Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale

• Main Authors: Angelini, A. (Author), Bognár, Z. (Author), Bortoli Chapalay, J. (Author), Cendron, L. (Author), Díaz-Perlas, C. (Author), Habeshian, S. (Author), Heinis, C. (Author), Merz, M.L (Author), Mothukuri, G.K (Author), Sangouard, G. (Author), Schüttel, M. (Author), Turcatti, G. (Author), Vesin, J. (Author)
• Format: Article
• Language: English
• Published: Nature Research 2022
• Online Access: View Fulltext in Publisher
• ISBN: 20411723 (ISSN)
• DOI: 10.1038/s41467-022-31428-8

Macrocycles have excellent potential as therapeutics due to their ability to bind challenging targets. However, generating macrocycles against new targets is hindered by a lack of large macrocycle libraries for high-throughput screening. To overcome this, we herein established a combinatorial approach by tethering a myriad of chemical fragments to peripheral groups of structurally diverse macrocyclic scaffolds in a combinatorial fashion, all at a picomole scale in nanoliter volumes using acoustic droplet ejection technology. In a proof-of-concept, we generate a target-tailored library of 19,968 macrocycles by conjugating 104 carboxylic-acid fragments to 192 macrocyclic scaffolds. The high reaction efficiency and small number of side products of the acylation reactions allowed direct assay without purification and thus a large throughput. In screens, we identify nanomolar inhibitors against thrombin (Ki = 44 ± 1 nM) and the MDM2:p53 protein-protein interaction (Kd MDM2 = 43 ± 18 nM). The increased efficiency of macrocycle synthesis and screening and general applicability of this approach unlocks possibilities for generating leads against any protein target. © 2022, The Author(s).