Small-molecule discovery through DNA-encoded libraries

Abstract

The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.

Fig. 1 |. DNA-encoded libraries as a small molecule discovery platform.

a, Architecture of a DNA-encoded library member. Individual building blocks (green, yellow, and purple shapes) that comprise the entire molecular structure are encoded by regions of DNA (green, yellow, and purple DNA, respectively) on a covalently attached DNA oligonucleotide. PCR binding sites on the appended DNA allow the amplification of the entire DNA barcode by PCR for downstream identification and quantification. b, General cycle of a DNA-encoded library selection campaign. The target of interest is prepared in a form suitable for in vitro selection (1) and incubated with the entire pooled DNA-encoded library (2). Library members with target affinity are selectively retained, resulting in their enrichment over non-binding library members (3). Target-bound library members are isolated (4). Surviving library members can then either be reintroduced back into the selection for further rounds of selection (5a) or amplified by PCR and sequenced (5b) to identify and quantify these hit candidates.

Fig. 2 |. Publications reporting novel small molecules discovered from DNA-encoded libraries.

a, Publications are binned by year and are only included if the study reports new chemical matter with in vitro activity against the target of interest. b, Number of novel DNA-encoded library discovered ligands per target type. Examples are binned by target type and are only included if the study reports new chemical matter with in vitro activity against the target of interest. One representative ligand for each compound series with a target is counted.

Fig. 3 |. Highlighted studies that use the typical immobilization DEL selection workflow to discover novel ligands.

a, The discovery and development of non-covalent, non-β-lactam based OXA-48 inhibitors. b, First example of small molecules that inhibited polymerization of Z α1-antitrypsin. Compound #18 (GSK716) selectively bound to Z mutant over wild-type in a novel pocket containing the E342K mutant residue and increased monomeric Z α1-antitrypsin in mice.

Figure 4 |. Clinical candidates discovered from DNA-encoded libraries.

a, A lead sEH inhibitor that has been used in Phase I and Phase II trials. b, A series of RIP1 kinase inhibitors used in Phase I and Phase II trials, encompassing a variety of drug formulations, patient cohorts, and disease types. c, An autotaxin inhibitor that attenuated lung fibrosis in vivo and has been approved for Phase I clinical trials.

Fig. 5 |. Highlighted studies showing successful implementation of concurrent selection conditions to develop tailored ligands.

a) Discovery of ERα wild-type and mutant inhibitors. A VHL-based PROTAC, #42 (Compound 21) was also developed from lead compounds, which inhibited proliferation of many ER positive cancer cell lines and exhibited in vivo tumor suppression. b) BRDT-BD2 inhibitors that were selective for BET family BD2 domains. c) GPCR allosteric agonists, (#61 (AZ2429)) and allosteric antagonists (#62 (Compound 2) and #63 (AZ3451)). #63 (AZ3451) exhibited bioactivity in cellular and in vivo inflammatory disease models.

Fig. 6 |. Studies that incorporate non-immobilized selections or library retooling to enhance ligand discovery efforts.

a, Employing non-immobilized selection conditions to discover ligands that act as c-Src substrates. Methyl ester version of lead compound, #69 (SrcDEL10), showed bioactivity by reducing STAT3 phosphorylation in cellular models. b, Leveraging library resynthesis to discover and iteratively improve CBX chromodomain ligands. Lead CBX8 inhibitor, #74 (SW2_110A) was selective for CBX8 over other PRC1 CBX chromodomains, decreased transcription of CBX8 dependent genes, and inhibited proliferation of CBX8 dependent cell lines. CBX2 inhibitor, #75 (SW2_152F), was selective for CBX2 over other PRC1 CBX chromodomains, displaced CBX2 from chromatin, and inhibited cell proliferation in NED prostate cancer models synergistically with androgen receptor antagonists.

Fig. 7 |. On-cell DEL-based small molecule discovery.

Novel ligand discovery was mediated through selections with natively expressed FR and EGFR on whole cells, without overexpression of target needed.