Insights into Cyclin Groove Recognition: Complex Crystal Structures and Inhibitor Design through Ligand Exchange

• Published in: Structure (London) Vol. 11; no. 12; pp. 1537 - 1546
• Main Authors: Kontopidis, George, Andrews, Martin J.I., McInnes, Campbell, Cowan, Angela, Powers, Helen, Innes, Lorraine, Plater, Andy, Griffiths, Gary, Paterson, Dougie, Zheleva, Daniella I., Lane, David P., Green, Stephen, Walkinshaw, Malcolm D., Fischer, Peter M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2003
• Subjects: Amino Acid Motifs; Binding Sites; CDC2-CDC28 Kinases - antagonists & inhibitors; CDC2-CDC28 Kinases - chemistry; Crystallography, X-Ray; Cyclin A - antagonists & inhibitors; Cyclin A - chemistry; Cyclin-Dependent Kinase 2; Cyclin-Dependent Kinase Inhibitor p21; Cyclins - chemistry; Humans; Ligands; Models, Molecular; Peptides - chemistry; Protein Binding; Protein Conformation; Protein Structure, Secondary; Structure-Activity Relationship
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2003.11.006

Inhibition of CDK2/CA (cyclin-dependent kinase 2/cyclin A complex) activity through blocking of the substrate recognition site in the cyclin A subunit has been demonstrated to be an effective method for inducing apoptosis in tumor cells. We have used the cyclin binding motif (CBM) present in the tumor suppressor proteins p21 WAF1 and p27 KIP1 as a template to optimize the minimal sequence necessary for CDK2/CA inhibition. A series of peptides were prepared, containing nonnatural amino acids, which possess nano- to micromolar CDK2-inhibitory activity. Here we present X-ray structures of the protein complex CDK2/CA, together with the cyclin groove-bound peptides H-Ala-Ala-Abu-Arg-Ser-Leu-Ile-( p-F-Phe)-NH 2 (peptide 1), H-Arg-Arg-Leu-Ile-Phe-NH 2 (peptide 2), Ac-Arg-Arg-Leu-Asn-( m-Cl-Phe)-NH 2 (peptide 3), H-Arg-Arg-Leu-Asn-( p-F-Phe)-NH 2 (peptide 4), and H-Cit-Cit-Leu-Ile-(p- F-Phe)-NH 2 (peptide 5). Some of the peptide complexes presented here were obtained through the novel technique of ligand exchange within protein crystals. This method may find general application for obtaining complex structures of proteins with surface-bound ligands.