep26225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/25/2016] [Indexed: 11/08/2022] Open
Abstract
Cadmium is a toxic metal that inactivates DNA-repair proteins via multiple mechanisms, including zinc substitution. In this study, we investigated the effect of Cd(2+) on the Bloom protein (BLM), a DNA-repair helicase carrying a zinc-binding domain (ZBD) and playing a critical role to ensure genomic stability. One characteristics of BLM-deficient cells is the elevated rate of sister chromatid exchanges, a phenomenon that is also induced by Cd(2+). Here, we show that Cd(2+) strongly inhibits both ATPase and helicase activities of BLM. Cd(2+) primarily prevents BLM-DNA interaction via its binding to sulfhydryl groups of solvent-exposed cysteine residues and, concomitantly, promotes the formation of large BLM multimers/aggregates. In contrast to previously described Cd(2+) effects on other zinc-containing DNA-repair proteins, the ZBD appears to play a minor role in the Cd(2+)-mediated inhibition. While the Cd(2+)-dependent formation of inactive multimers and the defect of DNA-binding were fully reversible upon addition of EDTA, the inhibition of the DNA unwinding activity was not counteracted by EDTA, indicating another mechanism of inhibition by Cd(2+) relative to the targeting of a catalytic residue. Altogether, our results provide new clues for understanding the mechanism behind the ZBD-independent inactivation of BLM by Cd(2+) leading to accumulation of DNA double-strand breaks.
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10
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Mitochondria-targeted Triphenylamine Derivatives Activatable by Two-Photon Excitation for Triggering and Imaging Cell Apoptosis. Sci Rep 2016; 6:21458. [PMID: 26947258 PMCID: PMC4780088 DOI: 10.1038/srep21458] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Photodynamic therapy (PDT) leads to cell death by using a combination of a photosensitizer and an external light source for the production of lethal doses of reactive oxygen species (ROS). Since a major limitation of PDT is the poor penetration of UV-visible light in tissues, there is a strong need for organic compounds whose activation is compatible with near-infrared excitation. Triphenylamines (TPAs) are fluorescent compounds, recently shown to efficiently trigger cell death upon visible light irradiation (458 nm), however outside the so-called optical/therapeutic window. Here, we report that TPAs target cytosolic organelles of living cells, mainly mitochondria, triggering a fast apoptosis upon two-photon excitation, thanks to their large two-photon absorption cross-sections in the 760–860 nm range. Direct ROS imaging in the cell context upon multiphoton excitation of TPA and three-color flow cytometric analysis showing phosphatidylserine externalization indicate that TPA photoactivation is primarily related to the mitochondrial apoptotic pathway via ROS production, although significant differences in the time courses of cell death-related events were observed, depending on the compound. TPAs represent a new class of water-soluble organic photosensitizers compatible with direct two-photon excitation, enabling simultaneous multiphoton fluorescence imaging of cell death since a concomitant subcellular TPA re-distribution occurs in apoptotic cells.
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El Shafey N, Guesnon M, Simon F, Deprez E, Cosette J, Stockholm D, Scherman D, Bigey P, Kichler A. Inhibition of the myostatin/Smad signaling pathway by short decorin-derived peptides. Exp Cell Res 2016; 341:187-95. [PMID: 26844629 DOI: 10.1016/j.yexcr.2016.01.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/27/2016] [Accepted: 01/31/2016] [Indexed: 02/06/2023]
Abstract
Myostatin, also known as growth differentiation factor 8, is a member of the transforming growth factor-beta superfamily that has been shown to play a key role in the regulation of the skeletal muscle mass. Indeed, while myostatin deletion or loss of function induces muscle hypertrophy, its overexpression or systemic administration causes muscle atrophy. Since myostatin blockade is effective in increasing skeletal muscle mass, myostatin inhibitors have been actively sought after. Decorin, a member of the small leucine-rich proteoglycan family is a metalloprotein that was previously shown to bind and inactivate myostatin in a zinc-dependent manner. Furthermore, the myostatin-binding site has been shown to be located in the decorin N-terminal domain. In the present study, we investigated the anti-myostatin activity of short and soluble fragments of decorin. Our results indicate that the murine decorin peptides DCN48-71 and 42-65 are sufficient for inactivating myostatin in vitro. Moreover, we show that the interaction of mDCN48-71 to myostatin is strictly zinc-dependent. Binding of myostatin to activin type II receptor results in the phosphorylation of Smad2/3. Addition of the decorin peptide 48-71 decreased in a dose-dependent manner the myostatin-induced phosphorylation of Smad2 demonstrating thereby that the peptide inhibits the activation of the Smad signaling pathway. Finally, we found that mDCN48-71 displays a specificity towards myostatin, since it does not inhibit other members of the transforming growth factor-beta family.
