Download MendeleyCovalent flexible peptide docking in Rosetta.
Tivon, B., Gabizon, R., Somsen, B.A., Cossar, P.J., Ottmann, C., London, N.(2021) Chem Sci 12: 10836-10847
- PubMed: 34476063 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1039/d1sc02322e
- Primary Citation Related Structures:
7O07 - PubMed Abstract:
Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present Rosetta CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. We applied CovPepDock retrospectively to a dataset of 115 disulfide-bound peptides and a dataset of 54 electrophilic peptides. It produced a top-five scoring, near-native model, in 89% and 100% of the cases when docking from the native conformation, and 20% and 90% when docking from an extended peptide conformation, respectively. In addition, we developed a protocol for designing electrophilic peptide binders based on known non-covalent binders or protein-protein interfaces. We identified 7154 peptide candidates in the PDB for application of this protocol. As a proof-of-concept we validated the protocol on the non-covalent complex of 14-3-3σ and YAP1 phosphopeptide. The protocol identified seven highly potent and selective irreversible peptide binders. The predicted binding mode of one of the peptides was validated using X-ray crystallography. This case-study demonstrates the utility and impact of CovPepDock. It suggests that many new electrophilic peptide binders can be rapidly discovered, with significant potential as therapeutic molecules and chemical probes.
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel nir.london@weizmann.ac.il.
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