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Bis-3-Chloropiperidines Targeting TAR RNA as A Novel Strategy to Impair the HIV-1 Nucleocapsid Protein. Molecules 2021; 26:molecules26071874. [PMID: 33810333 PMCID: PMC8038054 DOI: 10.3390/molecules26071874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Specific RNA sequences regulate functions essential to life. The Trans-Activation Response element (TAR) is an RNA stem-bulge-loop structure involved in several steps of HIV-1 replication. In this work, we show how RNA targeting can inhibit HIV-1 nucleocapsid (NC), a highly conserved protein known to catalyze nucleic acid melting and strand transfers during reverse transcription. Our RNA targeting strategy consists of the employment of bis-3-chloropiperidines (B-CePs) to impair RNA melting through bifunctional alkylation. Specific interactions between B-CePs and TAR RNA were analytically investigated by gel electrophoresis and mass spectrometry, allowing the elucidation of B-CePs' recognition of TAR, and highlighting an RNA-directed mechanism of protein inhibition. We propose that B-CePs can freeze TAR tridimensional conformation, impairing NC-induced dynamics and finally inhibiting its functions in vitro.
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2
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Gamba E, Sosic A, Saccone I, Magli E, Frecentese F, Gatto B. Multiple in Vitro Inhibition of HIV-1 Proteins by 2,6-Dipeptidyl-anthraquinone Conjugates Targeting the PBS RNA. ACS Med Chem Lett 2020; 11:949-955. [PMID: 32435410 DOI: 10.1021/acsmedchemlett.9b00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/23/2020] [Indexed: 11/28/2022] Open
Abstract
We recently reported a series of 2,6-dipeptidyl-anthraquinone conjugates (AQs) as Trans-Activation Response element (TAR) RNA-binding agents able to inhibit in vitro the HIV-1 nucleocapsid (NC) protein-mediated processes. Because NC is a highly adaptable nucleic acid chaperone assisting several crucial steps along reverse transcription, in this study we investigate the ability of AQs to interact with other virus-derived nucleic acid structures thus potentially inhibiting multiple NC functions. Focusing on the HIV-1 Primer Binding Site (PBS) RNA sequence, we demonstrate that properly substituted dipeptidyl-anthraquinone conjugates efficiently inhibit the NC-mediated primer annealing in the low micromolar range. Similarly, we extended the analysis to the HIV-1 trans-activator of transcription (Tat) peptide, which has been recently shown to mimic the annealer functions of NC upon interacting with the same nucleic acid regulatory sequences. Our results highlight how RNA-targeting agents can act as multimode inhibitors of key viral proteins affecting their chaperone activity in reverse transcription processes.
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Affiliation(s)
- Elia Gamba
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Alice Sosic
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Irene Saccone
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Elisa Magli
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Francesco Frecentese
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
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3
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Ciaco S, Humbert N, Real E, Boudier C, Francesconi O, Roelens S, Nativi C, Seguin-Devaux C, Mori M, Mély Y. A Class of Potent Inhibitors of the HIV-1 Nucleocapsid Protein Based on Aminopyrrolic Scaffolds. ACS Med Chem Lett 2020; 11:698-705. [PMID: 32435373 DOI: 10.1021/acsmedchemlett.9b00558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/27/2020] [Indexed: 01/08/2023] Open
Abstract
The HIV-1 nucleocapsid protein 7 (NC) is a potential target for effective antiretroviral therapy due to its central role in virus replication, mainly linked to nucleic acid (NA) chaperone activity, and low susceptibility to drug resistance. By screening a compounds library, we identified the aminopyrrolic compound CN14_17, a known carbohydrate binding agent, that inhibits the NC chaperone activity in the low micromolar range. Different from most of available NC inhibitors, CN14_17 fully prevents the NC-induced annealing of complementary NA sequences. Using fluorescence assays and isothermal titration calorimetry, we found that CN14_17 competes with NC for the binding to NAs, preferentially targeting single-stranded sequences. Molecular dynamics simulations confirmed that binding to cTAR occurs preferably within the guanosine-rich single stranded sequence. Finally, CN14_17 exhibited antiretroviral activity in the low micromolar range, although with a moderate therapeutic index. Overall, CN14_17 might be the progenitor of a new promising class of NC inhibitors.
