1
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Tipo J, Gottipati K, Choi KH. High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. RNA (NEW YORK, N.Y.) 2024; 30:609-623. [PMID: 38383158 PMCID: PMC11098461 DOI: 10.1261/rna.079796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae The flavivirus genome contains a 5' end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5' guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small molecule inhibitors to disrupt the promoter function. To facilitate the identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of the bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures, and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.
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Affiliation(s)
- Jerricho Tipo
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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2
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Olenginski LT, Attionu SK, Henninger EN, LeBlanc RM, Longhini AP, Dayie TK. Hepatitis B Virus Epsilon (ε) RNA Element: Dynamic Regulator of Viral Replication and Attractive Therapeutic Target. Viruses 2023; 15:1913. [PMID: 37766319 PMCID: PMC10534774 DOI: 10.3390/v15091913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatitis B virus (HBV) chronically infects millions of people worldwide, which underscores the importance of discovering and designing novel anti-HBV therapeutics to complement current treatment strategies. An underexploited but attractive therapeutic target is ε, a cis-acting regulatory stem-loop RNA situated within the HBV pregenomic RNA (pgRNA). The binding of ε to the viral polymerase protein (P) is pivotal, as it triggers the packaging of pgRNA and P, as well as the reverse transcription of the viral genome. Consequently, small molecules capable of disrupting this interaction hold the potential to inhibit the early stages of HBV replication. The rational design of such ligands necessitates high-resolution structural information for the ε-P complex or its individual components. While these data are currently unavailable for P, our recent structural elucidation of ε through solution nuclear magnetic resonance spectroscopy marks a significant advancement in this area. In this review, we provide a brief overview of HBV replication and some of the therapeutic strategies to combat chronic HBV infection. These descriptions are intended to contextualize our recent experimental efforts to characterize ε and identify ε-targeting ligands, with the ultimate goal of developing novel anti-HBV therapeutics.
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Affiliation(s)
- Lukasz T. Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Solomon K. Attionu
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Erica N. Henninger
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Andrew P. Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
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3
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Malbert B, Labaurie V, Dorme C, Paget E. Group I Intron as a Potential Target for Antifungal Compounds: Development of a Trans-Splicing High-Throughput Screening Strategy. Molecules 2023; 28:molecules28114460. [PMID: 37298936 DOI: 10.3390/molecules28114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The search for safe and efficient new antifungal compounds for agriculture has led to more efforts in finding new modes of action. This involves the discovery of new molecular targets, including coding and non-coding RNA. Rarely found in plants and animals but present in fungi, group I introns are of interest as their complex tertiary structure may allow selective targeting using small molecules. In this work, we demonstrate that group I introns present in phytopathogenic fungi have a self-splicing activity in vitro that can be adapted in a high-throughput screening to find new antifungal compounds. Ten candidate introns from different filamentous fungi were tested and one group ID intron found in F. oxysporum showed high self-splicing efficiency in vitro. We designed the Fusarium intron to act as a trans-acting ribozyme and used a fluorescence-based reporter system to monitor its real time splicing activity. Together, these results are opening the way to study the druggability of such introns in crop pathogen and potentially discover small molecules selectively targeting group I introns in future high-throughput screenings.
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Affiliation(s)
- Bastien Malbert
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Virginie Labaurie
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Cécile Dorme
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
| | - Eric Paget
- Early Discovery, Biochemistry Excellence, Centre de Recherche La Dargoire, Bayer SAS, 69009 Lyon, France
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4
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Chaudhry T, Coxon CR, Ross K. Trading places: Peptide and small molecule alternatives to oligonucleotide-based modulation of microRNA expression. Drug Discov Today 2022; 27:103337. [PMID: 35995360 DOI: 10.1016/j.drudis.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
It is well established that microRNA (miRNA) dysregulation is involved in the development and progression of various diseases, especially cancer. Emerging evidence suggests that small molecule and peptide agents can interfere with miRNA disease pathways. Despite this, very little is known about structural features that drive drug-miRNA interactions and subsequent inhibition. In this review, we highlight the advances made in the development of small molecule and peptide inhibitors of miRNA processing. Specifically, we attempt to draw attention to peptide features that may be critical for interaction with the miRNA secondary structure to regulate miRNA expression. We hope that this review will help to establish peptides as exciting miRNA expression modulators and will contribute towards the development of the first miRNA-targeting peptide therapy.
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Affiliation(s)
- Talhat Chaudhry
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK; Institute for Health Research, Liverpool John Moores University, Liverpool, UK
| | - Christopher R Coxon
- EaStChem School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH14 4AS, UK
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK; Institute for Health Research, Liverpool John Moores University, Liverpool, UK.
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5
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Chang Z, Zheng YY, Mathivanan J, Valsangkar VA, Du J, Abou-Elkhair RAI, Hassan AEA, Sheng J. Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats. Int J Mol Sci 2022; 23:ijms23063321. [PMID: 35328743 PMCID: PMC8955525 DOI: 10.3390/ijms23063321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Pathogenic CUG and CCUG RNA repeats have been associated with myotonic dystrophy type 1 and 2 (DM1 and DM2), respectively. Identifying small molecules that can bind these RNA repeats is of great significance to develop potential therapeutics to treat these neurodegenerative diseases. Some studies have shown that aminoglycosides and their derivatives could work as potential lead compounds targeting these RNA repeats. In this work, sisomicin, previously known to bind HIV-1 TAR, is investigated as a possible ligand for CUG RNA repeats. We designed a novel fluorescence-labeled RNA sequence of r(CUG)10 to mimic cellular RNA repeats and improve the detecting sensitivity. The interaction of sisomicin with CUG RNA repeats is characterized by the change of fluorescent signal, which is initially minimized by covalently incorporating the fluorescein into the RNA bases and later increased upon ligand binding. The results show that sisomicin can bind and stabilize the folded RNA structure. We demonstrate that this new fluorescence-based binding characterization assay is consistent with the classic UV Tm technique, indicating its feasibility for high-throughput screening of ligand-RNA binding interactions and wide applications to measure the thermodynamic parameters in addition to binding constants and kinetics when probing such interactions.
