1
|
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; 24:9139. [PMID: 37298089 PMCID: PMC10252837 DOI: 10.3390/ijms24119139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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; (Y.H.S.); (D.-E.K.); (K.L.Y.); (K.-C.K.); (S.B.)
| | - 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; (Y.H.S.); (D.-E.K.); (K.L.Y.); (K.-C.K.); (S.B.)
| | - 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; (Y.H.S.); (D.-E.K.); (K.L.Y.); (K.-C.K.); (S.B.)
| | - 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; (C.M.P.); (H.G.K.)
| | - 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; (C.M.P.); (H.G.K.)
| | - 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; (Y.H.S.); (D.-E.K.); (K.L.Y.); (K.-C.K.); (S.B.)
| | - 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; (Y.H.S.); (D.-E.K.); (K.L.Y.); (K.-C.K.); (S.B.)
| | - 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; (Y.H.S.); (D.-E.K.); (K.L.Y.); (K.-C.K.); (S.B.)
| |
Collapse
|
2
|
Qi L, Zhang J, Gao Y, Gong P, Liang C, Su Y, Zeng Q, Zhang Y. Peptide-RNA complexation-induced fluorescence "turn on" displacement assay for the recognition of small ligands targeting HIV-1 RNA. J Pharm Anal 2022; 12:923-928. [PMID: 36605574 PMCID: PMC9805967 DOI: 10.1016/j.jpha.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023] Open
Abstract
The regulator of expression of virion (Rev) protein binds specifically to the Rev-responsive element (RRE) RNA in order to regulate the expression of the human immunodeficiency virus (HIV)-1 genes. Fluorescence indicator displacement assays have been used to identify ligands that can inhibit the Rev-RRE interaction; however, the small fluorescence indicators cannot fully replace the Rev peptide or protein. As a result, a single rhodamine B labeled Rev (RB-Rev) model peptide was utilized in this study to develop a direct and efficient Rev-RRE inhibitor screening model. Due to photon-induced electron transfer quenching of the tryptophan residue on the RB fluorophore, the fluorescence of RB in Rev was weakened and could be dramatically reactivated by interaction with RRE RNA in ammonium acetate buffer (approximately six times). The interaction could reduce the electron transfer between tryptophan and RB, and RRE could also increase RB fluorescence. The inhibitor screening model was evaluated using three known positive Rev-RRE inhibitors, namely, proflavin, 6-chloro-9-[3-(2-chloroethylamino)propylamino]-2-methoxyacridine (ICR 191), and neomycin, as well as a negative drug, arginine. With the addition of the positive drugs, the fluorescence of the Rev-RRE decreased, indicating the displacement of RB-Rev. This was confirmed using atomic force microscopy (AFM) and the fluorescence was essentially unaffected by the addition of arginine. The results demonstrated that RB-Rev can be used as a fluorescent probe for recognizing small ligands that target RRE RNA. The Rev-RRE inhibitor screening model offers a novel approach to evaluating and identifying long-acting Rev inhibitors.
Collapse
Affiliation(s)
- Liang Qi
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China,Corresponding author.
| | - Jiayun Zhang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Ying Gao
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Pin Gong
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Chengyuan Liang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yao Su
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Qiao Zeng
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yafeng Zhang
- Xi'an Institute for Food and Drug Control, Xi'an, 710054, China
| |
Collapse
|
3
|
Targeting Tat-TAR RNA Interaction for HIV-1 Inhibition. Viruses 2021; 13:v13102004. [PMID: 34696435 PMCID: PMC8536978 DOI: 10.3390/v13102004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 Tat protein interacts with TAR RNA and recruits CDK9/cyclin T1 and other host factors to induce HIV-1 transcription. Thus, Tat–TAR RNA interaction, which is unique for HIV-1, represents an attractive target for anti-HIV-1 therapeutics. To target Tat–TAR RNA interaction, we used a crystal structure of acetylpromazine bound to the bulge of TAR RNA, to dock compounds from the Enamine database containing over two million individual compounds. The docking procedure identified 173 compounds that were further analyzed for the inhibition of HIV-1 infection. The top ten inhibitory compounds with IC50 ≤ 6 µM were selected and the three least toxic compounds, T6780107 (IC50 = 2.97 μM), T0516-4834 (IC50 = 0.2 μM) and T5628834 (IC50 = 3.46 μM), were further tested for HIV-1 transcription inhibition. Only the T0516-4834 compound showed selective inhibition of Tat-induced HIV-1 transcription, whereas the T6780107 compound inhibited equally basal and Tat-induced transcription and the T5628834 compound only inhibited basal HIV-1 transcription. The compounds were tested for the inhibition of translation and showed minimal (<25%) effect. The T0516-4834 compound also showed the strongest inhibition of HIV-1 RNA expression and p24 production in CEM T cells and peripheral blood mononuclear cells infected with HIV-1 IIIB. Of the three compounds, only the T0516-4834 compound significantly disrupted Tat–TAR RNA interaction. Additionally, of the three tested compounds, T5628834 and, to a lesser extent, T0516-4834 disrupted Tat–CDK9/cyclin T1 interaction. None of the three compounds showed significant inhibition of the cellular CDK9 and cyclin T1 levels. In silico modelling showed that the T0516-4834 compound interacted with TAR RNA by binding to the bulge formed by U23, U25, C39, G26,C39 and U40 residues. Taken together, our study identified a novel benzoxazole compound that disrupted Tat–TAR RNA interaction and inhibited Tat-induced transcription and HIV-1 infection, suggesting that this compound might serve as a new lead for anti-HIV-1 therapeutics.
Collapse
|
4
|
Alamer E, Zhong C, Hajnik R, Soong L, Hu H. Modulation of BRD4 in HIV epigenetic regulation: implications for finding an HIV cure. Retrovirology 2021; 18:3. [PMID: 33413475 PMCID: PMC7792063 DOI: 10.1186/s12977-020-00547-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/30/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Following reverse transcription, HIV viral DNA is integrated into host cell genomes and establishes a stable latent infection, which has posed a major obstacle for obtaining a cure for HIV. HIV proviral transcription is regulated in cellular reservoirs by complex host epigenetic and transcriptional machineries. The Bromodomain (BD) and Extra-Terminal Domain (ET) protein, BRD4, is an important epigenetic reader that interacts with acetyl-histones and a variety of chromatin and transcriptional regulators to control gene expression, including HIV. Modulation of BRD4 by a pan BET inhibitor (JQ1) has been shown to activate HIV transcription. Recent studies by my group and others indicate that the function of BRD4 is versatile and its effects on HIV transcription may depend on the partner proteins or pathways engaged by BRD4. Our studies have reported a novel class of small-molecule modulators that are distinct from JQ1 but induce HIV transcriptional suppression through BRD4. Herein, we reviewed recent research on the modulation of BRD4 in HIV epigenetic regulation and discussed their potential implications for finding an HIV cure.
Collapse
Affiliation(s)
- Edrous Alamer
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA.,Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.,Medical Research Center, Jazan University, Jazan, 45142, Saudi Arabia
| | - Chaojie Zhong
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA
| | - Renee Hajnik
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA
| | - Lynn Soong
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA.,Institute for Human Infections and Immunity, Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), MRB 4.142A, 301 University Blvd, Galveston, TX, 77555, USA. .,Institute for Human Infections and Immunity, Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| |
Collapse
|
5
|
Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA (NEW YORK, N.Y.) 2021; 27:12-26. [PMID: 33028652 PMCID: PMC7749633 DOI: 10.1261/rna.076257.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/26/2020] [Indexed: 05/30/2023]
Abstract
Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to nonspecific binding of aminoglycosides and intercalators to many stem-loop RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities. However, target engagement and cellular selectivity assays are not routinely performed, and it is often unclear whether functional activity directly results from specific binding to the target RNA. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activities of distinct stem-loop RNAs, to bind and inhibit the cellular activities of two unrelated HIV-1 stem-loop RNAs: the transactivation response element (TAR) and the rev response element stem IIB (RREIIB). All compounds bound TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting off-target interactions consistent with nonspecific activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that aminoglycosides and drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, in contrast to ligands that specifically bind riboswitches. Our results demonstrate that drug-like molecules can nonspecifically bind stem-loop RNAs most likely through hydrogen bonding and electrostatic interactions and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.
