Addressing the Glycine‐Rich Loop of Protein Kinases by a Multi‐Facetted Interaction Network: Inhibition of PKA and a PKB Mimic

Abstract

Protein kinases continue to be hot targets in drug discovery research, as they are involved in many essential cellular processes and their deregulation can lead to a variety of diseases. A series of 32 enantiomerically pure inhibitors was synthesized and tested towards protein kinase A (PKA) and protein kinase B mimic PKAB3 (PKA triple mutant). The ligands bind to the hinge region, ribose pocket, and glycine-rich loop at the ATP site. Biological assays showed high potency against PKA, with Ki values in the low nanomolar range. The investigation demonstrates the significance of targeting the often neglected glycine-rich loop for gaining high binding potency. X-ray co-crystal structures revealed a multi-facetted network of ligand-loop interactions for the tightest binders, involving orthogonal dipolar contacts, sulfur and other dispersive contacts, amide-π stacking, and H-bonding to organofluorine, besides efficient water replacement. The network was analyzed in a computational approach.

Stacking Interactions of Heterocyclic Drug Fragments with Protein Amide Backbones

“…Optimizing amide stacking has also been used to improve inhibition of an umber of targets, includingt he aspartic protease endothiapepsin, [14] protein kinase A( PKA), [15] and the cysteine proteasea utophagin-1. [16] Most recently,D iederich et al [17] tried to design an inhibitor for the cysteine protease cathepsin Lb ym aximizing amide stackingi nteractions.…”

“…Optimizing amide stacking has also been used to improve inhibition of a number of targets, including the aspartic protease endothiapepsin, protein kinase A (PKA), and the cysteine protease autophagin‐1 . Most recently, Diederich et al .…”

The Route to ‘Chemobrain’ - Computational probing of neuronal LTP pathway

“…The off-target interactions have been shown to be involving the residues Gly 50, Thr 51, Gly 52, Ser 53, which are part of the Glycine rich loop (spanning from residue 50–55), an integral part of ATP binding site, and the residue Glu 170, part of ribose pocket, which carries the phosphate binding cassette 145 . Interestingly, the Glycine rich loop is one of the targeted sites for the development of PKA inhibitors 77 . Moreover, off-target interactions have also been observed in the activation loop hooking residues Phe 187, Thr 201, Pro 202 and Glu 203.…”

“…In case of PKA, the inhibitor 4L7 had been bound to glycine rich loop and β2–3 loop (ribose pocket). The 5 Å area around the residues involved in interactions with 4L7 was used as active site for docking studies 77 . In ERK2, the co-crystallize ligand had been 82 A that bound to protein kinase and glycine rich loop.…”

Inhibitor binding to mutants of protein kinase A with GGGxxG and GxGxxA glycine‐rich loop motifs

“…The binding of staurosporine to PKA was seen to displace a residue characteristic of the AGC group of kinases 20 The inhibitor H89, one of a series of Rho kinase inhibitors, was seen to possess hydrophobic interactions between its bromine moiety and the glycine‐rich loop, with both exhibiting flexibility 21,22 . Of great interest for this manuscript are a set of quinazoline‐based compounds (Figure 2) designed specifically to optimize interactions by varying substituents and geometries of interactions with the glycine‐rich loop, 23 keeping the hinge anchoring quinazoline group unchanged.…”