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Affiliation(s)
- Zhihua Chang
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Ya Ying Zheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Johnsi Mathivanan
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Vibhav A. Valsangkar
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Jinxi Du
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Reham A. I. Abou-Elkhair
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44523, Egypt;
| | - Abdalla E. A. Hassan
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44523, Egypt;
- Correspondence: (A.E.A.H.); (J.S.)
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
- Correspondence: (A.E.A.H.); (J.S.)
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6
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Zhan X, Deng L, Chen G. Mechanisms and applications of peptide nucleic acids selectively binding to double-stranded RNA. Biopolymers 2021; 113:e23476. [PMID: 34581432 DOI: 10.1002/bip.23476] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022]
Abstract
RNAs form secondary structures containing double-stranded base paired regions and single-stranded regions. Probing, detecting and modulating RNA structures and dynamics requires the development of molecular sensors that can differentiate the sequence and structure of RNAs present in viruses and cells, as well as in extracellular space. In this review, we summarize the recent progress on the development of chemically modified peptide nucleic acids (PNAs) for the selective recognition of double-stranded RNA (dsRNA) sequences over both single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) sequences. We also briefly discuss the applications of sequence-specific dsRNA-binding PNAs in sensing and stabilizing dsRNA structures and inhibiting dsRNA-protein interactions.
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Affiliation(s)
- Xuan Zhan
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Liping Deng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
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7
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Levintov L, Vashisth H. Role of conformational heterogeneity in ligand recognition by viral RNA molecules. Phys Chem Chem Phys 2021; 23:11211-11223. [PMID: 34010381 DOI: 10.1039/d1cp00679g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example of conformationally adapting molecules that have evolved to switch between many functional conformations. The transactivation response element (TAR) RNA from the type-1 human immunodeficiency virus (HIV-1) is a viral RNA molecule that is being increasingly explored as a potential therapeutic target due to its role in the viral replication process. In this work, we have studied the dynamics in TAR RNA in apo and liganded states by performing explicit-solvent molecular dynamics (MD) simulations initiated with 27 distinct structures. We determined that the TAR RNA structure is significantly stabilized on ligand binding with especially decreased fluctuations in its two helices. This rigidity is further coupled with the decreased flipping of bulge nucleotides, which were observed to flip more frequently in the absence of ligands. We found that initially-distinct structures of TAR RNA converged to similar conformations on removing ligands. We also report that conformational dynamics in unliganded TAR structures leads to the formation of binding pockets capable of accommodating ligands of various sizes.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, USA.
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, USA.
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8
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LeBlanc RM, Kasprzak WK, Longhini AP, Olenginski LT, Abulwerdi F, Ginocchio S, Shields B, Nyman J, Svirydava M, Del Vecchio C, Ivanic J, Schneekloth JS, Shapiro BA, Dayie TK, Le Grice SFJ. Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA. J Biomol Struct Dyn 2021; 40:9761-9773. [PMID: 34155954 PMCID: PMC10167916 DOI: 10.1080/07391102.2021.1934544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022]
Abstract
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral polymerase with a cis-acting regulatory signal, designated epsilon (ε), located at the 5'-end of its pre-genomic RNA (pgRNA). Binding of polymerase to ε is also necessary for pgRNA encapsidation. While the mechanistic basis of this interaction remains elusive, mutagenesis studies suggest its internal 6-nt "priming loop" provides an important structural contribution. ε might therefore be considered a promising target for small molecule interventions to complement current nucleoside-analog based anti-HBV therapies. An ideal prerequisite to any RNA-directed small molecule strategy would be a detailed structural description of this important element. Herein, we present a solution NMR structure for HBV ε which, in combination with molecular dynamics and docking simulations, reports on a flexible ligand "pocket", reminiscent of those observed in proteins. We also demonstrate the binding of the selective estrogen receptor modulators (SERMs) Raloxifene, Bazedoxifene, and a de novo derivative to the priming loop.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Regan M. LeBlanc
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew P. Longhini
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Fardokht Abulwerdi
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Stefano Ginocchio
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Brigit Shields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Julie Nyman
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Maryia Svirydava
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Bruce A. Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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9
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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10
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Singh AK, Ghosh M, Kumar V, Aggarwal S, Patil SA. Interplay between miRNAs and Mycobacterium tuberculosis: diagnostic and therapeutic implications. Drug Discov Today 2021; 26:1245-1255. [PMID: 33497829 DOI: 10.1016/j.drudis.2021.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/14/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Increasing evidence suggests that mycobacteria change the host miRNA profile to their advantage. The active participation of miRNAs in controlling immune responses in TB has raised the possibility of utilizing miRNA-based therapy itself or canonically with a standard drug regimen for shortening the duration of treatment. The development of delivery systems for optimal delivery of oligonucleotides, including small interfering (si)RNA/miRNAs-based therapeutics has shown potential as a new therapeutic intervention. However, studies related to the exploitation of miRNAs as both biomarkers and as therapeutics in TB are scarce; thus, more in vitro and in vivo studies are required to fully determine the role of miRNAs as potential diagnostic biomarkers and to improve the pharmacological profile of this class of therapeutics.
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Affiliation(s)
- Amit Kumar Singh
- Experimental Animal Facility, ICMR-National JALMA Institute For Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India.
