Rational design of glycosaminoglycan binding cyclic peptides using cPEPmatch.

ABSTRACT: Cyclic peptides present a robust platform for drug design, offering high specificity and stability due to their conformationally constrained structures. In this study, we introduce an updated version of the Cyclic Peptide Matching program (cPEPmatch) tailored for the identification of cyclic peptides capable of mimicking protein-glycosaminoglycan (GAG) binding sites. We focused on engineering cyclic peptides to replicate the GAG-binding affinity of antithrombin III (ATIII), a protein that plays a crucial role in modulating anticoagulation through interaction with the GAG heparin. By integrating computational and experimental methods, we successfully identified a cyclic peptide binder with promising potential for future optimization. MD simulations and MM-GBSA calculations were used to asse

SUBMITTER: Santini BL 

PROVIDER: S-EPMC11318538 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature