Due to the great potentials of cyclic peptides as therapeutic agents, several phage-displayed peptide libraries in which cyclization is achieved by the covalent linkage of cysteines have been previously demonstrated to identify cyclic-peptide ligands for therapeutic targets. While problems remain in these cysteine conjugation strategies, we have invented a phage display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded N-acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of a potent ligand, CycH8a, for histone deacetylase 8 (HDAC8). We believe this approach will find broad applications in drug discovery.
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http://dx.doi.org/10.1007/978-1-0716-1617-8_17 | DOI Listing |
Microb Cell Fact
January 2025
Chair of Technical Biochemistry, Technische Universität Dresden, Bergstraße 66, 01069, Dresden, Germany.
Background: The biosynthesis of the natural product family of the polycyclic tetramate macrolactams (PoTeMs) employs an uncommon iterative polyketide synthase/non-ribosomal peptide synthetase (iPKS/NRPS). This machinery produces a universal PoTeM biosynthetic precursor that contains a tetramic acid moiety connected to two unsaturated polyene side chains. The enormous structural and hence functional diversity of PoTeMs is enabled by pathway-specific tailoring enzymes, particularly cyclization-catalyzing oxidases that process the polyene chains to form distinct ring systems, and further modifying enzymes.
View Article and Find Full Text PDFOrg Lett
January 2025
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
The cyclic structure of non-ribosomal peptides (NRPs) is critical for enhancing their stability and bioactivity, which highlights the importance of exploring NRP cyclization enzymes for natural product discovery. Thioesterases (TEs) are crucial enzymes that catalyze the formation of various lactams, including macrolactams, β-lactams, and γ-lactams; however, their potential to produce other lactam types remains largely unexplored. In this study, we identified spinactin A () and novel derivatives, spinactin B-E (-), from NRRL 18395 and characterized the biosynthetic enzymes involved, particularly a unique TE SncF, responsible for δ-lactam formation.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, Texas 78712, United States.
Language modeling applied to biological data has significantly advanced the prediction of membrane penetration for small-molecule drugs and natural peptides. However, accurately predicting membrane diffusion for peptides with pharmacologically relevant modifications remains a substantial challenge. Here, we introduce PeptideCLM, a peptide-focused chemical language model capable of encoding peptides with chemical modifications, unnatural or noncanonical amino acids, and cyclizations.
View Article and Find Full Text PDFACS Chem Biol
January 2025
Texas A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.
Current methods for the macrocyclization of phage-displayed peptides often rely on small molecule linkers that nonspecifically react with targeted amino acid residues. To expand tool kits for more regioselective macrocyclization of phage-displayed peptides, this study explores the unique condensation reaction between an N-terminal cysteine and nitrile along with the reactivity of an internal cysteine. Five 2-cyanopyrimidine derivatives were synthesized for this purpose and evaluated for their selective macrocyclization of a protein-fused model peptide.
View Article and Find Full Text PDFJ Med Chem
January 2025
Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Glutaminyl cyclases, including glutaminyl-peptide cyclotransferase (QPCT) and glutaminyl-peptide cyclotransferase-like protein (QPCTL), primarily catalyze the cyclization of N-terminal glutamine or glutamate to pyroglutamate (pGlu). QPCTL, in particular, modifies the N-terminus of CD47, thereby regulating its interaction with signal-regulatory protein alpha (SIRPα) and modulating phagocytosis of tumor cells by immune cells. Additionally, QPCTL cyclizes the N-termini of CCL2, CCL7, and CX3CL1, influencing the tumor microenvironment and inflammatory responses in cancer and other disorders.
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