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Bagnolini G, Luu TB, Hargrove AE. Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA. RNA (NEW YORK, N.Y.) 2023; 29:473-488. [PMID: 36693763 PMCID: PMC10019373 DOI: 10.1261/rna.079497.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA structures regulate a wide range of processes in biology and disease, yet small molecule chemical probes or drugs that can modulate these functions are rare. Machine learning and other computational methods are well poised to fill gaps in knowledge and overcome the inherent challenges in RNA targeting, such as the dynamic nature of RNA and the difficulty of obtaining RNA high-resolution structures. Successful tools to date include principal component analysis, linear discriminate analysis, k-nearest neighbor, artificial neural networks, multiple linear regression, and many others. Employment of these tools has revealed critical factors for selective recognition in RNA:small molecule complexes, predictable differences in RNA- and protein-binding ligands, and quantitative structure activity relationships that allow the rational design of small molecules for a given RNA target. Herein we present our perspective on the value of using machine learning and other computation methods to advance RNA:small molecule targeting, including select examples and their validation as well as necessary and promising future directions that will be key to accelerate discoveries in this important field.
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Affiliation(s)
- Greta Bagnolini
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - TinTin B Luu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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2
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Donlic A, Swanson EG, Chiu LY, Wicks SL, Umuhire Juru A, Cai Z, Kassam K, Laudeman C, Sanaba BG, Sugarman A, Han E, Tolbert BS, Hargrove AE. R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures. ACS Chem Biol 2022; 17:1556-1566. [PMID: 35594415 PMCID: PMC9343015 DOI: 10.1021/acschembio.2c00224] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Discoveries of RNA roles in cellular physiology and pathology are increasing the need for new tools that modulate the structure and function of these biomolecules, and small molecules are proving useful. In 2017, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND) and discovered distinguishing physicochemical properties of RNA-targeting ligands, leading us to propose the existence of an "RNA-privileged" chemical space. Biennial updates of the database and the establishment of a website platform (rbind.chem.duke.edu) have provided new insights and tools to design small molecules based on the analyzed physicochemical and spatial properties. In this report and R-BIND 2.0 update, we refined the curation approach and ligand classification system as well as conducted analyses of RNA structure elements for the first time to identify new targeting strategies. Specifically, we curated and analyzed RNA target structural motifs to determine the properties of small molecules that may confer selectivity for distinct RNA secondary and tertiary structures. Additionally, we collected sequences of target structures and incorporated an RNA structure search algorithm into the website that outputs small molecules targeting similar motifs without a priori secondary structure knowledge. Cheminformatic analyses revealed that, despite the 50% increase in small molecule library size, the distinguishing properties of R-BIND ligands remained significantly different from that of proteins and are therefore still relevant to RNA-targeted probe discovery. Combined, we expect these novel insights and website features to enable the rational design of RNA-targeted ligands and to serve as a resource and inspiration for a variety of scientists interested in RNA targeting.
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Affiliation(s)
| | | | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 441106, United States
| | - Sarah L. Wicks
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Aline Umuhire Juru
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Zhengguo Cai
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Kamillah Kassam
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Chris Laudeman
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Bilva G. Sanaba
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 441106, United States
| | - Eunseong Han
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 441106, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
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Madeddu S, Ibba R, Sanna G, Piras S, Riu F, Marongiu A, Ambrosino A, Caria P, Onnis V, Franci G, Manzin A, Carta A. Human Enterovirus B: Selective Inhibition by Quinoxaline Derivatives and Bioinformatic RNA-Motif Identification as New Targets. Pharmaceuticals (Basel) 2022; 15:ph15020181. [PMID: 35215294 PMCID: PMC8878107 DOI: 10.3390/ph15020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
The Enterovirus genus includes many viruses that are pathogenic in humans, including Coxsackie viruses and rhinoviruses, as well as the emerging enteroviruses D68 and A71. Currently, effective antiviral agents are not available for the treatment or prevention of enterovirus infections, which remain an important threat to public health. We recently identified a series of quinoxaline derivatives that were provento be potent inhibitors of coxsackievirus B5, the most common and a very important human pathogen belonging to the enterovirus genus. We have shown how most active derivatives interfere with the earliest stages of viral replication, blocking infection. Considering the broad antiviral spectrum, a very attractive property for an antiviral drug, we aimed to investigate the antiviral activity of the most promising compounds against other Enterovirus species. Here, we investigated the susceptibility of a panel of representatives of Enterovirus genus (enterovirus A71, belonging to A species; coxsackieviruses B4 and B3; echovirus 9, belonging to B species; and enterovirus D68, belonging to D species) to quinoxaline inhibitors. We also tested cytotoxicity and selectivity indices of the selected compounds, as well as their effects on virus yield. We also investigated their potential mechanism of action by a time course assay. In addition, a bioinformatic analysis was carried out to discover potential new conserved motifs in CVB3 and CVB4 compared to the other enterovirus species that can be used as new targets.
