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Robello M, Nikolayevskiy H, Scerba MT, Nahui Palomino RA, Mercurio V, Appella DH. Prodrug Strategy Extends the Use of Anti-HIV Sulfanylbenzamides for Application In Vivo. ACS Pharmacol Transl Sci 2024; 7:259-273. [PMID: 38250006 PMCID: PMC10795369 DOI: 10.1021/acsptsci.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/23/2024]
Abstract
Sulfanylbenzamide thioesters are molecules with anti-HIV activity that disrupt zinc coordination in the viral protein NCp7. These molecules are useful as topical microbicides; however, they are too unstable to be used systemically. In this article, a nitroimidazole prodrug was used to protect the sulfanylbenzamide to convey blood stability and oral bioavailability to the molecule. Studies on the molecule called nipamovir were performed to assess the rate of prodrug cleavage, antiviral activity, mechanism of metabolism, and in vivo pharmacokinetics in several different species. An efficient and inexpensive synthesis of nipamovir is also described. The results indicate that nipamovir could be further developed as a new type of drug to treat HIV infection.
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Affiliation(s)
- Marco Robello
- Synthetic Bioactive Molecules Section, Laboratory of
Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney
Diseases (NIDDK), National Institutes of Health, 8 Center
Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Herman Nikolayevskiy
- Synthetic Bioactive Molecules Section, Laboratory of
Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney
Diseases (NIDDK), National Institutes of Health, 8 Center
Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Michael T. Scerba
- Synthetic Bioactive Molecules Section, Laboratory of
Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney
Diseases (NIDDK), National Institutes of Health, 8 Center
Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Rogers Alberto Nahui Palomino
- Section on Intercellular Interactions, Eunice Kennedy
Shriver National Institute of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20892, United
States
| | - Vincenzo Mercurio
- Section on Intercellular Interactions, Eunice Kennedy
Shriver National Institute of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20892, United
States
| | - Daniel H. Appella
- Synthetic Bioactive Molecules Section, Laboratory of
Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney
Diseases (NIDDK), National Institutes of Health, 8 Center
Drive, Room 404, Bethesda, Maryland 20892, United States
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2
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Persistent prevalence of non-covalent interaction in pyrimidine containing sulfonamide derivative: A quantum computational analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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3
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Yang R, Bi XD, Li Y, Liu M, Hu MQ, Zhao LM, Zhang H, Gao F. Scorpion-Shaped Zinc Porphyrins as Tetrafunctional TAR RNA Predators and HIV-1 Reverse Transcriptase Inhibitors. Inorg Chem 2022; 61:10774-10780. [PMID: 35796528 DOI: 10.1021/acs.inorgchem.2c00975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 reverse transcriptase (RT) inhibitors are fundamental to the discovery and development of anti-HIV drugs. Their main target is RT, and only a tiny number of them can bind to viral RNA. In this paper, five new Zn(II) porphyrin compounds were developed with different characters. ZnTPP4 has both the appearance and the functions of a scorpion with a rigid tail and stinger to selectively hunt HIV-1 TAR RNA based on the molecular recognition of hydrogen bonds, a fierce chelicera to bite RNA by metal coordination, mighty pedipalps to grasp the bound RNA by supramolecular inclusion, and a broad body maintaining the configuration of each functional area so that they can cooperate with each other and providing accommodation space for the bound RNA. This tetrafunctional Zn(II) porphyrin is relatively nontoxic to normal cells and can produce sensitive responses for RNA. Moreover, this work offers practical construction methodologies for medication of AIDS and other diseases closely related to RT like EBOV and SARS-CoV-2.
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Affiliation(s)
- Rong Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Xu-Dan Bi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Yan Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Meng Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Man-Qi Hu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Li-Min Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
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Hsu JN, Chen JS, Lin SM, Hong JY, Chen YJ, Jeng US, Luo SY, Hou MH. Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation. Front Mol Biosci 2022; 9:871499. [PMID: 35517857 PMCID: PMC9061996 DOI: 10.3389/fmolb.2022.871499] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/17/2022] [Indexed: 12/20/2022] Open
Abstract
Epidemics caused by coronaviruses (CoVs), namely the severe acute respiratory syndrome (SARS) (2003), Middle East respiratory syndrome (MERS) (2012), and coronavirus disease 2019 (COVID-19) (2019), have triggered a global public health emergency. Drug development against CoVs is inherently arduous. The nucleocapsid (N) protein forms an oligomer and facilitates binding with the viral RNA genome, which is critical in the life cycle of the virus. In the current study, we found a potential allosteric site (Site 1) using PARS, an online allosteric site predictor, in the CoV N-N-terminal RNA-binding domain (NTD) to modulate the N protein conformation. We identified 5-hydroxyindole as the lead via molecular docking to target Site 1. We designed and synthesized four 5-hydroxyindole derivatives, named P4-1 to P4-4, based on the pose of 5-hydroxyindole in the docking model complex. Small-angle X-ray scattering (SAXS) data indicate that two 5-hydroxyindole compounds with higher hydrophobic R-groups mediate the binding between N-NTD and N-C-terminal dimerization domain (CTD) and elicit high-order oligomerization of the whole N protein. Furthermore, the crystal structures suggested that these two compounds act on this novel cavity and create a flat surface with higher hydrophobicity, which may mediate the interaction between N-NTD and N-CTD. Taken together, we discovered an allosteric binding pocket targeting small molecules that induces abnormal aggregation of the CoV N protein. These novel concepts will facilitate protein-protein interaction (PPI)-based drug design against various CoVs.
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Affiliation(s)
- Jia-Ning Hsu
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jyun-Siao Chen
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Shan-Meng Lin
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jhen-Yi Hong
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Jheng Chen
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Shun-Yuan Luo
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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5
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Investigation of the Low-Populated Excited States of the HIV-1 Nucleocapsid Domain. Viruses 2022; 14:v14030632. [PMID: 35337039 PMCID: PMC8950434 DOI: 10.3390/v14030632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
The nucleocapsid domain (NCd), located at the C-terminus of the HIV-1 Gag protein, is involved in numerous stages of the replication cycle, such as the packaging of the viral genome and reverse transcription. It exists under different forms through the viral life cycle, depending on the processing of Gag by the HIV-1 protease. NCd is constituted of two adjacent zinc knuckles (ZK1 and ZK2), separated by a flexible linker and flanked by disordered regions. Here, conformational equilibria between a major and two minor states were highlighted exclusively in ZK2, by using CPMG and CEST NMR experiments. These minor states appear to be temperature dependent, and their populations are highest at physiological temperature. These minor states are present both in NCp7, the mature form of NCd, and in NCp9 and NCp15, the precursor forms of NCd, with increased populations. The role of these minor states in the targeting of NCd by drugs and its binding properties is discussed.
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6
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Fullerene Derivatives Prevent Packaging of Viral Genomic RNA into HIV-1 Particles by Binding Nucleocapsid Protein. Viruses 2021; 13:v13122451. [PMID: 34960720 PMCID: PMC8705927 DOI: 10.3390/v13122451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 02/02/2023] Open
Abstract
Fullerene derivatives with hydrophilic substituents have been shown to exhibit a range of biological activities, including antiviral ones. For a long time, the anti-HIV activity of fullerene derivatives was believed to be due to their binding into the hydrophobic pocket of HIV-1 protease, thereby blocking its activity. Recent work, however, brought new evidence of a novel, protease-independent mechanism of fullerene derivatives' action. We studied in more detail the mechanism of the anti-HIV-1 activity of N,N-dimethyl[70]fulleropyrrolidinium iodide fullerene derivatives. By using a combination of in vitro and cell-based approaches, we showed that these C70 derivatives inhibited neither HIV-1 protease nor HIV-1 maturation. Instead, our data indicate effects of fullerene C70 derivatives on viral genomic RNA packaging and HIV-1 cDNA synthesis during reverse transcription-without impairing reverse transcriptase activity though. Molecularly, this could be explained by a strong binding affinity of these fullerene derivatives to HIV-1 nucleocapsid domain, preventing its proper interaction with viral genomic RNA, thereby blocking reverse transcription and HIV-1 infectivity. Moreover, the fullerene derivatives' oxidative activity and fluorescence quenching, which could be one of the reasons for the inconsistency among reported anti-HIV-1 mechanisms, are discussed herein.