| | - Mrinmoy Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar-751024
| | - Vimal Kumar
- Experimental Animal Facility, ICMR-National JALMA Institute For Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India
| | - Sumit Aggarwal
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Shripad A Patil
- Immunology Division, ICMR-National JALMA Institute For Leprosy & Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
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11
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Levintov L, Vashisth H. Ligand Recognition in Viral RNA Necessitates Rare Conformational Transitions. J Phys Chem Lett 2020; 11:5426-5432. [PMID: 32551654 DOI: 10.1021/acs.jpclett.0c01390] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ribonucleic acids (RNAs) are conformationally flexible molecules that fold into three-dimensional structures and play an important role in different cellular processes as well as in the development of many diseases. RNA has therefore become an important target for developing novel therapeutic approaches. The biophysical processes underlying RNA function are often associated with rare structural transitions that play a key role in ligand recognition. In this work, we probe these rarely occurring transitions using nonequilibrium simulations by characterizing the dissociation of a ligand molecule from an HIV-1 viral RNA element. Specifically, we observed base-flipping rare events that are coupled with ligand binding/unbinding and also provided mechanistic details underlying these transitions.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
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12
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Bissaro M, Sturlese M, Moro S. Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules? Front Chem 2020; 8:107. [PMID: 32175307 PMCID: PMC7057144 DOI: 10.3389/fchem.2020.00107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/04/2020] [Indexed: 11/30/2022] Open
Abstract
Although proteins have represented the molecular target of choice in the development of new drug candidates, the pharmaceutical importance of ribonucleic acids has gradually been growing. The increasing availability of structural information has brought to light the existence of peculiar three-dimensional RNA arrangements, which can, contrary to initial expectations, be recognized and selectively modulated through small chemical entities or peptides. The application of classical computational methodologies, such as molecular docking, for the rational development of RNA-binding candidates is, however, complicated by the peculiarities characterizing these macromolecules, such as the marked conformational flexibility, the singular charges distribution, and the relevant role of solvent molecules. In this work, we have thus validated and extended the applicability domain of SuMD, an all-atoms molecular dynamics protocol that allows to accelerate the sampling of molecular recognition events on a nanosecond timescale, to ribonucleotide targets of pharmaceutical interest. In particular, we have proven the methodological ability by reproducing the binding mode of viral or prokaryotic ribonucleic complexes, as well as that of artificially engineered aptamers, with an impressive degree of accuracy.
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Affiliation(s)
- Maicol Bissaro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Mattia Sturlese
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
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13
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Van Meter EN, Onyango JA, Teske KA. A review of currently identified small molecule modulators of microRNA function. Eur J Med Chem 2020; 188:112008. [DOI: 10.1016/j.ejmech.2019.112008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022]
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14
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Henderson CA, Rail CA, Butt LE, Vincent HA, Callaghan AJ. Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers. Methods 2019; 167:39-53. [PMID: 31055072 PMCID: PMC7068705 DOI: 10.1016/j.ymeth.2019.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 12/23/2022] Open
Abstract
The discovery and engineering of more and more functions of RNA has highlighted the utility of RNA-targeting small molecules. Recently, several fluorogen-binding RNA aptamers have been developed that have been applied to live cell imaging of RNA and metabolites as RNA tags or biosensors, respectively. Although the design and application of these fluorogen-binding RNA aptamer-based devices is straightforward in theory, in practice, careful optimisation is required. For this reason, high throughput in vitro screening techniques, capable of quantifying fluorogen-RNA aptamer interactions, would be beneficial. We recently developed a method for generating functional-RNA arrays and demonstrated that they could be used to detect fluorogen-RNA aptamer interactions. Specifically, we were able to visualise the interaction between malachite green and the malachite green-binding aptamer. Here we expand this study to demonstrate that functional-RNA arrays can be used to quantify fluorogen-aptamer interactions. As proof-of-concept, we provide detailed protocols for the production of malachite green-binding RNA aptamer and DFHBI-binding Spinach RNA aptamer arrays. Furthermore, we discuss the potential utility of the technology to fluorogen-binding RNA aptamers, including application as a molecular biosensor platform. We anticipate that functional-RNA array technology will be beneficial for a wide variety of biological disciplines.
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Affiliation(s)
- Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Callum A Rail
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
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15
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Krishna MS, Wang Z, Zheng L, Bowry J, Ong AAL, Mu Y, Prabakaran M, Chen G. Incorporating G-C Pair-Recognizing Guanidinium into PNAs for Sequence and Structure Specific Recognition of dsRNAs over dsDNAs and ssRNAs. Biochemistry 2019; 58:3777-3788. [PMID: 31424191 DOI: 10.1021/acs.biochem.9b00608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recognition of RNAs under physiological conditions is important for the development of chemical probes and therapeutic ligands. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) are promising for the recognition of dsRNAs in a sequence and structure specific manner under near-physiological conditions. Guanidinium is often present in proteins and small molecules for the recognition of G bases in nucleic acids, in cell-penetrating carriers, and in bioactive drug molecules, which might be due to the fact that guanidinium is amphiphilic and has unique hydrogen bonding and stacking properties. We hypothesized that a simple guanidinium moiety can be directly incorporated into PNAs to facilitate enhanced molecular recognition of G-C pairs in dsRNAs and improved bioactivity. We grafted a guanidinium moiety directly into a PNA monomer (designated as R) using a two-carbon linker as guided by computational modeling studies. The synthetic scheme of the PNA R monomer is relatively simple compared to that of the previously reported L monomer. We incorporated the R residue into various dbPNAs for binding studies. dbPNAs incorporated with R residues are excellent in sequence specifically recognizing G-C pairs in dsRNAs over dsDNA and ssRNAs. We demonstrated that the R residue is compatible with unmodified T and C and previously developed modified L and Q residues in dbPNAs for targeting model dsRNAs, the influenza A viral panhandle duplex structure, and the HIV-1 frameshift site RNA hairpin. Furthermore, R residues enhance the cellular uptake of PNAs.
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Affiliation(s)
- Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhenzhang Wang
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604
| | - Liangzhen Zheng
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Jogesh Bowry
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,Department of Chemistry , University of Southampton , Southampton SO17 1BJ , U.K
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yuguang Mu
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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16
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Hewitt WM, Calabrese DR, Schneekloth JS. Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. Bioorg Med Chem 2019; 27:2253-2260. [PMID: 30982658 PMCID: PMC8283815 DOI: 10.1016/j.bmc.2019.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
Abstract
RNA has attracted considerable attention as a target for small molecules. However, methods to identify, study, and characterize suitable RNA targets have lagged behind strategies for protein targets. One approach that has received considerable attention for protein targets has been to utilize computational analysis to investigate ligandable "pockets" on proteins that are amenable to small molecule binding. These studies have shown that selected physical properties of pockets are important parameters that govern the ability of a structure to bind to small molecules. This work describes a similar analysis to study pockets on all RNAs in the Protein Data Bank (PDB). Using parameters such as buriedness, hydrophobicity, volume, and other properties, the set of all RNAs is analyzed and compared to all proteins. Considerable overlap is observed between the properties of pockets on RNAs and proteins. Thus, many RNAs are capable of populating conformations with pockets that are likely suitable for small molecule binding. Further, principal moment of inertia (PMI) calculations reveal that liganded RNAs exist in diverse structural space, much of which overlaps with protein structural space. Taken together, these results suggest that complex folded RNAs adopt unique structures with pockets that may represent viable opportunities for small molecule targeting.
