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Sawant AA, Jadav SS, Nayani K, Mainkar PS. Development of Synthetic Approaches Towards HIV Integrase Strand Transfer Inhibitors (INSTIs). ChemistrySelect 2022. [DOI: 10.1002/slct.202201915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashwini Amol Sawant
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surender Singh Jadav
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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Saez-Ayala M, Laban Yekwa E, Mondielli C, Roux L, Hernández S, Bailly F, Cotelle P, Rogolino D, Canard B, Ferron F, Alvarez K. Metal chelators for the inhibition of the lymphocytic choriomeningitis virus endonuclease domain. Antiviral Res 2018; 162:79-89. [PMID: 30557576 DOI: 10.1016/j.antiviral.2018.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022]
Abstract
Arenaviridae is a viral family whose members are associated with rodent-transmitted infections to humans responsible of severe diseases. The current lack of a vaccine and limited therapeutic options make the development of efficacious drugs of high priority. The cap-snatching mechanism of transcription of Arenavirus performed by the endonuclease domain of the L-protein is unique and essential, so we developed a drug design program targeting the endonuclease activity of the prototypic Lymphocytic ChorioMeningitis Virus. Since the endonuclease activity is metal ion dependent, we designed a library of compounds bearing chelating motifs (diketo acids, polyphenols, and N-hydroxyisoquinoline-1,3-diones) able to block the catalytic center through the chelation of the critical metal ions, resulting in a functional impairment. We pre-screened 59 compounds by Differential Scanning Fluorimetry. Then, we characterized the binding affinity by Microscale Thermophoresis and evaluated selected compounds in in vitro and in cellula assays. We found several potent binders and inhibitors of the endonuclease activity. This study validates the proof of concept that the endonuclease domain of Arenavirus can be used as a target for anti-arena-viral drug discovery and that both diketo acids and N-hydroxyisoquinoline-1,3-diones can be considered further as potential metal-chelating pharmacophores.
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Affiliation(s)
- Magali Saez-Ayala
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France; Aix-Marseille Université, CRCM, INSERM U1068, CNRS UMR7258, 13273, Marseille, France
| | - Elsie Laban Yekwa
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Clémence Mondielli
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France
| | - Loic Roux
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France; Department of Physiology Anatomy and Genetics, Oxford University, Oxford, UK
| | - Sergio Hernández
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France
| | - Fabrice Bailly
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000, Lille, France
| | - Philippe Cotelle
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences et Cancer, F-59000, Lille, France; ENSCL, F-59000, Lille, France
| | - Dominga Rogolino
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, P.co Area delle Scienze 17/A, Parma, Italy
| | - Bruno Canard
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France
| | - François Ferron
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France
| | - Karine Alvarez
- Aix-Marseille Université, CNRS UMR 7257, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288, Marseille, France.
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Leonel CA, Lima WG, dos Santos M, Ferraz AC, Taranto AG, de Magalhães JC, dos Santos LL, Ferreira JMS. Pharmacophoric characteristics of dengue virus NS2B/NS3pro inhibitors: a systematic review of the most promising compounds. Arch Virol 2017; 163:575-586. [DOI: 10.1007/s00705-017-3641-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/29/2017] [Indexed: 12/18/2022]
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Design and synthesis of N-methylpyrimidone derivatives as HIV-1 integrase inhibitors. Bioorg Med Chem 2015; 23:735-41. [PMID: 25618597 DOI: 10.1016/j.bmc.2014.12.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/25/2014] [Accepted: 12/26/2014] [Indexed: 01/23/2023]
Abstract
A series of novel β-diketo derivatives which combined the virtues of dihydroxypyrimidine carboxamide derived from the evolution of DKA and polyhydroxylated aromatics moieties, were designed and synthesized as potential HIV-1 integrase (IN) inhibitors and evaluated their inhibition to the strand transfer process of HIV-1 integrase and anti-HIV-1 activity. The result indicates that 3,4,5-trihydroxylated aromatic derivatives exhibit good inhibition to HIV-1 integrase, but dihydroxylated aromatic derivatives appear little inhibition to HIV-1 integrase. In addition, the preliminary structure-activity relationship (SAR) of these new derivatives was rationalized by docking studies.