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Affiliation(s)
- Nelly El Shafey
- Unité de Technologies Chimiques et Biologiques pour la Santé, CNRS UMR8258-Inserm, U1022 - Université Paris Descartes, Chimie ParisTech, 75006 Paris, France
| | - Mickaël Guesnon
- Unité de Technologies Chimiques et Biologiques pour la Santé, CNRS UMR8258-Inserm, U1022 - Université Paris Descartes, Chimie ParisTech, 75006 Paris, France
| | - Françoise Simon
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, UMR8113 CNRS, IDA FR3242, 94230 Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, UMR8113 CNRS, IDA FR3242, 94230 Cachan, France
| | - Jérémie Cosette
- Inserm, UMR 951, Université d'Evry Val d'Essonne, Genethon, 91000 Evry, France
| | - Daniel Stockholm
- Inserm, UMR 951, Université d'Evry Val d'Essonne, Genethon, 91000 Evry, France
| | - Daniel Scherman
- Unité de Technologies Chimiques et Biologiques pour la Santé, CNRS UMR8258-Inserm, U1022 - Université Paris Descartes, Chimie ParisTech, 75006 Paris, France
| | - Pascal Bigey
- Unité de Technologies Chimiques et Biologiques pour la Santé, CNRS UMR8258-Inserm, U1022 - Université Paris Descartes, Chimie ParisTech, 75006 Paris, France
| | - Antoine Kichler
- Unité de Technologies Chimiques et Biologiques pour la Santé, CNRS UMR8258-Inserm, U1022 - Université Paris Descartes, Chimie ParisTech, 75006 Paris, France; Laboratoire de Conception et Application de Molécules Bioactives UMR7199 CNRS-Université de Strasbourg, LabEx Medalis, Faculté de Pharmacie, 67401 Illkirch, France.
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12
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Thierry E, Deprez E, Delelis O. Different Pathways Leading to Integrase Inhibitors Resistance. Front Microbiol 2016. [PMID: 28123383 DOI: 10.3389/fmicb.2016.02165/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs), such as raltegravir (RAL), elvitegravir, or dolutegravir (DTG), are efficient antiretroviral agents used in HIV treatment in order to inhibit retroviral integration. By contrast to RAL treatments leading to well-identified mutation resistance pathways at the integrase level, recent clinical studies report several cases of patients failing DTG treatment without clearly identified resistance mutation in the integrase gene raising questions for the mechanism behind the resistance. These compounds, by impairing the integration of HIV-1 viral DNA into the host DNA, lead to an accumulation of unintegrated circular viral DNA forms. This viral DNA could be at the origin of the INSTI resistance by two different ways. The first one, sustained by a recent report, involves 2-long terminal repeat circles integration and the second one involves expression of accumulated unintegrated viral DNA leading to a basal production of viral particles maintaining the viral information.
