1
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Haga CL, Yang XD, Gheit IS, Phinney DG. Graph neural networks for the identification of novel inhibitors of a small RNA. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:402-409. [PMID: 37839522 DOI: 10.1016/j.slasd.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/16/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
MicroRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation and have been implicated in various diseases, including cancers and lung disease. In recent years, Graph Neural Networks (GNNs) have emerged as powerful tools for analyzing graph-structured data, making them well-suited for the analysis of molecular structures. In this work, we explore the application of GNNs in ligand-based drug screening for small molecules targeting miR-21. By representing a known dataset of small molecules targeting miR-21 as graphs, GNNs can learn complex relationships between their structures and activities, enabling the prediction of potential miRNA-targeting small molecules by capturing the structural features and similarity between known miRNA-targeting compounds. The use of GNNs in miRNA-targeting drug screening holds promise for the discovery of novel therapeutic agents and provides a computational framework for efficient screening of large chemical libraries.
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Affiliation(s)
- Christopher L Haga
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA.
| | - Xue D Yang
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
| | - Ibrahim S Gheit
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
| | - Donald G Phinney
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
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2
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Maucort C, Bonnet M, Ortuno JC, Tucker G, Quissac E, Verreault M, Azoulay S, Di Giorgio C, Di Giorgio A, Duca M. Synthesis of Bleomycin-Inspired RNA Ligands Targeting the Biogenesis of Oncogenic miRNAs. J Med Chem 2023; 66:10639-10657. [PMID: 37449818 DOI: 10.1021/acs.jmedchem.3c00797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Noncoding RNAs (ncRNAs) play pivotal roles in the regulation of gene expression and represent a promising target for the development of new therapeutic approaches. Among these ncRNAs, microRNAs (miRNAs or miRs) are involved in the regulation of gene expression, and their dysregulation has been linked to several diseases such as cancers. Indeed, oncogenic miRNAs are overexpressed in cancer cells, thus promoting tumorigenesis and maintenance of cancer stem cells that are resistant to chemotherapy and often responsible for therapeutic failure. Here, we describe the design and synthesis of new small-molecule RNA binders able to inhibit the biogenesis of oncogenic miRNAs and target efficiently cancer stem cells. Through the biochemical study of their interaction with the target and thanks to intracellular assays, we describe the structure-activity relationships for this new series of RNA ligands, and we identify compounds bearing a very promising antiproliferative activity against cancer stem cells.
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Affiliation(s)
- Chloé Maucort
- CNRS, Institute of Chemistry of Nice (ICN), Université Côte d'Azur, 28 avenue Valrose, 06100 Nice, France
| | - Maurinne Bonnet
- CNRS, Institute of Chemistry of Nice (ICN), Université Côte d'Azur, 28 avenue Valrose, 06100 Nice, France
| | - Jean-Claude Ortuno
- Institut de Recherche Servier, 125 chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Gordon Tucker
- Institut de Recherche Servier, 125 chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Emie Quissac
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Sorbonne Université, F-75013 Paris, France
| | - Maïté Verreault
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Sorbonne Université, F-75013 Paris, France
| | - Stéphane Azoulay
- CNRS, Institute of Chemistry of Nice (ICN), Université Côte d'Azur, 28 avenue Valrose, 06100 Nice, France
| | - Christophe Di Giorgio
- CNRS, Institute of Chemistry of Nice (ICN), Université Côte d'Azur, 28 avenue Valrose, 06100 Nice, France
| | - Audrey Di Giorgio
- CNRS, Institute of Chemistry of Nice (ICN), Université Côte d'Azur, 28 avenue Valrose, 06100 Nice, France
| | - Maria Duca
- CNRS, Institute of Chemistry of Nice (ICN), Université Côte d'Azur, 28 avenue Valrose, 06100 Nice, France
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3
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H. Al-Zuaini H, Rafiq Zahid K, Xiao X, Raza U, Huang Q, Zeng T. Hypoxia-driven ncRNAs in breast cancer. Front Oncol 2023; 13:1207253. [PMID: 37583933 PMCID: PMC10424730 DOI: 10.3389/fonc.2023.1207253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/06/2023] [Indexed: 08/17/2023] Open
Abstract
Low oxygen tension, or hypoxia is the driving force behind tumor aggressiveness, leading to therapy resistance, metastasis, and stemness in solid cancers including breast cancer, which now stands as the leading cause of cancer-related mortality in women. With the great advancements in exploring the regulatory roles of the non-coding genome in recent years, the wide spectrum of hypoxia-responsive genome is not limited to just protein-coding genes but also includes multiple types of non-coding RNAs, such as micro RNAs, long non-coding RNAs, and circular RNAs. Over the years, these hypoxia-responsive non-coding molecules have been greatly implicated in breast cancer. Hypoxia drives the expression of these non-coding RNAs as upstream modulators and downstream effectors of hypoxia inducible factor signaling in the favor of breast cancer through a myriad of molecular mechanisms. These non-coding RNAs then contribute in orchestrating aggressive hypoxic tumor environment and regulate cancer associated cellular processes such as proliferation, evasion of apoptotic death, extracellular matrix remodeling, angiogenesis, migration, invasion, epithelial-to-mesenchymal transition, metastasis, therapy resistance, stemness, and evasion of the immune system in breast cancer. In addition, the interplay between hypoxia-driven non-coding RNAs as well as feedback and feedforward loops between these ncRNAs and HIFs further contribute to breast cancer progression. Although the current clinical implications of hypoxia-driven non-coding RNAs are limited to prognostics and diagnostics in breast cancer, extensive explorations have established some of these hypoxia-driven non-coding RNAs as promising targets to treat aggressive breast cancers, and future scientific endeavors hold great promise in targeting hypoxia-driven ncRNAs at clinics to treat breast cancer and limit global cancer burden.
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Affiliation(s)
| | - Kashif Rafiq Zahid
- Department of Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Radiation Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiangyan Xiao
- Department of Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Umar Raza
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Qiyuan Huang
- Department of Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Zeng
- Department of Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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4
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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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5
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Haga CL, Phinney DG. Strategies for targeting RNA with small molecule drugs. Expert Opin Drug Discov 2023; 18:135-147. [PMID: 35934990 DOI: 10.1080/17460441.2022.2111414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Historically, therapeutic treatment of disease has been restricted to targeting proteins. Of the approximately 20,000 translated human proteins, approximately 1600 are associated with diseases. Strikingly, less than 15% of disease-associated proteins are predicted or known to be 'druggable.' While the concept and narrative of protein druggability continue to evolve with the development of novel technological and pharmacological advances, most of the human proteome remains undrugged. Recent genomic studies indicate that less than 2% of the human genome encodes for proteins, and while as much as 75% of the genome is transcribed, RNA has largely been ignored as a druggable target for therapeutic interventions. AREAS COVERED This review delineates the theory and techniques involved in the development of small molecule inhibitors of RNAs from brute force, high-throughput screening technologies to de novo molecular design using computational machine and deep learning. We will also highlight the potential pitfalls and limitations of targeting RNA with small molecules. EXPERT OPINION Although significant advances have recently been made in developing systems to identify small molecule inhibitors of RNAs, many challenges remain. Focusing on RNA structure and ligand binding sites may help bring drugging RNA in line with traditional protein drug targeting.