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Kong Y, Xuan S, Yan A. Computational models on quantitative prediction of bioactivity of HIV-1 integrase 3' processing inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:729-746. [PMID: 25121566 DOI: 10.1080/1062936x.2014.942695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this study, four computational quantitative structure-activity relationship (QSAR) models were built to predict the bioactivity of 3' processing (3'P) inhibitors of HIV-1 integrase. Some 453 inhibitors whose bioactivity values were detected by the radiolabelling method were collected. The molecular structures were represented with MOE descriptors. In total, 21 descriptors were selected for modelling. All inhibitors were divided into a training set and a test set with two methods: (1) by a Kohonen's self-organizing map (SOM); (2) by a random selection. For every training set and test set, a multilinear regression (MLR) analysis and a support vector machine (SVM) were used to establish models, respectively. For the training/test set divided by SOM, the correlation coefficients (r) were over 0.84, and for the training/test set split randomly, the r values were over 0.86. Some molecular properties such as hydrogen bond donor capacity, atomic partial charge properties, molecular refractivity, the number of aromatic bonds and molecular surface area, volume and shape properties played important roles for inhibiting 3' processing step of HIV-1 integrase.
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Affiliation(s)
- Y Kong
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , China
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Xuan S, Wang M, Kang H, Kirchmair J, Tan L, Yan A. Support Vector Machine (SVM) Models for Predicting Inhibitors of the 3′ Processing Step of HIV-1 Integrase. Mol Inform 2013; 32:811-26. [DOI: 10.1002/minf.201300107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/26/2013] [Indexed: 01/24/2023]
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Hu L, Zhang S, He X, Luo Z, Wang X, Liu W, Qin X. Design and synthesis of novel β-diketo derivatives as HIV-1 integrase inhibitors. Bioorg Med Chem 2012; 20:177-82. [DOI: 10.1016/j.bmc.2011.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/08/2011] [Accepted: 11/08/2011] [Indexed: 10/15/2022]
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Serafin K, Mazur P, Bak A, Laine E, Tchertanov L, Mouscadet JF, Polanski J. Ethyl malonate amides: A diketo acid offspring fragment for HIV integrase inhibition. Bioorg Med Chem 2011; 19:5000-5. [DOI: 10.1016/j.bmc.2011.06.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/16/2011] [Accepted: 06/18/2011] [Indexed: 12/24/2022]
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Crosby DC, Lei X, Gibbs CG, McDougall BR, Robinson WE, Reinecke MG. Design, synthesis, and biological evaluation of novel hybrid dicaffeoyltartaric/diketo acid and tetrazole-substituted L-chicoric acid analogue inhibitors of human immunodeficiency virus type 1 integrase. J Med Chem 2010; 53:8161-75. [PMID: 20977258 DOI: 10.1021/jm1010594] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourteen analogues of the anti-HIV-1 integrase (IN) inhibitor L-chicoric acid (L-CA) were prepared. Their IC(50) values for 3'-end processing and strand transfer against recombinant HIV-1 IN were determined in vitro, and their cell toxicities and EC(50) against HIV-1 were measured in cells (ex vivo). Compounds 1-6 are catechol/β-diketoacid hybrids, the majority of which exhibit submicromolar potency against 3'-end processing and strand transfer, though only with modest antiviral activities. Compounds 7-10 are L-CA/p-fluorobenzylpyrroloyl hybrids, several of which were more potent against strand transfer than 3'-end processing, a phenomenon previously attributed to the β-diketo acid pharmacophore. Compounds 11-14 are tetrazole bioisosteres of L-CA and its analogues, whose in vitro potencies were comparable to L-CA but with enhanced antiviral potency. The trihydroxyphenyl analogue 14 was 30-fold more potent than L-CA at relatively nontoxic concentrations. These data indicate that L-CA analogues are attractive candidates for development into clinically relevant inhibitors of HIV-1 IN.
