DNA-Encoded Libraries and Their Application to RNA

被引:4
作者
Yang, Xueyi [1 ,2 ]
Childs-Disney, Jessica L. [1 ,2 ]
Paegel, M. [3 ]
Disney, Matthew D. [1 ,2 ]
机构
[1] Herbert Wertheim UF Scripps Inst Biomed Innovat &, Dept Chem, 130 Scripps Way, Jupiter, FL 33458 USA
[2] Scripps Res Inst, 130 Scripps Way, Jupiter, FL 33458 USA
[3] Univ Calif Irvine, Dept Chem & Pharmaceut Sci, Irvine, CA 92617 USA
基金
美国国家卫生研究院;
关键词
RNA; DNA-encoded library; drug discovery; small molecules; SMALL-MOLECULE; COMBINATORIAL LIBRARIES; SECONDARY STRUCTURE; LIGAND-BINDING; G-QUADRUPLEX; DISCOVERY; SELECTION; DESIGN; IDENTIFICATION; INHIBITION;
D O I
10.1002/ijch.202300073
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The functional roles of structured RNAs in the regulation of biological processes, and hence RNA's potential as an effective therapeutic target, have only recently been appreciated. Robust and high-throughput methods that identify potent RNA ligands are critical to the development of chemical probes and therapeutics. DNA-encoded libraries (DEL) technology has emerged as a powerful tool for protein ligand discovery, and its ability to generate large, custom-tailored, and novel chemical space offers unprecedented opportunities to discover the rules of RNA ligand design. In this review, we discuss the basic principles of DEL selection, current progress on the application of DEL to RNA targets, and the outlook of targeting RNA by DEL.
引用
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页数:12
相关论文
共 92 条
[1]   Targeting Xist with compounds that disrupt RNA structure and X inactivation [J].
Aguilar, Rodrigo ;
Spencer, Kerrie B. ;
Kesner, Barry ;
Rizvi, Noreen F. ;
Badmalia, Maulik D. ;
Mrozowich, Tyler ;
Mortison, Jonathan D. ;
Rivera, Carlos ;
Smith, Graham F. ;
Burchard, Julja ;
Dandliker, Peter J. ;
Patel, Trushar R. ;
Nickbarg, Elliott B. ;
Lee, Jeannie T. .
NATURE, 2022, 604 (7904) :160-+
[2]   ScanFold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV [J].
Andrews, Ryan J. ;
Roche, Julien ;
Moss, Walter N. .
PEERJ, 2018, 6
[3]   Bleomycin Can Cleave an Oncogenic Noncoding RNA [J].
Angelbello, Alicia J. ;
Disney, Matthew D. .
CHEMBIOCHEM, 2018, 19 (01) :43-47
[4]   Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site [J].
Barbieri, Christopher M. ;
Kaul, Malvika ;
Pilch, Daniel S. .
TETRAHEDRON, 2007, 63 (17) :3567-3574
[5]   PROTAC targeted protein degraders: the past is prologue [J].
Bekes, Miklos ;
Langley, David R. ;
Crews, Craig M. .
NATURE REVIEWS DRUG DISCOVERY, 2022, 21 (03) :181-200
[6]   DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor [J].
Benhamou, Raphael I. ;
Suresh, Blessy M. ;
Tong, Yuquan ;
Cochran, Wesley G. ;
Cavett, Valerie ;
Vezina-Dawod, Simon ;
Abegg, Daniel ;
Childs-Disney, Jessica L. ;
Adibekian, Alexander ;
Paegel, Brian M. ;
Disney, Matthew D. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2022, 119 (06)
[7]   A simple, high-resolution method for establishing DNA binding affinity and sequence selectivity [J].
Boger, DL ;
Fink, BE ;
Brunette, SR ;
Tse, WC ;
Hedrick, MP .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2001, 123 (25) :5878-5891
[8]   ENCODED COMBINATORIAL CHEMISTRY [J].
BRENNER, S ;
LERNER, RA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (12) :5381-5383
[9]   Generalized DNA Barcode Design Based on Hamming Codes [J].
Bystrykh, Leonid V. .
PLOS ONE, 2012, 7 (05)
[10]   Selection of DNA-Encoded Libraries to Protein Targets within and on Living Cells [J].
Cai, Bo ;
Kim, Dongwook ;
Akhand, Saeed ;
Sun, Yixing ;
Cassell, Robert J. ;
Alpsoy, Aktan ;
Dykhuizen, Emily C. ;
Van Rijn, Richard M. ;
Wendt, Michael K. ;
Krusemark, Casey J. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2019, 141 (43) :17057-17061