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7
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Lyonnais S, Sadiq SK, Lorca-Oró C, Dufau L, Nieto-Marquez S, Escribà T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart JC, Meyerhans A, Tisné C, Gorelick RJ, Mirambeau G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation. Viruses 2021; 13:v13112312. [PMID: 34835118 PMCID: PMC8625067 DOI: 10.3390/v13112312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase-separated molecular ‘sponges’, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retroviruses such as HIV-1 form by self-assembly when their genomic RNA (gRNA) traps Gag and GagPol polyprotein precursors. Infectivity requires extracellular budding of the particle followed by maturation, an ordered processing of ∼2400 Gag and ∼120 GagPol by the viral protease (PR). This leads to a condensed gRNA-NCp7 nucleocapsid and a CAp24-self-assembled capsid surrounding the RNP. The choreography by which all of these components dynamically interact during virus maturation is one of the missing milestones to fully depict the HIV life cycle. Here, we describe how HIV-1 has evolved a dynamic RNP granule with successive weak–strong–moderate quinary NC-gRNA networks during the sequential processing of the GagNC domain. We also reveal two palindromic RNA-binding triads on NC, KxxFxxQ and QxxFxxK, that provide quinary NC-gRNA interactions. Consequently, the nucleocapsid complex appears properly aggregated for capsid reassembly and reverse transcription, mandatory processes for viral infectivity. We show that PR is sequestered within this RNP and drives its maturation/condensation within minutes, this process being most effective at the end of budding. We anticipate such findings will stimulate further investigations of quinary interactions and emergent mechanisms in crowded environments throughout the wide and growing array of RNP granules.
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Affiliation(s)
- Sébastien Lyonnais
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Centre d’Etudes des Maladies Infectieuses et Pharmacologie Anti-Infectieuse (CEMIPAI), CNRS UAR 3725, Université de Montpellier, 1919 Route de Mende, CEDEX 05, 34293 Montpellier, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - S. Kashif Sadiq
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence: (S.L.); (S.K.S.); (G.M.)
| | - Cristina Lorca-Oró
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Laure Dufau
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Sara Nieto-Marquez
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Tuixent Escribà
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Natalia Gabrielli
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Xiao Tan
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - Mohamed Ouizougun-Oubari
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Josephine Okoronkwo
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
| | - Michèle Reboud-Ravaux
- Biological Adaptation and Ageing (B2A), CNRS UMR 8256 & INSERM ERL U1164, Institut de Biologie Paris-Seine (IBPS), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 7 Quai St Bernard, CEDEX 05, 75252 Paris, France; (L.D.); (M.R.-R.)
| | - José Maria Gatell
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Facultat de Medicina y Ciencias de la Salud, Universitat de Barcelona, Carrer de Casanova 143, 08036 Barcelona, Spain
| | - Roland Marquet
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l’ARN, CNRS UPR 9002, Université de Strasbourg, 2 Allée Conrad Roentgen, 67000 Strasbourg, France; (R.M.); (J.-C.P.)
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain
| | - Carine Tisné
- Expression Génétique Microbienne, CNRS UMR 8261, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA;
| | - Gilles Mirambeau
- Infectious Disease & AIDS Research Unit, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Villaroel 170, 08036 Barcelona, Spain; (C.L.-O.); (S.N.-M.); (T.E.); (N.G.); (X.T.); (M.O.-O.); (J.O.); (J.M.G.)
- Biologie Intégrative des Organismes Marins (BIOM), CNRS UMR 7232, Observatoire Océanologique de Banyuls (OOB), Faculté des Sciences et d’Ingénierie (FSI), Sorbonne Université, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
- Correspondence: (S.L.); (S.K.S.); (G.M.)
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8
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Skoreński M, Sieńczyk M. The Fellowship of Privileged Scaffolds-One Structure to Inhibit Them All. Pharmaceuticals (Basel) 2021; 14:ph14111164. [PMID: 34832946 PMCID: PMC8622370 DOI: 10.3390/ph14111164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past few years, the application of privileged structure has emerged as a powerful approach to the discovery of new biologically active molecules. Privileged structures are molecular scaffolds with binding properties to the range of different biological targets. Moreover, privileged structures typically exhibit good drug-like properties, thus assuring more drug-like properties of modified compound. Our main objective is to discuss the privileged structures used for the development of antiviral agents.
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9
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Wang R, Wei Y, Wang M, Yan P, Jiang H, Du Z. Interaction of Natural Compounds in Licorice and Turmeric with HIV-NCp7 Zinc Finger Domain: Potential Relevance to the Mechanism of Antiviral Activity. Molecules 2021; 26:molecules26123563. [PMID: 34200973 PMCID: PMC8230585 DOI: 10.3390/molecules26123563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023] Open
Abstract
Nucleocapsid proteins (NCp) are zinc finger (ZF) proteins, and they play a central role in HIV virus replication, mainly by interacting with nucleic acids. Therefore, they are potential targets for anti-HIV therapy. Natural products have been shown to be able to inhibit HIV, such as turmeric and licorice, which is widely used in traditional Chinese medicine. Liquiritin (LQ), isoliquiritin (ILQ), glycyrrhizic acid (GL), glycyrrhetinic acid (GA) and curcumin (CUR), which were the major active components, were herein chosen to study their interactions with HIV-NCp7 C-terminal zinc finger, aiming to find the potential active compounds and reveal the mechanism involved. The stacking interaction between NCp7 tryptophan and natural compounds was evaluated by fluorescence. To elucidate the binding mode, mass spectrometry was used to characterize the reaction mixture between zinc finger proteins and active compounds. Subsequently, circular dichroism (CD) spectroscopy and molecular docking were used to validate and reveal the binding mode from a structural perspective. The results showed that ILQ has the strongest binding ability among the tested compounds, followed by curcumin, and the interaction between ILQ and the NCp7 zinc finger peptide was mediated by a noncovalent interaction. This study provided a scientific basis for the antiviral activity of turmeric and licorice.
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Affiliation(s)
- Runjing Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
- Ningxia Pharmaceutical Inspection and Research Institute, Yinchuan 750001, China
| | - Yinyu Wei
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Meiqin Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Pan Yan
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Hongliang Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
| | - Zhifeng Du
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China; (R.W.); (Y.W.); (M.W.); (P.Y.); (H.J.)
- Correspondence:
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10
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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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11
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Inhibitory Effect of Lithospermic Acid on the HIV-1 Nucleocapsid Protein. Molecules 2020; 25:molecules25225434. [PMID: 33233563 PMCID: PMC7699738 DOI: 10.3390/molecules25225434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a desirable target in antiretroviral therapy due to its high conservation among HIV-1 strains, and to its multiple and crucial roles in the HIV-1 replication cycle. Natural products represent a valuable source of NC inhibitors, with the catechol group being a privileged scaffold in NC inhibition. By coupling molecular modeling with NMR spectroscopy and fluorescence-based assays, we disclosed lithospermic acid, a catechol derivative extracted from Salvia miltiorrhizza, as a potent and chemically stable non-covalent inhibitor of the NC. Being different from other catechol derivative reported so far, lithospermic acid does not undergo spontaneous oxidation in physiological conditions, thus becoming a profitable starting point for the development of efficient NC inhibitors.
