1
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Emanuelson C, Ankenbruck N, Kumbhare R, Thomas M, Connelly C, Baktash Y, Randall G, Deiters A. Transcriptional Inhibition of MicroRNA miR-122 by Small Molecules Reduces Hepatitis C Virus Replication in Liver Cells. J Med Chem 2022; 65:16338-16352. [PMID: 36449366 PMCID: PMC9942140 DOI: 10.1021/acs.jmedchem.2c01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
MicroRNAs (miRNAs) are noncoding RNA molecules of 22-24 nucleotides that are estimated to regulate thousands of genes in humans, and their dysregulation has been implicated in many diseases. MicroRNA-122 (miR-122) is the most abundant miRNA in the liver and has been linked to the development of hepatocellular carcinoma and hepatitis C virus (HCV) infection. Its role in these diseases renders miR-122 a potential target for small-molecule therapeutics. Here, we report the discovery of a new sulfonamide class of small-molecule miR-122 inhibitors from a high-throughput screen using a luciferase-based reporter assay. Structure-activity relationship (SAR) studies and secondary assays led to the development of potent and selective miR-122 inhibitors. Preliminary mechanism-of-action studies suggest a role in the promoter-specific transcriptional inhibition of miR-122 expression through direct binding to the liver-enriched transcription factor hepatocyte nuclear factor 4α. Importantly, the developed inhibitors significantly reduce HCV replication in human liver cells.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rohan Kumbhare
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Meryl Thomas
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Colleen Connelly
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yasmine Baktash
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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2
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Chaudhry T, Coxon CR, Ross K. Trading places: Peptide and small molecule alternatives to oligonucleotide-based modulation of microRNA expression. Drug Discov Today 2022; 27:103337. [PMID: 35995360 DOI: 10.1016/j.drudis.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022]
Abstract
It is well established that microRNA (miRNA) dysregulation is involved in the development and progression of various diseases, especially cancer. Emerging evidence suggests that small molecule and peptide agents can interfere with miRNA disease pathways. Despite this, very little is known about structural features that drive drug-miRNA interactions and subsequent inhibition. In this review, we highlight the advances made in the development of small molecule and peptide inhibitors of miRNA processing. Specifically, we attempt to draw attention to peptide features that may be critical for interaction with the miRNA secondary structure to regulate miRNA expression. We hope that this review will help to establish peptides as exciting miRNA expression modulators and will contribute towards the development of the first miRNA-targeting peptide therapy.
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Affiliation(s)
- Talhat Chaudhry
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK; Institute for Health Research, Liverpool John Moores University, Liverpool, UK
| | - Christopher R Coxon
- EaStChem School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH14 4AS, UK
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool, UK; Institute for Health Research, Liverpool John Moores University, Liverpool, UK.
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3
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Soares S, Guerreiro SG, Cruz-Martins N, Faria I, Baylina P, Sales MG, Correa-Duarte MA, Fernandes R. The Influence of miRNAs on Radiotherapy Treatment in Prostate Cancer - A Systematic Review. Front Oncol 2021; 11:704664. [PMID: 34414113 PMCID: PMC8369466 DOI: 10.3389/fonc.2021.704664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/06/2021] [Indexed: 11/21/2022] Open
Abstract
In the last years, extensive investigation on miRNomics have shown to have great advantages in cancer personalized medicine regarding diagnosis, treatment and even clinical outcomes. Prostate cancer (PCa) is the second most common male cancer and about 50% of all PCa patients received radiotherapy (RT), despite some of them develop radioresistance. Here, we aim to provide an overview on the mechanisms of miRNA biogenesis and to discuss the functional impact of miRNAs on PCa under radiation response. As main findings, 23 miRNAs were already identified as being involved in genetic regulation of PCa cell response to RT. The mechanisms of radioresistance are still poorly understood, despite it has been suggested that miRNAs play an important role in cell signaling pathways. Identification of miRNAs panel can be thus considered an upcoming and potentially useful strategy in PCa diagnosis, given that radioresistance biomarkers, in both prognosis and therapy still remains a challenge.