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Affiliation(s)
- William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States.
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17
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Krishna MS, Toh DFK, Meng Z, Ong AAL, Wang Z, Lu Y, Xia K, Prabakaran M, Chen G. Sequence- And Structure-Specific Probing of RNAs by Short Nucleobase-Modified dsRNA-Binding PNAs Incorporating a Fluorescent Light-up Uracil Analog. Anal Chem 2019; 91:5331-5338. [PMID: 30873827 DOI: 10.1021/acs.analchem.9b00280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNAs are emerging as important biomarkers and therapeutic targets. The strategy of directly targeting double-stranded RNA (dsRNA) by triplex-formation is relatively underexplored mainly due to the weak binding at physiological conditions for the traditional triplex-forming oligonucleotides (TFOs). Compared to DNA and RNA, peptide nucleic acids (PNAs) are chemically stable and have a neutral peptide-like backbone, and thus, they show significantly enhanced binding to natural nucleic acids. We have successfully developed nucleobase-modified dsRNA-binding PNAs (dbPNAs) to facilitate structure-specific and selective recognition of dsRNA over single-stranded RNA (ssRNA) and dsDNA regions at near-physiological conditions. The triplex formation strategy facilitates the targeting of not only the sequence but also the secondary structure of RNA. Here, we report the development of novel dbPNA-based fluorescent light-up probes through the incorporation of A-U pair-recognizing 5-benzothiophene uracil (btU). The incorporation of btU into dbPNAs does not affect the binding affinity toward dsRNAs significantly, in most cases, as evidenced by our nondenaturing gel shift assay data. The blue fluorescence emission intensity of btU-modified dbPNAs is sequence- and structure-specifically enhanced by dsRNAs, including the influenza viral RNA panhandle duplex and HIV-1-1 ribosomal frameshift-inducing RNA hairpin, but not ssRNAs or DNAs, at 200 mM NaCl, pH 7.5. Thus, dbPNAs incorporating btU-modified and other further modified fluorescent nucleobases will be useful biochemical tools for probing and detecting RNA structures, interactions, and functions.
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Affiliation(s)
- Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Zhenyu Meng
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Zhenzhang Wang
- Temasek Life Science Laboratory , 1 Research Link, National University of Singapore , 117604 , Singapore
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory , 1 Research Link, National University of Singapore , 117604 , Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
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18
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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19
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Kesy J, Patil KM, Kumar SR, Shu Z, Yong HY, Zimmermann L, Ong AAL, Toh DFK, Krishna MS, Yang L, Decout JL, Luo D, Prabakaran M, Chen G, Kierzek E. A Short Chemically Modified dsRNA-Binding PNA (dbPNA) Inhibits Influenza Viral Replication by Targeting Viral RNA Panhandle Structure. Bioconjug Chem 2019; 30:931-943. [PMID: 30721034 DOI: 10.1021/acs.bioconjchem.9b00039] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNAs play critical roles in diverse catalytic and regulatory biological processes and are emerging as important disease biomarkers and therapeutic targets. Thus, developing chemical compounds for targeting any desired RNA structures has great potential in biomedical applications. The viral and cellular RNA sequence and structure databases lay the groundwork for developing RNA-binding chemical ligands through the recognition of both RNA sequence and RNA structure. Influenza A virion consists of eight segments of negative-strand viral RNA (vRNA), all of which contain a highly conserved panhandle duplex structure formed between the first 13 nucleotides at the 5' end and the last 12 nucleotides at the 3' end. Here, we report our binding and cell culture anti-influenza assays of a short 10-mer chemically modified double-stranded RNA (dsRNA)-binding peptide nucleic acid (PNA) designed to bind to the panhandle duplex structure through novel major-groove PNA·RNA2 triplex formation. We demonstrated that incorporation of chemically modified PNA residues thio-pseudoisocytosine (L) and guanidine-modified 5-methyl cytosine (Q) previously developed by us facilitates the sequence-specific recognition of Watson-Crick G-C and C-G pairs, respectively, at physiologically relevant conditions. Significantly, the chemically modified dsRNA-binding PNA (dbPNA) shows selective binding to the dsRNA region in panhandle structure over a single-stranded RNA (ssRNA) and a dsDNA containing the same sequence. The panhandle structure is not accessible to traditional antisense DNA or RNA with a similar length. Conjugation of the dbPNA with an aminosugar neamine enhances the cellular uptake. We observed that 2-5 μM dbPNA-neamine conjugate results in a significant reduction of viral replication. In addition, the 10-mer dbPNA inhibits innate immune receptor RIG-I binding to panhandle structure and thus RIG-I ATPase activity. These findings would provide the foundation for developing novel dbPNAs for the detection of influenza viral RNAs and therapeutics with optimal antiviral and immunomodulatory activities.
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Affiliation(s)
- Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | | | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Hui Yee Yong
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 636921 , Singapore
| | - Louis Zimmermann
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Jean-Luc Decout
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Dahai Luo
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link , National University of Singapore , 117604 , Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
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20
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Abulwerdi FA, Xu W, Ageeli AA, Yonkunas MJ, Arun G, Nam H, Schneekloth JS, Dayie TK, Spector D, Baird N, Le Grice SFJ. Selective Small-Molecule Targeting of a Triple Helix Encoded by the Long Noncoding RNA, MALAT1. ACS Chem Biol 2019; 14:223-235. [PMID: 30620551 DOI: 10.1021/acschembio.8b00807] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 ( Malat1/ MALAT1, mouse/human), a highly conserved long noncoding (lnc) RNA, has been linked with several physiological processes, including the alternative splicing, nuclear organization, and epigenetic modulation of gene expression. MALAT1 has also been implicated in metastasis and tumor proliferation in multiple cancer types. The 3' terminal stability element for nuclear expression (ENE) assumes a triple-helical configuration that promotes its nuclear accumulation and persistent function. Utilizing a novel small molecule microarray strategy, we identified multiple Malat1 ENE triplex-binding chemotypes, among which compounds 5 and 16 reduced Malat1 RNA levels and branching morphogenesis in a mammary tumor organoid model. Computational modeling and Förster resonance energy transfer experiments demonstrate distinct binding modes for each chemotype, conferring opposing structural changes to the triplex. Compound 5 modulates Malat1 downstream genes without affecting Neat1, a nuclear lncRNA encoded in the same chromosomal region as Malat1 with a structurally similar ENE triplex. Supporting this observation, the specificity of compound 5 for Malat1 over Neat1 and a virus-coded ENE was demonstrated by nuclear magnetic resonance spectroscopy. Small molecules specifically targeting the MALAT1 ENE triplex lay the foundation for new classes of anticancer therapeutics and molecular probes for the treatment and investigation of MALAT1-driven cancers.
