Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects

Abstract

While it is currently estimated that 40–50% of eukaryotic proteins are phosphorylated, little is known about the frequency and local effects of phosphorylation near pharmaceutical inhibitor binding sites. In this study, we investigated how frequently phosphorylation may affect the binding of drug inhibitors to target proteins. We examined the 453 non-redundant structures of soluble mammalian drug target proteins bound to inhibitors currently available in the Protein Data Bank (PDB). We cross-referenced these structures with phosphorylation data available from the PhosphoSitePlus database. 322/453 (71%) of drug targets have evidence of phosphorylation that has been validated by multiple methods or labs. For 132/453 (29%) of those, the phosphorylation site is within 12Å of the small molecule-binding site, where it would likely alter small molecule binding affinity. We propose a framework for distinguishing between drug-phosphorylation site interactions that are likely to alter the efficacy of drugs vs. those that are not. In addition we highlight examples of well-established drug targets, such as estrogen receptor alpha, for which phosphorylation may affect drug affinity and clinical efficacy. Our data suggest that phosphorylation may affect drug binding and efficacy for a significant fraction of drug target proteins.

Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity

“…The major inclusion criteria for further characterization of individual residues were their predictive score and location in the structure. Thus, Ser 28 and Ser 36 had the highest probability scores of 0.810 and 0.987, respectively, whereas serine residues at positions 23, 57, 100, and 111 exhibited very low probability scores ranging from 0.002 to 0.159. Because Ser 23 , Ser 28 , Ser 57 , Tyr 97 , and Ser 111 are located within the membrane lipid bilayer (Fig.…”

“…Thus, Ser 28 and Ser 36 had the highest probability scores of 0.810 and 0.987, respectively, whereas serine residues at positions 23, 57, 100, and 111 exhibited very low probability scores ranging from 0.002 to 0.159. Because Ser 23 , Ser 28 , Ser 57 , Tyr 97 , and Ser 111 are located within the membrane lipid bilayer (Fig. 1, B and C) with poor accessibility for kinases, we reasoned that the probability that these residues will be phosphorylated is very low.…”

“…Phosphomimetic Mutant S36E Is Less Sensitive to a Synthetic Inhibitor-A recent study suggests that protein phosphorylation may affect drug inhibitor binding to target proteins (28). They classified two types of mechanisms by which phosphorylation affects drug efficacy.…”

“…They classified two types of mechanisms by which phosphorylation affects drug efficacy. In one type, phosphorylation inhibits both drug binding and target activity, whereas in the other type, phosphorylation inhibits drug binding while increasing target activity (28). Here, we used the phosphomimetic mutant S36E to test the effect of phosphorylation on inhibitor binding to LTC4S.…”

In silico prediction and characterization of protein post-translational modifications

“…Once validated against a set of small molecule interactions from the PDB, 60% of the interactions predicted this way matched the experimental ligand. A specialized survey has been devoted to the effects of PTM on soluble mammalian drug target proteins [86]. Evidence from PDB entries shows that in approximately 30% of these proteins phosphorylation may occur within 12 Å of the drug binding sites.…”