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Joshi H, Tuli HS, Ranjan A, Chauhan A, Haque S, Ramniwas S, Bhatia GK, Kandari D. The Pharmacological Implications of Flavopiridol: An Updated Overview. Molecules 2023; 28:7530. [PMID: 38005250 PMCID: PMC10673037 DOI: 10.3390/molecules28227530] [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: 10/15/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Flavopiridol is a flavone synthesized from the natural product rohitukine, which is derived from an Indian medicinal plant, namely Dysoxylum binectariferum Hiern. A deeper understanding of the biological mechanisms by which such molecules act may allow scientists to develop effective therapeutic strategies against a variety of life-threatening diseases, such as cancer, viruses, fungal infections, parasites, and neurodegenerative diseases. Mechanistic insight of flavopiridol reveals its potential for kinase inhibitory activity of CDKs (cyclin-dependent kinases) and other kinases, leading to the inhibition of various processes, including cell cycle progression, apoptosis, tumor proliferation, angiogenesis, tumor metastasis, and the inflammation process. The synthetic derivatives of flavopiridol have overcome a few demerits of its parent compound. Moreover, these derivatives have much improved CDK-inhibitory activity and therapeutic abilities for treating severe human diseases. It appears that flavopiridol has potential as a candidate for the formulation of an integrated strategy to combat and alleviate human diseases. This review article aims to unravel the potential therapeutic effectiveness of flavopiridol and its possible mechanism of action.
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Affiliation(s)
- Hemant Joshi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India;
| | - Hardeep Singh Tuli
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala 133207, India;
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-on-Don 344090, Russia;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Sector 125, Noida 201301, India;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 11022801, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 13306, United Arab Emirates
| | - Seema Ramniwas
- University Centre for Research and Development, University Institute of Pharmaceutical Sciences, Chandigarh University, Gharuan, Mohali 140413, India;
| | - Gurpreet Kaur Bhatia
- Department of Physics, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, India;
| | - Divya Kandari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India;
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2
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Manna S, Das K, Santra S, Nosova EV, Zyryanov GV, Halder S. Structural and Synthetic Aspects of Small Ring Oxa- and Aza-Heterocyclic Ring Systems as Antiviral Activities. Viruses 2023; 15:1826. [PMID: 37766233 PMCID: PMC10536032 DOI: 10.3390/v15091826] [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: 03/31/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Antiviral properties of different oxa- and aza-heterocycles are identified and properly correlated with their structural features and discussed in this review article. The primary objective is to explore the activity of such ring systems as antiviral agents, as well as their synthetic routes and biological significance. Eventually, the structure-activity relationship (SAR) of the heterocyclic compounds, along with their salient characteristics are exhibited to build a suitable platform for medicinal chemists and biotechnologists. The synergistic conclusions are extremely important for the introduction of a newer tool for the future drug discovery program.
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Affiliation(s)
- Sibasish Manna
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| | - Koushik Das
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| | - Sougata Santra
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
| | - Emily V. Nosova
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, 620219 Yekaterinburg, Russia
| | - Grigory V. Zyryanov
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, 620219 Yekaterinburg, Russia
| | - Sandipan Halder
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
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3
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Xu S, Sun L, Liu X, Zhan P. Opportunities and challenges in new HIV therapeutic discovery: what is the next step? Expert Opin Drug Discov 2023; 18:1195-1199. [PMID: 37561085 DOI: 10.1080/17460441.2023.2246872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023]
Affiliation(s)
- Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
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4
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Targeting Human Proteins for Antiviral Drug Discovery and Repurposing Efforts: A Focus on Protein Kinases. Viruses 2023; 15:v15020568. [PMID: 36851782 PMCID: PMC9966946 DOI: 10.3390/v15020568] [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: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Despite the great technological and medical advances in fighting viral diseases, new therapies for most of them are still lacking, and existing antivirals suffer from major limitations regarding drug resistance and a limited spectrum of activity. In fact, most approved antivirals are directly acting antiviral (DAA) drugs, which interfere with viral proteins and confer great selectivity towards their viral targets but suffer from resistance and limited spectrum. Nowadays, host-targeted antivirals (HTAs) are on the rise, in the drug discovery and development pipelines, in academia and in the pharmaceutical industry. These drugs target host proteins involved in the virus life cycle and are considered promising alternatives to DAAs due to their broader spectrum and lower potential for resistance. Herein, we discuss an important class of HTAs that modulate signal transduction pathways by targeting host kinases. Kinases are considered key enzymes that control virus-host interactions. We also provide a synopsis of the antiviral drug discovery and development pipeline detailing antiviral kinase targets, drug types, therapeutic classes for repurposed drugs, and top developing organizations. Furthermore, we detail the drug design and repurposing considerations, as well as the limitations and challenges, for kinase-targeted antivirals, including the choice of the binding sites, physicochemical properties, and drug combinations.
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Minadakis G, Tomazou M, Dietis N, Spyrou GM. Vir2Drug: a drug repurposing framework based on protein similarities between pathogens. Brief Bioinform 2022; 24:6895455. [PMID: 36513376 PMCID: PMC9851336 DOI: 10.1093/bib/bbac536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
We draw from the assumption that similarities between pathogens at both pathogen protein and host protein level, may provide the appropriate framework to identify and rank candidate drugs to be used against a specific pathogen. Vir2Drug is a drug repurposing tool that uses network-based approaches to identify and rank candidate drugs for a specific pathogen, combining information obtained from: (a) ranked pathogen-to-pathogen networks based on protein similarities between pathogens, (b) taxonomy distance between pathogens and (c) drugs targeting specific pathogen's and host proteins. The underlying pathogen networks are used to screen drugs by means of specific methodologies that account for either the host or pathogen's protein targets. Vir2Drug is a useful and yet informative tool for drug repurposing against known or unknown pathogens especially in periods where the emergence for repurposed drugs plays significant role in handling viral outbreaks, until reaching a vaccine. The web tool is available at: https://bioinformatics.cing.ac.cy/vir2drug, https://vir2drug.cing-big.hpcf.cyi.ac.cy.
