Fragments vs COMT revisited

Catechol O-methyltransferase (COMT) metabolizes neurotransmitters such as dopamine and is a validated target for Parkinson’s disease. In theory other diseases could be treated with COMT inhibitors too, but most of these contain – like dopamine itself – catechol moieties, and thus have lousy pharmacokinetics and poor brain penetration. Catechols in general are best avoided, and in a recent paper in J. Med. Chem. María Sarmiento and colleagues at Roche have found an alternate scaffold.

COMT is a magnesium-dependent enzyme, and the catechol binds to the magnesium ion. The researchers decided to target the pocket that binds the cofactor, S-adenosyl-L-methionine (SAM). They screened 6000 rule-of-three compliant fragments at 200 µM using surface plasmon resonance (SPR). First they examined wild-type enzyme in the absence of magnesium and SAM, and they also counter-screened against six variants containing mutations in the SAM binding site to exclude fragments that bound elsewhere. Even after this specificity profiling 600 hits remained. Dose-response curves whittled the number down to 200, all of which were examined using ligand-detected (CPMG) NMR. Hits from CPMG NMR were further studied using protein-detected (¹H/¹⁵N HSQC) NMR. Finally, all 600 of the hits from the initial SPR screen/counter-screen assays were tested in an enzymatic assay. Only four fragments made it through all of these filters, three of which were pyrazoles such as compound 1.

Two years ago Teddy highlighted a paper from Takeda also focused on COMT, and there too pyrazoles predominated – an observation that didn’t escape the Roche researchers. In fact, compound 1 in the current paper is almost identical to compound 5 in the Takeda paper. Substructure searching and screening led to compound 4, which is identical to compound 7 in the Takeda paper. Whether COMT is really this choosy when it comes to fragment hits, or whether this reflects similarities in fragment libraries remains an open question.

But happily there’s more. The researchers used an iterative structure-guided fragment-growing approach to improve affinity. This ultimately resulted in compound 24, which is competitive with SAM and has mid-nanomolar activity. The solubility could be improved, and no other biological data are presented, but at least this paper demonstrates that it is possible to find potent inhibitors of COMT that are not phenols or catechols.