Directed evolution of small molecules to solve the molecular recognition problem
Abstract/Contents
- Abstract
- Directed evolution of large combinatorial chemistry libraries is an emerging approach for small-molecule discovery. To advance this field, we have developed a DNA‑programmed chemistry technique that enables breeding of drug-like compounds over multiple generations. The progeny from each cycle of synthesis, selection, and amplification act as the starting point for a subsequent generation; thus the evolutionary cycle can be iterated. The linkage between genotype and phenotype is accomplished by coupling each unique compound to a DNA gene that programs its synthesis. Here we establish the behavior of our technology using a model selection for kinase substrates. We show that the platform behaves in a predictable manner and that it should be capable of identifying useful molecules from very large compound libraries. We then use the technology to discover novel biologically active small molecules by applying a purifying selection to a naive DNA‑programmed library comprising 1.1 billion distinct compounds. Given the comprehensive nature of the combinatorial synthesis and the deep sampling enabled by high throughput sequencing, we can observe the simultaneous enrichment of different chemical families, increasing our chances of identifying a true hit. We have thus identified the first known non-peptidic substrate for protein kinase. This work demonstrates the feasibility to chemically probe the substrate binding sites of kinases. More broadly, we have performed the first directed evolution of a billion member combinatorial library. We anticipate that our approach will lead to the discovery of novel small‑molecule affinity reagents, pharmaceutical compound leads, imaging probes and other high‑value compounds. This could substantially increase global access to small‑molecule reagents, and open up new areas of biological inquiry.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2013 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Tilmans, Nicolas | |
|---|---|---|
| Associated with | Stanford University, Department of Biochemistry. | |
| Primary advisor | Harbury, Pehr | |
| Thesis advisor | Harbury, Pehr | |
| Thesis advisor | Brown, Patrick O'Reilly, 1954- | |
| Thesis advisor | Khosla, Chaitan, 1964- | |
| Advisor | Brown, Patrick O'Reilly, 1954- | |
| Advisor | Khosla, Chaitan, 1964- |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Nicolas Tilmans. |
|---|---|
| Note | Submitted to the Department of Biochemistry. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2013. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2013 by Nicolas Pierre Tilmans
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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