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Lan T, Peng C, Yao X, Chan RST, Wei T, Rupanya A, Radakovic A, Wang S, Chen S, Lovell S, Snyder SA, Bogyo M, Dickinson BC. Discovery of Thioether-Cyclized Macrocyclic Covalent Inhibitors by mRNA Display. J Am Chem Soc 2024; 146:24053-24060. [PMID: 39136646 DOI: 10.1021/jacs.4c07851] [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: 08/29/2024]
Abstract
Macrocyclic peptides are promising scaffolds for the covalent ligand discovery. However, platforms enabling the direct identification of covalent macrocyclic ligands in a high-throughput manner are limited. In this study, we present an mRNA display platform allowing selection of covalent macrocyclic inhibitors using 1,3-dibromoacetone-vinyl sulfone (DBA-VS). Testcase selections on TEV protease resulted in potent covalent inhibitors with diverse cyclic structures, among which cTEV6-2, a macrocyclic peptide with a unique C-terminal cyclization, emerged as the most potent covalent inhibitor of TEV protease described to-date. This study outlines the workflow for integrating chemical functionalization─installation of a covalent warhead─with mRNA display and showcases its application in targeted covalent ligand discovery.
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Affiliation(s)
- Tong Lan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Cheng Peng
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Xiyuan Yao
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Rachel Shu Ting Chan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Tongyao Wei
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Anuchit Rupanya
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksandar Radakovic
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sijie Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Scott A Snyder
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Chan Zuckerberg Biohub, Chicago, Illinois 60642, United States
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2
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Abou Madawi NA, Darwish ZE, Omar EM. Targeted gene therapy for cancer: the impact of microRNA multipotentiality. Med Oncol 2024; 41:214. [PMID: 39088082 PMCID: PMC11294399 DOI: 10.1007/s12032-024-02450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024]
Abstract
Cancer is a life-threatening disease and its management is difficult due to its complex nature. Cancer is characterized by genomic instability and tumor-associated inflammation of the supporting stoma. With the advances in omics science, a treatment strategy for cancer has emerged, which is based on targeting cancer-driving molecules, known as targeted therapy. Gene therapy, a form of targeted therapy, is the introduction of nucleic acids into living cells to replace a defective gene, promote or repress gene expression to treat a disease. MicroRNAs (miRNAs) are non-coding RNAs (ncRNAs) that regulate gene expression and thus are involved in physiological processes like cell proliferation, differentiation, and cell death. miRNAs control the actions of many genes. They are deregulated in cancer and their abnormal expression influences genetic and epigenetic alterations inducing carcinogenesis. In this review, we will explain the role of miRNAs in normal and abnormal gene expression and their usefulness in monitoring cancer patients. Besides, we will discuss miRNA-based therapy as a method of gene therapy and its impact on the success of cancer management.
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Affiliation(s)
- Nourhan A Abou Madawi
- Oral Pathology Department, Faculty of Dentistry, Alexandria University, Champollion Street, Azarita, 21521, Alexandria, Egypt.
| | - Zeinab E Darwish
- Oral Pathology Department, Faculty of Dentistry, Alexandria University, Champollion Street, Azarita, 21521, Alexandria, Egypt
| | - Enas M Omar
- Oral Pathology Department, Faculty of Dentistry, Alexandria University, Champollion Street, Azarita, 21521, Alexandria, Egypt
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3
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Ma S, Howden SA, Keane SC. Use of steric blocking antisense oligonucleotides for the targeted inhibition of junction containing precursor microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588531. [PMID: 38645194 PMCID: PMC11030329 DOI: 10.1101/2024.04.08.588531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antisense oligonucleotides (ASOs) are widely used as therapeutics for neurodegenerative diseases, cancers, and virus infections. One class of ASOs functions to enhance protein expression by sequestering the mature microRNA (miRNA) in a double-stranded structure within the RNA-induced silencing complex (RISC). An alternative approach for the targeted control of gene expression is to use ASOs that bind to the pre-elements of miRNAs (pre-miRNAs) and modulate their enzymatic processing. Here, we demonstrate that ASOs can be used to disrupt a specific structural feature, "junction," within pre-miR-31 that is important in directing efficient processing by the Dicer/TRBP complex. Furthermore, we extend and validate this strategy to pre-miR-144, which has a similar junction-dependent structure-function relationship. We found that a significant number of human pre-miRNAs are predicted to contain junctions, and validated our ASO approach on several members of this group. Importantly, we also verified the application of junction-targeting ASOs for the specific inhibition of pre-miRNA processing in cell . Our study reemphasizes the important roles of RNA structure in regulating Dicer/TRBP processing of pre-miRNAs and provides the framework to develop structure-informed ASOs that serve to inhibit miRNA production.