Collapse
Affiliation(s)
- Megan L Kelly
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Honglue Shi
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Laura R Ganser
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kelly Huynh
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yuze Hou
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| |
Collapse
|
6
|
Kodadek T, Paciaroni NG, Balzarini M, Dickson P. Beyond protein binding: recent advances in screening DNA-encoded libraries. Chem Commun (Camb) 2019; 55:13330-13341. [PMID: 31633708 PMCID: PMC6939232 DOI: 10.1039/c9cc06256d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library (DEL) screening has emerged as an important method for early stage drug and probe molecule discovery. The vast majority of screens using DELs have been relatively simple binding assays. The library is incubated with a target molecule, which is almost always a protein, and the DNAs that remain associated with the target after thorough washing are amplified and deep sequenced to reveal the chemical structures of the ligands they encode. Recently however, a number of different screening formats have been introduced that demand more than simple binding. These include a format that demands hits exhibit high selectivity for target vs. off-targets, a protocol to screen for enzyme inhibitors and another to identify organocatalysts in a DEL. These and other novel assay formats are reviewed in this article. We also consider some of the most significant remaining challenges in DEL assay development.
Collapse
Affiliation(s)
- Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Nicholas G Paciaroni
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Madeline Balzarini
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Paige Dickson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
7
|
Abstract
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates). These circuits offer the opportunity for a new class of antivirals that could lead to intrinsic combination-antiviral therapies within a single molecule-evolutionary escape from such circuit-disrupting antivirals would require simultaneous evolution of both the viral cis regulatory element (e.g., the DNA-binding site) and the trans element (e.g., the transcription factor) in order for the virus to recapitulate a circuit that would not be disrupted. We review the architectures of these fate-regulating master circuits in HIV-1 and the human herpesvirus cytomegalovirus along with potential circuit-disruption strategies that may ultimately enable escape-resistant antiviral therapies.
Collapse
Affiliation(s)
- Anand Pai
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158;
| | - Leor S Weinberger
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158; .,Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| |
Collapse
|
8
|
Qi L, Zhang J, He T, Huo Y, Zhang ZQ. Probing interaction of a fluorescent ligand with HIV TAR RNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:93-98. [PMID: 27611591 DOI: 10.1016/j.saa.2016.08.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/15/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.
Collapse
MESH Headings
- Aminacrine/analogs & derivatives
- Aminacrine/chemistry
- Aminacrine/metabolism
- Aminacrine/pharmacology
- Binding, Competitive
- Circular Dichroism
- Drug Evaluation, Preclinical/methods
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Framycetin/chemistry
- Framycetin/metabolism
- HIV Long Terminal Repeat
- Models, Molecular
- Molecular Docking Simulation
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- tat Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- tat Gene Products, Human Immunodeficiency Virus/chemistry
- tat Gene Products, Human Immunodeficiency Virus/metabolism
Collapse
Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Tian He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China.
| |
Collapse
|
9
|
Identification of Binding Mode and Prospective Structural Features of Novel Nef Protein Inhibitors as Potential Anti-HIV Drugs. Cell Biochem Biophys 2016; 75:49-64. [DOI: 10.1007/s12013-016-0774-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022]
|
10
|
Le Douce V, Ait-Amar A, Forouzan Far F, Fahmi F, Quiel J, El Mekdad H, Daouad F, Marban C, Rohr O, Schwartz C. Improving combination antiretroviral therapy by targeting HIV-1 gene transcription. Expert Opin Ther Targets 2016; 20:1311-1324. [PMID: 27266557 DOI: 10.1080/14728222.2016.1198777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Combination Antiretroviral Therapy (cART) has not allowed the cure of HIV. The main obstacle to HIV eradication is the existence of quiescent reservoirs. Several other limitations of cART have been described, such as strict life-long treatment and high costs, restricting it to Western countries, as well as the development of multidrug resistance. Given these limitations and the impetus to find a cure, the development of new treatments is necessary. Areas covered: In this review, we discuss the current status of several efficient molecules able to suppress HIV gene transcription, including NF-kB and Tat inhibitors. We also assess the potential of new proteins belonging to the intriguing DING family, which have been reported to have potential anti-HIV-1 activity by inhibiting HIV gene transcription. Expert opinion: Targeting HIV-1 gene transcription is an alternative approach, which could overcome cART-related issues, such as the emergence of multidrug resistance. Improving cART will rely on the identification and characterization of new actors inhibiting HIV-1 transcription. Combining such efforts with the use of new technologies, the development of new models for preclinical studies, and improvement in drug delivery will considerably reduce drug toxicity and thus increase patient adherence.
Collapse
Affiliation(s)
- Valentin Le Douce
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France.,c UCD Centre for Research in Infectious Diseases (CRID) School of Medicine and Medical Science , University College Dublin , Dublin 4 , Ireland
| | - Amina Ait-Amar
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Faezeh Forouzan Far
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Faiza Fahmi
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Jose Quiel
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Hala El Mekdad
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Fadoua Daouad
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Céline Marban
- d Faculté de Chirurgie Dentaire , Inserm UMR 1121 , Strasbourg , France
| | - Olivier Rohr
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France.,e Institut Universitaire de France , Paris , France
| | - Christian Schwartz
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France
| |
Collapse
|
11
|
Ulbrich K, Holá K, Šubr V, Bakandritsos A, Tuček J, Zbořil R. Targeted Drug Delivery with Polymers and Magnetic Nanoparticles: Covalent and Noncovalent Approaches, Release Control, and Clinical Studies. Chem Rev 2016; 116:5338-431. [DOI: 10.1021/acs.chemrev.5b00589] [Citation(s) in RCA: 1120] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Karel Ulbrich
- Institute
of Macromolecular Chemistry, The Czech Academy of Sciences, v.v.i., Heyrovsky Square 2, 162 06 Prague 6, Czech Republic
| | - Kateřina Holá
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, 17 Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Vladimir Šubr
- Institute
of Macromolecular Chemistry, The Czech Academy of Sciences, v.v.i., Heyrovsky Square 2, 162 06 Prague 6, Czech Republic
| | - Aristides Bakandritsos
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, 17 Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Jiří Tuček
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, 17 Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Radek Zbořil
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, 17 Listopadu 1192/12, 771 46 Olomouc, Czech Republic
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | | |
Collapse
|
13
|
Abstract
The transacting activator of transduction (TAT) protein plays a key role in the progression of AIDS. Studies have shown that a +8 charged sequence of amino acids in the protein, called the TAT peptide, enables the TAT protein to penetrate cell membranes. To probe mechanisms of binding and translocation of the TAT peptide into the cell, investigators have used phospholipid liposomes as cell membrane mimics. We have used the method of surface potential sensitive second harmonic generation (SHG), which is a label-free and interface-selective method, to study the binding of TAT to anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-1'-rac-glycerol (POPG) and neutral 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) liposomes. It is the SHG sensitivity to the electrostatic field generated by a charged interface that enabled us to obtain the interfacial electrostatic potential. SHG together with the Poisson-Boltzmann equation yielded the dependence of the surface potential on the density of adsorbed TAT. We obtained the dissociation constants Kd for TAT binding to POPC and POPG liposomes and the maximum number of TATs that can bind to a given liposome surface. For POPC Kd was found to be 7.5 ± 2 μM, and for POPG Kd was 29.0 ± 4.0 μM. As TAT was added to the liposome solution the POPC surface potential changed from 0 mV to +37 mV, and for POPG it changed from -57 mV to -37 mV. A numerical calculation of Kd, which included all terms obtained from application of the Poisson-Boltzmann equation to the TAT liposome SHG data, was shown to be in good agreement with an approximated solution.
Collapse
|
14
|
Sztuba-Solinska J, Shenoy SR, Gareiss P, Krumpe LH, Le Grice SJ, O’Keefe BR, Schneekloth JS. Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays. J Am Chem Soc 2014; 136:8402-10. [PMID: 24820959 PMCID: PMC4227816 DOI: 10.1021/ja502754f] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 12/16/2022]
Abstract
Identifying small molecules that selectively bind to structured RNA motifs remains an important challenge in developing potent and specific therapeutics. Most strategies to find RNA-binding molecules have identified highly charged compounds or aminoglycosides that commonly have modest selectivity. Here we demonstrate a strategy to screen a large unbiased library of druglike small molecules in a microarray format against an RNA target. This approach has enabled the identification of a novel chemotype that selectively targets the HIV transactivation response (TAR) RNA hairpin in a manner not dependent on cationic charge. Thienopyridine 4 binds to and stabilizes the TAR hairpin with a Kd of 2.4 μM. Structure-activity relationships demonstrate that this compound achieves activity through hydrophobic and aromatic substituents on a heterocyclic core, rather than cationic groups typically required. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis was performed on a 365-nucleotide sequence derived from the 5' untranslated region (UTR) of the HIV-1 genome to determine global structural changes in the presence of the molecule. Importantly, the interaction of compound 4 can be mapped to the TAR hairpin without broadly disrupting any other structured elements of the 5' UTR. Cell-based anti-HIV assays indicated that 4 inhibits HIV-induced cytopathicity in T lymphocytes with an EC50 of 28 μM, while cytotoxicity was not observed at concentrations approaching 1 mM.