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Affiliation(s)
- Christopher L Haga
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Donald G Phinney
- Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL, USA
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6
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Suresh BM, Akahori Y, Taghavi A, Crynen G, Gibaut QMR, Li Y, Disney MD. Low-Molecular Weight Small Molecules Can Potently Bind RNA and Affect Oncogenic Pathways in Cells. J Am Chem Soc 2022; 144:20815-20824. [PMID: 36322830 PMCID: PMC9930674 DOI: 10.1021/jacs.2c08770] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA is challenging to target with bioactive small molecules, particularly those of low molecular weight that bind with sufficient affinity and specificity. In this report, we developed a platform to address this challenge, affording a novel bioactive interaction. An RNA-focused small-molecule fragment collection (n = 2500) was constructed by analyzing features in all publicly reported compounds that bind RNA, the largest collection of RNA-focused fragments to date. The RNA-binding landscape for each fragment was studied by using a library-versus-library selection with an RNA library displaying a discrete structural element, probing over 12.8 million interactions, the greatest number of interactions between fragments and biomolecules probed experimentally. Mining of this dataset across the human transcriptome defined a drug-like fragment that potently and specifically targeted the microRNA-372 hairpin precursor, inhibiting its processing into the mature, functional microRNA and alleviating invasive and proliferative oncogenic phenotypes in gastric cancer cells. Importantly, this fragment has favorable properties, including an affinity for the RNA target of 300 ± 130 nM, a molecular weight of 273 Da, and quantitative estimate of drug-likeness (QED) score of 0.8. (For comparison, the mean QED of oral medicines is 0.6 ± 0.2). Thus, these studies demonstrate that a low-molecular weight, fragment-like compound can specifically and potently modulate RNA targets.
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Affiliation(s)
- Blessy M. Suresh
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yoshihiro Akahori
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Amirhossein Taghavi
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Quentin M. R. Gibaut
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
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7
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Rouse WB, O'Leary CA, Booher NJ, Moss WN. Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome. Sci Rep 2022; 12:14515. [PMID: 36008510 PMCID: PMC9403969 DOI: 10.1038/s41598-022-18699-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
RNA plays vital functional roles in almost every component of biology, and these functional roles are often influenced by its folding into secondary and tertiary structures. An important role of RNA secondary structure is in maintaining proper gene regulation; therefore, making accurate predictions of the structures involved in these processes is important. In this study, we have expanded on our previous work that led to the creation of the RNAStructuromeDB. Unlike this previous study that analyzed the human genome at low resolution, we have now scanned the protein-coding human transcriptome at high (single nt) resolution. This provides more robust structure predictions for over 100,000 isoforms of known protein-coding genes. Notably, we also utilize the motif identification tool, ScanFold, to model structures with high propensity for ordered/evolved stability. All data have been uploaded to the RNAStructuromeDB, allowing for easy searching of transcripts, visualization of data tracks (via the Integrative Genomics Viewer or IGV), and download of ScanFold data—including unique highly-ordered motifs. Herein, we provide an example analysis of MAT2A to demonstrate the utility of ScanFold at finding known and novel secondary structures, highlighting regions of potential functionality, and guiding generation of functional hypotheses through use of the data.
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Affiliation(s)
- Warren B Rouse
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nicholas J Booher
- Infrastructure and Research IT Services, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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8
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Sawai S, Wong PF, Ramasamy TS. Hypoxia-regulated microRNAs: the molecular drivers of tumor progression. Crit Rev Biochem Mol Biol 2022; 57:351-376. [PMID: 35900938 DOI: 10.1080/10409238.2022.2088684] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Hypoxia is a common feature of the tumor microenvironment (TME) of nearly all solid tumors, leading to therapeutic failure. The changes in stiffness of the extracellular matrix (ECM), pH gradients, and chemical balance that contribute to multiple cancer hallmarks are closely regulated by intratumoral oxygen tension via its primary mediators, hypoxia-inducible factors (HIFs). HIFs, especially HIF-1α, influence these changes in the TME by regulating vital cancer-associated signaling pathways and cellular processes including MAPK/ERK, NF-κB, STAT3, PI3K/Akt, Wnt, p53, and glycolysis. Interestingly, research has revealed the involvement of epigenetic regulation by hypoxia-regulated microRNAs (HRMs) of downstream target genes involved in these signaling. Through literature search and analysis, we identified 48 HRMs that have a functional role in the regulation of 5 key cellular processes: proliferation, metabolism, survival, invasion and migration, and immunoregulation in various cancers in hypoxic condition. Among these HRMs, 17 were identified to be directly associated with HIFs which include miR-135b, miR-145, miR-155, miR-181a, miR-182, miR-210, miR-224, miR-301a, and miR-675-5p as oncomiRNAs, and miR-100-5p, miR-138, miR-138-5p, miR-153, miR-22, miR-338-3p, miR-519d-3p, and miR-548an as tumor suppressor miRNAs. These HRMs serve as a potential lead in the development of miRNA-based targeted therapy for advanced solid tumors. Future development of combined HIF-targeted and miRNA-targeted therapy is possible, which requires comprehensive profiling of HIFs-HRMs regulatory network, and improved formula of the delivery vehicles to enhance the therapeutic kinetics of the targeted cancer therapy (TCT) moving forward.
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Affiliation(s)
- Sakunie Sawai
- Stem Cell Biology Laboratory, Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Pooi-Fong Wong
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Thamil Selvee Ramasamy
- Stem Cell Biology Laboratory, Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Wilayah Persekutuan Kuala Lumpur, Malaysia
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9
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Ražná K, Harenčár Ľ, Kučka M. The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View. Cells 2022; 11:cells11142151. [PMID: 35883592 PMCID: PMC9323225 DOI: 10.3390/cells11142151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.
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10
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Silveira GO, Coelho HS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. Parasitol Res 2021; 121:1091-1115. [PMID: 34859292 DOI: 10.1007/s00436-021-07384-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/14/2021] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) emerged in the past 20 years due to massive amounts of scientific data regarding transcriptomic analyses. They have been implicated in a plethora of cellular processes in higher eukaryotes. However, little is known about lncRNA possible involvement in parasitic diseases, with most studies only detecting their presence in parasites of human medical importance. Here, we review the progress on lncRNA studies and their functions in protozoans and helminths. In addition, we show an example of knockdown of one lncRNA in Schistosoma mansoni, SmLINC156349, which led to in vitro parasite adhesion, motility, and pairing impairment, with a 20% decrease in parasite viability and 33% reduction in female oviposition. Other observed phenotypes were a decrease in the proliferation rate of both male and female worms and their gonads, and reduced female lipid and vitelline droplets that are markers for well-developed vitellaria. Impairment of female worms' vitellaria in SmLINC156349-silenced worms led to egg development deficiency. All those results demonstrate the great potential of the tools and methods to characterize lncRNAs as potential new therapeutic targets. Further, we discuss the challenges and limitations of current methods for studying lncRNAs in parasites and possible solutions to overcome them, and we highlight the future directions of this exciting field.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Helena S Coelho
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Murilo S Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil. .,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
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11
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Orlandella FM, Auletta L, Greco A, Zannetti A, Salvatore G. Preclinical Imaging Evaluation of miRNAs' Delivery and Effects in Breast Cancer Mouse Models: A Systematic Review. Cancers (Basel) 2021; 13:6020. [PMID: 34885130 PMCID: PMC8656589 DOI: 10.3390/cancers13236020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND We have conducted a systematic review focusing on the advancements in preclinical molecular imaging to study the delivery and therapeutic efficacy of miRNAs in mouse models of breast cancer. METHODS A systematic review of English articles published in peer-reviewed journals using PubMed, EMBASE, BIOSIS™ and Scopus was performed. Search terms included breast cancer, mouse, mice, microRNA(s) and miRNA(s). RESULTS From a total of 2073 records, our final data extraction was from 114 manuscripts. The most frequently used murine genetic background was Balb/C (46.7%). The most frequently used model was the IV metastatic model (46.8%), which was obtained via intravenous injection (68.9%) in the tail vein. Bioluminescence was the most used frequently used tool (64%), and was used as a surrogate for tumor growth for efficacy treatment or for the evaluation of tumorigenicity in miRNA-transfected cells (29.9%); for tracking, evaluation of engraftment and for response to therapy in metastatic models (50.6%). CONCLUSIONS This review provides a systematic and focused analysis of all the information available and related to the imaging protocols with which to test miRNA therapy in an in vivo mice model of breast cancer, and has the purpose of providing an important tool to suggest the best preclinical imaging protocol based on available evidence.
