Crystal Structures of DPP-IV (CD26) from Rat Kidney Exhibit Flexible Accommodation of Peptidase-Selective Inhibitors

• Published in: Biochemistry (Easton) Vol. 45; no. 24; pp. 7474 - 7482
• Main Authors: Longenecker, Kenton L, Stewart, Kent D, Madar, David J, Jakob, Clarissa G, Fry, Elizabeth H, Wilk, Sherwin, Lin, Chun W, Ballaron, Stephen J, Stashko, Michael A, Lubben, Thomas H, Yong, Hong, Pireh, Daisy, Pei, Zhonghua, Basha, Fatima, Wiedeman, Paul E, von Geldern, Thomas W, Trevillyan, James M, Stoll, Vincent S
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 20.06.2006
• Subjects: Animals; Binding Sites; Crystallization; Dimerization; Dipeptidases - antagonists & inhibitors; Dipeptidases - chemistry; Dipeptidases - metabolism; Dipeptidyl Peptidase 4 - chemistry; Dipeptidyl Peptidase 4 - genetics; Dipeptidyl Peptidase 4 - isolation & purification; Dipeptidyl Peptidase 4 - metabolism; Glucagon-Like Peptide 1 - chemistry; Glucagon-Like Peptide 1 - metabolism; Humans; Kidney - enzymology; Kinetics; Models, Molecular; Molecular Structure; Protein Conformation; Rats; Recombinant Proteins - chemistry; Recombinant Proteins - metabolism; Structure-Activity Relationship; Tyrosine - chemistry; X-Ray Diffraction
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi060184f

Dipeptidyl peptidase IV (DPP-IV) belongs to a family of serine peptidases, and due to its indirect regulatory role in plasma glucose modulation, DPP-IV has become an attractive pharmaceutical target for diabetes therapy. DPP-IV inactivates the glucagon-like peptide (GLP-1) and several other naturally produced bioactive peptides that contain preferentially a proline or alanine residue in the second amino acid sequence position by cleaving the N-terminal dipeptide. To elucidate the details of the active site for structure-based drug design, we crystallized a natural source preparation of DPP-IV isolated from rat kidney and determined its three-dimensional structure using X-ray diffraction techniques. With a high degree of similarity to structures of human DPP-IV, the active site architecture provides important details for the design of inhibitory compounds, and structures of inhibitor−protein complexes offer detailed insight into three-dimensional structure−activity relationships that include a conformational change of Tyr548. Such accommodation is exemplified by the response to chemical substitution on 2-cyanopyrrolidine inhibitors at the 5 position, which conveys inhibitory selectivity for DPP-IV over closely related homologues. A similar conformational change is also observed in the complex with an unrelated synthetic inhibitor containing a xanthine core that is also selective for DPP-IV. These results suggest the conformational flexibility of Tyr548 is unique among protein family members and may be utilized in drug design to achieve peptidase selectivity.