PDBsum entry 4ym9

Hydrolase

PDB id: 4ym9

Contents

Protein chain

240 a.a.

Ligands

4E4

SO4 ×5

ACT ×5

GOL

Metals

_NA

Waters ×161

References listed in PDB file

Key reference

• Title: Clickable 4-Oxo-β-Lactam-Based selective probing for human neutrophil elastase related proteomes.
• Authors: E.F.Ruivo, L.M.Gonçalves, L.A.Carvalho, R.C.Guedes, S.Hofbauer, J.A.Brito, M.Archer, R.Moreira, S.D.Lucas.
• Ref.: ChemMedChem, 2016, 11, 2037-2042. [DOI no: 10.1002/cmdc.201600258]
• PubMed id: 27465595

Abstract

Human neutrophil elastase (HNE) is a serine protease associated with several inflammatory processes such as chronic obstructive pulmonary disease (COPD). The precise involvement of HNE in COPD and other inflammatory disease mechanisms has yet to be clarified. Herein we report a copper-catalyzed alkyne-azide 1,3-dipolar cycloaddition (CuAAC, or 'click' chemistry) approach based on the 4-oxo-β-lactam warhead that yielded potent HNE inhibitors containing a triazole moiety. The resulting structure-activity relationships set the basis to develop fluorescent and biotinylated activity-based probes as tools for molecular functional analysis. Attaching the tags to the 4-oxo-β-lactam scaffold did not affect HNE inhibitory activity, as revealed by the IC50 values in the nanomolar range (56-118 nm) displayed by the probes. The nitrobenzoxadiazole (NBD)-based probe presented the best binding properties (ligand efficiency (LE)=0.31) combined with an excellent lipophilic ligand efficiency (LLE=4.7). Moreover, the probes showed adequate fluorescence properties, internalization in human neutrophils, and suitable detection of HNE in the presence of a large excess of cell lysate proteins. This allows the development of activity-based probes with promising applications in target validation and identification, as well as diagnostic tools.