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Affiliation(s)
- George Minadakis
- Corresponding author: George Minadakis, Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus. Tel.: +357-22-392852; Fax: +357-22-358238; E-mail:
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683 Nicosia, Cyprus,The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus
| | - Nikolas Dietis
- Medical School, University of Cyprus, Nicosia 1678, Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683 Nicosia, Cyprus,The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus
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Mediouni S, Lyu S, Schader SM, Valente ST. Forging a Functional Cure for HIV: Transcription Regulators and Inhibitors. Viruses 2022; 14:1980. [PMID: 36146786 PMCID: PMC9502519 DOI: 10.3390/v14091980] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Current antiretroviral therapy (ART) increases the survival of HIV-infected individuals, yet it is not curative. The major barrier to finding a definitive cure for HIV is our inability to identify and eliminate long-lived cells containing the dormant provirus, termed viral reservoir. When ART is interrupted, the viral reservoir ensures heterogenous and stochastic HIV viral gene expression, which can reseed infection back to pre-ART levels. While strategies to permanently eradicate the virus have not yet provided significant success, recent work has focused on the management of this residual viral reservoir to effectively limit comorbidities associated with the ongoing viral transcription still observed during suppressive ART, as well as limit the need for daily ART. Our group has been at the forefront of exploring the viability of the block-and-lock remission approach, focused on the long-lasting epigenetic block of viral transcription such that without daily ART, there is no risk of viral rebound, transmission, or progression to AIDS. Numerous studies have reported inhibitors of both viral and host factors required for HIV transcriptional activation. Here, we highlight and review some of the latest HIV transcriptional inhibitor discoveries that may be leveraged for the clinical exploration of block-and-lock and revolutionize the way we treat HIV infections.
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Affiliation(s)
- Sonia Mediouni
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, 130 Scripps Way, 3C1, Jupiter, FL 33458, USA
| | - Shuang Lyu
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, 130 Scripps Way, 3C1, Jupiter, FL 33458, USA
| | - Susan M. Schader
- Department of Infectious Disease Research, Drug Development Division, Southern Research, 431 Aviation Way, Frederick, MD 21701, USA
| | - Susana T. Valente
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, 130 Scripps Way, 3C1, Jupiter, FL 33458, USA
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Cyclin-dependent Kinases as Emerging Targets for Developing Novel Antiviral Therapeutics. Trends Microbiol 2021; 29:836-848. [PMID: 33618979 DOI: 10.1016/j.tim.2021.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022]
Abstract
Besides its prominent role in cell proliferation, cyclin-dependent kinases (CDKs) are key players in viral infections as both DNA and RNA viruses modify CDK function to favor viral replication. Recently, a number of specific pharmacological CDK inhibitors have been developed and approved for cancer treatment. The repurposing of these specific CDK inhibitors for the treatment of viral infections may represent a novel effective therapeutic strategy to combat old and emergent viruses. In this review, we describe the role, mechanisms of action, and potential of CDKs as antiviral drug targets. We also discuss the current clinical state of novel specific CDK inhibitors, focusing on their putative use as antivirals, especially against new emerging viruses.
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Flavonoid-based inhibition of cyclin-dependent kinase 9 without concomitant inhibition of histone deacetylases durably reinforces HIV latency. Biochem Pharmacol 2021; 186:114462. [PMID: 33577894 DOI: 10.1016/j.bcp.2021.114462] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
While combination antiretroviral therapy (cART) durably suppresses HIV replication, virus persists in CD4+ T-cells that harbor latent but spontaneously inducible and replication-competent provirus. One strategy to inactivate these viral reservoirs involves the use of agents that continue to reinforce HIV latency even after their withdrawal. To identify new chemical leads with such properties, we investigated a series of naturally-occurring flavones (chrysin, apigenin, luteolin, and luteolin-7-glucoside (L7G)) and functionally-related cyclin dependent kinase 9 (CDK9) inhibitors (flavopiridol and atuveciclib) which are reported or presumed to suppress HIV replication in vitro. We found that, while all compounds inhibit provirus expression induced by latency-reversing agents in vitro, only aglycone flavonoids (chrysin, apigenin, luteolin, flavopiridol) and atuveciclib, but not the glycosylated flavonoid L7G, inhibit spontaneous latency reversal. Aglycone flavonoids and atuveciclib, but not L7G, also inhibit CDK9 and the HIV Tat protein. Aglycone flavonoids do not reinforce HIV latency following their in vitro withdrawal, which corresponds with their ability to also inhibit class I/II histone deacetylases (HDAC), a well-established mechanism of latency reversal. In contrast, atuveciclib and flavopiridol, which exhibit little or no HDAC inhibition, continue to reinforce latency for 9 to 14+ days, respectively, following their withdrawal in vitro. Finally, we show that flavopiridol also inhibits spontaneous ex vivo viral RNA production in CD4+ T cells from donors with HIV. These results implicate CDK9 inhibition (in the absence of HDAC inhibition) as a potentially favorable property in the search for compounds that durably reinforce HIV latency.
