Fragments vs Lp-PLA2 – third time’s the charm?

The enzyme lipoprotein-associated phospholipase A2 (Lp-PLA₂) cleaves phospholipids into inflammatory molecules. As such, it has been pursued as a target for several indications, from atherosclerosis to Alzheimer’s disease. In 2016 we highlighted two fragment success stories against this target (here and here). A recent paper in J. Med. Chem. provides a third, this one by Jianhua Shen, Yechun Xu, and colleagues at the Shanghai Institute of Materia Medica, ShanghaiTech University, and the University of Chinese Academy of Sciences. The fact that all the scientists are from China illustrates the growth of FBLD in that country, as we reported last November.

The researchers started by screening a 500 fragment library in an enzymatic assay. Compound 10 was a weak hit but had good ligand efficiency and was unlike known Lp-PLA₂ binders. Moreover, crystallography revealed multiple interactions between the sulfonamide and the protein. This information was used to perform a similarity search followed by docking of 200,000 compounds. The top 500 were manually inspected and 100 were purchased and tested, with compound 11 showing low micromolar activity.

A crystal structure of compound 11 bound to the protein revealed a similar binding mode as the initial fragment, and also suggested further improvements, such as adding substituents to fill a small pocket (as in compound 14a). Further optimization for both affinity and stability ultimately led to compound 37, which inhibited Lp-PLA₂ in human and rat plasma. It also exhibited good oral bioavailablilty in rats and promising pharmacokinetics. The researchers state that further optimization is ongoing.

How far will this go? The most advanced Lp-PLA2 inhibitor to make it to the clinic, darapladib, failed two phase 3 clinical trials (with nearly 30,000 patients!) for coronary diseases, casting a pall over the target. Darapladib, which was not fragment derived, can fairly be described as molecularly obese. Molecules such as compound 37 and the other fragment-derived series we previously mentioned do appear more attractive, but whether anyone will invest the massive resources needed to move them forward remains the billion yuan question.