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Monette A, Mouland AJ. Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates. Viruses 2020; 12:E1179. [PMID: 33081049 PMCID: PMC7589941 DOI: 10.3390/v12101179] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a rapidly growing research focus due to numerous demonstrations that many cellular proteins phase-separate to form biomolecular condensates (BMCs) that nucleate membraneless organelles (MLOs). A growing repertoire of mechanisms supporting BMC formation, composition, dynamics, and functions are becoming elucidated. BMCs are now appreciated as required for several steps of gene regulation, while their deregulation promotes pathological aggregates, such as stress granules (SGs) and insoluble irreversible plaques that are hallmarks of neurodegenerative diseases. Treatment of BMC-related diseases will greatly benefit from identification of therapeutics preventing pathological aggregates while sparing BMCs required for cellular functions. Numerous viruses that block SG assembly also utilize or engineer BMCs for their replication. While BMC formation first depends on prion-like disordered protein domains (PrLDs), metal ion-controlled RNA-binding domains (RBDs) also orchestrate their formation. Virus replication and viral genomic RNA (vRNA) packaging dynamics involving nucleocapsid (NC) proteins and their orthologs rely on Zinc (Zn) availability, while virus morphology and infectivity are negatively influenced by excess Copper (Cu). While virus infections modify physiological metal homeostasis towards an increased copper to zinc ratio (Cu/Zn), how and why they do this remains elusive. Following our recent finding that pan-retroviruses employ Zn for NC-mediated LLPS for virus assembly, we present a pan-virus bioinformatics and literature meta-analysis study identifying metal-based mechanisms linking virus-induced BMCs to neurodegenerative disease processes. We discover that conserved degree and placement of PrLDs juxtaposing metal-regulated RBDs are associated with disease-causing prion-like proteins and are common features of viral proteins responsible for virus capsid assembly and structure. Virus infections both modulate gene expression of metalloproteins and interfere with metal homeostasis, representing an additional virus strategy impeding physiological and cellular antiviral responses. Our analyses reveal that metal-coordinated virus NC protein PrLDs initiate LLPS that nucleate pan-virus assembly and contribute to their persistence as cell-free infectious aerosol droplets. Virus aerosol droplets and insoluble neurological disease aggregates should be eliminated by physiological or environmental metals that outcompete PrLD-bound metals. While environmental metals can control virus spreading via aerosol droplets, therapeutic interference with metals or metalloproteins represent additional attractive avenues against pan-virus infection and virus-exacerbated neurological diseases.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
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13
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Occupation of a thermoresistant-scaffold (αRep) at SP1-NC cleavage site disturbs the function of HIV-1 protease. Biosci Rep 2020; 40:225239. [PMID: 32519747 PMCID: PMC7313444 DOI: 10.1042/bsr20201131] [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: 04/09/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 11/25/2022] Open
Abstract
HIV-1 nucleocapsid (NC) becomes an attractive target for the development of novel anti-HIV-1 agents. Discovering of non-antibody scaffolds that disrupt the function of NC will be a potential aspect for disturbing viral maturation process. Correspondingly, we explored the specific binding site of the thermoresistant-scaffold protein, αRep9A8 which formerly demonstrated the inhibitory effect on HIV-1 replication. The portion of Gag, CA21-SP1-NC has been used as a template for designing nine overlapping peptides (P4–P12). The P9 peptide showed the strongest binding activity followed by P8 and P12 respectively. The amino acid sequences on those peptides resemble the N-terminal domain of the NC proximity to the SP1-NC initial cleavage site and across the conserved CCHC zinc finger 1 (ZF1) of NC. The interaction KD between αRep9A8 with its target was 224.9 ± 57.4 nM. Consequently, αRep9A8 demonstrated the interference of the HIV-1 protease function by hindering a protease cleavage site. The released NC product from CA21-SP1-NC was diminished. The present study provided an additional information of αRep9A8 function in interfering of viral maturation processes resulting in the decremental efficiency of viral infectivity.
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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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15
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Malancona S, Mori M, Fezzardi P, Santoriello M, Basta A, Nibbio M, Kovalenko L, Speziale R, Battista MR, Cellucci A, Gennari N, Monteagudo E, Di Marco A, Giannini A, Sharma R, Pires M, Real E, Zazzi M, Dasso Lang MC, De Forni D, Saladini F, Mely Y, Summa V, Harper S, Botta M. 5,6-Dihydroxypyrimidine Scaffold to Target HIV-1 Nucleocapsid Protein. ACS Med Chem Lett 2020; 11:766-772. [PMID: 32435383 DOI: 10.1021/acsmedchemlett.9b00608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/19/2020] [Indexed: 01/27/2023] Open
Abstract
The HIV-1 nucleocapsid (NC) protein is a small basic DNA and RNA binding protein that is absolutely necessary for viral replication and thus represents a target of great interest to develop new anti-HIV agents. Moreover, the highly conserved sequence offers the opportunity to escape the drug resistance (DR) that emerged following the highly active antiretroviral therapy (HAART) treatment. On the basis of our previous research, nordihydroguaiaretic acid 1 acts as a NC inhibitor showing moderate antiviral activity and suboptimal drug-like properties due to the presence of the catechol moieties. A bioisosteric catechol replacement approach led us to identify the 5-dihydroxypyrimidine-6-carboxamide substructure as a privileged scaffold of a new class of HIV-1 NC inhibitors. Hit validation efforts led to the identification of optimized analogs, as represented by compound 28, showing improved NC inhibition and antiviral activity as well as good ADME and PK properties.
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Affiliation(s)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Paola Fezzardi
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | | | - Andreina Basta
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Martina Nibbio
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | | | | | | | - Nadia Gennari
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | | | | | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Manuel Pires
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | | | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Vincenzo Summa
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
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16
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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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17
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Humbert N, Kovalenko L, Saladini F, Giannini A, Pires M, Botzanowski T, Cherenok S, Boudier C, Sharma KK, Real E, Zaporozhets OA, Cianférani S, Seguin-Devaux C, Poggialini F, Botta M, Zazzi M, Kalchenko VI, Mori M, Mély Y. (Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity. ACS Infect Dis 2020; 6:687-702. [PMID: 32045204 DOI: 10.1021/acsinfecdis.9b00290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties mediated by its two zinc fingers and basic residues. NC is a promising target for antiviral therapy, particularly to control viral strains resistant to currently available drugs. Since calixarenes with antiviral properties have been described, we explored the ability of calixarene hydroxymethylphosphonic or sulfonic acids to inhibit NC chaperone properties and exhibit antiviral activity. By using fluorescence-based assays, we selected four calixarenes inhibiting NC chaperone activity with submicromolar IC50 values. These compounds were further shown by mass spectrometry, isothermal titration calorimetry, and fluorescence anisotropy to bind NC with no zinc ejection and to compete with nucleic acids for the binding to NC. Molecular dynamic simulations further indicated that these compounds interact via their phosphonate or sulfonate groups with the basic surface of NC but not with the hydrophobic plateau at the top of the folded fingers. Cellular studies showed that the most soluble compound CIP201 inhibited the infectivity of wild-type and drug-resistant HIV-1 strains at low micromolar concentrations, primarily targeting the early steps of HIV-1 replication. Moreover, CIP201 was also found to inhibit the flipping and polymerization activity of reverse transcriptase. Calixarenes thus form a class of noncovalent NC inhibitors, endowed with a new binding mode and multitarget antiviral activity.