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Affiliation(s)
- Fardokht A. Abulwerdi
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wenbo Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
- Stony Brook University, Molecular and Cellular Biology Program, Stony Brook, New York 11794, United States
| | - Abeer A. Ageeli
- University of the Sciences, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Michael J. Yonkunas
- University of the Sciences, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
| | - Hyeyeon Nam
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Theodore Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - David Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
| | - Nathan Baird
- University of the Sciences, 600 South 43rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Stuart F. J. Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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21
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Abstract
Our current knowledge on the unique roles of RNA in cells makes it vital to investigate the properties of RNA systems using computational methods because of the potential pharmaceutical applications. With the continuous advancement of computer technology, it is now possible to study RNA folding. Molecular mechanics calculations are useful in discovering the structural and thermodynamic properties of RNA systems. Yet, the predictions depend on the quality of the RNA force field, which is a set of parameters describing the potential energy of the system. Torsional parameters are one of the terms in a force field that can be revised using physics-based approaches. This chapter focuses on improvements provided by revisions of torsional parameters of the AMBER (Assisted Model Building with Energy Refinement) RNA force field. The theory behind torsional revisions and re-parameterization of several RNA torsions is briefly described. Applications of the revised torsional parameters to study RNA nucleosides, single-stranded RNA tetramers, and RNA repeat expansions are described in detail. It is concluded that RNA force fields require constant revisions and should be benchmarked against diverse RNA systems such as single strands and internal loops in order to test their qualities.
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22
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Eubanks CS, Hargrove AE. RNA Structural Differentiation: Opportunities with Pattern Recognition. Biochemistry 2018; 58:199-213. [PMID: 30513196 DOI: 10.1021/acs.biochem.8b01090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Our awareness and appreciation of the many regulatory roles of RNA have dramatically increased in the past decade. This understanding, in addition to the impact of RNA in many disease states, has renewed interest in developing selective RNA-targeted small molecule probes. However, the fundamental guiding principles in RNA molecular recognition that could accelerate these efforts remain elusive. While high-resolution structural characterization can provide invaluable insight, examples of well-characterized RNA structures, not to mention small molecule:RNA complexes, remain limited. This Perspective provides an overview of the current techniques used to understand RNA molecular recognition when high-resolution structural information is unavailable. We will place particular emphasis on a new method, pattern recognition of RNA with small molecules (PRRSM), that provides rapid insight into critical components of RNA recognition and differentiation by small molecules as well as into RNA structural features.
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Affiliation(s)
- Christopher S Eubanks
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0354 , United States
| | - Amanda E Hargrove
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0354 , United States
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23
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Effect of double mutations T790M/L858R on conformation and drug-resistant mechanism of epidermal growth factor receptor explored by molecular dynamics simulations. RSC Adv 2018; 8:39797-39810. [PMID: 35558225 PMCID: PMC9091310 DOI: 10.1039/c8ra06844e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/18/2018] [Indexed: 12/28/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is one of the most promising targets for the treatment of cancers. Double mutations T790M/L858R lead to different degrees of drug resistance toward inhibitors. In this study, molecular dynamics (MD) simulations followed by principal component analysis are performed to study the conformational changes of EGFR induced by T790M/L858R. The results suggest that T790M/L858R cause obvious disturbance of the structural stability of EGFR. Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) and residue-based free energy decomposition methods are integrated to explore the drug-resistant mechanism of T790M/L858R toward inhibitors. The results show that the decrease in van der Waals interactions of inhibitors with the mutated EFGR relative to the wild-type (WT) one is the main force inducing drug resistance of T790M/L858R toward inhibitors TAK-285, while drug resistance toward W2P and HKI-272 is dominated by the decrease in van der Waals interactions and the increase in polar interactions. We expect that the information obtained from this study can aid rational design of effective drugs to relieve drug resistance of EGFR induced by T790M/L858R.
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Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250357 China
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24
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Fluorescent Trimethylated Naphthyridine Derivative with an Aminoalkyl Side Chain as the Tightest Non-aminoglycoside Ligand for the Bacterial A-site RNA. Chemistry 2018; 24:13862-13870. [DOI: 10.1002/chem.201802320] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Indexed: 12/31/2022]
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25
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Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1477. [PMID: 29726113 PMCID: PMC6002909 DOI: 10.1002/wrna.1477] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]
Abstract
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
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26
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Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes. Nat Commun 2018; 9:2032. [PMID: 29795225 PMCID: PMC5966403 DOI: 10.1038/s41467-018-04110-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/04/2018] [Indexed: 01/04/2023] Open
Abstract
Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5' splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformations of TSL2 and promotes a shift to triloop conformations that display enhanced E7 splicing. Collectively, our study validates TSL2 as a target for small-molecule drug discovery in SMA, identifies a novel mechanism of action for an E7 splicing modifier, and sets a precedent for other splicing-mediated diseases where RNA structure could be similarly targeted.
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27
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Ganser LR, Lee J, Rangadurai A, Merriman DK, Kelly ML, Kansal AD, Sathyamoorthy B, Al-Hashimi HM. High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nat Struct Mol Biol 2018; 25:425-434. [PMID: 29728655 PMCID: PMC5942591 DOI: 10.1038/s41594-018-0062-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Dynamic ensembles hold great promise in advancing RNA-targeted drug discovery. Here we subjected the transactivation response element (TAR) RNA from human immunodeficiency virus type-1 to experimental high-throughput screening against ~100,000 drug-like small molecules. Results were augmented with 170 known TAR-binding molecules and used to generate sublibraries optimized for evaluating enrichment when virtually screening a dynamic ensemble of TAR determined by combining NMR spectroscopy data and molecular dynamics simulations. Ensemble-based virtual screening scores molecules with an area under the receiver operator characteristic curve of ~0.85-0.94 and with ~40-75% of all hits falling within the top 2% of scored molecules. The enrichment decreased significantly for ensembles generated from the same molecular dynamics simulations without input NMR data and for other control ensembles. The results demonstrate that experimentally determined RNA ensembles can significantly enrich libraries with true hits and that the degree of enrichment is dependent on the accuracy of the ensemble.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Janghyun Lee
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Megan L Kelly
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Aman D Kansal
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Chemistry, Duke University, Durham, NC, USA.
