51
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Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim HY, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker PJ, Smith GF, Nickbarg EB. Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry. ACS Chem Biol 2018; 13:820-831. [PMID: 29412640 DOI: 10.1021/acschembio.7b01013] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule-ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.
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Affiliation(s)
- Noreen F. Rizvi
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - John A. Howe
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ali Nahvi
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J. Klein
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Hai-Young Kim
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Mark A. McCoy
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Scott S. Walker
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Alan Hruza
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Chad Chamberlin
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Peter Saradjian
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Gabriel Mercado
- Biodesy, Inc., South San Francisco, California 94080, United States
| | - Julja Burchard
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | | | - Graham F. Smith
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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52
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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53
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Xiao Z, Shen J, Zhang L, Li M, Hu W, Cho C. Therapeutic targeting of noncoding RNAs in hepatocellular carcinoma: Recent progress and future prospects. Oncol Lett 2018; 15:3395-3402. [PMID: 29467864 PMCID: PMC5796293 DOI: 10.3892/ol.2018.7758] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Due to the high mortality rate and unsatisfactory treatment options available, hepatocellular carcinoma (HCC) remains one of the most common malignancies and a leading cause of cancer-associated mortality. Novel therapeutic targets for HCC are urgently required. Advanced RNA sequencing technology enables the identification of considerable amounts of noncoding RNAs (ncRNAs), including small noncoding RNAs and long noncoding RNAs, which exhibit no protein-coding activities. In this respect, ncRNAs and their regulatory processes are important factors in liver tumorigenesis. The present review focuses on the characteristics and biological roles of ncRNAs in HCC. Potential therapeutic applications of ncRNAs in HCC are also evaluated.
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Affiliation(s)
- Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Lin Zhang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Wei Hu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Chihin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China.,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
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54
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RNA as a small molecule druggable target. Bioorg Med Chem Lett 2017; 27:5083-5088. [PMID: 29097169 DOI: 10.1016/j.bmcl.2017.10.052] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/11/2017] [Accepted: 10/22/2017] [Indexed: 12/20/2022]
Abstract
Small molecule drugs have readily been developed against many proteins in the human proteome, but RNA has remained an elusive target for drug discovery. Increasingly, we see that RNA, and to a lesser extent DNA elements, show a persistent tertiary structure responsible for many diverse and complex cellular functions. In this digest, we have summarized recent advances in screening approaches for RNA targets and outlined the discovery of novel, drug-like small molecules against RNA targets from various classes and therapeutic areas. The link of structure, function, and small-molecule Druggability validates now for the first time that RNA can be the targets of therapeutic agents.
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55
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Yamamoto H, Unbehaun A, Spahn CMT. Ribosomal Chamber Music: Toward an Understanding of IRES Mechanisms. Trends Biochem Sci 2017; 42:655-668. [PMID: 28684008 DOI: 10.1016/j.tibs.2017.06.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 12/31/2022]
Abstract
Internal initiation is a 5'-end-independent mode of translation initiation engaged by many virus- and putatively some cell-encoded templates. Internal initiation is facilitated by specific RNA tertiary folds, called internal ribosomal entry sites (IRESs), in the 5' untranslated region (UTR) of the respective transcripts. In this review we discuss recent structural insight into how established IRESs first capture and then manipulate the eukaryotic translation machinery through non-canonical interactions and by guiding the intrinsic conformational flexibility of the eukaryotic ribosome. Because IRESs operate with reduced complexity and constitute minimal systems of initiation, comparison with canonical initiation may allow common mechanistic principles of the ribosome to be delineated.
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Affiliation(s)
- Hiroshi Yamamoto
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Medizinische Physik und Biophysik, Charitéplatz 1, 10117 Berlin, Germany
| | - Anett Unbehaun
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Medizinische Physik und Biophysik, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian M T Spahn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Medizinische Physik und Biophysik, Charitéplatz 1, 10117 Berlin, Germany.
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56
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Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan USA
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57
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Velagapudi SP, Luo Y, Tran T, Haniff HS, Nakai Y, Fallahi M, Martinez GJ, Childs-Disney JL, Disney MD. Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA. ACS CENTRAL SCIENCE 2017; 3:205-216. [PMID: 28386598 PMCID: PMC5364451 DOI: 10.1021/acscentsci.7b00009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 05/03/2023]
Abstract
RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yiling Luo
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Tuan Tran
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Hafeez S. Haniff
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yoshio Nakai
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Mohammad Fallahi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Gustavo J. Martinez
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Jessica L. Childs-Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Matthew D. Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
- E-mail:
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58
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Structure-Based Discovery of Small Molecules Binding to RNA. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_29] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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59
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Charrette BP, Boerneke MA, Hermann T. Ligand Optimization by Improving Shape Complementarity at a Hepatitis C Virus RNA Target. ACS Chem Biol 2016; 11:3263-3267. [PMID: 27775338 DOI: 10.1021/acschembio.6b00687] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Crystal structure analysis revealed key interactions of a 2-amino-benzimidazole viral translation inhibitor that captures an elongated conformation of an RNA switch target in the internal ribosome entry site (IRES) of hepatitis C virus (HCV). Here, we have designed and synthesized quinazoline derivatives with improved shape complementarity at the ligand binding site of the viral RNA target. A spiro-cyclopropyl modification aimed at filling a pocket in the back of the RNA binding site led to a 5-fold increase of ligand affinity while a slightly more voluminous dimethyl substitution at the same position did not improve binding. We demonstrate that precise shape complementarity based solely on hydrophobic interactions contributes significantly to ligand binding even at a hydrophilic RNA target site such as the HCV IRES conformational switch.