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Affiliation(s)
- Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Manuel Pires
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Sergiy Cherenok
- Institute of Organic Chemistry, National Academy of Science of Ukraine, Murmanska str. 5, Kyiv 02660, Ukraine
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Kamal K. Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Olga A. Zaporozhets
- Department of Chemistry, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg
| | - Federica Poggialini
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 Università degli Studi di Siena, via Aldo Moro 2, I-53019 Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, viale Mario Bracci no. 16, 53100 Siena, Italy
| | - Vitaly I. Kalchenko
- Institute of Organic Chemistry, National Academy of Science of Ukraine, Murmanska str. 5, Kyiv 02660, Ukraine
| | - 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, Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
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18
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Dick A, Cocklin S. Recent Advances in HIV-1 Gag Inhibitor Design and Development. Molecules 2020; 25:molecules25071687. [PMID: 32272714 PMCID: PMC7181048 DOI: 10.3390/molecules25071687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
Acquired Immune Deficiency Syndrome (AIDS) treatment with combination antiretroviral therapy (cART) has improved the life quality of many patients since its implementation. However, resistance mutations and the accumulation of severe side effects associated with cART remain enormous challenges that need to be addressed with the continual design and redesign of anti-HIV drugs. In this review, we focus on the importance of the HIV-1 Gag polyprotein as the master coordinator of HIV-1 assembly and maturation and as an emerging drug target. Due to its multiple roles in the HIV-1 life cycle, the individual Gag domains are attractive but also challenging targets for inhibitor design. However, recent encouraging developments in targeting the Gag domains such as the capsid protein with highly potent and potentially long-acting inhibitors, as well as the exploration and successful targeting of challenging HIV-1 proteins such as the matrix protein, have demonstrated the therapeutic viability of this important protein. Such Gag-directed inhibitors have great potential for combating the AIDS pandemic and to be useful tools to dissect HIV-1 biology.
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19
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Mori M, Manetti F, Botta B, Tafi A. In Memory of Maurizio Botta: His Contribution to the Development of Computer-Aided Drug Design. J Chem Inf Model 2019; 59:4961-4967. [PMID: 31804073 DOI: 10.1021/acs.jcim.9b01043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 Siena , Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 Siena , Italy
| | - Bruno Botta
- Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022 , Sapienza University of Rome , Piazzale Aldo Moro 5 , 00185 Rome , Italy
| | - Andrea Tafi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022 , University of Siena , via Aldo Moro 2 , 53100 Siena , Italy
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20
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Wu B, Zhao L, Wang Y, Dong H, Yu H. Er 3+/Yb 3+ co-doped nanocrystals modified with 6-aminocaproic acid for temperature sensing in biomedicine. RSC Adv 2019; 9:42228-42235. [PMID: 35542838 PMCID: PMC9076559 DOI: 10.1039/c9ra08447a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/04/2019] [Indexed: 11/21/2022] Open
Abstract
We report β-PbF2:Er3+/Yb3+ nanocrystals (NCs) modified with 6-aminocaproic acid (6AA) via wet chemical etching of glass ceramics (GCs). NCs body-doped with trivalent rare-earth (RE3+) ions were released from the GCs by etching of the glass matrix and modified with bifunctional 6AA ligands to enhance their water solubility. They have good stability in water with an average diameter of 56 nm and display efficient green (521, 550 nm) and red (660 nm) emission under the excitation of a 940 nm laser. High absolute sensitivity (S A) and relative sensitivity (S R) (0.0027 K-1 and 1.18% K-1, respectively) and high resolution (0.25 K) were achieved for temperature sensing in the biological temperature range, using the fluorescence intensity ratio (FIR) technique. All of the experimental results indicate that the Er3+/Yb3+ co-doped NCs modified with 6AA may potentially be useful as fluorescent biological temperature sensors.
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Affiliation(s)
- Bing Wu
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics, Nankai University Tianjin 300071 China
| | - Lijuan Zhao
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics, Nankai University Tianjin 300071 China
| | - Ying Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University 23 Hongda Street, TEDA Tianjin 300457 China
| | - Haotian Dong
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics, Nankai University Tianjin 300071 China
| | - Hua Yu
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics, Nankai University Tianjin 300071 China
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21
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Ku T, Lopresti N, Shirley M, Mori M, Marchant J, Heng X, Botta M, Summers MF, Seley-Radtke KL. Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1. Bioorg Med Chem 2019; 27:2883-2892. [PMID: 31126822 PMCID: PMC6556414 DOI: 10.1016/j.bmc.2019.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/01/2019] [Accepted: 05/11/2019] [Indexed: 11/29/2022]
Abstract
Anti-HIV-1 drug design has been notably challenging due to the virus’ ability to mutate and develop immunity against commercially available drugs. The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The compounds were predicted by computational studies not to function via zinc ejection, which would endow them with significant advantages over non-specific and thus toxic zinc-ejectors. The target fleximer bases were synthesized using palladium-catalyzed cross-coupling techniques and subsequently tested against NC and HIV-1. The results of those studies are described herein.
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Affiliation(s)
- Therese Ku
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Natalie Lopresti
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Matthew Shirley
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Mattia Mori
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, via Aldo Moro 2, 53100 Siena, Italy
| | - Jan Marchant
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Xiao Heng
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Maurizio Botta
- University of Siena, Department of Biotechnology, Chemistry and Pharmacy, via Aldo Moro 2, 53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Bldg., Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA
| | - Michael F Summers
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA; Howard Hughes Medical Institute, USA
| | - Katherine L Seley-Radtke
- University of Maryland, Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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22
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Mori M, Dasso Lang MC, Saladini F, Palombi N, Kovalenko L, De Forni D, Poddesu B, Friggeri L, Giannini A, Malancona S, Summa V, Zazzi M, Mely Y, Botta M. Synthesis and Evaluation of Bifunctional Aminothiazoles as Antiretrovirals Targeting the HIV-1 Nucleocapsid Protein. ACS Med Chem Lett 2019; 10:463-468. [PMID: 30996780 DOI: 10.1021/acsmedchemlett.8b00506] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
Small molecule inhibitors of the HIV-1 nucleocapsid protein (NC) are considered as promising agents in the treatment of HIV/AIDS. In an effort to exploit the privileged 2-amino-4-phenylthiazole moiety in NC inhibition, here we conceived, synthesized, and tested in vitro 18 NC inhibitors (NCIs) bearing a double functionalization. In these NCIs, one part of the molecule is deputed to interact noncovalently with the NC hydrophobic pocket, while the second portion is designed to interact with the N-terminal domain of NC. This binding hypothesis was verified by molecular dynamics simulations, while the linkage between these two pharmacophores was found to enhance antiretroviral activity both on the wild-type virus and on HIV-1 strains with resistance to currently licensed drugs. The two most interesting compounds 6 and 13 showed no cytotoxicity, thus becoming valuable leads for further investigations.
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Affiliation(s)
- Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 53100 Siena, Italy
| | - Nastasja Palombi
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Faculté
de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Davide De Forni
- ViroStatics S.r.l., Viale Umberto I 46, 07100 Sassari, Italy
| | - Barbara Poddesu
- ViroStatics S.r.l., Viale Umberto I 46, 07100 Sassari, Italy
| | - Laura Friggeri
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 53100 Siena, Italy
| | - Savina Malancona
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Vincenzo Summa
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 53100 Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Faculté
de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Bldg., Suite
333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, 53019 Castelnuovo, Berardenga, Italy
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23
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Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP. Molecular Application of Aptamers in the Diagnosis and Treatment of Cancer and Communicable Diseases. Pharmaceuticals (Basel) 2018; 11:ph11040093. [PMID: 30274155 PMCID: PMC6315466 DOI: 10.3390/ph11040093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer and infectious diseases such as Ebola, HIV, tuberculosis, Zika, hepatitis, measles and human schistosomiasis are serious global health hazards. The increasing annual morbidities and mortalities of these diseases have been blamed on drug resistance and the inefficacy of available diagnostic tools, particularly those which are immunologically-based. Antibody-based tools rely solely on antibody production for diagnosis and for this reason they are the major cause of diagnostic delays. Unfortunately, the control of these diseases depends on early detection and administration of effective treatment therefore any diagnostic delay is a huge challenge to curbing these diseases. Hence, there is a need for alternative diagnostic tools, discovery and development of novel therapeutic agents. Studies have demonstrated that aptamers could potentially offer one of the best solutions to these problems. Aptamers are short sequences of either DNA or RNA molecules, which are identified in vitro through a SELEX process. They are sensitive and bind specifically to target molecules. Their promising features suggest they may serve as better diagnostic agents and can be used as drug carriers for therapeutic purposes. In this article, we review the applications of aptamers in the theranostics of cancer and some infectious diseases.
