1
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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2
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Rana N, Grover P, Singh H. Recent Developments and Future Perspectives of Purine Derivatives as a Promising Scaffold in Drug Discovery. Curr Top Med Chem 2024; 24:541-579. [PMID: 38288806 DOI: 10.2174/0115680266290152240110074034] [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: 10/30/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Numerous purine-containing compounds have undergone extensive investigation for their medical efficacy across various diseases. The swift progress in purine-based medicinal chemistry has brought to light the therapeutic capabilities of purine-derived compounds in addressing challenging medical conditions. Defined by a heterocyclic ring comprising a pyrimidine ring linked with an imidazole ring, purine exhibits a diverse array of therapeutic attributes. This review systematically addresses the multifaceted potential of purine derivatives in combating various diseases, including their roles as anticancer agents, antiviral compounds (anti-herpes, anti-HIV, and anti-influenzae), autoimmune and anti-inflammatory agents, antihyperuricemic and anti-gout solutions, antimicrobial agents, antitubercular compounds, anti-leishmanial agents, and anticonvulsants. Emphasis is placed on the remarkable progress made in developing purine-based compounds, elucidating their significant target sites. The article provides a comprehensive exploration of developments in both natural and synthetic purines, offering insights into their role in managing a diverse range of illnesses. Additionally, the discussion delves into the structure-activity relationships and biological activities of the most promising purine molecules. The intriguing capabilities revealed by these purine-based scaffolds unequivocally position them at the forefront of drug candidate development. As such, this review holds potential significance for researchers actively involved in synthesizing purine-based drug candidates, providing a roadmap for the continued advancement of this promising field.
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Affiliation(s)
- Neha Rana
- School of Pharmacy (SOP), Noida International University, Yamuna Expressway, Gautam Budh Nagar, 203201, India
| | - Parul Grover
- KIET School of Pharmacy, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206, India
| | - Hridayanand Singh
- Dr. K. N. Modi Institute of Pharmaceutical Education and Research, Modinagar, 201204, Uttar Pradesh, India
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3
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Shin YH, Kim DE, Yu KL, Park CM, Kim HG, Kim KC, Bae S, Yoon CH. A Novel Time-Resolved Fluorescence Resonance Energy Transfer Assay for the Discovery of Small-Molecule Inhibitors of HIV-1 Tat-Regulated Transcription. Int J Mol Sci 2023; 24:ijms24119139. [PMID: 37298089 DOI: 10.3390/ijms24119139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) transactivator (Tat)-mediated transcription is essential for HIV-1 replication. It is determined by the interaction between Tat and transactivation response (TAR) RNA, a highly conserved process representing a prominent therapeutic target against HIV-1 replication. However, owing to the limitations of current high-throughput screening (HTS) assays, no drug that disrupts the Tat-TAR RNA interaction has been uncovered yet. We designed a homogenous (mix-and-read) time-resolved fluorescence resonance energy transfer (TR-FRET) assay using europium cryptate as a fluorescence donor. It was optimized by evaluating different probing systems for Tat-derived peptides or TAR RNA. The specificity of the optimal assay was validated by mutants of the Tat-derived peptides and TAR RNA fragment, individually and by competitive inhibition with known TAR RNA-binding peptides. The assay generated a constant Tat-TAR RNA interaction signal, discriminating the compounds that disrupted the interaction. Combined with a functional assay, the TR-FRET assay identified two small molecules (460-G06 and 463-H08) capable of inhibiting Tat activity and HIV-1 infection from a large-scale compound library. The simplicity, ease of operation, and rapidity of our assay render it suitable for HTS to identify Tat-TAR RNA interaction inhibitors. The identified compounds may also act as potent molecular scaffolds for developing a new HIV-1 drug class.
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Affiliation(s)
- Young Hyun Shin
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Dong-Eun Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Kyung Lee Yu
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Chul Min Park
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Hong Gi Kim
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Kyung-Chang Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Songmee Bae
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
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4
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Chocron ES, Munkácsy E, Kim HS, Karpowicz P, Jiang N, Van Skike CE, DeRosa N, Banh AQ, Palavicini JP, Wityk P, Kalinowski L, Galvan V, Osmulski PA, Jankowska E, Gaczynska M, Pickering AM. Genetic and pharmacologic proteasome augmentation ameliorates Alzheimer's-like pathology in mouse and fly APP overexpression models. SCIENCE ADVANCES 2022; 8:eabk2252. [PMID: 35675410 PMCID: PMC9177073 DOI: 10.1126/sciadv.abk2252] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/21/2022] [Indexed: 05/27/2023]
Abstract
The proteasome has key roles in neuronal proteostasis, including the removal of misfolded and oxidized proteins, presynaptic protein turnover, and synaptic efficacy and plasticity. Proteasome dysfunction is a prominent feature of Alzheimer's disease (AD). We show that prevention of proteasome dysfunction by genetic manipulation delays mortality, cell death, and cognitive deficits in fly and cell culture AD models. We developed a transgenic mouse with neuronal-specific proteasome overexpression that, when crossed with an AD mouse model, showed reduced mortality and cognitive deficits. To establish translational relevance, we developed a set of TAT-based proteasome-activating peptidomimetics that stably penetrated the blood-brain barrier and enhanced 20S/26S proteasome activity. These agonists protected against cell death, cognitive decline, and mortality in cell culture, fly, and mouse AD models. The protective effects of proteasome overexpression appear to be driven, at least in part, by the proteasome's increased turnover of the amyloid precursor protein along with the prevention of overall proteostatic dysfunction.
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Affiliation(s)
- E. Sandra Chocron
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
| | - Erin Munkácsy
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
| | - Harper S. Kim
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX, USA
- Center for Neurodegeneration and Experimental Therapeutics (CNET), Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
- Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Przemyslaw Karpowicz
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Nisi Jiang
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Candice E. Van Skike
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Cellular and Integrative Physiology, UT Health San Antonio, San Antonio, TX, USA
| | - Nicholas DeRosa
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Cellular and Integrative Physiology, UT Health San Antonio, San Antonio, TX, USA
| | - Andy Q. Banh
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Cellular and Integrative Physiology, UT Health San Antonio, San Antonio, TX, USA
| | - Juan P. Palavicini
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
| | - Paweł Wityk
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gdańsk, Poland
- Department of Medical Laboratory Diagnostics–Fahrenheit Biobank BBMRI.pl, Medical University of Gdańsk, Gdańsk, Poland
- BioTechMed Centre/Department of Mechanics of Materials and Structures, Gdańsk University of Technology, Gdańsk, Poland
| | - Leszek Kalinowski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gdańsk, Poland
- Department of Medical Laboratory Diagnostics–Fahrenheit Biobank BBMRI.pl, Medical University of Gdańsk, Gdańsk, Poland
- BioTechMed Centre/Department of Mechanics of Materials and Structures, Gdańsk University of Technology, Gdańsk, Poland
| | - Veronica Galvan
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- College of Medicine, Oklahoma Health Science Center, Oklahoma City, OK, USA
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- South Texas VA Health Care System, San Antonio, TX, USA
- Oklahoma City VA Health Care System, Oklahoma City, OK, USA
| | - Pawel A. Osmulski
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Elzbieta Jankowska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Maria Gaczynska
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Andrew M. Pickering
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX, USA
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX, USA
- Center for Neurodegeneration and Experimental Therapeutics (CNET), Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
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5
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Bis-3-Chloropiperidines Targeting TAR RNA as A Novel Strategy to Impair the HIV-1 Nucleocapsid Protein. Molecules 2021; 26:molecules26071874. [PMID: 33810333 PMCID: PMC8038054 DOI: 10.3390/molecules26071874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Specific RNA sequences regulate functions essential to life. The Trans-Activation Response element (TAR) is an RNA stem-bulge-loop structure involved in several steps of HIV-1 replication. In this work, we show how RNA targeting can inhibit HIV-1 nucleocapsid (NC), a highly conserved protein known to catalyze nucleic acid melting and strand transfers during reverse transcription. Our RNA targeting strategy consists of the employment of bis-3-chloropiperidines (B-CePs) to impair RNA melting through bifunctional alkylation. Specific interactions between B-CePs and TAR RNA were analytically investigated by gel electrophoresis and mass spectrometry, allowing the elucidation of B-CePs' recognition of TAR, and highlighting an RNA-directed mechanism of protein inhibition. We propose that B-CePs can freeze TAR tridimensional conformation, impairing NC-induced dynamics and finally inhibiting its functions in vitro.
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6
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Khan N, Chen X, Geiger JD. Role of Divalent Cations in HIV-1 Replication and Pathogenicity. Viruses 2020; 12:E471. [PMID: 32326317 PMCID: PMC7232465 DOI: 10.3390/v12040471] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/09/2020] [Accepted: 04/18/2020] [Indexed: 12/22/2022] Open
Abstract
Divalent cations are essential for life and are fundamentally important coordinators of cellular metabolism, cell growth, host-pathogen interactions, and cell death. Specifically, for human immunodeficiency virus type-1 (HIV-1), divalent cations are required for interactions between viral and host factors that govern HIV-1 replication and pathogenicity. Homeostatic regulation of divalent cations' levels and actions appear to change as HIV-1 infection progresses and as changes occur between HIV-1 and the host. In people living with HIV-1, dietary supplementation with divalent cations may increase HIV-1 replication, whereas cation chelation may suppress HIV-1 replication and decrease disease progression. Here, we review literature on the roles of zinc (Zn2+), iron (Fe2+), manganese (Mn2+), magnesium (Mg2+), selenium (Se2+), and copper (Cu2+) in HIV-1 replication and pathogenicity, as well as evidence that divalent cation levels and actions may be targeted therapeutically in people living with HIV-1.
