Large Libraries of Structurally Diverse Macrocycles Suitable for Membrane Permeation

• Published in: Angewandte Chemie International Edition Vol. 63; no. 26; pp. e202400350 - n/a
• Main Authors: Nielsen, Alexander L., Bognar, Zsolt, Mothukuri, Ganesh K., Zarda, Anne, Schüttel, Mischa, Merz, Manuel L., Ji, Xinjian, Will, Edward J., Chinellato, Monica, Bartling, Christian R. O., Strømgaard, Kristian, Cendron, Laura, Angelini, Alessandro, Heinis, Christian
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 21.06.2024
• Edition: International ed. in English
• Subjects: Binding; Cell Membrane Permeability; Cell membranes; cell permeability; Chemical synthesis; Combinatorial analysis; Combinatorial libraries; Crystallography, X-Ray; cyclization; Drug development; Format; high-throughput screening; Humans; Invariants; Libraries; macrocycle; Macrocyclic Compounds - chemical synthesis; Macrocyclic Compounds - chemistry; Membrane permeability; Membranes; Models, Molecular; Molecular Structure; Peptides; Peptides, Cyclic - chemical synthesis; Peptides, Cyclic - chemistry; Peptides, Cyclic - metabolism; Plasma kallikrein; protease inhibitor; Small Molecule Libraries - chemical synthesis; Small Molecule Libraries - chemistry; Small Molecule Libraries - metabolism; Small Molecule Libraries - pharmacology; Structural analysis; Sulfhydryl Compounds - chemistry; Thrombin; Thrombin - antagonists & inhibitors; Thrombin - chemistry; Thrombin - metabolism; cell permeability; macrocycle; protease inhibitor; cyclization; high-throughput screening
• ISSN: 1433-7851; 1521-3773; 1521-3773
• DOI: 10.1002/anie.202400350

Macrocycles offer an attractive format for drug development due to their good binding properties and potential to cross cell membranes. To efficiently identify macrocyclic ligands for new targets, methods for the synthesis and screening of large combinatorial libraries of small cyclic peptides were developed, many of them using thiol groups for efficient peptide macrocyclization. However, a weakness of these libraries is that invariant thiol‐containing building blocks such as cysteine are used, resulting in a region that does not contribute to library diversity but increases molecule size. Herein, we synthesized a series of structurally diverse thiol‐containing elements and used them for the combinatorial synthesis of a 2,688‐member library of small, structurally diverse peptidic macrocycles with unprecedented skeletal complexity. We then used this library to discover potent thrombin and plasma kallikrein inhibitors, some also demonstrating favorable membrane permeability. X‐ray structure analysis of macrocycle‐target complexes showed that the size and shape of the newly developed thiol elements are key for binding. The strategy and library format presented in this work significantly enhance structural diversity by allowing combinatorial modifications to a previously invariant region of peptide macrocycles, which may be broadly applied in the development of membrane permeable therapeutics. Macrocycles are promising for drug development due to their good binding properties and the potential to cross membranes. A synthetic strategy and chemical building blocks are developed to produce and screen thousands of small, structurally highly diverse peptidic macrocycles. HTS identifies potent thrombin inhibitors with good membrane permeability. The strategy may be broadly applied in the development of membrane permeable therapeutics.