Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase

Abstract

Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46. Because S46 peptidases are not found in mammals, these enzymes are attractive targets for novel antibiotics. However, potent and selective inhibitors of these peptidases have not been developed to date. In this study, a high-resolution crystal structure analysis of PgDPP11 using a space-grown crystal enabled us to identify the binding of citrate ion, which could be regarded as a lead fragment mimicking the binding of a substrate peptide with acidic amino acids, in the S1 subsite. The citrate-based pharmacophore was utilized for in silico inhibitor screening. The screening resulted in an active compound SH-5, the first nonpeptidyl inhibitor of S46 peptidases. SH-5 and a lipophilic analog of SH-5 showed a dose-dependent inhibitory effect against the growth of P. gingivalis. The binding mode of SH-5 was confirmed by crystal structure analysis. Thus, these compounds could be lead structures for the development of selective inhibitors of PgDPP11.

7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk

“…S46 peptidases, bacterial DPP7s, and DPP11s are important enzymes for bacterial growth and are promising targets for antimicrobial agents. 28 The dipeptidyl ACA substrates developed in this study are useful for screening antimicrobial compounds targeting S46 peptidases from natural compounds. Since ACA can modify substrates such as peptides, its range of applications will extend to peptidases other than bacterial DPP.…”

“…mexicana WO24 (PmDAP BII), DPP7 from Stenotrophomonas maltophilia (SmDPP7), DPP11 from S. maltophilia (SmDPP11), and DPP11 from Porphyromonas gingivalis (PgDPP11) were overexpressed and purified as described in the literature. ,, …”

Dipeptidyl‐peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis

“…In this line, Sakamoto et al. (2019) developed nonpeptidyl DPP11 inhibitor SH‐5 with IC 50 of 90.1 µM, which showed a dose‐dependent inhibition of the growth of P. gingivalis .…”

Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7

“…Family S46 peptidases are serine proteases showing dipeptidyl peptidase activity and are widely distributed in Bacteroidetes and Proteobacteria, but are not found in mammals 11 , 12 . Since S46 peptidases are important enzymes for the growth of bacteria 13 , 14 , these peptidases are anticipated as a novel molecular target of antibiotics 15 . However, a clear difference in the specificity at the P1 position of the substrate between the two types of S46 peptidases has been an obstacle when designing a universal inhibitor.…”