Design and Application of a DNA-Encoded Macrocyclic Peptide Library

A DNA-encoded macrocyclic peptide library was designed and synthesized with 2.4 × 10¹² members composed of 4–20 natural and non-natural amino acids. Affinity-based selection was performed against two therapeutic targets, VHL and RSV N protein. On the basis of selection data, some peptides were selected for resynthesis without a DNA tag, and their activity was confirmed

Cell-Based Selection Expands the Utility of DNA-Encoded Small-Molecule Library Technology to Cell Surface Drug Targets: Identification of Novel Antagonists of the NK3 Tachykinin Receptor

DNA-encoded small-molecule library technology has recently emerged as a new paradigm for identifying ligands against drug targets. To date, this technology has been used with soluble protein targets that are produced and used in a purified state. Here, we describe a cell-based method for identifying small-molecule ligands from DNA-encoded libraries against integral membrane protein targets. We use this method to identify novel, potent, and specific inhibitors of NK3, a member of the tachykinin family of G-protein coupled receptors (GPCRs). The method is simple and broadly applicable to other GPCRs and integral membrane proteins. We have extended the application of DNA-encoded library technology to membrane-associated targets and demonstrate the feasibility of selecting DNA-tagged, small-molecule ligands from complex combinatorial libraries against targets in a heterogeneous milieu, such as the surface of a cell

Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase

Undecaprenyl pyrophosphate synthase (UppS) is an essential enzyme in bacterial cell wall synthesis. Here we report the discovery of <i>Staphylococcus aureus</i> UppS inhibitors from an Encoded Library Technology screen and demonstrate binding to the hydrophobic substrate site through cocrystallography studies. The use of bacterial strains with regulated <i>uppS</i> expression and inhibitor resistant mutant studies confirmed that the whole cell activity was the result of UppS inhibition, validating UppS as a druggable antibacterial target

Discovery and Optimization of Potent, Selective, and <i>in Vivo</i> Efficacious 2‑Aryl Benzimidazole BCATm Inhibitors

To identify BCATm inhibitors suitable for <i>in vivo</i> study, Encoded Library Technology (ELT) was used to affinity screen a 117 million member benzimidazole based DNA encoded library, which identified an inhibitor series with both biochemical and cellular activities. Subsequent SAR studies led to the discovery of a highly potent and selective compound, 1-(3-(5-bromothiophene-2-carboxamido)­cyclohexyl)-<i>N</i>-methyl-2-(pyridin-2-yl)-1<i>H</i>-benzo­[d]­imidazole-5-carboxamide (<b>8b</b>) with much improved PK properties. X-ray structure revealed that <b>8b</b> binds to the active site of BACTm in a unique mode via multiple H-bond and van der Waals interactions. After oral administration, <b>8b</b> raised mouse blood levels of all three branched chain amino acids as a consequence of BCATm inhibition

Discovery, SAR, and X‑ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library

As a potential target for obesity, human BCATm was screened against more than 14 billion DNA encoded compounds of distinct scaffolds followed by off-DNA synthesis and activity confirmation. As a consequence, several series of BCATm inhibitors were discovered. One representative compound (<i>R</i>)-3-((1-(5-bromothiophene-2-carbonyl)­pyrrolidin-3-yl)­oxy)-<i>N</i>-methyl-2′-(methylsulfonamido)-[1,1′-biphenyl]-4-carboxamide (<b>15e</b>) from a novel compound library synthesized via on-DNA Suzuki–Miyaura cross-coupling showed BCATm inhibitory activity with IC₅₀ = 2.0 μM. A protein crystal structure of <b>15e</b> revealed that it binds to BCATm within the catalytic site adjacent to the PLP cofactor. The identification of this novel inhibitor series plus the establishment of a BCATm protein structure provided a good starting point for future structure-based discovery of BCATm inhibitors