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Kobayashi-Ishihara M, Tsunetsugu-Yokota Y. Post-Transcriptional HIV-1 Latency: A Promising Target for Therapy? Viruses 2024; 16:666. [PMID: 38793548 PMCID: PMC11125802 DOI: 10.3390/v16050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) latency represents a significant hurdle in finding a cure for HIV-1 infections, despite tireless research efforts. This challenge is partly attributed to the intricate nature of HIV-1 latency, wherein various host and viral factors participate in multiple physiological processes. While substantial progress has been made in discovering therapeutic targets for HIV-1 transcription, targets for the post-transcriptional regulation of HIV-1 infections have received less attention. However, cumulative evidence now suggests the pivotal contribution of post-transcriptional regulation to the viral latency in both in vitro models and infected individuals. In this review, we explore recent insights on post-transcriptional latency in HIV-1 and discuss the potential of its therapeutic targets, illustrating some host factors that restrict HIV-1 at the post-transcriptional level.
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Affiliation(s)
- Mie Kobayashi-Ishihara
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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Chumillas S, Loharch S, Beltrán M, Szewczyk MP, Bernal S, Puertas MC, Martinez-Picado J, Alcamí J, Bedoya LM, Marchán V, Gallego J. Exploring the HIV-1 Rev Recognition Element (RRE)-Rev Inhibitory Capacity and Antiretroviral Action of Benfluron Analogs. Molecules 2023; 28:7031. [PMID: 37894510 PMCID: PMC10609163 DOI: 10.3390/molecules28207031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Human immunodeficiency virus-type 1 (HIV-1) remains one of the leading contributors to the global burden of disease, and novel antiretroviral agents with alternative mechanisms are needed to cure this infection. Here, we describe an exploratory attempt to optimize the antiretroviral properties of benfluron, a cytostatic agent previously reported to exhibit strong anti-HIV activity likely based on inhibitory actions on virus transcription and Rev-mediated viral RNA export. After obtaining six analogs designed to modify the benzo[c]fluorenone system of the parent molecule, we examined their antiretroviral and toxicity properties together with their capacity to recognize the Rev Recognition Element (RRE) of the virus RNA and inhibit the RRE-Rev interaction. The results indicated that both the benzo[c] and cyclopentanone components of benfluron are required for strong RRE-Rev target engagement and antiretroviral activity and revealed the relative impact of these moieties on RRE affinity, RRE-Rev inhibition, antiviral action and cellular toxicity. These data provide insights into the biological properties of the benzo[c]fluorenone scaffold and contribute to facilitating the design of new anti-HIV agents based on the inhibition of Rev function.
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Affiliation(s)
- Sergi Chumillas
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Saurabh Loharch
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain; (S.L.); (M.P.S.)
| | - Manuela Beltrán
- Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.B.); (L.M.B.)
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mateusz P. Szewczyk
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain; (S.L.); (M.P.S.)
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - Silvia Bernal
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain
- Infectious Diseases and Immunity Department, University of Vic—Central University of Catalonia, 08500 Vic, Spain
| | - Maria C. Puertas
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain
- Germans Trias i Pujol Research Institute, 08916 Badalona, Spain
| | - Javier Martinez-Picado
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain
- Infectious Diseases and Immunity Department, University of Vic—Central University of Catalonia, 08500 Vic, Spain
- Germans Trias i Pujol Research Institute, 08916 Badalona, Spain
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain
| | - José Alcamí
- Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.B.); (L.M.B.)
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Luis M. Bedoya
- Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.B.); (L.M.B.)
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Vicente Marchán
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - José Gallego
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain; (S.L.); (M.P.S.)
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Simba-Lahuasi Á, Alcamí J, Beltrán M, Bedoya LM, Gallego J. Novel HIV-1 RNA biogenesis inhibitors identified by virtual pharmacophore-based screening. Biochem Pharmacol 2023; 215:115734. [PMID: 37549794 DOI: 10.1016/j.bcp.2023.115734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
The complex between the Rev protein of HIV-1 and the Rev Recognition Element (RRE) within the virus RNA promotes nuclear export of unspliced or incompletely spliced viral transcripts and is required for virus transmission. Here, we have screened a virtual collection of compounds using a pharmacophore based on the chemical similarity of previously characterized inhibitors to identify new chemical scaffolds blocking the RRE-Rev interaction. The best molecules discovered with this strategy inhibited the complex by binding to the RRE and exhibited substantial antiretroviral activity (between 0.582 and 11.3 μM EC50 values) likely associated to inhibitory actions on viral transcription and Rev function. These results have allowed us to identify structural features required for RRE-Rev inhibition as well as to add new compounds to the pool of possible candidates for developing antiretroviral agents based on blockage of HIV-1 RNA biogenesis.
