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Unusual binding modes of two inhibitors to their target enzymes human leukocyte elastase (HLE) and protein kinase CK2 revealed by protein crystallography
Jennifer Hochscherf, Karsten Niefind
University of Cologne, Institute of Biochemistry

Published: 31 October 2018 by MDPI AG in Proceedings of 4th International Electronic Conference on Medicinal Chemistry in 4th International Electronic Conference on Medicinal Chemistry session ECMC-4
MDPI AG, 10.3390/ecmc-4-05572
Abstract:

The main subjects of this keynote are protein kinase CK2 and human leukocyte elastase (HLE), two biomedically important enzymes and pharmacologically attractive targets.

CK2 - more precisely its catalytic subunit CK2alpha - is a member of the superfamily of eukaryotic protein kinases. Its antiapoptotic activity is exploited by tumour cells in order to escape cell death. The indeno[1,2-b]indole scaffold, a flat annulated 4-ring system, is a relatively novel lead structure for the development of ATP-competitive CK2 inhibitors. Complex structures of CK2alpha and a number of indeno[1,2-b]indole-type compounds had been predicted previously. In such an in silico model the inhibitor sticks in the ATP cavity in an apparently plausible way, namely such that its hydrophobic side is directed inwards while its hydrophilic side has access to the solvent. However, when we determined the first co-crystal of CK2alpha with an indeno[1,2-b]indole-type inhibitor, we realized to our surprise that the orientation of the inhibitor was reversed: the "hydrophobic-out/oxygen-out" binding mode that we discovered is determined by hydrogen bonds of the inhibitor to a hidden and conserved water molecule. This molecular arrangement requires an inhibitor orientation in which hydrophobic substitutents are at the outer surface which opens the possibility for further modifications.

The second target enzyme, human leukocyte elastase (HLE), is a chymotrypsin-type serine protease which is produced by neutrophilic granulocytes, the most abundant cells of the innate immune system [therefore the synonym "human neutrophil elastase" (HNE)]. The activity of HLE must be strictly controlled to avoid proteolytic damage of the connective tissue which is a particular problem in chronic obstructive pulmonary disease (COPD) and other inflammatory diseases. Naturally, HLE is downregulated by alpha1-antitrypsin, a serpin-type protease inhibitor, which is likewise produced by neutrophils. Synthetic HLE inhibitors are useful in cases of inbalance of the natural HLE control system. Typically, HLE inhibibitors block the S1 pocket of the enzyme, the most critical of several substrate binding cavities. The S1 pocket recognizes the side chain of the substrate directly N-terminal of the peptide bond to be hydrolyzed. In our study we co-crystallized HLE with a 1,3-thiazolidine-2,4-dione derivative with antibacterial activity that had been observed to inhibit HLE as well. In the complex structure the inhibitor is bound to the S2' site, i.e. at a region responsible for harbouring residues at the C-terminal side of the scissile peptide bond. In addition, the inhibitor seems to induce a dimerization of the enzyme by which the access to the active site region is prohibited.

Keywords: cell death, Protein, hydrophobic, inhibitor, innate immune, CK2, complex structure, hle, Binding mode
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