Flipping fragments in PDE2

A common assumption in fragment growing is that the binding mode of the fragment remains the same throughout optimization (for example here, here, and here). However, this is not always the case (as described here, here, and here). A recent paper in Bioorg. Med. Chem. Lett. by Ashley Forster and colleagues from Merck falls into this latter category.

The researchers were interested in phosphodiesterase 2 (PDE2), which hydrolyzes the cyclic nucleotides cAMP and cGMP. PDE2 is highly expressed in the frontal cortex and hippocampus and has been implicated in cognition and proposed as a target for Alzheimer’s Disease. But because PDE2 is just one member of a large class of enzymes, selectivity is important. Indeed, Merck researchers previously used fragment-based methods to discover selective inhibitors of another member of the family, PDE10A.

In this case the researchers used both high-concentration biochemical screens as well as an SPR screen of a library of 1940 fragments, all with molecular weights < 250 Da. This resulted in 54 competitive inhibitors of PDE2 with affinities better than 200 µM. (No details were provided on numbers of hits from each screen.) Compound 1 was progressed into lead optimization due to its high ligand efficiency and attractive physicochemical properties.

A crystal structure of compound 1 bound to PDE2 revealed the potential to grow into a hydrophobic pocket exploited by previously reported molecules, leading to compound 5. Modeling suggested that bulking up the benzylic linker could improve the binding mode, and indeed compound 8 had submicromolar affinity. Surprisingly however, a crystal structure of a related molecule (having a single methyl group off the linker instead of two) revealed that the initial fragment had flipped orientation.

Further modeling suggested replacing the two methyl groups with a cyclopropyl group, as in compound 12. This simple change gave a 100-fold boost in potency, which was attributed to the free form of the compound more closely matching the bound form. Finally, the remaining methyl group was removed to reduce lipophilicity and remove a potential metabolic liability, leading to compound 16. Crystallography revealed that this binds as expected (gray), with the fragment moiety in the “flipped” conformation.

Compound 16 is at least 100-fold selective for PDE2 against a panel of other PDEs. The attention to physicochemical properties paid off in the form of good oral bioavailability, low clearance, and a satisfactory half life in rats. Although the paper does not mention how long the program took, it does state that only 25 analogs were made to get from the initial fragment to compound 16, and also mentions further optimization. This is another nice example of how the union of crystallography, modeling, and medicinal chemistry can rapidly lead to useful molecules.