The protein farnesyl pyrophosphate synthase (FPPS) has long been a target of drugs for osteoporosis, and some data have suggested it could be a productive target for other diseases too. However, approved drugs that target FPPS contain two phosphonates, highly negatively charged moieties that, while nicely directing the drugs to bone, lead to low plasma and soft tissue levels. Researchers at Novartis have now identified fragments that bind to an allosteric site on FPPS and so lack the phosphonate moieties. An article in the September issue of Nature Chemical Biology describes the discovery of these fragments and how they were advanced to nanomolar inhibitors.
The researchers, led to Wolfgang Jahnke in Basel, Switzerland, started by screening a library of only 400 fragments using NMR. Several low affinity (millimolar) hits such as compound 1 were identified, but surprisingly these were not competitive with bisphoshonate drugs, and some even bound synergistically. Crystallography revealed that they were binding in a previously undiscovered allosteric site. (The same group also used fragment screening to explore an allosteric site in another protein.)
To follow up on these observations, the researchers tested 40 related compounds in the Novartis internal compound collection, again using NMR to detect binding. This led to the more potent compound 5, and two rounds of focused library assembly and screening led to low micromolar inhibitors such as compound 7. Structure-based design led to molecules such as compound 11, which has comparable potency to approved drugs that target FPPS. Compound 11 was further characterized using ITC and crystallography, and although its two carboxylic acids likely account for a relatively low cellular permeability, it does not show any affinity for bone.
Interestingly, a high-throughput screen conducted against FPPS did not yield any inhibitors with an IC50 better than 5 micromolar. So in this case not only did a fragment-based approach discover a new series of molecules against a new site on an old target, it succeeded where conventional HTS didn’t.