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Affiliation(s)
- Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Eléonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
| | - Oscar Francesconi
- Dipartimento di Chimica “Ugo Schiff” and INSTM, University of Florence, via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Stefano Roelens
- Dipartimento di Chimica “Ugo Schiff” and INSTM, University of Florence, via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Cristina Nativi
- Dipartimento di Chimica “Ugo Schiff” and INSTM, University of Florence, via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France
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4
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Sosic A, Saccone I, Carraro C, Kenderdine T, Gamba E, Caliendo G, Corvino A, Di Vaio P, Fiorino F, Magli E, Perissutti E, Santagada V, Severino B, Spada V, Fabris D, Frecentese F, Gatto B. Non-Natural Linker Configuration in 2,6-Dipeptidyl-Anthraquinones Enhances the Inhibition of TAR RNA Binding/Annealing Activities by HIV-1 NC and Tat Proteins. Bioconjug Chem 2018; 29:2195-2207. [PMID: 29791798 DOI: 10.1021/acs.bioconjchem.8b00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The HIV-1 nucleocapsid (NC) protein represents an excellent molecular target for the development of anti-retrovirals by virtue of its well-characterized chaperone activities, which play pivotal roles in essential steps of the viral life cycle. Our ongoing search for candidates able to impair NC binding/annealing activities led to the identification of peptidyl-anthraquinones as a promising class of nucleic acid ligands. Seeking to elucidate the inhibition determinants and increase the potency of this class of compounds, we have now explored the effects of chirality in the linker connecting the planar nucleus to the basic side chains. We show here that the non-natural linker configuration imparted unexpected TAR RNA targeting properties to the 2,6-peptidyl-anthraquinones and significantly enhanced their potency. Even if the new compounds were able to interact directly with the NC protein, they manifested a consistently higher affinity for the TAR RNA substrate and their TAR-binding properties mirrored their ability to interfere with NC-TAR interactions. Based on these findings, we propose that the viral Tat protein, sharing the same RNA substrate but acting in distinct phases of the viral life cycle, constitutes an additional druggable target for this class of peptidyl-anthraquinones. The inhibition of Tat-TAR interaction for the test compounds correlated again with their TAR-binding properties, while simultaneously failing to demonstrate any direct Tat-binding capabilities. These considerations highlighted the importance of TAR RNA in the elucidation of their inhibition mechanism, rather than direct protein inhibition. We have therefore identified anti-TAR compounds with dual in vitro inhibitory activity on different viral proteins, demonstrating that it is possible to develop multitarget compounds capable of interfering with processes mediated by the interactions of this essential RNA domain of HIV-1 genome with NC and Tat proteins.
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Affiliation(s)
- Alice Sosic
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Irene Saccone
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Caterina Carraro
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Thomas Kenderdine
- The RNA Institute and Department of Chemistry , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Elia Gamba
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Giuseppe Caliendo
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Angela Corvino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Paola Di Vaio
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Ferdinando Fiorino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Elisa Magli
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Elisa Perissutti
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Vincenzo Santagada
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Beatrice Severino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Valentina Spada
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Dan Fabris
- The RNA Institute and Department of Chemistry , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Francesco Frecentese
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
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5
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Iraci N, Tabarrini O, Santi C, Sancineto L. NCp7: targeting a multitask protein for next-generation anti-HIV drug development part 2. Noncovalent inhibitors and nucleic acid binders. Drug Discov Today 2018; 23:687-695. [PMID: 29326078 DOI: 10.1016/j.drudis.2018.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Nucleocapsid protein 7 (NCp7) represents a viable target not yet reached by the currently available antiretrovirals. It is a small and highly basic protein, which is essential for multiple stages of the viral replicative cycle, with its structure preserved in all viral strains, including clinical isolates. NCp7 can be inhibited covalently, noncovalently and by shielding the nucleic acid (NA) substrates of its chaperone activity. Although covalent NCp7 inhibitors have already been detailed in the first part of this review series, the focus here is based on noncovalent and NA-binder inhibitors and on the analysis of the NCp7 3D structure to deliver fruitful insights for future drug design strategies.
