1
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Kodadek T. Catalytic Protein Inhibitors. Angew Chem Int Ed Engl 2024; 63:e202316726. [PMID: 38064411 DOI: 10.1002/anie.202316726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Indexed: 01/13/2024]
Abstract
Many of the highest priority targets in a wide range of disease states are difficult-to-drug proteins. The development of reversible small molecule inhibitors for the active sites of these proteins with sufficient affinity and residence time on-target is an enormous challenge. This has engendered interest in strategies to increase the potency of a given protein inhibitor by routes other than further improvement in gross affinity. Amongst these, the development of catalytic protein inhibitors has garnered the most attention and investment, particularly with respect to protein degraders, which catalyze the destruction of the target protein. This article discusses the genesis of the burgeoning field of catalytic inhibitors, the current state of the art, and exciting future directions.
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Affiliation(s)
- Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, FL 33458, USA
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2
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Kovachka S, Panosetti M, Grimaldi B, Azoulay S, Di Giorgio A, Duca M. Small molecule approaches to targeting RNA. Nat Rev Chem 2024; 8:120-135. [PMID: 38278932 DOI: 10.1038/s41570-023-00569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/28/2024]
Abstract
The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest in RNA targeting reflects the need to better understand complex intracellular processes involving RNA. In this context, small molecules are privileged tools used to explore the biological functions of RNA and to validate RNAs as therapeutic targets, and they eventually are to become new drugs. Despite recent progress, the rational design of specific RNA binders requires a better understanding of the interactions which occur with the RNA target to reach the desired biological response. In this Review, we discuss the challenges to approaching this underexplored chemical space, together with recent strategies to bind, interact and affect biologically relevant RNAs.
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Affiliation(s)
- Sandra Kovachka
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Marc Panosetti
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Benedetto Grimaldi
- Molecular Medicine Research Line, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Stéphane Azoulay
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France.
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3
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Nacheva K, Kulkarni SS, Kassu M, Flanigan D, Monastyrskyi A, Iyamu ID, Doi K, Barber M, Namelikonda N, Tipton JD, Parvatkar P, Wang HG, Manetsch R. Going beyond Binary: Rapid Identification of Protein-Protein Interaction Modulators Using a Multifragment Kinetic Target-Guided Synthesis Approach. J Med Chem 2023; 66:5196-5207. [PMID: 37000900 PMCID: PMC10620989 DOI: 10.1021/acs.jmedchem.3c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Indexed: 04/03/2023]
Abstract
Kinetic target-guided synthesis (KTGS) is a powerful screening approach that enables identification of small molecule modulators for biomolecules. While many KTGS variants have emerged, a majority of the examples suffer from limited throughput and a poor signal/noise ratio, hampering reliable hit detection. Herein, we present our optimized multifragment KTGS screening strategy that tackles these limitations. This approach utilizes selected reaction monitoring liquid chromatography tandem mass spectrometry for hit detection, enabling the incubation of 190 fragment combinations per screening well. Consequentially, our fragment library was expanded from 81 possible combinations to 1710, representing the largest KTGS screening library assembled to date. The expanded library was screened against Mcl-1, leading to the discovery of 24 inhibitors. This work unveils the true potential of KTGS with respect to the rapid and reliable identification of hits, further highlighting its utility as a complement to the existing repertoire of screening methods used in drug discovery.
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Affiliation(s)
- Katya Nacheva
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Sameer S. Kulkarni
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Mintesinot Kassu
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - David Flanigan
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Sciences, Hillsborough Community College, Tampa, Florida 33619, United States
| | - Andrii Monastyrskyi
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Iredia D. Iyamu
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Kenichiro Doi
- Department
of Pediatrics, Division of Pediatric Hematology and Oncology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Megan Barber
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Niranjan Namelikonda
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Jeremiah D. Tipton
- Proteomics
and Mass Spectrometry Core Facility, University
of South Florida, Tampa, Florida 33620, United States
| | - Prakash Parvatkar
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Hong-Gang Wang
- Department
of Pediatrics, Division of Pediatric Hematology and Oncology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Roman Manetsch
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Center for
Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Barnett
Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
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4
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Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
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Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
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5
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Chaudhuri R, Prasanth T, Dash J. Expanding the Toolbox of Target Directed Bio-Orthogonal Synthesis: In Situ Direct Macrocyclization by DNA Templates. Angew Chem Int Ed Engl 2023; 62:e202215245. [PMID: 36437509 DOI: 10.1002/anie.202215245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
Herein, we demonstrate for the first time that noncanonical DNA can direct macrocyclization-like challenging reactions to synthesize gene modulators. The planar G-quartets present in DNA G-quadruplexes (G4s) provide a size complementary reaction platform for the bio-orthogonal macrocyclization of bifunctional azide and alkyne fragments over oligo- and polymerization. G4s immobilized on gold-coated magnetic nanoparticles have been used as target templates to enable easy identification of a selective peptidomimetic macrocycle. Structurally similar macrocycles have been synthesized to understand their functional role in the modulation of gene function. The innate fluorescence of the in situ formed macrocycle has been utilized to monitor its cellular localization using a G4 antibody and its in cell formation from the corresponding azide and alkyne fragments. The successful execution of in situ macrocyclization in vitro and in cells would open up a new dimension for target-directed therapeutic applications.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
| | - Thumpati Prasanth
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Kolkata, Chunilal Bhawan,168, Maniktala Main Road, P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata, 700054, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700099, India
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6
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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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7
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Abstract
RNAs are involved in an enormous range of cellular processes, including gene regulation, protein synthesis, and cell differentiation, and dysfunctional RNAs are associated with disorders such as cancers, neurodegenerative diseases, and viral infections. Thus, the identification of compounds with the ability to bind RNAs and modulate their functions is an exciting approach for developing next-generation therapies. Numerous RNA-binding agents have been reported over the past decade, but the design of synthetic molecules with selectivity for specific RNA sequences is still in its infancy. In this perspective, we highlight recent advances in targeting RNAs with synthetic molecules, and we discuss the potential value of this approach for the development of innovative therapeutic agents.