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Affiliation(s)
- Philisiwe Fortunate Molefe
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Priscilla Masamba
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
- Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria.
| | - Londiwe Simphiwe Mbatha
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Mervin Meyer
- DST/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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24
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René B, Mauffret O, Fossé P. Retroviral nucleocapsid proteins and DNA strand transfers. BIOCHIMIE OPEN 2018; 7:10-25. [PMID: 30109196 PMCID: PMC6088434 DOI: 10.1016/j.biopen.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022]
Abstract
An infectious retroviral particle contains 1000-1500 molecules of the nucleocapsid protein (NC) that cover the diploid RNA genome. NC is a small zinc finger protein that possesses nucleic acid chaperone activity that enables NC to rearrange DNA and RNA molecules into the most thermodynamically stable structures usually those containing the maximum number of base pairs. Thanks to the chaperone activity, NC plays an essential role in reverse transcription of the retroviral genome by facilitating the strand transfer reactions of this process. In addition, these reactions are involved in recombination events that can generate multiple drug resistance mutations in the presence of anti-HIV-1 drugs. The strand transfer reactions rely on base pairing of folded DNA/RNA structures. The molecular mechanisms responsible for NC-mediated strand transfer reactions are presented and discussed in this review. Antiretroviral strategies targeting the NC-mediated strand transfer events are also discussed.
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Affiliation(s)
- Brigitte René
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Olivier Mauffret
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Philippe Fossé
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
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25
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Shvadchak V, Zgheib S, Basta B, Humbert N, Langedijk J, Morris MC, Ciaco S, Maskri O, Darlix JL, Mauffret O, Fossé P, Réal E, Mély Y. Rationally Designed Peptides as Efficient Inhibitors of Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein. Biochemistry 2018; 57:4562-4573. [PMID: 30019894 DOI: 10.1021/acs.biochem.8b00527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to its essential roles in the viral replication cycle and to its highly conserved sequence, the nucleocapsid protein (NCp7) of the human immunodeficiency virus type 1 is a target of choice for inhibiting replication of the virus. Most NCp7 inhibitors identified so far are small molecules. A small number of short peptides also act as NCp7 inhibitors by competing with its nucleic acid (NA) binding and chaperone activities but exhibit antiviral activity only at relatively high concentrations. In this work, in order to obtain more potent NCp7 competitors, we designed a library of longer peptides (10-17 amino acids) whose sequences include most of the NCp7 structural determinants responsible for its specific NA binding and destabilizing activities. Using an in vitro assay, the most active peptide (pE) was found to inhibit the NCp7 destabilizing activity, with a 50% inhibitory concentration in the nanomolar range, by competing with NCp7 for binding to its NA substrates. Formulated with a cell-penetrating peptide (CPP), pE was found to accumulate into HeLa cells, with low cytotoxicity. However, either formulated with a CPP or overexpressed in cells, pE did not show any antiviral activity. In vitro competition experiments revealed that its poor antiviral activity may be partly due to its sequestration by cellular RNAs. The selected peptide pE therefore appears to be a useful tool for investigating NCp7 properties and functions in vitro, but further work will be needed to design pE-derived peptides with antiviral activity.
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Affiliation(s)
- Volodymyr Shvadchak
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Sarwat Zgheib
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Beata Basta
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Nicolas Humbert
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | | | - May C Morris
- Institut des biomolécules Max Mousseron, CNRS, UMR 5247 , Université de Montpellier Faculté de Pharmacie , 15 av Charles Flahault 34093 Montpellier , France
| | - Stefano Ciaco
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Ouerdia Maskri
- LBPA, ENS Paris Saclay, CNRS , Université Paris-Saclay , 94235 , Cachan Cedex , France
| | - Jean-Luc Darlix
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Olivier Mauffret
- LBPA, ENS Paris Saclay, CNRS , Université Paris-Saclay , 94235 , Cachan Cedex , France
| | - Philippe Fossé
- LBPA, ENS Paris Saclay, CNRS , Université Paris-Saclay , 94235 , Cachan Cedex , France
| | - Eléonore Réal
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS , Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France
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26
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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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27
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Mori M, Kovalenko L, Malancona S, Saladini F, De Forni D, Pires M, Humbert N, Real E, Botzanowski T, Cianférani S, Giannini A, Dasso Lang MC, Cugia G, Poddesu B, Lori F, Zazzi M, Harper S, Summa V, Mely Y, Botta M. Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains. ACS Chem Biol 2018; 13:253-266. [PMID: 29235845 DOI: 10.1021/acschembio.7b00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of the HIV-1 life cycle are efficient in blocking viral replication but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR. Here, using a multidisciplinary approach combining in silico screening, fluorescence-based molecular assays, and cellular antiviral assays, we identified nordihydroguaiaretic acid (6), as a novel natural product inhibitor of NC. By using NMR, mass spectrometry, fluorescence spectroscopy, and molecular modeling, 6 was found to act through a dual mechanism of action never highlighted before for NC inhibitors (NCIs). First, the molecule recognizes and binds NC noncovalently, which results in the inhibition of the nucleic acid chaperone properties of NC. In a second step, chemical oxidation of 6 induces a potent chemical inactivation of the protein. Overall, 6 inhibits NC and the replication of wild-type and drug-resistant HIV-1 strains in the low micromolar range with moderate cytotoxicity that makes it a profitable tool compound as well as a good starting point for the development of pharmacologically relevant NCIs.