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Affiliation(s)
| | - Luigi Auletta
- Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, 80145 Naples, Italy; (L.A.); (A.Z.)
| | - Adelaide Greco
- InterDepartmental Center of Veterinary Radiology, University of Naples Federico II, 80131 Naples, Italy
| | - Antonella Zannetti
- Institute of Biostructures and Bioimaging, National Research Council, IBB-CNR, 80145 Naples, Italy; (L.A.); (A.Z.)
| | - Giuliana Salvatore
- IRCCS SDN, 80143 Naples, Italy;
- Department of Motor Sciences and Wellness, University of Naples Parthenope, 80133 Naples, Italy
- CEINGE-Biotecnologie Avanzate S.C.A.R.L., 80145 Naples, Italy
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12
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Garrido-Cano I, Pattanayak B, Adam-Artigues A, Lameirinhas A, Torres-Ruiz S, Tormo E, Cervera R, Eroles P. MicroRNAs as a clue to overcome breast cancer treatment resistance. Cancer Metastasis Rev 2021; 41:77-105. [PMID: 34524579 PMCID: PMC8924146 DOI: 10.1007/s10555-021-09992-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 12/31/2022]
Abstract
Breast cancer is the most frequent cancer in women worldwide. Despite the improvement in diagnosis and treatments, the rates of cancer relapse and resistance to therapies remain higher than desirable. Alterations in microRNAs have been linked to changes in critical processes related to cancer development and progression. Their involvement in resistance or sensitivity to breast cancer treatments has been documented by different in vivo and in vitro experiments. The most significant microRNAs implicated in modulating resistance to breast cancer therapies are summarized in this review. Resistance to therapy has been linked to cellular processes such as cell cycle, apoptosis, epithelial-to-mesenchymal transition, stemness phenotype, or receptor signaling pathways, and the role of microRNAs in their regulation has already been described. The modulation of specific microRNAs may modify treatment response and improve survival rates and cancer patients' quality of life. As a result, a greater understanding of microRNAs, their targets, and the signaling pathways through which they act is needed. This information could be useful to design new therapeutic strategies, to reduce resistance to the available treatments, and to open the door to possible new clinical approaches.
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Affiliation(s)
| | | | | | - Ana Lameirinhas
- INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | | | - Eduardo Tormo
- INCLIVA Biomedical Research Institute, 46010, Valencia, Spain.,Center for Biomedical Network Research On Cancer, CIBERONC-ISCIII, 28029, Madrid, Spain
| | | | - Pilar Eroles
- INCLIVA Biomedical Research Institute, 46010, Valencia, Spain. .,Center for Biomedical Network Research On Cancer, CIBERONC-ISCIII, 28029, Madrid, Spain. .,Department of Physiology, University of Valencia, 46010, Valencia, Spain.
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13
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Targeting RNA structures in diseases with small molecules. Essays Biochem 2021; 64:955-966. [PMID: 33078198 PMCID: PMC7724634 DOI: 10.1042/ebc20200011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/16/2020] [Accepted: 09/30/2020] [Indexed: 01/08/2023]
Abstract
RNA is crucial for gene expression and regulation. Recent advances in understanding of RNA biochemistry, structure and molecular biology have revealed the importance of RNA structure in cellular processes and diseases. Various approaches to discovering drug-like small molecules that target RNA structure have been developed. This review provides a brief introduction to RNA structural biology and how RNA structures function as disease regulators. We summarize approaches to targeting RNA with small molecules and highlight their advantages, shortcomings and therapeutic potential.
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14
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Bush JA, Williams CC, Meyer SM, Tong Y, Haniff HS, Childs-Disney JL, Disney MD. Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models. ACS Chem Biol 2021; 16:1111-1127. [PMID: 34166593 PMCID: PMC8867596 DOI: 10.1021/acschembio.1c00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interrogation and manipulation of biological systems by small molecules is a powerful approach in chemical biology. Ideal compounds selectively engage a target and mediate a downstream phenotypic response. Although historically small molecule drug discovery has focused on proteins and enzymes, targeting RNA is an attractive therapeutic alternative, as many disease-causing or -associated RNAs have been identified through genome-wide association studies. As the field of RNA chemical biology emerges, the systematic evaluation of target validation and modulation of target-associated pathways is of paramount importance. In this Review, through an examination of case studies, we outline the experimental characterization, including methods and tools, to evaluate comprehensively the impact of small molecules that target RNA on cellular phenotype.
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Affiliation(s)
- Jessica A Bush
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christopher C Williams
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Samantha M Meyer
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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15
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Raue R, Frank AC, Syed SN, Brüne B. Therapeutic Targeting of MicroRNAs in the Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms22042210. [PMID: 33672261 PMCID: PMC7926641 DOI: 10.3390/ijms22042210] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
The tumor-microenvironment (TME) is an amalgamation of various factors derived from malignant cells and infiltrating host cells, including cells of the immune system. One of the important factors of the TME is microRNAs (miRs) that regulate target gene expression at a post transcriptional level. MiRs have been found to be dysregulated in tumor as well as in stromal cells and they emerged as important regulators of tumorigenesis. In fact, miRs regulate almost all hallmarks of cancer, thus making them attractive tools and targets for novel anti-tumoral treatment strategies. Tumor to stroma cell cross-propagation of miRs to regulate protumoral functions has been a salient feature of the TME. MiRs can either act as tumor suppressors or oncogenes (oncomiRs) and both miR mimics as well as miR inhibitors (antimiRs) have been used in preclinical trials to alter cancer and stromal cell phenotypes. Owing to their cascading ability to regulate upstream target genes and their chemical nature, which allows specific pharmacological targeting, miRs are attractive targets for anti-tumor therapy. In this review, we cover a recent update on our understanding of dysregulated miRs in the TME and provide an overview of how these miRs are involved in current cancer-therapeutic approaches from bench to bedside.
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Affiliation(s)
- Rebecca Raue
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.R.); (A.-C.F.)
| | - Ann-Christin Frank
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.R.); (A.-C.F.)
| | - Shahzad Nawaz Syed
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.R.); (A.-C.F.)
