Discovery of Leukotriene A4 Hydrolase Inhibitors Using Metabolomics Biased Fragment Crystallography

Abstract

We describe a novel fragment library termed fragments of life (FOL) for structure-based drug discovery. The FOL library includes natural small molecules of life, derivatives thereof, and biaryl protein architecture mimetics. The choice of fragments facilitates the interrogation of protein active sites, allosteric binding sites, and protein−protein interaction surfaces for fragment binding. We screened the FOL library against leukotriene A4 hydrolase (LTA4H) by X-ray crystallography. A diverse set of fragments including derivatives of resveratrol, nicotinamide, and indole were identified as efficient ligands for LTA4H. These fragments were elaborated in a small number of synthetic cycles into potent inhibitors of LTA4H representing multiple novel chemotypes for modulating leukotriene biosynthesis. Analysis of the fragment-bound structures also showed that the fragments comprehensively recapitulated key chemical features and binding modes of several reported LTA4H inhibitors.

Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening

“…Fragment screening was performed on preformed GCDH crystals with a metabolome-derived small-molecule library of 1440 fragments following previously published methods (Davies et al, 2009;Begley et al, 2011). Briefly, pools of up to eight fragment ligands were prepared from concentrated methanol stock solutions with each ligand at 6.25 mM in the mixture.…”

“…Among these differences, a tyrosine side chain adjacent to the catalytic glutamate residue in apo BpGCDH is rotated nearly 180 from its position in the human ternary complex and appears to block the flavin-binding site. By soaking our Fragments of Life small-molecule library (Davies et al, 2009;Begley et al, 2011) into crystals of apo BpGCDH, complexes were formed whose crystal structures showed backbone hydrogen-bond interactions replaced by the catalytic glutamate side chain. These structures shed light on the structural flexibility available to GCDH and demonstrated the use of smallmolecular fragments as chemical probes for capturing alternative conformational states.…”

Resveratrol: Is It Really Good for Liver Health?

“…apoptosis (50). Moreover, a structure-based drug discovery study claimed RES as a binding partner for leukotriene A4 hydrolase (LTA4H) (51). This enzyme participates in arachidonic acid metabolism and plays important roles in immediate hyposensitivity reactions and inflammation.…”

Leukotriene A4 Hydrolase – An Evolving Therapeutic Target

“…Most of the published structures contain a co-crystallized substrate. Drug discovery efforts by deCODE Genetics, an Icelandbased pharmaceutical company, utilized the facility in which the leukotriene A 4 hydrolase enzyme could be co-crystallized with small molecule substrates to identify molecular fragments that could be pieced together to design a new drug [181,182].…”