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Affiliation(s)
- Farzad Zamani
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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8
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Bhattacharyya T, Panda D, Dash J. Supramolecular Template-Directed In Situ Click Chemistry: A Bioinspired Approach to Synthesize G-Quadruplex DNA Ligands. Org Lett 2021; 23:3004-3009. [PMID: 33830771 DOI: 10.1021/acs.orglett.1c00685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of guanosine and boronic acids produces anionic hydrogels (G-B hydrogels) that mimic the topology of the DNA G-quadruplex. We herein demonstrate an unconventional approach of using the G-B hydrogel as a supramolecular template that assembles the irreversible formation of DNA G-quadruplex-selective 1,4-triazole ligands from a pool of alkyne-azide building blocks. These generated ligands could also stabilize and strengthen the gel assembly.
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Affiliation(s)
- Tanima Bhattacharyya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Deepanjan Panda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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9
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Shibata T, Nagano K, Ueyama M, Ninomiya K, Hirose T, Nagai Y, Ishikawa K, Kawai G, Nakatani K. Small molecule targeting r(UGGAA) n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat Commun 2021; 12:236. [PMID: 33431896 PMCID: PMC7801683 DOI: 10.1038/s41467-020-20487-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here we report our discovery that naphthyridine carbamate dimer (NCD) targets disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31 (SCA31). Structural analysis of the NCD-UGGAA/UGGAA complex by nuclear magnetic resonance (NMR) spectroscopy clarifies the mode of binding that recognizes four guanines in the UGGAA/UGGAA pentad by hydrogen bonding with four naphthyridine moieties of two NCD molecules. Biological studies show that NCD disrupts naturally occurring RNA foci built on r(UGGAA)n repeat RNA known as nuclear stress bodies (nSBs) by interfering with RNA–protein interactions resulting in the suppression of nSB-mediated splicing events. Feeding NCD to larvae of the Drosophila model of SCA31 alleviates the disease phenotype induced by toxic r(UGGAA)n repeat RNA. These studies demonstrate that small molecules targeting toxic repeat RNAs are a promising chemical tool for studies on repeat expansion diseases. Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here the authors show the mechanism by which a small molecule targets the disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31.
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Affiliation(s)
- Tomonori Shibata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki, Japan
| | - Konami Nagano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Morio Ueyama
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kinya Ishikawa
- Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki, Japan.
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10
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Kaur J, Bhardwaj A, Wuest F. In Cellulo Generation of Fluorescent Probes for Live-Cell Imaging of Cylooxygenase-2. Chemistry 2020; 27:3326-3337. [PMID: 32786126 DOI: 10.1002/chem.202003315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Indexed: 02/01/2023]
Abstract
Live-cell imaging with fluorescent probes is an essential tool in chemical biology to visualize the dynamics of biological processes in real-time. Intracellular disease biomarker imaging remains a formidable challenge due to the intrinsic limitations of conventional fluorescent probes and the complex nature of cells. This work reports the in cellulo assembly of a fluorescent probe to image cyclooxygenase-2 (COX-2). We developed celecoxib-azide derivative 14, possessing favorable biophysical properties and excellent COX-2 selectivity profile. In cellulo strain-promoted fluorogenic click chemistry of COX-2-engaged compound 14 with non/weakly-fluorescent compounds 11 and 17 formed fluorescent probes 15 and 18 for the detection of COX-2 in living cells. Competitive binding studies, biophysical, and comprehensive computational analyses were used to describe protein-ligand interactions. The reported new chemical toolbox enables precise visualization and tracking of COX-2 in live cells with superior sensitivity in the visible range.
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Affiliation(s)
- Jatinder Kaur
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Atul Bhardwaj
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank Wuest
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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11
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Costales MG, Childs-Disney JL, Haniff HS, Disney MD. How We Think about Targeting RNA with Small Molecules. J Med Chem 2020; 63:8880-8900. [PMID: 32212706 PMCID: PMC7486258 DOI: 10.1021/acs.jmedchem.9b01927] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA offers nearly unlimited potential as a target for small molecule chemical probes and lead medicines. Many RNAs fold into structures that can be selectively targeted with small molecules. This Perspective discusses molecular recognition of RNA by small molecules and highlights key enabling technologies and properties of bioactive interactions. Sequence-based design of ligands targeting RNA has established rules for affecting RNA targets and provided a potentially general platform for the discovery of bioactive small molecules. The RNA targets that contain preferred small molecule binding sites can be identified from sequence, allowing identification of off-targets and prediction of bioactive interactions by nature of ligand recognition of functional sites. Small molecule targeted degradation of RNA targets (ribonuclease-targeted chimeras, RIBOTACs) and direct cleavage by small molecules have also been developed. These growing technologies suggest that the time is right to provide small molecule chemical probes to target functionally relevant RNAs throughout the human transcriptome.