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Affiliation(s)
- Mattia Mori
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Lesia Kovalenko
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
- Department
of Chemistry, Kyiv National Taras Shevchenko University, 01033 Kyiv, Ukraine
| | - Savina Malancona
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Francesco Saladini
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | | | - Manuel Pires
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Nicolas Humbert
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Thomas Botzanowski
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Alessia Giannini
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Giulia Cugia
- ViroStatics S.r.l, Viale Umberto
I 46, 07100 Sassari, Italy
| | | | - Franco Lori
- ViroStatics S.r.l, Viale Umberto
I 46, 07100 Sassari, Italy
| | - Maurizio Zazzi
- Department
of Medical Biotechnologies, University of Siena, Viale Mario Bracci,
16, 50100 Siena, Italy
| | - Steven Harper
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Vincenzo Summa
- IRBM Science Park S.p.A., Via Pontina Km 30.600, 00071 Pomezia (RM), Italy
| | - Yves Mely
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Botta
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Center for Biotechnology,
College of Science and Technology, Temple University, BioLife Science
Bldg., Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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28
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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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29
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Abbehausen C, de Paiva REF, Bjornsson R, Gomes SQ, Du Z, Corbi PP, Lima FA, Farrell N. X-ray Absorption Spectroscopy Combined with Time-Dependent Density Functional Theory Elucidates Differential Substitution Pathways of Au(I) and Au(III) with Zinc Fingers. Inorg Chem 2017; 57:218-230. [DOI: 10.1021/acs.inorgchem.7b02406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Camilla Abbehausen
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box 6154, CEP, 13083-970 Campinas, São Paulo, Brazil
| | | | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3,
IS-107 Reykjavik, Iceland
| | - Saulo Quintana Gomes
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box 6154, CEP, 13083-970 Campinas, São Paulo, Brazil
| | - Zhifeng Du
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284-2006, United States
| | - Pedro Paulo Corbi
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box 6154, CEP, 13083-970 Campinas, São Paulo, Brazil
| | - Frederico Alves Lima
- Centro Nacional de Pesquisa em Energia
e Materiais, Brazilian Synchrotron Light Laboratory—LNLS, CP 6192, 13084-971 Campinas, São Paulo, Brazil
| | - Nicholas Farrell
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284-2006, United States
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30
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Hadpech S, Nangola S, Chupradit K, Fanhchaksai K, Furnon W, Urvoas A, Valerio-Lepiniec M, Minard P, Boulanger P, Hong SS, Tayapiwatana C. Alpha-helicoidal HEAT-like Repeat Proteins (αRep) Selected as Interactors of HIV-1 Nucleocapsid Negatively Interfere with Viral Genome Packaging and Virus Maturation. Sci Rep 2017; 7:16335. [PMID: 29180782 PMCID: PMC5703948 DOI: 10.1038/s41598-017-16451-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
A new generation of artificial proteins, derived from alpha-helicoidal HEAT-like repeat protein scaffolds (αRep), was previously characterized as an effective source of intracellular interfering proteins. In this work, a phage-displayed library of αRep was screened on a region of HIV-1 Gag polyprotein encompassing the C-terminal domain of the capsid, the SP1 linker and the nucleocapsid. This region is known to be essential for the late steps of HIV-1 life cycle, Gag oligomerization, viral genome packaging and the last cleavage step of Gag, leading to mature, infectious virions. Two strong αRep binders were isolated from the screen, αRep4E3 (32 kDa; 7 internal repeats) and αRep9A8 (28 kDa; 6 internal repeats). Their antiviral activity against HIV-1 was evaluated in VLP-producer cells and in human SupT1 cells challenged with HIV-1. Both αRep4E3 and αRep9A8 showed a modest but significant antiviral effects in all bioassays and cell systems tested. They did not prevent the proviral integration reaction, but negatively interfered with late steps of the HIV-1 life cycle: αRep4E3 blocked the viral genome packaging, whereas αRep9A8 altered both virus maturation and genome packaging. Interestingly, SupT1 cells stably expressing αRep9A8 acquired long-term resistance to HIV-1, implying that αRep proteins can act as antiviral restriction-like factors.
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Affiliation(s)
- Sudarat Hadpech
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Faculty of Pharmaceutical Science, Burapha University, Muang District, Chonburi Province, 20131, Thailand.,University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Sawitree Nangola
- Division of Clinical Immunology and Transfusion Sciences, School of Allied Health Sciences, University of Phayao, Phayao, 56000, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanda Fanhchaksai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wilhelm Furnon
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Pierre Boulanger
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Saw-See Hong
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France. .,Institut National de la Santé et de la Recherche Médicale, 101, rue de Tolbiac, 75654, Paris Cedex 13, France.
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
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de Paiva REF, Du Z, Peterson EJ, Corbi PP, Farrell NP. Probing the HIV-1 NCp7 Nucleocapsid Protein with Site-Specific Gold(I)–Phosphine Complexes. Inorg Chem 2017; 56:12308-12318. [DOI: 10.1021/acs.inorgchem.7b01762] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raphael E. F. de Paiva
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
| | - Zhifeng Du
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
| | - Erica J. Peterson
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
| | - Pedro P. Corbi
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
| | - Nicholas P. Farrell
- Institute of Chemistry, University of Campinas − UNICAMP, P.O. Box 6154, 13083-970 Campinas-SP, Brazil
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32
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Shimberg GD, Ok K, Neu HM, Splan KE, Michel SLJ. Cu(I) Disrupts the Structure and Function of the Nonclassical Zinc Finger Protein Tristetraprolin (TTP). Inorg Chem 2017; 56:6838-6848. [PMID: 28557421 DOI: 10.1021/acs.inorgchem.7b00125] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tristetraprolin (TTP) is a nonclassical zinc finger (ZF) protein that plays a key role in regulating inflammatory response. TTP regulates cytokines at the mRNA level by binding to AU-rich sequences present at the 3'-untranslated region, forming a complex that is then degraded. TTP contains two conserved CCCH domains with the sequence CysX8CysX5CysX3His that are activated to bind RNA when zinc is coordinated. During inflammation, copper levels are elevated, which is associated with increased inflammatory response. A potential target for Cu(I) during inflammation is TTP. To determine whether Cu(I) binds to TTP and how Cu(I) can affect TTP/RNA binding, two TTP constructs were prepared. One construct contained just the first CCCH domain (TTP-1D) and serves as a peptide model for a CCCH domain; the second construct contains both CCCH domains (TTP-2D) and is functional (binds RNA) when Zn(II) is coordinated. Cu(I) binding to TTP-1D was assessed via electronic absorption spectroscopy titrations, and Cu(I) binding to TTP-2D was assessed via both absorption spectroscopy and a spin filter/inductively coupled plasma mass spectrometry (ICP-MS) assay. Cu(I) binds to TTP-1D with a 1:1 stoichiometry and to TTP-2D with a 3:1 stoichiometry. The CD spectrum of Cu(I)-TTP-2D did not exhibit any secondary structure, matching that of apo-TTP-2D, while Zn(II)-TTP-2D exhibited a secondary structure. Measurement of RNA binding via fluorescence anisotropy revealed that Cu(I)-TTP-2D does not bind to the TTP-2D RNA target sequence UUUAUUUAUUU with any measurable affinity, while Zn(II)-TTP-2D binds to this site with nanomolar affinity. Similarly, addition of Cu(I) to the Zn(II)-TTP-2D/RNA complex resulted in inhibition of RNA binding. Together, these data indicate that, while Cu(I) binds to TTP-2D, it does not result in a folded or functional protein and that Cu(I) inhibits Zn(II)-TTP-2D/RNA binding.
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Affiliation(s)
- Geoffrey D Shimberg
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
| | - Kiwon Ok
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
| | - Heather M Neu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
| | - Kathryn E Splan
- Department of Chemistry, Macalester College , 1600 Grand Avenue, Saint Paul, Minnesota 55105, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
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Saha M, Scerba MT, Shank NI, Hartman TL, Buchholz CA, Buckheit RW, Durell SR, Appella DH. Probing Mercaptobenzamides as HIV Inactivators via Nucleocapsid Protein 7. ChemMedChem 2017; 12:714-721. [PMID: 28395128 DOI: 10.1002/cmdc.201700141] [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: 03/01/2017] [Revised: 04/10/2017] [Indexed: 01/22/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein 7 (NCp7), a zinc finger protein, plays critical roles in viral replication and maturation and is an attractive target for drug development. However, the development of drug-like molecules that inhibit NCp7 has been a significant challenge. In this study, a series of novel 2-mercaptobenzamide prodrugs were investigated for anti-HIV activity in the context of NCp7 inactivation. The molecules were synthesized from the corresponding thiosalicylic acids, and they are all crystalline solids and stable at room temperature. Derivatives with a range of amide side chains and aromatic substituents were synthesized and screened for anti-HIV activity. Wide ranges of antiviral activity were observed, with IC50 values ranging from 1 to 100 μm depending on subtle changes to the substituents on the aromatic ring and side chain. Results from these structure-activity relationships were fit to a probable mode of intracellular activation and interaction with NCp7 to explain variations in antiviral activity. Our strategy to make a series of mercaptobenzamide prodrugs represents a general new direction to make libraries that can be screened for anti-HIV activity.