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9
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Potent inhibition of HIV replication in primary human cells by novel synthetic polyketides inspired by Aureothin. Sci Rep 2020; 10:1326. [PMID: 31992748 PMCID: PMC6987146 DOI: 10.1038/s41598-020-57843-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/06/2020] [Indexed: 11/08/2022] Open
Abstract
Overcoming the global health threat of HIV infection requires continuous pipelines of novel drug candidates. We identified the γ-pyrone polyketides Aureothin/Neoaureothin as potent hits by anti-HIV screening of an extensive natural compound collection. Total synthesis of a structurally diverse group of Aureothin-derivatives successfully identified a lead compound (#7) superior to Aureothin that combines strong anti-HIV activity (IC90<45 nM), photostability and improved cell safety. Compound #7 inhibited de novo virus production from integrated proviruses by blocking the accumulation of HIV RNAs that encode the structural components of virions and include viral genomic RNAs. Thus, the mode-of-action displayed by compound #7 is different from those of all current clinical drugs. Proteomic analysis indicated that compound #7 does not affect global protein expression in primary blood cells and may modulate cellular pathways linked to HIV infection. Compound #7 inhibited multiple HIV genotypes, including HIV-type 1 and 2 and synergistically inhibited HIV in combination with clinical reverse transcriptase and integrase inhibitors. We conclude that compound #7 represents a promising new class of HIV inhibitors that will facilitate the identification of new virus-host interactions exploitable for antiviral attack and holds promise for further drug development.
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10
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Lin X, Ammosova T, Kumari N, Nekhai S. Protein Phosphatase-1 -targeted Small Molecules, Iron Chelators and Curcumin Analogs as HIV-1 Antivirals. Curr Pharm Des 2018; 23:4122-4132. [PMID: 28677499 DOI: 10.2174/1381612823666170704123620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Despite efficient suppression of HIV-1 replication, current antiviral drugs are not able to eradicate HIV-1 infection. Permanent HIV-1 suppression or complete eradication requires novel biological approaches and therapeutic strategies. Our previous studies showed that HIV-1 transcription is regulated by host cell protein phosphatase-1. We also showed that HIV-1 transcription is sensitive to the reduction of intracellular iron that affects cell cycle-dependent kinase 2. We developed protein phosphatase 1-targeting small molecules that inhibited HIV-1 transcription. We also found an additional class of protein phosphatase-1-targeting molecules that activated HIV-1 transcription and reported HIV-1 inhibitory iron chelators and novel curcumin analogs that inhibit HIV-1. Here, we review HIV-1 transcription and replication with focus on its regulation by protein phosphatase 1 and cell cycle dependent kinase 2 and describe novel small molecules that can serve as future leads for anti-HIV drug development. RESULTS Our review describes in a non-exhaustive manner studies in which HIV-1 transcription and replication are targeted with small molecules. Previously, published studies show that HIV-1 can be inhibited with protein phosphatase-1-targeting and iron chelating compounds and curcumin analogs. These results are significant in light of the current efforts to eradicate HIV-1 through permanent inhibition. Also, HIV-1 activating compounds can be useful for "kick and kill" therapy in which the virus is reactivated prior to its inhibition by the combination antiretroviral therapy. CONCLUSION The studies described in our review point to protein phosphatase-1 as a new drug target, intracellular iron as subject for iron chelation and novel curcumin analogs that can be developed for novel HIV-1 transcription- targeting therapeutics.
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Affiliation(s)
- Xionghao Lin
- Center for Sickle Cell Disease, 1840 7th Street, N.W. HURB1, Suite 202, Washington DC 20001. United States
| | - Tatyana Ammosova
- Center for Sickle Cell Disease, 1840 7th Street, N.W. HURB1, Suite 202, Washington DC 20001. United States
| | - Namita Kumari
- Center for Sickle Cell Disease, 1840 7th Street, N.W. HURB1, Suite 202, Washington DC 20001. United States
| | - Sergei Nekhai
- Center for Sickle Cell Disease, 1840 7th Street, N.W. HURB1, Suite 202, Washington DC 20001. United States
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11
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How to win the HIV-1 drug resistance hurdle race: running faster or jumping higher? Biochem J 2017; 474:1559-1577. [PMID: 28446620 DOI: 10.1042/bcj20160772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/17/2022]
Abstract
Infections by the human immunodeficiency virus type 1 (HIV-1), the causative agent of the acquired immunodeficiency syndrome (AIDS), are still totaling an appalling 36.7 millions worldwide, with 1.1 million AIDS deaths/year and a similar number of yearly new infections. All this, in spite of the discovery of HIV-1 as the AIDS etiological agent more than 30 years ago and the introduction of an effective combinatorial antiretroviral therapy (cART), able to control disease progression, more than 20 years ago. Although very effective, current cART is plagued by the emergence of drug-resistant viral variants and most of the efforts in the development of novel direct-acting antiviral agents (DAAs) against HIV-1 have been devoted toward the fighting of resistance. In this review, rather than providing a detailed listing of all the drugs and the corresponding resistance mutations, we aim, through relevant examples, at presenting to the general reader the conceptual shift in the approaches that are being taken to overcome the viral resistance hurdle. From the classic 'running faster' strategy, based on the development of novel DAAs active against the mutant viruses selected by the previous drugs and/or presenting to the virus a high genetic barrier toward the development of resilience, to a 'jumping higher' approach, which looks at the cell, rather than the virus, as a source of valuable drug targets, in order to make the cellular environment non-permissive toward the replication of both wild-type and mutated viruses.
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Abstract
Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the "torpedo" exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle.