Collapse
Affiliation(s)
- Joanna Sztuba-Solinska
- HIV
Drug Resistance Program, National Cancer
Institute, Frederick, Maryland, United States
| | - Shilpa R. Shenoy
- Molecular
Targets Laboratory, National Cancer Institute, Frederick, Maryland, United States
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory, Frederick, Maryland, United States
| | - Peter Gareiss
- Center
For Molecular Discovery, Yale University, New Haven, Connecticut, United States
| | - Lauren
R. H. Krumpe
- Molecular
Targets Laboratory, National Cancer Institute, Frederick, Maryland, United States
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory, Frederick, Maryland, United States
| | - Stuart
F. J. Le Grice
- HIV
Drug Resistance Program, National Cancer
Institute, Frederick, Maryland, United States
| | - Barry R. O’Keefe
- Molecular
Targets Laboratory, National Cancer Institute, Frederick, Maryland, United States
| | - John S. Schneekloth
- Chemical
Biology Laboratory, National Cancer Institute, Frederick, Maryland, United States
| |
Collapse
|
15
|
Human Immunodeficiency Virus Type 1 Tat and Rev as Potential Targets for Drug Development. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
16
|
Abstract
The most significant advance in the medical management of HIV-1 infection has been the treatment of patients with antiviral drugs, which can suppress HIV-1 replication to undetectable levels. The discovery of HIV-1 as the causative agent of AIDS together with an ever-increasing understanding of the virus replication cycle have been instrumental in this effort by providing researchers with the knowledge and tools required to prosecute drug discovery efforts focused on targeted inhibition with specific pharmacological agents. To date, an arsenal of 24 Food and Drug Administration (FDA)-approved drugs are available for treatment of HIV-1 infections. These drugs are distributed into six distinct classes based on their molecular mechanism and resistance profiles: (1) nucleoside-analog reverse transcriptase inhibitors (NNRTIs), (2) non-nucleoside reverse transcriptase inhibitors (NNRTIs), (3) integrase inhibitors, (4) protease inhibitors (PIs), (5) fusion inhibitors, and (6) coreceptor antagonists. In this article, we will review the basic principles of antiretroviral drug therapy, the mode of drug action, and the factors leading to treatment failure (i.e., drug resistance).
Collapse
Affiliation(s)
- Eric J Arts
- Ugandan CFAR Laboratories, Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA.
| | | |
Collapse
|
17
|
Strategies to Block HIV Transcription: Focus on Small Molecule Tat Inhibitors. BIOLOGY 2012; 1:668-97. [PMID: 24832514 PMCID: PMC4009808 DOI: 10.3390/biology1030668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023]
Abstract
After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replication. Basal transcription from the integrated HIV promoter is very low in the absence of the HIV transactivator of transcription (Tat) protein and is solely dependent on cellular transcription factors. The 5' terminal region (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loop structure called the Transactivation Responsive (TAR) element. Once Tat is made, it binds to TAR and drastically activates transcription from the HIV LTR promoter. Mutations in either the Tat protein or TAR sequence usually affect HIV replication, indicating a strong requirement for their conservation. The necessity of the Tat-mediated transactivation cascade for robust HIV replication renders Tat one of the most desirable targets for transcriptional therapy against HIV replication. Screening based on inhibition of the Tat-TAR interaction has identified a number of potential compounds, but none of them are currently used as therapeutics, partly because these agents are not easily delivered for an efficient therapy, emphasizing the need for small molecule compounds. Here we will give an overview of the different strategies used to inhibit HIV transcription and review the current repertoire of small molecular weight compounds that target HIV transcription.
Collapse
|
18
|
Li CH, Zuo ZC, Su JG, Xu XJ, Wang CX. The interactions and recognition of cyclic peptide mimetics of Tat with HIV-1 TAR RNA: a molecular dynamics simulation study. J Biomol Struct Dyn 2012; 31:276-87. [PMID: 22943434 DOI: 10.1080/07391102.2012.698248] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The interaction of HIV-1 trans-activator protein Tat with its cognate trans-activation response element (TAR) RNA is critical for viral transcription and replication. Therefore, it has long been considered as an attractive target for the development of antiviral compounds. Recently, the conformationally constrained cyclic peptide mimetics of Tat have been tested to be a promising family of lead peptides. Here, we focused on two representative cyclic peptides termed as L-22 and KP-Z-41, both of which exhibit excellent inhibitory potency against Tat and TAR interaction. By means of molecular dynamics simulations, we obtained a detailed picture of the interactions between them and HIV-1 TAR RNA. In results, it is found that the binding modes of the two cyclic peptides to TAR RNA are almost identical at or near the bulge regions, whereas the binding interfaces at the apical loop exhibit large conformational heterogeneity. In addition, it is revealed that electrostatic interaction energy contributes much more to KP-Z-41 complex formation than to L-22 complex, which is the main source of energy that results in a higher binding affinity of KP-Z-41 over-22 for TAR RNA. Furthermore, we identified a conserved motif RRK (Arg-Arg-Lys) that is shown to be essential for specific binding of this class of cyclic peptides to TAR RNA. This work can provide a useful insight into the design and modification of cyclic peptide inhibitors targeting the association of HIV-1 Tat and TAR RNA.
Collapse
Affiliation(s)
- Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Pingleyuan 100, Chaoyang District, Beijing 100124, China.
| | | | | | | | | |
Collapse
|
19
|
Preventing the formation of positive transcription elongation factor b by human cyclin T1-binding RNA aptamer for anti-HIV transcription. AIDS 2012; 26:1599-605. [PMID: 22569018 DOI: 10.1097/qad.0b013e3283554f7d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Development of an innovative antitranscriptional technique for HIV. DESIGN Systematic evolution of ligands by exponential enrichment (SELEX) technique that can characterize target-specific aptamer was employed to synthesize an aptamer that binds human cyclin T1 (CycT1). When CycT1-binding aptamer interferes the binding of cyclin-dependent kinase 9 (Cdk9) to CycT1, HIV transcription is likely to be discouraged. METHODS Throughout SELEX steps, RNA aptamers having high specific affinity toward CycT1 were characterized. The binding interaction between selected aptamers and CycT1 was analyzed via various techniques. RESULTS Both qualitative and quantitative analyses revealed Apt4 aptamer, among four candidates, has the highest specific affinity to CycT1. In the presence of Apt4, Cdk9 protein was unable to make interaction with CycT1. CONCLUSION A specific RNA aptamer that identifies and binds to CycT1 with high affinity was successfully characterized. As CycT1 plays an important role in HIV transcription, this novel method that interferes and inhibits the transcription of HIV has the potential of being exploited in extended research fields, such as clinical therapy.
Collapse
|
20
|
Kuzmina A, Hadad U, Fujinaga K, Taube R. Functional characterization of a human cyclin T1 mutant reveals a different binding surface for Tat and HEXIM1. Virology 2012; 426:152-61. [PMID: 22342181 DOI: 10.1016/j.virol.2012.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 01/17/2012] [Accepted: 01/27/2012] [Indexed: 11/25/2022]
Abstract
HIV transcription is regulated at the step of elongation by the viral Tat protein and the cellular positive transcription elongation factor b (P-TEFb; Cdk9/cyclin T1). Herein, a human cyclin T1 mutant, cyclin T1-U7, which contains four substitutions and one deletion in the N-terminal cyclin box, was stably expressed in HeLa cells. HIV transcription was efficiently inhibited in HeLa-HA-CycT1-U7 stable cells. Cyclin T1-U7 bound Tat but did not modulate its expression levels, which remained high. Importantly cyclin T1-U7 failed to interact with Cdk9 or HEXIM1 and did not interfere with endogenous P-TEFb activity to stimulate MEF2C or NFkB mediated transcription. In a T cell line and primary CD4+ cells, cyclin T1-U7 also inhibited HIV transcription. We conclude that cyclin T1-U7 sequesters Tat from P-TEFb and inhibits HIV transcription. Importantly, N-terminal residues in cyclin T1 are specifically involved in the binding of cyclin T1 to HEXIM1 but not to Tat.