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Affiliation(s)
- Brian P. Charrette
- Department
of Chemistry and Biochemistry, University of California, San Diego,
9500 Gilman Drive, La Jolla, California 92093, United States
| | - Mark A. Boerneke
- Department
of Chemistry and Biochemistry, University of California, San Diego,
9500 Gilman Drive, La Jolla, California 92093, United States
| | - Thomas Hermann
- Department
of Chemistry and Biochemistry, University of California, San Diego,
9500 Gilman Drive, La Jolla, California 92093, United States
- Center
for Drug Discovery Innovation, University of California, San Diego,
9500 Gilman Drive, La Jolla, California 92093, United States
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60
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Connelly CM, Moon MH, Schneekloth JS. The Emerging Role of RNA as a Therapeutic Target for Small Molecules. Cell Chem Biol 2016; 23:1077-1090. [PMID: 27593111 PMCID: PMC5064864 DOI: 10.1016/j.chembiol.2016.05.021] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/07/2016] [Accepted: 05/18/2016] [Indexed: 01/09/2023]
Abstract
Recent advances in understanding different RNAs and unique features of their biology have revealed a wealth of information. However, approaches to identify small molecules that target these newly discovered regulatory elements have been lacking. The application of new biochemical screening and design-based technologies, coupled with a resurgence of interest in phenotypic screening, has resulted in several compelling successes in targeting RNA. A number of recent advances suggest that achieving the long-standing goal of developing drug-like, biologically active small molecules that target RNA is possible. This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.
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Affiliation(s)
- Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Michelle H Moon
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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61
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Jan E, Mohr I, Walsh D. A Cap-to-Tail Guide to mRNA Translation Strategies in Virus-Infected Cells. Annu Rev Virol 2016; 3:283-307. [PMID: 27501262 DOI: 10.1146/annurev-virology-100114-055014] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although viruses require cellular functions to replicate, their absolute dependence upon the host translation machinery to produce polypeptides indispensable for their reproduction is most conspicuous. Despite their incredible diversity, the mRNAs produced by all viruses must engage cellular ribosomes. This has proven to be anything but a passive process and has revealed a remarkable array of tactics for rapidly subverting control over and dominating cellular regulatory pathways that influence translation initiation, elongation, and termination. Besides enforcing viral mRNA translation, these processes profoundly impact host cell-intrinsic immune defenses at the ready to deny foreign mRNA access to ribosomes and block protein synthesis. Finally, genome size constraints have driven the evolution of resourceful strategies for maximizing viral coding capacity. Here, we review the amazing strategies that work to regulate translation in virus-infected cells, highlighting both virus-specific tactics and the tremendous insight they provide into fundamental translational control mechanisms in health and disease.
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Affiliation(s)
- Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada;
| | - Ian Mohr
- Department of Microbiology and New York University Cancer Institute, New York University School of Medicine, New York, NY 10016;
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611;
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62
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Hermann T. Small molecules targeting viral RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:726-743. [PMID: 27307213 PMCID: PMC7169885 DOI: 10.1002/wrna.1373] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 02/06/2023]
Abstract
Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug‐like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug‐like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA‐binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect‐borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726–743. doi: 10.1002/wrna.1373 This article is categorized under:
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
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Affiliation(s)
- Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Center for Drug Discovery Innovation, University of California, San Diego, La Jolla, CA, USA.
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63
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Abstract
Ligand-responsive RNA mechanical switches represent a new class of simple switching modules that adopt well-defined ligand-free and bound conformational states, distinguishing them from metabolite-sensing riboswitches. Initially discovered in the internal ribosome entry site (IRES) of hepatitis C virus (HCV), these RNA switch motifs were found in the genome of diverse other viruses. Although large variations are seen in sequence and local secondary structure of the switches, their function in viral translation initiation that requires selective ligand recognition is conserved. We recently determined the crystal structure of an RNA switch from Seneca Valley virus (SVV) which is able to functionally replace the switch of HCV. The switches from both viruses recognize identical cognate ligands despite their sequence dissimilarity. Here, we describe the discovery of 7 new switches in addition to the previously established 5 examples. We highlight structural and functional features unique to this class of ligand-responsive RNA mechanical switches and discuss implications for therapeutic development and the construction of RNA nanostructures.
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Key Words
- AEV, avian encephalomyelitis virus
- BDV, border disease virus
- BVDV, bovine viral diarrhea virus
- CSFV, classical swine fever virus
- DHV, Duck hepatitis virus
- DPV, duck picornavirus
- GBV, GB virus
- GPV, giraffe pestivirus
- HCV, hepatitis C virus
- IRES
- IRES, internal ribosome entry site
- IVT, in vitro translation
- NPHV, non-primate hepacivirus
- RNA switch
- SPV, simian picornavirus
- SVV, Seneca Valley virus
- conformational switch
- hepatitis C virus
- riboswitch
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Affiliation(s)
- Mark A Boerneke
- a Department of Chemistry and Biochemistry ; University of California, San Diego ; La Jolla , CA USA
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64
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Dibrov SM, Hermann T. Structure of the HCV Internal Ribosome Entry Site Subdomain IIa RNA in Complex with a Viral Translation Inhibitor. Methods Mol Biol 2016; 1320:329-35. [PMID: 26227053 DOI: 10.1007/978-1-4939-2763-0_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The internal ribosome entry site (IRES) in the 5' untranslated region (UTR) of the hepatitis C virus (HCV) RNA genome is responsible for initiation of viral protein synthesis. The IRES RNA contains autonomously folding domains that are potential targets for antiviral translation inhibitors. Here, we describe the experimental crystal structure determination of the IRES subdomain IIa in complex with a previously discovered benzimidazole translation inhibitor. The structure of an inhibitor complex of the highly conserved IRES subdomain IIa holds promise for structure-based design of new anti-HCV drugs.