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Affiliation(s)
- Matthew G Costales
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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12
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Hagler LD, Luu LM, Tonelli M, Lee J, Hayes SM, Bonson SE, Vergara JI, Butcher SE, Zimmerman SC. Expanded DNA and RNA Trinucleotide Repeats in Myotonic Dystrophy Type 1 Select Their Own Multitarget, Sequence-Selective Inhibitors. Biochemistry 2020; 59:3463-3472. [PMID: 32856901 DOI: 10.1021/acs.biochem.0c00472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There are few methods available for the rapid discovery of multitarget drugs. Herein, we describe the template-assisted, target-guided discovery of small molecules that recognize d(CTG) in the expanded d(CTG·CAG) sequence and its r(CUG) transcript that cause myotonic dystrophy type 1. A positive cross-selection was performed using a small library of 30 monomeric alkyne- and azide-containing ligands capable of producing >5000 possible di- and trimeric click products. The monomers were incubated with d(CTG)16 or r(CUG)16 under physiological conditions, and both sequences showed selectivity in the proximity-accelerated azide-alkyne [3+2] cycloaddition click reaction. The limited number of click products formed in both selections and the even smaller number of common products suggests that this method is a useful tool for the discovery of single-target and multitarget lead therapeutic agents.
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Affiliation(s)
- Lauren D Hagler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Long M Luu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marco Tonelli
- National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - JuYeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Samuel M Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sarah E Bonson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - J Ignacio Vergara
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Angelbello AJ, Disney MD. A Toxic RNA Templates the Synthesis of Its Own Fluorogenic Inhibitor by Using a Bio-orthogonal Tetrazine Ligation in Cells and Tissues. ACS Chem Biol 2020; 15:1820-1825. [PMID: 32551539 DOI: 10.1021/acschembio.0c00417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Expanded RNA repeats cause more than 30 incurable diseases. One approach to mitigate their toxicity is by using small molecules that assemble into potent, oligomeric species upon binding to the disease-causing RNA in cells. Herein, we show that the expanded repeat [r(CUG)exp] that causes myotonic dystrophy type 1 (DM1) catalyzes the in situ synthesis of its own inhibitor using an RNA-templated tetrazine ligation in DM1 patient-derived cells. The compound synthesized on-site improved DM1-associated defects at picomolar concentrations, enhancing potency by 10 000-fold, compared to its parent compounds that cannot undergo oligomerization. A fluorogenic reaction is also described where r(CUG)exp templates the synthesis of its own imaging probe to enable visualization of the repeat in its native context in live cells and muscle tissue.
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Affiliation(s)
- Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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14
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Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 2020; 20:474-489. [PMID: 31182864 DOI: 10.1038/s41580-019-0136-0] [Citation(s) in RCA: 244] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNAs fold into 3D structures that range from simple helical elements to complex tertiary structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory RNAs depend on how their 3D structure changes in response to a diverse array of cellular conditions. In this Review, we examine how the structural characterization of RNA as dynamic ensembles of conformations, which form with different probabilities and at different timescales, is improving our understanding of RNA function in cells. We discuss the mechanisms of gene regulation by microRNAs, riboswitches, ribozymes, post-transcriptional RNA modifications and RNA-binding proteins, and how the cellular environment and processes such as liquid-liquid phase separation may affect RNA folding and activity. The emerging RNA-ensemble-function paradigm is changing our perspective and understanding of RNA regulation, from in vitro to in vivo and from descriptive to predictive.
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Affiliation(s)
- Laura R Ganser
- 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
| | - Daniel Herschlag
- Department of Biochemistry, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA.,Department of Chemical Engineering, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, 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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15
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Benhamou RI, Angelbello AJ, Andrews RJ, Wang ET, Moss WN, Disney MD. Structure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide. ACS Chem Biol 2020; 15:485-493. [PMID: 31927948 DOI: 10.1021/acschembio.9b00958] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy that is caused by an expanded repeat of r(CCUG) [r(CCUG)exp] in intron 1 of a CHC-type zinc finger nucleic acid binding protein (CNBP) pre-mRNA. Various mechanisms contribute to DM2 pathology including pre-mRNA splicing defects caused by sequestration of the RNA splicing regulator muscleblind-like-1 (MBNL1) by r(CCUG)exp. Herein, we study the biological impacts of the molecular recognition of r(CCUG)exp's structure by a designer dimeric small molecule that directly cleaves the RNA in patient-derived cells. The compound is comprised of two RNA-binding modules conjugated to a derivative of the natural product bleomycin. Careful design of the chimera affords RNA-specific cleavage, as attachment of the bleomycin cleaving module was done in a manner that disables DNA cleavage. The chimeric cleaver is more potent than the parent binding compound for alleviating DM2-associated defects. Importantly, oligonucleotides targeting the r(CCUG)exp sequence for cleavage exacerbate DM2 defects due to recognition of a short r(CCUG) sequence that is embedded in CNBP, argonaute-1 (AGO1), and MBNL1, reducing their levels. The latter event causes a greater depletion of functional MBNL1 than the amount already sequestered by r(CCUG)exp. Thus, compounds targeting RNA structures can have functional advantages over oligonucleotides that target the sequence in some disease settings, particularly in DM2.