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28
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Walton JW, Cross JM, Riedel T, Dyson PJ. Perfluorinated HDAC inhibitors as selective anticancer agents. Org Biomol Chem 2018; 15:9186-9190. [PMID: 29072756 DOI: 10.1039/c7ob02339a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A series of potent histone deacetylase inhibitors is presented that incorporate alkyl or perfluorinated alkyl chains. Several new compounds show greater in vitro antiproliferative activity than the clinically approved inhibitor, SAHA. Furthermore, the new compounds show up to 5-fold greater activity against cancer cells than healthy cells. This selectivity is in contrast to SAHA, which is more active against the healthy cell line than the cancer cell line tested. Finally, we report an increase in activity for SAHA under mild hyperthermia, indicating that it could be an interesting candidate to use in combination with thermal therapy.
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Affiliation(s)
- James W Walton
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.
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29
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Guyon H, Mavré F, Catala M, Turcaud S, Brachet F, Limoges B, Tisné C, Micouin L. Use of a redox probe for an electrochemical RNA-ligand binding assay in microliter droplets. Chem Commun (Camb) 2018; 53:1140-1143. [PMID: 28054050 DOI: 10.1039/c6cc07785d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we report an affordable, sensitive, fast and user-friendly electroanalytical method for monitoring the binding between unlabeled RNA and small compounds in microliter-size droplets using a redox-probe and disposable miniaturized screen-printed electrochemical cells.
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Affiliation(s)
- Hélène Guyon
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France. and Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - Marjorie Catala
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Serge Turcaud
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France.
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Laurent Micouin
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France.
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30
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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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31
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González ÀL, Konieczny P, Llamusi B, Delgado-Pinar E, Borrell JI, Teixidó J, García-España E, Pérez-Alonso M, Estrada-Tejedor R, Artero R. In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models. PLoS One 2017; 12:e0178931. [PMID: 28582438 PMCID: PMC5459475 DOI: 10.1371/journal.pone.0178931] [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: 12/21/2016] [Accepted: 05/22/2017] [Indexed: 12/24/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a rare multisystemic disorder associated with an expansion of CUG repeats in mutant DMPK (dystrophia myotonica protein kinase) transcripts; the main effect of these expansions is the induction of pre-mRNA splicing defects by sequestering muscleblind-like family proteins (e.g. MBNL1). Disruption of the CUG repeats and the MBNL1 protein complex has been established as the best therapeutic approach for DM1, hence two main strategies have been proposed: targeted degradation of mutant DMPK transcripts and the development of CUG-binding molecules that prevent MBNL1 sequestration. Herein, suitable CUG-binding small molecules were selected using in silico approaches such as scaffold analysis, similarity searching, and druggability analysis. We used polarization assays to confirm the CUG repeat binding in vitro for a number of candidate compounds, and went on to evaluate the biological activity of the two with the strongest affinity for CUG repeats (which we refer to as compounds 1–2 and 2–5) in DM1 mutant cells and Drosophila DM1 models with an impaired locomotion phenotype. In particular, 1–2 and 2–5 enhanced the levels of free MBNL1 in patient-derived myoblasts in vitro and greatly improved DM1 fly locomotion in climbing assays. This work provides new computational approaches for rational large-scale virtual screens of molecules that selectively recognize CUG structures. Moreover, it contributes valuable knowledge regarding two compounds with desirable biological activity in DM1 models.
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Affiliation(s)
- Àlex L. González
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
| | - Piotr Konieczny
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
| | - Beatriz Llamusi
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
| | | | - José I. Borrell
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
| | - Jordi Teixidó
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
| | | | - Manuel Pérez-Alonso
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
| | - Roger Estrada-Tejedor
- Grup d’Enginyeria Molecular (GEM), Institut Químic de Sarrià (IQS)–Universitat Ramon Llull (URL), Barcelona, Catalonia, Spain
- * E-mail:
| | - Rubén Artero
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain
- Incliva-CIPF joint unit, Valencia, Spain
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32
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Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE. Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. MEDCHEMCOMM 2017; 8:1022-1036. [PMID: 28798862 PMCID: PMC5546750 DOI: 10.1039/c6md00729e] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/14/2017] [Indexed: 12/23/2022]
Abstract
Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic routes for combinatorial C(5)- and C(6)-diversification. Iterative modifications at the C(5)- and C(6)- positions yielded derivative 24, which demonstrated a 100-fold increase in activity over the parent dimethylamiloride in peptide displacement assays. NMR chemical shift mapping was performed using the 2D SOFAST- [1H-13C] HMQC NMR method, which allowed for facile and rapid evaluation of binding modes for all library members. Cheminformatic analysis revealed distinct differences between selective and non-selective ligands. In this study, we evolved dimethylamiloride from a weak TAR ligand to one of the tightest binding selective TAR ligands reported to date through a novel combination of synthetic methods and analytical techniques. We expect these methods to allow for rapid library expansion and tuning of the amiloride scaffold for a range of RNA targets and for SOFAST NMR to allow unprecedented evaluation of small molecule:RNA interactions.
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Affiliation(s)
- Neeraj N. Patwardhan
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Laura R. Ganser
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Gary J. Kapral
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Christopher S. Eubanks
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Janghyun Lee
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Bharathwaj Sathyamoorthy
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Hashim M. Al-Hashimi
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Amanda E. Hargrove
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
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33
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Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan USA
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34
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Eubanks CS, Forte JE, Kapral GJ, Hargrove AE. Small Molecule-Based Pattern Recognition To Classify RNA Structure. J Am Chem Soc 2017; 139:409-416. [PMID: 28004925 PMCID: PMC5465965 DOI: 10.1021/jacs.6b11087] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes. Complete (100%) predictive ability for this RNA training set was achieved by incorporating two exhaustively guanidinylated aminoglycosides into the receptor library. The PCA was then externally validated using biologically relevant RNA constructs. In bulge-stem-loop constructs of HIV-1 transactivation response element (TAR) RNA, we achieved nucleotide-specific classification of two independent secondary structure motifs. Furthermore, examination of cheminformatic parameters and PCA loading factors revealed trends in aminoglycoside:RNA recognition, including the importance of shape-based discrimination, and suggested the potential for size and sequence discrimination within RNA structural motifs. These studies present a new approach to classifying RNA structure and provide direct evidence that RNA topology, in addition to sequence, is critical for the molecular recognition of RNA.