Collapse
Affiliation(s)
- Alona Kuzmina
- Department of Virology and Developmental Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | | | | | | |
Collapse
|
21
|
Mehla R, Bivalkar-Mehla S, Chauhan A. A flavonoid, luteolin, cripples HIV-1 by abrogation of tat function. PLoS One 2011; 6:e27915. [PMID: 22140483 PMCID: PMC3227592 DOI: 10.1371/journal.pone.0027915] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 10/27/2011] [Indexed: 12/17/2022] Open
Abstract
Despite the effectiveness of combination antiretroviral treatment (cART) against HIV-1, evidence indicates that residual infection persists in different cell types. Intensification of cART does not decrease the residual viral load or immune activation. cART restricts the synthesis of infectious virus but does not curtail HIV-1 transcription and translation from either the integrated or unintegrated viral genomes in infected cells. All treated patients with full viral suppression actually have low-level viremia. More than 60% of treated individuals also develop minor HIV-1 -associated neurocognitive deficits (HAND) due to residual virus and immune activation. Thus, new therapeutic agents are needed to curtail HIV-1 transcription and residual virus. In this study, luteolin, a dietary supplement, profoundly reduced HIV-1 infection in reporter cells and primary lymphocytes. HIV-1inhibition by luteolin was independent of viral entry, as shown by the fact that wild-type and VSV-pseudotyped HIV-1 infections were similarly inhibited. Luteolin was unable to inhibit viral reverse transcription. Luteolin had antiviral activity in a latent HIV-1 reactivation model and effectively ablated both clade-B- and -C -Tat-driven LTR transactivation in reporter assays but had no effect on Tat expression and its sub-cellular localization. We conclude that luteolin confers anti-HIV-1 activity at the Tat functional level. Given its biosafety profile and ability to cross the blood-brain barrier, luteolin may serve as a base flavonoid to develop potent anti-HIV-1 derivatives to complement cART.
Collapse
Affiliation(s)
- Rajeev Mehla
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
| | - Shalmali Bivalkar-Mehla
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
| | - Ashok Chauhan
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
- Department of Pharmacology, Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
- * E-mail:
| |
Collapse
|
22
|
Boll A, Jatho A, Czudnochowski N, Geyer M, Steinem C. Mechanistic insights into the translocation of full length HIV-1 Tat across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2685-93. [PMID: 21819963 DOI: 10.1016/j.bbamem.2011.07.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 06/19/2011] [Accepted: 07/20/2011] [Indexed: 11/28/2022]
Abstract
The mechanism of how full length Tat (aa 1-86) crosses artificial lipid membranes was elucidated by means of fluorescence spectroscopy and fluorescence microscopy. It was shown that full length Tat (aa 1-86) neither forms pores in large unilamellar vesicles (LUVs) nor in giant unilamellar vesicles (GUVs) composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). In contrast, an N-terminally truncated Tat protein (aa 35-86) that lacks the structurally defined proline- and cysteine-rich region as well as the highly conserved tryptophan residue at position 11 generates pores in artificial POPC-membranes, through which a water-soluble dye up to a size of 10kDa can pass. By means of fluorescence microscopy, the transfer of fluorescently labeled full length Tat across POPC-bilayers was unambiguously visualized with a concomitant accumulation of the protein in the membrane interface. However, if the dye was attached to the protein, also pore formation was induced. The size of the pores was, however smaller than the protein size, i.e. the labeled protein with a mass of 11.6kDa passed the membrane, while a fluorescent dye with a mass of 10kDa was excluded from the vesicles' interior. The results demonstrate that pore formation is not the prime mechanism by which full length Tat crosses a membrane.
Collapse
Affiliation(s)
- Annegret Boll
- Institute of Organic and Biomolecular Chemistry, Tammannstr. 2, Göttingen, Germany
| | | | | | | | | |
Collapse
|
23
|
Abstract
The current anti-HIV treatments fail to completely eradicate the virus in HIV-infected individuals, mainly as a result of a small pool of latently infected cells. This issue, together with the emergence of multidrug-resistant viruses, clearly highlights the need to find additional strategies. An overview of the Tat-mediated transcription inhibitors 6-desfluoroquinolones (6-DFQs), identified by our group, is given in this review along with a critical appraisal of their advantages and drawbacks. Attempts are also made to place them within the context of new potential anti-HIV therapeutics. Due to their innovative mechanism of action, the 6-DFQs could be interesting candidates for use in association with the currently used cocktail of drugs. Their potential as antivirals deserves further investigation.
Collapse
|
24
|
Functional Characterization of Human Cyclin T1 N-Terminal Region for Human Immunodeficiency Virus-1 Tat Transcriptional Activation. J Mol Biol 2011; 410:887-95. [DOI: 10.1016/j.jmb.2011.04.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 11/23/2022]
|
25
|
Inhibition of HIV-1 Tat-mediated transcription by a coumarin derivative, BPRHIV001, through the Akt pathway. J Virol 2011; 85:9114-26. [PMID: 21697490 DOI: 10.1128/jvi.00175-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1)-encoded RNA-binding protein Tat is known to play an essential role in viral gene expression. In the search for novel compounds to inhibit Tat transactivity, one coumarin derivative, BPRHIV001, was identified, with a 50% effective concentration (EC(50)) against HIV-1 at 1.3 nM. BPRHIV001 is likely to exert its effects at the stage after initiation of RNAPII elongation since Tat protein expression and the assembly of the Tat/P-TEFb complex remained unchanged. Next, a reduction of the p300 protein level, known to modulate Tat function through acetylation, was observed upon BPRHIV001 treatment, while the p300 mRNA level was unaffected. A concordant reduction of phosphorylated Akt, which was shown to be closely related to p300 stability, was observed in the presence of BPRHIV001 and was accompanied by a decrease of phosphorylated PDPK1, a well-known Akt activator. Furthermore, the docking analysis revealed that the reduced PDPK1 phosphorylation likely resulted from the allosteric effect of interaction between BPRHIV001 and PDPK1. With strong synergistic effects with current reverse transcriptase inhibitors, BPRHIV001 has the potential to become a promising lead compound for the development of a novel therapeutic agent against HIV-1 infection.
Collapse
|
26
|
Lalonde MS, Lobritz MA, Ratcliff A, Chamanian M, Athanassiou Z, Tyagi M, Wong J, Robinson JA, Karn J, Varani G, Arts EJ. Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA. PLoS Pathog 2011; 7:e1002038. [PMID: 21625572 PMCID: PMC3098202 DOI: 10.1371/journal.ppat.1002038] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 03/04/2011] [Indexed: 11/18/2022] Open
Abstract
The RNA response element TAR plays a critical role in HIV replication by
providing a binding site for the recruitment of the viral transactivator protein
Tat. Using a structure-guided approach, we have developed a series of
conformationally-constrained cyclic peptides that act as structural mimics of
the Tat RNA binding region and block Tat-TAR interactions at nanomolar
concentrations in vitro. Here we show that these compounds
block Tat-dependent transcription in cell-free systems and in cell-based
reporter assays. The compounds are also cell permeable, have low toxicity, and
inhibit replication of diverse HIV-1 strains, including both CXCR4-tropic and
CCR5-tropic primary HIV-1 isolates of the divergent subtypes A, B, C, D and
CRF01_AE. In human peripheral blood mononuclear cells, the cyclic peptidomimetic
L50 exhibited an IC50 ∼250 nM. Surprisingly, inhibition of
LTR-driven HIV-1 transcription could not account for the full antiviral
activity. Timed drug-addition experiments revealed that L-50 has a bi-phasic
inhibition curve with the first phase occurring after HIV-1 entry into the host
cell and during the initiation of HIV-1 reverse transcription. The second phase
coincides with inhibition of HIV-1 transcription. Reconstituted reverse
transcription assays confirm that HIV-1 (−) strand strong stop DNA
synthesis is blocked by L50-TAR RNA interactions in-vitro.
These findings are consistent with genetic evidence that TAR plays critical
roles both during reverse transcription and during HIV gene expression. Our
results suggest that antiviral drugs targeting TAR RNA might be highly effective
due to a dual inhibitory mechanism. The HIV-1 transactivator protein (Tat), together with the elongation factor
P-TEFb binds to an HIV-1 RNA secondary structure in the 5′-UTRs of nascent
viral mRNAs (TAR) and promotes transcription elongation. This process has been
an attractive target for drug development but previous inhibitors that bind
either Tat or TAR have been plagued by poor inhibition of virus replication,
limited cell penetration, and off-target effects. In this article, we describe a
series of rationally designed cyclic peptides that block Tat-TAR interactions.