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Affiliation(s)
- Sílvia Soares
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, Porto, Portugal.,LaBMI - Laboratory of Medical & Industrial Biotechnology, Porto Research, Technology & Innovation Center (PORTIC), P.PORTO - Polytechnic Institute of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), Porto, Portugal.,Faculty of Chemistry, University of Vigo, Vigo, Spain.,CEB, Centre of Biological Engineering of Minho University, Braga, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Susana G Guerreiro
- Institute for Research and Innovation in Health (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto-IPATIMUP, Porto, Portugal.,Department of Biomedicine, Biochemistry Unit, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Natália Cruz-Martins
- Institute for Research and Innovation in Health (i3S), Porto, Portugal.,Department of Biomedicine, Biochemistry Unit, Faculty of Medicine, University of Porto, Porto, Portugal.,Institute of Research and Advanced Training in Health Sciences and Technologies (CESPU), Gandra, Portugal
| | - Isabel Faria
- School of Health, Polytechnic of Porto, Porto, Portugal
| | - Pilar Baylina
- LaBMI - Laboratory of Medical & Industrial Biotechnology, Porto Research, Technology & Innovation Center (PORTIC), P.PORTO - Polytechnic Institute of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), Porto, Portugal.,School of Health, Polytechnic of Porto, Porto, Portugal
| | - Maria Goreti Sales
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, Porto, Portugal.,CEB, Centre of Biological Engineering of Minho University, Braga, Portugal.,Biomark@UC, Department of Chemical Engineering, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Miguel A Correa-Duarte
- Faculty of Chemistry, University of Vigo, Vigo, Spain.,CINBIO, University of Vigo, Vigo, Spain.,Southern Galicia Institute of Health Research (IISGS), and Biomedical Research Networking Center for Mental Health (CIBERSAM), Vigo, Spain
| | - Rúben Fernandes
- LaBMI - Laboratory of Medical & Industrial Biotechnology, Porto Research, Technology & Innovation Center (PORTIC), P.PORTO - Polytechnic Institute of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), Porto, Portugal.,School of Health, Polytechnic of Porto, Porto, Portugal
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4
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Das B, Murata A, Nakatani K. A small-molecule fluorescence probe ANP77 for sensing RNA internal loop of C, U and A/CC motifs and their binding molecules. Nucleic Acids Res 2021; 49:8462-8470. [PMID: 34358308 PMCID: PMC8421207 DOI: 10.1093/nar/gkab650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/02/2021] [Accepted: 08/04/2021] [Indexed: 11/12/2022] Open
Abstract
Small-molecules interacting with particular RNAs and modulating their functions are vital tools for RNA-targeting drug discovery. Considering the substantial distribution of the internal loops involving two contiguous cytosines opposite to a single-nucleotide base (Y/CC; Y = C, U or A) within the biologically significant functional RNAs, developing small-molecule probes targeting Y/CC sites should provide profound insight into their functions and roles in biochemical processes. Herein, we report ANP77 as the small-molecule probe for sensing RNA internal loop of Y/CC motifs and molecules binding to the motifs. The Y/CC motifs interact with ANP77 via the formation of a 1:1 complex and quench the fluorescence of ANP77. The flanking sequence-dependent binding to C/CC and U/CC sites was assessed by fluorometric screening, provided the binding heat maps. The quenching phenomena of ANP77 fluorescence was confirmed with intrinsic potential drug target pre-miR-1908. Finally, the binding-dependent fluorescence quenching of ANP77 was utilized in the fluorescence indicator displacement assay to demonstrate the potential of ANP77 as an indicator by using the RNA-binding drugs, risdiplam and branaplam.
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Affiliation(s)
- Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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5
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Xie J, Frank AT. Mining for Ligandable Cavities in RNA. ACS Med Chem Lett 2021; 12:928-934. [PMID: 34141071 DOI: 10.1021/acsmedchemlett.1c00068] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022] Open
Abstract
Identifying potential ligand binding cavities is a critical step in structure-based screening of biomolecular targets. Cavity mapping methods can detect such binding cavities; however, for ribonucleic acid (RNA) targets, determining which of the detected cavities are "ligandable" remains an unsolved challenge. In this study, we trained a set of machine learning classifiers to distinguish ligandable RNA cavities from decoy cavities. Application of our classifiers to two independent test sets demonstrated that we could recover ligandable cavities from decoys with an AUC > 0.83. Interestingly, when we applied our classifiers to a library of modeled structures of the HIV-1 transactivation response (TAR) element RNA, we found that several of the conformers that harbored cavities with high ligandability scores resembled known holo-TAR structures. On the basis of our results, we envision that our classifiers could find utility as a tool to parse RNA structures and prospectively mine for ligandable binding cavities and, in so doing, facilitate structure-based virtual screening efforts against RNA drug targets.
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Affiliation(s)
- Jingru Xie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aaron T. Frank
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Amin S, Alam MM, Akhter M, Najmi AK, Siddiqui N, Husain A, Shaquiquzzaman M. A review on synthetic procedures and applications of phosphorus oxychloride (POCl 3) in the last biennial period (2018–19). PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2020.1831499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shaista Amin
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - M. Mumtaz Alam
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Mymoona Akhter
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - A. K. Najmi
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Nadeem Siddiqui
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Asif Husain
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - M. Shaquiquzzaman
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
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7
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Liu D, Wan X, Shan X, Fan R, Zha W. Drugging the "undruggable" microRNAs. Cell Mol Life Sci 2021; 78:1861-1871. [PMID: 33052435 PMCID: PMC11073314 DOI: 10.1007/s00018-020-03676-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/07/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
As a naturally occurring class of gene regulators, microRNAs (miRNAs) have attracted much attention as promising targets for therapeutic development. However, RNAs including miRNAs have long been considered undruggable, and most efforts have been devoted to using synthetic oligonucleotides to regulate miRNAs. Encouragingly, recent findings have revealed that miRNAs can also be drugged with small molecules that directly target miRNAs. In this review paper, we give a summary of recently emerged small-molecule inhibitors (SMIs) and small-molecule degraders (SMDs) for miRNAs. SMIs are small molecules that directly bind to miRNAs to inhibit their biogenesis, and SMDs are bifunctional small molecules that upon binding to miRNAs induce miRNA degradation. Strategies for discovering SMIs and developing SMDs were summarized. Applications of SMIs and SMDs in miRNA inhibition and cancer therapy were also introduced. Overall, SMIs and SMDs introduced here have high potency and specificity in miRNA inhibition. We envision that these small molecules will pave the way for developing novel therapeutics toward miRNAs that were previously considered undruggable.
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Affiliation(s)
- Dejun Liu
- The Yancheng Clinical College of Xuzhou Medical University, Yancheng, 224001, China
| | - Xinqiang Wan
- Department of Gynaecology and Obstetrics, Yancheng City No.1 People's Hospital, Yancheng, 224001, China
| | - Xiangxiang Shan
- Department of Geraeology, Yancheng City No.1 People's Hospital, Yancheng, 224001, China
| | - Rengen Fan
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, 224001, China.
| | - Wenzhang Zha
- Department of General Surgery, Yancheng City No.1 People's Hospital, Yancheng, 224001, China.