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Affiliation(s)
- Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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65
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Han Li C, Chen Y. Small and Long Non-Coding RNAs: Novel Targets in Perspective Cancer Therapy. Curr Genomics 2016; 16:319-26. [PMID: 27047252 PMCID: PMC4763970 DOI: 10.2174/1389202916666150707155851] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/02/2015] [Accepted: 04/04/2015] [Indexed: 02/08/2023] Open
Abstract
Non-coding RNA refers to a large group of endogenous RNA molecules that have no protein coding capacity, while having specialized cellular and molecular functions. They possess wide range of functions such as the regulation of gene transcription and translation, post-transcriptional modification, epigenetic landscape establishment, protein scaffolding and cofactors recruitments. They are further divided into small non-coding RNAs with size < 200nt (e.g. miRNA, piRNA) and long non-coding RNAs with size >= 200nt (e.g. lincRNA, NAT). Increasing evidences suggest that both non-coding RNAs groups play important roles in cancer development, progression and pathology. Clinically, non-coding RNAs aberrations show high diagnostic and prognostic values. With improved understanding of the nature and roles of non-coding RNAs, it is believed that we can develop therapeutic treatment against cancer via the modulation of these RNA molecules. Advances in nucleic acid drug technology and computational simulation prompt the development of agents to intervene the malignant effects of non-coding RNAs. In this review, we will discuss the role of non-coding RNAs in cancer, and evaluate the potential of non-coding RNA-based cancer therapies.
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Affiliation(s)
- Chi Han Li
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong;; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China;; State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
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66
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Boerneke MA, Dibrov SM, Hermann T. Kristallstruktur-geleitetes Design selbstorganisierender RNA-Nanodreiecke. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mark A. Boerneke
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Sergey M. Dibrov
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
- Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
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67
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Boerneke MA, Dibrov SM, Hermann T. Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles. Angew Chem Int Ed Engl 2016; 55:4097-100. [PMID: 26914842 DOI: 10.1002/anie.201600233] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/25/2016] [Indexed: 12/11/2022]
Abstract
RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation.
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Affiliation(s)
- Mark A Boerneke
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. .,Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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68
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Lozano G, Trapote A, Ramajo J, Elduque X, Grandas A, Robles J, Pedroso E, Martínez-Salas E. Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation. RNA Biol 2016; 12:555-68. [PMID: 25775053 PMCID: PMC4615676 DOI: 10.1080/15476286.2015.1025190] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The internal ribosome entry site (IRES) element located at the 5'untranslated genomic region of various RNA viruses mediates cap-independent initiation of translation. Picornavirus IRES activity is highly dependent on both its structural organization and its interaction with host factors. Small molecules able to interfere with RNA function are valuable candidates for antiviral agents. Here we show that a small molecule based on benzimidazole (IRAB) inhibited foot-and-mouth disease virus (FMDV) IRES-dependent protein synthesis in cells transfected with infectious RNA leading to a decrease of the virus titer, which was higher than that induced by a structurally related benzimidazole derivative. Interestingly, IRAB preferentially inhibited IRES-dependent translation in cell free systems in a dose-dependent manner. RNA structural analysis by SHAPE demonstrated an increased local flexibility of the IRES structure upon incubation with IRAB, which affected 3 stem-loops (SL) of domain 3. Fluorescence binding assays conducted with individual aminopurine-labeled oligoribonucleotides indicated that the SL3A binds IRAB (EC50 18 μM). Taken together, the results derived from SHAPE reactivity and fluorescence binding assays suggested that the target site of IRAB within the FMDV IRES might be a folded RNA structure that involves the entire apical region of domain 3. Our data suggest that the conformational changes induced by this compound on a specific region of the IRES structure which is essential for its activity is, at least in part, responsible for the reduced IRES efficiency observed in cell free lysates and, particularly, in RNA-transfected cells.
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Affiliation(s)
- Gloria Lozano
- a Centro de Biología Molecular Severo Ochoa; CSIC-UAM; Madrid , Spain
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69
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Henley RY, Carson S, Wanunu M. Studies of RNA Sequence and Structure Using Nanopores. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 139:73-99. [PMID: 26970191 DOI: 10.1016/bs.pmbts.2015.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards to RNA sequencing, microRNA detection, RNA/ligand interactions, and RNA structural/conformational analysis.
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Affiliation(s)
- Robert Y Henley
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts, USA; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA.
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70
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Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nat Commun 2015; 6:8898. [PMID: 26638992 PMCID: PMC4686816 DOI: 10.1038/ncomms9898] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 10/07/2015] [Indexed: 01/22/2023] Open
Abstract
The structure and biological properties of RNAs are a function of changing cellular conditions, but comprehensive, simultaneous investigation of the effect of multiple interacting environmental variables is not easily achieved. We have developed an efficient, high-throughput method to characterize RNA structure and thermodynamic stability as a function of multiplexed solution conditions using Förster resonance energy transfer (FRET). In a single FRET experiment using conventional quantitative PCR instrumentation, 19,400 conditions of MgCl2, ligand and temperature are analysed to generate detailed empirical conformational and stability landscapes of the cyclic diguanylate (c-di-GMP) riboswitch. The method allows rapid comparison of RNA structure modulation by cognate and non-cognate ligands. Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. This demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules. The structure and biological properties of RNAs are a function of changing cellular conditions. Here, Baird et al. report a high-throughput Förster resonance energy transfer (FRET) method to rapidly compare RNA structure modulation by cognate and non-cognate ligands across multiplexed solution conditions.