L50, the most potent of these compounds, inhibits a wide range of HIV-1 strains
from around the world. Remarkably, L50 inhibits two distinct steps in the HIV-1
lifecycle. As expected, L50 inhibits Tat-dependent HIV-1 transcription, but the
majority of its anti-HIV activity is due to a block in reverse transcription,
i.e. synthesis of the proviral DNA from the RNA genome. L50 inhibition of
reverse transcription reveals an important role for TAR RNA during reverse
transcription as well as providing one of first examples of a drug with a dual
mechanism of action.
Collapse
Affiliation(s)
- Matthew S. Lalonde
- Department of Biochemistry, Case Western
Reserve University, Cleveland, Ohio, United States of America
| | - Michael A. Lobritz
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Annette Ratcliff
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Mastooreh Chamanian
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Zafiria Athanassiou
- Department of Chemistry and Department of
Biochemistry, University of Washington, Seattle, Washington, United States of
America
| | - Mudit Tyagi
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Julian Wong
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - John A. Robinson
- Department of Chemistry, University of Zurich,
Zurich, Switzerland
| | - Jonathan Karn
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
| | - Gabriele Varani
- Department of Chemistry and Department of
Biochemistry, University of Washington, Seattle, Washington, United States of
America
| | - Eric J. Arts
- Department of Molecular Biology and
Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of
America
- Division of Infectious Diseases, Department of
Medicine, Case Western Reserve University, Cleveland, Ohio, United States of
America
- * E-mail:
| |
Collapse
|
27
|
Mujtaba S, Zhou MM. Anti-viral opportunities during transcriptional activation of latent HIV in the host chromatin. Methods 2011; 53:97-101. [PMID: 20828615 PMCID: PMC3580173 DOI: 10.1016/j.ymeth.2010.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 08/12/2010] [Accepted: 09/01/2010] [Indexed: 10/19/2022] Open
Abstract
Human immunodeficiency virus (HIV) when integrated into a host chromosome exists in a transcriptionally inactive but replication-competent state. Such latent infection represents a major challenge to HIV eradication efforts because a permanent virus reservoir resided in the infected cell is able to spike the viral load on immune suppression or during interruption of highly active anti-retroviral therapy. Understanding the molecular mechanisms that control HIV proviral latency and its reactivation could provide new perspectives on host factors as therapeutic targets for abolishing cellular reservoirs of dormant HIV. Although the control of HIV latency is multifactorial, chromatin structure and the chromatin-associated transcriptional machinery are known to be important factors. For instance, transcription initiation of the HIV provirus involves a complex molecular interplay between chromatin-associated proteins and the virus-encoded trans-activator, Tat. The first part of this review discusses our current understanding of the elements involved in HIV transcriptional activation and viral mRNA elongation, mainly post-translational modifications of HIV Tat and its interactions with host chromatin-modifying enzymes and chromatin-remodeling complexes. The second part highlights new experimental therapeutic approaches aimed at administrating activators of HIV gene expression to reduce or eliminate the pool of latently HIV-infected cells.
Collapse
Affiliation(s)
- Shiraz Mujtaba
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
| |
Collapse
|
28
|
Kilareski EM, Shah S, Nonnemacher MR, Wigdahl B. Regulation of HIV-1 transcription in cells of the monocyte-macrophage lineage. Retrovirology 2009; 6:118. [PMID: 20030845 PMCID: PMC2805609 DOI: 10.1186/1742-4690-6-118] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 12/23/2009] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) has been shown to replicate productively in cells of the monocyte-macrophage lineage, although replication occurs to a lesser extent than in infected T cells. As cells of the monocyte-macrophage lineage become differentiated and activated and subsequently travel to a variety of end organs, they become a source of infectious virus and secreted viral proteins and cellular products that likely initiate pathological consequences in a number of organ systems. During this process, alterations in a number of signaling pathways, including the level and functional properties of many cellular transcription factors, alter the course of HIV-1 long terminal repeat (LTR)-directed gene expression. This process ultimately results in events that contribute to the pathogenesis of HIV-1 infection. First, increased transcription leads to the upregulation of infectious virus production, and the increased production of viral proteins (gp120, Tat, Nef, and Vpr), which have additional activities as extracellular proteins. Increased viral production and the presence of toxic proteins lead to enhanced deregulation of cellular functions increasing the production of toxic cellular proteins and metabolites and the resulting organ-specific pathologic consequences such as neuroAIDS. This article reviews the structural and functional features of the cis-acting elements upstream and downstream of the transcriptional start site in the retroviral LTR. It also includes a discussion of the regulation of the retroviral LTR in the monocyte-macrophage lineage during virus infection of the bone marrow, the peripheral blood, the lymphoid tissues, and end organs such as the brain. The impact of genetic variation on LTR-directed transcription during the course of retrovirus disease is also reviewed.
Collapse
Affiliation(s)
- Evelyn M Kilareski
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Center for Molecular Therapeutics and Resistance, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA
| | - Sonia Shah
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Center for Molecular Therapeutics and Resistance, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA
| | - Michael R Nonnemacher
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Center for Molecular Therapeutics and Resistance, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA
| | - Brian Wigdahl
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Center for Molecular Therapeutics and Resistance, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA
| |
Collapse
|
29
|
Wang D, Iera J, Baker H, Hogan P, Ptak R, Yang L, Hartman T, Buckheit RW, Desjardins A, Yang A, Legault P, Yedavalli V, Jeang KT, Appella DH. Multivalent binding oligomers inhibit HIV Tat-TAR interaction critical for viral replication. Bioorg Med Chem Lett 2009; 19:6893-7. [PMID: 19896372 DOI: 10.1016/j.bmcl.2009.10.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 10/19/2009] [Indexed: 12/11/2022]
Abstract
We describe the development of a new type of scaffold to target RNA structures. Multivalent binding oligomers (MBOs) are molecules in which multiple sidechains extend from a polyamine backbone such that favorable RNA binding occurs. We have used this strategy to develop MBO-based inhibitors to prevent the association of a protein-RNA complex, Tat-TAR, that is essential for HIV replication. In vitro binding assays combined with model cell-based assays demonstrate that the optimal MBOs inhibit Tat-TAR binding at low micromolar concentrations. Antiviral studies are also consistent with the in vitro and cell-based assays. MBOs provide a framework for the development of future RNA-targeting molecules.
Collapse
Affiliation(s)
- Deyun Wang
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, DHHS, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Romani B, Engelbrecht S, Glashoff RH. Functions of Tat: the versatile protein of human immunodeficiency virus type 1. J Gen Virol 2009; 91:1-12. [PMID: 19812265 DOI: 10.1099/vir.0.016303-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Tat is a multifunctional protein that contributes to several pathological symptoms of HIV-1 infection as well as playing a critical role in virus replication. Tat is a robust transactivating protein that induces a variety of effects by altering the expression levels of cellular and viral genes. The functions of Tat are therefore primarily related to its role in modulation of gene expression. In this review the functions of HIV-1 Tat that have been well documented, as well as a number of novel functions that have been proposed for this protein, are discussed. Since some of the functions of Tat vary in different cell types in a concentration-dependent manner and because Tat sometimes exerts the same activity through different pathways, study of this protein has at times yielded conflicting and controversial results. Due to its pivotal role in viral replication and in disease pathogenesis, Tat and the cellular pathways targeted by Tat are potential targets for new anti-HIV drugs.
Collapse
Affiliation(s)
- Bizhan Romani
- Division of Medical Virology, Department of Pathology, University of Stellenbosch, Tygerberg 7505, South Africa.
| | | | | |
Collapse
|
31
|
Role of Tat protein in HIV neuropathogenesis. Neurotox Res 2009; 16:205-20. [PMID: 19526283 DOI: 10.1007/s12640-009-9047-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/09/2009] [Accepted: 03/09/2009] [Indexed: 12/13/2022]
Abstract
The Tat protein of the human immunodeficiency virus (HIV) has been implicated in the pathophysiology of the neurocognitive deficits associated with HIV infection. This is the earliest protein to be produced by the proviral DNA in the infected cell. The protein not only drives the regulatory regions of the virus but may also be actively released from the cell and then interact with the cell surface receptors of other uninfected cells in the brain leading to cellular dysfunction. It may also be taken up by these cells and can then activate a number of host genes. The Tat protein is highly potent and has the unique ability to travel along neuronal pathways. Importantly, its production is not impacted by the use of antiretroviral drugs once the proviral DNA has been formed. This article reviews the pleomorphic actions of Tat protein and the evidence supporting its central role in the neuropathogenesis of the HIV infection.