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Affiliation(s)
- Eloïse Thierry
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
| | - Olivier Delelis
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, Université Paris-Saclay Cachan, France
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13
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Han YS, Xiao WL, Quashie PK, Mesplède T, Xu H, Deprez E, Delelis O, Pu JX, Sun HD, Wainberg MA. Development of a fluorescence-based HIV-1 integrase DNA binding assay for identification of novel HIV-1 integrase inhibitors. Antiviral Res 2013; 98:441-8. [PMID: 23583286 DOI: 10.1016/j.antiviral.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/25/2013] [Accepted: 04/01/2013] [Indexed: 10/27/2022]
Abstract
Human immunodeficiency virus integrase (HIV-1 IN) inhibitors that are currently approved or are in advanced clinical trials specifically target the strand transfer step of integration. However, considerable cross-resistance exists among some members of this class of IN inhibitors. Intriguingly, though, HIV-1 IN possesses multiple sites, distinct from those involved in the strand transfer step, that could be targeted to develop new HIV-1 IN inhibitors. We have developed a fluorescent HIV-1 IN DNA binding assay that can identify small molecules termed IN binding inhibitors (INBIs) that inhibit IN binding to viral DNA. This assay has been optimized with respect to concentrations of each protein, long terminal repeat (LTR) DNA substrate, salt, and time, and has been used successfully to measure the HIV-1 IN DNA binding activity of a well-characterized INBI termed FZ41. In addition, we have used the assay to screen a small library of natural products, resulting in the identification of nigranoic acid as a new INBI. The proposed fluorescence assay is easy and inexpensive, and provides a high-throughput detection method for determination of HIV-1 IN DNA binding activity, monitoring of enzyme kinetics, and high-throughput screening for the identification of new INBIs.
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Affiliation(s)
- Ying-Shan Han
- McGill University AIDS Centre, Lady Davis for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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14
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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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15
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Sample preparation and analytical strategies for large-scale phosphoproteomics experiments. Semin Cell Dev Biol 2012; 23:843-53. [DOI: 10.1016/j.semcdb.2012.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 05/29/2012] [Indexed: 12/28/2022]
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16
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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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17
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Korolev S, Knyazhanskaya E, Anisenko A, Tashlitskii V, Zatsepin TS, Gottikh M, Agapkina J. Modulation of HIV-1 integrase activity by single-stranded oligonucleotides and their conjugates with eosin. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:651-66. [PMID: 21888554 DOI: 10.1080/15257770.2011.592890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Integration of the DNA copy of the genomic RNA into an infected cell genome is one of the key steps of the replication cycle of all retroviruses. It is catalyzed by the viral enzyme, integrase. We have shown that conjugates of short single-stranded oligonucleotides with eosin efficiently inhibit the catalytic activity of the HIV-1 integrase. In this article, we have found that the dependence of the integrase catalytic activity on the concentration of oligonucleotides has a bell-shaped pattern. The modulation of HIV-1 integrase activity correlated with the oligonucleotide length and was not associated with specific sequences. Moreover, a similar mode of the oligonucleotide action was found for integrase from the prototype foamy virus. This dual effect of the oligonucleotide and their conjugates with eosin might be explained by their binding with retroviral integrase in two different sites; the oligodeoxynucleotide binding in the first site results in integrase activation, whereas interactions with another one lead to inhibition of the enzyme activity. Eosin coupling to oligonucleotides did not change the mode of their action but enhanced their affinity to both binding sites. The affinity increase was found to be much more important for the site responsible for the integrase inhibition, thus explaining the high inhibitory potency of oligonucleotide-eosin conjugates.