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Affiliation(s)
- Silvia Madeddu
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato (Cagliari), 09042 Monserrato, Italy; (S.M.); (A.M.); (P.C.); (A.M.)
| | - Roberta Ibba
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy; (R.I.); (S.P.); (F.R.); (A.C.)
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato (Cagliari), 09042 Monserrato, Italy; (S.M.); (A.M.); (P.C.); (A.M.)
- Correspondence: (G.S.); (V.O.)
| | - Sandra Piras
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy; (R.I.); (S.P.); (F.R.); (A.C.)
| | - Federico Riu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy; (R.I.); (S.P.); (F.R.); (A.C.)
| | - Alessandra Marongiu
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato (Cagliari), 09042 Monserrato, Italy; (S.M.); (A.M.); (P.C.); (A.M.)
- Department of Biomedical Sciences, University of Sassari, Viale S. Pietro, 43C, 07100 Sassari, Italy
| | - Annalisa Ambrosino
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Paola Caria
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato (Cagliari), 09042 Monserrato, Italy; (S.M.); (A.M.); (P.C.); (A.M.)
| | - Valentina Onnis
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato (Cagliari), 09042 Monserrato, Italy
- Correspondence: (G.S.); (V.O.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy;
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D’Aragona University Hospital, 84131 Salerno, Italy
| | - Aldo Manzin
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria di Monserrato (Cagliari), 09042 Monserrato, Italy; (S.M.); (A.M.); (P.C.); (A.M.)
| | - Antonio Carta
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy; (R.I.); (S.P.); (F.R.); (A.C.)
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Cheng Y, Ma Z, Liu S, Yang X, Li S. CircLPAR3 knockdown suppresses esophageal squamous cell carcinoma cell oncogenic phenotypes and Warburg effect through miR-873-5p/LDHA axis. Hum Exp Toxicol 2022; 41:9603271221143695. [PMID: 36484173 DOI: 10.1177/09603271221143695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) have been identified to participate in regulating multiple malignancies. Herein, this study aimed to explore the clinical significance, biological function, and regulatory mechanisms of circRNA lysophosphatidic acid receptor 3 (circLPAR3) in esophageal squamous cell carcinoma (ESCC) cell malignant phenotypes and Warburg effect. METHODS The qRT-PCR and Western blot were used to detect the levels of genes and proteins. Glucose uptake and lactate production were detected to determine the Warburg effect. The effects of circLPAR3 on ESCC cell proliferation, apoptosis, and metastasis were evaluated by MTT, 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, wound healing, and transwell assays. The binding interaction between miR-873-5p and circLPAR3 or lactate dehydrogenase A (LDHA) was verified using dual-luciferase reporter and RIP assays. Xenograft mice models were established to conduct in vivo analysis. RESULTS CircLPAR3 is a stable circRNA and was increased in ESCC tissues and cells. Functionally, circLPAR3 knockdown suppressed ESCC cell Warburg effect, proliferation, metastasis, and induced apoptosis in vitro, and impeded xenograft tumor growth and Warburg effect in ESCC mice models. Mechanistically, circLPAR3 served as a sponge for miR-873-5p, which targeted LDHA. Moreover, circLPAR3 could regulate LDHA expression by sponging miR-873-5p. Thereafter, rescue experiments suggested that miR-873-5p inhibition reversed the anticancer effects of circLPAR3 silencing on ESCC cells. Furthermore, miR-873-5p overexpression restrained ESCC cell Warburg effect and oncogenic phenotypes, which were abolished by LDHA up-regulation. CONCLUSION CircLPAR3 knockdown suppressed ESCC cell growth, metastasis, and Warburg effect by miR-873-5p/LDHA axis, implying a promising molecular target for ESCC therapy.