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Affiliation(s)
- David C Crosby
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California 92697-4800, USA
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Synthesis of polyhydroxylated aromatics having amidation of piperazine nitrogen as HIV-1 integrase inhibitor. Bioorg Med Chem Lett 2010; 20:5469-71. [DOI: 10.1016/j.bmcl.2010.07.087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 06/27/2010] [Accepted: 07/21/2010] [Indexed: 11/23/2022]
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Marchand C, Maddali K, Métifiot M, Pommier Y. HIV-1 IN inhibitors: 2010 update and perspectives. Curr Top Med Chem 2010; 9:1016-37. [PMID: 19747122 DOI: 10.2174/156802609789630910] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 06/13/2009] [Indexed: 12/29/2022]
Abstract
Integrase (IN) is the newest validated target against AIDS and retroviral infections. The remarkable activity of raltegravir (Isentress((R))) led to its rapid approval by the FDA in 2007 as the first IN inhibitor. Several other IN strand transfer inhibitors (STIs) are in development with the primary goal to overcome resistance due to the rapid occurrence of IN mutations in raltegravir-treated patients. Thus, many scientists and drug companies are actively pursuing clinically useful IN inhibitors. The objective of this review is to provide an update on the IN inhibitors reported in the last two years, including second generation STI, recently developed hydroxylated aromatics, natural products, peptide, antibody and oligonucleotide inhibitors. Additionally, the targeting of IN cofactors such as LEDGF and Vpr will be discussed as novel strategies for the treatment of AIDS.
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Affiliation(s)
- Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
PURPOSE OF REVIEW Most of the studies investigating inhibition of human immunodeficiency virus integration have focused on blocking the enzymatic functions of HIV integrase, with the predominant judgment that integration inhibitors need to block at least one of the integrase-catalyzed reactions. Recent studies, however, have highlighted the importance of other proteins and their contacts with integrase in the preintegration complex, and their involvement in chromosomal integration of the viral DNA. RECENT FINDINGS Promising results of clinical trials for two new integrase inhibitors were announced recently, providing the proof of the concept for using HIV-1 integrase inhibitors as antiretroviral therapy. Two strategies are currently employed for the development of novel inhibitors of HIV integrase: synthesis of hybrid molecules comprising core structures of two or more known inhibitors, and three-dimensional pharmacophore searches based on previously discovered compounds. By highlighting the role of the cellular cofactor LEDGF/p75 in HIV integration, novel approaches are indicated that aim to develop compounds altering contact between HIV integrase and integration cofactors. SUMMARY By the discovery of novel inhibitors and targets for HIV integration, coupled with recent studies in characterizing preintegration complex formation, new insight is provided for the rational design of anti-HIV integration inhibitors.
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Synthesis and antiviral properties of some polyphenols related to Salvia genus. Bioorg Med Chem Lett 2008; 18:4736-40. [PMID: 18674899 DOI: 10.1016/j.bmcl.2008.06.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 06/17/2008] [Accepted: 06/18/2008] [Indexed: 11/20/2022]
Abstract
An efficient synthesis of the acid part of salvianolic acid E 2 is described. Compound 2 was obtained from vanillin in 10 steps and 21% overall yield. During the synthesis of 2 an unexpected 5-oxo-4b,9b-dihydroindano[1,2-b]benzofuran rac-12 was isolated. Both compounds together with the acid part of salvianolic acid D were active as HIV-1 integrase inhibitors at the submicromolar level. But they did not inhibit the replication of the virus on MT-4 cells.
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Dayam R, Gundla R, Al-Mawsawi LQ, Neamati N. HIV-1 integrase inhibitors: 2005-2006 update. Med Res Rev 2008; 28:118-54. [PMID: 17979144 DOI: 10.1002/med.20116] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) catalyzes the integration of proviral DNA into the host genome, an essential step for viral replication. Inhibition of IN catalytic activity provides an attractive strategy for antiretroviral drug design. Currently two IN inhibitors, MK-0518 and GS-9137, are in advanced stages of human clinical trials. The IN inhibitors in clinical evaluation demonstrate excellent antiretroviral efficacy alone or in combination regimens as compared to previously used clinical antiretroviral agents in naive and treatment-experienced HIV-1 infected patients. However, the emergence of viral strains resistant to clinically studied IN inhibitors and the dynamic nature of the HIV-1 genome demand a continued effort toward the discovery of novel inhibitors to keep a therapeutic advantage over the virus. Continued efforts in the field have resulted in the discovery of compounds from diverse chemical classes. In this review, we provide a comprehensive report of all IN inhibitors discovered in the years 2005 and 2006.
