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Maiti BK. Can Papain-like Protease Inhibitors Halt SARS-CoV-2 Replication? ACS Pharmacol Transl Sci 2020; 3:1017-1019. [PMID: 33062954 PMCID: PMC7409920 DOI: 10.1021/acsptsci.0c00093] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2 encoded papain-like protease (PLpro) harbors a labile Zn site (Cys189-X-X-Cys192-X n -Cys224-X-Cys226) and a classic catalytic site (Cys111-His272-Asp286), which play key roles for viral replication and hence represent promising drug targets. In this Viewpoint, both sulfur-based drugs and peptides-based inhibitors may block Cys residues in the catalytic and/or Zn site of CoV-2-PLpro, leading to dysfunction of CoV-2-PLpro and thereby halting viral replication.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
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2
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Nucleocapsid Protein Precursors NCp9 and NCp15 Suppress ATP-Mediated Rescue of AZT-Terminated Primers by HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother 2020; 64:AAC.00958-20. [PMID: 32747359 DOI: 10.1128/aac.00958-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/29/2020] [Indexed: 01/20/2023] Open
Abstract
In HIV-1, development of resistance to AZT (3'-azido-3'-deoxythymidine) is mediated by the acquisition of thymidine analogue resistance mutations (TAMs) (i.e., M41L, D67N, K70R, L210W, T215F/Y, and K219E/Q) in the viral reverse transcriptase (RT). Clinically relevant combinations of TAMs, such as M41L/T215Y or D67N/K70R/T215F/K219Q, enhance the ATP-mediated excision of AZT monophosphate (AZTMP) from the 3' end of the primer, allowing DNA synthesis to continue. Additionally, during HIV-1 maturation, the Gag polyprotein is cleaved to release a mature nucleocapsid protein (NCp7) and two intermediate precursors (NCp9 and NCp15). NC proteins interact with the viral genome and facilitate the reverse transcription process. Using wild-type and TAM-containing RTs, we showed that both NCp9 and NCp15 inhibited ATP-mediated rescue of AZTMP-terminated primers annealed to RNA templates but not DNA templates, while NCp7 had no effect on rescue activity. RNase H inactivation by introducing the active-site mutation E478Q led to the loss of the inhibitory effect shown by NCp9. NCp15 had a stimulatory effect on the RT's RNase H activity not observed with NCp7 and NCp9. However, analysis of RNase H cleavage patterns revealed that in the presence of NCp9, RNA/DNA complexes containing duplexes of 12 bp had reduced stability in comparison with those obtained in the absence of NC or with NCp7 or NCp15. These effects are expected to have a strong influence on the inhibitory action of NCp9 and NCp15 by affecting the efficiency of RNA-dependent DNA polymerization after unblocking DNA primers terminated with AZTMP and other nucleotide analogues.
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3
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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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4
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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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5
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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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6
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Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guérin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B. Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights. Int J Mol Sci 2020; 21:ijms21062058. [PMID: 32192183 PMCID: PMC7139703 DOI: 10.3390/ijms21062058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 02/06/2023] Open
Abstract
DNA glycosylases are emerging as relevant pharmacological targets in inflammation, cancer and neurodegenerative diseases. Consequently, the search for inhibitors of these enzymes has become a very active research field. As a continuation of previous work that showed that 2-thioxanthine (2TX) is an irreversible inhibitor of zinc finger (ZnF)-containing Fpg/Nei DNA glycosylases, we designed and synthesized a mini-library of 2TX-derivatives (TXn) and evaluated their ability to inhibit Fpg/Nei enzymes. Among forty compounds, four TXn were better inhibitors than 2TX for Fpg. Unexpectedly, but very interestingly, two dithiolated derivatives more selectively and efficiently inhibit the zincless finger (ZnLF)-containing enzymes (human and mimivirus Neil1 DNA glycosylases hNeil1 and MvNei1, respectively). By combining chemistry, biochemistry, mass spectrometry, blind and flexible docking and X-ray structure analysis, we localized new TXn binding sites on Fpg/Nei enzymes. This endeavor allowed us to decipher at the atomic level the mode of action for the best TXn inhibitors on the ZnF-containing enzymes. We discovered an original inhibition mechanism for the ZnLF-containing Fpg/Nei DNA glycosylases by disulfide cyclic trimeric forms of dithiopurines. This work paves the way for the design and synthesis of a new structural class of inhibitors for selective pharmacological targeting of hNeil1 in cancer and neurodegenerative diseases.
