1
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Tipo J, Gottipati K, Choi KH. High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. RNA (NEW YORK, N.Y.) 2024; 30:609-623. [PMID: 38383158 PMCID: PMC11098461 DOI: 10.1261/rna.079796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae The flavivirus genome contains a 5' end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5' guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small molecule inhibitors to disrupt the promoter function. To facilitate the identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of the bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures, and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.
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Affiliation(s)
- Jerricho Tipo
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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2
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Mikutis S, Rebelo M, Yankova E, Gu M, Tang C, Coelho AR, Yang M, Hazemi ME, Pires de Miranda M, Eleftheriou M, Robertson M, Vassiliou GS, Adams DJ, Simas JP, Corzana F, Schneekloth JS, Tzelepis K, Bernardes GJL. Proximity-Induced Nucleic Acid Degrader (PINAD) Approach to Targeted RNA Degradation Using Small Molecules. ACS CENTRAL SCIENCE 2023; 9:892-904. [PMID: 37252343 PMCID: PMC10214512 DOI: 10.1021/acscentsci.3c00015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Indexed: 05/31/2023]
Abstract
Nature has evolved intricate machinery to target and degrade RNA, and some of these molecular mechanisms can be adapted for therapeutic use. Small interfering RNAs and RNase H-inducing oligonucleotides have yielded therapeutic agents against diseases that cannot be tackled using protein-centered approaches. Because these therapeutic agents are nucleic acid-based, they have several inherent drawbacks which include poor cellular uptake and stability. Here we report a new approach to target and degrade RNA using small molecules, proximity-induced nucleic acid degrader (PINAD). We have utilized this strategy to design two families of RNA degraders which target two different RNA structures within the genome of SARS-CoV-2: G-quadruplexes and the betacoronaviral pseudoknot. We demonstrate that these novel molecules degrade their targets using in vitro, in cellulo, and in vivo SARS-CoV-2 infection models. Our strategy allows any RNA binding small molecule to be converted into a degrader, empowering RNA binders that are not potent enough to exert a phenotypic effect on their own. PINAD raises the possibility of targeting and destroying any disease-related RNA species, which can greatly expand the space of druggable targets and diseases.
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Affiliation(s)
- Sigitas Mikutis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Maria Rebelo
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Eliza Yankova
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Muxin Gu
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
| | - Cong Tang
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Ana R. Coelho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Mo Yang
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Madoka E. Hazemi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Marta Pires de Miranda
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Maria Eleftheriou
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Max Robertson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - George S. Vassiliou
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
| | - David J. Adams
- Experimental
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, U.K.
| | - J. Pedro Simas
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
- Católica
Biomedical Research and Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisboa, Portugal
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - John S. Schneekloth
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Konstantinos Tzelepis
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Cambridge CB2 0AW, U.K.
- Milner
Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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3
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Lightfoot HL, Smith GF. Targeting RNA with small molecules-A safety perspective. Br J Pharmacol 2023. [PMID: 36631428 DOI: 10.1111/bph.16027] [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: 02/24/2022] [Revised: 06/30/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
RNA is a major player in cellular function, and consequently can drive a number of disease pathologies. Over the past several years, small molecule-RNA targeting (smRNA targeting) has developed into a promising drug discovery approach. Numerous techniques, tools, and assays have been developed to support this field, and significant investments have been made by pharmaceutical and biotechnology companies. To date, the focus has been on identifying disease validated primary targets for smRNA drug development, yet RNA as a secondary (off) target for all small molecule drug programs largely has been unexplored. In this perspective, we discuss structure, target, and mechanism-driven safety aspects of smRNAs and highlight how these parameters can be evaluated in drug discovery programs to produce potentially safer drugs.