- Correspondence: (S.N.S.); (B.B.); Tel.: +49-69-6301-7424 (B.B.)
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; (R.R.); (A.-C.F.)
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology, 60596 Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, 60590 Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe-University Frankfurt, 60596 Frankfurt, Germany
- Correspondence: (S.N.S.); (B.B.); Tel.: +49-69-6301-7424 (B.B.)
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16
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Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA (NEW YORK, N.Y.) 2021; 27:12-26. [PMID: 33028652 PMCID: PMC7749633 DOI: 10.1261/rna.076257.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/26/2020] [Indexed: 05/30/2023]
Abstract
Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to nonspecific binding of aminoglycosides and intercalators to many stem-loop RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities. However, target engagement and cellular selectivity assays are not routinely performed, and it is often unclear whether functional activity directly results from specific binding to the target RNA. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activities of distinct stem-loop RNAs, to bind and inhibit the cellular activities of two unrelated HIV-1 stem-loop RNAs: the transactivation response element (TAR) and the rev response element stem IIB (RREIIB). All compounds bound TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting off-target interactions consistent with nonspecific activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that aminoglycosides and drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, in contrast to ligands that specifically bind riboswitches. Our results demonstrate that drug-like molecules can nonspecifically bind stem-loop RNAs most likely through hydrogen bonding and electrostatic interactions and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.
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Affiliation(s)
- Megan L Kelly
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Honglue Shi
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Laura R Ganser
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kelly Huynh
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yuze Hou
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
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17
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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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18
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Costales MG, Childs-Disney JL, Haniff HS, Disney MD. How We Think about Targeting RNA with Small Molecules. J Med Chem 2020; 63:8880-8900. [PMID: 32212706 PMCID: PMC7486258 DOI: 10.1021/acs.jmedchem.9b01927] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA offers nearly unlimited potential as a target for small molecule chemical probes and lead medicines. Many RNAs fold into structures that can be selectively targeted with small molecules. This Perspective discusses molecular recognition of RNA by small molecules and highlights key enabling technologies and properties of bioactive interactions. Sequence-based design of ligands targeting RNA has established rules for affecting RNA targets and provided a potentially general platform for the discovery of bioactive small molecules. The RNA targets that contain preferred small molecule binding sites can be identified from sequence, allowing identification of off-targets and prediction of bioactive interactions by nature of ligand recognition of functional sites. Small molecule targeted degradation of RNA targets (ribonuclease-targeted chimeras, RIBOTACs) and direct cleavage by small molecules have also been developed. These growing technologies suggest that the time is right to provide small molecule chemical probes to target functionally relevant RNAs throughout the human transcriptome.
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Affiliation(s)
- Matthew G Costales
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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19
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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20
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Ursu A, Childs-Disney JL, Angelbello AJ, Costales MG, Meyer SM, Disney MD. Gini Coefficients as a Single Value Metric to Define Chemical Probe Selectivity. ACS Chem Biol 2020; 15:2031-2040. [PMID: 32568503 PMCID: PMC7442733 DOI: 10.1021/acschembio.0c00486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Selectivity is a key requirement of high-quality chemical probes and lead medicines; however, methods to quantify and compare the selectivity of small molecules have not been standardized across the field. Herein, we discuss the origins and use of a comprehensive, single value term to quantify selectivity, the Gini coefficient. Case studies presented include compounds that target protein kinases, small molecules that bind RNA structures, and small molecule chimeras that bind to and degrade the target RNA. With an increasing number of transcriptome- and proteome-wide studies, we submit that reporting Gini coefficients as a quantitative descriptor of selectivity should be used broadly.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | | | | | | | - Samantha M. Meyer
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
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21
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Zhang Z, Qiu M, Du H, Li Q, Yu C, Gan W, Peng H, Xia B, Xiong X, Song X, Yang L, Hu C, Chen J, Yang C, Jiang X. Identification of long noncoding RNAs involved in adaptability to chronic hypoxic by whole transcriptome sequencing. 3 Biotech 2020; 10:269. [PMID: 32523863 DOI: 10.1007/s13205-020-02272-8] [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: 04/15/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
Hypoxia affects the physiology of cells and organisms; however, the mechanisms associated with hypoxia adaptation remain unknown in Tibetan chickens. In this study, we aimed to identify long noncoding RNAs (lncRNAs) involved in hypoxia adaptation in Tibetan chickens and Daheng broilers, to provide insights into the mechanisms underlying hypoxia induction. RNA sequencing results revealed that a total of 5504 lncRNAs and 16,779 microRNAs were differentially expressed in four Tibetan chickens and four Daheng broilers; 70 lncRNAs were up-regulated and 113 lncRNAs were down-regulated in the Tibetan chickens compared to the expression levels in the Daheng broilers. The differentially expressed lncRNAs (DElncRNAs) were enriched in the following Gene ontology terms: protein complex localization, small-molecule metabolic process, and RNA splicing. Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DElncRNAs were mainly enriched in pathways that regulate cell junctions and intercellular spaces and oxygen or energy metabolism, mainly involved in hypoxic adaption. Moreover, a predicted ceRNA network with five DElncRNAs interacted with three miRNAs that acted on 42 pathways through 19 target genes. Quantitative real-time polymerase chain reaction was used to verify that the expression levels of ENSGALG00000008047, ENSGALG00000050044, and ENSGALG00000053982 were significantly lower in Tibetan chickens than in the Daheng broilers, consistent with the RNA sequencing results. We obtained lncRNA expression profiles for the heart tissue of Tibetan chickens for the first time and have provided novel data that may aid research on biological adaptation to hypoxic stress.
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22
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Zhang S, Zhou Y, Wang Y, Wang Z, Xiao Q, Zhang Y, Lou Y, Qiu Y, Zhu F. The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years. Brief Bioinform 2020; 22:1860-1883. [PMID: 32249290 DOI: 10.1093/bib/bbaa023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Despite The Central Dogma states the destiny of gene as 'DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic information but also, surprisingly, join in intracellular vital movement as a regulator of gene expression. Bioinformatics has contributed to knowledge for a series of emerging novel nucleic acids molecules. For typical cases, microRNA (miRNA), long noncoding RNA (lncRNA) and circular RNA (circRNA) exert crucial role in regulating vital biological processes, especially in malignant diseases. Due to extraordinarily heterogeneity among all malignancies, hepatocellular carcinoma (HCC) has emerged enormous limitation in diagnosis and therapy. Mechanistic, diagnostic and therapeutic nucleic acids for HCC emerging in past score years have been systematically reviewed. Particularly, we have organized recent advances on nucleic acids of HCC into three facets: (i) summarizing diverse nucleic acids and their modification (miRNA, lncRNA, circRNA, circulating tumor DNA and DNA methylation) acting as potential biomarkers in HCC diagnosis; (ii) concluding different patterns of three key noncoding RNAs (miRNA, lncRNA and circRNA) in gene regulation and (iii) outlining the progress of these novel nucleic acids for HCC diagnosis and therapy in clinical trials, and discuss their possibility for clinical applications. All in all, this review takes a detailed look at the advances of novel nucleic acids from potential of biomarkers and elaboration of mechanism to early clinical application in past 20 years.