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Affiliation(s)
- Charlotte Rieux
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Stéphane Goffinont
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Zahira Tber
- Institut de Chimie Organique et Analytique, UMR7311 CNRS-Orleans University, Université d’Orléans, Pôle de Chimie, rue de Chartres, F-45100 Orléans, France; (Z.T.); (S.B.); (L.A.)
| | - Julien Cros
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Vincent Roy
- Institut de Chimie Organique et Analytique, UMR7311 CNRS-Orleans University, Université d’Orléans, Pôle de Chimie, rue de Chartres, F-45100 Orléans, France; (Z.T.); (S.B.); (L.A.)
- Université d’Orléans, UFR Sciences et Techniques, rue de Chartres, 45100 Orléans, France
- Correspondence: (V.R.); (N.G.); (B.C.)
| | - Martine Guérin
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
- Université d’Orléans, UFR Sciences et Techniques, rue de Chartres, 45100 Orléans, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique, UMR7311 CNRS-Orleans University, Université d’Orléans, Pôle de Chimie, rue de Chartres, F-45100 Orléans, France; (Z.T.); (S.B.); (L.A.)
| | - Artur Biela
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
| | - Luigi Agrofoglio
- Institut de Chimie Organique et Analytique, UMR7311 CNRS-Orleans University, Université d’Orléans, Pôle de Chimie, rue de Chartres, F-45100 Orléans, France; (Z.T.); (S.B.); (L.A.)
- Université d’Orléans, UFR Sciences et Techniques, rue de Chartres, 45100 Orléans, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
- Université d’Orléans, UFR Sciences et Techniques, rue de Chartres, 45100 Orléans, France
- Correspondence: (V.R.); (N.G.); (B.C.)
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071 Orléans, France; (C.R.); (S.G.); (F.C.); (J.C.); (M.G.); (V.G.); (A.B.); (V.A.)
- Correspondence: (V.R.); (N.G.); (B.C.)
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7
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Asquith CRM, Sil BC, Laitinen T, Tizzard GJ, Coles SJ, Poso A, Hofmann-Lehmann R, Hilton ST. Novel epidithiodiketopiperazines as anti-viral zinc ejectors of the Feline Immunodeficiency Virus (FIV) nucleocapsid protein as a model for HIV infection. Bioorg Med Chem 2019; 27:4174-4184. [PMID: 31395510 DOI: 10.1016/j.bmc.2019.07.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/22/2019] [Accepted: 07/28/2019] [Indexed: 01/02/2023]
Abstract
Focused libraries of multi-substituted epidithiodiketopiperazines (ETP) were prepared and evaluated for efficacy of inhibiting the nucleocapsid protein function of the Feline Immunodeficiency Virus (FIV) as a model for HIV. This activity was compared and contrasted to observed toxicity utilising an in-vitro cell culture approach. This resulted in the identification of several promising lead compounds with nanomolar potency in cells with low toxicity and a favorable therapeutic index.
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Affiliation(s)
- Christopher R M Asquith
- School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom; Clinical Laboratory & Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Bruno C Sil
- School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom; School of Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, United Kingdom
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom
| | - Simon J Coles
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Regina Hofmann-Lehmann
- Clinical Laboratory & Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Stephen T Hilton
- School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom.
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8
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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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9
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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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10
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Nikolayevskiy H, Scerba MT, Deschamps JR, Appella DH. Reaction Kinetics Direct a Rational Synthesis of an HIV-1 Inactivator of Nucleocapsid Protein 7 and Provide Mechanistic Insight into Cellular Metabolism and Antiviral Activity. Chemistry 2018; 24:9485-9489. [PMID: 29653024 DOI: 10.1002/chem.201801253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Indexed: 12/14/2022]
Abstract
Mercaptobenzamide thioester SAMT-247 is a non-toxic, mutation-resistant HIV-1 maturation inhibitor with a unique mechanism of antiviral activity. NMR spectroscopic analyses of model reactions that mimic the cellular environment answered fundamental questions about the antiviral mechanism and inspired a high-yielding (64 % overall), scalable (75 mmol), and cost-effective ($4 mmol-1 ) three-step synthesis that will enable additional preclinical evaluation.
