Backbone Cyclic Peptide Inhibitors of Protein Kinase B (PKB/Akt)

Abstract

Elevated levels of activated protein kinase B (PKB/Akt) have been detected in many types of cancer. Substrate-based peptide inhibitors have the advantage of selectivity due to their extensive interactions with the kinase-specific substrate binding site but often lack necessary pharmacological properties. Chemical modifications of potent peptide inhibitors, such as cyclization, may overcome these drawbacks while maintaining potency. We present an extensive structure-activity relationship (SAR) study of a potent peptide-based PKB/Akt inhibitor. Two backbone cyclic (BC) peptide libraries with varying modes of cyclization, bridge chemistry, and ring size were synthesized and evaluated for in vitro PKB/Akt inhibition. Backbone-to-backbone urea BC peptides were more potent than N-terminus-to-backbone amide BC peptides. Several analogues were up to 10-fold more active than the parent linear peptide. Some activity trends could be rationalized using computational surface mapping of the PKB/Akt kinase catalytic domain. The novel molecules have enhanced pharmacological properties which make them promising lead candidates.

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

“…Thus it is particularly useful in the design of kinase peptide inhibitors, as opposed to the design of optimal kinase substrates. Indeed, ANCHORSmap results were recently used to rationalize the structure-activity relations of a peptidomimetic library of novel PKB kinase inhibitors [76].…”

“…Computational mapping of amino acid-anchoring spots on kinase surfaces can provide testable hypotheses regarding kinase specificity and peptidomimetics affinity [77] and may be used as input for anchor-driven peptide-docking [14] to predict 3D structures of kinase-peptide complexes. It is therefore expected to promote our understanding of kinase regulation and expand the possibilities for the design of kinase-specific signaling modulators.…”

Development of a Peptidase-Resistant Substrate for Single-Cell Measurement of Protein Kinase B Activation

“…Peptide cyclization yields degradation-resistant peptides, but this often results in poor substrate recognition by the kinase and these constructs can be synthetically challenging. 22, 23 Modifications to the C- and N-terminus are relatively simple to accomplish and provide protection against amino- and carboxy-peptidases, but not endopeptidases. 24 Terminal modifications can be used in combination with non-native residues, including N-methylated and D-amino acids, to impart additional stability to peptide bonds.…”

Targeting kinase signaling pathways with constrained peptide scaffolds

“…This synthetic modification improved in vitro potency with an IC 50 value in the high nanomolar range (640 nM) and also improved proteolytic stability as compared to the non-modified parent sequence. GSK3β peptides were also designed as macrocyclic Akt substrates via urea backbone cyclization or head-to-tail amide backbone cyclization, of which several cyclized peptides were found to have increased in vitro inhibitory activity against Akt as compared to their linear counterparts (Tal-Gan, et al, 2011). Since Akt has over 100 known substrates (Mundi, et al, 2016), these strategies outlined above may provide additional opportunities to design alternative constrained pseudosubstrate targeting sequences for Akt inhibition.…”