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Affiliation(s)
| | | | - Jonathan D. Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA; (N.K.); (X.C.)
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7
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Chen K, Phan T, Lin A, Sardo L, Mele AR, Nonnemacher MR, Klase Z. Morphine exposure exacerbates HIV-1 Tat driven changes to neuroinflammatory factors in cultured astrocytes. PLoS One 2020; 15:e0230563. [PMID: 32210470 PMCID: PMC7094849 DOI: 10.1371/journal.pone.0230563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Despite antiretroviral therapy human immunodeficiency virus type-1 (HIV-1) infection results in neuroinflammation of the central nervous system that can cause HIV-associated neurocognitive disorders (HAND). The molecular mechanisms involved in the development of HAND are unclear, however, they are likely due to both direct and indirect consequences of HIV-1 infection and inflammation of the central nervous system. Additionally, opioid abuse in infected individuals has the potential to exacerbate HIV-comorbidities, such as HAND. Although restricted for productive HIV replication, astrocytes (comprising 40-70% of all brain cells) likely play a significant role in neuropathogenesis in infected individuals due to the production and response of viral proteins. The HIV-1 protein Tat is critical for viral transcription, causes neuroinflammation, and can be secreted from infected cells to affect uninfected bystander cells. The Wnt/β-catenin signaling cascade plays an integral role in restricting HIV-1 infection in part by negatively regulating HIV-1 Tat function. Conversely, Tat can overcome this negative regulation and inhibit β-catenin signaling by sequestering the critical transcription factor TCF-4 from binding to β-catenin. Here, we aimed to explore how opiate exposure affects Tat-mediated suppression of β-catenin in astrocytes and the downstream modulation of neuroinflammatory genes. We observed that morphine can potentiate Tat suppression of β-catenin activity in human astrocytes. In contrast, Tat mutants deficient in secretion, and lacking neurotoxic effects, do not affect β-catenin activity in the presence or absence of morphine. Finally, morphine treatment of astrocytes was sufficient to reduce the expression of genes involved in neuroinflammation. Examining the molecular mechanisms of how HIV-1 infection and opiate exposure exacerbate neuroinflammation may help us inform or predict disease progression prior to HAND development.
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Affiliation(s)
- Kenneth Chen
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Thienlong Phan
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Angel Lin
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Luca Sardo
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
- Current institution – Department of Infectious Diseases and Vaccines, MRL, Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | - Anthony R. Mele
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Zachary Klase
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
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8
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Osmulski PA, Karpowicz P, Jankowska E, Bohmann J, Pickering AM, Gaczyńska M. New Peptide-Based Pharmacophore Activates 20S Proteasome. Molecules 2020; 25:E1439. [PMID: 32235805 PMCID: PMC7145288 DOI: 10.3390/molecules25061439] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 02/01/2023] Open
Abstract
The proteasome is a pivotal element of controlled proteolysis, responsible for the catabolic arm of proteostasis. By inducing apoptosis, small molecule inhibitors of proteasome peptidolytic activities are successfully utilized in treatment of blood cancers. However, the clinical potential of proteasome activation remains relatively unexplored. In this work, we introduce short TAT peptides derived from HIV-1 Tat protein and modified with synthetic turn-stabilizing residues as proteasome agonists. Molecular docking and biochemical studies point to the α1/α2 pocket of the core proteasome α ring as the binding site of TAT peptides. We postulate that the TATs' pharmacophore consists of an N-terminal basic pocket-docking "activation anchor" connected via a β turn inducer to a C-terminal "specificity clamp" that binds on the proteasome α surface. By allosteric effects-including destabilization of the proteasomal gate-the compounds substantially augment activity of the core proteasome in vitro. Significantly, this activation is preserved in the lysates of cultured cells treated with the compounds. We propose that the proteasome-stimulating TAT pharmacophore provides an attractive lead for future clinical use.
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Affiliation(s)
- Paweł A. Osmulski
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
| | - Przemysław Karpowicz
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Elżbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Jonathan Bohmann
- Southwest Research Institute, San Antonio, Texas, TX 78238, USA;
| | - Andrew M. Pickering
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
- The Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, UT Health San Antonio, TX 78229, USA
| | - Maria Gaczyńska
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
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9
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Peralta AN, Dai Y, Sherpa C, Le Grice SFJ, Santos WL. Molecular recognition of HIV-1 RNAs with branched peptides. Methods Enzymol 2019; 623:373-400. [PMID: 31239054 DOI: 10.1016/bs.mie.2019.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Targeting RNA offers the potential in many diseases of a therapeutic treatment. Due to its large surface area and ability to adopt different conformations, targeting RNA has proven challenging. Medium-sized branched peptides are of the size to competitively bind RNA while remaining cell permeable, stable in vivo, and non-toxic. Additionally, the ease in generating a large library followed by high-throughput screening provides a way to suggest a scaffold with high diversity that is capable of targeting the structure and sequence of RNA. The ability to select various types of amino acid modifications in the branched peptide allows for variable structures and interactions of the branched peptide but can result in too large a task if not approached properly. In this chapter, we discuss a strategy to selectively recognize RNAs of interest through high throughput screening of branched peptides, validation of hits and biophysical characterization, leading by example with our experience in targeting HIV-1 RNAs with branched peptides.
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Affiliation(s)
- Ashley N Peralta
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States
| | - Yumin Dai
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Webster L Santos
- Department of Chemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.
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10
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Arjmand F, Afsan Z, Sharma S, Parveen S, Yousuf I, Sartaj S, Siddique HR, Tabassum S. Recent advances in metallodrug-like molecules targeting non-coding RNAs in cancer chemotherapy. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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11
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Dai Y, Peralta AN, Wynn JE, Sherpa C, Li H, Verma A, Le Grice SFJ, Santos WL. Molecular recognition of a branched peptide with HIV-1 Rev Response Element (RRE) RNA. Bioorg Med Chem 2019; 27:1759-1765. [PMID: 30879859 PMCID: PMC6476629 DOI: 10.1016/j.bmc.2019.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 01/27/2023]
Abstract
Interaction of HIV-1 rev response element (RRE) RNA with its cognate protein, Rev, is critical for HIV-1 replication. Understanding the mode of interaction between RRE RNA and ligands at the binding site can facilitate RNA molecular recognition as well as provide a strategy for developing anti-HIV therapeutics. Our approach utilizes branched peptides as a scaffold for multivalent binding to RRE IIB (high affinity rev binding site) with incorporation of unnatural amino acids to increase affinity via non-canonical interactions with the RNA. Previous high throughput screening of a 46,656-member library revealed several hits that bound RRE IIB RNA in the sub-micromolar range. In particular, the lead compound, 4B3, displayed a Kd value of 410 nM and demonstrated selectivity towards RRE. A ribonuclease protection assay revealed that 4B3 binds to the stem-loop structure of RRE IIB RNA, which was confirmed by SHAPE analysis with 234 nt long NL4-3 RRE RNA. Our studies further indicated interaction of 4B3 with both primary and secondary Rev binding sites.
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Affiliation(s)
- Yumin Dai
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Ashley N Peralta
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Hao Li
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Astha Verma
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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12
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Li XD, Liu L, Cheng L. Identification of thienopyridine carboxamides as selective binders of HIV-1 trans Activation Response (TAR) and Rev Response Element (RRE) RNAs. Org Biomol Chem 2019; 16:9191-9196. [PMID: 30465585 DOI: 10.1039/c8ob02753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Small organic molecules that can selectively bind to RNA with specificity are relatively rare. Here we report the synthesis, biochemical and structural studies of thienopyridine carboxamide derivatives with the capacity of selectively recognizing and binding with HIV-1 TAR and RRE RNAs that are essential elements for viral replication.
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Affiliation(s)
- Xue-Dong Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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13
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Spector C, Mele AR, Wigdahl B, Nonnemacher MR. Genetic variation and function of the HIV-1 Tat protein. Med Microbiol Immunol 2019; 208:131-169. [PMID: 30834965 DOI: 10.1007/s00430-019-00583-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/11/2019] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) encodes a transactivator of transcription (Tat) protein, which has several functions that promote viral replication, pathogenesis, and disease. Amino acid variation within Tat has been observed to alter the functional properties of Tat and, depending on the HIV-1 subtype, may produce Tat phenotypes differing from viruses' representative of each subtype and commonly used in in vivo and in vitro experimentation. The molecular properties of Tat allow for distinctive functional activities to be determined such as the subcellular localization and other intracellular and extracellular functional aspects of this important viral protein influenced by variation within the Tat sequence. Once Tat has been transported into the nucleus and becomes engaged in transactivation of the long terminal repeat (LTR), various Tat variants may differ in their capacity to activate viral transcription. Post-translational modification patterns based on these amino acid variations may alter interactions between Tat and host factors, which may positively or negatively affect this process. In addition, the ability of HIV-1 to utilize or not utilize the transactivation response (TAR) element within the LTR, based on genetic variation and cellular phenotype, adds a layer of complexity to the processes that govern Tat-mediated proviral DNA-driven transcription and replication. In contrast, cytoplasmic or extracellular localization of Tat may cause pathogenic effects in the form of altered cell activation, apoptosis, or neurotoxicity. Tat variants have been shown to differentially induce these processes, which may have implications for long-term HIV-1-infected patient care in the antiretroviral therapy era. Future studies concerning genetic variation of Tat with respect to function should focus on variants derived from HIV-1-infected individuals to efficiently guide Tat-targeted therapies and elucidate mechanisms of pathogenesis within the global patient population.