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Affiliation(s)
- 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 (NIH), 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - 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 (NIH), 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - Jeffrey R Deschamps
- Naval Research Laboratory, Code 6910, 4555 Overlook Ave. SW, Washington D.C., 20375, USA
| | - 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 (NIH), 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
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11
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Ren W, Ji D, Xu X. Metal cofactor modulated folding and target recognition of HIV-1 NCp7. PLoS One 2018; 13:e0196662. [PMID: 29715277 PMCID: PMC5929515 DOI: 10.1371/journal.pone.0196662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 nucleocapsid 7 (NCp7) plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3) recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.
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Affiliation(s)
- Weitong Ren
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Dongqing Ji
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Xiulian Xu
- School of Physical Science and Technology, Yangzhou University, Yangzhou 225002, China
- * E-mail:
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12
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Deshmukh L, Tugarinov V, Appella DH, Clore GM. Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lalit Deshmukh
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0520 USA
- Present address: Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0520 USA
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0830 USA
| | - G. Marius Clore
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0520 USA
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13
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Deshmukh L, Tugarinov V, Appella DH, Clore GM. Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:2687-2691. [PMID: 29345807 DOI: 10.1002/anie.201713172] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 12/22/2022]
Abstract
HIV-1 nucleocapsid (NCp7) is a two Cys2 HisCys zinc knuckle (N-Zn and C-Zn) protein that plays a key role in viral replication. NCp7 conformational dynamics is characterized by NMR relaxation dispersion and chemical exchange saturation transfer measurements. While the N-Zn knuckle is conformationally stable, the C-Zn knuckle interconverts on the millisecond timescale between the major state, in which the zinc is coordinated by three cysteines and a histidine, and two folded minor species (with populations around 1 %) in which one of the coordination bonds (Cys413-Sγ-Zn or His421-Nϵ2-Zn) is hydrolyzed. These findings explain why antiretroviral thioesters specifically disrupt the C-Zn knuckle by initial acylation of Cys413, and show that transient, sparsely-populated ("dark"), excited states of proteins can present effective targets for rational drug design.
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Affiliation(s)
- Lalit Deshmukh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0520, USA.,Present address: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0520, USA
| | - Daniel H Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0830, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0520, USA
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14
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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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15
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Meanwell NA. Drug-target interactions that involve the replacement or displacement of magnesium ions. Bioorg Med Chem Lett 2017; 27:5355-5372. [DOI: 10.1016/j.bmcl.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 01/11/2023]
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16
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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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17
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Sancineto L, Iraci N, Tabarrini O, Santi C. NCp7: targeting a multitasking protein for next-generation anti-HIV drug development part 1: covalent inhibitors. Drug Discov Today 2017; 23:260-271. [PMID: 29107765 DOI: 10.1016/j.drudis.2017.10.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/02/2017] [Accepted: 10/17/2017] [Indexed: 11/16/2022]
Abstract
The major internal component of the HIV virion core is the nucleocapsid protein 7 (NCp7), a small, highly basic protein that is essential for multiple stages of the viral replicative cycle, and whose structure is preserved in all viral strains, including clinical isolates from therapy-experienced patients. This key protein is recognised as a potential target for an effective next-generation antiretroviral therapy, because it could offer the possibility to develop broad-spectrum agents that are less prone to select for resistant strains. Here, we provide a comprehensive overview of the covalent NCp7 inhibitors that have emerged over the past 25 years of drug discovery campaigns, emphasising, where possible, their structure-activity relationships (SARs) and pharmacophoric features.