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Affiliation(s)
- Sergey Korolev
- Department of Chemistry, Belozersky Institute of Physical and Chemical Biology, Moscow State University, Moscow, Russia
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18
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Xue W, Liu H, Yao X. Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. J Comput Chem 2011; 33:527-36. [DOI: 10.1002/jcc.22887] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 09/25/2011] [Accepted: 10/20/2011] [Indexed: 01/03/2023]
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19
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McNeely M, Hendrix J, Busschots K, Boons E, Deleersnijder A, Gerard M, Christ F, Debyser Z. In vitro DNA tethering of HIV-1 integrase by the transcriptional coactivator LEDGF/p75. J Mol Biol 2011; 410:811-30. [PMID: 21763490 DOI: 10.1016/j.jmb.2011.03.073] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 12/21/2022]
Abstract
Although LEDGF/p75 is believed to act as a cellular cofactor of lentiviral integration by tethering integrase (IN) to chromatin, there is no good in vitro model to analyze this functionality. We designed an AlphaScreen assay to study how LEDGF/p75 modulates the interaction of human immunodeficiency virus type 1 IN with DNA. IN bound with similar affinity to DNA mimicking the long terminal repeat or to random DNA. While LEDGF/p75 bound DNA strongly, a mutant of LEDGF/p75 with compromised nuclear localization signal (NLS)/AT hook interacted weakly, and the LEDGF/p75 PWWP domain did not interact, corroborating previous reports on the role of NLS and AT hooks in charge-dependent DNA binding. LEDGF/p75 stimulated IN binding to DNA 10-fold to 30-fold. Stimulation of IN-DNA binding required a direct interaction between IN and the C-terminus of LEDGF/p75. Addition of either the C-terminus of LEDGF/p75 (amino acids 325-530) or LEDGF/p75 mutated in the NLS/AT hooks interfered with IN binding to DNA. Our results are consistent with an in vitro model of LEDGF/p75-mediated tethering of IN to DNA. The inhibition of IN-DNA interaction by the LEDGF/p75 C-terminus may provide a novel strategy for the inhibition of HIV IN activity and may explain the potent inhibition of HIV replication observed after the overexpression of C-terminal fragments in cell culture.
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Affiliation(s)
- Melissa McNeely
- Laboratory for Molecular Virology and Gene Therapy, Molecular Medicine, KULeuven and IRC Kulak, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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20
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Zamborlini A, Coiffic A, Beauclair G, Delelis O, Paris J, Koh Y, Magne F, Giron ML, Tobaly-Tapiero J, Deprez E, Emiliani S, Engelman A, de Thé H, Saïb A. Impairment of human immunodeficiency virus type-1 integrase SUMOylation correlates with an early replication defect. J Biol Chem 2011; 286:21013-22. [PMID: 21454548 PMCID: PMC3121452 DOI: 10.1074/jbc.m110.189274] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 02/23/2011] [Indexed: 11/06/2022] Open
Abstract
HIV-1 integrase (IN) orchestrates the integration of the reverse transcribed viral cDNA into the host cell genome and participates also in other steps of HIV-1 replication. Cellular and viral factors assist IN in performing its multiple functions, and post-translational modifications contribute to modulate its activities. Here, we show that HIV-1 IN is modified by SUMO proteins and that phylogenetically conserved SUMOylation consensus motifs represent major SUMO acceptor sites. Viruses harboring SUMOylation site IN mutants displayed a replication defect that was mapped during the early stages of infection, before integration but after reverse transcription. Because SUMOylation-defective IN mutants retained WT catalytic activity, we hypothesize that SUMOylation might regulate the affinity of IN for co-factors, contributing to efficient HIV-1 replication.