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Affiliation(s)
- Helen L Lightfoot
- Safety and Mechanistic Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Graham F Smith
- Data Science and AI, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
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4
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Torrez RM, Ohi MD, Garner AL. Structural Insights into the Advances and Mechanistic Understanding of Human Dicer. Biochemistry 2023; 62:1-16. [PMID: 36534787 DOI: 10.1021/acs.biochem.2c00570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The RNase III endoribonuclease Dicer was discovered to be associated with cleavage of double-stranded RNA in 2001. Since then, many advances in our understanding of Dicer function have revealed that the enzyme plays a major role not only in microRNA biology but also in multiple RNA interference-related pathways. Yet, there is still much to be learned regarding Dicer structure-function in relation to how Dicer and Dicer-like enzymes initiate their cleavage reaction and release the desired RNA product. This Perspective describes the latest advances in Dicer structural studies, expands on what we have learned from this data, and outlines key gaps in knowledge that remain to be addressed. More specifically, we focus on human Dicer and highlight the intermediate processing steps where there is a lack of structural data to understand how the enzyme traverses from pre-cleavage to cleavage-competent states. Understanding these details is necessary to model Dicer's function as well as develop more specific microRNA-targeted therapeutics for the treatment of human diseases.
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Affiliation(s)
- Rachel M Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States.,Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States.,Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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5
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Hua L, Zhang Q, Zhu X, Wang R, You Q, Wang L. Beyond Proteolysis-Targeting Chimeric Molecules: Designing Heterobifunctional Molecules Based on Functional Effectors. J Med Chem 2022; 65:8091-8112. [PMID: 35686733 DOI: 10.1021/acs.jmedchem.2c00316] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, with the successful development of proteolysis-targeting chimeric molecules (PROTACs), the potential of heterobifunctional molecules to contribute to reenvisioning drug design, especially small-molecule drugs, has been increasingly recognized. Inspired by PROTACs, diverse heterobifunctional molecules have been reported to simultaneously bind two or more molecules and bring them into proximity to interaction, such as ribonuclease-recruiting, autophagy-recruiting, lysosome-recruiting, kinase-recruiting, phosphatase-recruiting, glycosyltransferase-recruiting, and acetyltransferase-recruiting chimeras. On the basis of the heterobifunctional principle, more opportunities for advancing drug design by linking potential effectors to a protein of interest (POI) have emerged. Herein, we introduce heterobifunctional molecules other than PROTACs, summarize the limitations of existing molecules, list the main challenges, and propose perspectives for future research directions, providing insight into alternative design strategies based on substrate-proximity-based targeting.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Xinyue Zhu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Ruoning Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
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6
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Vidović M, Rikalovic MG. Alpha-Synuclein Aggregation Pathway in Parkinson's Disease: Current Status and Novel Therapeutic Approaches. Cells 2022; 11:cells11111732. [PMID: 35681426 PMCID: PMC9179656 DOI: 10.3390/cells11111732] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Following Alzheimer’s, Parkinson’s disease (PD) is the second-most common neurodegenerative disorder, sharing an unclear pathophysiology, a multifactorial profile, and massive social costs worldwide. Despite this, no disease-modifying therapy is available. PD is tightly associated with α-synuclein (α-Syn) deposits, which become organised into insoluble, amyloid fibrils. As a typical intrinsically disordered protein, α-Syn adopts a monomeric, random coil conformation in an aqueous solution, while its interaction with lipid membranes drives the transition of the molecule part into an α-helical structure. The central unstructured region of α-Syn is involved in fibril formation by converting to well-defined, β-sheet rich secondary structures. Presently, most therapeutic strategies against PD are focused on designing small molecules, peptides, and peptidomimetics that can directly target α-Syn and its aggregation pathway. Other approaches include gene silencing, cell transplantation, stimulation of intracellular clearance with autophagy promoters, and degradation pathways based on immunotherapy of amyloid fibrils. In the present review, we sum marise the current advances related to α-Syn aggregation/neurotoxicity. These findings present a valuable arsenal for the further development of efficient, nontoxic, and non-invasive therapeutic protocols for disease-modifying therapy that tackles disease onset and progression in the future.
