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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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Sosic A, Olivato G, Carraro C, Göttlich R, Fabris D, Gatto B. In Vitro Evaluation of Bis-3-Chloropiperidines as RNA Modulators Targeting TAR and TAR-Protein Interaction. Int J Mol Sci 2022; 23:ijms23020582. [PMID: 35054766 PMCID: PMC8776071 DOI: 10.3390/ijms23020582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabilizing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analytical approaches for the study of multicomponent RNA-based interactions.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Giulia Olivato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany;
| | - Dan Fabris
- Department of Chemistry, University of Connecticut, 55 North Eagleville Rd., Storrs, CT 06269, USA;
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
- Correspondence:
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3
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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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4
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Carraro C, Helbing T, Francke A, Zuravka I, Sosic A, De Franco M, Gandin V, Gatto B, Göttlich DR. Appended Aromatic Moieties in Flexible Bis-3-chloropiperidines Confer Tropism against Pancreatic Cancer Cells. ChemMedChem 2021; 16:860-868. [PMID: 33200541 PMCID: PMC7984046 DOI: 10.1002/cmdc.202000814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 12/24/2022]
Abstract
Nitrogen mustards (NMs) are an old but still largely diffused class of anticancer drugs. However, spreading mechanisms of resistance undermine their efficacy and therapeutic applicability. To expand their antitumour value, we developed bis-3-chloropiperidines (B-CePs), a new class of mustard-based alkylating agent, and we recently reported the striking selectivity for BxPC-3 pancreatic tumour cells of B-CePs bearing aromatic moieties embedded in the linker. In this study, we demonstrate that such tropism is shared by bis-3-chloropiperidines bearing appended aromatic groups in flexible linkers, whereas esters substituted by aliphatic groups or by efficient DNA-interacting groups are potent but nonselective cytotoxic agents. Besides, we describe how the critical balance between water stability and DNA reactivity can affect the properties of bis-3-chloropiperidines. Together, these findings support the exploitation of B-CePs as potential antitumour clinical candidates.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Tim Helbing
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Alexander Francke
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Ivonne Zuravka
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - D. Richard Göttlich
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
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5
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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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Butovskaya E, Soldà P, Scalabrin M, Nadai M, Richter SN. HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands. ACS Infect Dis 2019; 5:2127-2135. [PMID: 31646863 PMCID: PMC6909241 DOI: 10.1021/acsinfecdis.9b00272] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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The G-quadruplexes that form in the
HIV-1 RNA genome hinder progression
of reverse transcriptase
in vitro, but not in infected cells. We investigated the possibility
that the HIV-1 nucleocapsid protein NCp7, which remains associated
with the viral RNA during reverse transcription, modulated HIV-1 RNA
G-quadruplex stability. By electrophoresis, circular dichroism, mass
spectrometry, and reverse transcriptase stop assays, we demonstrated
that NCp7 binds and unfolds the HIV-1 RNA G-quadruplexes and promotes
DNA/RNA duplex formation, allowing reverse transcription to proceed.
The G-quadruplex ligand BRACO-19 was able to partially counteract
this effect. These results indicate NCp7 as the first known viral
protein able to unfold RNA G-quadruplexes, and they explain how the
extra-stable HIV-1 RNA G-quadruplexes are processed; they also point
out that the reverse transcription process is hindered by G-quadruplex
ligands at both reverse transcriptase and NCp7 level. This information
can lead to the development of more effective anti-HIV-1 drugs with
a new mechanism of action.
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Affiliation(s)
- Elena Butovskaya
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Paola Soldà
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
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