A comparative study of the binding modes of recently launched dipeptidyl peptidase IV inhibitors in the active site
Introduction
Dipeptidyl peptidase IV (DPP-4, EC 3.4.14.5) inhibitors are a new class of oral anti-hyperglycemic agents for the treatment of type 2 diabetes. The glucose lowering effect of DPP-4 inhibitors is mediated by suppressing the degradation of the incretin hormone glucagon-like peptide-1 and stimulating insulin secretion in response to increased blood glucose levels [1]. Prescriptions for recently launched DPP-4 inhibitors for type 2 diabetes have been expanding because of their high effectiveness and safety.
Among the recently marketed DPP-4 inhibitors (Table 1), vildagliptin [2], saxagliptin [3] and teneligliptin [4] are peptide mimetic compounds, which have been discovered by replacing segments of peptide-based substrates [5]. In contrast, sitagliptin [6], alogliptin [7] and linagliptin [8] are non-peptide mimetic compounds, which have been discovered by optimization of the initial lead compounds identified by random screening [5]. Therefore, their chemical structures are diverse, suggesting that each of their binding modes in DPP-4 would be unique.
DPP-4 is a highly specific serine protease that recognizes an amino acid sequence having proline or alanine at the N-terminal penultimate (P1) position and inactivates or generates biologically active peptides [9]. The amino acid sequence and three-dimensional structure of DPP-4 are well known [10], [11]. The structure comprises a β-propeller domain and a catalytic domain, which together embrace an internal cavity housing the active center. This cavity is connected to the bulk solvent by a “propeller opening” and a “side opening” [12]. The conventional hypothesis suggests that substrates and inhibitors enter or leave the active site via the side opening [12], [13].
While some comparative studies on the pharmacological effects of DPP-4 inhibitors have been reported [14], there have been no reports comparing their binding modes in DPP-4. X-ray co-crystal structures of five inhibitors, sitagliptin [6], saxagliptin [15], alogliptin [16], linagliptin [8] and teneligliptin [4], with DPP-4 were determined by each originator except vildagliptin. Because these inhibitors have diverse chemical structures, a comparative study of their binding modes in DPP-4 is of considerable interest. Although it is well known that all DPP-4 inhibitors bind to the S1 and S2 subsites in common, it has not been systematically understood whether other subsites exist and whether each inhibitor binds to these in a distinct manner. In this study, we determined the co-crystal structure of vildagliptin with DPP-4, analyzed those of the six inhibitors in parallel and studied the relationships between their binding interactions with DPP-4 and their inhibitory activity.
Section snippets
Synthesis of vildagliptin
Vildagliptin was prepared according to the method described by Villhauer et al. [2].
X-ray crystallographic studies
The protein of human DPP-4 (33-766) secreted from insect cells was purified and crystallized according to the method reported by Hiramatsu et al. [17] The protein–inhibitor complex was obtained by soaking a preformed DPP-4 crystal in the presence of vildagliptin and preserving it in liquid nitrogen for data collection at 100 K. X-ray diffraction data were collected at the High Energy Accelerator Research
Definition of subsites in the active site of DPP-4
In the active site of a protease, subsites are generally defined by the binding site of the substrate peptide [20]. The amino acids in the substrate peptide are numbered from the point of cleavage (P2, P1, P1′, P2′ …), and the protein subsites occupied by the respective amino acids are also numbered in the same fashion (S2, S1, S1′, S2′…). In the case of DPP-4, the N-terminus of the substrate peptide is recognized by Glu205 and Glu206, and Ser630 cleaves at the N-terminus penultimate position (P
Acknowledgments
The authors thank Dr. Hideo Kubodera, Dr. Okimasa Okada and Dr. Kunitomo Adachi for their helpful discussion.
References (27)
- et al.
Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3- methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl] thiazolidine): a highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes
Bioorg. Med. Chem.
(2012) Dipeptidyl-peptidase IV (CD26)-role in the inactivation of regulatory peptides
Regul. Pept.
(1999)- et al.
Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV
Structure
(2003) - et al.
Rigidity and flexibility of dipeptidyl peptidase IV: crystal structures of and docking experiments with DPIV
J. Mol. Biol.
(2006) - et al.
Processing of X-ray diffraction data collected in oscillation mode
Meth. Enzymol.
(1997) - et al.
On the size of the active site in proteases I. Papain
Biochem. Biophys. Res. Commun.
(1967) - et al.
Fused bicyclic heteroarylpiperazine-substituted l-prolylthiazolidines as highly potent DPP-4 inhibitors lacking the electrophilic nitrile group
Bioorg. Med. Chem.
(2012) - et al.
Crystal structures of HIV-1 Tat-derived nonapeptides Tat-(1–9) and Trp2-Tat-(1–9) bound to the active site of dipeptidyl-peptidase IV (CD26)
J. Biol. Chem.
(2005) - et al.
[(S)-γ-(4-Aryl-1-piperazinyl)-l-prolyl]thiazolidines as a novel series of highly potent and long-lasting DPP-IV inhibitors
Bioorg. Med. Chem. Lett.
(2007) - et al.
Discovery of potent and selective β-homophenylalanine based dipeptidyl peptidase IV inhibitors
Bioorg. Med. Chem. Lett.
(2004)
Structural and kinetic analysis of the substrate specificity of human fibroblast activation protein α
J. Biol. Chem.
Long-term treatment with the dipeptidyl peptidase IV inhibitor P32/98 causes sustained improvements in glucose tolerance, insulin sensitivity, hyperinsulinemia, and β-cell glucose responsiveness in VDF (fa/fa) zucker rats
Diabetes
1-[[(3-Hydroxy-1-adamantyl)amino]acetyl]-2-cyano-(S)-pyrrolidine: a potent, selective, and orally bioavailable dipeptidyl peptidase IV inhibitor with antihyperglycemic properties
J. Med. Chem.
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