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4
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Borgelt L, Wu P. Targeting Ribonucleases with Small Molecules and Bifunctional Molecules. ACS Chem Biol 2023; 18:2101-2113. [PMID: 37382390 PMCID: PMC10594538 DOI: 10.1021/acschembio.3c00191] [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] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Ribonucleases (RNases) cleave and process RNAs, thereby regulating the biogenesis, metabolism, and degradation of coding and noncoding RNAs. Thus, small molecules targeting RNases have the potential to perturb RNA biology, and RNases have been studied as therapeutic targets of antibiotics, antivirals, and agents for autoimmune diseases and cancers. Additionally, the recent advances in chemically induced proximity approaches have led to the discovery of bifunctional molecules that target RNases to achieve RNA degradation or inhibit RNA processing. Here, we summarize the efforts that have been made to discover small-molecule inhibitors and activators targeting bacterial, viral, and human RNases. We also highlight the emerging examples of RNase-targeting bifunctional molecules and discuss the trends in developing such molecules for both biological and therapeutic applications.
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Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max
Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
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5
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Tregub PP, Ibrahimli I, Averchuk AS, Salmina AB, Litvitskiy PF, Manasova ZS, Popova IA. The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies. Int J Mol Sci 2023; 24:12899. [PMID: 37629078 PMCID: PMC10454825 DOI: 10.3390/ijms241612899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
In recent times, there has been a significant increase in researchers' interest in the functions of microRNAs and the role of these molecules in the pathogenesis of many multifactorial diseases. This is related to the diagnostic and prognostic potential of microRNA expression levels as well as the prospects of using it in personalized targeted therapy. This review of the literature analyzes existing scientific data on the involvement of microRNAs in the molecular and cellular mechanisms underlying the development of pathologies such as Alzheimer's disease, cerebral ischemia and reperfusion injury, and dysfunction of the blood-brain barrier.
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Affiliation(s)
- Pavel P. Tregub
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia
- Research Center of Neurology, 125367 Moscow, Russia
| | - Irada Ibrahimli
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | | | - Alla B. Salmina
- Research Center of Neurology, 125367 Moscow, Russia
- Research Institute of Molecular Medicine and Pathobiochemistry, Prof. V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Peter F. Litvitskiy
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Zaripat Sh. Manasova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Inga A. Popova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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Cornelius VA, Fulton JR, Margariti A. Alternative Splicing: A Key Mediator of Diabetic Vasculopathy. Genes (Basel) 2021; 12:1332. [PMID: 34573314 PMCID: PMC8469645 DOI: 10.3390/genes12091332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 12/25/2022] Open
Abstract
Cardiovascular disease is the leading cause of death amongst diabetic individuals. Atherosclerosis is the prominent driver of diabetic vascular complications, which is triggered by the detrimental effects of hyperglycemia and oxidative stress on the vasculature. Research has extensively shown diabetes to result in the malfunction of the endothelium, the main component of blood vessels, causing severe vascular complications. The pathogenic mechanism in which diabetes induces vascular dysfunction, however, remains largely unclear. Alternative splicing of protein coding pre-mRNAs is an essential regulatory mechanism of gene expression and is accepted to be intertwined with cellular physiology. Recently, a role for alternative splicing has arisen within vascular health, with aberrant mis-splicing having a critical role in disease development, including in atherosclerosis. This review focuses on the current knowledge of alternative splicing and the roles of alternatively spliced isoforms within the vasculature, with a particular focus on disease states. Furthermore, we explore the recent elucidation of the alternatively spliced QKI gene within vascular cell physiology and the onset of diabetic vasculopathy. Potential therapeutic strategies to restore aberrant splicing are also discussed.
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Affiliation(s)
| | | | - Andriana Margariti
- The Wellcome-Wolfson Institute of Experimental Medicine, Belfast BT9 7BL, UK; (V.A.C.); (J.R.F.)
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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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