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Affiliation(s)
- Raphael I. Benhamou
- Department of Chemistry, The Scripps Research Institute, 110 Scripps Way, Jupiter, Florida 33458, United States
| | - Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute, 110 Scripps Way, Jupiter, Florida 33458, United States
| | - Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, UF Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, Florida 32610, United States
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 110 Scripps Way, Jupiter, Florida 33458, United States
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16
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Short Tandem Repeat-Enriched Architectural RNAs in Nuclear Bodies: Functions and Associated Diseases. Noncoding RNA 2020; 6:ncrna6010006. [PMID: 32093161 PMCID: PMC7151548 DOI: 10.3390/ncrna6010006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear bodies are membraneless, phase-separated compartments that concentrate specific proteins and RNAs in the nucleus. They are believed to serve as sites for the modification, sequestration, and storage of specific factors, and to act as organizational hubs of chromatin structure to control gene expression and cellular function. Architectural (arc) RNA, a class of long noncoding RNA (lncRNA), plays essential roles in the formation of nuclear bodies. Herein, we focus on specific arcRNAs containing short tandem repeat-enriched sequences and introduce their biological functions and recently elucidated underlying molecular mechanism. In various neurodegenerative diseases, abnormal nuclear and cytoplasmic bodies are built on disease-causing RNAs or toxic RNAs with aberrantly expanded short tandem repeat-enriched sequences. We discuss the possible analogous functions of natural arcRNAs and toxic RNAs with short tandem repeat-enriched sequences. Finally, we describe the technical utility of short tandem repeat-enriched arcRNAs as a model for exploring the structures and functions of nuclear bodies, as well as the pathogenic mechanisms of neurodegenerative diseases.
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17
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Saha P, Panda D, Müller D, Maity A, Schwalbe H, Dash J. In situ formation of transcriptional modulators using non-canonical DNA i-motifs. Chem Sci 2020; 11:2058-2067. [PMID: 32180928 PMCID: PMC7047845 DOI: 10.1039/d0sc00514b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
Herein, i-motif DNA-immobilized magnetic nanoparticles are used as templates to promote the in situ cycloaddition generating specific binders for i-motifs.
Non-canonical DNA i-motifs and G-quadruplexes are postulated as genetic switches for the transcriptional regulation of proto-oncogenes. However, in comparison to G-quadruplexes, the therapeutic potential of i-motifs is less explored. The development of i-motif selective ligands by conventional approaches is challenging due to the structural complexity of i-motifs. The target guided synthetic (TGS) approach involving in situ cycloaddition could provide specific ligands for these dynamic DNA structures. Herein, we have used i-motif forming C-rich DNA and their complementary G-quadruplex forming DNA sequences of c-MYC and BCL2 promoter regions as well as a control self-complementary duplex DNA sequence as the templates to generate selective ligands from a pool of reactive azide–alkyne building blocks. In our approach, thiolated DNA targets are immobilized on the surface of gold-coated iron nanoparticles to enable efficient isolation of the newly generated ligands from the solution mixture by simple magnetic decantation. The combinatorial in situ cycloaddition generated cell-membrane permeable triazole leads for respective DNA targets (c-MYC and BCL2 i-motifs and G-quadruplexes) that selectively promote their formation. In vitro cellular studies reveal that the c-MYC i-motif and G-quadruplex leads downregulate c-MYC gene expression whereas the BCL2 i-motif lead upregulates and the BCL2 G-quadruplex lead represses BCL2 gene expression. The TGS strategy using i-motif DNA nanotemplates represents a promising platform for the direct in situ formation of i-motif specific ligands for therapeutic intervention.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Deepanjan Panda
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Diana Müller
- Institute of Organic Chemistry and Chemical Biology , Center for Biomolecular Magnetic Resonance (BMRZ) , Goethe University , Max-von-Laue Strasse 7 , Frankfurt , D-60438 , Germany
| | - Arunabha Maity
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology , Center for Biomolecular Magnetic Resonance (BMRZ) , Goethe University , Max-von-Laue Strasse 7 , Frankfurt , D-60438 , Germany
| | - Jyotirmayee Dash
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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18
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Benhamou RI, Angelbello AJ, Wang ET, Disney MD. A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways. Cell Chem Biol 2020; 27:223-231.e4. [PMID: 31981476 DOI: 10.1016/j.chembiol.2020.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/22/2019] [Accepted: 01/03/2020] [Indexed: 12/12/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetically defined disease caused by a toxic expanded repeat of r(CCUG) [r(CCUG)exp], harbored in intron 1 of CCHC-type zinc-finger nucleic acid binding protein (CNBP) pre-mRNA. This r(CCUG)exp causes toxicity via a gain-of-function mechanism, resulting in three pathological hallmarks: aggregation into nuclear foci; sequestration of muscleblind-like-1 (MBNL1) protein, leading to splicing defects; and retention of CNBP intron 1. We studied two types of small molecules with different modes of action, ones that simply bind and ones that are templated by r(CCUG)exp in cells, i.e., the RNA synthesizes its own drug. Indeed, our studies completed in DM2 patient-derived fibroblasts showed that the compounds disrupt the r(CCUG)exp-MBNL1 complex, reduce intron retention, subjecting the liberated intronic r(CCUG)exp to native decay pathways, and rescue other DM2-associated cellular defects. Importantly, this study shows that small molecules can modulate RNA biology by shunting toxic transcripts toward native decay pathways.
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Affiliation(s)
- Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, UF Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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19
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Bosc D, Camberlein V, Gealageas R, Castillo-Aguilera O, Deprez B, Deprez-Poulain R. Kinetic Target-Guided Synthesis: Reaching the Age of Maturity. J Med Chem 2019; 63:3817-3833. [PMID: 31820982 DOI: 10.1021/acs.jmedchem.9b01183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinetic target-guided synthesis (KTGS) is an original discovery strategy allowing a target to catalyze the irreversible synthesis of its own ligands from a pool of reagents. Although pioneered almost two decades ago, it only recently proved its usefulness in medicinal chemistry, as exemplified by the increasing number of protein targets used, the wider range of target and pocket types, and the diversity of therapeutic areas explored. In recent years, two new leads for in vivo studies were released. Amidations and multicomponent reactions expanded the armamentarium of reactions beyond triazole formation and two new examples of in cellulo KTGS were also disclosed. Herein, we analyze the origins and the chemical space of both KTGS ligands and warhead-bearing reagents. We review the KTGS timeline focusing on recent cases in order to give medicinal chemists the full scope of this strategy which has great potential for hit discovery and hit or lead optimization.
