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Jurj A, Fontana B, Varani G, Calin GA. Small molecules targeting microRNAs: new opportunities and challenges in precision cancer therapy. Trends Cancer 2024; 10:809-824. [PMID: 39107162 DOI: 10.1016/j.trecan.2024.06.006] [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: 11/27/2023] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 08/09/2024]
Abstract
Noncoding RNAs, especially miRNAs, play a pivotal role in cancer initiation and metastasis, underscoring their susceptibility to precise modulation via small molecule inhibitors. This review examines the innovative strategy of targeting oncogenic miRNAs with small drug-like molecules, an approach that can reshape the cancer treatment landscape. We review the current understanding of the multifaceted roles of miRNAs in oncogenesis, highlighting emerging therapeutic paradigms that have the potential to expand cancer treatment options. As research on small molecule inhibitors of miRNA is still in its early stages, ongoing investigative efforts and the development of new technologies and chemical matter are essential to fulfill the significant potential of this innovative approach to cancer treatment.
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Affiliation(s)
- Ancuta Jurj
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beatrice Fontana
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Abstract
Although fragment-based drug discovery (FBDD) has been successfully implemented and well-explored for protein targets, its feasibility for RNA targets is emerging. Despite the challenges associated with the selective targeting of RNA, efforts to integrate known methods of RNA binder discovery with fragment-based approaches have been fruitful, as a few bioactive ligands have been identified. Here, we review various fragment-based approaches implemented for RNA targets and provide insights into experimental design and outcomes to guide future work in the area. Indeed, investigations surrounding the molecular recognition of RNA by fragments address rather important questions such as the limits of molecular weight that confer selective binding and the physicochemical properties favorable for RNA binding and bioactivity.
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Affiliation(s)
- Blessy M. Suresh
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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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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Shortridge MD, Chaubey B, Zhang HJ, Pavelitz T, Vidadala V, Tang C, Olsen GL, Calin GA, Varani G. Drug-Like Small Molecules That Inhibit Expression of the Oncogenic MicroRNA-21. ACS Chem Biol 2023; 18:237-250. [PMID: 36727622 PMCID: PMC10593481 DOI: 10.1021/acschembio.2c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report the discovery of drug-like small molecules that bind specifically to the precursor of the oncogenic and pro-inflammatory microRNA-21 with mid-nanomolar affinity. The small molecules target a local structure at the Dicer cleavage site and induce distinctive structural changes in the RNA, which correlate with specific inhibition of miRNA processing. Structurally conservative single nucleotide substitutions eliminate the conformational change induced by the small molecules, which is also not observed in other miRNA precursors. The most potent of these compounds reduces cellular proliferation and miR-21 levels in cancer cell lines without inhibiting kinases or classical receptors, while closely related compounds without this specific binding activity are inactive in cells. These molecules are highly ligand-efficient (MW < 330) and display specific biochemical and cellular activity by suppressing the maturation of miR-21, thereby providing an avenue toward therapeutic development in multiple diseases where miR-21 is abnormally expressed.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bhawna Chaubey
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Huanyu J Zhang
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Venkata Vidadala
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gregory L Olsen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - George A Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Walsh L, Erlanson DA, de Esch IJP, Jahnke W, Woodhead A, Wren E. Fragment-to-Lead Medicinal Chemistry Publications in 2021. J Med Chem 2023; 66:1137-1156. [PMID: 36622056 DOI: 10.1021/acs.jmedchem.2c01827] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This Perspective is the seventh in an annual series that summarizes successful Fragment-to-Lead (F2L) case studies published in a given year. A tabulated summary of relevant articles published in 2021 is provided, and features such as target class, screening methods, and ligand efficiency are discussed, both for the 2021 examples and for the combined examples over the years 2015-2021. In addition, trends and new developments in the field are summarized. In particular, the use of structural information in fragment-based drug discovery is discussed.
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Affiliation(s)
- Louise Walsh
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Ella Wren
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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Falco N, Garfio CM, Spitalny L, Spitale RC. A Fluorescent Reverse-Transcription Assay to Detect Chemical Adducts on RNA. Biochemistry 2022; 61:1665-1668. [PMID: 35876726 PMCID: PMC10010264 DOI: 10.1021/acs.biochem.2c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we detail a novel reverse-transcription (RT) assay to directly detect chemical adducts on RNA. We optimize a fluorescence quenching assay to detect RT polymerization and employ our approach to detect N1-alkylation of inosine, an important post-transcriptional modification, using a phenylacrylamide as a model compound. We anticipate our approach can be expanded to identify novel reagents that form adducts with RNA and further explored to understand the relationship between RT processivity and natural post-transcriptional modifications in RNA.
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