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71
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Qi L, Huo Y, Wang H, Zhang J, Dang FQ, Zhang ZQ. Fluorescent DNA-Protected Silver Nanoclusters for Ligand-HIV RNA Interaction Assay. Anal Chem 2015; 87:11078-83. [PMID: 26447651 DOI: 10.1021/acs.analchem.5b03166] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Studying ligand-biomacromolecule interactions provides opportunities for creating new compounds that can efficiently regulate specific biological processes. Ribonucleic acid (RNA) molecules have become attractive drug targets since the discovery of their roles in modulating gene expression, while only a limited number of studies have investigated interactions between ligands and functional RNA molecules, especially those based on nanotechnology. DNA-protected silver nanoclusters (AgNCs) were used to investigate ligand-RNA interactions for the first time in this study. The anthracycline anticancer drug mitoxantrone (MTX) was found to quench the fluorescence of AgNCs. After adding human immunodeficiency virus trans-activation responsive region (TAR) RNA or Rev-response element (RRE) RNA to AgNCs-MTX mixtures, the fluorescence of the AgNCs recovered due to interactions between MTX with RNAs. The binding constants and number of binding sites of MTX to TAR and RRE RNA were determined through theoretical calculations. MTX-RNA interactions were further confirmed in fluorescence polarization and mass spectrometry experiments. The mechanism of MTX-based fluorescence quenching of the AgNCs was also explored. This study provides a new strategy for ligand-RNA binding interaction assay.
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, 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, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Huan Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Fu-Quan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, 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, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
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72
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Conformational flexibility of viral RNA switches studied by FRET. Methods 2015; 91:35-39. [PMID: 26381686 DOI: 10.1016/j.ymeth.2015.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
The function of RNA switches involved in the regulation of transcription and translation relies on their ability to adopt different, structurally well-defined states. A new class of ligand-responsive RNA switches, which we recently discovered in positive strand RNA viruses, are distinct from conventional riboswitches. The viral switches undergo large conformational changes in response to ligand binding while retaining the same secondary structure in their free and ligand-bound forms. Here, we describe FRET experiments to study folding and ligand binding of the viral RNA switches. In addition to reviewing previous approaches involving RNA model constructs which were directly conjugated with fluorescent dyes, we outline the design and application of new modular constructs for FRET experiments, in which dye labeling is achieved by hybridization of a core RNA switch module with universal DNA fluorescent probes. As an example, folding and ligand binding of the RNA switch from the internal ribosome entry site of hepatitis C virus is studied comparatively with conventional and modular FRET constructs.
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73
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Velagapudi SP, Vummidi BR, Disney MD. Small molecule chemical probes of microRNA function. Curr Opin Chem Biol 2014; 24:97-103. [PMID: 25500006 DOI: 10.1016/j.cbpa.2014.10.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/27/2014] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as progress is made in understanding small molecule recognition of RNA.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458, United States
| | - Balayeshwanth R Vummidi
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, FL 33458, United States.
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74
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Fragment based search for small molecule inhibitors of HIV-1 Tat-TAR. Bioorg Med Chem Lett 2014; 24:5576-5580. [DOI: 10.1016/j.bmcl.2014.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/28/2014] [Accepted: 11/01/2014] [Indexed: 01/06/2023]
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75
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Boerneke MA, Dibrov SM, Gu J, Wyles DL, Hermann T. Functional conservation despite structural divergence in ligand-responsive RNA switches. Proc Natl Acad Sci U S A 2014; 111:15952-7. [PMID: 25349403 PMCID: PMC4234586 DOI: 10.1073/pnas.1414678111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An internal ribosome entry site (IRES) initiates protein synthesis in RNA viruses, including the hepatitis C virus (HCV). We have discovered ligand-responsive conformational switches in viral IRES elements. Modular RNA motifs of greatly distinct sequence and local secondary structure have been found to serve as functionally conserved switches involved in viral IRES-driven translation and may be captured by identical cognate ligands. The RNA motifs described here constitute a new paradigm for ligand-captured switches that differ from metabolite-sensing riboswitches with regard to their small size, as well as the intrinsic stability and structural definition of the constitutive conformational states. These viral RNA modules represent the simplest form of ligand-responsive mechanical switches in nucleic acids.
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Affiliation(s)
| | | | - Jing Gu
- Department of Chemistry and Biochemistry
| | - David L Wyles
- Division of Infectious Diseases, Department of Medicine, and
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, La Jolla, CA 92093
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76
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Ohlmann T, Mengardi C, López-Lastra M. Translation initiation of the HIV-1 mRNA. ACTA ACUST UNITED AC 2014; 2:e960242. [PMID: 26779410 DOI: 10.4161/2169074x.2014.960242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/23/2014] [Accepted: 06/17/2014] [Indexed: 12/17/2022]
Abstract
Translation initiation of the full-length mRNA of the human immunodeficiency virus can occur via several different mechanisms to maintain production of viral structural proteins throughout the replication cycle. HIV-1 viral protein synthesis can occur by the use of both a cap-dependant and IRES-driven mechanism depending on the physiological conditions of the cell and the status of the ongoing infection. For both of these mechanisms there is a need for several viral and cellular co-factors for optimal translation of the viral mRNA. In this review we will describe the mechanism used by the full-length mRNA to initiate translation highlighting the role of co-factors within this process. A particular emphasis will be given to the role of the DDX3 RNA helicase in HIV-1 mRNA translation initiation.