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Affiliation(s)
- Luca Sancineto
- Department of Heterorganic Chemistry, Centre of Molecular and Macromolecular Studies, Lodz, Poland.
| | - Nunzio Iraci
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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18
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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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19
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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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20
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Diversity in Gold Finger Structure Elucidated by Traveling‐Wave Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612494] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Du Z, de Paiva REF, Nelson K, Farrell NP. Diversity in Gold Finger Structure Elucidated by Traveling‐Wave Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:4464-4467. [DOI: 10.1002/anie.201612494] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/13/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Zhifeng Du
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | | | - Kristina Nelson
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
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22
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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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23
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Spearman P. HIV-1 Gag as an Antiviral Target: Development of Assembly and Maturation Inhibitors. Curr Top Med Chem 2016; 16:1154-66. [PMID: 26329615 DOI: 10.2174/1568026615666150902102143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/18/2015] [Accepted: 06/21/2015] [Indexed: 01/10/2023]
Abstract
HIV-1 Gag is the master orchestrator of particle assembly. The central role of Gag at multiple stages of the HIV lifecycle has led to efforts to develop drugs that directly target Gag and prevent the formation and release of infectious particles. Until recently, however, only the catalytic site protease inhibitors have been available to inhibit late stages of HIV replication. This review summarizes the current state of development of antivirals that target Gag or disrupt late events in the retrovirus lifecycle such as maturation of the viral capsid. Maturation inhibitors represent an exciting new series of antiviral compounds, including those that specifically target CA-SP1 cleavage and the allosteric integrase inhibitors that inhibit maturation by a completely different mechanism. Numerous small molecules and peptides targeting CA have been studied in attempts to disrupt steps in assembly. Efforts to target CA have recently gained considerable momentum from the development of small molecules that bind CA and alter capsid stability at the post-entry stage of the lifecycle. Efforts to develop antivirals that inhibit incorporation of genomic RNA or to inhibit late budding events remain in preliminary stages of development. Overall, the development of novel antivirals targeting Gag and the late stages in HIV replication appears much closer to success than ever, with the new maturation inhibitors leading the way.
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Affiliation(s)
- Paul Spearman
- Department of Pediatrics; Pediatric Infectious Diseases, Emory University, 2015 Uppergate Drive, Atlanta, GA 30322.
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24
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Tsotsoros SD, Lutz PB, Daniel AG, Peterson EJ, de Paiva REF, Rivera E, Qu Y, Bayse CA, Farrell NP. Enhancement of the physicochemical properties of [Pt(dien)(nucleobase)] 2+ for HIVNCp7 targeting. Chem Sci 2016; 8:1269-1281. [PMID: 28451269 PMCID: PMC5369524 DOI: 10.1039/c6sc03445d] [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: 08/03/2016] [Accepted: 10/06/2016] [Indexed: 12/31/2022] Open
Abstract
Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]2+ ([PtN4]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN4 coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified as having significantly enhanced stacking capability over guanosine. Correlation of the LUMO energies of the modified nucleobases with the DFT π-stacking energies shows that frontier orbital energies of the individual monomers can be used as a first estimate of the π-stacking strength to Trp. Cellular accumulation studies showed no significant correlation with lipophilicity of the compounds, but all compounds had very low cytotoxicity suggesting the potential for antiviral selectivity. The conceptual similarities between nucleobase alkylation and platination validates the design of formally substitution-inert coordination complexes as weak Lewis acid electrophiles for selective peptide targeting.
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Affiliation(s)
- S D Tsotsoros
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - P B Lutz
- Department of Science , Technology and Mathematics , Regent University , Virginia Beach , Virginia 23464 , USA.,Department of Chemistry and Biochemistry , Old Dominion University , Norfolk , VA 23529 , USA .
| | - A G Daniel
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - E J Peterson
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA . .,Massey Cancer Center , Virginia Commonwealth University , Richmond , VA , USA
| | - R E F de Paiva
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - E Rivera
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - Y Qu
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA .
| | - C A Bayse
- Department of Chemistry and Biochemistry , Old Dominion University , Norfolk , VA 23529 , USA .
