CycloSELs – Massive Screening Platform of barcode-free macrocycle libraries enables the identification of cell-penetrating PPI inhibitors

ChemRxiv

Abstract

Synthetic macrocycles offer exceptional potential as therapeutics, combining the ability to engage challenging biological targets with favorable drug-like properties. However, most high-throughput discovery platforms rely on genetically encoded libraries of large peptide macrocycles, which typically exhibit poor cell permeability. Here we report CycloSEL (Cyclic Self-Encoded Libraries): a barcode-free, fully synthetic, ultra–high-throughput platform for the discovery of drug-like macrocycles. CycloSEL couples the combinatorial synthesis of massive macrocycle libraries with affinity-based selection and de novo hit identification by tandem mass spectrometry, eliminating the need for genetic barcodes and expanding chemical space. We constructed a 16 million-member macrocycle library enriched in druglike features and validated the approach against the oncology target carbonic anhydrase IX, achieving robust enrichment and accurate identification of true binders. Applying CycloSEL to the acute myeloid leukemia target WDR5 yielded a macrocycle with 8 nM affinity, which we rapidly optimized to a compound that potently disrupts the oncogenic WDR5–MLL interaction (IC₅₀ = 128 nM), displays excellent serum stability, passive membrane permeability and anti-proliferative activity against leukemia cells. Taken together, CycloSEL is a powerful discovery platform for identifying therapeutic leads against challenging intracellular targets.

Authors 7

1. J. Miguel Mata Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

2. Jingming Liu Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

3. Marije Havermans

   Erasmus MC · Oncode Institute

   Affiliation as printed

   Erasmus MC

   Oncode Institute

4. Sean M. McKenna Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

5. Edith van der Nol Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute

6. Ruud Delwel

   Erasmus MC · Oncode Institute

   Affiliation as printed

   Erasmus MC

   Oncode Institute

7. Sebastian J. Pomplun Aachen

   Leiden University · Oncode Institute

   Affiliation as printed

   Leiden University

   Oncode Institute