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Affiliation(s)
- Song Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China.,College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China
| | - Yanan Wang
- School of Life Sciences in Nanchang University, China
| | - Zhengwen Wang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Qitao Xiao
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Yan Lou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China
| | - Feng Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China.,College of Pharmaceutical Sciences in Zhejiang University, China
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23
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Van Meter EN, Onyango JA, Teske KA. A review of currently identified small molecule modulators of microRNA function. Eur J Med Chem 2020; 188:112008. [DOI: 10.1016/j.ejmech.2019.112008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022]
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24
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Martin C, De Piccoli S, Gaysinski M, Becquart C, Azoulay S, Di Giorgio A, Duca M. Unveiling RNA‐Binding Properties of Verapamil and Preparation of New Derivatives as Inhibitors of HIV‐1 Tat‐TAR Interaction. Chempluschem 2020. [DOI: 10.1002/cplu.201900650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Céline Martin
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Serena De Piccoli
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Marc Gaysinski
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Cécile Becquart
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Stéphane Azoulay
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Audrey Di Giorgio
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Maria Duca
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
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25
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Di Giorgio A, Duca M. Synthetic small-molecule RNA ligands: future prospects as therapeutic agents. MEDCHEMCOMM 2019; 10:1242-1255. [PMID: 31534649 PMCID: PMC6748380 DOI: 10.1039/c9md00195f] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2022]
Abstract
RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in many pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified. Among the most important ones, one can mention prokaryotic ribosomal RNA which is the target of several marketed antibiotics, viral RNAs or oncogenic microRNAs that are tightly involved in the development and progression of various cancers. Oligonucleotides are efficient and specific RNA targeting agents but suffer from poor pharmacodynamic and pharmacokinetic properties. For this reason, a number of synthetic small-molecule ligands have been identified and studied upon screening of chemical libraries or focused design of RNA binders. In this review, we report the most relevant examples of synthetic compounds bearing sufficient selectivity to envisage clinical studies and future therapeutic applications with a particular attention for the main strategies that can be undertaken toward the improvement of selectivity and biological activity.
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Affiliation(s)
- A Di Giorgio
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
| | - M Duca
- Université Côte d'Azur , CNRS , Institute of Chemistry of Nice (ICN) , Nice , France .
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26
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Morgan BS, Forte JE, Hargrove AE. Insights into the development of chemical probes for RNA. Nucleic Acids Res 2019; 46:8025-8037. [PMID: 30102391 PMCID: PMC6144806 DOI: 10.1093/nar/gky718] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/27/2018] [Indexed: 12/18/2022] Open
Abstract
Over the past decade, the RNA revolution has revealed thousands of non-coding RNAs that are essential for cellular regulation and are misregulated in disease. While the development of methods and tools to study these RNAs has been challenging, the power and promise of small molecule chemical probes is increasingly recognized. To harness existing knowledge, we compiled a list of 116 ligands with reported activity against RNA targets in biological systems (R-BIND). In this survey, we examine the RNA targets, design and discovery strategies, and chemical probe characterization techniques of these ligands. We discuss the applicability of current tools to identify and evaluate RNA-targeted chemical probes, suggest criteria to assess the quality of RNA chemical probes and targets, and propose areas where new tools are particularly needed. We anticipate that this knowledge will expedite the discovery of RNA-targeted ligands and the next phase of the RNA revolution.
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Affiliation(s)
| | - Jordan E Forte
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, NC 27708, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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27
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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28
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Yan H, Liang FS. miRNA inhibition by proximity-enabled Dicer inactivation. Methods 2019; 167:117-123. [PMID: 31077820 DOI: 10.1016/j.ymeth.2019.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/22/2019] [Accepted: 05/05/2019] [Indexed: 11/17/2022] Open
Abstract
microRNAs (miRNAs) are considered as master regulators of biological processes. Dysregulation of miRNA expression has been implicated in many human diseases. Driven by the key biological roles and the therapeutic potential, developing methods for miRNA regulation has become an intense research area. Due to favorable pharmacological properties, small molecule-based miRNA inhibition emerges as a promising strategy and significant progresses have been made. However, it remains challenging to regulate miRNA using small molecules because of the inherent difficulty in RNA targeting and inhibition. Herein we outline the workflow of generating bifunctional small molecule inhibitors blocking miRNA biogenesis through proximity-enabled inactivation of Dicer, an enzyme required for the processing of precursor miRNA (pre-miRNA) into mature miRNA. By conjugating a weak Dicer inhibitor with a pre-miRNA binder, the inhibitor can be delivered to the Dicer processing site associated with the targeted pre-miRNA, and as a result inhibiting Dicer-mediated pre-miRNA processing. This protocol can be applicable in producing bifunctional inhibitors for different miRNAs.
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Affiliation(s)
- Hao Yan
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
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29
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Disney MD. Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine. J Am Chem Soc 2019; 141:6776-6790. [PMID: 30896935 DOI: 10.1021/jacs.8b13419] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biology of healthy and disease-affected cells is often mediated by RNA structures, desirable targets for small molecule chemical probes and lead medicines. Although structured regions are found throughout the transcriptome, some even with demonstrated functionality, human RNAs are considered recalcitrant to small molecule targeting. However, targeting structured regions with small molecules provides an important alternative to oligonucleotides that target sequence. In this Perspective, we describe challenges and progress in developing small molecules interacting with RNA (SMIRNAs) to capture their significant opportunities at the intersection of chemistry, biology, and medicine. Key to establishing a new paradigm in chemical biology and medicine is the development of methods to obtain, preferably by design, bioactive compounds that modulate RNA targets and companion methods that validate their direct effects in cells and pre-clinical models. While difficult, demonstration of direct target engagement in the complex cellular milieu, along with methods to establish modes of action, is required to push this field forward. We also describe frameworks for accelerated advancements in this burgeoning area, their implications, key new technologies for development of SMIRNAs, and milestones that have led to broader acceptance of RNA as a small molecule druggable target.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
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Fan R, Xiao C, Wan X, Cha W, Miao Y, Zhou Y, Qin C, Cui T, Su F, Shan X. Small molecules with big roles in microRNA chemical biology and microRNA-targeted therapeutics. RNA Biol 2019; 16:707-718. [PMID: 30900502 DOI: 10.1080/15476286.2019.1593094] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that post-transcriptionally regulate gene expression. Aberrant miRNA expression or function have close links with various human diseases. Therefore, therapeutic treatments with disease-associated miRNAs as targets are emerging. However, the intracellular miRNA networks are extremely complicated and poorly understood, which thus hinder the development of miRNA-targeted therapeutics. Small molecules that are able to regulate endogenous miRNAs hold great potential in both elucidation of miRNA networks and treatment of miRNA-related diseases. Herein, we summarize current strategies for discovery of small molecule modifiers of miRNAs, and we highlight aspects of miRNA cellular biology elucidated by using these small molecules and miRNA-targeted therapeutics realized by these small molecules. We envision that this area will expand dramatically in the near future and will ultimately contribute to a better understanding of miRNA-involved cellular processes and development of therapeutic agents for miRNA-associated diseases.
