Design, synthesis and selection of DNA-encoded small-molecule libraries

Abstract

Biochemical combinatorial techniques such as phage display, RNA display and oligonucleotide aptamers have proven to be reliable methods for generation of ligands to protein targets. Adapting these techniques to small synthetic molecules has been a long-sought goal. We report the synthesis and interrogation of an 800-million-member DNA-encoded library in which small molecules are covalently attached to an encoding oligonucleotide. The library was assembled by a combination of chemical and enzymatic synthesis, and interrogated by affinity selection. We describe methods for the selection and deconvolution of the chemical display library, and the discovery of inhibitors for two enzymes: Aurora A kinase and p38 MAP kinase.

Addressing the Right Targets in Oncology: Challenges and Alternative Approaches

“…95,96 Finally, DNA-encoded chemical libraries have the potential for the synthesis and interrogation of hundreds of millions of compounds through affinity selection followed by deconvolution of the chemical display library to identify discrete screening hits. 97 Collaborative models, such as the one recently described by AstraZeneca and Bayer Pharma AG, 98,99 are also forging new ways to improve the chemical diversity of screening libraries. In this instance, the sharing of compound collections between the two companies, with suitable measures in place to protect intellectual property, was shown to be a valid strategy to quickly enhance the coverage of chemical space in respective screening collections.…”

High-Throughput Affinity-Based Technologies for Small-Molecule Drug Discovery

“…The library sizes that can be made by the last approach are limited only by the number of available building blocks with particular reactive groups and can be as large as 100,000,000 compounds, 52 2 orders of magnitude higher than the compound deck for traditional HTS. The diversity and size of these types of libraries will most likely increase the probability of finding hits for therapeutic targets.…”

“…This process is repeated for several cycles to produce very large combinatorial libraries of compounds that each contain unique DNA tags. 52,53 The first two approaches are collectively described as template-directed synthesis, in which building blocks are first conjugated to nucleotides, DNA pieces, or a strand of DNA. This conjugation requirement significantly limits the number of building blocks that can be used and thus the diversity of the assembled library.…”

A Handbook for DNA‐Encoded Chemistry

“…Therefore, while library size exclusively depends on the number of combinatorial split-and-pool steps and building blocks employed, the gain in size and chemical diversity often correspond to an unwanted increase of the average molecular weight, beyond the generally accepted drug-like criteria (e.g., according to Lipinski's rule of 5) [27,28], and decrease of library quality, due to incomplete reactions [3].…”