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Affiliation(s)
- Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Virgyl Camberlein
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Omar Castillo-Aguilera
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France.,Institut Universitaire de France, F- 75005 Paris, France
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20
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Di Giorgio A, Duca M. Synthetic small-molecule RNA ligands: future prospects as therapeutic agents. MEDCHEMCOMM 2019; 10:1242-1255. [PMID: 31534649 PMCID: PMC6748380 DOI: 10.1039/c9md00195f] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
Abstract
RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in many pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified. Among the most important ones, one can mention prokaryotic ribosomal RNA which is the target of several marketed antibiotics, viral RNAs or oncogenic microRNAs that are tightly involved in the development and progression of various cancers. Oligonucleotides are efficient and specific RNA targeting agents but suffer from poor pharmacodynamic and pharmacokinetic properties. For this reason, a number of synthetic small-molecule ligands have been identified and studied upon screening of chemical libraries or focused design of RNA binders. In this review, we report the most relevant examples of synthetic compounds bearing sufficient selectivity to envisage clinical studies and future therapeutic applications with a particular attention for the main strategies that can be undertaken toward the improvement of selectivity and biological activity.
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Affiliation(s)
- A Di Giorgio
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
| | - M Duca
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
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21
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Sackler Prize in Physical Sciences Innovation Prize in Medicinal/Pharmaceutical Chemistry. Angew Chem Int Ed Engl 2019; 58:8973. [PMID: 31148347 DOI: 10.1002/anie.201906251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Sackler Prize in Physical Sciences Innovationspreis der GDCh‐Fachgruppe Medizinische Chemie. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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A Massively Parallel Selection of Small Molecule-RNA Motif Binding Partners Informs Design of an Antiviral from Sequence. Chem 2018; 4:2384-2404. [PMID: 30719503 DOI: 10.1016/j.chempr.2018.08.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many RNAs cause disease; however, RNA is rarely exploited as a small-molecule drug target. Our programmatic focus is to define privileged RNA motif small-molecule interactions to enable the rational design of compounds that modulate RNA biology starting from only sequence. We completed a massive, library-versus-library screen that probed over 50 million binding events between RNA motifs and small molecules. The resulting data provide a rich encyclopedia of small-molecule RNA recognition patterns, defining chemotypes and RNA motifs that confer selective, avid binding. The resulting interaction maps were mined against the entire viral genome of hepatitis C virus (HCV). A small molecule was identified that avidly bound RNA motifs present in the HCV 30 UTR and inhibited viral replication while having no effect on host cells. Collectively, this study represents the first whole-genome pattern recognition between small molecules and RNA folds.
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24
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Jin X, Daher SS, Lee M, Buttaro B, Andrade RB. Ribosome-Templated Azide-Alkyne Cycloadditions Using Resistant Bacteria as Reaction Vessels: in Cellulo Click Chemistry. ACS Med Chem Lett 2018; 9:907-911. [PMID: 30258539 DOI: 10.1021/acsmedchemlett.8b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/13/2018] [Indexed: 01/21/2023] Open
Abstract
In situ click chemistry has been a powerful method for fragment-based drug design since its discovery in 2002. Recently, we demonstrated that the bacterial ribosome can template the azide-alkyne cycloaddition reaction to expedite the discovery of novel antibiotics. We now report this process can be performed in an antibiotic-resistant bacterial cell. The corresponding triazole products formed in cellulo are potent antibiotics that inhibit bacterial growth; moreover, the potency of each cycloadduct can be visualized using the traditional MIC assay in a 96-well plate format. We characterized the in cellulo clicked products by independent chemical synthesis and LC-MS analysis, which showed that mass count percent increase was directly proportional to 1/MIC. In other words, potent compounds detected by MIC were formed in greater amounts. Control experiments unambiguously showed the ribosome was responsible for templating triazole formation. Significantly, our method (1) obviates the need to isolate bacterial ribosomes; (2) could be applied to different bacterial strains, which broadens the scope and facilitates the discovery of narrow-spectrum antibiotics; and (3) does not require the knowledge of mode-of-action and thus could uncover novel antibiotic targets. We believe this method could be expanded and implemented as a novel approach for antibiotic drug discovery.
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Affiliation(s)
- Xiao Jin
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Samer S. Daher
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Miseon Lee
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Bettina Buttaro
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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25
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Haniff HS, Graves A, Disney MD. Selective Small Molecule Recognition of RNA Base Pairs. ACS COMBINATORIAL SCIENCE 2018; 20:482-491. [PMID: 29966095 PMCID: PMC6325646 DOI: 10.1021/acscombsci.8b00049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many types of RNAs exist in the human transcriptome, yet only the bacterial ribosome has been exploited as a small molecule drug target. Aside from rRNA, other cellular RNAs such as noncoding RNAs have primarily secondary structure and limited tertiary structure. Within these secondary structures of noncanonically paired and unpaired regions, more than 50% are base paired, with most efforts to target these structures focused on looped regions. A void exists in the availability of small molecules capable of targeting RNA base pairs. Using chemoinformatics, an RNA-focused library enriched for nitrogen-containing heterocycles was developed and tested for binding RNA base pairs, leading to the identification of six selective and previously unknown binders. While all binders were derivatives of benzimidazoles, those with expanded aromatic polycycles bound selectively to AU pairs, while those with flexible urea side chains bound selectively to GC pairs. Two of the three selective GC pair binders can distinguish between two different orientations, 5'GG/3'CC and 5'GC/3'CG pairs. Furthermore, all six molecules showed >50-fold selectivity for RNA over DNA. These studies provide foundational knowledge to better exploit RNA as targets for small molecule chemical probes or lead therapeutics by using modules that target RNA base pairs.