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Affiliation(s)
- Rengen Fan
- a Department of General Surgery, Yancheng City No. 1 People's Hospital , Yancheng , China
| | - Chaocheng Xiao
- b Department of General Surgery, Yancheng City No. 1 People's Hospital , Yancheng , China
| | - Xinqiang Wan
- c Department of Gynaecology and Obstetrics, Yancheng City No. 1 People's Hospital , Yancheng , China
| | - Wenzhang Cha
- a Department of General Surgery, Yancheng City No. 1 People's Hospital , Yancheng , China
| | - Yufeng Miao
- d Department of Medical Oncology , Wuxi Third People's Hospital , Wuxi , China
| | - Yong Zhou
- a Department of General Surgery, Yancheng City No. 1 People's Hospital , Yancheng , China
| | - Chenglin Qin
- a Department of General Surgery, Yancheng City No. 1 People's Hospital , Yancheng , China
| | - Ting Cui
- e Department of Cardiology, The Third People's Hospital of Yancheng , Yancheng , China
| | - Fenglian Su
- f School of Medical University, Xuzhou , Xuzhou , China
| | - Xiangxiang Shan
- g Department of Geraeology, Yancheng City No.1 People's Hospital , Yancheng , China
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LEF1-AS1 contributes to proliferation and invasion through regulating miR-544a/ FOXP1 axis in lung cancer. Invest New Drugs 2019; 37:1127-1134. [PMID: 30734202 PMCID: PMC6856024 DOI: 10.1007/s10637-018-00721-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/26/2018] [Indexed: 11/29/2022]
Abstract
Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulators in tumor development. This study aims to investigate the potential role oflncRNALEF1-AS1, in the progression of lung cancer. Quantitative real-time PCR (qRT-PCR) and western blot assays showed that LEF1-AS1 was upregulated while miR-544a was downregulated in lung cancer specimens and cells. Overexpression of LEF1-AS1 led to the enhancement of cell proliferation and invasion, revealed by CCK-8 assay and transwell assay. A negative correlation was found between LEF1-AS1 and miR-544a. BLAST analysis and dual-luciferase assay confirmed that FOXP1 is a downstream effector of miR-544a. Therefore, the LEF1-AS1/miR-544a/FOXP1 axis is an important contributor to lung cancer progression. Collectively, our novel data uncovers a new mechanism that governs tumor progression in lung cancer and provides new targets that may be used for disease monitoring and therapeutic intervention of lung cancer.
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Qu J, Chen X, Sun YZ, Zhao Y, Cai SB, Ming Z, You ZH, Li JQ. In Silico Prediction of Small Molecule-miRNA Associations Based on the HeteSim Algorithm. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:274-286. [PMID: 30654189 PMCID: PMC6348698 DOI: 10.1016/j.omtn.2018.12.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/15/2018] [Accepted: 12/04/2018] [Indexed: 01/27/2023]
Abstract
Targeting microRNAs (miRNAs) with drug small molecules (SMs) is a new treatment method for many human complex diseases. Unsurprisingly, identification of potential miRNA-SM associations is helpful for pharmaceutical engineering and disease therapy in the field of medical research. In this paper, we developed a novel computational model of HeteSim-based inference for SM-miRNA Association prediction (HSSMMA) by implementing a path-based measurement method of HeteSim on a heterogeneous network combined with known miRNA-SM associations, integrated miRNA similarity, and integrated SM similarity. Through considering paths from an SM to a miRNA in the heterogeneous network, the model can capture the semantics information under each path and predict potential miRNA-SM associations based on all the considered paths. We performed global, miRNA-fixed local and SM-fixed local leave one out cross validation (LOOCV) as well as 5-fold cross validation based on the dataset of known miRNA-SM associations to evaluate the prediction performance of our approach. The results showed that HSSMMA gained the corresponding areas under the receiver operating characteristic (ROC) curve (AUCs) of 0.9913, 0.9902, 0.7989, and 0.9910 ± 0.0004 based on dataset 1 and AUCs of 0.7401, 0.8466, 0.6149, and 0.7451 ± 0.0054 based on dataset 2, respectively. In case studies, 2 of the top 10 and 13 of the top 50 predicted potential miRNA-SM associations were confirmed by published literature. We further implemented case studies to test whether HSSMMA was effective for new SMs without any known related miRNAs. The results from cross validation and case studies showed that HSSMMA could be a useful prediction tool for the identification of potential miRNA-SM associations.
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Affiliation(s)
- Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Shu-Bin Cai
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhong Ming
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Ürümqi 830011, China.
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
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Lee J, Heo J, Kang H. miR-92b-3p-TSC1 axis is critical for mTOR signaling-mediated vascular smooth muscle cell proliferation induced by hypoxia. Cell Death Differ 2018; 26:1782-1795. [PMID: 30518907 PMCID: PMC6748132 DOI: 10.1038/s41418-018-0243-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 01/05/2023] Open
Abstract
Pulmonary artery smooth muscle cells (PASMCs) undergo proliferation by the mammalian target of rapamycin (mTOR) signaling pathway under hypoxia. Hypoxia induces expression of a specific set of microRNAs (miRNAs) in a variety of cell types. We integrated genomic analyses of both small non-coding RNA and coding transcripts using next-generation sequencing (NGS)-based RNA sequencing with the molecular mechanism of the mTOR signaling pathway in hypoxic PASMCs. These analyses revealed hypoxia-induced miR-92b-3p as a potent regulator of the mTOR signaling pathway. We demonstrated that miR-92b-3p directly targets the 3′-UTR of a negative regulator in the mTOR signaling pathway, TSC1. mTOR signaling and consequent cell proliferation were promoted by enforced expression of miR-92b-3p but inhibited by knocking down endogenous miR-92b-3p. Furthermore, inhibition of miR-92b-3p attenuated hypoxia-induced proliferation of vascular smooth muscle cells (VSMCs). Therefore, this study elucidates a novel role of miR-92b-3p as a hypoxamir in the regulation of the mTOR signaling pathway and the pathological VSMC proliferative response under hypoxia. These findings will help us better understand the miRNA-mediated molecular mechanism of the proliferative response of hypoxic VSMCs through the mTOR signaling pathway.
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Affiliation(s)
- Jihui Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea
| | - Jeongyeon Heo
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea
| | - Hara Kang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 406-772, Republic of Korea.
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Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1477. [PMID: 29726113 PMCID: PMC6002909 DOI: 10.1002/wrna.1477] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]
Abstract
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
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Cha W, Fan R, Miao Y, Zhou Y, Qin C, Shan X, Wan X, Cui T. MicroRNAs as novel endogenous targets for regulation and therapeutic treatments. MEDCHEMCOMM 2018; 9:396-408. [PMID: 30108932 PMCID: PMC6072415 DOI: 10.1039/c7md00285h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 12/10/2017] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have been identified as key endogenous biomolecules that are able to regulate gene expression at the post-transcriptional level. The abnormal expression or function of miRNAs has been demonstrated to be closely related to the occurrence or development of various human diseases, including cancers. Regulation of these abnormal miRNAs thus holds great promise for therapeutic treatments. In this review, we summarize exogenous molecules that are able to regulate endogenous miRNAs, including small molecule regulators of miRNAs and synthetic oligonucleotides. Strategies for screening small molecule regulators of miRNAs and recently reported small molecules are introduced and summarized. Synthetic oligonucleotides including antisense miRNA oligonucleotides and miRNA mimics, as well as delivery systems for these synthetic oligonucleotides to enter cells, that regulate endogenous miRNAs are also summarized. In addition, we discuss recent applications of these small molecules and synthetic oligonucleotides in therapeutic treatments. Overall, this review aims to provide a brief synopsis of recent achievements of using both small molecule regulators and synthetic oligonucleotides to regulate endogenous miRNAs and achieve therapeutic outcomes. We envision that these regulators of endogenous miRNAs will ultimately contribute to the development of new therapies in the future.
