Inhibition of Human Neutrophil Elastase. 4. Design, Synthesis, X-ray Crystallographic Analysis, and Structure−Activity Relationships for a Series of P₂-Modified, Orally Active Peptidyl Pentafluoroethyl Ketones

Abstract

A series of P2-modified, orally active peptidic inhibitors of human neutrophil elastase (HNE) are reported. These pentafluoroethyl ketone-based inhibitors were designed using pentafluoroethyl ketone 1 as a model. Rational structural modifications were made at the P3, P2, and activating group (AG) portions of 1 based on structure-activity relationships (SAR) developed from in vitro (measured Ki) data and information provided by modeling studies that docked inhibitor 1 into the active site of HNE. The modeling-based design was corroborated with X-ray crystallographic analysis of the complex between 1 and porcine pancreatic elastase (PPE) and subsequently the complex between 1 and HNE.

Unexpected Active-Site Flexibility in the Structure of Human Neutrophil Elastase in Complex with a New Dihydropyrimidone Inhibitor

“…31 The determined overall threedimensional structures of HNE in the DHPI complex ( Fig. 1a) and free HNE are very similar and closely resemble those of previously published HNE:inhibitor complexes [24][25][26][27][28][29][30] with RMSD between 0.14 Å and 0.47 Å for C α atoms. We observed N-linked sugar moieties at both potential glycosylation sites.…”

“…[24][25][26][27][28] In addition, two complexes of HNE with inhibitory domains of macromolecular inhibitors have been determined. 29,30 Three of the smallmolecule inhibitors are peptidic compounds, 24,27,28 whereas the compounds described by MacDonald et al 26 and Huang et al 25 are based on a pyrrolidine trans-lactam and a 1,2,5-thiadiazolidin-3-one 1,1-dioxide scaffold, respectively. In contrast, porcine pancreatic elastase (PPE), which shares 40% amino acid identity with HNE, is structurally very well characterized 31 with more than 100 structures deposited in the Protein Data Bank (PDB).…”

“…24,[27][28][29][30] It builds two hydrogen bonds with the main chain of peptidic inhibitors, which are arranged in a β-sheetlike fashion. DHPI interacts with Val216 via a hydrogen bond between the carbonyl-O of the central pyrimidine ring system and the backbone amide of Val216 (3.16 Å).…”

Direct interaction of ONO-5046 with human neutrophil elastase through 1H NMR and molecular docking

“…The crystal structure (PDB ID: 1B0F) of HNE in complex with the inhibitor SEI (1-{3-methyl-2-[4-(morpholine-4-carbonyl)-benzoylamino]-butyryl}-pyrrolidine-2-carboxylic acid (3,3,4,4,4-pentafluoro-1-isopropyl-2-oxo-butyl)-amide) was downloaded from the RCSB protein data bank [18]. The potential of the 3D structure of HNE was assigned according to the Amber force field with Kollman-United-atom charges encoded in the molecular modeling software Sybyl 7.3 (Linux-os2x).…”

Mutations in the ELA2 gene correlate with more severe expression of neutropenia: a study of 81 patients from the French Neutropenia Register

“…Bioinformatics analyses of ELA2 missense mutations were based on the crystal structures of human NE protein reported by Navia et al 18 (Protein Data Bank entry, 1HNE) and Cregge et al 19 (Protein Data Bank entry, 1B0F). Structures were analyzed by using the DeepView-SwissPdbViewer program.…”