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Affiliation(s)
- Robert P Fisher
- a Department of Oncological Sciences , Icahn School of Medicine at Mount Sinai , New York , NY , USA
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13
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Sonawane YA, Taylor MA, Napoleon JV, Rana S, Contreras JI, Natarajan A. Cyclin Dependent Kinase 9 Inhibitors for Cancer Therapy. J Med Chem 2016; 59:8667-8684. [PMID: 27171036 PMCID: PMC5636177 DOI: 10.1021/acs.jmedchem.6b00150] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Cyclin dependent kinase (CDK) inhibitors
have been the topic of intense research for nearly 2 decades due to
their widely varied and critical functions within the cell. Recently
CDK9 has emerged as a druggable target for the development of cancer
therapeutics. CDK9 plays a crucial role in transcription regulation;
specifically, CDK9 mediated transcriptional regulation of short-lived
antiapoptotic proteins is critical for the survival of transformed
cells. Focused chemical libraries based on a plethora of scaffolds
have resulted in mixed success with regard to the development of selective
CDK9 inhibitors. Here we review the regulation of CDK9, its cellular
functions, and common core structures used to target CDK9, along with
their selectivity profile and efficacy in vitro and in vivo.
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Affiliation(s)
- Yogesh A Sonawane
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, Nebraska 68198-6805, United States
| | - Margaret A Taylor
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, Nebraska 68198-6805, United States
| | - John Victor Napoleon
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, Nebraska 68198-6805, United States
| | - Sandeep Rana
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, Nebraska 68198-6805, United States
| | - Jacob I Contreras
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, Nebraska 68198-6805, United States
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, Nebraska 68198-6805, United States
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14
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Sansó M, Levin RS, Lipp JJ, Wang VYF, Greifenberg AK, Quezada EM, Ali A, Ghosh A, Larochelle S, Rana TM, Geyer M, Tong L, Shokat KM, Fisher RP. P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Genes Dev 2016; 30:117-31. [PMID: 26728557 PMCID: PMC4701974 DOI: 10.1101/gad.269589.115] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sansó et al. identified ∼100 putative substrates of human positive transcription elongation factor b (P-TEFb), which were enriched for proteins implicated in transcription and RNA catabolism. Among the RNA processing factors phosphorylated by Cdk9 was the 5′-to-3′ “torpedo” exoribonuclease Xrn2, required in transcription termination by Pol II. The transcription cycle of RNA polymerase II (Pol II) is regulated at discrete transition points by cyclin-dependent kinases (CDKs). Positive transcription elongation factor b (P-TEFb), a complex of Cdk9 and cyclin T1, promotes release of paused Pol II into elongation, but the precise mechanisms and targets of Cdk9 action remain largely unknown. Here, by a chemical genetic strategy, we identified ∼100 putative substrates of human P-TEFb, which were enriched for proteins implicated in transcription and RNA catabolism. Among the RNA processing factors phosphorylated by Cdk9 was the 5′-to-3′ “torpedo” exoribonuclease Xrn2, required in transcription termination by Pol II, which we validated as a bona fide P-TEFb substrate in vivo and in vitro. Phosphorylation by Cdk9 or phosphomimetic substitution of its target residue, Thr439, enhanced enzymatic activity of Xrn2 on synthetic substrates in vitro. Conversely, inhibition or depletion of Cdk9 or mutation of Xrn2-Thr439 to a nonphosphorylatable Ala residue caused phenotypes consistent with inefficient termination in human cells: impaired Xrn2 chromatin localization and increased readthrough transcription of endogenous genes. Therefore, in addition to its role in elongation, P-TEFb regulates termination by promoting chromatin recruitment and activation of a cotranscriptional RNA processing enzyme, Xrn2.
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Affiliation(s)
- Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rebecca S Levin
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jesse J Lipp
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Vivien Ya-Fan Wang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Ann Katrin Greifenberg
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany
| | - Elizabeth M Quezada
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Animesh Ghosh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Stéphane Larochelle
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Tariq M Rana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA
| | - Matthias Geyer
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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15
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Recent advances in the identification of Tat-mediated transactivation inhibitors: progressing toward a functional cure of HIV. Future Med Chem 2016; 8:421-42. [PMID: 26933891 DOI: 10.4155/fmc.16.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The current anti-HIV combination therapy does not eradicate the virus that persists mainly in quiescent infected CD4(+) T cells as a latent integrated provirus that resumes after therapy interruption. The Tat-mediated transactivation (TMT) is a critical step in the HIV replication cycle that could give the opportunity to reduce the size of latent reservoirs. More than two decades of research led to the identification of various TMT inhibitors. While none of them met the criteria to reach the market, the search for a suitable TMT inhibitor is still actively pursued. Really promising compounds, including one in a Phase III clinical trial, have been recently identified, thus warranting an update.
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16
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Srikumar T, Padmanabhan J. Potential Use of Flavopiridol in Treatment of Chronic Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 929:209-228. [PMID: 27771926 DOI: 10.1007/978-3-319-41342-6_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This chapter describes the potential use of flavopiridol, a CDK inhibitor with anti-inflammatory and anti-proliferative activities, in the treatment of various chronic diseases. Flavopiridol arrests cell cycle progression in the G1 or G2 phase by inhibiting the kinase activities of CDK1, CDK2, CDK4/6, and CDK7. Additionally, it binds tightly to CDK9, a component of the P-TEFb complex (CDK9/cyclin T), and interferes with RNA polymerase II activation and associated transcription. This in turn inhibits expression of several pro-survival and anti-apoptotic genes, and enhances cytotoxicity in transformed cells or differentiation in growth-arrested cells. Recent studies indicate that flavopiridol elicits anti-inflammatory activity via CDK9 and NFκB-dependent signaling. Overall, these effects of flavopiridol potentiate its ability to overcome aberrant cell cycle activation and/or inflammatory stimuli, which are mediators of various chronic diseases.