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8
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Clinico-Pathological Importance of miR-146a in Lung Cancer. Diagnostics (Basel) 2021; 11:diagnostics11020274. [PMID: 33578944 PMCID: PMC7916675 DOI: 10.3390/diagnostics11020274] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is a well-known malignant tumor of the respiratory tract, which has caused a significant level of damage to human health in the 21st century. Micro-RNAs (miRNAs) are tiny, non-coding RNA stem-loop structures with a length of roughly 20–25 nucleotides that function as powerful modulators of mRNA and protein products of a gene. miRNAs may modulate many biological processes involving growth, differentiation, proliferation, and cell death and play a key role in the pathogenesis of various types of malignancies. Several accumulating pieces of evidence have proven that miRNA, especially miR-146a, are crucial modulators of innate immune response sequences. A novel and exciting cancer research field has involved miRNA for the detection and suppression of cancer. However, the actual mechanism which is adopted by these miRNA is still unclear. miRNAs have been used as a cancer-associated biomarker in several studies, suggesting their altered expression in various cancers compared to the normal cells. The amount of expression of miRNA can also be used to determine the stage of the disease, aiding in early detection. In breast, pancreatic, and hepatocellular carcinoma, and gastric cancer, cancer cell proliferation and metastasis has been suppressed by miR-146a. Changes in miR-146a expression levels have biomarker importance and possess a high potential as a therapeutic target in lung cancer. It retards epithelial-mesenchymal transition and promotes the therapeutic action of anticancer agents in lung cancer. Studies have also suggested that miR-146a affects gene expression through different signaling pathways viz. TNF-α, NF-κB and MEK-1/2, and JNK-1/2. Further research is required for understanding the molecular mechanisms of miR-146a in lung cancer. The potential role of miR-146a as a diagnostic marker of lung cancer must also be analyzed. This review summarizes the tumor-suppressing, anti-inflammatory, and antichemoresistive nature of miR-146a in lung cancer.
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9
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Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA. Methods Mol Biol 2021; 2105:157-172. [PMID: 32088869 DOI: 10.1007/978-1-0716-0243-0_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the important roles noncoding RNAs play in gene expression, their sequence-specific recognition is important for both fundamental science and the pharmaceutical industry. However, most noncoding RNAs fold in complex helical structures that are challenging problems for molecular recognition. Herein, we describe a method for sequence-specific recognition of double-stranded RNA using peptide nucleic acids (PNAs) that form triple helices in the major grove of RNA under physiologically relevant conditions. We also outline methods for solid-phase conjugation of PNA with cell-penetrating peptides and fluorescent dyes. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.
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10
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Daws SE, Miller CA. Targeting persistent stress-enhanced memory through microRNAs. Neuropsychopharmacology 2021; 46:236. [PMID: 32843704 PMCID: PMC7689484 DOI: 10.1038/s41386-020-00816-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephanie E Daws
- Department of Anatomy & Cell Biology, Temple University, Philadelphia, PA, USA
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA
| | - Courtney A Miller
- Department of Molecular Medicine, The Scripps Research Institute, San Diego, CA, USA.
- Department of Neuroscience, The Scripps Research Institute, San Diego, CA, USA.
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11
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Abstract
The structural and regulatory elements in therapeutically relevant RNAs offer many opportunities for targeting by small molecules, yet fundamental understanding of what drives selectivity in small molecule:RNA recognition has been a recurrent challenge. In particular, RNAs tend to be more dynamic and offer less chemical functionality than proteins, and biologically active ligands must compete with the highly abundant and highly structured RNA of the ribosome. Indeed, the only small molecule drug targeting RNA other than the ribosome was just approved in August 2020, and our recent survey of the literature revealed fewer than 150 reported chemical probes that target non-ribosomal RNA in biological systems. This Feature outlines our efforts to improve small molecule targeting strategies and gain fundamental insights into small molecule:RNA recognition by analyzing patterns in both RNA-biased small molecule chemical space and RNA topological space privileged for differentiation. First, we synthesized libraries based on RNA binding scaffolds that allowed us to reveal general principles in small molecule:recognition and to ask precise chemical questions about drivers of affinity and selectivity. Elaboration of these scaffolds has led to recognition of medicinally relevant RNA targets, including viral and long noncoding RNA structures. More globally, we identified physicochemical, structural, and spatial properties of biologically active RNA ligands that are distinct from those of protein-targeted ligands, and we have provided the dataset and associated analytical tools as part of a publicly available online platform to facilitate RNA ligand discovery. At the same time, we used pattern recognition protocols to identify RNA topologies that can be differentially recognized by small molecules and have elaborated this technique to visualize conformational changes in RNA secondary structure. These fundamental insights into the drivers of RNA recognition in vitro have led to functional targeting of RNA structures in biological systems. We hope that these initial guiding principles, as well as the approaches and assays developed in their pursuit, will enable rapid progress toward the development of RNA-targeted chemical probes and ultimately new therapeutic approaches to a wide range of deadly human diseases.