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Affiliation(s)
- Álvaro Simba-Lahuasi
- CITSAM, Fundación Universidad Católica de Valencia San Vicente Mártir, C/Quevedo 2 46001, Valencia, Spain; Escuela de Doctorado, Fundación Universidad Católica de Valencia San Vicente Mártir, Spain
| | - José Alcamí
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2 28220, Majadahonda, Spain; CIBERINFEC, Instituto de Salud Carlos III, Spain
| | - Manuela Beltrán
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2 28220, Majadahonda, Spain; CIBERINFEC, Instituto de Salud Carlos III, Spain
| | - Luis M Bedoya
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2 28220, Majadahonda, Spain; CIBERINFEC, Instituto de Salud Carlos III, Spain; Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n 28040, Madrid, Spain.
| | - José Gallego
- CITSAM, Fundación Universidad Católica de Valencia San Vicente Mártir, C/Quevedo 2 46001, Valencia, Spain.
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SARS-CoV-2 Inhibitors Identified by Phenotypic Analysis of a Collection of Viral RNA-Binding Molecules. Pharmaceuticals (Basel) 2022; 15:ph15121448. [PMID: 36558898 PMCID: PMC9784969 DOI: 10.3390/ph15121448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Antiviral agents are needed for the treatment of SARS-CoV-2 infections and to control other coronavirus outbreaks that may occur in the future. Here we report the identification and characterization of RNA-binding compounds that inhibit SARS-CoV-2 replication. The compounds were detected by screening a small library of antiviral compounds previously shown to bind HIV-1 or HCV RNA elements with a live-virus cellular assay detecting inhibition of SARS-CoV-2 replication. These experiments allowed detection of eight compounds with promising anti-SARS-CoV-2 activity in the sub-micromolar to micromolar range and wide selectivity indexes. Examination of the mechanism of action of three selected hit compounds excluded action on the entry or egress stages of the virus replication cycle and confirmed recognition by two of the molecules of conserved RNA elements of the SARS-CoV-2 genome, including the highly conserved S2m hairpin located in the 3'-untranslated region of the virus. While further studies are needed to clarify the mechanism of action responsible for antiviral activity, these results facilitate the discovery of RNA-targeted antivirals and provide new chemical scaffolds for developing therapeutic agents against coronaviruses.
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Taxonomic Characterization, Antiviral Activity and Induction of Three New Kenalactams in Nocardiopsis sp. CG3. Curr Microbiol 2022; 79:284. [PMID: 35947206 PMCID: PMC9363871 DOI: 10.1007/s00284-022-02954-x] [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: 02/07/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022]
Abstract
Exploration of secondary metabolites secreted by new Actinobacteria taxa isolated from unexplored areas, can increase the possibility to obtain new compounds which can be developed into new drugs for the treatment of serious diseases such as hepatitis C. In this context, one actinobacterial strain, CG3, has been selected based on the results of polyphasic characterization, which indicate that it represents a new putative species within the genus Nocardiopsis. Two fractions (F2 and F3), prepared from the culture of strain CG3 in soybean medium, exhibited a pronounced antiviral activity against the HCV strain Luc-Jc1. LC–HRESIMS analysis showed different bioactive compounds in both active fractions (F2 and F3), including five polyenic macrolactams (kenalactams A-E), three isoflavone metabolites, along with mitomycin C and one p-phenyl derivative. Furthermore, feeding with 1% of methionine, lysine or alanine as a unique nitrogen source, induced the production of three novel kenalactam derivatives.
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Crespo R, Rao S, Mahmoudi T. HibeRNAtion: HIV-1 RNA Metabolism and Viral Latency. Front Cell Infect Microbiol 2022; 12:855092. [PMID: 35774399 PMCID: PMC9237370 DOI: 10.3389/fcimb.2022.855092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023] Open
Abstract
HIV-1 infection remains non-curative due to the latent reservoir, primarily a small pool of resting memory CD4+ T cells bearing replication-competent provirus. Pharmacological reversal of HIV-1 latency followed by intrinsic or extrinsic cell killing has been proposed as a promising strategy to target and eliminate HIV-1 viral reservoirs. Latency reversing agents have been extensively studied for their role in reactivating HIV-1 transcription in vivo, although no permanent reduction of the viral reservoir has been observed thus far. This is partly due to the complex nature of latency, which involves strict intrinsic regulation at multiple levels at transcription and RNA processing. Still, the molecular mechanisms that control HIV-1 latency establishment and maintenance have been almost exclusively studied in the context of chromatin remodeling, transcription initiation and elongation and most known LRAs target LTR-driven transcription by manipulating these. RNA metabolism is a largely understudies but critical mechanistic step in HIV-1 gene expression and latency. In this review we provide an update on current knowledge on the role of RNA processing mechanisms in viral gene expression and latency and speculate on the possible manipulation of these pathways as a therapeutic target for future cure studies.