| | - N P Farrell
- Department of Chemistry , Virginia Commonwealth University , 1001 W. Main Street , Richmond , VA 23284-2006 , USA . .,Massey Cancer Center , Virginia Commonwealth University , Richmond , VA , USA
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25
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Asquith CRM, Konstantinova LS, Laitinen T, Meli ML, Poso A, Rakitin OA, Hofmann-Lehmann R, Hilton ST. Evaluation of Substituted 1,2,3-Dithiazoles as Inhibitors of the Feline Immunodeficiency Virus (FIV) Nucleocapsid Protein via a Proposed Zinc Ejection Mechanism. ChemMedChem 2016; 11:2119-2126. [DOI: 10.1002/cmdc.201600260] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/21/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher R. M. Asquith
- School of Pharmacy; Faculty of Life Sciences; University College London; London WC1N 1AX UK
- Clinical Laboratory & Center for Clinical Studies; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Lidia S. Konstantinova
- Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Moscow 119991 Russian Federation
- Nanotechnology Education and Research Center; South Ural State, University; Lenina Ave. 76 Chelyabinsk 454080 Russian Federation
| | - Tuomo Laitinen
- School of Pharmacy; Faculty of Health Sciences; University of Eastern, Finland; Kuopio 70211 Finland
| | - Marina L. Meli
- Clinical Laboratory & Center for Clinical Studies; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Antti Poso
- School of Pharmacy; Faculty of Health Sciences; University of Eastern, Finland; Kuopio 70211 Finland
| | - Oleg A. Rakitin
- Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Moscow 119991 Russian Federation
- Nanotechnology Education and Research Center; South Ural State, University; Lenina Ave. 76 Chelyabinsk 454080 Russian Federation
| | - Regina Hofmann-Lehmann
- Clinical Laboratory & Center for Clinical Studies; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Stephen T. Hilton
- School of Pharmacy; Faculty of Life Sciences; University College London; London WC1N 1AX UK
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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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Nahalka J, Hrabarova E, Talafova K. Protein-RNA and protein-glycan recognitions in light of amino acid codes. Biochim Biophys Acta Gen Subj 2015; 1850:1942-52. [PMID: 26145579 DOI: 10.1016/j.bbagen.2015.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND RNA-binding proteins, in cooperation with non-coding RNAs, play important roles in post-transcriptional regulation. Non-coding micro-RNAs control information flow from the genome to the glycome by interacting with glycan-synthesis enzymes. Glycan-binding proteins read the cell surface and cytoplasmic glycome and transfer signals back to the nucleus. The profiling of the protein-RNA and protein-glycan interactomes is of significant medicinal importance. SCOPE OF REVIEW This review discusses the state-of-the-art research in the protein-RNA and protein-glycan recognition fields and proposes the application of amino acid codes in profiling and programming the interactomes. MAJOR CONCLUSIONS The deciphered PUF-RNA and PPR-RNA amino acid recognition codes can be explained by the protein-RNA amino acid recognition hypothesis based on the genetic code. The tripartite amino acid code is also involved in protein-glycan interactions. At present, the results indicate that a system of four codons ("gnc", where n=g - guanine, c - cytosine, u - uracil or a - adenine) and four amino acids (G - glycine, A - alanine, V - valine, D - aspartic acid) could be the original genetic code that imprinted "rules" into both recognition processes. GENERAL SIGNIFICANCE Amino acid recognition codes have provocative potential in the profiling and programming of the protein-RNA and protein-glycan interactomes. The profiling and even programming of the interactomes will play significant roles in diagnostics and the development of therapeutic procedures against cancer and neurodegenerative, developmental and other diseases.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic.
| | - Eva Hrabarova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic
| | - Klaudia Talafova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic
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Abstract
Major advances have occurred in recent years in our understanding of HIV-1 assembly, release and maturation, as work in this field has been propelled forwards by developments in imaging technology, structural biology, and cell and molecular biology. This increase in basic knowledge is being applied to the development of novel inhibitors designed to target various aspects of virus assembly and maturation. This Review highlights recent progress in elucidating the late stages of the HIV-1 replication cycle and the related interplay between virology, cell and molecular biology, and drug discovery.
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Affiliation(s)
- Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Bg. 535, Room 110, 1050 Boyles St., Frederick, Maryland 21702-1201, USA
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