Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors

Many
protein kinases are valid drug targets in oncology because
they are key components of signal transduction pathways. The number
of clinical kinase inhibitors is on the rise, but these molecules
often exhibit polypharmacology, potentially eliciting desired and
toxic effects. Therefore, a comprehensive assessment of a compound’s
target space is desirable for a better understanding of its biological
effects. The enzyme ferrochelatase (FECH) catalyzes the conversion
of protoporphyrin IX into heme and was recently found to be an off-target
of the BRAF inhibitor Vemurafenib, likely explaining the phototoxicity
associated with this drug in melanoma patients. This raises the question
of whether FECH binding is a more general feature of kinase inhibitors.
To address this, we applied a chemical proteomics approach using kinobeads
to evaluate 226 clinical kinase inhibitors for their ability to bind
FECH. Surprisingly, low or submicromolar FECH binding was detected
for 29 of all compounds tested and isothermal dose response measurements
confirmed target engagement in cells. We also show that Vemurafenib,
Linsitinib, Neratinib, and MK-2461 reduce heme levels in K562 cells,
verifying that drug binding leads to a loss of FECH activity. Further
biochemical and docking experiments identified the protoporphyrin
pocket in FECH as one major drug binding site. Since the genetic loss
of FECH activity leads to photosensitivity in humans, our data strongly
suggest that FECH inhibition by kinase inhibitors is the molecular
mechanism triggering photosensitivity in patients. We therefore suggest
that a FECH assay should generally be part of the preclinical molecular
toxicology package for the development of kinase inhibitors.