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Affiliation(s)
- Marija Vidović
- Laboratory for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
- Correspondence: ; Tel.: +38-16-4276-3221
| | - Milena G. Rikalovic
- Environment and Sustainable Development, Singidunum Univeristy, Danijelova 32, 11010 Belgrade, Serbia;
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7
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DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor. Proc Natl Acad Sci U S A 2022; 119:2114971119. [PMID: 35110406 PMCID: PMC8833215 DOI: 10.1073/pnas.2114971119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/31/2022] Open
Abstract
Drug discovery generally investigates one target at a time, in sharp contrast to living organisms, which mold ligands and targets by evolution of highly complex molecular interaction networks. We recapitulate this modality of discovery by encoding drug structures in DNA, allowing the entire DNA-encoded library to interact with thousands of RNA fold targets, and then decoding both drug and target by sequencing. This information serves as a filter to identify human RNAs aberrantly produced in cancer that are also binding partners of the discovered ligand, leading to a precision medicine candidate that selectively ablates an oncogenic noncoding RNA, reversing a disease-associated phenotype in cells. Nature evolves molecular interaction networks through persistent perturbation and selection, in stark contrast to drug discovery, which evaluates candidates one at a time by screening. Here, nature’s highly parallel ligand-target search paradigm is recapitulated in a screen of a DNA-encoded library (DEL; 73,728 ligands) against a library of RNA structures (4,096 targets). In total, the screen evaluated ∼300 million interactions and identified numerous bona fide ligand–RNA three-dimensional fold target pairs. One of the discovered ligands bound a 5′GAG/3′CCC internal loop that is present in primary microRNA-27a (pri-miR-27a), the oncogenic precursor of microRNA-27a. The DEL-derived pri-miR-27a ligand was cell active, potently and selectively inhibiting pri-miR-27a processing to reprogram gene expression and halt an otherwise invasive phenotype in triple-negative breast cancer cells. By exploiting evolutionary principles at the earliest stages of drug discovery, it is possible to identify high-affinity and selective target–ligand interactions and predict engagements in cells that short circuit disease pathways in preclinical disease models.
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8
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Grosso Jasutkar H, Oh SE, Mouradian MM. Therapeutics in the Pipeline Targeting α-Synuclein for Parkinson's Disease. Pharmacol Rev 2022; 74:207-237. [PMID: 35017177 PMCID: PMC11034868 DOI: 10.1124/pharmrev.120.000133] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/21/2021] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder and the fastest growing neurologic disease in the world, yet no disease-modifying therapy is available for this disabling condition. Multiple lines of evidence implicate the protein α-synuclein (α-Syn) in the pathogenesis of PD, and as such, there is intense interest in targeting α-Syn for potential disease modification. α-Syn is also a key pathogenic protein in other synucleionpathies, most commonly dementia with Lewy bodies. Thus, therapeutics targeting this protein will have utility in these disorders as well. Here we discuss the various approaches that are being investigated to prevent and mitigate α-Syn toxicity in PD, including clearing its pathologic aggregates from the brain using immunization strategies, inhibiting its misfolding and aggregation, reducing its expression level, enhancing cellular clearance mechanisms, preventing its cell-to-cell transmission within the brain and perhaps from the periphery, and targeting other proteins associated with or implicated in PD that contribute to α-Syn toxicity. We also discuss the therapeutics in the pipeline that harness these strategies. Finally, we discuss the challenges and opportunities for the field in the discovery and development of therapeutics for disease modification in PD. SIGNIFICANCE STATEMENT: PD is the second most common neurodegenerative disorder, for which disease-modifying therapies remain a major unmet need. A large body of evidence points to α-synuclein as a key pathogenic protein in this disease as well as in dementia with Lewy bodies, making it of leading therapeutic interest. This review discusses the various approaches being investigated and progress made to date toward discovering and developing therapeutics that would slow and stop progression of these disabling diseases.