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Affiliation(s)
- Mrinmoy Saha
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - Michael T Scerba
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - Nathaniel I Shank
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - Tracy L Hartman
- ImQuest Biosciences, 7340 Executive Way, Suite R, Frederick, MD, 21704, USA
| | - Caitlin A Buchholz
- ImQuest Biosciences, 7340 Executive Way, Suite R, Frederick, MD, 21704, USA
| | - Robert W Buckheit
- ImQuest Biosciences, 7340 Executive Way, Suite R, Frederick, MD, 21704, USA
| | - Stewart R Durell
- Laboratory of Cell Biology, NCI, NIH, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
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Kessl JJ, Kutluay SB, Townsend D, Rebensburg S, Slaughter A, Larue RC, Shkriabai N, Bakouche N, Fuchs JR, Bieniasz PD, Kvaratskhelia M. HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis. Cell 2016; 166:1257-1268.e12. [PMID: 27565348 DOI: 10.1016/j.cell.2016.07.044] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/16/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
While an essential role of HIV-1 integrase (IN) for integration of viral cDNA into human chromosome is established, studies with IN mutants and allosteric IN inhibitors (ALLINIs) have suggested that IN can also influence viral particle maturation. However, it has remained enigmatic as to how IN contributes to virion morphogenesis. Here, we demonstrate that IN directly binds the viral RNA genome in virions. These interactions have specificity, as IN exhibits distinct preference for select viral RNA structural elements. We show that IN substitutions that selectively impair its binding to viral RNA result in eccentric, non-infectious virions without affecting nucleocapsid-RNA interactions. Likewise, ALLINIs impair IN binding to viral RNA in virions of wild-type, but not escape mutant, virus. These results reveal an unexpected biological role of IN binding to the viral RNA genome during virion morphogenesis and elucidate the mode of action of ALLINIs.
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Affiliation(s)
- Jacques J Kessl
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Dana Townsend
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie Rebensburg
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Alison Slaughter
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Ross C Larue
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Nordine Bakouche
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - James R Fuchs
- College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA; Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA.
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Spell SR, Mangrum JB, Peterson EJ, Fabris D, Ptak R, Farrell NP. Au(iii) compounds as HIV nucleocapsid protein (NCp7)-nucleic acid antagonists. Chem Commun (Camb) 2016; 53:91-94. [PMID: 27858001 PMCID: PMC7086404 DOI: 10.1039/c6cc07970a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HIV nucleocapsid NCp7-SL2 RNA interaction is interrupted in the presence of a formally substitution-inert gold(dien)-nucleobase/N-heterocycle AuN4 compound where the N-heterocycle serves the dual purposes of a template for "non-covalent" molecular recognition of the essential tryptophan of the protein, mimicking the natural reaction and subsequent "fixation" by Au-Cys bond formation providing a chemotype for a new distinct class of nucleocapsid-nucleic acid antagonist.
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Affiliation(s)
- Sarah R Spell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - John B Mangrum
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Erica J Peterson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
| | - Daniele Fabris
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Roger Ptak
- Southern Research Institute, 431 Aviation Way, Frederick, Maryland 21701, USA
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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36
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Bernardes VHF, Qu Y, Du Z, Beaton J, Vargas MD, Farrell NP. Interaction of the HIV NCp7 Protein with Platinum(II) and Gold(III) Complexes Containing Tridentate Ligands. Inorg Chem 2016; 55:11396-11407. [PMID: 27934299 DOI: 10.1021/acs.inorgchem.6b01925] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human immunodeficiency virus (HIV) nucleocapsid protein (NCp7) plays significant roles in the virus life cycle and has been targeted by compounds that could lead to its denaturation or block its interaction with viral RNA. Herein, we describe the interactions of platinum(II) and gold(III) complexes with NCp7 and how the reactivity/affinity of potential inhibitors can be modulated by judicious choice of ligands. The interactions of [MCl(N3)]n+ (M = Pt2+ (n = 1) and Au3+ (n = 2); N3 = tridentate chelate ligands: bis(2-pyridylmethyl)methylamine (Mebpma, L1) and bis(2-pyridylmethyl)amine (bpma, L2) with the C-terminal zinc finger of NCp7 (ZF2) were investigated by electrospray ionization-mass spectroscopy (ESI-MS). Mass spectra from the incubation of [MCl(Mebpma)]n+ complexes (PtL1 and AuL1) with ZF2 indicated that they were more reactive than the previously studied diethylenetriamine-containing analogues [MCl(dien)]n+. The initial product of reaction of PtL1 with ZF2 results in loss of all ligands and release of zinc to give the platinated apopeptide {PtF} (F = apopeptide). This is in contrast to the incubation with [PtCl(dien)]+, in which {Pt(dien)}-peptide adducts are observed. Incubation of the Au3+ complex AuL1 with ZF2 gave AuxFn+ species (x = 1, 2, 4, F = apopeptide) again with loss of all ligands. Furthermore, the formally substitution-inert analogues [Pt(N3)L]2+ (L = 4-methylpyridine (4-pic), 4-dimethylaminopyridine (dmap), and 9-ethylguanine (9-EtGua)) were prepared to examine stacking interactions with N-acetyltryptophan (N-AcTrp), the Trp-containing ZF2, and the "full" two-finger NCp7 itself using fluorescence quenching titration. Use of bpma and Mebpma gave slightly higher affinity than analogous [Pt(dien)L)]2+ complexes. The dmap-containing complexes (PtL1a and PtL2a) had the greatest association constants (Ka) for N-AcTrp and ZF2 peptide. The complex PtL1a had the highest Ka when compared with other known Pt2+ analogues: [Pt(dien)(9-EtGua)]2+ < [Pt(bpma)(9-EtGua)]2+ < [Pt(dien)(dmap)]2+< PtL2a < PtL1a. A Ka value of ca. 40.6 ± 1.0 × 103 M-1 was obtained for the full NCp7 peptide with PtL1a. In addition, the mass spectrum of the interaction between ZF2 and PtL1a confirms formation of a 1:1 PtL1a/ZF2 adduct. The reactivity of selected complexes with sulfur-containing amino acid N-acetylcysteine (N-AcCys) was also investigated by 195Pt and 1H NMR spectroscopy and ESI-MS. The precursor compounds [PtCl(N3)]+ PtL1 and PtL2 reacted readily, whereas their [Pt(N3)L]2+ analogues PtL1a and PtL2a were inert to substitution.