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Affiliation(s)
- Thejal Srikumar
- Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, USA
| | - Jaya Padmanabhan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, USA. .,USF Health Byrd Alzheimer's Institute, University of South Florida, 4001 E. Fletcher Ave., Tampa, Florida, 33613, USA.
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17
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Gao J, Fang C, Xiao Z, Huang L, Chen CH, Wang LT, Lee KH. Discovery of novel 5-fluoro- N2, N4-diphenylpyrimidine-2,4-diamines as potent inhibitors against CDK2 and CDK9. MEDCHEMCOMM 2015; 6:444-454. [PMID: 25914804 DOI: 10.1039/c4md00412d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Based on a 3D-QSAR pharmacophore derived from a diverse set of known cyclin-dependent kinase 9 (CDK9) inhibitors and a composite pharmacophore extracted from the complex structure of flavopiridol (FVP)-CDK9, thirty novel 5-fluoro-N2,N4-diphenylpyrimidine-2,4-diamine derivatives were designed and synthesized. Initial tests against four tumor cell lines with the sulforhodamine B (SRB) assay identified a series of potent compounds with GI50 values at lower micromolar or submicromolar level. Most of the highly cytotoxic compounds exhibited potent inhibitory activities against both CDK2/cyclin E1 and CDK9/cyclin T1. Notably, inhibitions against the two enzymes were generally correlated well with the cytotoxicity of these compounds. Appreciable inhibition was also observed for selected compounds in the anti-HIV-1 assay. Docking studies on compounds 6d and 9g provided conducive clues to further structural optimization.
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Affiliation(s)
- Jiadi Gao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Cheng Fang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Li Huang
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Chin-Ho Chen
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Li-Ting Wang
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA ; Chinese Medicine Research and Development Center, China Medical University and Hospital, Taichung, Taiwan
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18
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Abstract
Antiretroviral therapy (ART) potently suppresses HIV-1 replication, but the virus persists in quiescent infected CD4(+)T cells as a latent integrated provirus, and patients must indefinitely remain on therapy. If ART is terminated, these integrated proviruses can reactivate, driving new rounds of infection. A functional cure for HIV requires eliminating low-level ongoing viral replication that persists in certain tissue sanctuaries and preventing viral reactivation. The HIV Tat protein plays an essential role in HIV transcription by recruiting the kinase activity of the P-TEFb complex to the viral mRNA's stem-bulge-loop structure, TAR, activating transcriptional elongation. Because the Tat-mediated transactivation cascade is critical for robust HIV replication, the Tat/TAR/P-TEFb complex is one of the most attractive targets for drug development. Importantly, compounds that interfere with transcription could impair viral reactivation, low-level ongoing replication, and replenishment of the latent reservoir, thereby reducing the size of the latent reservoir pool. Here, we discuss the potential importance of transcriptional inhibitors in the treatment of latent HIV-1 disease and review recent findings on targeting Tat, TAR, and P-TEFb individually or as part of a complex. Finally, we discuss the impact of extracellular Tat in HIV-associated neurocognitive disorders and cancers.
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19
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Yamamoto M, Onogi H, Kii I, Yoshida S, Iida K, Sakai H, Abe M, Tsubota T, Ito N, Hosoya T, Hagiwara M. CDK9 inhibitor FIT-039 prevents replication of multiple DNA viruses. J Clin Invest 2014; 124:3479-88. [PMID: 25003190 DOI: 10.1172/jci73805] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 05/23/2014] [Indexed: 01/09/2023] Open
Abstract
A wide range of antiviral drugs is currently available; however, drug-resistant viruses have begun to emerge and represent a potential public health risk. Here, we explored the use of compounds that inhibit or interfere with the action of essential host factors to prevent virus replication. In particular, we focused on the cyclin-dependent kinase 9 (CDK9) inhibitor, FIT-039, which suppressed replication of a broad spectrum of DNA viruses through inhibition of mRNA transcription. Specifically, FIT-039 inhibited replication of herpes simplex virus 1 (HSV-1), HSV-2, human adenovirus, and human cytomegalovirus in cultured cells, and topical application of FIT-039 ointment suppressed skin legion formation in a murine HSV-1 infection model. FIT-039 did not affect cell cycle progression or cellular proliferation in host cells. Compared with the general CDK inhibitor flavopiridol, transcriptome analyses of FIT-039-treated cells revealed that FIT-039 specifically inhibited CDK9. Given at concentrations above the inhibitory concentration, FIT-039 did not have a cytotoxic effect on mammalian cells. Importantly, administration of FIT-039 ameliorated the severity of skin lesion formation in mice infected with an acyclovir-resistant HSV-1, without noticeable adverse effects. Together, these data indicate that FIT-039 has potential as an antiviral agent for clinical therapeutics.
