posted on 2018-08-17, 00:00authored byErnest Awoonor-Williams, Christopher N. Rowley
Targeted covalent inhibitors (TCIs)
have been successfully developed as high-affinity and selective inhibitors
of enzymes of the protein kinase family. These drugs typically act
by undergoing an electrophilic addition with an active-site cysteine
residue, so design of a TCI begins with the identification of a “druggable”
cysteine. These electrophilic additions generally require deprotonation
of the thiol to form a reactive anionic thiolate, so the acidity of
the residue is a critical factor. Few experimental measurements of
the pKa’s of druggable cysteines
have been reported, so computational prediction could prove to be
very important in selecting reactive cysteine targets. Here we report
the computed pKa’s of druggable
cysteines in selected protein kinases that are of clinical relevance
for targeted therapies. The pKa’s
of the cysteines were calculated using advanced computational methods
based on all-atom replica-exchange thermodynamic integration molecular
dynamics simulations in explicit solvent. We found that the acidities
of druggable cysteines within protein kinases are diverse and elevated,
indicating enormous differences in their reactivity. Constant-pH molecular
dynamics simulations were also performed on selected protein kinases,
and the results confirmed this varied range in the acidities of druggable
cysteines. Many of these active-site cysteines have low exposure to
solvent molecules, elevating their pKa values. Electrostatic interactions with nearby anionic residues
also elevate the pKa’s of cysteine
residues in the active site. The results suggest that some cysteine
residues within kinase binding sites will be slow to react with a
TCI because of their low acidity. Several oncogenic kinase mutations
were also modeled and found to have pKa’s similar to that of the wild-type kinase.