Fragments vs Lp-PLA2: A new hope

A few months ago we highlighted work out of Astex and GlaxoSmithKline describing the fragment-based discovery of inhibitors of lipoprotein-associated phospholipase A2 (Lp-PLA₂), an inflammatory disease target. Although low nanomolar compounds were identified, they had high clearance in rats. In a new J. Med. Chem. paper the team – led by Alison Woolford of Astex and Vipul Patel of GlaxoSmithKline – describes a completely new series of molecules with better pharmacokinetic properties.

Recall that the researchers had previously solved the crystal structures of 50 fragments bound to the “canyon-like” active groove of Lp-PLA_2. Hydantoin 3 was one of these, and although it had no detectable activity in a biochemical assay, it did make contacts with residues in the catalytic site of the enzyme. A virtual screen of 16,000 related compounds identified 33 potential hits, and crystallographic and biochemical screening of these led to compound 5, with low micromolar activity.

The researchers were able to trim back the cyclohexyl group and remove one of the carbonyls with only a modest loss in affinity. They could also take advantage of extensive structural information from other fragment hits. For example, adding a nitrile from another fragment produced compound 13, with improved affinity.

Next, the researchers turned to the left side of the molecule, adding substituents to make a stacking interaction with a tryptophan residue in the protein – an interaction seen previously with a uracil fragment. Simple aromatic rings worked, but aliphatic heterocycles such as amines and sulfones were even better, with compound (S)-23 being among the best.

Although compound (S)-23 has only high-nanomolar potency in a biochemical assay, it is equipotent with darapladib in a whole plasma assay – despite the fact that darapladib is a picomolar inhibitor in the biochemical assay. The researchers attribute this difference to the fact that darapladib, which reached phase 3 trials, is a poster child for molecular obesity, while (S)-23 comes in with a svelte molecular weight below 400, very low plasma protein binding, and a solubility of at least 3.5 mM. The molecule is also permeable, does not inhibit CYP450s, is selective against the closely related PLA2-VIIB, and has low clearance in dogs. The clearance is higher in rats, but a closely related compound is better and also has high oral bioavailability.

This paper provides another example of finding a fragment with no detectable activity and advancing it to an attractive series. It illustrates the power of crystallography to reveal useful fragments as well as the importance of crystallography during lead optimization. Darapladib failed in two massive phase 3 clinical trials for cardiovascular disease, which probably poisoned GlaxoSmithKline's appetite for Lp-PLA₂. Still, if future biological discoveries suggest new indications for this target, molecules from this series may provide a path back into the clinic.