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Affiliation(s)
- Hilary Grosso Jasutkar
- Robert Wood Johnson Medical School Institute for Neurological Therapeutics, and Department of Neurology, Rutgers Biomedical and Health Sciences, Piscataway, New Jersey
| | - Stephanie E Oh
- Robert Wood Johnson Medical School Institute for Neurological Therapeutics, and Department of Neurology, Rutgers Biomedical and Health Sciences, Piscataway, New Jersey
| | - M Maral Mouradian
- Robert Wood Johnson Medical School Institute for Neurological Therapeutics, and Department of Neurology, Rutgers Biomedical and Health Sciences, Piscataway, New Jersey
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9
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Kargbo RB. RIBOTACs: Small Molecules Selectively Destroy Cancer-Associated RNA. ACS Med Chem Lett 2021; 12:1872-1873. [PMID: 34917240 DOI: 10.1021/acsmedchemlett.1c00576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Robert B. Kargbo
- Usona Institute, 277 Granada Drive, San Luis Obispo, California 93401-7337, United States
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10
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Liu H, Rauch S, Dickinson BC. Programmable technologies to manipulate gene expression at the RNA level. Curr Opin Chem Biol 2021; 64:27-37. [PMID: 33930627 DOI: 10.1016/j.cbpa.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
RNA has long been an enticing therapeutic target, but is now garnering increased attention, largely driven by clinical successes of RNA interference-based drugs. While gene knockdown by well-established RNA interference- and other oligonucleotide-based strategies continues to advance in the clinic, the repertoire of targetable effectors capable of altering gene expression at the RNA level is also rapidly expanding. In this review, we focus on several recently developed bifunctional molecular technologies that both interact with and act upon a target RNA. These new approaches for programmable RNA knockdown, editing, splicing, translation, and chemical modifications stand to provide impactful new modalities for therapeutic development in the coming decades.
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Affiliation(s)
- Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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12
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Liu D, Wan X, Shan X, Fan R, Zha W. Drugging the "undruggable" microRNAs. Cell Mol Life Sci 2021; 78:1861-1871. [PMID: 33052435 PMCID: PMC11073314 DOI: 10.1007/s00018-020-03676-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/07/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
As a naturally occurring class of gene regulators, microRNAs (miRNAs) have attracted much attention as promising targets for therapeutic development. However, RNAs including miRNAs have long been considered undruggable, and most efforts have been devoted to using synthetic oligonucleotides to regulate miRNAs. Encouragingly, recent findings have revealed that miRNAs can also be drugged with small molecules that directly target miRNAs. In this review paper, we give a summary of recently emerged small-molecule inhibitors (SMIs) and small-molecule degraders (SMDs) for miRNAs. SMIs are small molecules that directly bind to miRNAs to inhibit their biogenesis, and SMDs are bifunctional small molecules that upon binding to miRNAs induce miRNA degradation. Strategies for discovering SMIs and developing SMDs were summarized. Applications of SMIs and SMDs in miRNA inhibition and cancer therapy were also introduced. Overall, SMIs and SMDs introduced here have high potency and specificity in miRNA inhibition. We envision that these small molecules will pave the way for developing novel therapeutics toward miRNAs that were previously considered undruggable.
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Affiliation(s)
- Dejun Liu
- The Yancheng Clinical College of Xuzhou Medical University, Yancheng, 224001, China
| | - Xinqiang Wan
- Department of Gynaecology and Obstetrics, Yancheng City No.1 People's Hospital, Yancheng, 224001, China
| | - Xiangxiang Shan
- Department of Geraeology, Yancheng City No.1 People's Hospital, Yancheng, 224001, China
| | - Rengen Fan
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, 224001, China.
| | - Wenzhang Zha
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, 224001, China.
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Feng Y, Li J, Zhang Y. Chemical Knockdown of MicroRNA with Small-Molecule Chimeras. Chembiochem 2020; 21:3180-3185. [PMID: 32495978 DOI: 10.1002/cbic.202000287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/02/2020] [Indexed: 11/09/2022]
Abstract
This concept article introduces the emerging area of small-molecule chimeras (SMCs) for knocking down microRNAs (miRNAs), which are endogenous gene silencers involved in diverse pathological processes. Compared with agents for genetic knockdown, small-molecules hold significant promise in this field due to their ideal pharmacokinetic and pharmacodynamic properties. The SMCs introduced here are hetero-bifunctional molecules comprising small-molecule binders (SMBs) of miRNAs and chemical functionalities that either directly cleave RNAs or recruit ribonucleases to destroy RNAs. Binding of SMBs to miRNAs brings SMCs' chemical functionalities close to the miRNA, eventually causing miRNA degradation. Compared with parent SMBs, SMCs exhibit remarkably enhanced potency and specificity in miRNA inhibition. The development and application of SMCs for miRNAs will be discussed.
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Affiliation(s)
- Yi Feng
- State Key Laboratory of Analytical Chemistry for Life Sciences Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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