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Affiliation(s)
- Nunzio Iraci
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Luca Sancineto
- Department of Heterorganic Chemistry, Centre of Molecular and Macromulecular Studies, Lodz, Poland.
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6
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Identification of novel 2-benzoxazolinone derivatives with specific inhibitory activity against the HIV-1 nucleocapsid protein. Eur J Med Chem 2017; 145:154-164. [PMID: 29324338 DOI: 10.1016/j.ejmech.2017.12.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/16/2017] [Accepted: 12/20/2017] [Indexed: 11/23/2022]
Abstract
In this report, we present a new benzoxazole derivative endowed with inhibitory activity against the HIV-1 nucleocapsid protein (NC). NC is a 55-residue basic protein with nucleic acid chaperone properties, which has emerged as a novel and potential pharmacological target against HIV-1. In the pursuit of novel NC-inhibitor chemotypes, we performed virtual screening and in vitro biological evaluation of a large library of chemical entities. We found that compounds sharing a benzoxazolinone moiety displayed putative inhibitory properties, which we further investigated by considering a series of chemical analogues. This approach provided valuable information on the structure-activity relationships of these compounds and, in the process, demonstrated that their anti-NC activity could be finely tuned by the addition of specific substituents to the initial benzoxazolinone scaffold. This study represents the starting point for the possible development of a new class of antiretroviral agents targeting the HIV-1 NC protein.
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7
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Zoidis G, Sosic A, Da Ros S, Gatto B, Sissi C, Palluotto F, Carotti A, Catto M. Indenocinnoline derivatives as G-quadruplex binders, topoisomerase IIα inhibitors and antiproliferative agents. Bioorg Med Chem 2017; 25:2625-2634. [PMID: 28342691 DOI: 10.1016/j.bmc.2017.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/21/2017] [Accepted: 03/07/2017] [Indexed: 11/30/2022]
Abstract
DNA intercalating agents are a consolidated therapeutic option in the treatment of tumor diseases. Starting from previous findings in the antiproliferative efficacy of a series of indeno[1,2-c]cinnoline-11-one derivatives, we performed a suitable decoration of this scaffold by means of a simple and straightforward chemistry, aiming to a) enlarge the planar core to a pentacyclic benzo[h]indeno[1,2-c]cinnoline-13-one and b) introduce a basic head tethered through a simple polymethylene chain. In fluorescence melting and fluorescence intercalator displacement assays, these new compounds displayed fair to very good intercalating properties on different nucleic acid strands, with preference for G-quadruplex sequences. Inhibition of human topoisomerase IIα and antiproliferative assays on HeLa and MCF7 tumor cell lines outlined a multitarget antiproliferative profile for tetracyclic 6 and pentacyclic derivative 20, both bearing a N,N-dimethylamine as the protonatable moiety. Particularly, compound 6 displayed a very potent inhibition of tumor cell proliferation, while 20 returned the highest thermal stabilization in melting experiments. In summary, these results outlined a potential of such highly planar scaffolds for nucleic acid binding and antiproliferative effects.
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Affiliation(s)
- Grigoris Zoidis
- School of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimioupoli-Zografou, GR-15771 Athens, Greece
| | - Alice Sosic
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Silvia Da Ros
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Claudia Sissi
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Fausta Palluotto
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy
| | - Angelo Carotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy
| | - Marco Catto
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy.
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8
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Ghose A, Maltsev OV, Humbert N, Hintermann L, Arntz Y, Naumov P, Mély Y, Didier P. Oxyluciferin Derivatives: A Toolbox of Environment-Sensitive Fluorescence Probes for Molecular and Cellular Applications. J Phys Chem B 2017; 121:1566-1575. [PMID: 28118001 DOI: 10.1021/acs.jpcb.6b12616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this work, we used firefly oxyluciferin (OxyLH2) and its polarity-dependent fluorescence mechanism as a sensitive tool to monitor biomolecular interactions. The chromophores, OxyLH2, and its two analogues, 4-MeOxyLH and 4,6'-DMeOxyL, were modified trough carboxylic functionalization and then coupled to the N-terminus part of Tat and NCp7 peptides of human immunodeficiency virus type-1 (HIV-1). The photophysical properties of the labeled peptides were studied in live cells as well as in complex with different oligonucleotides in solution. By monitoring the emission properties of these derivatives we were able, for the first time, to study in vitro biomolecular interactions using oxyluciferin as a sensor. As an additional application, cyclopropyl-oxyluciferin (5,5-Cpr-OxyLH) was site-specifically conjugated to the thiol group (Cys-232) of the human protein α-1 antytripsin to investigate its interaction with porcine pancreatic elastase. Our data demonstrate that OxyLH2 and its derivatives can be used as fluorescence reporters for monitoring biomolecular interactions.
