Selection of Carbonic Anhydrase IX Inhibitors from One Million DNA-Encoded Compounds

Abstract

DNA-encoded chemical libraries, i.e., collections of compounds individually coupled to distinctive DNA fragments serving as amplifiable identification barcodes, represent a new tool for the de novo discovery of small molecule ligands to target proteins of pharmaceutical interest. Here, we describe the design and synthesis of a novel DNA-encoded chemical library containing one million small molecules. The library was synthesized by combinatorial assembly of three sets of chemical building blocks using Diels-Alder cycloadditions and by the stepwise build-up of the DNA barcodes. Model selections were performed to test library performance and to develop a statistical method for the analysis of high-throughput sequencing data. A library selection against carbonic anhydrase IX revealed a new class of submicromolar bis(sulfonamide) inhibitors. One of these inhibitors was synthesized in the absence of the DNA-tag and showed accumulation in hypoxic tumor tissue sections in vitro and tumor targeting in vivo.

Prognostic relevance of carbonic anhydrase IX expression is distinct in various subtypes of breast cancer and its silencing suppresses self-renewal capacity of breast cancer cells

“…CAIX has been previously proposed to serve as a therapeutic target in breast [16,45] and renal cancer [46][47][48]. Depletion of CAIX expression in mouse and human breast cancer cells has been found to attenuate tumour growth and inhibited formation of spontaneous lung metastasis in mouse models [16].…”

Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery

“…Single-pharmacophore libraries are made up of a small organic molecule bound to an oligonucleotide and can be further defined into two subdivisions: libraries that are created combinatorially using a split-and-pool method as first imagined by Brenner and Lerner or libraries that are created using DNA-templated synthesis (DTS). The combinatorial split-and-pool synthesis approach is a robust method for creating DNA-encoded libraries of large magnitude (between 10 5 and 10 8 ) 68 and has identified inhibitors for tumor necrosis factor, 69 carbonic anhydrase IX, 70 polyclonal human IgG, 71 and trypsin. 72 DTS involves the DNA fragments not just as encoding tags but also as a means of directing the generation of the library.…”

A Handbook for DNA‐Encoded Chemistry

“…Thanks to the striking sensitivity and specificity of small-molecule DNA-encoding/decoding, today DNA-Encoded Chemical Library (DECL) technology holds a concrete promise to elegantly tackle this formidable task. The appeal of DECL technology mainly relies on the unrivalled opportunity to rapidly synthesize and probe by means of simple affinitycapture selection procedures chemical libraries of unprecedented size in a single test tube [1][2][3][4][5][6].…”

“…Today, cutting-edge, deep-sequencing platforms are capable of collecting millions to billions of DNA-sequence reads per run in just a week [22][23][24], thus allowing the simultaneous deconvolution of multiple panning experiments using libraries containing millions of compounds in a single shot. Employing DNA-encoded strategies, researchers are quickly provided with instant (structure-activity relationship) databases after each selection experiment: an invaluable set of information for medicinal chemistry optimization of the selected structures and/or the design of successive DNA-encoded affinity maturation libraries [1,2,25].…”