8QGZ

NbE201 a nanobody binding human neutrophil elastase

Summary for 8QGZ

• Entry DOI: 10.2210/pdb8qgz/pdb
• Descriptor: NbE201, ACETATE ION (3 entities in total)
• Functional Keywords: nanobody, elastase, inhibitor, single-domain antibody, immune system
• Biological source: Lama glama
• Total number of polymer chains: 4
• Total formula weight: 57581.19

Authors

Redeghieri, P.,Morales-Yanez, F.,Moray, J.,Dumoulin, M.,Kerff, F. (deposition date: 2023-09-06, release date: 2024-12-25)

Primary citation

Redeghieri, P.,Moray, J.,Kerff, F.,Gohy, S.,Leal, T.,Muyldermans, S.,Vanbever, R.,Morales-Yanez, F.J.,Dumoulin, M.
Enzymatic, structural, and biophysical characterization of a single-domain antibody (VHH) selectively and tightly inhibiting neutrophil elastase and exhibiting favorable developability properties.
Protein Sci., 33:e5227-e5227, 2024

PubMed Abstract: Human neutrophil elastase (hNE), a serine protease released by neutrophils during inflammation, plays a major role in the pathophysiology of several conditions especially in inflammatory lung diseases. Its inhibition constitutes, therefore, a promising therapeutic strategy to combat these diseases. In this work, we characterized the in vitro properties of a VHH (i.e., the antigen binding domain of camelid heavy chain-only antibodies), referred to as NbE201. This VHH is able to inhibit tightly, selectively and competitively both human and murine elastases with the inhibition constants (K) of 4.1 ± 0.9 nM and 36.8 ± 3.9 nM, respectively. The IC for the inhibition of the hydrolysis of elastin is in the same range to that of alpha-1 antitrypsin (i.e., the main endogenous inhibitor of hNE also used in the clinic) and 14 times better than that of Sivelestat (i.e., the 2nd clinically approved hNE inhibitor). The X-ray crystal structure of the NbE201-hNE complex reveals that the Complementarity Determining Regions CDR1 and CDR3 of the VHH bind into the substrate binding pocket of hNE and prevent the access to small or macromolecular substrates. They do not, however, bind deep enough into the pocket to be hydrolyzed. NbE201 is highly stable towards oxidation, deamidation, and chemical or thermal denaturation. NbE201 is therefore likely to tolerate manufacturing processes during drug development. These results highlight the high potential of NbE201 as a (pre)clinical tool to diagnose and treat diseases associated with excessive hNE activity, and for fundamental research to better understand the role of hNE in these conditions.

PubMed: 39604162
DOI: 10.1002/pro.5227

Experimental method

X-RAY DIFFRACTION (1.8 Å)