1
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Tong Y, Zanon PRA, Yang X, Su X, Childs-Disney JL, Disney MD. Transcriptome-wide mapping of small-molecule RNA-binding sites in live cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596700. [PMID: 38853865 PMCID: PMC11160777 DOI: 10.1101/2024.05.30.596700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Small molecules targeting RNA can be valuable chemical probes and potential therapeutics. The interactions between small molecules, particularly fragments, and RNA, however, can be difficult to detect due to their modest affinities and short residence times. Here, we describe the procedures for mapping the molecular fingerprints of small molecules in vitro and throughout the human transcriptome in live cells, identifying both the targets bound by the small molecule and the sites of binding therein. For complete details on the use and execution of this protocol, please refer to 1.
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2
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Kovachka S, Tong Y, Childs-Disney JL, Disney MD. Heterobifunctional small molecules to modulate RNA function. Trends Pharmacol Sci 2024; 45:449-463. [PMID: 38641489 DOI: 10.1016/j.tips.2024.03.006] [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: 03/02/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
RNA has diverse cellular functionality, including regulating gene expression, protein translation, and cellular response to stimuli, due to its intricate structures. Over the past decade, small molecules have been discovered that target functional structures within cellular RNAs and modulate their function. Simple binding, however, is often insufficient, resulting in low or even no biological activity. To overcome this challenge, heterobifunctional compounds have been developed that can covalently bind to the RNA target, alter RNA sequence, or induce its cleavage. Herein, we review the recent progress in the field of RNA-targeted heterobifunctional compounds using representative case studies. We identify critical gaps and limitations and propose a strategic pathway for future developments of RNA-targeted molecules with augmented functionalities.
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Affiliation(s)
- Sandra Kovachka
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yuquan Tong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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3
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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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4
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [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: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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5
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Tang Z, Hegde S, Hao S, Selvaraju M, Qiu J, Wang J. Chemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5' untranslated region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535453. [PMID: 37066172 PMCID: PMC10103992 DOI: 10.1101/2023.04.03.535453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
One of the hallmarks of RNA viruses is highly structured untranslated regions (UTRs) in their genomes. These conserved RNA structures are often essential for viral replication, transcription, or translation. In this report, we discovered and optimized a new type of coumarin derivatives, such as C30 and C34, which bind to a four-way RNA helix called SL5 in the 5' UTR of the SARS-CoV-2 RNA genome. To locate the binding site, we developed a novel sequencing-based method namely cgSHAPE-seq, in which the acylating chemical probe was directed to crosslink with the 2'-OH groups of ribose at the ligand binding site. This crosslinked RNA could then create read-through mutations during reverse transcription (i.e., primer extension) at single-nucleotide resolution to uncover the acylation locations. cgSHAPE-seq unambiguously determined that a bulged G in SL5 was the primary binding site of C30 in the SARS-CoV-2 5' UTR, which was validated through mutagenesis and in vitro binding experiments. C30 was further used as a warhead in RNA-degrading chimeras to reduce viral RNA expression levels. We demonstrated that replacing the acylating moiety in the cgSHAPE probe with ribonuclease L recruiter (RLR) moieties yielded RNA degraders active in the in vitro RNase L degradation assay and SARS-CoV-2 5' UTR expressing cells. We further explored another RLR conjugation site on the E ring of C30/C34 and discovered improved RNA degradation activities in vitro and in cells. The optimized RNA-degrading chimera C64 inhibited live virus replication in lung epithelial carcinoma cells.