Collapse
|
32
|
Chirayil S, Chirayil R, Luebke KJ. Discovering ligands for a microRNA precursor with peptoid microarrays. Nucleic Acids Res 2009; 37:5486-97. [PMID: 19561197 PMCID: PMC2760809 DOI: 10.1093/nar/gkp549] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have screened peptoid microarrays to identify specific ligands for the RNA hairpin precursor of miR-21, a microRNA involved in cancer and heart disease. Microarrays were printed by spotting a library of 7680 N-substituted oligoglycines (peptoids) onto glass slides. Two compounds on the array specifically bind RNA having the sequence and predicted secondary structure of the miR-21 precursor hairpin and have specific affinity for the target in solution. Their binding induces a conformational change around the hairpin loop, and the most specific compound recognizes the loop sequence and a bulged uridine in the proximal duplex. Functional groups contributing affinity and specificity were identified, and by varying a critical methylpyridine group, a compound with a dissociation constant of 1.9 μM for the miR-21 precursor hairpin and a 20-fold discrimination against a closely-related hairpin was created. This work describes a systematic approach to discovery of ligands for specific pre-defined novel RNA structures. It demonstrates discovery of new ligands for an RNA for which no specific lead compounds were previously known by screening a microarray of small molecules.
Collapse
Affiliation(s)
- Sara Chirayil
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9185, USA
| | | | | |
Collapse
|
33
|
Bonnard V, Azoulay S, Di Giorgio A, Patino N. Polyamide amino acids: a new class of RNA ligands. Chem Commun (Camb) 2009:2302-4. [DOI: 10.1039/b815324h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Jadlowsky JK, Nojima M, Okamoto T, Fujinaga K. Dominant negative mutant cyclin T1 proteins that inhibit HIV transcription by forming a kinase inactive complex with Tat. J Gen Virol 2008; 89:2783-2787. [DOI: 10.1099/vir.0.2008/002857-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription of the human immunodeficiency virus type 1 (HIV) requires the interaction of the cyclin T1 (CycT1) subunit of a host cellular factor, the positive transcription elongation factor b (P-TEFb), with the viral Tat protein, at the transactivation response element (TAR) of nascent transcripts. Because of this virus-specific interaction, CycT1 may potentially serve as a target for the development of anti-HIV therapies. Here we report the development of a mutant CycT1 protein, containing three threonine-to-alanine substitutions in the linker region between two of the cyclin boxes, which displays a potent dominant negative effect on HIV transcription. Investigation into the inhibitory mechanism revealed that this mutant CycT1 interacted with Tat and the cyclin-dependent kinase 9 (Cdk9) subunit of P-TEFb, but failed to stimulate the Cdk9 kinase activity critical for elongation. This mutant CycT1 protein may represent a novel class of specific inhibitors of HIV transcription which could lead to development of new antiviral therapies.
Collapse
Affiliation(s)
- Julie K. Jadlowsky
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4984, USA
| | - Masanori Nojima
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4984, USA
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Koh Fujinaga
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4984, USA
| |
Collapse
|
35
|
Krishnamurthy M, Schirle NT, Beal PA. Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay. Bioorg Med Chem 2008; 16:8914-21. [PMID: 18789700 DOI: 10.1016/j.bmc.2008.08.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 08/22/2008] [Accepted: 08/26/2008] [Indexed: 11/19/2022]
Abstract
The fluorescent intercalator displacement assay using thiazole orange has been adapted to the study of RNA-binding helix-threading peptides (HTPs). This assay is highly sensitive with HTP-binding RNAs and provides binding affinity data in good agreement with quantitative ribonuclease footprinting without the need for radiolabeling or gel electrophoresis. The FID assay was used to define structure activity relationships for a small library of helix-threading peptides. Results of these studies indicate their RNA binding is dependent on peptide sequence, alpha-amino acid stereochemistry, and cyclization (vs linear peptides), but independent of macrocyclic ring size for the penta-, tetra- and tri-peptides analyzed.
Collapse
Affiliation(s)
- Malathy Krishnamurthy
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | | | | |
Collapse
|
36
|
Jadlowsky JK, Nojima M, Schulte A, Geyer M, Okamoto T, Fujinaga K. Dominant negative mutant cyclin T1 proteins inhibit HIV transcription by specifically degrading Tat. Retrovirology 2008; 5:63. [PMID: 18620576 PMCID: PMC2492875 DOI: 10.1186/1742-4690-5-63] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 07/11/2008] [Indexed: 11/28/2022] Open
Abstract
Background The positive transcription elongation factor b (P-TEFb) is an essential cellular co-factor for the transcription of the human immunodeficiency virus type 1 (HIV-1). The cyclin T1 (CycT1) subunit of P-TEFb associates with a viral protein, Tat, at the transactivation response element (TAR). This represents a critical and necessary step for the stimulation of transcriptional elongation. Therefore, CycT1 may serve as a potential target for the development of anti-HIV therapies. Results To create effective inhibitors of HIV transcription, mutant CycT1 proteins were constructed based upon sequence similarities between CycT1 and other cyclin molecules, as well as the defined crystal structure of CycT1. One of these mutants, termed CycT1-U7, showed a potent dominant negative effect on Tat-dependent HIV transcription despite a remarkably low steady-state expression level. Surprisingly, the expression levels of Tat proteins co-expressed with CycT1-U7 were significantly lower than Tat co-expressed with wild type CycT1. However, the expression levels of CycT1-U7 and Tat were restored by treatment with proteasome inhibitors. Concomitantly, the dominant negative effect of CycT1-U7 was abolished by these inhibitors. Conclusion These results suggest that CycT1-U7 inhibits HIV transcription by promoting a rapid degradation of Tat. These mutant CycT1 proteins represent a novel class of specific inhibitors for HIV transcription that could potentially be used in the design of anti-viral therapy.
Collapse
Affiliation(s)
- Julie K Jadlowsky
- Division of Infectious Diseases, Department of Medicine, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
| | | | | | | | | | | |
Collapse
|
37
|
Wang H, Ghosh A, Baigude H, Yang CS, Qiu L, Xia X, Zhou H, Rana TM, Xu Z. Therapeutic gene silencing delivered by a chemically modified small interfering RNA against mutant SOD1 slows amyotrophic lateral sclerosis progression. J Biol Chem 2008; 283:15845-52. [PMID: 18367449 PMCID: PMC2414310 DOI: 10.1074/jbc.m800834200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 03/17/2008] [Indexed: 02/01/2023] Open
Abstract
Inherited neurodegenerative diseases, such as Huntington disease and subset of Alzheimer disease, Parkinson disease, and amyotrophic lateral sclerosis, are caused by the mutant genes that have gained undefined properties that harm cells in the nervous system, causing neurodegeneration and clinical phenotypes. Lowering the mutant gene expression is predicted to slow the disease progression and produce clinical benefit. Administration of small interfering RNA (siRNA) can silence specific genes. However, long term delivery of siRNA to silence the mutant genes, a requirement for treatment of these chronic central nervous system (CNS) diseases, remains a critical unsolved issue. Here we designed and tested a chemically stabilized siRNA against human Cu,Zn-superoxide dismutase (SOD1) in a mouse model for amyotrophic lateral sclerosis. We show that the modified siRNA has enhanced stability and retains siRNA activity. Administration of this siRNA at the disease onset by long term infusion into the CNS resulted in widespread distribution of this siRNA, knocked down the mutant SOD1 expression, slowed the disease progression, and extended the survival. These results bring RNA interference therapy one step closer to its clinical application for treatment of chronic, devastating, and fatal CNS disorders.
Collapse
Affiliation(s)
- Hongyan Wang
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Animesh Ghosh
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Huricha Baigude
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Chao-shun Yang
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Linghua Qiu
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Xugang Xia
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Hongxia Zhou
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Tariq M. Rana
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| | - Zuoshang Xu
- Department of Biochemistry and Molecular
Pharmacology, Chemical Biology Program,
Cell Biology, and
Neuroscience Program, University of Massachusetts
Medical School, Worcester, Massachusetts 01605
| |
Collapse
|
38
|
Guilbert C, James TL. Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. J Chem Inf Model 2008; 48:1257-68. [PMID: 18510306 DOI: 10.1021/ci8000327] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based drug design is now well-established for proteins as a key first step in the lengthy process of developing new drugs. In many ways, RNA may be a better target to treat disease than a protein because it is upstream in the translation pathway, so inhibiting a single mRNA molecule could prevent the production of thousands of protein gene products. Virtual screening is often the starting point for structure-based drug design. However, computational docking of a small molecule to RNA seems to be more challenging than that to protein due to the higher intrinsic flexibility and highly charged structure of RNA. Previous attempts at docking to RNA showed the need for a new approach. We present here a novel algorithm using molecular simulation techniques to account for both nucleic acid and ligand flexibility. In this approach, with both the ligand and the receptor permitted some flexibility, they can bind one another via an induced fit, as the flexible ligand probes the surface of the receptor. A possible ligand can explore a low-energy path at the surface of the receptor by carrying out energy minimization with root-mean-square-distance constraints. Our procedure was tested on 57 RNA complexes (33 crystal and 24 NMR structures); this is the largest data set to date to reproduce experimental RNA binding poses. With our procedure, the lowest-energy conformations reproduced the experimental binding poses within an atomic root-mean-square deviation of 2.5 A for 74% of tested complexes.
