Exploiting the S4–S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis

Carla Guarino (1) , Natalia Gruba (2) , Renata Grzywa (3) , Edyta Dyguda-Kazimierowicz (4) , Yveline Hamon (5, 1) , Monika Łȩgowska (2) , Marcin Skoreński (3) , Sandrine Dallet-Choisy (6, 1) , Adam Marchand-Adam (1) , Christine Kellenberger (7) , Dieter Jenne (8) , Marcin Sieńczyk (3) , Adam Lesner (9, 2) , Francis Gauthier (1) , Brice Korkmaz (1, 10)

1 Pathologies Respiratoires : Protéolyse et Aérosolthérapie
2 UG - University of Gdańsk
3 UWr - University of Wrocław [Poland]
4 Wroclaw University of Science and Technology
5 Comprehensive Pneumology Center - Institute of Lung Biology and Disease (iLBD)
6 Université Francois Rabelais [Tours]
7 AFMB - Architecture et fonction des macromolécules biologiques
8 Department of Neuroimmunology
9 Faculty of Chemistry
10 CEPR - Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100

The neutrophilic serine protease proteinase 3 (PR3) is involved in inflammation and immune response and thus appears as a therapeutic target for a variety of infectious and inflammatory diseases. Here we combined kinetic and molecular docking studies to increase the potency of peptidyl-diphenyl phosphonate PR3 inhibitors. Occupancy of the S1 subsite of PR3 by a nVal residue and of the S4-S5 subsites by a biotinylated Val residue as obtained in biotin-VYDnVP(O-C6H4-4-Cl)2 enhanced the second-order inhibition constant kobs/[I] toward PR3 by more than 10 times ( kobs/[I] = 73000 ± 5000 M-1 s-1) as compared to the best phosphonate PR3 inhibitor previously reported. This inhibitor shows no significant inhibitory activity toward human neutrophil elastase and resists proteolytic degradation in sputa from cystic fibrosis patients. It also inhibits macaque PR3 but not the PR3 from rodents and can thus be used for in vivo assays in a primate model of inflammation.

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Biochemistry [q-bio.BM]

Carla Guarino, Natalia Gruba, Renata Grzywa, Edyta Dyguda-Kazimierowicz, Yveline Hamon, et al.. Exploiting the S4–S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis. Journal of Medicinal Chemistry, 2018, 61 (5), pp.1858-1870. ⟨10.1021/acs.jmedchem.7b01416⟩. ⟨hal-02094546⟩