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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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2
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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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Alenazi NA, Fawzi Qarah A, Alsahag M, Alharbi H, Bayazeed A, Al-Qahtani SD, El-Metwaly NM. Synthesis, molecular modelling and docking studies of new thieno[2,3-b:4,5-b′] dipyridine compounds as antimicrobial agents. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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4
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Modern Methods for the Synthesis of Cyano-Substituted Bipyridine Derivatives (microreview). Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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5
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Nucleic acid recognition and antiviral activity of 1,4-substituted terphenyl compounds mimicking all faces of the HIV-1 Rev protein positively-charged α-helix. Sci Rep 2020; 10:7190. [PMID: 32346097 PMCID: PMC7188855 DOI: 10.1038/s41598-020-64120-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/09/2020] [Indexed: 11/08/2022] Open
Abstract
Small synthetic molecules mimicking the three-dimensional structure of α-helices may find applications as inhibitors of therapeutically relevant protein-protein and protein-nucleic acid interactions. However, the design and use of multi-facial helix mimetics remains in its infancy. Here we describe the synthesis and application of novel bilaterally substituted p-terphenyl compounds containing positively-charged aminoalkyl groups in relative 1,4 positions across the aromatic scaffold. These compounds were specifically designed to mimic all faces of the arginine-rich α-helix of the HIV-1 protein Rev, which forms deeply embedded RNA complexes and plays key roles in the virus replication cycle. Two of these molecules recognized the Rev site in the viral RNA and inhibited the formation of the RRE-Rev ribonucleoprotein complex, a currently unexploited target in HIV chemotherapy. Cellular assays revealed that the most active compounds blocked HIV-1 replication with little toxicity, and likely exerted this effect through a multi-target mechanism involving inhibition of viral LTR promoter-dependent transcription and Rev function. Further development of this scaffold may open new avenues for targeting nucleic acids and may complement current HIV therapies, none of which involve inhibitors interfering with the gene regulation processes of the virus.
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6
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Jackson PEH, Huang J, Sharma M, Rasmussen SK, Hammarskjold ML, Rekosh D. A novel retroviral vector system to analyze expression from mRNA with retained introns using fluorescent proteins and flow cytometry. Sci Rep 2019; 9:6467. [PMID: 31015546 PMCID: PMC6478720 DOI: 10.1038/s41598-019-42914-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
The ability to overcome cellular restrictions that exist for the export and translation of mRNAs with retained introns is a requirement for the replication of retroviruses and also for the expression of many mRNA isoforms transcribed from cellular genes. In some cases, RNA structures have been identified in the mRNA that directly interact with cellular factors to promote the export and expression of isoforms with retained introns. In other cases, a viral protein is also required to act as an adapter. In this report we describe a novel vector system that allows measurement of the ability of cis- and trans-acting factors to promote the export and translation of mRNAs with retained introns. One reporter vector used in this system is derived from an HIV proviral clone engineered to express two different fluorescent proteins from spliced and unspliced transcripts. The ratio of fluorescent signals is a measurement of the efficiency of export and translation. A second vector utilizes a third fluorescent protein to measure the expression of viral export proteins that interact with some of the export elements. Both vectors can be packaged into viral particles and be used to transduce cells, allowing expression at physiological levels from the integrated vector.
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Affiliation(s)
- Patrick E H Jackson
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Jing Huang
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Monika Sharma
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Sara K Rasmussen
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - David Rekosh
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA.
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7
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Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD. Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability. Sci Rep 2019; 9:5139. [PMID: 30914719 PMCID: PMC6435700 DOI: 10.1038/s41598-019-41582-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/05/2019] [Indexed: 11/12/2022] Open
Abstract
HIV-1 Rev is an essential viral regulatory protein that facilitates the nuclear export of intron-containing viral mRNAs. It is organized into structured, functionally well-characterized motifs joined by less understood linker regions. Our recent competitive deep mutational scanning study confirmed many known constraints in Rev’s established motifs, but also identified positions of mutational plasticity, most notably in surrounding linker regions. Here, we probe the mutational limits of these linkers by testing the activities of multiple truncation and mass substitution mutations. We find that these regions possess previously unknown structural, functional or regulatory roles, not apparent from systematic point mutational approaches. Specifically, the N- and C-termini of Rev contribute to protein stability; mutations in a turn that connects the two main helices of Rev have different effects in different contexts; and a linker region which connects the second helix of Rev to its nuclear export sequence has structural requirements for function. Thus, Rev function extends beyond its characterized motifs, and is tuned by determinants within seemingly plastic portions of its sequence. Additionally, Rev’s ability to tolerate many of these massive truncations and substitutions illustrates the overall mutational and functional robustness inherent in this viral protein.
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Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.,UCSC Genomics Institute/Howard Hughes Medical Institute, University of Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Shumin Yang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.,School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Cynthia Smith
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.
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8
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Prado S, Beltrán M, Moreno Á, Bedoya LM, Alcamí J, Gallego J. A small-molecule inhibitor of HIV-1 Rev function detected by a diversity screen based on RRE-Rev interference. Biochem Pharmacol 2018; 156:68-77. [PMID: 30071201 DOI: 10.1016/j.bcp.2018.07.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/27/2018] [Indexed: 11/18/2022]
Abstract
The Rev protein of HIV-1 binds to the Rev Recognition Element (RRE) in the virus RNA to promote nuclear export of unspliced and partially spliced transcripts, an essential step in the virus transmission cycle. Here, we describe the screening of a library of chemically diverse compounds with an assay based on monitoring the interaction between the RNA-binding α-helix of Rev and its high-affinity binding site in the RRE. This screen allowed the identification of a benzofluorenone compound that inhibited the formation of the full-length RRE-Rev ribonucleoprotein by associating to the RRE, and blocked HIV-1 transcription and Rev action in cells. This molecule, previously studied as a cytostatic agent, had substantial antiretroviral activity. Together with other screening hits, it provides a new chemical scaffold for the development of antiretroviral agents based on blockage of HIV-1 RNA biogenesis.
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Affiliation(s)
- Silvia Prado
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Manuela Beltrán
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain
| | - Ángela Moreno
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Luis M Bedoya
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain; Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - José Alcamí
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain.
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain.
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