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Affiliation(s)
- Yao Cheng
- Department of Thoracic Surgery, 12480Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhenchuan Ma
- Department of Thoracic Surgery, 12480Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shiyuan Liu
- Department of Thoracic Surgery, 12480Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoping Yang
- Department of Thoracic Surgery, 12480Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shaomin Li
- Department of Thoracic Surgery, 12480Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Pandey M, Ojha D, Bansal S, Rode AB, Chawla G. From bench side to clinic: Potential and challenges of RNA vaccines and therapeutics in infectious diseases. Mol Aspects Med 2021; 81:101003. [PMID: 34332771 DOI: 10.1016/j.mam.2021.101003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/27/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The functional and structural versatility of Ribonucleic acids (RNAs) makes them ideal candidates for overcoming the limitations imposed by small molecule-based drugs. Hence, RNA-based biopharmaceuticals such as messenger RNA (mRNA) vaccines, antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNA mimics, anti-miRNA oligonucleotides (AMOs), aptamers, riboswitches, and CRISPR-Cas9 are emerging as vital tools for the treatment and prophylaxis of many infectious diseases. Some of the major challenges to overcome in the area of RNA-based therapeutics have been the instability of single-stranded RNAs, delivery to the diseased cell, and immunogenicity. However, recent advancements in the delivery systems of in vitro transcribed mRNA and chemical modifications for protection against nucleases and reducing the toxicity of RNA have facilitated the entry of several exogenous RNAs into clinical trials. In this review, we provide an overview of RNA-based vaccines and therapeutics, their production, delivery, current advancements, and future translational potential in treating infectious diseases.
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Affiliation(s)
- Manish Pandey
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Divya Ojha
- Laboratory of Synthetic Biology, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Sakshi Bansal
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Ambadas B Rode
- Laboratory of Synthetic Biology, Regional Centre for Biotechnology, Faridabad, 121001, India.
| | - Geetanjali Chawla
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India.
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6
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Paananen J, Fortino V. An omics perspective on drug target discovery platforms. Brief Bioinform 2019; 21:1937-1953. [PMID: 31774113 PMCID: PMC7711264 DOI: 10.1093/bib/bbz122] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 01/28/2023] Open
Abstract
The drug discovery process starts with identification of a disease-modifying target. This critical step traditionally begins with manual investigation of scientific literature and biomedical databases to gather evidence linking molecular target to disease, and to evaluate the efficacy, safety and commercial potential of the target. The high-throughput and affordability of current omics technologies, allowing quantitative measurements of many putative targets (e.g. DNA, RNA, protein, metabolite), has exponentially increased the volume of scientific data available for this arduous task. Therefore, computational platforms identifying and ranking disease-relevant targets from existing biomedical data sources, including omics databases, are needed. To date, more than 30 drug target discovery (DTD) platforms exist. They provide information-rich databases and graphical user interfaces to help scientists identify putative targets and pre-evaluate their therapeutic efficacy and potential side effects. Here we survey and compare a set of popular DTD platforms that utilize multiple data sources and omics-driven knowledge bases (either directly or indirectly) for identifying drug targets. We also provide a description of omics technologies and related data repositories which are important for DTD tasks.
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Affiliation(s)
- Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Finland.,Blueprint Genetics Ltd, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Finland
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7
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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8
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Chen YL, Lee T, Elber R, Pollack L. Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations. Biophys J 2018; 116:19-30. [PMID: 30558889 DOI: 10.1016/j.bpj.2018.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 11/02/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022] Open
Abstract
RNA is involved in a broad range of biological processes that extend far beyond translation. Many of RNA's recently discovered functions rely on folding to a specific conformation or transitioning between conformations. The RNA structure contains rigid, short basepaired regions connected by more flexible linkers. Studies of model constructs such as small helix-junction-helix (HJH) motifs are useful in understanding how these elements work together to determine RNA conformation. Here, we reveal the full ensemble of solution structures assumed by a model RNA HJH. We apply small-angle x-ray scattering and an ensemble optimization method to selectively refine models generated by all-atom molecular dynamics simulations. The expectation of a broad distribution of helix orientations, at and above physiological ionic strength, is not met. Instead, this analysis shows that the HJH structures are dominated by two distinct conformations at moderate to high ionic strength. Atomic structures, selected from the molecular dynamics simulations, reveal strong base-base interactions in the junction that critically constrain the conformational space available to the HJH molecule and lead to a surprising re-extension at high salt. These results are corroborated by comparison with previous single-molecule fluorescence resonance energy transfer experiments on the same constructs.
