Expanding the DNA-encoded library toolbox: identifying small molecules targeting RNA

Abstract

DNA-encoded library (DEL) technology is a powerful tool for small molecule identification in drug discovery, yet the reported DEL selection strategies were applied primarily on protein targets in either purified form or in cellular context. To expand the application of this technology, we employed DEL selection on an RNA target HIV-1 TAR (trans-acting responsive region), but found that the majority of signals were resulted from false positive DNA–RNA binding. We thus developed an optimized selection strategy utilizing RNA patches and competitive elution to minimize unwanted DNA binding, followed by k-mer analysis and motif search to differentiate false positive signal. This optimized strategy resulted in a very clean background in a DEL selection against Escherichia coli FMN Riboswitch, and the enriched compounds were determined with double digit nanomolar binding affinity, as well as similar potency in functional FMN competition assay. These results demonstrated the feasibility of small molecule identification against RNA targets using DEL selection. The developed experimental and computational strategy provided a promising opportunity for RNA ligand screening and expanded the application of DEL selection to a much wider context in drug discovery.

A Riboswitch-Driven Era of New Antibacterials

“…Another technology that facilitates the screening of billions of compounds simultaneously in a single reaction is the DNA-encoded library (DEL); however, it is not well established for RNA targets yet, although one successful attempt has identified two compounds, HGC-1 and HGC-2, with binding affinities for E. coli FMN riboswitch of 11.38 and 15.03 nM, respectively. Nonetheless, these compounds must be further investigated for their ability to penetrate the bacterial cell wall and antimicrobial activity [ 90 ].…”

DNA-encoded librariesvialate-stage functionalization strategies: a review

“…Several reviews have been published to highlight the various synthetic methodologies for obtaining DEL. [37][38][39][40][41] However, a focused perspective on the recent developments in the utilization of metal-mediated late-stage modification of conjugated DNA for DNA-encoded library synthesis has been missing, and warrants a thorough analysis of what such an approach can offer to those interested in furthering this exciting area of research. The review also critically analyzes the problems associated with the synthetic methodologies, identifies the possible shortcomings, and provides future directions for improving the DEL synthesis.…”

Incorporation of viridicatin alkaloid-like scaffolds into DNA-encoded chemical libraries

“…The construction of such a competent compound collection can enable researchers to rapidly select NP derivatives of interest. 4 Among those prevalent technologies in current drug discovery, DNA-encoded chemical library (DEL) technology, conceptualized by Lerner and Brenner in 1992, 5 has been widely recognized by industry [6][7][8][9][10] and academia [11][12][13][14][15][16][17][18][19] in the past three decades. This technology features miniature-scale library construction with a huge number of generated members, easy storage, and convenient screening.…”