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Affiliation(s)
- Alessia Zamborlini
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
- the Conservatoire des Arts et Métiers, Paris, France
| | - Audrey Coiffic
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
| | - Guillaume Beauclair
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
| | - Olivier Delelis
- Laboratoire de Biotechnologies et Pharmacologie Génétique Appliquée, CNRS UMR8113, Ecole Normale Supérieure, 94235 Cachan, France
| | - Joris Paris
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
| | - Yashuiro Koh
- the Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Fabian Magne
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
- the Conservatoire des Arts et Métiers, Paris, France
| | - Marie-Lou Giron
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
| | - Joelle Tobaly-Tapiero
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
| | - Eric Deprez
- Laboratoire de Biotechnologies et Pharmacologie Génétique Appliquée, CNRS UMR8113, Ecole Normale Supérieure, 94235 Cachan, France
| | - Stephane Emiliani
- INSERM U1016, CNRS UMR8104, Université Paris Descartes, Institut Cochin, 75014 Paris, France, and
| | - Alan Engelman
- the Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Hugues de Thé
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
| | - Ali Saïb
- From the CNRS UMR7212, INSERM U944, Institut Universitaire d'Hématologie-Université Paris7 Diderot, 75475 Paris, France
- the Conservatoire des Arts et Métiers, Paris, France
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21
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Gupta P, Garg P, Roy N. Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors. Mol Divers 2011; 15:733-50. [DOI: 10.1007/s11030-011-9304-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 01/05/2011] [Indexed: 12/01/2022]
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22
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Al-Mawsawi LQ, Neamati N. Allosteric inhibitor development targeting HIV-1 integrase. ChemMedChem 2011; 6:228-41. [PMID: 21275045 PMCID: PMC3115487 DOI: 10.1002/cmdc.201000443] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/06/2010] [Indexed: 12/16/2022]
Abstract
HIV-1 integrase (IN) is one of three essential enzymes for viral replication, and is a focus of ardent antiretroviral drug discovery and development efforts. Diligent research has led to the development of the strand-transfer-specific chemical class of IN inhibitors, with two compounds from this group, raltegravir and elvitegravir, advancing the farthest in the US Food and Drug Administration (FDA) approval process for any IN inhibitor discovered thus far. Raltegravir, developed by Merck & Co., has been approved by the FDA for HIV-1 therapy, whereas elvitegravir, developed by Gilead Sciences and Japan Tobacco, has reached phase III clinical trials. Although this is an undoubted success for the HIV-1 IN drug discovery field, the emergence of HIV-1 IN strand-transfer-specific drug-resistant viral strains upon clinical use of these compounds is expected. Furthermore, the problem of strand-transfer-specific IN drug resistance will be exacerbated by the development of cross-resistant viral strains due to an overlapping binding orientation at the IN active site and an equivalent inhibitory mechanism for the two compounds. This inevitability will result in no available IN-targeted therapeutic options for HIV-1 treatment-experienced patients. The development of allosterically targeted IN inhibitors presents an extremely advantageous approach for the discovery of compounds effective against IN strand-transfer drug-resistant viral strains, and would likely show synergy with all available FDA-approved antiretroviral HIV-1 therapeutics, including the IN strand-transfer-specific compounds. Herein we review the concept of allosteric IN inhibition, and the small molecules that have been investigated to bind non-active-site regions to inhibit IN function.
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Affiliation(s)
- Laith Q. Al-Mawsawi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089
| | - Nouri Neamati
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089
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23
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Billamboz M, Bailly F, Lion C, Calmels C, Andréola ML, Witvrouw M, Christ F, Debyser Z, De Luca L, Chimirri A, Cotelle P. 2-hydroxyisoquinoline-1,3(2H,4H)-diones as inhibitors of HIV-1 integrase and reverse transcriptase RNase H domain: influence of the alkylation of position 4. Eur J Med Chem 2010; 46:535-46. [PMID: 21185110 DOI: 10.1016/j.ejmech.2010.11.033] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/15/2010] [Accepted: 11/20/2010] [Indexed: 11/16/2022]
Abstract
We report herein the synthesis of a series of fifteen 2-hydroxyisoquinoline-1,3(2H,4H)-dione derivatives. Alkyl and arylalkyl groups were introduced on position 4 of the basis scaffold. All the compounds presented poor inhibitory properties against HIV-1 reverse transcriptase ribonuclease H (RNase H). Four compounds inhibited HIV-1 integrase at a low micromolar level. A docking study using the later crystallographic data available for PFV integrase allowed us to explain the slightly improved integrase inhibitory activities of 4-pentyl and 4-(3-phenylpropyl)-2-hydroxyisoquinoline-1,3(2H,4H)-diones, when compared to the basis scaffold. Physicochemical studies were consistent with 1:1 and 1:2 (metal/ligand) stoichiometries of the magnesium complexes in solution. Unfortunately all tested compounds exhibited high cellular cytotoxicity in cell culture which limited their applications as antiviral agents. However these identified integrase inhibitors provide a very good basis for the development of new hits.
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