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Affiliation(s)
- Yen-Lin Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Tongsik Lee
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas
| | - Ron Elber
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas; Institute of Computational Sciences and Engineering, University of Texas at Austin, Austin, Texas
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
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9
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Pocock GM, Zimdars LL, Yuan M, Eliceiri KW, Ahlquist P, Sherer NM. Diverse activities of viral cis-acting RNA regulatory elements revealed using multicolor, long-term, single-cell imaging. Mol Biol Cell 2017; 28:476-487. [PMID: 27903772 PMCID: PMC5341730 DOI: 10.1091/mbc.e16-08-0612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023] Open
Abstract
Cis-acting RNA structural elements govern crucial aspects of viral gene expression. How these structures and other posttranscriptional signals affect RNA trafficking and translation in the context of single cells is poorly understood. Herein we describe a multicolor, long-term (>24 h) imaging strategy for measuring integrated aspects of viral RNA regulatory control in individual cells. We apply this strategy to demonstrate differential mRNA trafficking behaviors governed by RNA elements derived from three retroviruses (HIV-1, murine leukemia virus, and Mason-Pfizer monkey virus), two hepadnaviruses (hepatitis B virus and woodchuck hepatitis virus), and an intron-retaining transcript encoded by the cellular NXF1 gene. Striking behaviors include "burst" RNA nuclear export dynamics regulated by HIV-1's Rev response element and the viral Rev protein; transient aggregations of RNAs into discrete foci at or near the nuclear membrane triggered by multiple elements; and a novel, pulsiform RNA export activity regulated by the hepadnaviral posttranscriptional regulatory element. We incorporate single-cell tracking and a data-mining algorithm into our approach to obtain RNA element-specific, high-resolution gene expression signatures. Together these imaging assays constitute a tractable, systems-based platform for studying otherwise difficult to access spatiotemporal features of viral and cellular gene regulation.
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MESH Headings
- Active Transport, Cell Nucleus/physiology
- Cell Nucleus/metabolism
- Gene Expression Regulation, Viral
- Gene Products, rev/metabolism
- Genes, env/physiology
- HIV-1
- Mason-Pfizer monkey virus
- Molecular Imaging/methods
- RNA Processing, Post-Transcriptional/physiology
- RNA, Messenger/metabolism
- RNA, Viral
- Regulatory Sequences, Nucleic Acid/genetics
- Regulatory Sequences, Nucleic Acid/physiology
- Regulatory Sequences, Ribonucleic Acid/genetics
- Regulatory Sequences, Ribonucleic Acid/physiology
- Single-Cell Analysis/methods
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Affiliation(s)
- Ginger M Pocock
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Laraine L Zimdars
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
| | - Ming Yuan
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706
| | - Kevin W Eliceiri
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
- Laboratory for Optical and Computational Instrumentation and Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
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10
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Gorzelnik KV, Cui Z, Reed CA, Jakana J, Young R, Zhang J. Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ. Proc Natl Acad Sci U S A 2016; 113:11519-11524. [PMID: 27671640 PMCID: PMC5068298 DOI: 10.1073/pnas.1609482113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.
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Affiliation(s)
- Karl V Gorzelnik
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Zhicheng Cui
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Catrina A Reed
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Ry Young
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843;
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11
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Garg D, Torbett BE. Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy. Virus Res 2014; 193:135-43. [PMID: 25026536 PMCID: PMC4252855 DOI: 10.1016/j.virusres.2014.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.