Collapse
Affiliation(s)
- Christophe Guilbert
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | | |
Collapse
|
39
|
Affiliation(s)
- Jason R Thomas
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61822, USA
| | | |
Collapse
|
40
|
Suhartono M, Weidlich M, Stein T, Karas M, Dürner G, Göbel MW. Synthesis of Non-Natural Aromatic α-Amino Acids by a Heck Reaction. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701124] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
41
|
Ludwig V, Krebs A, Stoll M, Dietrich U, Ferner J, Schwalbe H, Scheffer U, Dürner G, Göbel MW. Tripeptides from synthetic amino acids block the Tat-TAR association and slow down HIV spread in cell cultures. Chembiochem 2008; 8:1850-6. [PMID: 17886825 DOI: 10.1002/cbic.200700232] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Non-natural amino acids with aromatic or heteroaromatic side chains were incorporated into tripeptides of the general structure Arg-X-Arg and tested as ligands of the HIV RNA element TAR. Some of these compounds could compete efficiently with the association of TAR and Tat and downregulated a TAR-controlled reporter gene in HeLa cells. Peptide 7, which contains a 2-pyrimidinyl-alkyl chain, also inhibited the spread of HIV-1 in cell cultures. NMR studies of 7 bound to HIV-2-TAR gave evidence for contacts in the bulge region.
Collapse
Affiliation(s)
- Verena Ludwig
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Mao H, Thakur CS, Chattopadhyay S, Silverman RH, Gudkov A, Banerjee AK. Inhibition of human parainfluenza virus type 3 infection by novel small molecules. Antiviral Res 2007; 77:83-94. [PMID: 17964670 DOI: 10.1016/j.antiviral.2007.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 08/31/2007] [Accepted: 09/04/2007] [Indexed: 01/07/2023]
Abstract
Human parainfluenza virus type 3 (HPIV3) is an important respiratory tract pathogen of infants and children. There are no vaccines or antivirals currently approved for prevention or treatment of HPIV3 infection. Towards developing an antiviral therapy to combat HPIV3 infection, we have established a green fluorescent protein (GFP)-tagged HPIV3 infected-cell assay and used it for screening of a small molecule library obtained from ChemBridge Diver. Two novel small molecules (C5 and C7) which shared structural similarities were identified and their inhibitory effects on HPIV3 were confirmed in CV-1 and human lung epithelium A549 cells by plaque assay, Western blot and Northern blot analyses. C5 and C7 effectively prevented the cytopathic effect in cells infected with HPIV3, achieving IC(50) values of 2.36 microM and 0.08 microM, respectively, for infectious virus production. The inhibition appears to be at the primary transcriptional level of HPIV3 life cycle based on sequential time course test, binding and internalization assays, and finally by a minigenome transcription assay in cells as well as measuring viral transcripts in cells in the presence of anisomycin. Interestingly, vesicular stomatitis virus (VSV), another member of mononegavirales order, was also inhibited by these compounds, whereas poliovirus-a picornavirus was not. Use of these inhibitors has a strong potential to develop novel antiviral agents against this important human pathogen.
Collapse
Affiliation(s)
- Hongxia Mao
- Department of Molecular Genetics, Virology Section NN10, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | | | | | | | | | | |
Collapse
|
43
|
Agbottah ET, Traviss C, McArdle J, Karki S, St Laurent GC, Kumar A. Nuclear Factor 90(NF90) targeted to TAR RNA inhibits transcriptional activation of HIV-1. Retrovirology 2007; 4:41. [PMID: 17565699 PMCID: PMC1910605 DOI: 10.1186/1742-4690-4-41] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 06/12/2007] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Examination of host cell-based inhibitors of HIV-1 transcription may be important for attenuating viral replication. We describe properties of a cellular double-stranded RNA binding protein with intrinsic affinity for HIV-1 TAR RNA that interferes with Tat/TAR interaction and inhibits viral gene expression. RESULTS Utilizing TAR affinity fractionation, North-Western blotting, and mobility-shift assays, we show that the C-terminal variant of nuclear factor 90 (NF90ctv) with strong affinity for the TAR RNA, competes with Tat/TAR interaction in vitro. Analysis of the effect of NF90ctv-TAR RNA interaction in vivo showed significant inhibition of Tat-transactivation of HIV-1 LTR in cells expressing NF90ctv, as well as changes in histone H3 lysine-4 and lysine-9 methylation of HIV chromatin that are consistent with the epigenetic changes in transcriptionally repressed gene. CONCLUSION Structural integrity of the TAR element is crucial in HIV-1 gene expression. Our results show that perturbation Tat/TAR RNA interaction by the dsRNA binding protein is sufficient to inhibit transcriptional activation of HIV-1.
Collapse
Affiliation(s)
- Emmanuel T Agbottah
- Department of Biochemistry & Molecular Biology, School of Medicine, The George Washington University, Washington D.C. USA
| | - Christine Traviss
- Department of Biochemistry & Molecular Biology, School of Medicine, The George Washington University, Washington D.C. USA
| | - James McArdle
- Department of Biochemistry & Molecular Biology, School of Medicine, The George Washington University, Washington D.C. USA
| | - Sambhav Karki
- Department of Biochemistry & Molecular Biology, School of Medicine, The George Washington University, Washington D.C. USA
| | - Georges C St Laurent
- Department of Biochemistry & Molecular Biology, School of Medicine, The George Washington University, Washington D.C. USA
| | - Ajit Kumar
- Department of Biochemistry & Molecular Biology, School of Medicine, The George Washington University, Washington D.C. USA
| |
Collapse
|
44
|
Stevens M, Pollicita M, Pannecouque C, Verbeken E, Tabarrini O, Cecchetti V, Aquaro S, Perno CF, Fravolini A, De Clercq E, Schols D, Balzarini J. Novel in vivo model for the study of human immunodeficiency virus type 1 transcription inhibitors: evaluation of new 6-desfluoroquinolone derivatives. Antimicrob Agents Chemother 2007; 51:1407-13. [PMID: 17242146 PMCID: PMC1855509 DOI: 10.1128/aac.01251-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Two novel 6-desfluoroquinolone derivatives, HM-12 and HM-13, were evaluated for anti-human immunodeficiency virus (anti-HIV) activity in acutely, chronically, and latently HIV type 1 (HIV-1)-infected cell cultures and were found to behave as potent HIV-1 transcription inhibitors. In order to extend this result in vivo, we developed an artificial hu-SCID mouse model for HIV-1 latency based on SCID mice engrafted with latently HIV-1-infected promyelocytic OM-10.1 cells in which HIV-1 can be reactivated in vivo by the administration of human tumor necrosis factor alpha (hTNF-alpha). Treating these SCID mice with HM-12 or HM-13 prior to hTNF-alpha stimulation resulted in a pronounced suppressive effect on viral reactivation. Since both quinolone derivatives were able to inhibit the reactivation of HIV-1 from this artificial viral reservoir in vivo, we provide encouraging evidence for the use of quinolones in the control of HIV-1 infections.
Collapse
Affiliation(s)
- Miguel Stevens
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, and Division of Histopathology, University Hospitals, Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mayer M, Lang PT, Gerber S, Madrid PB, Pinto IG, Guy RK, James TL. Synthesis and testing of a focused phenothiazine library for binding to HIV-1 TAR RNA. ACTA ACUST UNITED AC 2006; 13:993-1000. [PMID: 16984889 DOI: 10.1016/j.chembiol.2006.07.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 07/12/2006] [Accepted: 07/25/2006] [Indexed: 11/25/2022]
Abstract
We have synthesized a series of phenothiazine derivatives, which were used to test the structure-activity relationship of binding to HIV-1 TAR RNA. Variations from our initial compound, 2-acetylphenothiazine, focused on two moieties: ring substitutions and n-alkyl substitutions. Binding characteristics were ascertained via NMR, principally by saturation transfer difference spectra of the ligand and imino proton resonance shifts of the RNA. Both ring and alkyl substitutions manifested NMR changes upon binding. In general, the active site, while somewhat flexible, has regions that can be capitalized for increased binding through van der Waals interactions and others that can be optimized for solubility in subsequent stages of development. However, binding can be nontrivially enhanced several-fold through optimization of van der Waals and hydrophilic sites of the scaffold.