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Affiliation(s)
- Wenzhang Cha
- Department of General Surgery , 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
| | - Yufeng Miao
- Department of Medical Oncology , Wuxi Third People's Hospital , Wuxi 214000 , China
| | - Yong Zhou
- Department of General Surgery , Yancheng City No.1 People's Hospital , Yancheng 224001 , China
| | - Chenglin Qin
- Department of General Surgery , 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 .
| | - Xinqiang Wan
- Department of Clinical Medicine , Nantong University Xinglin College , Nantong 226000 , China .
| | - Ting Cui
- Department of Cardiology , The Third People's Hospital of Yancheng , Yancheng 224001 , China .
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36
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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37
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Rapid Generation of miRNA Inhibitor Leads by Bioinformatics and Efficient High-Throughput Screening Methods. Methods Mol Biol 2018; 1517:179-198. [PMID: 27924483 DOI: 10.1007/978-1-4939-6563-2_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The discovery of microRNAs (miRNAs) has opened an entire new avenue for drug development. These short (15-22 nucleotides) noncoding RNAs, which function in RNA silencing and posttranscriptional regulation of gene expression, have been shown to critically affect numerous pathways in both development and disease progression. Current miRNA drug development focuses on either reintroducing the miRNA into cells through the use of a miRNA mimic or inhibiting its function via use of a synthetic antagomir. Although these methods have shown some success as therapeutics, they face challenges particularly with regard to cellular uptake and for use as systemic reagents. We recently presented a novel mechanism of inhibiting miR-544 by directed inhibition of miRNA biogenesis. We found that inhibition of DICER processing of miR-544 through the use of a small molecule abolished miR-544 function in regulating adaptation of breast cancer cells to hypoxic stress. Herein, we describe a protocol that utilizes bioinformatics to first identify lead small molecules that bind to DICER cleavage sites in pre-miRNAs and then employ an efficient, high-throughput fluorescent-based screening system to determine the inhibitory potential of the lead compounds and their derivatives.
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38
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Yao GD, Zhang YF, Chen P, Ren XB. MicroRNA-544 promotes colorectal cancer progression by targeting forkhead box O1. Oncol Lett 2017; 15:991-997. [PMID: 29422969 PMCID: PMC5772941 DOI: 10.3892/ol.2017.7381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 09/07/2017] [Indexed: 01/07/2023] Open
Abstract
Dysregulation of microRNAs has been confirmed to serve an important role in cancer development and progression. However, the role of microRNA (miR)-544 in colorectal cancer progression remains unknown. In the present study, it was observed that the expression level of miR-544 was increased in breast cancer cell lines and tissues using the quantitative polymerase chain reaction. Overexpression of miR-544 promoted cell proliferation and invasion in colorectal cancer, whereas inhibition of miR-544 suppressed colorectal cancer progression as determined using MTT, colony formation and Transwell assays. Furthermore, forkhead box O1 (FOXO1) was a direct target of miR-544. FOXO1 mediated miR-544-regulated colorectal cancer progression and cell cycle distribution. In conclusion, the results of the present study revealed that miR-544 serves an important role in promoting human colorectal cancer cell progression.
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Affiliation(s)
- Guo-Dong Yao
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, P.R. China.,Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, P.R. China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, P.R. China.,Department of Surgery, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia Autonomous Region 010050, P.R. China
| | - Ya-Feng Zhang
- Department of Surgery, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia Autonomous Region 010050, P.R. China
| | - Peng Chen
- Department of Surgery, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia Autonomous Region 010050, P.R. China
| | - Xiu-Bao Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, P.R. China.,Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, P.R. China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, P.R. China
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Zhu Z, Wang S, Zhu J, Yang Q, Dong H, Huang J. MicroRNA-544 down-regulates both Bcl6 and Stat3 to inhibit tumor growth of human triple negative breast cancer. Biol Chem 2017; 397:1087-95. [PMID: 27186677 DOI: 10.1515/hsz-2016-0104] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/09/2016] [Indexed: 01/03/2023]
Abstract
Triple negative breast cancer lacking estrogen receptor (ER), progesterone receptor and Her2 account for account for the majority of the breast cancer deaths, due to the lack of specific gene targeted therapy. Our current study aimed to investigate the role of miR-544 in triple negative breast cancer. Endogenous levels of miR-544 were significantly lower in breast cancer cell lines than in human breast non-tumorigenic and mammary epithelial cell lines. We found that miR-544 directly targeted the 3'-untranslated region (UTR) on both Bcl6 and Stat3 mRNAs, and overexpression of miR-544 in triple negative breast cancer cells significantly down-regulated expressions of Bcl6 and Stat3, which in turn severely inhibited cancer cell proliferation, migration and invasion in vitro. Employing a mouse xenograft model to examine the in vivo function of miR-544, we found that expression of miR-544 significantly repressed the growth of xenograft tumors. Our current study reported miR-544 as a tumor-suppressor microRNA particularly in triple negative breast cancer. Our data supported the role of miR-544 as a potential biomarker in developing gene targeted therapies in the clinical treatment of triple negative breast cancer.
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Velagapudi SP, Luo Y, Tran T, Haniff HS, Nakai Y, Fallahi M, Martinez GJ, Childs-Disney JL, Disney MD. Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA. ACS CENTRAL SCIENCE 2017; 3:205-216. [PMID: 28386598 PMCID: PMC5364451 DOI: 10.1021/acscentsci.7b00009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 05/03/2023]
Abstract
RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yiling Luo
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Tuan Tran
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Hafeez S. Haniff
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yoshio Nakai
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Mohammad Fallahi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Gustavo J. Martinez
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Jessica L. Childs-Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Matthew D. Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
- E-mail:
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41
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Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Disney MD, Angelbello AJ. Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence. Acc Chem Res 2016; 49:2698-2704. [PMID: 27993012 DOI: 10.1021/acs.accounts.6b00326] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1-2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions. RNA's diverse roles are often a consequence of the various folds that it adopts. The single-stranded nature of the biopolymer enables it to adopt intramolecular folds with noncanonical pairings to lower its free energy. These folds can be scaffolds to bind proteins or to form frameworks to interact with other RNAs. Not surprisingly, dysregulation of certain noncoding RNAs has been shown to be causative of disease. Given this as the background, it is easy to see why it would be useful to develop methods that target RNA and manipulate its biology in rational and predictable ways. The antisense approach has afforded strategies to target RNAs via Watson-Crick base pairing and has typically focused on targeting partially unstructured regions of RNA. Small molecule strategies to target RNA would be desirable not only because compounds could be lead optimized via medicinal chemistry but also because structured regions within an RNA of interest could be targeted to directly interfere with RNA folds that contribute to disease. Additionally, small molecules have historically been the most successful drug candidates. Until recently, the ability to design small molecules that target non-ribosomal RNAs has been elusive, creating the perception that they are "undruggable". In this Account, approaches to demystify targeting RNA with small molecules are described. Rather than bulk screening for compounds that bind to singular targets, which is the purview of the pharmaceutical industry and academic institutions with high throughput screening facilities, we focus on methods that allow for the rational design of small molecules toward biological RNAs. One enabling and foundational technology that has been developed is two-dimensional combinatorial screening (2DCS), a library-versus-library selection approach that allows the identification of the RNA motif binding preferences of small molecules from millions of combinations. A landscape map of the 2DCS-defined and annotated RNA motif-small molecule interactions is then placed into Inforna, a computational tool that allows one to mine these interactions against an RNA of interest or an entire transcriptome. Indeed, this approach has been enabled by tools to annotate RNA structure from sequence, an invaluable asset to the RNA community and this work, and has allowed for the rational identification of "druggable" RNAs in a target agnostic fashion.