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Affiliation(s)
- Divita Garg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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12
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In vitro and in vivo protection against enterovirus 71 by an antisense phosphorothioate oligonucleotide. Arch Virol 2014; 159:2339-47. [PMID: 24756344 DOI: 10.1007/s00705-014-2054-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 03/10/2014] [Indexed: 12/17/2022]
Abstract
Enterovirus 71 (EV71) is a highly infectious virus that is a major cause of hand, foot, and mouth disease (HFMD), which can lead to severe neurological complications. Currently, there is no effective therapy against EV71. Five antisense oligodeoxynucleotides targeting the 5'-terminal conserved domain of the viral genome were designed using a method based on multiple predicted target mRNA structures. They were then screened for anti-EV71 activity in vitro based on their ability to inhibit an EV71-induced cytopathic effect (CPE). A novel antisense oligonucleotide (EV5) was tested both in rhabdomyosarcoma (RD) cells and in vivo using a mouse model, with a random oligonucleotide (EV5R) of EV5 as a control. EV5 was identified as having significant anti-EV71 activity in vitro and in vivo without significant cytotoxicity. Treatment of RD and Vero cells with antisense oligodeoxynucleotide EV5 significantly and specifically alleviated the cytopathic effect of EV71 in vitro. The inhibitory effect was dose dependent and specific, with a corresponding decrease in viral RNA and viral protein levels. In vivo, EV5 was specifically effective against EV71 virus in preventing death, decreasing weight reduction and reducing the viral RNA copy number and the level of viral proteins in the lungs, intestines and muscles. These results demonstrate the potential and feasibility of using antisense oligodeoxynucleotides specific for the 5'-terminal conserved domain of the viral genome as an antiviral therapy for EV71 disease.
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Warui DM, Baranger AM. Identification of small molecule inhibitors of the HIV-1 nucleocapsid-stem-loop 3 RNA complex. J Med Chem 2012; 55:4132-41. [PMID: 22480197 DOI: 10.1021/jm2007694] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serves as a principle determinant for viral packaging. Viral encapsulation is critical for viral replication, and disruption of the nucleocapsid-ψ-RNA complex interferes with viral replication. We have used SL3 RNA as a target for identification of small molecule inhibitors of the interactions of nucleocapsid protein (NCp7) and ψ-RNA. We report the use of computational and high-throughput screening approaches to identify 16 compounds that bind SL3 RNA with micromolar affinities. Among the identified ligands, two molecules, compounds 7 and 17, bind with higher affinity to SL3 RNA than to double- and single-stranded RNAs. Four of the 16 SL3 RNA ligands inhibit interactions between SL3 RNA and NCp7 with micromolar inhibition constants. In general, the identified SL3 ligands have simple molecular structures and low molecular weights and are, therefore, possible lead compounds for the development of ligands that target the elements of ψ-RNA of HIV-1 with high affinity and specificity.
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Affiliation(s)
- Douglas M Warui
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Cheng CW, Su ECY, Hwang JK, Sung TY, Hsu WL. Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics 2008; 9 Suppl 12:S6. [PMID: 19091029 PMCID: PMC2638146 DOI: 10.1186/1471-2105-9-s12-s6] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. Identification of RNA-binding sites in proteins provides valuable insights for biologists. However, experimental determination of RNA-protein interaction remains time-consuming and labor-intensive. Thus, computational approaches for prediction of RNA-binding sites in proteins have become highly desirable. Extensive studies of RNA-binding site prediction have led to the development of several methods. However, they could yield low sensitivities in trade-off for high specificities. Results We propose a method, RNAProB, which incorporates a new smoothed position-specific scoring matrix (PSSM) encoding scheme with a support vector machine model to predict RNA-binding sites in proteins. Besides the incorporation of evolutionary information from standard PSSM profiles, the proposed smoothed PSSM encoding scheme also considers the correlation and dependency from the neighboring residues for each amino acid in a protein. Experimental results show that smoothed PSSM encoding significantly enhances the prediction performance, especially for sensitivity. Using five-fold cross-validation, our method performs better than the state-of-the-art systems by 4.90%~6.83%, 0.88%~5.33%, and 0.10~0.23 in terms of overall accuracy, specificity, and Matthew's correlation coefficient, respectively. Most notably, compared to other approaches, RNAProB significantly improves sensitivity by 7.0%~26.9% over the benchmark data sets. To prevent data over fitting, a three-way data split procedure is incorporated to estimate the prediction performance. Moreover, physicochemical properties and amino acid preferences of RNA-binding proteins are examined and analyzed. Conclusion Our results demonstrate that smoothed PSSM encoding scheme significantly enhances the performance of RNA-binding site prediction in proteins. This also supports our assumption that smoothed PSSM encoding can better resolve the ambiguity of discriminating between interacting and non-interacting residues by modelling the dependency from surrounding residues. The proposed method can be used in other research areas, such as DNA-binding site prediction, protein-protein interaction, and prediction of posttranslational modification sites.