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MESH Headings
- Acyclovir/pharmacology
- Adenoviruses, Human/drug effects
- Adenoviruses, Human/physiology
- Animals
- Antiviral Agents/chemistry
- Antiviral Agents/pharmacology
- Antiviral Agents/toxicity
- Cyclin-Dependent Kinase 9/antagonists & inhibitors
- Cytomegalovirus/drug effects
- Cytomegalovirus/physiology
- DNA Viruses/drug effects
- DNA Viruses/genetics
- DNA Viruses/physiology
- Disease Models, Animal
- Drug Resistance, Viral
- Flavonoids/pharmacology
- HEK293 Cells
- HeLa Cells
- Herpes Simplex/drug therapy
- Herpes Simplex/pathology
- Herpes Simplex/virology
- Herpesvirus 1, Human/drug effects
- Herpesvirus 1, Human/physiology
- Herpesvirus 2, Human/drug effects
- Herpesvirus 2, Human/physiology
- Host-Pathogen Interactions/drug effects
- Host-Pathogen Interactions/genetics
- Humans
- Mice
- Mice, Inbred ICR
- Piperidines/pharmacology
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/toxicity
- Pyridines/chemistry
- Pyridines/pharmacology
- Pyridines/toxicity
- Rats
- Rats, Wistar
- Transcription, Genetic/drug effects
- Transcriptome/drug effects
- Virus Replication/drug effects
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20
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Heredia A, Natesan S, Le NM, Medina-Moreno S, Zapata JC, Reitz M, Bryant J, Redfield RR. Indirubin 3'-monoxime, from a Chinese traditional herbal formula, suppresses viremia in humanized mice infected with multidrug-resistant HIV. AIDS Res Hum Retroviruses 2014; 30:403-6. [PMID: 24401082 DOI: 10.1089/aid.2013.0249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alonso Heredia
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Senthilkumar Natesan
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nhut M. Le
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Sandra Medina-Moreno
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Juan C. Zapata
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Marvin Reitz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Joseph Bryant
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Robert R. Redfield
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland
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21
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Dürr R, Keppler O, Christ F, Crespan E, Garbelli A, Maga G, Dietrich U. Targeting Cellular Cofactors in HIV Therapy. TOPICS IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1007/7355_2014_45] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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22
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Sancineto L, Iraci N, Massari S, Attanasio V, Corazza G, Barreca ML, Sabatini S, Manfroni G, Avanzi NR, Cecchetti V, Pannecouque C, Marcello A, Tabarrini O. Computer-Aided Design, Synthesis and Validation of 2-Phenylquinazolinone Fragments as CDK9 Inhibitors with Anti-HIV-1 Tat-Mediated Transcription Activity. ChemMedChem 2013; 8:1941-53. [DOI: 10.1002/cmdc.201300287] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 12/20/2022]
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23
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Strategies to Block HIV Transcription: Focus on Small Molecule Tat Inhibitors. BIOLOGY 2012; 1:668-97. [PMID: 24832514 PMCID: PMC4009808 DOI: 10.3390/biology1030668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023]
Abstract
After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replication. Basal transcription from the integrated HIV promoter is very low in the absence of the HIV transactivator of transcription (Tat) protein and is solely dependent on cellular transcription factors. The 5' terminal region (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loop structure called the Transactivation Responsive (TAR) element. Once Tat is made, it binds to TAR and drastically activates transcription from the HIV LTR promoter. Mutations in either the Tat protein or TAR sequence usually affect HIV replication, indicating a strong requirement for their conservation. The necessity of the Tat-mediated transactivation cascade for robust HIV replication renders Tat one of the most desirable targets for transcriptional therapy against HIV replication. Screening based on inhibition of the Tat-TAR interaction has identified a number of potential compounds, but none of them are currently used as therapeutics, partly because these agents are not easily delivered for an efficient therapy, emphasizing the need for small molecule compounds. Here we will give an overview of the different strategies used to inhibit HIV transcription and review the current repertoire of small molecular weight compounds that target HIV transcription.
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24
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Merrick KA, Fisher RP. Why minimal is not optimal: driving the mammalian cell cycle--and drug discovery--with a physiologic CDK control network. Cell Cycle 2012; 11:2600-5. [PMID: 22732498 DOI: 10.4161/cc.20758] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Progression through the eukaryotic cell division cycle is governed by the activity of cyclin-dependent kinases (CDKs). For a CDK to become active it must (1) bind a positive regulatory subunit (cyclin) and (2) be phosphorylated on its activation (T) loop. In metazoans, multiple CDK catalytic subunits, each with a distinct set of preferred cyclin partners, regulate the cell cycle, but it has been difficult to assign functions to individual CDKs in vivo. Biochemical analyses and experiments with dominant-negative alleles suggested that specific CDK/cyclin complexes regulate different events, but genetic loss of interphase CDKs (Cdk2, -4 and -6), alone or in combination, did not block proliferation of cells in culture. These knockout and knockdown studies suggested redundancy or plasticity built into the CDK network but did not address whether there was true redundancy in normal cells with a full complement of CDKs. Here, we discuss recent work that took a chemical-genetic approach to reveal that the activity of a genetically non-essential CDK, Cdk2, is required for cell proliferation when normal cyclin pairing is maintained. These results have implications for the systems-level organization of the cell cycle, for regulation of the restriction point and G 1/S transition and for efforts to target Cdk2 therapeutically in human cancers.