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Affiliation(s)
- Raveendra Dayam
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, USA
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HIV‐1 Integrase Inhibitors: Update and Perspectives. HIV-1: MOLECULAR BIOLOGY AND PATHOGENESIS 2008; 56:199-228. [DOI: 10.1016/s1054-3589(07)56007-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Dubey S, Satyanarayana YD, Lavania H. Development of integrase inhibitors for treatment of AIDS: An overview. Eur J Med Chem 2007; 42:1159-68. [PMID: 17367896 DOI: 10.1016/j.ejmech.2007.01.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Revised: 01/18/2007] [Accepted: 01/19/2007] [Indexed: 11/22/2022]
Abstract
HIV-1 integrase (IN) is an essential enzyme for retroviral replication. It is involved in the integration of HIV DNA into host chromosomal DNA. The unique properties of IN makes it an ideal target for drug design. First, there appears to have no functional equivalent in human cells and the reactions catalyzed by IN are unique. Second, IN is absolutely required for viral replication and mutations in a number of key residues block the viral replication. Third, IN has been validated as a legitimate target and the results from the molecules like S-1,360, JKT-303 which are under phase II/III clinical trials suggest synergistic effect with reverse transcriptase (RT) and protease (PR) inhibitors. During the past 10 years a plethora of inhibitors have been identified and some were shown to be selective against IN and block viral replication. The classes under which inhibitors of integrase can be classified are catechol-containing hydroxylated aromatics, diketoacid-containing aromatics, quninolines and others (non-catechol containing). In the present article we review all the recent small molecules reported to inhibit recombinant HIV-1 IN under these heads. It seems likely that the efficient use of HIV IN as target for rational design can give potent anti-HIV agents, which can be used alone or in combination regimens with other classes of anti-HIV drugs.
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Affiliation(s)
- Sonal Dubey
- K.L.E.S. College of Pharmacy, Rajajinagar II Block, Bangalore 560010, Karnataka, India.
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Tchertanov L, Mouscadet JF. Target recognition by catechols and beta-ketoenols: potential contribution of hydrogen bonding and Mn/Mg chelation to HIV-1 integrase inhibition. J Med Chem 2007; 50:1133-45. [PMID: 17302399 DOI: 10.1021/jm061375j] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catechol and beta-ketoenol are important pharmacophores of HIV-1 integrase (IN) inhibitors. We investigated their recognition of the divalent metals, Mg and Mn, and of hydrogen bond donors (HBD) and acceptors (HBA). We used data retrieved from the Cambridge Structural Database (CSD), applying a 3-D structure-based, in silico-driven approach. We found that both biophores were stabilized by intramolecular H-bonding (IHB), which was weak in catechols and very strong in beta-ketoenols. Catechols tended to recognize environmental HBD and HBA, demonstrating their ability to make use of both hydroxyl groups to form multiple, strong intermolecular H-bonds. In contrast, beta-ketoenols stabilized by strong IHB inefficiently formed intermolecular H-bonds. beta-Ketoenolate chelated both Mg and Mn ions much more efficiently than dioxolene, which was highly selective for Mn cations. The significant differences in the ability of these two pharmacophores to bind HBD and HBA and in their ability to chelate Mg and Mn have important consequences for competitive inhibitor binding and selectivity for metals and integrase DNA-binding sites.
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Affiliation(s)
- Luba Tchertanov
- Laboratoire de Biotechnologie et Pharmacologie Génétique Appliquée, CNRS UMR 8113, Ecole Normale Supérieure de Cachan, 61 av. Président Wilson, 94235 Cachan, France.
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