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Affiliation(s)
- Hafeez S Haniff
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Amanda Graves
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
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26
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Antti H, Sellstedt M. Cell-Based Kinetic Target-Guided Synthesis of an Enzyme Inhibitor. ACS Med Chem Lett 2018; 9:351-353. [PMID: 29670699 DOI: 10.1021/acsmedchemlett.7b00535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/04/2018] [Indexed: 12/22/2022] Open
Abstract
Finding a new drug candidate for a selected target is an expensive and time-consuming process. Target guided-synthesis, or in situ click chemistry, is a concept where the drug target is used to template the formation of its own inhibitors from reactive building blocks. This could simplify the identification of drug candidates. However, with the exception of one example of an RNA-target, target-guided synthesis has always employed purified targets. This limits the number of targets that can be screened by the method. By applying methods from the field of metabolomics, we demonstrate that target-guided synthesis with protein targets also can be performed directly in cell-based systems. These methods offer new possibilities to conduct screening for drug candidates of difficult protein targets in cellular environments.
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Affiliation(s)
- Henrik Antti
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
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27
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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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28
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Hilimire TA, Chamberlain JM, Anokhina V, Bennett RP, Swart O, Myers JR, Ashton JM, Stewart RA, Featherston AL, Gates K, Helms ED, Smith HC, Dewhurst S, Miller BL. HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells. ACS Chem Biol 2017; 12:1674-1682. [PMID: 28448121 PMCID: PMC5477779 DOI: 10.1021/acschembio.7b00052] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
The
HIV-1 frameshift-stimulating (FSS) RNA, a regulatory RNA of
critical importance in the virus’ life cycle, has been posited
as a novel target for anti-HIV drug development. We report the synthesis
and evaluation of triazole-containing compounds able to bind the FSS
with high affinity and selectivity. Readily accessible synthetically,
these compounds are less toxic than previously reported olefin congeners.
We show for the first time that FSS-targeting compounds have antiviral
activity against replication-competent HIV in human cells, including
a highly cytopathic, multidrug-resistant strain. These results support
the viability of the HIV-1 FSS RNA as a therapeutic target and more
generally highlight opportunities for synthetic molecule-mediated
interference with protein recoding in a wide range of organisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Eric D. Helms
- Department of Chemistry, SUNY Geneseo, Geneseo, New York 14454, United States
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29
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Urbanek MO, Fiszer A, Krzyzosiak WJ. Reduction of Huntington's Disease RNA Foci by CAG Repeat-Targeting Reagents. Front Cell Neurosci 2017; 11:82. [PMID: 28400719 PMCID: PMC5368221 DOI: 10.3389/fncel.2017.00082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022] Open
Abstract
In several human polyglutamine diseases caused by expansions of CAG repeats in the coding sequence of single genes, mutant transcripts are detained in nuclear RNA foci. In polyglutamine disorders, unlike other repeat-associated diseases, both RNA and proteins exert pathogenic effects; therefore, decreases of both RNA and protein toxicity need to be addressed in proposed treatments. A variety of oligonucleotide-based therapeutic approaches have been developed for polyglutamine diseases, but concomitant assays for RNA foci reduction are lacking. Here, we show that various types of oligonucleotide-based reagents affect RNA foci number in Huntington’s disease cells. We analyzed the effects of reagents targeting either CAG repeat tracts or specific HTT sequences in fibroblasts derived from patients. We tested reagents that either acted as translation blockers or triggered mRNA degradation via the RNA interference pathway or RNase H activation. We also analyzed the effect of chemical modifications of CAG repeat-targeting siRNAs on their efficiency in the foci decline. Our results suggest that the decrease of RNA foci number may be considered as a readout of treatment outcomes for oligonucleotide reagents.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
| | - Agnieszka Fiszer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
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30
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Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Nat Chem Biol 2016; 13:188-193. [PMID: 27941760 DOI: 10.1038/nchembio.2251] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023]
Abstract
Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context.
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Park H, Tran T, Lee JH, Park H, Disney MD. Controlled dehydration improves the diffraction quality of two RNA crystals. BMC STRUCTURAL BIOLOGY 2016; 16:19. [PMID: 27809904 PMCID: PMC5093936 DOI: 10.1186/s12900-016-0069-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/18/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND Post-crystallization dehydration methods, applying either vapor diffusion or humidity control devices, have been widely used to improve the diffraction quality of protein crystals. Despite the fact that RNA crystals tend to diffract poorly, there is a dearth of reports on the application of dehydration methods to improve the diffraction quality of RNA crystals. RESULTS We use dehydration techniques with a Free Mounting System (FMS, a humidity control device) to recover the poor diffraction quality of RNA crystals. These approaches were applied to RNA constructs that model various RNA-mediated repeat expansion disorders. CONCLUSION The method we describe herein could serve as a general tool to improve diffraction quality of RNA crystals to facilitate structure determinations.