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Affiliation(s)
- Cheng-Wei Cheng
- Institute of Information Systems and Applications, National Tsing Hua University, Hsinchu, Taiwan.
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15
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Wang L, Brown SJ. Prediction of RNA-binding residues in protein sequences using support vector machines. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2008; 2006:5830-3. [PMID: 17946337 DOI: 10.1109/iembs.2006.260025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Understanding the molecular recognition between RNA and proteins is central to elucidation of many biological processes in the cell. Although structural data are available for some protein-RNA complexes, the interaction patterns are still mostly unclear. In this study, support vector machines as well as artificial neural networks have been trained to predict RNA binding residues from five sequence-derived features, including the solvent accessible surface area, BLAST-based conservation score, hydrophobicity index, side chain pK(a) value and molecular mass of an amino acid. It is found that support vector machines outperform neural networks for prediction of RNA-binding residues. The best support vector machine achieves 70.74% of prediction strength (average of sensitivity and specificity), whereas the performance measure reaches 67.79% for the neural networks. The results suggest that RNA binding residues can be predicted directly from amino acid sequence information. Online prediction of RNA-binding residues is available at http://bioinformatics.ksu.edu/bindn/
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Affiliation(s)
- Liangjiang Wang
- Bioinformatics Center, Div. of Biol., Kansas State Univ., Manhattan, KS 66506, USA.
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16
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Duan M, Zhou Z, Lin RX, Yang J, Xia XZ, Wang SQ. In vitro and in vivo Protection against the Highly Pathogenic H5N1 Influenza virus by an Antisense Phosphorothioate Oligonucleotide. Antivir Ther 2008. [DOI: 10.1177/135965350801300112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Current vaccination strategies and antiviral drugs only provide limited protection against influenza virus infection. In this study, we investigated the use of a novel antisense oligonucleotide (named IV-AS), which is specific for the 5’-terminal conserved sequence found in all eight viral RNA segments of influenza A virus. Methods The activity of IV-AS was monitored both in vitro, in Madin-Darby canine kidney (MDCK) cells, and in vivo using a mouse model. IV-AS was given intranasally to H5N1-infected mice once daily for 6 days starting 6 h after infection. A three-base mismatch of IV-AS was used as a control. Results IV-AS inhibited influenza virus A induced cytopathic effects in MDCK cells with the 50% effective concentration (EC50) ranging from 2.2 to 4.4 μM. IV-AS was effective against H5N1 virus in preventing death, lessening weight reduction, inhibiting lung consolidation and reducing lung virus titres. Dosages of 40 and 60 mg/kg/day provided 40% and 60% survival rates and prolonged mean survival days in comparison with the infected control group ( P<0.05). The lung index in mice treated with IV-AS, at a dose of 20, 40 or 60 mg/kg/day, had been inhibited on day 4 or 6 ( P<0.05 or P<0.01); virus titres in lung had declined to 2.42, 1.51 and 1.54 log10 TCID50/g of lung, respectively, whereas the yields in the infected control mice were 6.00 log10 TCID50/g of lung. Conclusions Our results suggest that the 5’-terminal conserved region of influenza A virus RNA segments can be targeted using antisense technology; therefore, IV-AS is a potential drug for prophylaxis and control of influenza virus infections.
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Affiliation(s)
- Ming Duan
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, China
| | - Zhe Zhou
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, China
| | - Ru-Xian Lin
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, China
| | - Jing Yang
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, China
| | - Xian-Zhu Xia
- Changchun Institute of Veterinary Science, 1068 Qinglong Road, Changchun, 130062, China
| | - Sheng-Qi Wang
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, China
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Gooch BD, Krishnamurthy M, Shadid M, Beal PA. Binding of helix-threading peptides to E. coli 16S ribosomal RNA and inhibition of the S15-16S complex. Chembiochem 2006; 6:2247-54. [PMID: 16245373 DOI: 10.1002/cbic.200500285] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Helix-threading peptides (HTPs) constitute a new class of small molecules that bind selectively to duplex RNA structures adjacent to helix defects and project peptide functionality into the dissimilar duplex grooves. To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified helix 22 of the prokaryotic ribosomal RNA 16S as a target. This helix is a component of the binding site for the ribosomal protein S15. In addition, the S15-16S RNA interaction is important for the ordered assembly of the bacterial ribosome. Here we present the synthesis and characterization of helix-threading peptides that bind selectively to helix 22 of E. coli 16S RNA. These compounds bind helix 22 by threading intercalation placing the N termini in the minor groove and the C termini in the major groove. Binding is dependent on the presence of a highly conserved purine-rich internal loop in the RNA, whereas removal of the loop minimally affects binding of the classical intercalators ethidium bromide and methidiumpropyl-EDTAFe (MPEFe). Moreover, binding selectivity translates into selective inhibition of formation of the S15-16S complex.