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Affiliation(s)
- Cassandra Spector
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Anthony R Mele
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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14
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Lata S, Mishra R, Banerjea AC. Proteasomal Degradation Machinery: Favorite Target of HIV-1 Proteins. Front Microbiol 2018; 9:2738. [PMID: 30524389 PMCID: PMC6262318 DOI: 10.3389/fmicb.2018.02738] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/26/2018] [Indexed: 12/17/2022] Open
Abstract
Proteasomal degradation pathways play a central role in regulating a variety of protein functions by controlling not only their turnover but also the physiological behavior of the cell. This makes it an attractive target for the pathogens, especially viruses which rely on the host cellular machinery for their propagation and pathogenesis. Viruses have evolutionarily developed various strategies to manipulate the host proteasomal machinery thereby creating a cellular environment favorable for their own survival and replication. Human immunodeficiency virus-1 (HIV-1) is one of the most dreadful viruses which has rapidly spread throughout the world and caused high mortality due to its high evolution rate. Here, we review the various mechanisms adopted by HIV-1 to exploit the cellular proteasomal machinery in order to escape the host restriction factors and components of host immune system for supporting its own multiplication, and successfully created an infection.
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Affiliation(s)
- Sneh Lata
- Virology Lab II, National Institute of Immunology, New Delhi, India
| | - Ritu Mishra
- Virology Lab II, National Institute of Immunology, New Delhi, India
| | - Akhil C Banerjea
- Virology Lab II, National Institute of Immunology, New Delhi, India
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15
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Carmona-Martínez V, Ruiz-Alcaraz AJ, Vera M, Guirado A, Martínez-Esparza M, García-Peñarrubia P. Therapeutic potential of pteridine derivatives: A comprehensive review. Med Res Rev 2018; 39:461-516. [PMID: 30341778 DOI: 10.1002/med.21529] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 07/07/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022]
Abstract
Pteridines are aromatic compounds formed by fused pyrazine and pyrimidine rings. Many living organisms synthesize pteridines, where they act as pigments, enzymatic cofactors, or immune system activation molecules. This variety of biological functions has motivated the synthesis of a huge number of pteridine derivatives with the aim of studying their therapeutic potential. This review gathers the state-of-the-art of pteridine derivatives, describing their biological activities and molecular targets. The antitumor activity of pteridine-based compounds is one of the most studied and advanced therapeutic potentials, for which several molecular targets have been identified. Nevertheless, pteridines are also considered as very promising therapeutics for the treatment of chronic inflammation-related diseases. On the other hand, many pteridine derivatives have been tested for antimicrobial activities but, although some of them resulted to be active in preliminary assays, a deeper research is needed in this area. Moreover, pteridines may be of use in the treatment of many other diseases, such as diabetes, osteoporosis, ischemia, or neurodegeneration, among others. Thus, the diversity of the biological activities shown by these compounds highlights the promising therapeutic use of pteridine derivatives. Indeed, methotrexate, pralatrexate, and triamterene are Food and Drug Administration approved pteridines, while many others are currently under study in clinical trials.
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Affiliation(s)
- Violeta Carmona-Martínez
- Departamento de Bioquímica, Biología Molecular (B) e Inmunología, Facultad de Medicina, IMIB and Regional Campus of International Excellence "Campus Mare Nostrum," Universidad de Murcia, Murcia, Spain
| | - Antonio J Ruiz-Alcaraz
- Departamento de Bioquímica, Biología Molecular (B) e Inmunología, Facultad de Medicina, IMIB and Regional Campus of International Excellence "Campus Mare Nostrum," Universidad de Murcia, Murcia, Spain
| | - María Vera
- Departamento de Química Orgánica, Universidad de Murcia, Campus de Espinardo, Murcia, Spain
| | - Antonio Guirado
- Departamento de Química Orgánica, Universidad de Murcia, Campus de Espinardo, Murcia, Spain
| | - María Martínez-Esparza
- Departamento de Bioquímica, Biología Molecular (B) e Inmunología, Facultad de Medicina, IMIB and Regional Campus of International Excellence "Campus Mare Nostrum," Universidad de Murcia, Murcia, Spain
| | - Pilar García-Peñarrubia
- Departamento de Bioquímica, Biología Molecular (B) e Inmunología, Facultad de Medicina, IMIB and Regional Campus of International Excellence "Campus Mare Nostrum," Universidad de Murcia, Murcia, Spain
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16
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Sosic A, Saccone I, Carraro C, Kenderdine T, Gamba E, Caliendo G, Corvino A, Di Vaio P, Fiorino F, Magli E, Perissutti E, Santagada V, Severino B, Spada V, Fabris D, Frecentese F, Gatto B. Non-Natural Linker Configuration in 2,6-Dipeptidyl-Anthraquinones Enhances the Inhibition of TAR RNA Binding/Annealing Activities by HIV-1 NC and Tat Proteins. Bioconjug Chem 2018; 29:2195-2207. [PMID: 29791798 DOI: 10.1021/acs.bioconjchem.8b00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The HIV-1 nucleocapsid (NC) protein represents an excellent molecular target for the development of anti-retrovirals by virtue of its well-characterized chaperone activities, which play pivotal roles in essential steps of the viral life cycle. Our ongoing search for candidates able to impair NC binding/annealing activities led to the identification of peptidyl-anthraquinones as a promising class of nucleic acid ligands. Seeking to elucidate the inhibition determinants and increase the potency of this class of compounds, we have now explored the effects of chirality in the linker connecting the planar nucleus to the basic side chains. We show here that the non-natural linker configuration imparted unexpected TAR RNA targeting properties to the 2,6-peptidyl-anthraquinones and significantly enhanced their potency. Even if the new compounds were able to interact directly with the NC protein, they manifested a consistently higher affinity for the TAR RNA substrate and their TAR-binding properties mirrored their ability to interfere with NC-TAR interactions. Based on these findings, we propose that the viral Tat protein, sharing the same RNA substrate but acting in distinct phases of the viral life cycle, constitutes an additional druggable target for this class of peptidyl-anthraquinones. The inhibition of Tat-TAR interaction for the test compounds correlated again with their TAR-binding properties, while simultaneously failing to demonstrate any direct Tat-binding capabilities. These considerations highlighted the importance of TAR RNA in the elucidation of their inhibition mechanism, rather than direct protein inhibition. We have therefore identified anti-TAR compounds with dual in vitro inhibitory activity on different viral proteins, demonstrating that it is possible to develop multitarget compounds capable of interfering with processes mediated by the interactions of this essential RNA domain of HIV-1 genome with NC and Tat proteins.
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Affiliation(s)
- Alice Sosic
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Irene Saccone
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Caterina Carraro
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Thomas Kenderdine
- The RNA Institute and Department of Chemistry , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Elia Gamba
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Giuseppe Caliendo
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Angela Corvino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Paola Di Vaio
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Ferdinando Fiorino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Elisa Magli
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Elisa Perissutti
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Vincenzo Santagada
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Beatrice Severino
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Valentina Spada
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Dan Fabris
- The RNA Institute and Department of Chemistry , State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Francesco Frecentese
- Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II" , Via D. Montesano 49 , 80131 Napoli , Italy
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco , Università di Padova , via Marzolo 5 , 35131 Padova , Italy
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17
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Yang Y, Wang S. RNA Characterization by Solid-State NMR Spectroscopy. Chemistry 2018; 24:8698-8707. [DOI: 10.1002/chem.201705583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
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18
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Gaskill PJ, Miller DR, Gamble-George J, Yano H, Khoshbouei H. HIV, Tat and dopamine transmission. Neurobiol Dis 2017; 105:51-73. [PMID: 28457951 PMCID: PMC5541386 DOI: 10.1016/j.nbd.2017.04.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/04/2017] [Accepted: 04/16/2017] [Indexed: 01/02/2023] Open
Abstract
Human Immunodeficiency Virus (HIV) is a progressive infection that targets the immune system, affecting more than 37 million people around the world. While combinatorial antiretroviral therapy (cART) has lowered mortality rates and improved quality of life in infected individuals, the prevalence of HIV associated neurocognitive disorders is increasing and HIV associated cognitive decline remains prevalent. Recent research has suggested that HIV accessory proteins may be involved in this decline, and several studies have indicated that the HIV protein transactivator of transcription (Tat) can disrupt normal neuronal and glial function. Specifically, data indicate that Tat may directly impact dopaminergic neurotransmission, by modulating the function of the dopamine transporter and specifically damaging dopamine-rich regions of the CNS. HIV infection of the CNS has long been associated with dopaminergic dysfunction, but the mechanisms remain undefined. The specific effect(s) of Tat on dopaminergic neurotransmission may be, at least partially, a mechanism by which HIV infection directly or indirectly induces dopaminergic dysfunction. Therefore, precisely defining the specific effects of Tat on the dopaminergic system will help to elucidate the mechanisms by which HIV infection of the CNS induces neuropsychiatric, neurocognitive and neurological disorders that involve dopaminergic neurotransmission. Further, this will provide a discussion of the experiments needed to further these investigations, and may help to identify or develop new therapeutic approaches for the prevention or treatment of these disorders in HIV-infected individuals.