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Affiliation(s)
- Christopher S Eubanks
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Jordan E Forte
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Gary J Kapral
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
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35
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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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36
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Vo DD, Duca M. Design of Multimodal Small Molecules Targeting miRNAs Biogenesis: Synthesis and In Vitro Evaluation. Methods Mol Biol 2017; 1517:137-154. [PMID: 27924480 DOI: 10.1007/978-1-4939-6563-2_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
microRNAs (miRNAs) are emerging as novel biological targets for medicinal chemists to develop chemical tools for intracellular regulation. In this context, the discovery of small-molecule drugs targeting specific miRNAs and modulating their production or function represents a very promising approach that could be further developed for targeted therapy in miRNA-related pathologies. Here, we describe the design of multimodal small molecules as RNA ligands targeting DICER-mediated miRNA maturation. The synthesis and the biochemical evaluation as ligands of stem-loop-structured precursor microRNAs (pre-miRNAs) are reported.
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Affiliation(s)
- Duc D Vo
- Institute of Chemistry of Nice, University of Nice Sophia Antipolis, UMR7272 CNRS, Parc Valrose, 06100, Nice, France
| | - Maria Duca
- Institute of Chemistry of Nice, University of Nice Sophia Antipolis, UMR7272 CNRS, Parc Valrose, 06100, Nice, France.
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37
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Paul P, Mati SS, Bhattacharya SC, Kumar GS. Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach. Phys Chem Chem Phys 2017; 19:6636-6653. [DOI: 10.1039/c6cp07888e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA targeting by small molecules.
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Affiliation(s)
- Puja Paul
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | | | | | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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38
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Toh DFK, Devi G, Patil KM, Qu Q, Maraswami M, Xiao Y, Loh TP, Zhao Y, Chen G. Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine-purine inversion site of an RNA duplex. Nucleic Acids Res 2016; 44:9071-9082. [PMID: 27596599 PMCID: PMC5100590 DOI: 10.1093/nar/gkw778] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/20/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022] Open
Abstract
RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair. Remarkably, the relatively short PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. The attached guanidine group stabilizes the base triple through hydrogen bonding with the G base in a C-G pair. Selective binding towards an RNA duplex over a single-stranded RNA can be rationalized by the fact that alkylation of the amine of a 5-methyl C base blocks the Watson-Crick edge. PNAs incorporating multiple guanidine-modified cytosine residues are able to enter HeLa cells without any transfection agent.
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Affiliation(s)
- Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Qiuyu Qu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Manikantha Maraswami
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yunyun Xiao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Teck Peng Loh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yanli Zhao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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39
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Development of pharmacophore models for small molecules targeting RNA: Application to the RNA repeat expansion in myotonic dystrophy type 1. Bioorg Med Chem Lett 2016; 26:5792-5796. [PMID: 27839685 DOI: 10.1016/j.bmcl.2016.10.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/07/2016] [Accepted: 10/12/2016] [Indexed: 01/29/2023]
Abstract
RNA is an important drug target, but current approaches to identify bioactive small molecules have been engineered primarily for protein targets. Moreover, the identification of small molecules that bind a specific RNA target with sufficient potency remains a challenge. Computer-aided drug design (CADD) and, in particular, ligand-based drug design provide a myriad of tools to identify rapidly new chemical entities for modulating a target based on previous knowledge of active compounds without relying on a ligand complex. Herein we describe pharmacophore virtual screening based on previously reported active molecules that target the toxic RNA that causes myotonic dystrophy type 1 (DM1). DM1-associated defects are caused by sequestration of muscleblind-like 1 protein (MBNL1), an alternative splicing regulator, by expanded CUG repeats (r(CUG)exp). Several small molecules have been found to disrupt the MBNL1-r(CUG)exp complex, ameliorating DM1 defects. Our pharmacophore model identified a number of potential lead compounds from which we selected 11 compounds to evaluate. Of the 11 compounds, several improved DM1 defects both in vitro and in cells.
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40
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Alberti E, Zampakou M, Donghi D. Covalent and non-covalent binding of metal complexes to RNA. J Inorg Biochem 2016; 163:278-291. [DOI: 10.1016/j.jinorgbio.2016.04.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/12/2016] [Accepted: 04/12/2016] [Indexed: 01/19/2023]
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41
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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: 206] [Impact Index Per Article: 25.8] [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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42
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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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43
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Small-molecule approaches toward the targeting of oncogenic miRNAs: roadmap for the discovery of RNA modulators. Future Med Chem 2016; 8:803-16. [DOI: 10.4155/fmc-2016-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
miRNAs are a recently discovered class of small noncoding RNAs implicated in the regulation of gene expression. The deregulation of miRNAs levels has been linked to the development of various cancers where oncogenic miRNAs are overexpressed and tumor suppressor miRNAs are underexpressed. Here we report the three main strategies developed in order to discover small-molecule drugs able to selectively interfere with oncogenic miRNAs: the high throughput screening of large libraries of compounds, the focused screening of small libraries of molecules that are known to be able to interact with RNA thus being supposed modulators of miRNAs pathway and the design of small molecules based on the secondary structure of targeted RNA and/or three-dimensional structure of enzymes involved in miRNAs pathway.