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Affiliation(s)
- Théophile Ohlmann
- CIRI; International Center for Infectiology Research; Université de Lyon; Lyon, France; Inserm; Lyon, France; Ecole Normale Supérieure de Lyon; Lyon, France; Université Lyon 1; Center International de Recherche en Infectiologie; Lyon, France; CNRS; Lyon, France
| | - Chloé Mengardi
- CIRI; International Center for Infectiology Research; Université de Lyon; Lyon, France; Inserm; Lyon, France; Ecole Normale Supérieure de Lyon; Lyon, France; Université Lyon 1; Center International de Recherche en Infectiologie; Lyon, France; CNRS; Lyon, France
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular; Instituto Milenio de Inmunología e Inmunoterapia; Centro de Investigaciones Médicas; Escuela de Medicina; Pontificia Universidad Católica de Chile ; Santiago, Chile
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77
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Khawaja A, Vopalensky V, Pospisek M. Understanding the potential of hepatitis C virus internal ribosome entry site domains to modulate translation initiation via their structure and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:211-24. [PMID: 25352252 PMCID: PMC4361049 DOI: 10.1002/wrna.1268] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/31/2014] [Accepted: 09/02/2014] [Indexed: 12/16/2022]
Abstract
Translation initiation in the hepatitis C virus (HCV) occurs through a cap-independent mechanism that involves an internal ribosome entry site (IRES) capable of interacting with and utilizing the eukaryotic translational machinery. In this review, we focus on the structural configuration of the different HCV IRES domains and the impact of IRES primary sequence variations on secondary structure conservation and function. In some cases, multiple mutations, even those scattered across different domains, led to restoration of the translational activity of the HCV IRES, although the individual occurrences of these mutations were found to be deleterious. We propose that such observation may be attributed to probable long-range inter- and/or intra-domain functional interactions. The precise functioning of the HCV IRES requires the specific interaction of its domains with ribosomal subunits and a subset of eukaryotic translation initiation factors (eIFs). The structural conformation, sequence preservation and variability, and translational machinery association with the HCV IRES regions are also thoroughly discussed, along with other factors that can affect and influence the formation of translation initiation complexes. WIREs RNA 2015, 6:211–224. doi: 10.1002/wrna.1268
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Affiliation(s)
- Anas Khawaja
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
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78
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Ding K, Wang A, Boerneke MA, Dibrov SM, Hermann T. Aryl-substituted aminobenzimidazoles targeting the hepatitis C virus internal ribosome entry site. Bioorg Med Chem Lett 2014; 24:3113-7. [PMID: 24856063 PMCID: PMC4096041 DOI: 10.1016/j.bmcl.2014.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 02/07/2023]
Abstract
We describe the exploration of N1-aryl-substituted benzimidazoles as ligands for the hepatitis C virus (HCV) internal ribosome entry site (IRES) RNA. The design of the compounds was guided by the co-crystal structure of a benzimidazole viral translation inhibitor in complex with the RNA target. Structure-binding activity relationships of aryl-substituted benzimidazole ligands were established that were consistent with the crystal structure of the translation inhibitor complex.
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Affiliation(s)
- Kejia Ding
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Annie Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Mark A Boerneke
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States.
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79
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Shasha C, Henley RY, Stoloff DH, Rynearson KD, Hermann T, Wanunu M. Nanopore-based conformational analysis of a viral RNA drug target. ACS NANO 2014; 8:6425-6430. [PMID: 24861167 PMCID: PMC4729693 DOI: 10.1021/nn501969r] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nanopores are single-molecule sensors that show exceptional promise as a biomolecular analysis tool by enabling label-free detection of small amounts of sample. In this paper, we demonstrate that nanopores are capable of detecting the conformation of an antiviral RNA drug target. The hepatitis C virus uses an internal ribosome entry site (IRES) motif in order to initiate translation by docking to ribosomes in its host cell. The IRES is therefore a viable and important drug target. Drug-induced changes to the conformation of the HCV IRES motif, from a bent to a straight conformation, have been shown to inhibit HCV replication. However, there is presently no straightforward method to analyze the effect of candidate small-molecule drugs on the RNA conformation. In this paper, we show that RNA translocation dynamics through a 3 nm diameter nanopore is conformation-sensitive by demonstrating a difference in transport times between bent and straight conformations of a short viral RNA motif. Detection is possible because bent RNA is stalled in the 3 nm pore, resulting in longer molecular dwell times than straight RNA. Control experiments show that binding of a weaker drug does not produce a conformational change, as consistent with independent fluorescence measurements. Nanopore measurements of RNA conformation can thus be useful for probing the structure of various RNA motifs, as well as structural changes to the RNA upon small-molecule binding.
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Affiliation(s)
- Carolyn Shasha
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniel H. Stoloff
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kevin D. Rynearson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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80
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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.