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Affiliation(s)
- Peter J Gaskill
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States.
| | - Douglas R Miller
- Department of Neuroscience, University of Florida, Gainesville, FL 32611, United States
| | - Joyonna Gamble-George
- Department of Neuroscience, University of Florida, Gainesville, FL 32611, United States
| | - Hideaki Yano
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, United States
| | - Habibeh Khoshbouei
- Department of Neuroscience, University of Florida, Gainesville, FL 32611, United States.
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19
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Ronsard L, Rai T, Rai D, Ramachandran VG, Banerjea AC. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity. Front Microbiol 2017; 8:1467. [PMID: 28848502 PMCID: PMC5550727 DOI: 10.3389/fmicb.2017.01467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Tat transactivates viral genes through strong interaction with TAR RNA. The stem-loop bulged region of TAR consisting of three nucleotides at the position 23–25 and the loop region consisting of six nucleotides at the position 30–35 are essential for viral transactivation. The arginine motif of Tat (five arginine residues on subtype TatC) is critically important for TAR interaction. Any mutations in this motif could lead to reduce transactivation ability and pathogenesis. Here, we identified structurally important residues (arginine and lysine residues) of Tat in this motif could bind to TAR via hydrogen bond interactions which is critical for transactivation. Natural mutant Ser46Phe in the core motif could likely led to conformational change resulting in more hydrogen bond interactions than the wild type Tat making it highly potent transactivator. Importantly, we report the possible probabilities of number of hydrogen bond interactions in the wild type Tat and the mutants with TAR complexes. This study revealed the differential transactivation of subtype B and C Tat could likely be due to the varying number of hydrogen bonds with TAR. Our data support that the N-terminal and the C-terminal domains of Tat is involved in the TAR interactions through hydrogen bonds which is important for transactivation. This study highlights the evolving pattern of structurally important determinants of Tat in the arginine motif for viral transactivation.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesNew Delhi, India
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesNew Delhi, India
| | - Vishnampettai G Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India
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20
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Ronsard L, Ganguli N, Singh VK, Mohankumar K, Rai T, Sridharan S, Pajaniradje S, Kumar B, Rai D, Chaudhuri S, Coumar MS, Ramachandran VG, Banerjea AC. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction. Front Microbiol 2017; 8:706. [PMID: 28484443 PMCID: PMC5399533 DOI: 10.3389/fmicb.2017.00706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities. Molecular dynamics simulation data verified that the variants with this mutation had a higher binding affinity for TAR than both the wild-type Tat and other variants that lacked Ser46Phe and Ser61Arg. Other mutations in Tat conferred varying affinities for TAR interaction leading to differential transactivation abilities. This is the first report from North India with a clinical validation of CD4 counts to demonstrate the influence of Tat genetic variations affecting the stability of Tat and its interaction with TAR. This study highlights the co-evolution pattern of Tat and predominant nucleotides for Tat activity, facilitating the identification of genetic determinants for the attenuation of viral gene expression.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyDelhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalDelhi, India
| | - Nilanjana Ganguli
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
| | - Vivek K Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | - Kumaravel Mohankumar
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Veterinary Physiology and Pharmacology, Texas A&M University, College StationTX, USA
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesDelhi, India
| | - Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Symptom Research, The University of Texas MD Anderson Cancer Center, HoustonTX, USA
| | - Sankar Pajaniradje
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India
| | - Binod Kumar
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, ChicagoIL, USA
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesDelhi, India
| | - Suhnrita Chaudhuri
- Department of Neurological Surgery, Northwestern University, ChicagoIL, USA
| | - Mohane S Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | | | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
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21
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Kamori D, Ueno T. HIV-1 Tat and Viral Latency: What We Can Learn from Naturally Occurring Sequence Variations. Front Microbiol 2017; 8:80. [PMID: 28194140 PMCID: PMC5276809 DOI: 10.3389/fmicb.2017.00080] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/11/2017] [Indexed: 01/25/2023] Open
Abstract
Despite the effective use of antiretroviral therapy, the remainder of a latently HIV-1-infected reservoir mainly in the resting memory CD4+ T lymphocyte subset has provided a great setback toward viral eradication. While host transcriptional silencing machinery is thought to play a dominant role in HIV-1 latency, HIV-1 protein such as Tat, may affect both the establishment and the reversal of latency. Indeed, mutational studies have demonstrated that insufficient Tat transactivation activity can result in impaired transcription of viral genes and the establishment of latency in cell culture experiments. Because Tat protein is one of highly variable proteins within HIV-1 proteome, it is conceivable that naturally occurring Tat mutations may differentially modulate Tat functions, thereby influencing the establishment and/or the reversal of viral latency in vivo. In this mini review, we summarize the recent findings of Tat naturally occurring polymorphisms associating with host immune responses and we highlight the implication of Tat sequence variations in relation to HIV latency.
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Affiliation(s)
- Doreen Kamori
- Center for AIDS Research, Kumamoto University Kumamoto, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto UniversityKumamoto, Japan; International Research Center for Medical Sciences, Kumamoto UniversityKumamoto, Japan
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22
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Liu MC, Chen CY, Chiang CH, Wang WM, Cheng RP. Effect of lysine methylation and acetylation on the RNA recognition and cellular uptake of Tat-derived peptides. Bioorg Med Chem 2016; 24:5047-5051. [DOI: 10.1016/j.bmc.2016.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 11/25/2022]
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23
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Kumar S, Ranjan N, Kellish P, Gong C, Watkins D, Arya DP. Multivalency in the recognition and antagonism of a HIV TAR RNA-TAT assembly using an aminoglycoside benzimidazole scaffold. Org Biomol Chem 2016; 14:2052-6. [PMID: 26765486 DOI: 10.1039/c5ob02016f] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recognition of RNA by high-affinity binding small molecules is crucial for expanding existing approaches in RNA recognition, and for the development of novel RNA binding drugs. A novel neomycin dimer benzimidazole conjugate 5 (DPA 83) was synthesized by conjugating a neomycin-dimer with a benzimidazole alkyne using click chemistry to target multiple binding sites on HIV TAR RNA. Ligand 5 significantly enhances the thermal stability of HIV TAR RNA and interacts stoichiometrically with HIV TAR RNA with a low nanomolar affinity. 5 displayed enhanced binding compared to its individual building blocks including the neomycin dimer azide and benzimidazole alkyne. In essence, a high affinity multivalent ligand was designed and synthesized to target HIV TAR RNA.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA. and Nubad LLC, 900 B West Faris Road, Greenville, SC 29630, USA
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | - Changjun Gong
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | | | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
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24
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Aralaguppe SPG, Sharma S, Menon M, Prasad VR, Saravanan S, Murugavel KG, Solomon S, Ranga U. The Evolving Profile of the Signature Amino Acid Residues in HIV-1 Subtype C Tat. AIDS Res Hum Retroviruses 2016; 32:503-14. [PMID: 26678403 DOI: 10.1089/aid.2015.0208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Using several HIV-1 tat exon 1 amino acid sequences available from public databases and additional sequences derived from a southern Indian clinical cohort, we compared the profile of the signature amino acid residues (SAR) between two different time periods, 1986-2004 and 2005-2014. The analysis identified eight positions as signature residues in subtype C Tat and demonstrated a changing pattern at four of these positions between the two periods. At three locations (histidine 29, serine 57, and proline 60), there appears to be a nonuniform negative selection against the SAR. The negative selection appears to be severe, especially against histidine 29 (p < .0001) and moderate against proline 60 (p < .0001). The negative selection against serine 57 is statistically insignificant and appears to have begun recently. At position 63, the frequency of signature residue glutamic acid increased over the past decade, although the difference was not significant. Importantly, at the three locations where the negative selection is in progress, the substitute amino acids are the generic residues present in most of the other HIV-1 subtypes. Our data demonstrate that viral evolution can subject specific amino acid residues to subtle and progressive selection pressures without affecting the prevalence of other amino acid residues.
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Affiliation(s)
- Shambhu Prasad G. Aralaguppe
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Shilpee Sharma
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Malini Menon
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Vinayaka R. Prasad
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, New York
| | | | | | - Suniti Solomon
- YRG Centre for AIDS Research and Education, Chennai, India
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV-AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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25
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Zhao X, Qian L, Zhou D, Qi D, Liu C, Kong X. Stability of HIV-1 subtype B and C Tat is associated with variation in the carboxyl-terminal region. Virol Sin 2016; 31:199-206. [PMID: 27007880 DOI: 10.1007/s12250-016-3681-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/01/2016] [Indexed: 12/14/2022] Open
Abstract
The multifunctional trans-activator Tat is an essential regulatory protein for HIV-1 replication and is characterized by high sequence diversity. Numerous experimental studies have examined Tat in HIV-1 subtype B, but research on subtype C Tat is lacking, despite the high prevalence of infections caused by subtype C worldwide. We hypothesized that amino acid differences contribute to functional differences among Tat proteins. In the present study, we found that subtype B NL4-3 Tat and subtype C isolate HIV1084i Tat exhibited differences in stability by overexpressing the fusion protein Tat-Flag. In addition, 1084i Tat can activate LTR and NF-κB more efficiently than NL4-3 Tat. In analyses of the activities of the truncated forms of Tat, we found that the carboxyl-terminal region of Tat regulates its stability and transactivity. According to our results, we speculated that the differences in stability between B-Tat and C-Tat result in differences in transactivation ability.
