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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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2
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Chan KH, Wang Y, Zheng BX, Long W, Feng X, Wong WL. RNA-Selective Small-Molecule Ligands: Recent Advances in Live-Cell Imaging and Drug Discovery. ChemMedChem 2023; 18:e202300271. [PMID: 37649155 DOI: 10.1002/cmdc.202300271] [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: 05/20/2023] [Revised: 08/13/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
RNA structures, including those formed from coding and noncoding RNAs, alternative to protein-based drug targets, could be a promising target of small molecules for drug discovery against various human diseases, particularly in anticancer, antibacterial and antivirus development. The normal cellular activity of cells is critically dependent on the function of various RNA molecules generated from DNA transcription. Moreover, many studies support that mRNA-targeting small molecules may regulate the synthesis of disease-related proteins via the non-covalent mRNA-ligand interactions that do not involve gene modification. RNA-ligand interaction is thus an attractive approach to address the challenge of "undruggable" proteins in drug discovery because the intracellular activity of these proteins is hard to be suppressed with small molecule ligands. We selectively surveyed a specific area of RNA structure-selective small molecule ligands in fluorescence live cell imaging and drug discovery because the area was currently underexplored. This state-of-the-art review thus mainly focuses on the research published within the past three years and aims to provide the most recent information on this research area; hopefully, it could be complementary to the previously reported reviews and give new insights into the future development on RNA-specific small molecule ligands for live cell imaging and drug discovery.
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Affiliation(s)
- Ka Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Yakun Wang
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Xinxin Feng
- State Key Laboratory of Chem-/Bio-Sensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
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Pascual-Gilabert M, Artero R, López-Castel A. The myotonic dystrophy type 1 drug development pipeline: 2022 edition. Drug Discov Today 2023; 28:103489. [PMID: 36634841 DOI: 10.1016/j.drudis.2023.103489] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
The beginning of the 20th decade has witnessed an increase in drug development programs for myotonic dystrophy type 1 (DM1). We have collected nearly 20 candidate drugs with accomplished preclinical and clinical phases, updating our previous drug development pipeline review with new entries and relevant milestones for pre-existing candidates. Three interventional first-in-human clinical trials got underway with distinct drug classes, namely AOC 1001 and DYNE-101 nucleic acid-based therapies, and the small molecule pitolisant, which joins the race toward market authorization with other repurposed drugs, including tideglusib, metformin, or mexiletine, already in clinical evaluation. Furthermore, newly disclosed promising preclinical data for several additional nucleic-acid therapeutic candidates and a CRISPR-based approach, as well as the advent into the pipeline of novel therapeutic programs, increase the plausibility of success in the demanding task of providing valid treatments to patients with DM1.
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Affiliation(s)
| | - Ruben Artero
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain; Translational Genomics Group, Incliva Biomedical Research Institute, Valencia, Spain.
| | - Arturo López-Castel
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain; Translational Genomics Group, Incliva Biomedical Research Institute, Valencia, Spain.
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Barraza SJ, Bhattacharyya A, Trotta CR, Woll MG. Targeting strategies for modulating pre-mRNA splicing with small molecules: Recent advances. Drug Discov Today 2023; 28:103431. [PMID: 36356786 DOI: 10.1016/j.drudis.2022.103431] [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: 08/03/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
The concept of using small molecules to therapeutically modulate pre-mRNA splicing was validated with the US Food and Drug Administration (FDA) approval of Evrysdi® (risdiplam) in 2020. Since then, efforts have continued unabated toward the discovery of new splicing-modulating drugs. However, the drug development world has evolved in the 10 years since risdiplam precursors were first identified in high-throughput screening (HTS). Now, new mechanistic insights into RNA-processing pathways and regulatory networks afford increasingly feasible targeted approaches. In this review, organized into classes of biological target, we compile and summarize small molecules discovered, devised, and developed since 2020 to alter pre-mRNA splicing.