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Affiliation(s)
- Barry D Gooch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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18
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Khan AU. Ribozyme: A clinical tool. Clin Chim Acta 2006; 367:20-7. [PMID: 16426595 DOI: 10.1016/j.cca.2005.11.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 11/18/2005] [Accepted: 11/22/2005] [Indexed: 01/15/2023]
Abstract
Catalytic RNAs (ribozymes) are capable of specifically cleaving RNA molecules, a property that enables them to act as potential antiviral and anti-cancer agents, as well as powerful tools for functional genomic studies. Recently, ribozymes have been used successfully to inhibit gene expression in a variety of biological systems in vitro and in vivo. Phase I clinical trials using ribozyme gene therapy to treat AIDS patients have been conducted. Despite initial success, there are many areas that require further investigation. These include stability of ribozymes in cells and designing highly active ribozymes in vivo, identification of target sequence sites and co-localization of ribozymes and substrates, and their delivery to specific tissues and maintenance of its stable long-term expression. This review gives a brief introduction to ribozyme structure, catalysis and its potential applications in biological systems as therapeutic agents.
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Affiliation(s)
- Asad U Khan
- Interdisciplinary Biotechnology unit, Aligarh Muslim University, Aligarh 202002, India.
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19
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Abstract
In the age of extensive global traffic systems, the close neighborhood of man and livestock in some regions of the world, as well as inadequate prevention measures and medical care in poorer countries, greatly facilitates the emergence and dissemination of new virus strains. The appearance of avian influenza viruses that can infect humans, the spread of the severe acute respiratory syndrome (SARS) virus, and the unprecedented raging of human immunodeficiency virus (HIV) illustrate the threat of a global virus pandemic. In addition, viruses like hepatitis B and C claim more than one million lives every year for want of efficient therapy. Thus, new approaches to prevent virus propagation are urgently needed. Antisense strategies are considered a very attractive means of inhibiting viral replication, as oligonucleotides can be designed to interact with any viral RNA, provided its sequence is known. The ensuing targeted destruction of viral RNA should interfere with viral replication without entailing negative effects on ongoing cellular processes. In this review, we will give some examples of the employment of antisense oligonucleotides, ribozymes, and RNA interference strategies for antiviral purposes. Currently, in spite of encouraging results in preclinical studies, only a few antisense oligonucleotides and ribozymes have turned out to be efficient antiviral compounds in clinical trials. The advent of RNA interference now seems to be refueling hopes for decisive progress in the field of therapeutic employment of antisense strategies.
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Affiliation(s)
- Volker Erdmann
- Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Scienes, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jürgen Brosius
- Institute of Experimental Pathology, Molecular Neurobiology (ZMBE), University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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Xing F, Song G, Ren J, Chaires JB, Qu X. Molecular recognition of nucleic acids: Coralyne binds strongly to poly(A). FEBS Lett 2005; 579:5035-9. [PMID: 16125177 DOI: 10.1016/j.febslet.2005.07.091] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 07/22/2005] [Accepted: 07/25/2005] [Indexed: 11/30/2022]
Abstract
The small molecule coralyne was found to bind preferentially and strongly to single-stranded poly(A) with an apparent association constant (Ka) of (1.8+/-0.3) x 10(6)M(-1). Binding of coralyne to poly(A) is predominantly enthalpically driven with a stoichiometry of one coralyne per four adenine bases. Poly(A) forms a coralyne dependent secondary structure with a melting temperature of 60 degrees C, for the conditions of our study.