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Affiliation(s)
- Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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12
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Bhattarai U, Hsieh WC, Yan H, Guo ZF, Shaikh AY, Soltani A, Song Y, Ly DH, Liang FS. Bifunctional small molecule-oligonucleotide hybrid as microRNA inhibitor. Bioorg Med Chem 2020; 28:115394. [PMID: 32139203 DOI: 10.1016/j.bmc.2020.115394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 10/25/2022]
Abstract
miRNAs are key regulators of various biological processes. Dysregulation of miRNA is linked to many diseases. Development of miRNA inhibitor has implication in disease therapy and study of miRNA function. The biogenesis pathway of miRNA involves the processing of pre-miRNA into mature miRNA by Dicer enzyme. We previously reported a proximity enabled approach that employs bifunctional small molecules to regulate miRNA maturation through inhibiting the enzymatic activity of Dicer. By conjugating to an RNA targeting unit, an RNase inhibitor could be delivered to the cleavage site of specific pre-miRNA to deactivate the complexed Dicer enzyme. Herein, we expanded this bifunctional strategy by showing that antisense oligonucleotides (ASOs), including morpholinos and γPNAs, could be readily used as the RNA recognition unit to generate bifunctional small molecule-oligonucleotide hybrids as miRNA inhibitors. A systematic comparison revealed that the potency of these hybrids is mainly determined by the RNA binding of the targeting ASO molecules. Since the lengths of the ASO molecules used in this approach were much shorter than commonly used anti-miRNA ASOs, this may provide benefits to the specificity and cellular delivery of these hybrids. We expect that this approach could be complementary to traditional ASO and small molecule based miRNA inhibition and contribute to the study of miRNA.
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Affiliation(s)
- Umesh Bhattarai
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, USA
| | - Wei-Che Hsieh
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Hao Yan
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, USA; Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Zhi-Fo Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, USA
| | - Ashif Yasin Shaikh
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Aria Soltani
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Yabin Song
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, USA
| | - Danith H Ly
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, USA; Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA.
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13
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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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14
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Maity D, Kumar S, Curreli F, Debnath AK, Hamilton AD. α‐Helix‐Mimetic Foldamers for Targeting HIV‐1 TAR RNA. Chemistry 2019; 25:7265-7269. [DOI: 10.1002/chem.201900139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/22/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Debabrata Maity
- Department of ChemistryNew York University New York New York 10003 USA
| | - Sunil Kumar
- Department of ChemistryNew York University New York New York 10003 USA
| | - Francesca Curreli
- Lindsey F. Kimball Research InstituteNew York Blood Center New York New York 10065 USA
| | - Asim K. Debnath
- Lindsey F. Kimball Research InstituteNew York Blood Center New York New York 10065 USA
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15
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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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16
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Vo DD, Becquart C, Tran TPA, Di Giorgio A, Darfeuille F, Staedel C, Duca M. Building of neomycin-nucleobase-amino acid conjugates for the inhibition of oncogenic miRNAs biogenesis. Org Biomol Chem 2019; 16:6262-6274. [PMID: 30116813 DOI: 10.1039/c8ob01858h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers, thus being oncogenic. The inhibition of oncogenic miRNAs (defined as the blocking of miRNAs' production or function) would find application in the therapy of different types of cancer in which these miRNAs are implicated. In this work, we describe the design and synthesis of new small-molecule RNA ligands with the aim of inhibiting Dicer-mediated processing of oncogenic miRNAs. One of the synthesized compound (4b) composed of the aminoglycoside neomycin conjugated to an artificial nucleobase and to amino acid histidine is able to selectively decrease miR-372 levels in gastric adenocarcinoma (AGS) cells and to restore the expression of the target LATS2 protein. This activity led to the inhibition of proliferation of these cells. The study of the interactions of 4b with pre-miR-372 allowed for the elucidation of the molecular mechanism of the conjugate, thus leading to new perspectives for the design of future inhibitors.
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Affiliation(s)
- Duc Duy Vo
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), Nice, France.
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17
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Abstract
While <2% of DNA encodes for functional proteins, >70% is transcribed into RNA. Although the function of most RNA transcripts is unknown, such non-coding RNAs are attractive targets for molecular recognition because of the potentially important roles they play in regulation of gene expression and development of disease. In this chapter, we describe peptide nucleic acids (PNAs) that form sequence-specific triple helices with double-stranded RNA (dsRNA). We provide protocols for sequence design and biophysical characterization of PNAs and discuss first examples where such PNAs have been used for functional modulation of dsRNA. The triplex-forming PNAs represent a new approach for RNA recognition that may find future applications in fundamental science, biotechnology and medicine.
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18
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19
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Yan H, Bhattarai U, Song Y, Liang FS. Design, synthesis and activity of light deactivatable microRNA inhibitor. Bioorg Chem 2018; 80:492-497. [PMID: 29990897 DOI: 10.1016/j.bioorg.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/25/2018] [Accepted: 07/01/2018] [Indexed: 12/28/2022]
Abstract
miRNAs are key cellular regulators and their dysregulation is associated with many human diseases. They are usually produced locally in a spatiotemporally controlled manner to target mRNAs and regulate gene expression. Thus, developing chemical tools for manipulating miRNA with spatiotemporal precise is critical for studying miRNA. Herein, we designed a strategy to control miRNA biogenesis with light controllable inhibitor targeting the pre-miRNA processing by Dicer. By conjugating two non-inhibiting units, a low affinity Dicer inhibitor and a pre-miRNA binder, through a photocleavable linker, the bifunctional molecule obtained could inhibit miRNA production. Taking advantage of the photocleavable property of the linker, the bifunctional inhibitor can be fragmented into separate non-inhibiting units and therefore be deactivated by light. We expect that this strategy could be applied to generate chemical biological tools that allow light-mediated spatiotemporal control of miRNA maturation and contribute to the study of miRNA function.