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Affiliation(s)
- Avisek Ghose
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 du CNRS, Faculté de Pharmacie, Université de Strasbourg , 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Oleg V Maltsev
- Department Chemie, Technische Universität München , Lichtenbergstr. 4, 85748 Garching bei München, Germany
| | - Nicolas Humbert
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 du CNRS, Faculté de Pharmacie, Université de Strasbourg , 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Lukas Hintermann
- Department Chemie, Technische Universität München , Lichtenbergstr. 4, 85748 Garching bei München, Germany
| | - Youri Arntz
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 du CNRS, Faculté de Pharmacie, Université de Strasbourg , 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Panče Naumov
- New York University Abu Dhabi , P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 du CNRS, Faculté de Pharmacie, Université de Strasbourg , 74, Route du Rhin, 67401 Illkirch Cedex, France
| | - Pascal Didier
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 du CNRS, Faculté de Pharmacie, Université de Strasbourg , 74, Route du Rhin, 67401 Illkirch Cedex, France
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9
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Frecentese F, Sosic A, Saccone I, Gamba E, Link K, Miola A, Cappellini M, Cattelan MG, Severino B, Fiorino F, Magli E, Corvino A, Perissutti E, Fabris D, Gatto B, Caliendo G, Santagada V. Synthesis and in Vitro Screening of New Series of 2,6-Dipeptidyl-anthraquinones: Influence of Side Chain Length on HIV-1 Nucleocapsid Inhibitors. J Med Chem 2016; 59:1914-24. [PMID: 26797100 DOI: 10.1021/acs.jmedchem.5b01494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2,6-Dipeptidyl-anthraquinones are a promising class of nucleic acid-binding compounds that act as NC inhibitors in vitro. We designed, synthesized, and tested new series of 2,6-disubstituted-anthraquinones, which are able to bind viral nucleic acid substrates of NC. We demonstrate here that these novel derivatives interact preferentially with noncanonical structures of TAR and cTAR, stabilize their dynamics, and interfere with NC chaperone activity.
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Affiliation(s)
- Francesco Frecentese
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Alice Sosic
- Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
| | - Irene Saccone
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Elia Gamba
- Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
| | - Kristina Link
- Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
| | - Angelica Miola
- Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
| | - Marta Cappellini
- Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
| | | | - Beatrice Severino
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Ferdinando Fiorino
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Elisa Magli
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Angela Corvino
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Elisa Perissutti
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Dan Fabris
- The RNA Institute and Department of Chemistry, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
| | - Giuseppe Caliendo
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Santagada
- Dipartimento di Farmacia, Università di Napoli "Federico II" Via D. Montesano 49, 80131 Napoli, Italy
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10
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Sosic A, Sinigaglia L, Cappellini M, Carli I, Parolin C, Zagotto G, Sabatino G, Rovero P, Fabris D, Gatto B. Mechanisms of HIV-1 Nucleocapsid Protein Inhibition by Lysyl-Peptidyl-Anthraquinone Conjugates. Bioconjug Chem 2015; 27:247-56. [PMID: 26666402 DOI: 10.1021/acs.bioconjchem.5b00627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Nucleocapsid protein NCp7 (NC) is a nucleic acid chaperone responsible for essential steps of the HIV-1 life cycle and an attractive candidate for drug development. NC destabilizes nucleic acid structures and promotes the formation of annealed substrates for HIV-1 reverse transcription elongation. Short helical nucleic acid segments bordered by bulges and loops, such as the Trans-Activation Response element (TAR) of HIV-1 and its complementary sequence (cTAR), are nucleation elements for helix destabilization by NC and also preferred recognition sites for threading intercalators. Inspired by these observations, we have recently demonstrated that 2,6-disubstituted peptidyl-anthraquinone-conjugates inhibit the chaperone activities of recombinant NC in vitro, and that inhibition correlates with the stabilization of TAR and cTAR stem-loop structures. We describe here enhanced NC inhibitory activity by novel conjugates that exhibit longer peptidyl chains ending with a conserved N-terminal lysine. Their efficient inhibition of TAR/cTAR annealing mediated by NC originates from the combination of at least three different mechanisms, namely, their stabilizing effects on nucleic acids dynamics by threading intercalation, their ability to target TAR RNA substrate leading to a direct competition with the protein for the same binding sites on TAR, and, finally, their effective binding to the NC protein. Our results suggest that these molecules may represent the stepping-stone for the future development of NC-inhibitors capable of targeting the protein itself and its recognition site in RNA.