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Affiliation(s)
- Karl A Merrick
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY, USA
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25
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Ali A, Wang J, Nathans RS, Cao H, Sharova N, Stevenson M, Rana TM. Synthesis and structure-activity relationship studies of HIV-1 virion infectivity factor (Vif) inhibitors that block viral replication. ChemMedChem 2012; 7:1217-29. [PMID: 22555953 DOI: 10.1002/cmdc.201200079] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Indexed: 11/09/2022]
Abstract
The human immunodeficiency virus 1 (HIV-1) virion infectivity factor (Vif) protein, essential for in vivo viral replication, protects the virus from innate antiviral cellular factor apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (APOBEC3G; A3G) and is an attractive target for the development of novel antiviral therapeutics. We have evaluated the structure-activity relationships of N-(2-methoxyphenyl)-2-((4-nitrophenyl)thio)benzamide (RN-18), a small molecule recently identified as an inhibitor of Vif function that blocks viral replication only in nonpermissive cells expressing A3G, by inhibiting Vif-A3G interactions. Microwave-assisted cross-coupling reactions were developed to prepare a series of RN18 analogues with diverse linkages and substitutions on the phenyl rings. A dual cell-based assay system was used to assess antiviral activity against wild-type HIV-1 in both nonpermissive (H9) and permissive (MT4) cells that also allowed evaluation of specificity. In general, variations of phenyl substitutions were detrimental to antiviral potency and specificity, but isosteric replacements of amide and ether linkages were relatively well tolerated. These structure-activity relationship data define structural requirements for Vif-specific activity, identify new compounds with improved antiviral potency and specificity, and provide leads for further exploration to develop new antiviral therapeutics.
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Affiliation(s)
- Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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26
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Toossi Z, Wu M, Hirsch CS, Mayanja-Kizza H, Baseke J, Aung H, Canaday DH, Fujinaga K. Activation of P-TEFb at sites of dual HIV/TB infection, and inhibition of MTB-induced HIV transcriptional activation by the inhibitor of CDK9, Indirubin-3'-monoxime. AIDS Res Hum Retroviruses 2012; 28:182-7. [PMID: 21453127 DOI: 10.1089/aid.2010.0211] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
At sites of Mycobacterium tuberculosis (MTB) infection, HIV-1 replication is increased during tuberculosis (TB). Here we investigated the role of positive transcription elongation factor (P-TEFb), comprised of CycT1 and CDK9, as the cellular cofactor of HIV-1 Tat protein in transcriptional activation of HIV-1 in mononuclear cells from HIV-1-infected patients with pleural TB. Expression of CycT1 in response to MTB was assessed in mononuclear cells from pleural fluid (PFMC) and blood (PBMC) from HIV/TB patients with pleural TB, and in blood monocytes (MN) from singly infected HIV-1-seropositive subjects. We then examined whether the CDK9 inhibitor, Indirubin 3'-monoxime (IM), was effective in inhibition of MTB-induced HIV-1 mRNA expression. We found higher expression of CycT1 mRNA in PFMCs as compared to PBMCs from HIV/TB-coinfected subjects. MTB induced the expression of CycT1 and HIV-1 gag/pol mRNA in both PFMCs from HIV/TB subjects and MN from HIV-1-infected subjects. CycT1 protein was also induced by MTB stimulation in PFMCs from HIV/TB patients, and both MN and in vitro-derived macrophages. Inhibition of CDK9 by IM in both PFMCs from HIV/TB and MN from HIV-1-infected subjects in response to MTB led to inhibition of HIV-1 mRNA expression. These data imply that IM may be useful as an adjunctive therapy in control of HIV-1 replication in HIV/TB dually infected subjects.
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Affiliation(s)
- Zahra Toossi
- Case Western Reserve University, Cleveland, Ohio
- Veterans Affairs Medical Center, Cleveland, Ohio
| | - Mianda Wu
- Case Western Reserve University, Cleveland, Ohio
| | | | - Harriet Mayanja-Kizza
- Makerere University and National Tuberculosis and Leprosy Program, Kampala, Uganda
- Joint Clinical Research Center, Kampala, Uganda
| | - Joy Baseke
- Joint Clinical Research Center, Kampala, Uganda
| | - Htin Aung
- Case Western Reserve University, Cleveland, Ohio
| | | | - Koh Fujinaga
- Case Western Reserve University, Cleveland, Ohio
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27
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Victoriano AFB, Okamoto T. Transcriptional control of HIV replication by multiple modulators and their implication for a novel antiviral therapy. AIDS Res Hum Retroviruses 2012; 28:125-38. [PMID: 22077140 DOI: 10.1089/aid.2011.0263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Transcriptional regulation is critical for the human immunodeficiency virus 1 (HIV-1) life cycle and is the only step at which the virus amplifies the content of its genetic information. Numerous known and still unknown transcriptional factors, both host and viral, regulate HIV-1 gene expression and latency. This article is a comprehensive review of transcription factors involved in HIV-1 gene expression and presents the significant implications of nuclear factor kappa B (NF-κB) and the HIV-1 transactivator of transcription (Tat) protein. We include recent findings on chromatin remodeling toward HIV transcription and its therapeutic implication is also discussed. The current status of small-molecular-weight compounds that affect HIV transcription is also described.
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Affiliation(s)
- Ann Florence B. Victoriano
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School for Medical Sciences, Nagoya, Japan
- Japanese Foundation for AIDS Prevention, Tokyo, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School for Medical Sciences, Nagoya, Japan
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28
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O'Brien SK, Knight KL, Rana TM. Phosphorylation of histone H1 by P-TEFb is a necessary step in skeletal muscle differentiation. J Cell Physiol 2011; 227:383-9. [PMID: 21503884 DOI: 10.1002/jcp.22797] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Positive transcription elongation factor b (P-TEFb), the complex of Cyclin T1 and CDK9, activates the transcription of many viral and eukaryotic genes at the point of mRNA elongation. The activity of P-TEFb has been implicated in the differentiation of a number of cell types, including skeletal muscle. In order to promote transcription, P-TEFb hyperphosphorylates RNA Pol II, thereby increasing its processivity. Our previous work identified histone H1 as a P-TEFb substrate during HIV-1 and immediate-early transcription. Here, we examine the role of P-TEFb phosphorylation of histone H1 during differentiation, using the myoblast cell line C2C12 as a model for skeletal muscle differentiation. We found that H1 phosphorylation is elevated in differentiating C2C12, and this phosphorylation is sensitive to P-TEFb inhibition. H1 phosphorylation was also necessary for the induction of three muscle marker genes that require P-TEFb for expression. Additionally, ChIP experiments demonstrate that H1 dissociates from muscle differentiation marker genes in C2C12 cells under active P-TEFb conditions. We determine that both P-TEFb activity and H1 phosphorylation are necessary for the full differentiation of C2C12 myoblasts into myotubes.