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Affiliation(s)
- Xuechao Zhao
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Lingyu Qian
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Deyu Zhou
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Di Qi
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Chang Liu
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xiaohong Kong
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China.
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López-Huertas MR, Li J, Zafar A, Rodríguez-Mora S, García-Domínguez C, Mateos E, Alcamí J, Rao S, Coiras M. PKCθ and HIV-1 Transcriptional Regulator Tat Co-exist at the LTR Promoter in CD4(+) T Cells. Front Immunol 2016; 7:69. [PMID: 26973648 PMCID: PMC4770193 DOI: 10.3389/fimmu.2016.00069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
PKCθ is essential for the activation of CD4+ T cells. Upon TCR/CD28 stimulation, PKCθ is phosphorylated and migrates to the immunological synapse, inducing the activation of cellular transcription factors such as NF-κB and kinases as ERK that are critical for HIV-1 replication. We previously demonstrated that PKCθ is also necessary for HIV-1 replication but the precise mechanism is unknown. Efficient HIV-1 transcription and elongation are absolutely dependent on the synergy between NF-κB and the viral regulator Tat. Tat exerts its function by binding a RNA stem-loop structure proximal to the viral mRNA cap site termed TAR. Besides, due to its effect on cellular metabolic pathways, Tat causes profound changes in infected CD4+ T cells such as the activation of NF-κB and ERK. We hypothesized that the aberrant upregulation of Tat-mediated activation of NF-κB and ERK occurred through PKCθ signaling. In fact, Jurkat TetOff cells with stable and doxycycline-repressible expression of Tat (Jurkat-Tat) expressed high levels of mRNA for PKCθ. In these cells, PKCθ located at the plasma membrane was phosphorylated at T538 residue in undivided cells, in the absence of stimulation. Treatment with doxycycline inhibited PKCθ phosphorylation in Jurkat-Tat, suggesting that Tat expression was directly related to the activation of PKCθ. Both NF-κB and Ras/Raf/MEK/ERK signaling pathway were significantly activated in Jurkat-Tat cells, and this correlated with high transactivation of HIV-1 LTR promoter. RNA interference for PKCθ inhibited NF-κB and ERK activity, as well as LTR-mediated transactivation even in the presence of Tat. In addition to Tat-mediated activation of PKCθ in the cytosol, we demonstrated by sequential ChIP that Tat and PKCθ coexisted in the same complex bound at the HIV-1 LTR promoter, specifically at the region containing TAR loop. In conclusion, PKCθ-Tat interaction seemed to be essential for HIV-1 replication in CD4+ T cells and could be used as a therapeutic target.
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Affiliation(s)
- María Rosa López-Huertas
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III , Madrid , Spain
| | - Jasmine Li
- Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia
| | - Anjum Zafar
- Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra , Canberra, ACT , Australia
| | - Sara Rodríguez-Mora
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III , Madrid , Spain
| | - Carlota García-Domínguez
- Functional Research Unit in Chronic Diseases, National Center of Microbiology, Instituto de Salud Carlos III , Madrid , Spain
| | - Elena Mateos
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III , Madrid , Spain
| | - José Alcamí
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III , Madrid , Spain
| | - Sudha Rao
- Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra , Canberra, ACT , Australia
| | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III , Madrid , Spain
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27
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Sosic A, Sinigaglia L, Cappellini M, Carli I, Parolin C, Zagotto G, Sabatino G, Rovero P, Fabris D, Gatto B. Mechanisms of HIV-1 Nucleocapsid Protein Inhibition by Lysyl-Peptidyl-Anthraquinone Conjugates. Bioconjug Chem 2015; 27:247-56. [PMID: 26666402 DOI: 10.1021/acs.bioconjchem.5b00627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Nucleocapsid protein NCp7 (NC) is a nucleic acid chaperone responsible for essential steps of the HIV-1 life cycle and an attractive candidate for drug development. NC destabilizes nucleic acid structures and promotes the formation of annealed substrates for HIV-1 reverse transcription elongation. Short helical nucleic acid segments bordered by bulges and loops, such as the Trans-Activation Response element (TAR) of HIV-1 and its complementary sequence (cTAR), are nucleation elements for helix destabilization by NC and also preferred recognition sites for threading intercalators. Inspired by these observations, we have recently demonstrated that 2,6-disubstituted peptidyl-anthraquinone-conjugates inhibit the chaperone activities of recombinant NC in vitro, and that inhibition correlates with the stabilization of TAR and cTAR stem-loop structures. We describe here enhanced NC inhibitory activity by novel conjugates that exhibit longer peptidyl chains ending with a conserved N-terminal lysine. Their efficient inhibition of TAR/cTAR annealing mediated by NC originates from the combination of at least three different mechanisms, namely, their stabilizing effects on nucleic acids dynamics by threading intercalation, their ability to target TAR RNA substrate leading to a direct competition with the protein for the same binding sites on TAR, and, finally, their effective binding to the NC protein. Our results suggest that these molecules may represent the stepping-stone for the future development of NC-inhibitors capable of targeting the protein itself and its recognition site in RNA.
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Affiliation(s)
| | | | | | | | | | | | | | - Paolo Rovero
- Dipartimento NeuroFarBa, Sezione di Scienze Farmaceutiche e Nutraceutica, Università di Firenze , 50121 Firenze, Italy
| | - Dan Fabris
- Department of Chemistry, State University of New York , Albany, New York 12222, United States
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Fatin MF, Ruslinda AR, Md Arshad MK, Tee KK, Ayub RM, Hashim U, Kamarulzaman A, Gopinath SCB. HIV-1 Tat biosensor: Current development and trends for early detection strategies. Biosens Bioelectron 2015; 78:358-366. [PMID: 26655174 DOI: 10.1016/j.bios.2015.11.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/20/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus (HIV) has infected almost 35 million people worldwide. Various tests have been developed to detect the presence of HIV during the early stages of the disease in order to reduce the risk of transmission to other humans. The HIV-1 Tat protein is one of the proteins present in HIV that are released abundantly approximately 2-4 weeks after infection. In this review, we have outlined various strategies for detecting the Tat protein, which helps transcribe the virus and enhances replication. Detection strategies presented include immunoassays, biosensors and gene expression, which utilize antibodies or aptamers as common probes to sense the presence of Tat. Alternatively, measuring the levels of gene transcription is a direct method of analysing the HIV gene to confirm the presence of Tat. By detection of the Tat protein, virus transmission can be detected in high-risk individuals in the early stages of the disease to reduce the risk of an HIV pandemic.
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Affiliation(s)
- M F Fatin
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - A R Ruslinda
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia.
| | - M K Md Arshad
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - K K Tee
- Center of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - R M Ayub
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - A Kamarulzaman
- Center of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
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Lata S, Ali A, Sood V, Raja R, Banerjea AC. HIV-1 Rev downregulates Tat expression and viral replication via modulation of NAD(P)H:quinine oxidoreductase 1 (NQO1). Nat Commun 2015; 6:7244. [DOI: 10.1038/ncomms8244] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 04/22/2015] [Indexed: 12/30/2022] Open
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30
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Wynn JE, Santos WL. HIV-1 drug discovery: targeting folded RNA structures with branched peptides. Org Biomol Chem 2015; 13:5848-58. [PMID: 25958855 PMCID: PMC4511164 DOI: 10.1039/c5ob00589b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA.
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31
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Interactions of HIV-1 proteins as targets for developing anti-HIV-1 peptides. Future Med Chem 2015; 7:1055-77. [DOI: 10.4155/fmc.15.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein–protein interactions (PPI) are essential in every step of the HIV replication cycle. Mapping the interactions between viral and host proteins is a fundamental target for the design and development of new therapeutics. In this review, we focus on rational development of anti-HIV-1 peptides based on mapping viral–host and viral–viral protein interactions all across the HIV-1 replication cycle. We also discuss the mechanism of action, specificity and stability of these peptides, which are designed to inhibit PPI. Some of these peptides are excellent tools to study the mechanisms of PPI in HIV-1 replication cycle and for the development of anti-HIV-1 drug leads that modulate PPI.
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32
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Roy CN, Khandaker I, Furuse Y, Oshitani H. Molecular characterization of full-length Tat in HIV-1 subtypes B and C. Bioinformation 2015; 11:151-60. [PMID: 25914449 PMCID: PMC4403036 DOI: 10.6026/97320630011151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/02/2015] [Indexed: 12/13/2022] Open
Abstract
HIV-1Tat (trans-acting activator of transcription) plays essential roles in the replication through viral mRNA and genome transcription from the HIV-1 LTR promoter. However, Tat undergoes continuous amino acid substitutions. As a consequence, the virus escapes from host immunity indicating that genetic diversity of Tat protein in major HIV-1 subtypes is required to be continuously monitored. We analyzed available full-length HIV-1 sequences of subtypes B (n=493) and C (n=280) strains circulating worldwide. We observed 81% and 84% nucleotide sequence identities of HIV-1 Tat for subtypes B and C, respectively. Based on phylogenetic and mutation analyses, global diversity of subtype B was apparently higher compared to that of subtype C. Positively selected sites, such as positions Ser68 and Ser70 in both subtypes, were located in the Tat-transactivation responsive RNA (TAR) interaction domain. We also found positively selected sites in exon 2, such as positions Ser75, Pro77, Asp80, Pro81 and Ser87 for both subtypes. Our study provides useful information on the full-length HIV-1 Tat sequences in globally circulating strains.