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Affiliation(s)
- Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
- *Correspondence: Tokameh Mahmoudi,
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van Heuvel Y, Schatz S, Rosengarten JF, Stitz J. Infectious RNA: Human Immunodeficiency Virus (HIV) Biology, Therapeutic Intervention, and the Quest for a Vaccine. Toxins (Basel) 2022; 14:toxins14020138. [PMID: 35202165 PMCID: PMC8876946 DOI: 10.3390/toxins14020138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Different mechanisms mediate the toxicity of RNA. Genomic retroviral mRNA hijacks infected host cell factors to enable virus replication. The viral genomic RNA of the human immunodeficiency virus (HIV) encompasses nine genes encoding in less than 10 kb all proteins needed for replication in susceptible host cells. To do so, the genomic RNA undergoes complex alternative splicing to facilitate the synthesis of the structural, accessory, and regulatory proteins. However, HIV strongly relies on the host cell machinery recruiting cellular factors to complete its replication cycle. Antiretroviral therapy (ART) targets different steps in the cycle, preventing disease progression to the acquired immunodeficiency syndrome (AIDS). The comprehension of the host immune system interaction with the virus has fostered the development of a variety of vaccine platforms. Despite encouraging provisional results in vaccine trials, no effective vaccine has been developed, yet. However, novel promising vaccine platforms are currently under investigation.
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Affiliation(s)
- Yasemin van Heuvel
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Stefanie Schatz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jamila Franca Rosengarten
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jörn Stitz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Correspondence:
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Orel VB, Vitkovskaya NM, Bobkov AS, Semenova NV, Schmidt EY, Trofimov BA. Aldol Condensation Versus Superbase-Catalyzed Addition of Ketones to Acetylenes: A Quantum-Chemical and Experimental Study. J Org Chem 2021; 86:7439-7449. [PMID: 34014087 DOI: 10.1021/acs.joc.1c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The mechanism of aldol condensation of ketones in KOH/DMSO superbasic media has been investigated using the B2PLYP(D2)/6-311+G**//B3LYP/6-31+G* quantum-chemical approach. It is found that the interaction of three ketone molecules resulting in the formation of the cyclohex-2-enone structure [isophorone or 3,5-dicyclohexyl-5-methylspiro(5.5)undec-2-en-1-one] is thermodynamically more favorable than the interaction of two, three, or four molecules of ketone, resulting in the formation of linear products of the condensation. The formation of the condensation products with the isophorone skeleton can significantly hinder the cascade reactions of ketones with acetylenes [to afford 6,8-dioxabicyclo(3.2.1)octanes or acylcyclopentenols] promoted by superbases. In particular, the kinetically more preferable reactions of autovinylation of 2-methyl-3-butyn-2-ol and autocondensation of acetone are the reasons why interaction of acetone with acetylene does not lead to the products of the cascade assemblies. The predominant formation of the products of these side reactions is confirmed experimentally.
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Affiliation(s)
- Vladimir B Orel
- Laboratory of Quantum-Chemical Modeling of Molecular Systems, Irkutsk State University, 1 K. Marx Street, 664003 Irkutsk, Russian Federation.,A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
| | - Nadezhda M Vitkovskaya
- Laboratory of Quantum-Chemical Modeling of Molecular Systems, Irkutsk State University, 1 K. Marx Street, 664003 Irkutsk, Russian Federation
| | - Alexander S Bobkov
- Laboratory of Quantum-Chemical Modeling of Molecular Systems, Irkutsk State University, 1 K. Marx Street, 664003 Irkutsk, Russian Federation
| | - Nadezhda V Semenova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
| | - Elena Yu Schmidt
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
| | - Boris A Trofimov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation
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Algar S, Martín-Martínez M, González-Muñiz R. Evolution in non-peptide α-helix mimetics on the road to effective protein-protein interaction modulators. Eur J Med Chem 2020; 211:113015. [PMID: 33423841 DOI: 10.1016/j.ejmech.2020.113015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023]
Abstract
Modulation of interactome networks, essentially protein-protein interactions (PPIs), might represent valuable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs are mediated by α-helical structures at the interacting surface, the development of compounds able to reproduce the amino acid side-chain organization of α-helices (e.g. stabilized α-helix peptides and β-derivatives, proteomimetics, and α-helix small-molecule mimetics) focuses the attention of different research groups. This appraisal describes the recent progress in the non-peptide α-helix mimetics field, which has evolved from single-face to multi-face reproducing compounds and from oligomeric to monomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chains in canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules, oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomeric small-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeutically relevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development in clinical trials, are also remarked. The discovery of a continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcoming α-helix mimetics.
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Affiliation(s)
- Sergio Algar
- Instituto de Química Médica, IQM-CSIC, Juan de La Cierva 3, 28006, Madrid, Spain
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