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Affiliation(s)
- Matthew D. Disney
- Departments of
Chemistry
and Neuroscience, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, Florida 33458, United States
| | - Alicia J. Angelbello
- Departments of
Chemistry
and Neuroscience, The Scripps Research Institute, 130 Scripps Way, #3A1, Jupiter, Florida 33458, United States
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43
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Connelly CM, Moon MH, Schneekloth JS. The Emerging Role of RNA as a Therapeutic Target for Small Molecules. Cell Chem Biol 2016; 23:1077-1090. [PMID: 27593111 PMCID: PMC5064864 DOI: 10.1016/j.chembiol.2016.05.021] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/07/2016] [Accepted: 05/18/2016] [Indexed: 01/09/2023]
Abstract
Recent advances in understanding different RNAs and unique features of their biology have revealed a wealth of information. However, approaches to identify small molecules that target these newly discovered regulatory elements have been lacking. The application of new biochemical screening and design-based technologies, coupled with a resurgence of interest in phenotypic screening, has resulted in several compelling successes in targeting RNA. A number of recent advances suggest that achieving the long-standing goal of developing drug-like, biologically active small molecules that target RNA is possible. This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.
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Affiliation(s)
- Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Michelle H Moon
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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44
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Abulwerdi FA, Schneekloth JS. Microarray-based technologies for the discovery of selective, RNA-binding molecules. Methods 2016; 103:188-95. [PMID: 27109057 PMCID: PMC6314024 DOI: 10.1016/j.ymeth.2016.04.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/20/2022] Open
Abstract
The identification of small molecules that bind specifically to RNA is a challenge. However, the recent explosion in knowledge about the role RNA plays in a number of physiological processes apart from coding for protein sequences makes it a highly interesting target for chemical probes and therapeutics. One technology that has played an important role in the discovery of RNA-binding molecules is microarrays. Microarrays have been broadly employed to screen, profile, and quantify RNA interactions, and will likely play an important role in the discovery of new classes of ligands going forward. Here, we discuss the development of microarray technologies, including aminoglycoside, peptide, peptoid, and small molecule microarrays, and their use in studying RNA-interacting molecules.
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Affiliation(s)
- Fardokht A Abulwerdi
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States; Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States.
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45
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Potenza N, Castiello F, Panella M, Colonna G, Ciliberto G, Russo A, Costantini S. Human MiR-544a Modulates SELK Expression in Hepatocarcinoma Cell Lines. PLoS One 2016; 11:e0156908. [PMID: 27275761 PMCID: PMC4898719 DOI: 10.1371/journal.pone.0156908] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/20/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a multi-factorial cancer with a very poor prognosis; therefore, there are several investigations aimed at the comprehension of the molecular mechanisms leading to development and progression of HCC and at the definition of new therapeutic strategies. We have recently evaluated the expression of selenoproteins in HCC cell lines in comparison with normal hepatocytes. Recent results have shown that some of them are down- and others up-regulated, including the selenoprotein K (SELK), whose expression was also induced by sodium selenite treatment on cells. However, so far very few studies have been dedicated to a possible effect of microRNAs on the expression of selenoproteins and their implication in HCC. In this study, the analysis of SELK 3'UTR by bioinformatics tools led to the identification of eight sites potentially targeted by human microRNAs. They were then subjected to a validation test based on luciferase reporter constructs transfected in HCC cell lines. In this functional screening, miR-544a was able to interact with SELK 3'UTR suppressing the reporter activity. Transfection of a miR-544a mimic or inhibitor was then shown to decrease or increase, respectively, the translation of the endogenous SELK mRNA. Intriguingly, miR-544a expression was found to be modulated by selenium treatment, suggesting a possible role in SELK induction by selenium.
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Affiliation(s)
- Nicoletta Potenza
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta, Italia
| | - Filomena Castiello
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta, Italia
| | - Marta Panella
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta, Italia
| | - Giovanni Colonna
- Servizio di Informatica Medica, Azienda Ospedaliera Universitaria, Seconda Università di Napoli, Napoli, Italia
| | - Gennaro Ciliberto
- Direttore Scientifico, Istituto Nazionale Tumori “Fondazione G. Pascale”- IRCCS, Napoli, Italia
| | - Aniello Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta, Italia
| | - Susan Costantini
- CROM, Istituto Nazionale Tumori “Fondazione G. Pascale”—IRCCS, Napoli, Italia
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46
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Synthesis and investigation of novel benzimidazole derivatives as antifungal agents. Bioorg Med Chem 2016; 24:3680-6. [PMID: 27301676 DOI: 10.1016/j.bmc.2016.06.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 01/02/2023]
Abstract
The rise and emergence of resistance to antifungal drugs by diverse pathogenic fungal strains have resulted in an increase in demand for new antifungal agents. Various heterocyclic scaffolds with different mechanisms of action against fungi have been investigated in the past. Herein, we report the synthesis and antifungal activities of 18 alkylated mono-, bis-, and trisbenzimidazole derivatives, their toxicities against mammalian cells, as well as their ability to induce reactive oxygen species (ROS) in yeast cells. Many of our bisbenzimidazole compounds exhibited moderate to excellent antifungal activities against all tested fungal strains, with MIC values ranging from 15.6 to 0.975μg/mL. The fungal activity profiles of our bisbenzimidazoles were found to be dependent on alkyl chain length. Our most potent compounds were found to display equal or superior antifungal activity when compared to the currently used agents amphotericin B, fluconazole, itraconazole, posaconazole, and voriconazole against many of the strains tested.
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47
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Small-molecule approaches toward the targeting of oncogenic miRNAs: roadmap for the discovery of RNA modulators. Future Med Chem 2016; 8:803-16. [DOI: 10.4155/fmc-2016-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
miRNAs are a recently discovered class of small noncoding RNAs implicated in the regulation of gene expression. The deregulation of miRNAs levels has been linked to the development of various cancers where oncogenic miRNAs are overexpressed and tumor suppressor miRNAs are underexpressed. Here we report the three main strategies developed in order to discover small-molecule drugs able to selectively interfere with oncogenic miRNAs: the high throughput screening of large libraries of compounds, the focused screening of small libraries of molecules that are known to be able to interact with RNA thus being supposed modulators of miRNAs pathway and the design of small molecules based on the secondary structure of targeted RNA and/or three-dimensional structure of enzymes involved in miRNAs pathway.
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