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Affiliation(s)
- Chandra Nath Roy
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
| | - Irona Khandaker
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba-ku, Sendai city, Miyagi, Japan-9808575
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Luzzi A, Morettini F, Gazaneo S, Mundo L, Onnis A, Mannucci S, Rogena EA, Bellan C, Leoncini L, De Falco G. HIV-1 Tat induces DNMT over-expression through microRNA dysregulation in HIV-related non Hodgkin lymphomas. Infect Agent Cancer 2014; 9:41. [PMID: 25705251 PMCID: PMC4334912 DOI: 10.1186/1750-9378-9-41] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/14/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A close association between HIV infection and the development of cancer exists. Although the advent of highly active antiretroviral therapy has changed the epidemiology of AIDS-associated malignancies, a better understanding on how HIV can induce malignant transformation will help the development of novel therapeutic agents. METHODS HIV has been reported to induce the expression of DNMT1 in vitro, but still no information is available about the mechanisms regulating DNMT expression in HIV-related B-cell lymphomas. In this paper, we investigated the expression of DNMT family members (DNMT1, DNMT3a/b) in primary cases of aggressive B-cell lymphomas of HIV-positive subjects. RESULTS Our results confirmed the activation of DNMT1 by HIV in vivo, and reported for the first time a marked up-regulation of DNMT3a and DNMT3b in HIV-positive aggressive B-cell lymphomas. DNMT up-regulation in HIV-positive tumors correlated with down-regulation of specific microRNAs, as the miR29 family, the miR148-152 cluster, known to regulate their expression. Literature reports the activation of DNMTs by the human polyomavirus BKV large T-antigen and adenovirus E1a, through the pRb/E2F pathway. We have previously demonstrated that the HIV Tat protein is able to bind to the pocket proteins and to inactivate their oncosuppressive properties, resulting in uncontrolled cell proliferation. Therefore, we focused on the role of Tat, due to its capability to be released from infected cells and to dysregulate uninfected ones, using an in vitro model in which Tat was ectopically expressed in B-cells. CONCLUSIONS Our findings demonstrated that the ectopic expression of Tat was per se sufficient to determine DNMT up-regulation, based on microRNA down-regulation, and that this results in aberrant hypermethylation of target genes and microRNAs. These results point at a direct role for Tat in participating in uninfected B-cell lymphomagenesis, through dysregulation of the epigenetical control of gene expression.
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Affiliation(s)
- Anna Luzzi
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Federica Morettini
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sara Gazaneo
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Lucia Mundo
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Anna Onnis
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Susanna Mannucci
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Emily A Rogena
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
- />Department of Pathology, University of Nairobi, Nairobi, Kenya
| | - Cristiana Bellan
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Lorenzo Leoncini
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulia De Falco
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
- />School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Zhang L, Qin J, Li Y, Wang J, He Q, Zhou J, Liu M, Li D. Modulation of the stability and activities of HIV-1 Tat by its ubiquitination and carboxyl-terminal region. Cell Biosci 2014; 4:61. [PMID: 25328666 PMCID: PMC4201738 DOI: 10.1186/2045-3701-4-61] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/27/2014] [Indexed: 11/28/2022] Open
Abstract
Background The transactivator of transcription (Tat) protein of human immunodeficiency virus type 1 (HIV-1) is known to undergo ubiquitination. However, the roles of ubiquitination in regulating Tat stability and activities are unclear. In addition, although the 72- and 86-residue forms are commonly used for in vitro studies, the 101-residue form is predominant in the clinical isolates of HIV-1. The influence of the carboxyl-terminal region of Tat on its functions remains unclear. Results In this study, we find that Tat undergoes lysine 48-linked ubiquitination and is targeted to proteasome-dependent degradation. Expression of various ubiquitin mutants modulates Tat activities, including the transactivation of transcription, induction of apoptosis, interaction with tubulin, and stabilization of microtubules. Moreover, the 72-, 86- and 101-residue forms of Tat also exhibit different stability and aforementioned activities. Conclusions Our findings demonstrate that the ubiquitination and carboxyl-terminal region of Tat are critical determinants of its stability and activities.
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Affiliation(s)
- Linlin Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Juan Qin
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Yuanyuan Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Jian Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Qianqian He
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Jun Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Min Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
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Kellish PC, Kumar S, Mack TS, Spano MN, Hennig M, Arya DP. Multivalent Amino Sugars to Recognize Different TAR RNA Conformations. MEDCHEMCOMM 2014; 5:1235-1246. [PMID: 27076899 PMCID: PMC4828046 DOI: 10.1039/c4md00165f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neomycin dimers synthesized using "click chemistry" with varying functionality and length in the linker region have been shown to be effective in targeting the HIV-1 TAR RNA region of the HIV virus. TAR (Transactivation Response) RNA region, a 59 base pair stem loop structure located at the 5'-end of all nascent viral transcripts interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Ethidium bromide displacement and FRET competition assays have revealed nanomolar binding affinity between neomycin dimers and wildtype TAR RNA while in case of neomycin, only a weak binding was detected. Here, NMR and FID-based comparisons reveal an extended binding interface for neomycin dimers involving the upper stem of the TAR RNA thereby offering an explanation for increased affinities. To further explore the potential of these modified aminosugars we have extended binding studies to include four TAR RNA mutants that display conformational differences with minimal sequence variation. The differences in binding between neomycin and neomycin dimers is characterized with TAR RNA mutants that include mutations to the bulge region, hairpin region, and both the bulge and hairpin regions. Our results demonstrate the effect of these mutations on neomycin binding and our results show that linker functionalities between dimeric units of neomycin can distinguish between the conformational differences of mutant TAR RNA structures.
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Affiliation(s)
- Patrick C. Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Todd S. Mack
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | | | - Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, 900B West Faris Rd., Greenville, SC 29605
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Effect of each guanidinium group on the RNA recognition and cellular uptake of Tat-derived peptides. Bioorg Med Chem 2014; 22:3016-20. [DOI: 10.1016/j.bmc.2014.03.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/19/2014] [Accepted: 03/21/2014] [Indexed: 11/18/2022]
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Ronsard L, Lata S, Singh J, Ramachandran VG, Das S, Banerjea AC. Molecular and genetic characterization of natural HIV-1 Tat Exon-1 variants from North India and their functional implications. PLoS One 2014; 9:e85452. [PMID: 24465566 PMCID: PMC3900424 DOI: 10.1371/journal.pone.0085452] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/27/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Designing an ideal vaccine against HIV-1 has been difficult due to enormous genetic variability as a result of high replication rate and lack of proofreading activity of reverse transcriptase leading to emergence of genetic variants and recombinants. Tat transactivates HIV-1 LTR, resulting in a remarkable increase in viral gene expression, and plays a vital role in pathogenesis. The aim of this study was to characterize the genetic variations of Tat exon-1 from HIV-1 infected patients from North India. METHODS Genomic DNA was isolated from PBMCs and Tat exon-1 was PCR amplified with specific primers followed by cloning, sequencing and sequence analyses using bioinformatic tools for predicting HIV-1 subtypes, recombination events, conservation of domains and phosphorylation sites, and LTR transactivation by luciferase assay. RESULTS Phylogenetic analysis of Tat exon-1 variants (n = 120) revealed sequence similarity with South African Tat C sequences and distinct geographical relationships were observed for B/C recombinants. Bootscan analysis of our variants showed 90% homology to Tat C and 10% to B/C recombinants with a precise breakpoint. Natural substitutions were observed with high allelic frequencies which may be beneficial for virus. High amino acid conservation was observed in Tat among Anti Retroviral Therapy (ART) recipients. Barring few changes, most of the functional domains, predicted motifs and phosphorylation sites were well conserved in most of Tat variants. dN/dS analysis revealed purifying selection, implying the importance of functional conservation of Tat exon-1. Our Indian Tat C variants and B/C recombinants showed differential LTR transactivation. CONCLUSIONS The possible role of Tat exon-1 variants in shaping the current HIV-1 epidemic in North India was highlighted. Natural substitutions across conserved functional domains were observed and provided evidence for the emergence of B/C recombinants within the ORF of Tat exon-1. These events are likely to have implications for viral pathogenesis and vaccine formulations.
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Affiliation(s)
- Larance Ronsard
- Virology Laboratory, National Institute of Immunology, New Delhi, India
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Sneh Lata
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Jyotsna Singh
- Virology Laboratory, National Institute of Immunology, New Delhi, India
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | | | - Shukla Das
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Akhil C. Banerjea
- Virology Laboratory, National Institute of Immunology, New Delhi, India
- * E-mail: ,
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Stefanovic L, Longo L, Zhang Y, Stefanovic B. Characterization of binding of LARP6 to the 5' stem-loop of collagen mRNAs: implications for synthesis of type I collagen. RNA Biol 2014; 11:1386-401. [PMID: 25692237 PMCID: PMC4615758 DOI: 10.1080/15476286.2014.996467] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 01/11/2023] Open
Abstract
Type I collagen is composed of 2 polypeptides, α1(I) and α2(I), which fold into triple helix. Collagen α1(I) and α2(I) mRNAs have a conserved stem-loop structure in their 5' UTRs, the 5'SL. LARP6 binds the 5'SL to regulate type I collagen expression. We show that 5 nucleotides within the single stranded regions of 5'SL contribute to the high affinity of LARP6 binding. Mutation of individual nucleotides abolishes the binding in gel mobility shift assay. LARP6 binding to 5'SL of collagen α2(I) mRNA is more stable than the binding to 5'SL of α1(I) mRNA, although the equilibrium binding constants are similar. The more stable binding to α2(I) mRNA may favor synthesis of the heterotrimeric type I collagen. LARP6 needs 2 domains to contact 5'SL, the La domain and the RRM. T133 in the La domain is critical for folding of the protein, while loop 3 in the RRM is critical for binding 5'SL. Loop 3 is also involved in the interaction of LARP6 and protein translocation channel SEC61. This interaction is essential for type I collagen synthesis, because LARP6 mutant which binds 5'SL but which does not interact with SEC61, suppresses collagen synthesis in a dominant negative manner. We postulate that LARP6 directly targets collagen mRNAs to the SEC61 translocons to facilitate coordinated translation of the 2 collagen mRNAs. The unique sequences of LARP6 identified in this work may have evolved to enable its role in type I collagen biosynthesis.