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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
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81
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Tanpure AA, Srivatsan SG. Synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue based on the Lucifer chromophore. Chembiochem 2014; 15:1309-16. [PMID: 24861713 DOI: 10.1002/cbic.201402052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/10/2022]
Abstract
The majority of fluorescent nucleoside analogues used in nucleic acid studies have excitation maxima in the UV region and show very low fluorescence within oligonucleotides (ONs); hence, they cannot be utilised with certain fluorescence methods and for cell-based analysis. Here, we describe the synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue, derived by attaching a Lucifer chromophore (1,8-naphthalimide core) at the 5-position of uracil. The emissive nucleoside displays excitation and emission maxima in the visible region and exhibits high quantum yield. Importantly, when incorporated into ON duplexes it retains appreciable fluorescence efficiency and is sensitive to the neighbouring base environment. Notably, the nucleoside signals the presence of purine repeats in ON duplexes with an enhancement in fluorescence intensity, a property rarely displayed by other nucleoside analogues.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008 (India)
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82
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Windisch MP, Jo S, Kim HY, Kim SH, Kim K, Kong S, Jeong H, Ahn S, No Z, Hwang JY. Discovery of 2-iminobenzimidazoles as potent hepatitis C virus inhibitors with a novel mechanism of action. Eur J Med Chem 2014; 78:35-42. [DOI: 10.1016/j.ejmech.2014.03.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/11/2014] [Accepted: 03/11/2014] [Indexed: 01/29/2023]
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83
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Chan SW. Establishment of chronic hepatitis C virus infection: Translational evasion of oxidative defence. World J Gastroenterol 2014; 20:2785-2800. [PMID: 24659872 PMCID: PMC3961964 DOI: 10.3748/wjg.v20.i11.2785] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/03/2013] [Accepted: 01/15/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) causes a clinically important disease affecting 3% of the world population. HCV is a single-stranded, positive-sense RNA virus belonging to the genus Hepacivirus within the Flaviviridae family. The virus establishes a chronic infection in the face of an active host oxidative defence, thus adaptation to oxidative stress is key to virus survival. Being a small RNA virus with a limited genomic capacity, we speculate that HCV deploys a different strategy to evade host oxidative defence. Instead of counteracting oxidative stress, it utilizes oxidative stress to facilitate its own survival. Translation is the first step in the replication of a plus strand RNA virus so it would make sense if the virus can exploit the host oxidative defence in facilitating this very first step. This is particularly true when HCV utilizes an internal ribosome entry site element in translation, which is distinctive from that of cap-dependent translation of the vast majority of cellular genes, thus allowing selective translation of genes under conditions when global protein synthesis is compromised. Indeed, we were the first to show that HCV translation was stimulated by an important pro-oxidant-hydrogen peroxide in hepatocytes, suggesting that HCV is able to adapt to and utilize the host anti-viral response to facilitate its own translation thus allowing the virus to thrive under oxidative stress condition to establish chronicity. Understanding how HCV translation is regulated under oxidative stress condition will advance our knowledge on how HCV establishes chronicity. As chronicity is the initiator step in disease progression this will eventually lead to a better understanding of pathogenicity, which is particularly relevant to the development of anti-virals and improved treatments of HCV patients using anti-oxidants.
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84
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Velagapudi SP, Gallo SM, Disney MD. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol 2014; 10:291-7. [PMID: 24509821 PMCID: PMC3962094 DOI: 10.1038/nchembio.1452] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 12/17/2013] [Indexed: 12/17/2022]
Abstract
Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide.
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Affiliation(s)
- Sai Pradeep Velagapudi
- 1] Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA. [2] The Department of Chemistry, The University at Buffalo, Buffalo, New York, USA
| | - Steven M Gallo
- The New York State Center of Excellence in Bioinformatics and Life Sciences, The University at Buffalo, Buffalo, New York, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA
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85
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Bell NM, L'Hernault A, Murat P, Richards JE, Lever AML, Balasubramanian S. Targeting RNA-protein interactions within the human immunodeficiency virus type 1 lifecycle. Biochemistry 2013; 52:9269-74. [PMID: 24358934 PMCID: PMC3928988 DOI: 10.1021/bi401270d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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RNA–protein
interactions are vital throughout the HIV-1
life cycle for the successful production of infectious virus particles.
One such essential RNA–protein interaction occurs between the
full-length genomic viral RNA and the major structural protein of
the virus. The initial interaction is between the Gag polyprotein
and the viral RNA packaging signal (psi or Ψ), a highly conserved
RNA structural element within the 5′-UTR of the HIV-1 genome,
which has gained attention as a potential therapeutic target. Here,
we report the application of a target-based assay to identify small
molecules, which modulate the interaction between Gag and Ψ.
We then demonstrate that one such molecule exhibits potent inhibitory
activity in a viral replication assay. The mode of binding of the
lead molecules to the RNA target was characterized by 1H NMR spectroscopy.
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Affiliation(s)
- Neil M Bell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K
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86
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Pawar MG, Srivatsan SG. Environment-responsive fluorescent nucleoside analogue probe for studying oligonucleotide dynamics in a model cell-like compartment. J Phys Chem B 2013; 117:14273-82. [PMID: 24161106 DOI: 10.1021/jp4071168] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of fluorescent nucleoside analogue probes that have been used in the in vitro study of nucleic acids are not suitable for cell-based biophysical assays because they exhibit excitation maxima in the UV region and low quantum yields within oligonucleotides. Therefore, we propose that the photophysical characterization of oligonucleotides labeled with a fluorescent nucleoside analogue in reverse micelles (RM), which are good biological membrane models and UV-transparent, could provide an alternative approach to studying the properties of nucleic acids in a cell-like confined environment. In this context, we describe the photophysical properties of an environment-sensitive fluorescent uridine analogue (1), based on the 5-(benzo[b]thiophen-2-yl)pyrimidine core, in micelles and RM. The emissive nucleoside, which is polarity- and viscosity-sensitive, reports the environment of the surfactant assemblies via changes in its fluorescence properties. The nucleoside analogue, incorporated into an RNA oligonucleotide and hybridized to its complementary DNA and RNA oligonucleotides, exhibits a significantly higher fluorescence intensity, lifetime, and anisotropy in RM than in aqueous buffer, which is consistent with the environment of RM. Collectively, our results demonstrate that nucleoside 1 could be utilized as a fluorescent label to study the function of nucleic acids in a model cellular milieu.