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Affiliation(s)
- Feifei Xing
- Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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22
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Ovenden SPB, Sberna G, Tait RM, Wildman HG, Patel R, Li B, Steffy K, Nguyen N, Meurer-Grimes BM. A diketopiperazine dimer from a marine-derived isolate of Aspergillus niger. JOURNAL OF NATURAL PRODUCTS 2004; 67:2093-2095. [PMID: 15620260 DOI: 10.1021/np0497494] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The new diketopiperazine dimer 1, as well as the known compounds TMC-256A1 (2), TMC-256C1 (3), and demethylkotanin (4), were isolated from a culture of Aspergillus niger. The gross structure of 1 was determined by 2D NMR studies and comparison with literature data, and the absolute stereochemistry was elucidated by chiral HPLC analysis of the hydrolysis products.
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Affiliation(s)
- Simon P B Ovenden
- Cerylid Biosciences, 576 Swan Street, Richmond, Victoria, 3121, Australia
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23
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Arzumanov A, Stetsenko DA, Malakhov AD, Reichelt S, Sørensen MD, Babu BR, Wengel J, Gait MJ. A structure-activity study of the inhibition of HIV-1 Tat-dependent trans-activation by mixmer 2'-O-methyl oligoribonucleotides containing locked nucleic acid (LNA), alpha-L-LNA, or 2'-thio-LNA residues. Oligonucleotides 2004; 13:435-53. [PMID: 15025911 DOI: 10.1089/154545703322860762] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The HIV-1 trans-activation responsive element (TAR) RNA stem-loop interacts with the HIV trans-activator protein Tat and other cellular factors to stimulate transcriptional elongation from the viral long terminal repeat (LTR). Inhibitors of these interactions block full-length transcription and, hence, would potentially inhibit HIV replication. We have studied structure-activity relationships in inhibition of trans-activation by steric block 2'-O-methyl (OMe) oligonucleotides chimeras (mixmers) containing locked nucleic acid (LNA) units. Inhibition was measured both in Tat-dependent in vitro transcription from an HIV-1 DNA template directed by HeLa cell nuclear extract and in a robust HeLa cell reporter assay that involves use of stably integrated plasmids to express firefly luciferase Tat dependently and Renilla luciferase Tat-independently. OMe oligonucleotides with optimally 40%-50% LNA units and a minimum of 12 residues in length were active in the cellular assay when delivered with cationic gemini surfactant GS11 at 50% inhibitory concentrations of 230 +/- 40 nM, whereas activity in the in vitro transcription assay was observed down to 9 residues. No cellular activity was observed for OMe oligonucleotides of 12 or 16 residues, which was shown to be due to poor cellular uptake. Both 12-mer mixmers containing alpha -L-LNA or 2'-thio-LNA (S-LNA) were also active in in vitro transcription and the former in cellular reporter inhibition assays, demonstrating that the property of promotion of cellular uptake by LNA is not due to specific sugar conformational effects. Covalent conjugates of OMe/LNA chimeras with Kaposi-fibroblast growth factor (K-FGF) or Transportan peptides failed to enter HeLa cells without a delivery agent but were fully active when delivered by cationic gemini surfactant, showing that in principle, peptide conjugation does not interfere with cellular activity. Thus, OMe/LNA mixmers are powerful reagents for use as steric block inhibitors of gene expression regulated by protein-RNA interactions within HeLa cell nuclei.
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Affiliation(s)
- Andrey Arzumanov
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
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24
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Abstract
The treatment of advanced nonsmall cell lung cancer (NSCLC) continues to pose great challenges for the thoracic surgeon. Current therapeutic strategies with chemotherapy and radiation are often ineffective adjuncts to surgery. Accordingly, preclinical research concentration has turned to molecular targets that may prove to be more effective. The Bcl-2 family consists of a homologous network of genes that regulate apoptosis or programmed cell death. Altered expression of members in this family leads to aberrant cell proliferation and malignant growth. This review will discuss the expression and significance of Bcl-2 family members in NSCLC and consider potential methods of intervention that are currently being tested and may have clinical applicability. In addition, the current experience with clinical trials involving Bcl-2 down-regulation in solid organ tumors will be summarized.
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Affiliation(s)
- Jonathan C Daniel
- Department of Thoracic and Cardiovascular Surgery, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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