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Affiliation(s)
- Victor H F Bernardes
- Chemistry Institute, Fluminense Federal University , Campus Valonguinho, CEP 24020-141, Niterói-RJ, Brazil.,Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - Yun Qu
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - Zhifeng Du
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - James Beaton
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
| | - Maria D Vargas
- Chemistry Institute, Fluminense Federal University , Campus Valonguinho, CEP 24020-141, Niterói-RJ, Brazil
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University , 1001 W. Main St., Richmond, Virginia 23284-2006, United States
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Hartman TL, Yang L, Helfrick AN, Hassink M, Shank NI, George Rosenker K, Scerba MT, Saha M, Hughes E, Wang AQ, Xu X, Gupta P, Buckheit RW, Appella DH. Preclinical evaluation of a mercaptobenzamide and its prodrug for NCp7-targeted inhibition of human immunodeficiency virus. Antiviral Res 2016; 134:216-225. [PMID: 27568924 PMCID: PMC7113734 DOI: 10.1016/j.antiviral.2016.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/01/2023]
Abstract
Although the effective use of highly active antiretroviral therapy results in the suppression of virus production in infected individuals, it does not eliminate the infection and low level virus production in cells harboring virus in sanctuary sites. Thus, the continued search for new antiretroviral agents with unique and different mechanisms of HIV inhibition remains critical, and compounds that can reduce the level of virus production from cells already infected with HIV, as opposed to preventing de novo infection, would be of great benefit. A mercaptobenzamide (MDH-1-38) and its prodrug (NS1040) are being developed as potential therapeutic compounds targeting the zinc finger of HIV nucleocapsid. In the presence of esterase enzymes, NS1040 is designed to be converted to MDH-1-38 which has antiviral activity. While we presume that NS1040 is rapidly converted to MDH-1-38 in all experiments, the two compounds were tested side-by-side to determine whether the presence of a prodrug affects the antiviral activity or mechanism of action. The two compounds were evaluated against a panel of HIV-1 clinical isolates in human PBMCs and monocyte-macrophages and yielded EC50 values ranging from 0.7 to 13 μM with no toxicity up to 100 μM. MDH-1-38 and NS1040 remained equally active in human PBMCs in the presence of added serum proteins as well as against HIV-1 isolates resistant to reverse transcriptase, integrase or protease inhibitors. Cell-based and biochemical mechanism of antiviral action assays demonstrated MDH-1-38 and NS1040 were virucidal at concentrations of 15 and 50 μM, respectively. Cell to cell transmission of HIV in multiple passages was significantly reduced in CEM-SS and human PBMCs by reducing progeny virus infectivity at compound concentrations greater than 2 μM. The combination of either MDH-1-38 or NS1040 with other FDA-approved HIV drugs yielded additive to synergistic antiviral interactions with no evidence of antiviral antagonism or synergistic toxicity. Serial dose escalation was used in attempts to select for HIV strains resistant to MDH-1-38 and NS1040. Virus at several passages failed to replicate in cells treated at increased compound concentrations, which is consistent with the proposed mechanism of action of the virus inactivating compounds. Through 14 passages, resistance to the compounds has not been achieved. Most HIV inhibitors with mechanism of antiviral action targeting a viral protein would have selected for a drug resistant virus within 14 passages. These studies indicate that these NCp7-targeted compounds represent new potent anti-HIV drug candidates which could be effectively used in combination with all approved anti-HIV drugs.
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Affiliation(s)
| | - L Yang
- ImQuest Biosciences, Frederick, MD, USA
| | | | - M Hassink
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | - N I Shank
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | | | - M T Scerba
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | - M Saha
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | | | | | - X Xu
- NCATS, NIH, Bethesda, MD, USA
| | - P Gupta
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | | | - D H Appella
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA.
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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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Sharma KK, Przybilla F, Restle T, Godet J, Mély Y. FRET-based assay to screen inhibitors of HIV-1 reverse transcriptase and nucleocapsid protein. Nucleic Acids Res 2016; 44:e74. [PMID: 26762982 PMCID: PMC4856972 DOI: 10.1093/nar/gkv1532] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/23/2015] [Indexed: 12/15/2022] Open
Abstract
During HIV-1 reverse transcription, the single-stranded RNA genome is converted into proviral double stranded DNA by Reverse Transcriptase (RT) within a reverse transcription complex composed of the genomic RNA and a number of HIV-1 encoded proteins, including the nucleocapsid protein NCp7. Here, we developed a one-step and one-pot RT polymerization assay. In this in vitro assay, RT polymerization is monitored in real-time by Förster resonance energy transfer (FRET) using a commercially available doubly-labeled primer/template DNA. The assay can monitor and quantify RT polymerization activity as well as its promotion by NCp7. Z-factor values as high as 0.89 were obtained, indicating that the assay is suitable for high-throughput drug screening. Using Nevirapine and AZT as prototypical RT inhibitors, reliable IC50 values were obtained from the changes in the RT polymerization kinetics. Interestingly, the assay can also detect NCp7 inhibitors, making it suitable for high-throughput screening of drugs targeting RT, NCp7 or simultaneously, both proteins.
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Affiliation(s)
- Kamal K Sharma
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Frédéric Przybilla
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Tobias Restle
- Institute für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401 Illkirch, France Département d'Information Médicale et de Biostatistiques, Hôpitaux Universitaires de Strasbourg, 1, pl de l'Hôpital, 67400 Strasbourg, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401 Illkirch, France
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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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Sancineto L, Mariotti A, Bagnoli L, Marini F, Desantis J, Iraci N, Santi C, Pannecouque C, Tabarrini O. Design and Synthesis of DiselenoBisBenzamides (DISeBAs) as Nucleocapsid Protein 7 (NCp7) Inhibitors with anti-HIV Activity. J Med Chem 2015; 58:9601-14. [PMID: 26613134 DOI: 10.1021/acs.jmedchem.5b01183] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The interest in the synthesis of Se-containing compounds is growing with the discovery of derivatives exhibiting various biological activities. In this manuscript, we have identified a series of 2,2'-diselenobisbenzamides (DISeBAs) as novel HIV retroviral nucleocapsid protein 7 (NCp7) inhibitors. Because of its pleiotropic functions in the whole viral life cycle and its mutation intolerant nature, NCp7 represents a target of great interest which is not reached by any anti-HIV agent in clinical use. Using the diselenobisbenzoic scaffold, amino acid, and benzenesulfonamide derivatives were prepared and biologically profiled against different models of HIV infection. The incorporation of amino acids such as glycine and glutamate into DISeBAs 7 and 8 resulted in selective anti-HIV activity against both acutely and chronically infected cells as well as an interesting virucidal effect. DISeBAs demonstrated broad antiretroviral activity, encompassing HIV-1 drug-resistant strains including clinical isolates, as well as simian immunodeficiency virus (SIV). Time of addition experiments, along with the observed dose dependent inhibition of the Gag precursor proper processing, confirmed that their mechanism of action is based on NCp7 inhibition.
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Affiliation(s)
- Luca Sancineto
- Department of Pharmaceutical Sciences, Group of Catalysis and Organic Green Chemistry, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Alice Mariotti
- Department of Pharmaceutical Sciences, Group of Catalysis and Organic Green Chemistry, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Luana Bagnoli
- Department of Pharmaceutical Sciences, Group of Catalysis and Organic Green Chemistry, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Francesca Marini
- Department of Pharmaceutical Sciences, Group of Catalysis and Organic Green Chemistry, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Nunzio Iraci
- Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, Group of Catalysis and Organic Green Chemistry, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
| | - Christophe Pannecouque
- Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven , B-3000 Leuven, Belgium
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo 1, Perugia 06100, Italy
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Sosic A, Cappellini M, Scalabrin M, Gatto B. Nucleocapsid Annealing-Mediated Electrophoresis (NAME) assay allows the rapid identification of HIV-1 nucleocapsid inhibitors. J Vis Exp 2015:52474. [PMID: 25650789 PMCID: PMC4354545 DOI: 10.3791/52474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA or DNA folded in stable tridimensional folding are interesting targets in the development of antitumor or antiviral drugs. In the case of HIV-1, viral proteins involved in the regulation of the virus activity recognize several nucleic acids. The nucleocapsid protein NCp7 (NC) is a key protein regulating several processes during virus replication. NC is in fact a chaperone destabilizing the secondary structures of RNA and DNA and facilitating their annealing. The inactivation of NC is a new approach and an interesting target for anti-HIV therapy. The Nucleocapsid Annealing-Mediated Electrophoresis (NAME) assay was developed to identify molecules able to inhibit the melting and annealing of RNA and DNA folded in thermodynamically stable tridimensional conformations, such as hairpin structures of TAR and cTAR elements of HIV, by the nucleocapsid protein of HIV-1. The new assay employs either the recombinant or the synthetic protein, and oligonucleotides without the need of their previous labeling. The analysis of the results is achieved by standard polyacrylamide gel electrophoresis (PAGE) followed by conventional nucleic acid staining. The protocol reported in this work describes how to perform the NAME assay with the full-length protein or its truncated version lacking the basic N-terminal domain, both competent as nucleic acids chaperones, and how to assess the inhibition of NC chaperone activity by a threading intercalator. Moreover, NAME can be performed in two different modes, useful to obtain indications on the putative mechanism of action of the identified NC inhibitors.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova
| | - Marta Cappellini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova
| | | | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova;
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