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Affiliation(s)
- Hao Yan
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States
| | - Umesh Bhattarai
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States
| | - Yabin Song
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States.
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20
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Idda ML, Munk R, Abdelmohsen K, Gorospe M. Noncoding RNAs in Alzheimer's disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9. [PMID: 29327503 PMCID: PMC5847280 DOI: 10.1002/wrna.1463] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the main cause of dementia among the elderly worldwide. Despite intense efforts to develop drugs for preventing and treating AD, no effective therapies are available as yet, posing a growing burden at the personal, medical, and socioeconomic levels. AD is characterized by the production and aggregation of amyloid β (Aβ) peptides derived from amyloid precursor protein (APP), the presence of hyperphosphorylated microtubule-associated protein Tau (MAPT), and chronic inflammation leading to neuronal loss. Aβ accumulation and hyperphosphorylated Tau are responsible for the main histopathological features of AD, Aβ plaques, and neurofibrillary tangles (NFTs), respectively. However, the full spectrum of molecular factors that contribute to AD pathogenesis is not known. Noncoding (nc)RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), regulate gene expression at the transcriptional and posttranscriptional levels in various diseases, serving as biomarkers and potential therapeutic targets. There is rising recognition that ncRNAs have been implicated in both the onset and pathogenesis of AD. Here, we review the ncRNAs implicated posttranscriptionally in the main AD pathways and discuss the growing interest in targeting regulatory ncRNAs therapeutically to combat AD pathology. WIREs RNA 2018, 9:e1463. doi: 10.1002/wrna.1463 This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
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21
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Li J, Lei K, Wu Z, Li W, Liu G, Liu J, Cheng F, Tang Y. Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs. Oncotarget 2018; 7:45584-45596. [PMID: 27329603 PMCID: PMC5216744 DOI: 10.18632/oncotarget.10052] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/28/2016] [Indexed: 02/05/2023] Open
Abstract
As the recent development of high-throughput technologies in cancer pharmacogenomics, there is an urgent need to develop new computational approaches for comprehensive identification of new pharmacogenomic biomarkers, such as microRNAs (miRNAs). In this study, a network-based framework, namely the SMiR-NBI model, was developed to prioritize miRNAs as potential biomarkers characterizing treatment responses of anticancer drugs on the basis of a heterogeneous network connecting drugs, miRNAs and genes. A high area under the receiver operating characteristic curve of 0.820 ± 0.013 was yielded during 10-fold cross validation. In addition, high performance was further validated in identifying new anticancer mechanism-of-action for natural products and non-steroidal anti-inflammatory drugs. Finally, the newly predicted miRNAs for tamoxifen and metformin were experimentally validated in MCF-7 and MDA-MB-231 breast cancer cell lines via qRT-PCR assays. High success rates of 60% and 65% were yielded for tamoxifen and metformin, respectively. Specifically, 11 oncomiRNAs (e.g. miR-20a-5p, miR-27a-3p, miR-29a-3p, and miR-146a-5p) from the top 20 predicted miRNAs were experimentally verified as new pharmacogenomic biomarkers for metformin in MCF-7 or MDA-MB-231 cell lines. In summary, the SMiR-NBI model would provide a powerful tool to identify potential pharmacogenomic biomarkers characterized by miRNAs in the emerging field of precision cancer medicine, which is available at http://lmmd.ecust.edu.cn/database/smir-nbi/.
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Affiliation(s)
- Jie Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Kecheng Lei
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jianwen Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Feixiong Cheng
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,Current address: Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.,Current address: Center for Complex Networks Research, Northeastern University, Boston, USA
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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22
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Modulation of oncogenic miRNA biogenesis using functionalized polyamines. Sci Rep 2018; 8:1667. [PMID: 29374231 PMCID: PMC5786041 DOI: 10.1038/s41598-018-20053-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/12/2018] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs are key factors in the regulation of gene expression and their deregulation has been directly linked to various pathologies such as cancer. The use of small molecules to tackle the overexpression of oncogenic miRNAs has proved its efficacy and holds the promise for therapeutic applications. Here we describe the screening of a 640-compound library and the identification of polyamine derivatives interfering with in vitro Dicer-mediated processing of the oncogenic miR-372 precursor (pre-miR-372). The most active inhibitor is a spermine-amidine conjugate that binds to the pre-miR-372 with a KD of 0.15 µM, and inhibits its in vitro processing with a IC50 of 1.06 µM. The inhibition of miR-372 biogenesis was confirmed in gastric cancer cells overexpressing miR-372 and a specific inhibition of proliferation through de-repression of the tumor suppressor LATS2 protein, a miR-372 target, was observed. This compound modifies the expression of a small set of miRNAs and its selective biological activity has been confirmed in patient-derived ex vivo cultures of gastric carcinoma. Polyamine derivatives are promising starting materials for future studies about the inhibition of oncogenic miRNAs and, to the best of our knowledge, this is the first report about the application of functionalized polyamines as miRNAs interfering agents.