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Affiliation(s)
- Zhichao Tang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Shalakha Hegde
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
| | - Siyuan Hao
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
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6
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Fang L, Velema WA, Lee Y, Xiao L, Mohsen MG, Kietrys AM, Kool ET. Pervasive transcriptome interactions of protein-targeted drugs. Nat Chem 2023; 15:1374-1383. [PMID: 37653232 DOI: 10.1038/s41557-023-01309-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/27/2023] [Indexed: 09/02/2023]
Abstract
The off-target toxicity of drugs targeted to proteins imparts substantial health and economic costs. Proteome interaction studies can reveal off-target effects with unintended proteins; however, little attention has been paid to intracellular RNAs as potential off-targets that may contribute to toxicity. To begin to assess this, we developed a reactivity-based RNA profiling methodology and applied it to uncover transcriptome interactions of a set of Food and Drug Administration-approved small-molecule drugs in vivo. We show that these protein-targeted drugs pervasively interact with the human transcriptome and can exert unintended biological effects on RNA functions. In addition, we show that many off-target interactions occur at RNA loci associated with protein binding and structural changes, allowing us to generate hypotheses to infer the biological consequences of RNA off-target binding. The results suggest that rigorous characterization of drugs' transcriptome interactions may help assess target specificity and potentially avoid toxicity and clinical failures.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Willem A Velema
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yujeong Lee
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Anna M Kietrys
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
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7
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Kallert E, Behrendt M, Frey A, Kersten C, Barthels F. Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications. Chem Sci 2023; 14:9827-9837. [PMID: 37736627 PMCID: PMC10510756 DOI: 10.1039/d3sc02993j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/27/2023] [Indexed: 09/23/2023] Open
Abstract
Microscale Thermophoresis (MST) is a powerful biophysical technique that measures the mobility of biomolecules in response to a temperature gradient, making it useful for investigating the interactions between biological molecules. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. This "mix-and-measure" protocol uses non-covalent dyes, such as those from the Syto or Sybr series, which lead to the statistical binding of one fluorophore per RNA oligo showing key advantages over traditional covalent labelling approaches. This new approach has been successfully used to study the binding of ligands to RNA molecules (e.g., SAM- and PreQ1 riboswitches) and the identification of modifications (e.g., m6A) in short RNA oligos which can be written by the RNA methyltransferase METTL3/14.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Malte Behrendt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
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8
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Gibaut QR, Bush JA, Tong Y, Baisden JT, Taghavi A, Olafson H, Yao X, Childs-Disney JL, Wang ET, Disney MD. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG) exp Degrader in Myotonic Dystrophy. ACS CENTRAL SCIENCE 2023; 9:1342-1353. [PMID: 37521782 PMCID: PMC10375898 DOI: 10.1021/acscentsci.2c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a highly structured RNA repeat expansion, r(CUG)exp, harbored in the 3' untranslated region (3' UTR) of dystrophia myotonica protein kinase (DMPK) mRNA and drives disease through a gain-of-function mechanism. A panel of low-molecular-weight fragments capable of reacting with RNA upon UV irradiation was studied for cross-linking to r(CUG)expin vitro, affording perimidin-2-amine diazirine (1) that bound to r(CUG)exp. The interactions between the small molecule and RNA were further studied by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Binding of 1 in DM1 myotubes was profiled transcriptome-wide, identifying 12 transcripts including DMPK that were bound by 1. Augmenting the functionality of 1 with cleaving capability created a chimeric degrader that specifically targets r(CUG)exp for elimination. The degrader broadly improved DM1-associated defects as assessed by RNA-seq, while having limited effects on healthy myotubes. This study (i) provides a platform to investigate molecular recognition of ligands directly in disease-affected cells; (ii) illustrates that RNA degraders can be more specific than the binders from which they are derived; and (iii) suggests that repeating transcripts can be selectively degraded due to the presence of multiple ligand binding sites.
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Affiliation(s)
- Quentin
M. R. Gibaut
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hailey Olafson
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Xiyuan Yao
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Eric T. Wang
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew D. Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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9
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Ortega AD. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors. Biomolecules 2023; 13:biom13050765. [PMID: 37238635 DOI: 10.3390/biom13050765] [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: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
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Affiliation(s)
- Alvaro Darío Ortega
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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10
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Garner AL. Contemporary Progress and Opportunities in RNA-Targeted Drug Discovery. ACS Med Chem Lett 2023; 14:251-259. [PMID: 36923915 PMCID: PMC10009794 DOI: 10.1021/acsmedchemlett.3c00020] [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: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The surprising discovery that RNAs are the predominant gene products to emerge from the human genome catalyzed a renaissance in RNA biology. It is now well-understood that RNAs act as more than just a messenger and comprise a large and diverse family of ribonucleic acids of differing sizes, structures, and functions. RNAs play expansive roles in the cell, contributing to the regulation and fine-tuning of nearly all aspects of gene expression and genome architecture. In line with the significance of these functions, we have witnessed an explosion in discoveries connecting RNAs with a variety of human diseases. Consequently, the targeting of RNAs, and more broadly RNA biology, has emerged as an untapped area of drug discovery, making the search for RNA-targeted therapeutics of great interest. In this Microperspective, I highlight contemporary learnings in the field and present my views on how to catapult us toward the systematic discovery of RNA-targeted medicines.
