Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 and structure-activity relationships based on inhibitor profiling

Abstract

The Gram-negative anaerobe Porphyromonas gingivalis is associated with chronic periodontitis. Clinical isolates of P. gingivalis strains with high dipeptidyl peptidase 4 (DPP4) expression also had a high capacity for biofilm formation and were more infective. The X-ray crystal structure of P. gingivalis DPP4 was solved at 2.2 Å resolution. Despite a sequence identity of 32%, the overall structure of the dimer was conserved between P. gingivalis DPP4 and mammalian orthologues. The structures of the substrate binding sites were also conserved, except for the region called S2-extensive, which is exploited by specific human DPP4 inhibitors currently used as antidiabetic drugs. Screening of a collection of 450 compounds as inhibitors revealed a structure-activity relationship that mimics in part that of mammalian DPP9. The functional similarity between human and bacterial DPP4 was confirmed using 124 potential peptide substrates.

The contribution of Tannerella forsythia dipeptidyl aminopeptidase IV in the breakdown of collagen

“…[37][38][39] DPP IV from P. gingivalis has recently been fully characterized. 27 As mentioned above, BFOR_1659 shares 62% and 44% amino acid sequence identity with the corresponding genes from P. gingivalis and the human DPP IV, respectively. All the critical features of the catalytic site are structurally conserved, including the S1-pocket accommodating the proline, the catalytic triad, the oxyanion hole required for stabilization of the transition state, and tetrahedral intermediates, the two glutamates that bind the positively charged N-terminus of the substrate and the S1' pocket that maintains a sharp bend in the substrate's backbone.…”

“…All these features have been described in detail for the human DPP IV . The analysis of the S1‐pocket, S2‐glutamates, S2‐extensive residues, and S1‐residues and the catalytic site, show a high similarity between human, P. gingivalis DPP IV, and BFOR_1659 . Based on the structural alignment, the residues flanking the S1‐pocket are identical in human, P. gingivalis , and T. forsythia DPP IV.…”

“…The analysis of the S1‐pocket, S2‐glutamates, S2‐extensive residues and S1‐residues are depicted in Figure . The S1‐pocket is located next to the catalytic site which is Ser 612 (Ser 593 on P. gingivalis DPP IV) . Based on the structural alignment, the residues flanking the S1‐pocket are identical in human, P. gingivalis , and T. forsythia DPP IV.…”

“…It has been shown that P. gingivalis secretes endopeptidases (Arg‐gingipains and Lys‐gingipains) as well as exopeptidases (DPP IV, DPP‐7, DPP11, PTP‐A, and CPG‐70) with the ability to degrade collagen type I . DPP IV from P. gingivalis has recently been fully characterized …”

“…The S1-pocket is located next to the catalytic site which is Ser 612 (Ser 593 on P. gingivalis DPP IV). 27 Based on the structural alignment, the residues flanking the S1-pocket are identical in human, P. gingivalis, not completely conserved in P. gingivalis DPP IV and BFOR_1659.…”