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23
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Shortridge MD, Walker MJ, Pavelitz T, Chen Y, Yang W, Varani G. A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing. ACS Chem Biol 2017; 12:1611-1620. [PMID: 28437065 DOI: 10.1021/acschembio.7b00180] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) help orchestrate cellular growth and survival through post-transcriptional mechanisms. The dysregulation of miRNA biogenesis can lead to cellular growth defects and chemotherapeutic resistance and plays a direct role in the development of many chronic diseases. Among these RNAs, miR-21 is consistently overexpressed in most human cancers, leading to the down-regulation of key tumor-suppressing and pro-apoptotic factors, suggesting that inhibition of miR-21 biogenesis could reverse these negative effects. However, targeted inhibition of miR-21 using small molecules has had limited success. To overcome difficulties in targeting RNA secondary structure with small molecules, we developed a class of cyclic β-hairpin peptidomimetics which bind to RNA stem-loop structures, such as miRNA precursors, with potent affinity and specificity. We screened an existing cyclic peptide library and discovered a lead structure which binds to pre-miR21 with KD = 200 nM and prefers it over other pre-miRNAs. The NMR structure of the complex shows that the peptide recognizes the Dicer cleavage site and alters processing of the precursor to the mature miRNA in vitro and in cultured cells. The structure provides a rationale for the peptide binding activity and clear guidance for further improvements in affinity and targeting.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Matthew J. Walker
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Yu Chen
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
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24
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Yan H, Bhattarai U, Guo ZF, Liang FS. Regulating miRNA-21 Biogenesis By Bifunctional Small Molecules. J Am Chem Soc 2017; 139:4987-4990. [PMID: 28287718 DOI: 10.1021/jacs.7b00610] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report a new strategy to regulate microRNAs (miRNAs) biogenesis by using bifunctional small molecules that consist of a pre-miRNA binding unit connected by a linker to a Dicer inhibiting unit. In this effort, fluorescence polarization-based screening was used to identify neomycin as a pre-miR-21 binding ligand. Although neomycin cannot inhibit miR-21 maturation, linking it to the RNase inhibitor 1 forms the bifunctional conjugate 7A, which inhibits the production of miR-21. We expect that this strategy will be applicable to design other molecules for miRNA regulation.
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Affiliation(s)
- Hao Yan
- Department of Chemistry and Chemical Biology, University of New Mexico , 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Umesh Bhattarai
- Department of Chemistry and Chemical Biology, University of New Mexico , 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Zhi-Fo Guo
- Department of Chemistry and Chemical Biology, University of New Mexico , 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico , 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
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25
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Vo DD, Duca M. Design of Multimodal Small Molecules Targeting miRNAs Biogenesis: Synthesis and In Vitro Evaluation. Methods Mol Biol 2017; 1517:137-154. [PMID: 27924480 DOI: 10.1007/978-1-4939-6563-2_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
microRNAs (miRNAs) are emerging as novel biological targets for medicinal chemists to develop chemical tools for intracellular regulation. In this context, the discovery of small-molecule drugs targeting specific miRNAs and modulating their production or function represents a very promising approach that could be further developed for targeted therapy in miRNA-related pathologies. Here, we describe the design of multimodal small molecules as RNA ligands targeting DICER-mediated miRNA maturation. The synthesis and the biochemical evaluation as ligands of stem-loop-structured precursor microRNAs (pre-miRNAs) are reported.
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Affiliation(s)
- Duc D Vo
- Institute of Chemistry of Nice, University of Nice Sophia Antipolis, UMR7272 CNRS, Parc Valrose, 06100, Nice, France
| | - Maria Duca
- Institute of Chemistry of Nice, University of Nice Sophia Antipolis, UMR7272 CNRS, Parc Valrose, 06100, Nice, France.
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26
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Alberti E, Zampakou M, Donghi D. Covalent and non-covalent binding of metal complexes to RNA. J Inorg Biochem 2016; 163:278-291. [DOI: 10.1016/j.jinorgbio.2016.04.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/12/2016] [Accepted: 04/12/2016] [Indexed: 01/19/2023]
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27
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Asada K, Canestrari E, Paroo Z. A druggable target for rescuing microRNA defects. Bioorg Med Chem Lett 2016; 26:4942-4946. [PMID: 27641467 DOI: 10.1016/j.bmcl.2016.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/15/2016] [Accepted: 09/06/2016] [Indexed: 01/06/2023]
Abstract
Despite immense promise, development of microRNA (miRNA) therapeutics remains limited by pharmacodynamic challenges that have hindered progress of related oligonucleotide-based technologies. Recent discovery of enzymes that mediate miRNA metabolism represent potential pharmacological targets for directing miRNA function, circumventing barriers associated with oligonucleotides. We previously identified the Translin/Trax (TN/TX) ribonuclease complex as a pre-miRNA degrading enzyme that competes with pre-miRNA processing by Dicer. Here, we establish a high-throughput TN/TX assay and screened 2320 drug and natural product compounds for inhibitors of TN/TX. Secondary analyses demonstrate small molecule mediated inhibition of pre-miRNA degradation by TN/TX and enhanced miRNA processing by Dicer. This application of traditional enzyme-inhibitor pharmacology to the miRNA pathway establishes a druggable target for rescuing global miRNA defects, providing an important complement to current approaches towards miRNA therapeutics. More broadly, demonstrating feasibility of pharmacological targeting of the 'ribonucleome' is particularly important given emerging classes of regulatory RNA and growing understanding of their importance in health and disease.
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Affiliation(s)
- Ken Asada
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Emanuele Canestrari
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Zain Paroo
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA.
