Fragments vs matrix metalloproteinase-13: avoiding the metal

Matrix metalloproteinases (MMPs), as their name suggests, are metal-dependent proteases that cleave the extracellular matrix. They have been implicated in a wide variety of diseases including cancer and inflammation. MMPs have also been used as model systems to study the effects of fragment linking. (In fact, the first successful example of SAR by NMR was conducted against MMP-3.) Most inhibitors, including those starting from fragments, interact with the catalytic zinc in order to achieve potency. However, with roughly two dozen human MMPs, all dependent on a zinc ion, selectivity has been tricky. A recent paper in J. Med. Chem. mostly from researchers at Boehringer Ingelheim sidesteps this problem nicely.

MMP-13 is one of the more interesting members of the family due to its apparent role in rheumatoid arthritis. The enzyme is crystallographically well-behaved, and has a large substrate-binding pocket (the S1’ pocket) near the catalytic zinc that is dissimilar from other S1’ pockets. Even better, there is an adjacent side pocket (S1’*) that can open when the S1’ pocket is occupied, providing further selectivity.

The researchers started by performing a virtual screen of their entire corporate library to look for fragments that might bind in the S1’ pocket. These were added to an in-house fragment collection, and the combined set of roughly 1000 compounds was screened at 0.5 mM concentration in a biochemical screen. Compounds were also assessed using NMR (saturation transfer difference) and size exclusion chromatography mass-spectrometry. One of the best hits was Compound 1, which came from the virtual screen and was originally made as a synthetic intermediate in a completely different program.

Crystallography revealed that Compound 1 does in fact bind in the S1’ pocket, making several hydrogen bonds, with the amide moiety pointed towards the S1’* portion of the protein. This compound also displayed some selectivity towards two other MMPs. Fragment growing towards the S1’* pocket led to compound 11, with increased potency and ligand efficiency, and ultimately to compound 15, with low nanomolar potency and > 1000-fold selectivity against 9 other MMPs. Crystallography revealed that, as expected, the compound binds with the benzoic acid moiety in the S1’* pocket. And despite the presence of the ethyl ester, compound 15 is orally bioavailable in rats.

The paper gives no indication of where the program is today, but it is another nice example of fragment growing, as well as taking an unconventional approach to achieve selectivity.