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Affiliation(s)
- Maroti G Pawar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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87
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Dibrov SM, Parsons J, Carnevali M, Zhou S, Rynearson KD, Ding K, Garcia Sega E, Brunn ND, Boerneke MA, Castaldi MP, Hermann T. Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site. J Med Chem 2013; 57:1694-707. [PMID: 24138284 DOI: 10.1021/jm401312n] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The internal ribosome entry site (IRES) in the 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome initiates translation of the viral polyprotein precursor. The unique structure and high sequence conservation of the 5' UTR render the IRES RNA a potential target for the development of selective viral translation inhibitors. Here, we provide an overview of approaches to block HCV IRES function by nucleic acid, peptide, and small molecule ligands. Emphasis will be given to the IRES subdomain IIa, which currently is the most advanced target for small molecule inhibitors of HCV translation. The subdomain IIa behaves as an RNA conformational switch. Selective ligands act as translation inhibitors by locking the conformation of the RNA switch. We review synthetic procedures for inhibitors as well as structural and functional studies of the subdomain IIa target and its ligand complexes.
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Affiliation(s)
- Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
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88
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Romero-López C, Berzal-Herranz A. Unmasking the information encoded as structural motifs of viral RNA genomes: a potential antiviral target. Rev Med Virol 2013; 23:340-54. [PMID: 23983005 PMCID: PMC7169113 DOI: 10.1002/rmv.1756] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 02/05/2023]
Abstract
RNA viruses show enormous capacity to evolve and adapt to new cellular and molecular contexts, a consequence of mutations arising from errors made by viral RNA-dependent RNA polymerase during replication. Sequence variation must occur, however, without compromising functions essential for the completion of the viral cycle. RNA viruses are safeguarded in this respect by their genome carrying conserved information that does not code only for proteins but also for the formation of structurally conserved RNA domains that directly perform these critical functions. Functional RNA domains can interact with other regions of the viral genome and/or proteins to direct viral translation, replication and encapsidation. They are therefore potential targets for novel therapeutic strategies. This review summarises our knowledge of the functional RNA domains of human RNA viruses and examines the achievements made in the design of antiviral compounds that interfere with their folding and therefore their function.
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Affiliation(s)
- Cristina Romero-López
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, PTS Granada, Armilla, Granada, Spain
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89
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Li CH, Chen Y. Targeting long non-coding RNAs in cancers: Progress and prospects. Int J Biochem Cell Biol 2013; 45:1895-910. [DOI: 10.1016/j.biocel.2013.05.030] [Citation(s) in RCA: 344] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 02/07/2023]
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90
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Dibrov SM, Parker MA, Bergdahl BM, Hermann T. Crystal structure of a benzimidazole hepatitis C virus inhibitor free and in complex with the viral RNA target. JOURNAL OF CHEMICAL CRYSTALLOGRAPHY 2013; 43:235-239. [PMID: 23750099 PMCID: PMC3673731 DOI: 10.1007/s10870-013-0410-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The crystal structure of 8-((dimethylamino)methyl)-1-(3-(dimethylamino)propyl)-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine (1), an inhibitor of the hepatitis C virus internal ribosome entry site, is described and compared to the structure of the compound in complex with the viral RNA target. Compound 1 crystallized by pentane vapor diffusion into dichloroethane solution. It crystallized in the monoclinic system, P21/c space group with unit cell parameters a = 15.7950(5) Å, b = 14.0128(4) Å, c = 8.8147(3) Å, β = 94.357(2)° and a cell volume of 1945.34(11) A-3. Packing interactions in the small molecule crystal lattice correspond to key interactions of the compound with the viral RNA target.
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Affiliation(s)
- Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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91
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Screening for inhibitors of the hepatitis C virus internal ribosome entry site RNA. Bioorg Med Chem 2013; 21:6139-44. [PMID: 23602522 DOI: 10.1016/j.bmc.2013.03.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/21/2013] [Indexed: 01/09/2023]
Abstract
The highly conserved internal ribosome entry site (IRES) of hepatitis C virus (HCV) regulates translation of the viral RNA genome and is essential for the expression of HCV proteins in infected host cells. The structured subdomain IIa of the IRES element is the target site of recently discovered benzimidazole inhibitors that selectively block viral translation through capture of an extended conformation of an RNA internal loop. Here, we describe the development of a FRET-based screening assay for similarly acting HCV translation inhibitors. The assay relies on monitoring fluorescence changes that indicate rearrangement of the RNA target conformation upon ligand binding. Screening of a small pilot set of potential RNA binders identified a benzoxazole scaffold as a ligand that bound selectively to IIa IRES target and was confirmed as an inhibitor of in vitro viral translation. The screening approach outlined here provides an efficient method to discover HCV translation inhibitors that may provide leads for the development of novel antiviral therapies directed at the highly conserved IRES RNA.
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92
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Walsh D, Mathews MB, Mohr I. Tinkering with translation: protein synthesis in virus-infected cells. Cold Spring Harb Perspect Biol 2013; 5:a012351. [PMID: 23209131 DOI: 10.1101/cshperspect.a012351] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Viruses are obligate intracellular parasites, and their replication requires host cell functions. Although the size, composition, complexity, and functions encoded by their genomes are remarkably diverse, all viruses rely absolutely on the protein synthesis machinery of their host cells. Lacking their own translational apparatus, they must recruit cellular ribosomes in order to translate viral mRNAs and produce the protein products required for their replication. In addition, there are other constraints on viral protein production. Crucially, host innate defenses and stress responses capable of inactivating the translation machinery must be effectively neutralized. Furthermore, the limited coding capacity of the viral genome needs to be used optimally. These demands have resulted in complex interactions between virus and host that exploit ostensibly virus-specific mechanisms and, at the same time, illuminate the functioning of the cellular protein synthesis apparatus.