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Affiliation(s)
| | | | | | | | | | | | | | - Paolo Rovero
- Dipartimento NeuroFarBa, Sezione di Scienze Farmaceutiche e Nutraceutica, Università di Firenze , 50121 Firenze, Italy
| | - Dan Fabris
- Department of Chemistry, State University of New York , Albany, New York 12222, United States
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11
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Mori M, Kovalenko L, Lyonnais S, Antaki D, Torbett BE, Botta M, Mirambeau G, Mély Y. Nucleocapsid Protein: A Desirable Target for Future Therapies Against HIV-1. Curr Top Microbiol Immunol 2015; 389:53-92. [PMID: 25749978 PMCID: PMC7122173 DOI: 10.1007/82_2015_433] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial to infected patients. However, clinical failures occur as a result of the ability of HIV-1 to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to noninfectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within the last few years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.
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Affiliation(s)
- Mattia Mori
- Dipartimento di Biotecnologie Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
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Sosic A, Cappellini M, Sinigaglia L, Jacquet R, Deffieux D, Fabris D, Quideau S, Gatto B. Polyphenolic C-glucosidic ellagitannins present in oak-aged wine inhibit HIV-1 nucleocapsid protein. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Garg D, Torbett BE. Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy. Virus Res 2014; 193:135-43. [PMID: 25026536 PMCID: PMC4252855 DOI: 10.1016/j.virusres.2014.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.
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Affiliation(s)
- Divita Garg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Retrospective on the all-in-one retroviral nucleocapsid protein. Virus Res 2014; 193:2-15. [PMID: 24907482 PMCID: PMC7114435 DOI: 10.1016/j.virusres.2014.05.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/11/2014] [Accepted: 05/11/2014] [Indexed: 01/08/2023]
Abstract
This retrospective reviews 30 years of research on the retroviral nucleocapsid protein (NC) focusing on HIV-1 NC. Originally considered as a non-specific nucleic-acid binding protein, NC has seminal functions in virus replication. Indeed NC turns out to be a all-in-one viral protein that chaperones viral DNA synthesis and integration, and virus formation. As a chaperone NC provides assistance to genetic recombination thus allowing the virus to escape the immune response and antiretroviral therapies against HIV-1.
This review aims at briefly presenting a retrospect on the retroviral nucleocapsid protein (NC), from an unspecific nucleic acid binding protein (NABP) to an all-in-one viral protein with multiple key functions in the early and late phases of the retrovirus replication cycle, notably reverse transcription of the genomic RNA and viral DNA integration into the host genome, and selection of the genomic RNA together with the initial steps of virus morphogenesis. In this context we will discuss the notion that NC protein has a flexible conformation and is thus a member of the growing family of intrinsically disordered proteins (IDPs) where disorder may account, at least in part, for its function as a nucleic acid (NA) chaperone and possibly as a protein chaperone vis-à-vis the viral DNA polymerase during reverse transcription. Lastly, we will briefly review the development of new anti-retroviral/AIDS compounds targeting HIV-1 NC because it represents an ideal target due to its multiple roles in the early and late phases of virus replication and its high degree of conservation.
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