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28
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Abstract
microRNAs (miRNA) are small non-coding RNAs (sRNA) that post-transcriptionally regulate gene (mRNA) expression and are implicated in many biological processes and diseases. Many miRNAs have been reported to be altered in cardiovascular disease (CVD); both cellular and extracellular miRNA levels are affected by hypercholesterolemia and atherosclerosis. We and other groups have reported that lipoproteins transport miRNAs in circulation and these lipoprotein signatures are significantly altered in hypercholesterolemia and coronary artery disease (CAD). Extracellular miRNAs are a new class of potential biomarkers for CVD; however, they may also be new drug targets as high-density lipoproteins (HDL) transfer functional miRNAs to recipient cells in an endocrine-like form of intercellular communication that likely suppresses vascular inflammation. Recently, RNA-based drugs have emerged as the next frontier in drug therapy, and there are many miRNA inhibitors and mimics in clinical development. Here, we discuss specific miRNA drug targets and how their manipulation may impact CVD. We also address the potential for manipulating HDL-miRNA levels to treat CVD and the use of HDL as a delivery vehicle for RNA and chemical drugs. Finally, we outline the current and future challenges for HDL and miRNA-based therapeutics for the prevention and treatment of CVD.
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Affiliation(s)
- Danielle L Michell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Kasey C Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States.
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29
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Vengut-Climent E, Gómez-Pinto I, Lucas R, Peñalver P, Aviñó A, Fonseca Guerra C, Bickelhaupt FM, Eritja R, González C, Morales JC. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Empar Vengut-Climent
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
| | | | - Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Pablo Peñalver
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Anna Aviñó
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
- Institute of Molecules and Materials (IMM); Radboud University; 6525 AJ Nijmegen The Netherlands
| | - Ramón Eritja
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”, CSIC, 28006; Madrid Spain
| | - Juan C. Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
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31
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Vengut-Climent E, Gómez-Pinto I, Lucas R, Peñalver P, Aviñó A, Fonseca Guerra C, Bickelhaupt FM, Eritja R, González C, Morales JC. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA. Angew Chem Int Ed Engl 2016; 55:8643-7. [DOI: 10.1002/anie.201603510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/19/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Empar Vengut-Climent
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
| | | | - Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Pablo Peñalver
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Anna Aviñó
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
- Institute of Molecules and Materials (IMM); Radboud University; 6525 AJ Nijmegen The Netherlands
| | - Ramón Eritja
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”, CSIC, 28006; Madrid Spain
| | - Juan C. Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
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32
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Yoon H, Flores LF, Kim J. MicroRNAs in brain cholesterol metabolism and their implications for Alzheimer's disease. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:2139-2147. [PMID: 27155217 DOI: 10.1016/j.bbalip.2016.04.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 01/01/2023]
Abstract
Cholesterol is important for various neuronal functions in the brain. Brain has elaborate regulatory mechanisms to control cholesterol metabolism that are distinct from the mechanisms in periphery. Interestingly, dysregulation of the cholesterol metabolism is strongly associated with a number of neurodegenerative diseases. MicroRNAs are short non-coding RNAs acting as post-transcriptional gene regulators. Recently, several microRNAs are demonstrated to be involved in regulating cholesterol metabolism in the brain. This article reviews the regulatory mechanisms of cellular cholesterol homeostasis in the brain. In addition, we discuss the role of microRNAs in brain cholesterol metabolism and their potential implications for the treatment of Alzheimer's disease. This article is part of a special issue entitled: MicroRNAs and lipid/energy metabolism and related diseases edited by Carlos Fernández-Hernando and Yajaira Suárez.
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Affiliation(s)
- Hyejin Yoon
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Jacksonville, FL, United States; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Luis F Flores
- Biochemistry and Molecular Biology Graduate Program, Mayo Graduate School, Jacksonville, FL, United States
| | - Jungsu Kim
- Neurobiology of Disease Graduate Program, Mayo Graduate School, Jacksonville, FL, United States; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States.
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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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Vo DD, Tran TPA, Staedel C, Benhida R, Darfeuille F, Di Giorgio A, Duca M. Oncogenic MicroRNAs Biogenesis as a Drug Target: Structure-Activity Relationship Studies on New Aminoglycoside Conjugates. Chemistry 2016; 22:5350-62. [DOI: 10.1002/chem.201505094] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Duc Duy Vo
- University of Nice Sophia Antipolis; Institute of Chemistry of Nice, UMR7272 CNRS, Parc Valrose; 06100 Nice France
| | - Thi Phuong Anh Tran
- University of Nice Sophia Antipolis; Institute of Chemistry of Nice, UMR7272 CNRS, Parc Valrose; 06100 Nice France
| | - Cathy Staedel
- University of Bordeaux; ARNA Laboratory; 33000 Bordeaux France
- INSERM, U869; 33000 Bordeaux France
| | - Rachid Benhida
- University of Nice Sophia Antipolis; Institute of Chemistry of Nice, UMR7272 CNRS, Parc Valrose; 06100 Nice France
| | - Fabien Darfeuille
- University of Bordeaux; ARNA Laboratory; 33000 Bordeaux France
- INSERM, U869; 33000 Bordeaux France
| | - Audrey Di Giorgio
- University of Nice Sophia Antipolis; Institute of Chemistry of Nice, UMR7272 CNRS, Parc Valrose; 06100 Nice France
| | - Maria Duca
- University of Nice Sophia Antipolis; Institute of Chemistry of Nice, UMR7272 CNRS, Parc Valrose; 06100 Nice France
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Abstract
UNLABELLED Dysregulation of amyloid-β (Aβ) metabolism is critical for Alzheimer's disease (AD) pathogenesis. Mounting evidence suggests that apolipoprotein E (ApoE) is involved in Aβ metabolism. ATP-binding cassette transporter A1 (ABCA1) is a key regulator of ApoE lipidation, which affects Aβ levels. Therefore, identifying regulatory mechanisms of ABCA1 expression in the brain may provide new therapeutic targets for AD. Here, we demonstrate that microRNA-33 (miR-33) regulates ABCA1 and Aβ levels in the brain. Overexpression of miR-33 impaired cellular cholesterol efflux and dramatically increased extracellular Aβ levels by promoting Aβ secretion and impairing Aβ clearance in neural cells. In contrast, genetic deletion of mir-33 in mice dramatically increased ABCA1 levels and ApoE lipidation, but it decreased endogenous Aβ levels in cortex. Most importantly, pharmacological inhibition of miR-33 via antisense oligonucleotide specifically in the brain markedly decreased Aβ levels in cortex of APP/PS1 mice, representing a potential therapeutic strategy for AD. SIGNIFICANCE STATEMENT Brain lipid metabolism, in particular Apolipoprotein E (ApoE) lipidation, is critical to Aβ metabolism and Alzheimer's disease (AD). Brain lipid metabolism is largely separated from the periphery due to blood-brain barrier and different repertoire of lipoproteins. Therefore, identifying the novel regulatory mechanism of brain lipid metabolism may provide a new therapeutic strategy for AD. Although there have been studies on brain lipid metabolism, its regulation, in particular by microRNAs, is relatively unknown. Here, we demonstrate that inhibition of microRNA-33 increases lipidation of brain ApoE and reduces Aβ levels by inducing ABCA1. We provide a unique approach for AD therapeutics to increase ApoE lipidation and reduce Aβ levels via pharmacological inhibition of microRNA in vivo.