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Affiliation(s)
- Derek Walsh
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
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93
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Piñeiro D, Martinez-Salas E. RNA structural elements of hepatitis C virus controlling viral RNA translation and the implications for viral pathogenesis. Viruses 2012. [PMID: 23202462 PMCID: PMC3497050 DOI: 10.3390/v4102233] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) genome multiplication requires the concerted action of the viral RNA, host factors and viral proteins. Recent studies have provided information about the requirement of specific viral RNA motifs that play an active role in the viral life cycle. RNA regulatory motifs controlling translation and replication of the viral RNA are mostly found at the 5' and 3' untranslated regions (UTRs). In particular, viral protein synthesis is under the control of the internal ribosome entry site (IRES) element, a complex RNA structure located at the 5'UTR that recruits the ribosomal subunits to the initiator codon. Accordingly, interfering with this RNA structural motif causes the abrogation of the viral cycle. In addition, RNA translation initiation is modulated by cellular factors, including miRNAs and RNA-binding proteins. Interestingly, a RNA structural motif located at the 3'end controls viral replication and establishes long-range RNA-RNA interactions with the 5'UTR, generating functional bridges between both ends on the viral genome. In this article, we review recent advances on virus-host interaction and translation control modulating viral gene expression in infected cells.
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Affiliation(s)
- David Piñeiro
- Centro de Biología Molecular Severo Ochoa, Nicolas Cabrera, 1, Cantoblanco, 28049 Madrid, Spain.
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94
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Chen L, Calin GA, Zhang S. Novel insights of structure-based modeling for RNA-targeted drug discovery. J Chem Inf Model 2012; 52:2741-53. [PMID: 22947071 DOI: 10.1021/ci300320t] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Substantial progress in RNA biology highlights the importance of RNAs (e.g., microRNAs) in diseases and the potential of targeting RNAs for drug discovery. However, the lack of RNA-specific modeling techniques demands the development of new tools for RNA-targeted rational drug design. Herein, we implemented integrated approaches of accurate RNA modeling and virtual screening for RNA inhibitor discovery with the most comprehensive evaluation to date of five docking and 11 scoring methods. For the first time, statistical analysis was heavily employed to assess the significance of our predictions. We found that GOLD:GOLD Fitness and rDock:rDock_solv could accurately predict the RNA ligand poses, and ASP rescoring further improved the ranking of ligand binding poses. Due to the weak correlations (R(2) < 0.3) of existing scoring with experimental binding affinities, we implemented two new RNA-specific scoring functions, iMDLScore1 and iMDLScore2, and obtained better correlations with R(2) = 0.70 and 0.79, respectively. We also proposed a multistep virtual screening approach and demonstrated that rDock:rDock_solv together with iMDLScore2 rescoring obtained the best enrichment on the flexible RNA targets, whereas GOLD:GOLD Fitness combined with rDock_solv rescoring outperformed other methods for rigid RNAs. This study provided practical strategies for RNA modeling and offered new insights into RNA-small molecule interactions for drug discovery.
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Affiliation(s)
- Lu Chen
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, 1901 East Road, Houston Texas 77054, USA
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95
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Chenoweth DM, Meier JL, Dervan PB. Pyrrole-imidazole polyamides distinguish between double-helical DNA and RNA. Angew Chem Int Ed Engl 2012; 52:415-8. [PMID: 22987334 DOI: 10.1002/anie.201205775] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Indexed: 12/14/2022]
Abstract
Groove specificity: pyrrole-imidazole polyamides are well-known for their specific interactions with the minor groove of DNA. However, polyamides do not show similar binding to duplex RNA, and a structural rationale for the molecular-level discrimination of nucleic acid duplexes by minor-groove-binding ligands is presented.
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Affiliation(s)
- David M Chenoweth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, 91125, USA
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96
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Chenoweth DM, Meier JL, Dervan PB. Pyrrole-Imidazole Polyamides Distinguish Between Double-Helical DNA and RNA. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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97
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Lombès T, Moumné R, Larue V, Prost E, Catala M, Lecourt T, Dardel F, Micouin L, Tisné C. Investigation of RNA-Ligand Interactions by 19F NMR Spectroscopy Using Fluorinated Probes. Angew Chem Int Ed Engl 2012; 51:9530-4. [DOI: 10.1002/anie.201204083] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 01/08/2023]
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98
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Lombès T, Moumné R, Larue V, Prost E, Catala M, Lecourt T, Dardel F, Micouin L, Tisné C. Investigation of RNA-Ligand Interactions by 19F NMR Spectroscopy Using Fluorinated Probes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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99
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Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches. Proc Natl Acad Sci U S A 2012; 109:5223-8. [PMID: 22431596 DOI: 10.1073/pnas.1118699109] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The internal ribosome entry site (IRES) in the hepatitis C virus (HCV) RNA genome is essential for the initiation of viral protein synthesis. IRES domains adopt well-defined folds that are potential targets for antiviral translation inhibitors. We have determined the three-dimensional structure of the IRES subdomain IIa in complex with a benzimidazole translation inhibitor at 2.2 Å resolution. Comparison to the structure of the unbound RNA in conjunction with studies of inhibitor binding to the target in solution demonstrate that the RNA undergoes a dramatic ligand-induced conformational adaptation to form a deep pocket that resembles the substrate binding sites in riboswitches. The presence of a well-defined ligand-binding pocket within the highly conserved IRES subdomain IIa holds promise for the development of unique anti-HCV drugs with a high barrier to resistance.
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100
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Abstract
RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void.
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Affiliation(s)
- Lirui Guan
- Department of Chemistry, The Kellogg School of Science
and Technology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458,
United States
| | - Matthew D. Disney
- Department of Chemistry, The Kellogg School of Science
and Technology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458,
United States
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