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Affiliation(s)
- Scott J Barraza
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, USA.
| | | | | | - Matthew G Woll
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, USA
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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: 132] [Impact Index Per Article: 66.0] [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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Development of Therapeutic Approaches for Myotonic Dystrophies Type 1 and Type 2. Int J Mol Sci 2022; 23:ijms231810491. [PMID: 36142405 PMCID: PMC9499601 DOI: 10.3390/ijms231810491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Myotonic Dystrophies type 1 (DM1) and type 2 (DM2) are complex multisystem diseases without disease-based therapies. These disorders are caused by the expansions of unstable CTG (DM1) and CCTG (DM2) repeats outside of the coding regions of the disease genes: DMPK in DM1 and CNBP in DM2. Multiple clinical and molecular studies provided a consensus for DM1 pathogenesis, showing that the molecular pathophysiology of DM1 is associated with the toxicity of RNA CUG repeats, which cause multiple disturbances in RNA metabolism in patients' cells. As a result, splicing, translation, RNA stability and transcription of multiple genes are misregulated in DM1 cells. While mutant CCUG repeats are the main cause of DM2, additional factors might play a role in DM2 pathogenesis. This review describes current progress in the translation of mechanistic knowledge in DM1 and DM2 to clinical trials, with a focus on the development of disease-specific therapies for patients with adult forms of DM1 and congenital DM1 (CDM1).
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Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ 1-Riboswitch. J Chem Inf Model 2022; 62:4134-4148. [PMID: 35994617 DOI: 10.1021/acs.jcim.2c00751] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Simon Schneider
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Maike Grimm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
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Wang W, He S, Dong G, Sheng C. Nucleic-Acid-Based Targeted Degradation in Drug Discovery. J Med Chem 2022; 65:10217-10232. [PMID: 35916496 DOI: 10.1021/acs.jmedchem.2c00875] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeted protein degradation (TPD), represented by proteolysis-targeting chimera (PROTAC), has emerged as a novel therapeutic modality in drug discovery. However, the application of conventional PROTACs is limited to protein targets containing cytosolic domains with ligandable sites. Recently, nucleic-acid-based modalities, such as modified oligonucleotide mimics and aptamers, opened new avenues to degrade protein targets and greatly expanded the scope of TPD. Beyond constructing protein-degrading chimeras, nucleic acid motifs can also serve as substrates for targeted degradation. Particularly, the new type of chimeric RNA degrader termed ribonuclease-targeting chimera (RIBOTAC) has shown promising features in drug discovery. Here, we provide an overview of the newly emerging TPD strategies based on nucleic acids as well as new strategies for targeted degradation of nucleic acid (RNA) targets. The design strategies, case studies, potential applications, and challenges are focused on.
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Affiliation(s)
- Wei Wang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
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Jenquin JR, O’Brien AP, Poukalov K, Lu Y, Frias JA, Shorrock HK, Richardson JI, Mazdiyasni H, Yang H, Huigens RW, Boykin D, Ranum LP, Cleary JD, Wang ET, Berglund JA. Molecular characterization of myotonic dystrophy fibroblast cell lines for use in small molecule screening. iScience 2022; 25:104198. [PMID: 35479399 PMCID: PMC9035709 DOI: 10.1016/j.isci.2022.104198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/30/2021] [Accepted: 04/01/2022] [Indexed: 01/05/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are common forms of adult onset muscular dystrophy. Pathogenesis in both diseases is largely driven by production of toxic-expanded repeat RNAs that sequester MBNL RNA-binding proteins, causing mis-splicing. Given this shared pathogenesis, we hypothesized that diamidines, small molecules that rescue mis-splicing in DM1 models, could also rescue mis-splicing in DM2 models. While several DM1 cell models exist, few are available for DM2 limiting research and therapeutic development. Here, we characterize DM1 and DM2 patient-derived fibroblasts for use in small molecule screens and therapeutic studies. We identify mis-splicing events unique to DM2 fibroblasts and common events shared with DM1 fibroblasts. We show that diamidines can partially rescue molecular phenotypes in both DM1 and DM2 fibroblasts. This study demonstrates the potential of fibroblasts as models for DM1 and DM2, which will help meet an important need for well-characterized DM2 cell models.
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Affiliation(s)
- Jana R. Jenquin
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Alana P. O’Brien
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kiril Poukalov
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yidan Lu
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jesus A. Frias
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hannah K. Shorrock
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jared I. Richardson
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hormoz Mazdiyasni
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hongfen Yang
- Department of Medicinal Chemistry, Center for Natural Products Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Robert W. Huigens
- Department of Medicinal Chemistry, Center for Natural Products Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - David Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Laura P.W. Ranum
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John Douglas Cleary
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - J. Andrew Berglund
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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