Collapse
Affiliation(s)
- Moriz Mayer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Baba M. Recent status of HIV-1 gene expression inhibitors. Antiviral Res 2006; 71:301-6. [PMID: 16488488 DOI: 10.1016/j.antiviral.2006.01.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 01/12/2006] [Accepted: 01/13/2006] [Indexed: 11/16/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) gene expression and transcription is a crucial step in the viral replication cycle, which is considered to be a potential target for inhibition of HIV-1. Among the factors involved in this step, the cellular protein nuclear factor (NF)-kappaB is the most powerful inducer of HIV-1 gene expression. On the other hand, the viral protein Tat plays a central role in sustaining a high level of HIV-1 replication. Several compounds have been reported to selectively inhibit the functions of Tat and NF-kappaB. Tat inhibitors target either the Tat/TAR RNA interaction or the Tat cofactor cyclin-dependent kinase 9/cyclin T1. Antioxidants, protein kinase C inhibitors, and IkappaB kinase inhibitors are known to suppress the activation of NF-kappaB. Although some of the compounds inhibit HIV-1 replication in cell cultures at low concentrations, they also have considerable toxicity to the host cells. Considering the increase of treatment failure cases in highly active antiretroviral therapy due to the emergence of multidrug resistance, HIV-1 gene expression inhibitors should be extensively studied as alternative approach to effective anti-HIV-1 chemotherapy.
Collapse
Affiliation(s)
- Masanori Baba
- Division of Antiviral Chemotherapy, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan.
| |
Collapse
|
47
|
Stevens M, De Clercq E, Balzarini J. The regulation of HIV-1 transcription: molecular targets for chemotherapeutic intervention. Med Res Rev 2006; 26:595-625. [PMID: 16838299 PMCID: PMC7168390 DOI: 10.1002/med.20081] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The regulation of transcription of the human immunodeficiency virus (HIV) is a complex event that requires the cooperative action of both viral and cellular components. In latently infected resting CD4(+) T cells HIV-1 transcription seems to be repressed by deacetylation events mediated by histone deacetylases (HDACs). Upon reactivation of HIV-1 from latency, HDACs are displaced in response to the recruitment of histone acetyltransferases (HATs) by NF-kappaB or the viral transcriptional activator Tat and result in multiple acetylation events. Following chromatin remodeling of the viral promoter region, transcription is initiated and leads to the formation of the TAR element. The complex of Tat with p-TEFb then binds the loop structures of TAR RNA thereby positioning CDK9 to phosphorylate the cellular RNA polymerase II. The Tat-TAR-dependent phosphorylation of RNA polymerase II plays an important role in transcriptional elongation as well as in other post-transcriptional events. As such, targeting of Tat protein (and/or cellular cofactors) provide an interesting perspective for therapeutic intervention in the HIV replicative cycle and may afford lifetime control of the HIV infection.
Collapse
Affiliation(s)
- Miguel Stevens
- Rega Institute for Medical Research, Minderbroedersstraat 10, B‐3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Minderbroedersstraat 10, B‐3000 Leuven, Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research, Minderbroedersstraat 10, B‐3000 Leuven, Belgium
| |
Collapse
|
48
|
Ennifar E, Paillart JC, Bodlenner A, Walter P, Weibel JM, Aubertin AM, Pale P, Dumas P, Marquet R. Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell. Nucleic Acids Res 2006; 34:2328-39. [PMID: 16679451 PMCID: PMC1458285 DOI: 10.1093/nar/gkl317] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The kissing-loop complex that initiates dimerization of genomic RNA is crucial for Human Immunodeficiency Virus Type 1 (HIV-1) replication. We showed that owing to its strong similitude with the bacterial ribosomal A site it can be targeted by aminoglycosides. Here, we present its crystal structure in complex with neamine, ribostamycin, neomycin and lividomycin. These structures explain the specificity for 4,5-disubstituted 2-deoxystreptamine (DOS) derivatives and for subtype A and subtype F kissing-loop complexes, and provide a strong basis for rational drug design. As a consequence of the different topologies of the kissing-loop complex and the A site, these aminoglycosides establish more contacts with HIV-1 RNA than with 16S RNA. Together with biochemical experiments, they showed that while rings I, II and III confer binding specificity, rings IV and V are important for affinity. Binding of neomycin, paromomycin and lividomycin strongly stabilized the kissing-loop complex by bridging the two HIV-1 RNA molecules. Furthermore, in situ footprinting showed that the dimerization initiation site (DIS) of HIV-1 genomic RNA could be targeted by these aminoglycosides in infected cells and virions, demonstrating its accessibility.
Collapse
Affiliation(s)
- Eric Ennifar
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
| | - Jean-Christophe Paillart
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
| | - Anne Bodlenner
- UMR 7123 CNRS—Université Louis Pasteur, Institut Le Bel4 rue Blaise Pascal, BP 1032/F, 67070, Strasbourg cedex, France
| | - Philippe Walter
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
| | - Jean-Marc Weibel
- UMR 7123 CNRS—Université Louis Pasteur, Institut Le Bel4 rue Blaise Pascal, BP 1032/F, 67070, Strasbourg cedex, France
| | - Anne-Marie Aubertin
- UMR 544 INSERM—Université Louis Pasteur, Institut de Virologie3 rue Koberlé, 67000 Strasbourg, France
| | - Patrick Pale
- UMR 7123 CNRS—Université Louis Pasteur, Institut Le Bel4 rue Blaise Pascal, BP 1032/F, 67070, Strasbourg cedex, France
| | - Philippe Dumas
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
- To whom correspondence should be addressed. Tel: +33388417002; Fax: +33388602218;
| | - Roland Marquet
- UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur, IBMC15 rue René Descartes, 67084, Strasbourg cedex, France
- Correspondence may also be addressed to Roland Marquet. Tel: +33388417054; Fax: +33388602218;
| |
Collapse
|
49
|
Lee CW, Cao H, Ichiyama K, Rana TM. Design and synthesis of a novel peptidomimetic inhibitor of HIV-1 Tat–TAR interactions: Squaryldiamide as a new potential bioisostere of unsubstituted guanidine. Bioorg Med Chem Lett 2005; 15:4243-6. [PMID: 16054360 DOI: 10.1016/j.bmcl.2005.06.077] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 06/21/2005] [Accepted: 06/23/2005] [Indexed: 11/24/2022]
Abstract
By performing RNA-targeted structure-activity relationship studies, we discovered a novel peptidomimetic containing squaryldiamide as a potential bioisostere replacement for guanidine that binds transactivation responsive RNA with high affinity.
Collapse
Affiliation(s)
- Chi-Wan Lee
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-2324, USA
| | | | | | | |
Collapse
|
50
|
Nielsen MH, Pedersen FS, Kjems J. Molecular strategies to inhibit HIV-1 replication. Retrovirology 2005; 2:10. [PMID: 15715913 PMCID: PMC553987 DOI: 10.1186/1742-4690-2-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 02/16/2005] [Indexed: 11/10/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) is the primary cause of the acquired immunodeficiency syndrome (AIDS), which is a slow, progressive and degenerative disease of the human immune system. The pathogenesis of HIV-1 is complex and characterized by the interplay of both viral and host factors. An intense global research effort into understanding the individual steps of the viral replication cycle and the dynamics during an infection has inspired researchers in the development of a wide spectrum of antiviral strategies. Practically every stage in the viral life cycle and every viral gene product is a potential target. In addition, several strategies are targeting host proteins that play an essential role in the viral life cycle. This review summarizes the main genetic approaches taken in such antiviral strategies.
Collapse
Affiliation(s)
- Morten Hjuler Nielsen
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Alle, Bldg. 130, Room 404, DK-8000 Aarhus C, Denmark
| | - Finn Skou Pedersen
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Alle, Bldg. 130, Room 404, DK-8000 Aarhus C, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Alle, Bldg. 130, Room 404, DK-8000 Aarhus C, Denmark
| |
Collapse
|