Replace: A Strategy for Iterative Design of Cyclin- Binding Groove InhibitorsAndrews, M.J., Kontopidis, G., Mcinnes, C., Plater, A., Innes, L., Cowan, A., Jewsbury, P., Fischer, P.M.
(2006) Chembiochem 7: 1909
- PubMed: 17051658
- DOI: 10.1002/cbic.200600189
- Primary Citation of Related Structures:
- PubMed Abstract:
- Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design
Kontopidis, G., Mcinnes, C., Pandalaneni, S.R., Mcnae, I., Gibson, D., Mezna, M., Thomas, M., Wood, G., Wang, S., Walkinshaw, M.D., Fische, P.M.
(2006) Chem Biol 13: 201
We describe a drug-design strategy termed REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) in which nonpeptidic surrogates for specific determinants of known peptide ligands are identified in silico by using a core ...
We describe a drug-design strategy termed REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) in which nonpeptidic surrogates for specific determinants of known peptide ligands are identified in silico by using a core peptide-bound protein structure as a design anchor. In the REPLACE application example, we present the effective replacement of two critical binding motifs in a lead protein-protein interaction inhibitor pentapeptide with more druglike phenyltriazole and diphenyl ether groups. These were identified through docking of fragment libraries into the volume of the cyclin-binding groove of CDK2/cyclin A vacated through truncation of the inhibitor peptide-binding determinants. Proof of concept for this strategy was obtained through the generation of potent peptide-small-molecule hybrids and by the confirmation of inhibitor-binding modes in X-ray crystal structures. This method therefore allows nonpeptide fragments to be identified without the requirement for a high-sensitivity binding assay and should be generally applicable in replacing amino acids as individual residues or groups in peptide inhibitors to generate pharmaceutically acceptable lead molecules.
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