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Affiliation(s)
- Lela Stefanovic
- Department of Biomedical Sciences; College of Medicine; Florida State University; Tallahassee, FL USA
- Current affiliation: Molecular Biophysics; Florida State University; Tallahassee, FL USA
| | - Liam Longo
- Current affiliation: Molecular Biophysics; Florida State University; Tallahassee, FL USA
| | - Yujie Zhang
- Department of Biomedical Sciences; College of Medicine; Florida State University; Tallahassee, FL USA
- Current affiliation: Molecular Biophysics; Florida State University; Tallahassee, FL USA
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Lata S, Ronsard L, Sood V, Dar SA, Ramachandran VG, Das S, Banerjea AC. Effect on HIV-1 gene expression, Tat-Vpr interaction and cell apoptosis by natural variants of HIV-1 Tat exon 1 and Vpr from Northern India. PLoS One 2013; 8:e82128. [PMID: 24367500 PMCID: PMC3868622 DOI: 10.1371/journal.pone.0082128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Since HIV-1 Tat and Vpr genes are involved in promoter transactivation, apoptosis, etc, we carried out studies to find out nature and extent of natural variation in the two genes from seropositive patients from Northern India and determined their functional implications. METHODS HIV-1 tat exon 1 and vpr were amplified from the genomic DNA isolated from the blood of HIV-1 infected individuals using specific primers by Polymerase Chain reaction (PCR) and subjected to extensive genetic analysis (CLUSTAL W, Simplot etc). Their expression was monitored by generating myc fusion clones. Tat exon 1 and Vpr variants were co-transfected with the reporter gene construct (LTR-luc) and their transactivation potential was monitored by measuring luciferase activity. Apoptosis and cell cycle analysis was done by Propidium Iodide (PI) staining followed by FACS. RESULTS Exon 1 of tat was amplified from 21 samples and vpr was amplified from 16 samples. One of the Tat exon 1 variants showed phylogenetic relatedness to subtype B & C and turned out to be a unique recombinant. Two of the Vpr variants were B/C/D recombinants. These natural variations were found to have no impact on the stability of Tat and Vpr. These variants differed in their ability to transactivate B LTR and C LTR promoters. B/C recombinant Tat showed better co-operative interaction with Vpr. B/C/D recombination in Vpr was found to have no effect on its co-operativity with Tat. Recombinant Tat (B/C) induced more apoptosis than wild type B and C Tat. The B/C/D recombination in Vpr did not affect its G2 arrest induction potential but reduced its apoptosis induction ability. CONCLUSIONS Extensive sequence and region-specific variations were observed in Tat and Vpr genes from HIV-1 infected individuals from Northern India. These variations have functional implications & therefore important for the pathogenicity of virus.
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Affiliation(s)
- Sneh Lata
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Larance Ronsard
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Vikas Sood
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Sajad A. Dar
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Vishnampettai G. Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- * E-mail: (VGR); (ACB)
| | - Shukla Das
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Akhil C. Banerjea
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
- * E-mail: (VGR); (ACB)
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40
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Planès R, Bahraoui E. HIV-1 Tat protein induces the production of IDO in human monocyte derived-dendritic cells through a direct mechanism: effect on T cells proliferation. PLoS One 2013; 8:e74551. [PMID: 24073214 PMCID: PMC3779232 DOI: 10.1371/journal.pone.0074551] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/02/2013] [Indexed: 12/21/2022] Open
Abstract
During HIV-1 infection, an increase of indoleamine 2,3 dioxygenase (IDO) expression, and dendritic cells (DC) dysfunction were often associated with AIDS disease progression. In this work, we investigated the effect of HIV-1 Tat protein on the expression of IDO, in MoDCs. We show that Tat induces IDO protein expression and activity in a dose dependent manner by acting at the cell membrane. Using Tat-mutants, we show that the N-Terminal domain, Tat 1–45, but not the central region, Tat 30–72, is sufficient to induce the expression of active IDO. Tat protein is also able to induce several cytokines in MoDCs, including IFN-γ, a strong inducer of IDO. In order to understand whether IDO is induced directly by Tat protein or indirectly following IFN-γ production, complementary experiments were performed and showed that: i) at the kinetic level, Tat induced IDO expression before the production of IFN-γ ii) treatment of MoDCs with Tat-conditioned medium was unable to stimulate IDO expression, iii) coculture of MoDCs in a transwell cell system did not allow IDO expression in MoDCs not previously treated by Tat, iv) direct contact between Tat-treated and untreated MoDCs was not sufficient to induce IDO expression in a Tat-independent manner, and v) treatment of MoDCs in the presence of IFN-γ pathway inhibitors, Jak I and Ly294002, inhibited IFN-γ-induced IDO but had no effect on Tat-induced IDO. At the functional level, our data showed that treatment of MoDCs with Tat led to the inhibition of their capacity to stimulate T cell proliferation. This impairement was totally abolished when the stimulation was performed in the presence of 1MT, an inhibitor of IDO activity, arguing for the implication of the kynurenine pathway. By inducing IDO, Tat protein may be considered, as a viral pathogenic factor, in the dysregulation of the DC functions during HIV-1 infection.
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Affiliation(s)
- Rémi Planès
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université Paul Sabatier, EA 3038, Toulouse, France
| | - Elmostafa Bahraoui
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université Paul Sabatier, EA 3038, Toulouse, France
- * E-mail:
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41
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Sampey GC, Guendel I, Das R, Jaworski E, Klase Z, Narayanan A, Kehn-Hall K, Kashanchi F. Transcriptional Gene Silencing (TGS) via the RNAi Machinery in HIV-1 Infections. BIOLOGY 2012; 1:339-69. [PMID: 24832229 PMCID: PMC4009781 DOI: 10.3390/biology1020339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/03/2012] [Accepted: 08/13/2012] [Indexed: 12/21/2022]
Abstract
Gene silencing via non-coding RNA, such as siRNA and miRNA, can occur at the transcriptional, post-transcriptional, and translational stages of expression. Transcriptional gene silencing (TGS) involving the RNAi machinery generally occurs through DNA methylation, as well as histone post-translational modifications, and corresponding remodeling of chromatin around the target gene into a heterochromatic state. The mechanism by which mammalian TGS occurs includes the recruitment of RNA-induced initiation of transcriptional gene silencing (RITS) complexes, DNA methyltransferases (DNMTs), and other chromatin remodelers. Additionally, virally infected cells encoding miRNAs have also been shown to manipulate the host cell RNAi machinery to induce TGS at the viral genome, thereby establishing latency. Furthermore, the introduction of exogenous siRNA and shRNA into infected cells that target integrated viral promoters can greatly suppress viral transcription via TGS. Here we examine the latest findings regarding mammalian TGS, specifically focusing on HIV-1 infected cells, and discuss future avenues of exploration in this field.
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Affiliation(s)
- Gavin C Sampey
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Irene Guendel
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Ravi Das
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Elizabeth Jaworski
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Zachary Klase
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, 9000 Rockville Pike, Bethesda, MD 20810, USA.
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Kylene Kehn-Hall
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Fatah Kashanchi
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
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42
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Impact of Tat Genetic Variation on HIV-1 Disease. Adv Virol 2012; 2012:123605. [PMID: 22899925 PMCID: PMC3414192 DOI: 10.1155/2012/123605] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 05/14/2012] [Indexed: 01/08/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) promoter or long-terminal repeat (LTR) regulates viral gene expression by interacting with multiple viral and host factors. The viral transactivator protein Tat plays an important role in transcriptional activation of HIV-1 gene expression. Functional domains of Tat and its interaction with transactivation response element RNA and cellular transcription factors have been examined. Genetic variation within tat of different HIV-1 subtypes has been shown to affect the interaction of the viral transactivator with cellular and/or viral proteins, influencing the overall level of transcriptional activation as well as its action as a neurotoxic protein. Consequently, the genetic variability within tat may impact the molecular architecture of functional domains of the Tat protein that may impact HIV pathogenesis and disease. Tat as a therapeutic target for anti-HIV drugs has also been discussed.