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Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, United States
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11
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Abstract
For more than three decades, RNA has been known to be a relevant and attractive macromolecule to target but figuring out which RNA should be targeted and how remains challenging. Recent years have seen the confluence of approaches for screening, drug optimization, and target validation that have led to the approval of a few RNA-targeting therapeutics for clinical applications. This focused perspective aims to highlight - but not exhaustively review - key factors accounting for these successes while pointing at crucial aspects worth considering for further breakthroughs.
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Affiliation(s)
- Quentin Vicens
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
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12
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West AV, Woo CM. Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions. Isr J Chem 2022. [DOI: 10.1002/ijch.202200081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Alexander V. West
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
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13
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Childs-Disney JL, Yang X, Gibaut QMR, Tong Y, Batey RT, Disney MD. Targeting RNA structures with small molecules. Nat Rev Drug Discov 2022; 21:736-762. [PMID: 35941229 PMCID: PMC9360655 DOI: 10.1038/s41573-022-00521-4] [Citation(s) in RCA: 141] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
RNA adopts 3D structures that confer varied functional roles in human biology and dysfunction in disease. Approaches to therapeutically target RNA structures with small molecules are being actively pursued, aided by key advances in the field including the development of computational tools that predict evolutionarily conserved RNA structures, as well as strategies that expand mode of action and facilitate interactions with cellular machinery. Existing RNA-targeted small molecules use a range of mechanisms including directing splicing - by acting as molecular glues with cellular proteins (such as branaplam and the FDA-approved risdiplam), inhibition of translation of undruggable proteins and deactivation of functional structures in noncoding RNAs. Here, we describe strategies to identify, validate and optimize small molecules that target the functional transcriptome, laying out a roadmap to advance these agents into the next decade.
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Affiliation(s)
| | - Xueyi Yang
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | | | - Yuquan Tong
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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14
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Sexton AN, Vandivier LE, Petter JC, Mukherjee H, Craig Blain J. Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq. Methods 2022; 205:83-88. [PMID: 35764246 DOI: 10.1016/j.ymeth.2022.06.009] [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: 02/01/2022] [Revised: 04/29/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
In the development of therapeutics, it is important to establish engagement of a compound to its intended target and identify other targets it binds to. Methods for demonstrating target engagement in the growing field of RNA-targeted therapeutics are therefore needed. We present a detailed protocol for Photoaffinity Evaluation of RNA Ligation-Sequencing (PEARL-seq), a platform for determining interactions between small molecule ligands and their target RNA(s). PEARL-seq allows detection of binding and crosslinking events with single nucleotide resolution and allows measurement of enrichment of the target RNA relative to all other RNAs. PEARL-seq is a valuable tool in the effort to verify bona fide RNA-ligand interactions.