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Affiliation(s)
- HaJeung Park
- X-ray Core Facility, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Tuan Tran
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990 Republic of Korea ,Department of Polar Sciences, University of Science and Technology, Incheon, 21990 Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990 Republic of Korea ,Department of Polar Sciences, University of Science and Technology, Incheon, 21990 Republic of Korea
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458 USA
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Disney MD, Winkelsas AM, Velagapudi SP, Southern M, Fallahi M, Childs-Disney JL. Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs. ACS Chem Biol 2016; 11:1720-8. [PMID: 27097021 DOI: 10.1021/acschembio.6b00001] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The development of small molecules that target RNA is challenging yet, if successful, could advance the development of chemical probes to study RNA function or precision therapeutics to treat RNA-mediated disease. Previously, we described Inforna, an approach that can mine motifs (secondary structures) within target RNAs, which is deduced from the RNA sequence, and compare them to a database of known RNA motif-small molecule binding partners. Output generated by Inforna includes the motif found in both the database and the desired RNA target, lead small molecules for that target, and other related meta-data. Lead small molecules can then be tested for binding and affecting cellular (dys)function. Herein, we describe Inforna 2.0, which incorporates all known RNA motif-small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. By incorporation of interactions identified by other laboratories, the database has been doubled, containing 1936 RNA motif-small molecule interactions, including 244 unique small molecules and 1331 motifs. Interestingly, chemotype analysis of the compounds that bind RNA in the database reveals features in small molecule chemotypes that are privileged for binding. Further, this updated database expanded the number of cellular RNAs to which lead compounds can be identified.
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Affiliation(s)
- Matthew D. Disney
- Department of Chemistry and ‡Informatics Core, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Audrey M. Winkelsas
- Department of Chemistry and ‡Informatics Core, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Sai Pradeep Velagapudi
- Department of Chemistry and ‡Informatics Core, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Mark Southern
- Department of Chemistry and ‡Informatics Core, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Mohammad Fallahi
- Department of Chemistry and ‡Informatics Core, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- Department of Chemistry and ‡Informatics Core, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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Shukla S, Parker R. Hypo- and Hyper-Assembly Diseases of RNA-Protein Complexes. Trends Mol Med 2016; 22:615-628. [PMID: 27263464 DOI: 10.1016/j.molmed.2016.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 12/14/2022]
Abstract
A key aspect of cellular function is the proper assembly and utilization of ribonucleoproteins (RNPs). Recent studies have shown that hyper- or hypo-assembly of various RNPs can lead to human diseases. Defects in the formation of RNPs lead to 'RNP hypo-assembly diseases', which can be caused by RNA degradation outcompeting RNP assembly. By contrast, excess RNP assembly, either in higher order RNP granules, or due to the expression of repeat-containing RNAs, can lead to 'RNP hyper-assembly diseases'. Here, we discuss the most recent advances in understanding the cause of disease onset, as well as potential therapies from the aspect of modulating RNP assembly in the cell, which presents a novel route to the treatment of these diseases.
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Affiliation(s)
- Siddharth Shukla
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Costales MG, Rzuczek SG, Disney MD. Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA. Bioorg Med Chem Lett 2016; 26:2605-9. [PMID: 27117425 DOI: 10.1016/j.bmcl.2016.04.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/09/2016] [Accepted: 04/11/2016] [Indexed: 11/29/2022]
Abstract
Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)(exp)) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example.
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Affiliation(s)
- Matthew G Costales
- Departments of Chemistry & Neuroscience, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Suzanne G Rzuczek
- Departments of Chemistry & Neuroscience, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Matthew D Disney
- Departments of Chemistry & Neuroscience, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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Glassford I, Teijaro CN, Daher SS, Weil A, Small MC, Redhu SK, Colussi DJ, Jacobson MA, Childers WE, Buttaro B, Nicholson AW, MacKerell AD, Cooperman BS, Andrade RB. Ribosome-Templated Azide-Alkyne Cycloadditions: Synthesis of Potent Macrolide Antibiotics by In Situ Click Chemistry. J Am Chem Soc 2016; 138:3136-44. [PMID: 26878192 PMCID: PMC4785600 DOI: 10.1021/jacs.5b13008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over half of all antibiotics target the bacterial ribosome-nature's complex, 2.5 MDa nanomachine responsible for decoding mRNA and synthesizing proteins. Macrolide antibiotics, exemplified by erythromycin, bind the 50S subunit with nM affinity and inhibit protein synthesis by blocking the passage of nascent oligopeptides. Solithromycin (1), a third-generation semisynthetic macrolide discovered by combinatorial copper-catalyzed click chemistry, was synthesized in situ by incubating either E. coli 70S ribosomes or 50S subunits with macrolide-functionalized azide 2 and 3-ethynylaniline (3) precursors. The ribosome-templated in situ click method was expanded from a binary reaction (i.e., one azide and one alkyne) to a six-component reaction (i.e., azide 2 and five alkynes) and ultimately to a 16-component reaction (i.e., azide 2 and 15 alkynes). The extent of triazole formation correlated with ribosome affinity for the anti (1,4)-regioisomers as revealed by measured Kd values. Computational analysis using the site-identification by ligand competitive saturation (SILCS) approach indicated that the relative affinity of the ligands was associated with the alteration of macrolactone+desosamine-ribosome interactions caused by the different alkynes. Protein synthesis inhibition experiments confirmed the mechanism of action. Evaluation of the minimal inhibitory concentrations (MIC) quantified the potency of the in situ click products and demonstrated the efficacy of this method in the triaging and prioritization of potent antibiotics that target the bacterial ribosome. Cell viability assays in human fibroblasts confirmed 2 and four analogues with therapeutic indices for bactericidal activity over in vitro mammalian cytotoxicity as essentially identical to solithromycin (1).