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43
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Li GH, Li W, Mumper RJ, Nath A. Molecular mechanisms in the dramatic enhancement of HIV-1 Tat transduction by cationic liposomes. FASEB J 2012; 26:2824-34. [PMID: 22447980 DOI: 10.1096/fj.11-203315] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) transactivator of transcription (Tat) protein possesses a unique membrane-transduction property. Interestingly, Tat transduction could be dramatically increased 1000-fold based on LTR-transactivation assay when complexed with cationic liposomes (lipo-Tat), compared with Tat alone. Therefore, underlining mechanisms were explored further. Microscopy and flow cytometry showed that this effect was associated with enhanced membrane binding, large particle formation (1-2 μm) and increased intracellular uptake of Tat fluorescent proteins. Using pharmacological assays and immune colocalizations, it was found that lipid raft-dependent endocytosis and macropinocytosis were major pathways involved in lipo-Tat uptake, and actin-filaments played a major role in intracellular trafficking of lipo-Tat to the nucleus. Furthermore, we found that the Tat hydrophobic domain (aa 36-47) mediated formation of two positively charged molecules into lipo-Tat complexes via hydrophobic bonds, based on LTR-transactivation inhibition assay. Thus, the hydrophobic domain may play an important role in Tat protein uptake and be useful for intracellular delivery of biomacromolecules if coupled together with Tat basic peptide, a cell-penetrating peptide.
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Affiliation(s)
- Guan-Han Li
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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44
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Kumar S, Kellish P, Robinson WE, Wang D, Appella DH, Arya DP. Click dimers to target HIV TAR RNA conformation. Biochemistry 2012; 51:2331-47. [PMID: 22339203 DOI: 10.1021/bi201657k] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of neomycin dimers have been synthesized using "click chemistry" with varying functionality and length in the linker region to target the human immunodeficiency virus type 1 (HIV-1) TAR RNA region of the HIV virus. The TAR (Trans-Activation Responsive) RNA region, a 59 bp stem-loop structure located at the 5'-end of all nascent viral transcripts, interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1. Neomycin, an aminosugar, has been shown to exhibit multiple binding sites on TAR RNA. This observation prompted us to design and synthesize a library of triazole-linked neomycin dimers using click chemistry. The binding between neomycin dimers and TAR RNA was characterized using spectroscopic techniques, including FID (fluorescent intercalator displacement), a FRET (fluorescence resonance energy transfer) competitive assay, circular dichroism (CD), and UV thermal denaturation. UV thermal denaturation studies demonstrate that binding of neomycin dimers increases the melting temperature (T(m)) of the HIV TAR RNA up to 10 °C. Ethidium bromide displacement (FID) and a FRET competition assay revealed nanomolar binding affinity between neomycin dimers and HIV TAR RNA, while in case of neomycin, only weak binding was detected. More importantly, most of the dimers exhibited lower IC(50) values toward HIV TAR RNA, when compared to the fluorescent Tat peptide, and show increased selectivity over mutant TAR RNA. Cytopathic effects investigated using MT-2 cells indicate a number of the dimers with high affinity toward TAR show promising anti-HIV activity.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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45
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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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46
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Bryson DI, Zhang W, McLendon PM, Reineke TM, Santos WL. Toward targeting RNA structure: branched peptides as cell-permeable ligands to TAR RNA. ACS Chem Biol 2012; 7:210-7. [PMID: 22003984 DOI: 10.1021/cb200181v] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rational design of RNA ligands continues to be a formidable challenge, but the potential powerful applications in biology and medicine catapults it to the forefront of chemical research. Indeed, small molecule and macromolecular intervention are attractive approaches, but selectivity and cell permeability can be a hurdle. An alternative strategy is to use molecules of intermediate molecular weight that possess large enough surface area to maximize interaction with the RNA structure but are small enough to be cell-permeable. Herein, we report the discovery of nontoxic and cell-permeable branched peptide (BP) ligands that bind to TAR RNA in the low micromolar range from on-bead high-throughput screening of 4,096 compounds. TAR is a short RNA motif in the 5'-UTR of HIV-1 that is responsible for efficient generation of full RNA transcripts. We demonstrate that BPs are selective for the native TAR RNA structure and that "branching" in peptides provides multivalent interaction, which increases binding affinity to RNA.
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Affiliation(s)
- David I. Bryson
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Wenyu Zhang
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Patrick M. McLendon
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Theresa M. Reineke
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Webster L. Santos
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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47
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Huang W, Varani G, Drobny GP. Interactions of protein side chains with RNA defined with REDOR solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:347-356. [PMID: 21947838 DOI: 10.1007/s10858-011-9573-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/11/2011] [Indexed: 05/31/2023]
Abstract
Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a combination of multiple solid state NMR REDOR experiments can be used to obtain multiple distance constraints from (15)N to (13)C spins within the backbone and side chain guanidinium groups of arginine in a Tat-derived peptide, using (19)F spins incorporated into the base of U23 in TAR and (31)P spins in the P22 and P23 phosphate groups. Distances between the side chain of Arg52 and the base and phosphodiester backbone near U23 measured by REDOR NMR are comparable to distances observed in solution NMR-derived structural models, indicating that interactions of TAR RNA with key amino acid side chains in Tat are the same in the amorphous solid state as in solution. This method is generally applicable to other protein-RNA complexes where crystallization or solution NMR has failed to provide high resolution structural information.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington, DC 98195, USA
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48
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Abstract
In the past 25 years revelations on the genesis of human cancer have come at an increasing pace. Research on oncogenic infectious agents, especially viruses, has helped us to understand the process of malignant transformation of cells because the cellular events in viral-driven transformation mirror, often brilliantly, basic cellular processes that culminate in cancer, even those not associated with viruses. Infectious agents, especially viruses, account for several of the most common malignancies-up to 20% of all cancers. Some of these cancers are endemic, with a high incidence in certain geographic locations, but sporadic/lower incidence in other parts of the world. Lymphomas arise frequently in association with infectious agents such as Epstein-Barr virus, human immunodeficiency virus, human herpes virus 8, Helicobacter pylori, and hepatitis C virus. In this review, we will focus on the association between infectious agents and lymphomas, with a look at the molecular mechanisms they use to disturb cell regulation and eventually result in cancer.
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Affiliation(s)
- Giulia De Falco
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
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49
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Kumar S, Arya DP. Recognition of HIV TAR RNA by triazole linked neomycin dimers. Bioorg Med Chem Lett 2011; 21:4788-92. [PMID: 21757341 PMCID: PMC3673547 DOI: 10.1016/j.bmcl.2011.06.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/10/2011] [Accepted: 06/13/2011] [Indexed: 10/18/2022]
Abstract
A series of neomycin dimers have been synthesized using 'click chemistry' with varying linker functionality and length to target the TAR RNA region of HIV virus. TAR (trans activation response) RNA region, a 59 base pair stem loop structure located at 5'-end of all nascent HIV-1 transcripts interacts with a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Neomycin, an aminosugar, has been shown to exhibit more than one binding site with HIV TAR RNA. Multiple TAR binding sites of neomycin prompted us to design and synthesize a small library of neomycin dimers using click chemistry. The binding between neomycin dimers and HIV TAR RNA was characterized using spectroscopic techniques including FID (Fluorescent Intercalator Displacement) titration and UV-thermal denaturation. UV thermal denaturation studies demonstrate that neomycin dimer binding increase the melting temperature (T(m)) of the HIV TAR RNA up to 10°C. Ethidium bromide displacement titrations revealed nanomolar IC(50) between neomycin dimers and HIV TAR RNA, whereas with neomycin, a much higher IC(50) in the micromolar range is observed.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
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50
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Cowley D, Gray LR, Wesselingh SL, Gorry PR, Churchill MJ. Genetic and functional heterogeneity of CNS-derived tat alleles from patients with HIV-associated dementia. J Neurovirol 2010; 17:70-81. [PMID: 21165788 DOI: 10.1007/s13365-010-0002-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 09/20/2010] [Accepted: 09/28/2010] [Indexed: 01/08/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) demonstrates a high degree of viral diversity which has an impact on viral fitness. Genetic compartmentalization of HIV-1 proteins between central nervous system (CNS) and lymphoid tissues is well established and reflects altered requirements for HIV-1 replication in macrophages/microglia, brain-specific immune selection pressures and possibly the timing of virus invasion of the CNS. Tat-encoding mRNA has been detected in the CNS of HIV-1 infected individuals and its neurotoxic effects in the CNS are well documented. However, while CNS-derived tat sequences have demonstrated significant diversity, the effect of this molecular diversity on transcriptional regulation and its impact on the pathogenesis of HIV-associated dementia (HAD) remains unclear. In this study, we cloned and characterised 44 unique tat alleles from brain, cerebral spinal fluid, spinal cord and blood/lymphoid tissue-derived HIV-1 isolates from five subjects with HAD. While phylogenetic analyses revealed tissue-specific compartmentalization of Tat variants for two patients, broad compartmentalization across the panel of tissue-derived viruses was not observed. Despite the lack of consistent tissue-specific compartmentalization, sequence variations within patients segregated CNS and non-CNS tat alleles. These amino acid alterations predominated within the transactivation domain of Tat and could account for alterations in the ability of particular Tat proteins to transactivate the LTR. Although a subset of patients demonstrated reduced transactivation capacity among CNS-derived Tat proteins compared to those from matched lymphoid tissues, overall Tat proteins from the CNS to lymphoid compartments maintained similar levels of transactivation function. Together, these data suggest that despite the observed heterogeneity in tat alleles isolated from matched lymphoid to CNS compartments, Tat function is maintained, highlighting the importance of Tat function in HIV-1 neuropathogenesis.
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Affiliation(s)
- Daniel Cowley
- Centre for Virology, Burnet Institute, 85 Commercial Rd, Melbourne, 3004 Victoria, Australia
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