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44
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA. Bioorg Med Chem 2016; 24:3947-3952. [PMID: 27091070 DOI: 10.1016/j.bmc.2016.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure-activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Denis M Tebit
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Laurie R Gray
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - David Rekosh
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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45
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McFadden EJ, Hargrove AE. Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. Biochemistry 2016; 55:1615-30. [PMID: 26859437 DOI: 10.1021/acs.biochem.5b01141] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200 nucleotides in length, are often differentially expressed throughout developmental stages, tissue types, and disease states. The identification, visualization, and suppression/overexpression of these sequences have revealed impacts on a wide range of biological processes, including epigenetic regulation. Biochemical investigations on select systems have revealed striking insight into the biological roles of lncRNAs and lncRNA:protein complexes, which in turn prompt even more unanswered questions. To begin, multiple protein- and RNA-centric technologies have been employed to isolate lncRNA:protein and lncRNA:chromatin complexes. LncRNA interactions with the multi-subunit protein complex PRC2, which acts as a transcriptional silencer, represent some of the few cases where the binding affinity, selectivity, and activity of a lncRNA:protein complex have been investigated. At the same time, recent reports of full-length lncRNA secondary structures suggest the formation of complex structures with multiple independent folding domains and pave the way for more detailed structural investigations and predictions of lncRNA three-dimensional structure. This review will provide an overview of the methods and progress made to date as well as highlight new methods that promise to further inform the molecular recognition, specificity, and function of lncRNAs.
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Affiliation(s)
- Emily J McFadden
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University , 124 Science Drive, Durham, North Carolina 27708, United States
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46
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Pascale L, González AL, Di Giorgio A, Gaysinski M, Teixido Closa J, Tejedor RE, Azoulay S, Patino N. Deciphering structure-activity relationships in a series of Tat/TAR inhibitors. J Biomol Struct Dyn 2016; 34:2327-38. [PMID: 26524629 DOI: 10.1080/07391102.2015.1114971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A series of pentameric "Polyamide Amino Acids" (PAAs) compounds derived from the same trimeric precursor have been synthesized and investigated as HIV TAR RNA ligands, in the absence and in the presence of a Tat fragment. All PAAs bind TAR with similar sub-micromolar affinities but their ability to compete efficiently with the Tat fragment strongly differs, IC50 ranging from 35 nM to >2 μM. While NMR and CD studies reveal that all PAA interact with TAR at the same site and induce globally the same RNA conformational change upon binding, a comparative thermodynamic study of PAA/TAR equilibria highlights distinct TAR binding modes for Tat competitor and non-competitor PAAs. This led us to suggest two distinct interaction modes that have been further validated by molecular modeling studies. While the binding of Tat competitor PAAs induces a contraction at the TAR bulge region, the binding of non-competitor ones widens it. This could account for the distinct PAA ability to compete with Tat fragment. Our work illustrates how comparative thermodynamic studies of a series of RNA ligands of same chemical family are of value for understanding their binding modes and for rationalizing structure-activity relationships.
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Affiliation(s)
- Lise Pascale
- a Institut de Chimie de Nice UMR7272, Université Nice Sophia Antipolis , 06108 Nice Cedex , France
| | - Alejandro López González
- b Molecular Design Lab, IQS School of Engineering , Universitat Ramon Llull , 08017 Barcelona , Spain
| | - Audrey Di Giorgio
- a Institut de Chimie de Nice UMR7272, Université Nice Sophia Antipolis , 06108 Nice Cedex , France
| | - Marc Gaysinski
- a Institut de Chimie de Nice UMR7272, Université Nice Sophia Antipolis , 06108 Nice Cedex , France
| | - Jordi Teixido Closa
- b Molecular Design Lab, IQS School of Engineering , Universitat Ramon Llull , 08017 Barcelona , Spain
| | - Roger Estrada Tejedor
- b Molecular Design Lab, IQS School of Engineering , Universitat Ramon Llull , 08017 Barcelona , Spain
| | - Stéphane Azoulay
- a Institut de Chimie de Nice UMR7272, Université Nice Sophia Antipolis , 06108 Nice Cedex , France
| | - Nadia Patino
- a Institut de Chimie de Nice UMR7272, Université Nice Sophia Antipolis , 06108 Nice Cedex , France
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47
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Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry 2015; 54:6769-82. [PMID: 26451676 PMCID: PMC4666457 DOI: 10.1021/acs.biochem.5b00833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Knowledge
of RNA
structure is necessary to determine structure–function relationships
and to facilitate design of potential therapeutics.
RNA secondary structure prediction can be improved by applying constraints
from nuclear magnetic resonance (NMR) experiments to a dynamic programming
algorithm. Imino proton walks from NOESY spectra reveal double-stranded
regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs,
UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to
identify constraints for the 5′ to 3′ directionality
of base pairs in helices. The 5′ to 3′ directionality
constraints were incorporated into an NMR-assisted prediction of secondary
structure (NAPSS-CS) program. When it was tested on 18 structures,
including nine pseudoknots, the sensitivity and positive predictive
value were improved relative to those of three unrestrained programs.
The prediction accuracy for the pseudoknots improved the most. The
program also facilitates assignment of chemical shifts to individual
nucleotides, a necessary step for determining three-dimensional structure.
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Affiliation(s)
- Jonathan L Chen
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jason D Tubbs
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Michael J Lopez
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
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48
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Stefaniak F, Chudyk EI, Bodkin M, Dawson WK, Bujnicki JM. Modeling of ribonucleic acid-ligand interactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1226] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw Poland
| | - Ewa I. Chudyk
- Research Informatics; Evotec (UK) Ltd; Milton Park UK
| | | | - Wayne K. Dawson
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
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49
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miRNA-based therapies: strategies and delivery platforms for oligonucleotide and non-oligonucleotide agents. Future Med Chem 2015; 6:1967-84. [PMID: 25495987 DOI: 10.4155/fmc.14.116] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The discovery of miRNAs as important regulatory agents for gene expression has expanded the therapeutic opportunities for oligonucleotides. In contrast to siRNA, miRNA-targeted therapy is able to influence not only a single gene, but entire cellular pathways or processes. It is possible to supplement downregulated or non-functional miRNAs by synthetic oligonucleotides, as well as alleviating effects caused by overexpression of malignant miRNAs through artificial antagonists, either oligonucleotides or small molecules. Chemical oligonucleotide modifications together with an efficient delivery system seem to be mandatory for successful therapeutic application. While miRNA-based therapy benefits from the decades of research spent on other therapeutic oligonucleotides, there are some specific challenges associated with miRNA therapy, mainly caused by the short target sequence. The current status and recent progress of miRNA-targeted therapeutics is described and future challenges and potential applications in treatment of cancer and viral infections are discussed.
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50
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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