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Affiliation(s)
- Ian Glassford
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | | | - Samer S. Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Amy Weil
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Meagan C. Small
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122
| | - Dennis J. Colussi
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Marlene A. Jacobson
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Wayne E. Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Bettina Buttaro
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140
| | | | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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Urbanek MO, Krzyzosiak WJ. RNA FISH for detecting expanded repeats in human diseases. Methods 2015; 98:115-123. [PMID: 26615955 DOI: 10.1016/j.ymeth.2015.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/18/2015] [Accepted: 11/21/2015] [Indexed: 12/14/2022] Open
Abstract
RNA fluorescence in situ hybridization (FISH) is a widely used technique for detecting transcripts in fixed cells and tissues. Many variants of RNA FISH have been proposed to increase signal strength, resolution and target specificity. The current variants of this technique facilitate the detection of the subcellular localization of transcripts at a single molecule level. Among the applications of RNA FISH are studies on nuclear RNA foci in diseases resulting from the expansion of tri-, tetra-, penta- and hexanucleotide repeats present in different single genes. The partial or complete retention of mutant transcripts forming RNA aggregates within the nucleoplasm has been shown in multiple cellular disease models and in the tissues of patients affected with these atypical mutations. Relevant diseases include, among others, myotonic dystrophy type 1 (DM1) with CUG repeats, Huntington's disease (HD) and spinocerebellar ataxia type 3 (SCA3) with CAG repeats, fragile X-associated tremor/ataxia syndrome (FXTAS) with CGG repeats, myotonic dystrophy type 2 (DM2) with CCUG repeats, amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) with GGGGCC repeats and spinocerebellar ataxia type 32 (SCA32) with GGCCUG. In this article, we summarize the results obtained with FISH to examine RNA nuclear inclusions. We provide a detailed protocol for detecting RNAs containing expanded CAG and CUG repeats in different cellular models, including fibroblasts, lymphoblasts, induced pluripotent stem cells and murine and human neuronal progenitors. We also present the results of the first single-molecule FISH application in a cellular model of polyglutamine disease.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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Childs-Disney JL, Disney MD. Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells. Annu Rev Pharmacol Toxicol 2015; 56:123-40. [PMID: 26514201 DOI: 10.1146/annurev-pharmtox-010715-103910] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA has become an increasingly important target for therapeutic interventions and for chemical probes that dissect and manipulate its cellular function. Emerging targets include human RNAs that have been shown to directly cause cancer, metabolic disorders, and genetic disease. In this review, we describe various routes to obtain bioactive compounds that target RNA, with a particular emphasis on the development of small molecules. We use these cases to describe approaches that are being developed for target validation, which include target-directed cleavage, classic pull-down experiments, and covalent cross-linking. Thus, tools are available to design small molecules to target RNA and to identify the cellular RNAs that are their targets.
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Affiliation(s)
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458; ,
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Bochicchio A, Rossetti G, Tabarrini O, Krauβ S, Carloni P. Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy. J Chem Theory Comput 2015; 11:4911-22. [PMID: 26574279 DOI: 10.1021/acs.jctc.5b00208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Huntington's disease is a fatal and devastating neurodegenerative genetic disorder for which there is currently no cure. It is characterized by Huntingtin protein's mRNA transcripts with 36 or more CAG repeats. Inhibiting the formation of pathological complexes between these expanded transcripts and target proteins may be a valuable strategy against the disease. Yet, the rational design of molecules specifically targeting the expanded CAG repeats is limited by the lack of structural information. Here, we use well-tempered metadynamics-based free energy calculations to investigate pose and affinity of two ligands targeting CAG repeats for which affinities have been previously measured. The first consists of two 4-guanidinophenyl rings linked by an ester group. It is the most potent ligand identified so far, with Kd = 60(30) nM. The second consists of a 4-phenyl dihydroimidazole and 4-1H-indole dihydroimidazole connected by a C-C bond (Kd = 700(80) nM). Our calculations reproduce the experimental affinities and uncover the recognition pattern between ligands' and their RNA target. They also provide a molecular basis for the markedly different affinity of the two ligands for CAG repeats as observed experimentally. These findings may pave the way for a structure-based hit-to-lead optimization to further improve ligand selectivity toward CAG repeat-containing mRNAs.
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Affiliation(s)
| | - Giulia Rossetti
- Department of Oncology, Hematology and Stem Cell Transplantation, RWTH Aachen University , D-52074 Aachen, North Rhine-Westphalia, Germany
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, Università di Perugia , Via del Liceo 1, I-06123 Perugia, Perugia, Italy
| | - Sybille Krauβ
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 25, D-53127 Bonn, North Rhine-Westphalia, Germany
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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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Abstract
![]()
Influenza A is an RNA virus with
a genome of eight negative sense
segments. Segment 7 mRNA contains a 3′ splice site for alternative
splicing to encode the essential M2 protein. On the basis of sequence
alignment and chemical mapping experiments, the secondary structure
surrounding the 3′ splice site has an internal loop, adenine
bulge, and hairpin loop when it is in the hairpin conformation that
exposes the 3′ splice site. We report structural features of
a three-dimensional model of the hairpin derived from nuclear magnetic
resonance spectra and simulated annealing with restrained molecular
dynamics. Additional insight was provided by modeling based on 1H chemical shifts. The internal loop containing the 3′
splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge
also appears to be dynamic with the A either stacked in the stem or
forming a base triple with a Watson–Crick GC pair. The hairpin
loop is a GAAA tetraloop closed by an AC pair.
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Affiliation(s)
- Jonathan L Chen
- †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
| | - 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 14627, United States
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