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Affiliation(s)
- Alec N Sexton
- Arrakis Therapeutics, 828 Winter Street, Waltham MA, USA
| | | | | | | | - J Craig Blain
- Arrakis Therapeutics, 828 Winter Street, Waltham MA, USA
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15
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Tong Y, Gibaut QMR, Rouse W, Childs-Disney JL, Suresh BM, Abegg D, Choudhary S, Akahori Y, Adibekian A, Moss WN, Disney MD. Transcriptome-Wide Mapping of Small-Molecule RNA-Binding Sites in Cells Informs an Isoform-Specific Degrader of QSOX1 mRNA. J Am Chem Soc 2022; 144:11620-11625. [PMID: 35737519 PMCID: PMC9594100 DOI: 10.1021/jacs.2c01929] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The interactions between cellular RNAs in MDA-MB-231 triple negative breast cancer cells and a panel of small molecules appended with a diazirine cross-linking moiety and an alkyne tag were probed transcriptome-wide in live cells. The alkyne tag allows for facile pull-down of cellular RNAs bound by each small molecule, and the enrichment of each RNA target defines the compound's molecular footprint. Among the 34 chemically diverse small molecules studied, six bound and enriched cellular RNAs. The most highly enriched interaction occurs between the novel RNA-binding compound F1 and a structured region in the 5' untranslated region of quiescin sulfhydryl oxidase 1 isoform a (QSOX1-a), not present in isoform b. Additional studies show that F1 specifically bound RNA over DNA and protein; that is, we studied the entire DNA, RNA, and protein interactome. This interaction was used to design a ribonuclease targeting chimera (RIBOTAC) to locally recruit Ribonuclease L to degrade QSOX1 mRNA in an isoform-specific manner, as QSOX1-a, but not QSOX1-b, mRNA and protein levels were reduced. The RIBOTAC alleviated QSOX1-mediated phenotypes in cancer cells. This approach can be broadly applied to discover ligands that bind RNA in cells, which could be bioactive themselves or augmented with functionality such as targeted degradation.
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Affiliation(s)
- Yuquan Tong
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Quentin M R Gibaut
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Warren Rouse
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Blessy M Suresh
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Shruti Choudhary
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yoshihiro Akahori
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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Crielaard S, Maassen R, Vosman T, Rempkens I, Velema WA. Affinity-Based Profiling of the Flavin Mononucleotide Riboswitch. J Am Chem Soc 2022; 144:10462-10470. [PMID: 35666649 PMCID: PMC9204756 DOI: 10.1021/jacs.2c02685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Riboswitches are
structural RNA elements that control gene expression.
These naturally occurring RNA sensors are of continued interest as
antibiotic targets, molecular sensors, and functional elements of
synthetic circuits. Here, we describe affinity-based profiling of
the flavin mononucleotide (FMN) riboswitch to characterize ligand
binding and structural folding. We designed and synthesized photoreactive
ligands and used them for photoaffinity labeling. We showed selective
labeling of the FMN riboswitch and used this covalent interaction
to quantitatively measure ligand binding, which we demonstrate with
the naturally occurring antibiotic roseoflavin. We measured conditional
riboswitch folding as a function of temperature and cation concentration.
Furthermore, combining photoaffinity labeling with reverse transcription
revealed ligand binding sites within the aptamer domain with single-nucleotide
resolution. The photoaffinity probe was applied to cellular extracts
of Bacillus subtilis to demonstrate conditional folding
of the endogenous low-abundant ribD FMN riboswitch
in biologically derived samples using quantitative PCR. Lastly, binding
of the riboswitch-targeting antibiotic roseoflavin to the FMN riboswitch
was measured in live bacteria using the photoaffinity probe.
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Affiliation(s)
- Stefan Crielaard
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rick Maassen
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tess Vosman
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ivy Rempkens
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Péczka N, Orgován Z, Ábrányi-Balogh P, Keserű GM. Electrophilic warheads in covalent drug discovery: an overview. Expert Opin Drug Discov 2022; 17:413-422. [PMID: 35129005 DOI: 10.1080/17460441.2022.2034783] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Covalent drugs have been used for more than hundred years, but gathered larger interest in the last two decades. There are currently over a 100 different electrophilic warheads used in covalent ligands, and there are several considerations tailoring their reactivity against the target of interest, which is still a challenging task. AREAS COVERED This review aims to give an overview of electrophilic warheads used for protein labeling in chemical biology and medicinal chemistry. The warheads are discussed by targeted residues, mechanism and selectivity, and analyzed through three different datasets including our collection of warheads, the CovPDB database, and the FDA approved covalent drugs. Moreover, the authors summarize general practices that facilitate the selection of the appropriate warhead for the target of interest. EXPERT OPINION In spite of the numerous electrophilic warheads, only a fraction of them is used in current drug discovery projects. Recent studies identified new tractable residues by applying a wider array of warhead chemistries. However, versatile, selective warheads are not available for all targetable amino acids, hence discovery of new warheads for these residues is needed. Broadening the toolbox of the warheads could result in novel inhibitors even for challenging targets developing with significant therapeutic potential.
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Affiliation(s)
- Nikolett Péczka
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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