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Affiliation(s)
- Siobhan K O'Brien
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Worcester, Massachusetts, USA
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29
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Hoque M, Shamanna RA, Guan D, Pe'ery T, Mathews MB. HIV-1 replication and latency are regulated by translational control of cyclin T1. J Mol Biol 2011; 410:917-32. [PMID: 21763496 DOI: 10.1016/j.jmb.2011.03.060] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/24/2011] [Accepted: 03/25/2011] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) exploits cellular proteins during its replicative cycle and latent infection. The positive transcription elongation factor b (P-TEFb) is a key cellular transcription factor critical for these viral processes and is a drug target. During viral replication, P-TEFb is recruited via interactions of its cyclin T1 subunit with the HIV Tat (transactivator of transcription) protein and TAR (transactivation response) element. Through RNA silencing and over-expression experiments, we discovered that nuclear factor 90 (NF90), a cellular RNA binding protein, regulates P-TEFb expression. NF90 depletion reduced cyclin T1 protein levels by inhibiting translation initiation. Regulation was mediated by the 3' untranslated region of cyclin T1 mRNA independently of microRNAs. Cyclin T1 induction is involved in the escape of HIV-1 from latency. We show that the activation of viral replication by phorbol ester in latently infected monocytic cells requires the posttranscriptional induction of NF90 and cyclin T1, implicating NF90 in protein kinase C signaling pathways. This investigation reveals a novel mechanism of cyclin T1 regulation and establishes NF90 as a regulator of HIV-1 replication during both productive infection and induction from latency.
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Affiliation(s)
- Mainul Hoque
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, PO Box 1709, Newark, NJ 07101-1709, USA
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30
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Abstract
The current anti-HIV treatments fail to completely eradicate the virus in HIV-infected individuals, mainly as a result of a small pool of latently infected cells. This issue, together with the emergence of multidrug-resistant viruses, clearly highlights the need to find additional strategies. An overview of the Tat-mediated transcription inhibitors 6-desfluoroquinolones (6-DFQs), identified by our group, is given in this review along with a critical appraisal of their advantages and drawbacks. Attempts are also made to place them within the context of new potential anti-HIV therapeutics. Due to their innovative mechanism of action, the 6-DFQs could be interesting candidates for use in association with the currently used cocktail of drugs. Their potential as antivirals deserves further investigation.
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31
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Narayanan A, Kehn-Hall K, Bailey C, Kashanchi F. Analysis of the roles of HIV-derived microRNAs. Expert Opin Biol Ther 2011; 11:17-29. [PMID: 21133815 DOI: 10.1517/14712598.2011.540564] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE OF THE FIELD HIV-1 is a retrovirus that has infected millions in recent decades. The level of life cycle complexity and host control exerted by this small virus with only nine proteins is astonishing. An interesting direction that has emerged in recent years is the role of small non-coding RNAs in viral gene expression. AREAS COVERED IN THIS REVIEW We focus on HIV-1 produced microRNAs (miRNAs), namely, TAR, Nef and miR-H1, and their roles in HIV-1 biogenesis. The article provides insights into TAR miRNA-mediated downregulation of viral and host gene expression by recruitment of chromatin remodeling components (HDAC1). WHAT THE READER WILL GAIN We address the influence of TAR miRNA on host cell cycle progression and apoptosis, and the role of Nef miRNA in the regulation of viral and host gene expression. The review also highlights an intriguing connection between miR-H1 and HIV-1-associated neurological pathogenesis, and the influence of the miRNA machinery in the establishment of latency. In the Expert Opinion section, we analyze the issue of host-based therapeutics against HIV-1 and how transcription inhibitors are influenced by viral miRNA production. TAKE HOME MESSAGE HIV-derived miRNAs are of significance not only to understand host-virus interactions, but also for the design of effective therapeutics.
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Affiliation(s)
- Aarthi Narayanan
- George Mason University, National Center for Biodefense and Infectious Diseases, Manassas, VA 20110, USA
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32
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Fang C, Xiao Z, Guo Z. Generation and validation of the first predictive pharmacophore model for cyclin-dependent kinase 9 inhibitors. J Mol Graph Model 2011; 29:800-8. [DOI: 10.1016/j.jmgm.2011.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 12/21/2010] [Accepted: 01/10/2011] [Indexed: 01/16/2023]
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33
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Dolle RE, Bourdonnec BL, Worm K, Morales GA, Thomas CJ, Zhang W. Comprehensive survey of chemical libraries for drug discovery and chemical biology: 2009. JOURNAL OF COMBINATORIAL CHEMISTRY 2010; 12:765-806. [PMID: 20923157 PMCID: PMC4140011 DOI: 10.1021/cc100128w] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Roland E Dolle
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, USA.
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Li LL, Hu ST, Wang SH, Lee HH, Wang YT, Ping YH. Positive transcription elongation factor b (P-TEFb) contributes to dengue virus-stimulated induction of interleukin-8 (IL-8). Cell Microbiol 2010; 12:1589-603. [DOI: 10.1111/j.1462-5822.2010.01493.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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