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Hesse M, Arenz C. A Rapid and Versatile Assay for Ago2-Mediated Cleavage by Using Branched Rolling Circle Amplification. Chembiochem 2016; 17:304-7. [DOI: 10.1002/cbic.201500537] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Marlen Hesse
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Christoph Arenz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
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Abstract
BACKGROUND High attrition rates in drug discovery call for new approaches to improve target validation. Academia is filling gaps, but often lacks the experience and resources of the pharmaceutical industry resulting in poorly characterized tool compounds. DISCUSSION The SGC has established an open access chemical probe consortium, currently encompassing ten pharmaceutical companies. One of its mandates is to create well-characterized inhibitors (chemical probes) for epigenetic targets to enable new biology and target validation for drug development. CONCLUSION Epigenetic probe compounds have proven to be very valuable and have not only spurred a plethora of novel biological findings, but also provided starting points for clinical trials. These probes have proven to be critical complementation to traditional genetic targeting strategies and provided sometimes surprising results.
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Affiliation(s)
- Peter J Brown
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Susanne Müller
- Structural Genomics Consortium, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
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Tran TPA, Vo DD, Di Giorgio A, Duca M. Ribosome-targeting antibiotics as inhibitors of oncogenic microRNAs biogenesis: Old scaffolds for new perspectives in RNA targeting. Bioorg Med Chem 2015; 23:5334-44. [PMID: 26264847 DOI: 10.1016/j.bmc.2015.07.062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 07/27/2015] [Indexed: 12/23/2022]
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression at the post-transcriptional level. It is now well established that the overexpression of some miRNAs (oncogenic miRNAs) is responsible for initiation and progression of human cancers and the discovery of new molecules able to interfere with their production and/or function represents one of the most important challenges of current medicinal chemistry of RNA ligands. In this work, we studied the ability of 18 different antibiotics, known as prokaryotic ribosomal RNA, to bind to oncogenic miRNA precursors (stem-loop structured pre-miRNAs) in order to inhibit miRNAs production. In vitro inhibition, binding constants, thermodynamic parameters and binding sites were investigated and highlighted that aminoglycosides and tetracyclines represent interesting pre-miRNA ligands with the ability to inhibit Dicer processing.
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Affiliation(s)
- Thi Phuong Anh Tran
- Institute of Chemistry of Nice, UMR7272 CNRS-University Nice Sophia Antipolis, Parc Valrose, 06100 Nice, France
| | - Duc Duy Vo
- Institute of Chemistry of Nice, UMR7272 CNRS-University Nice Sophia Antipolis, Parc Valrose, 06100 Nice, France
| | - Audrey Di Giorgio
- Institute of Chemistry of Nice, UMR7272 CNRS-University Nice Sophia Antipolis, Parc Valrose, 06100 Nice, France
| | - Maria Duca
- Institute of Chemistry of Nice, UMR7272 CNRS-University Nice Sophia Antipolis, Parc Valrose, 06100 Nice, France.
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Jeker LT, Marone R. Targeting microRNAs for immunomodulation. Curr Opin Pharmacol 2015; 23:25-31. [PMID: 26021286 DOI: 10.1016/j.coph.2015.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 12/29/2022]
Abstract
microRNAs (miRNA) are small regulatory RNAs exerting pleiotropic functions in virtually any immune cell-type. Dozens of miRNAs with a known function in the immune system constitute interesting drug targets for immunomodulation. Chemical modifications of nucleic acid-based miRNA mimics and inhibitors largely solved instability issues but delivery to immune cells remains a major challenge. However, recent success targeting the acidic tumor microenvironment is very promising for inflammatory diseases. Moreover, small molecules are being explored as an interesting alternative. Although RNA is often considered 'undruggable' by small molecules recent progress modulating miRNA function through small molecules is encouraging. Computational approaches even allow predictions about specific small molecule/RNA interactions. Finally, recent clinical success demonstrates that drugs targeting RNAs work in humans.
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Affiliation(s)
- Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
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