Optimization of Non-ATP Competitive CDK/Cyclin Groove Inhibitors through REPLACE-Mediated Fragment Assembly

Abstract

A major challenge in drug discovery is to develop and improve methods for targeting protein-protein interactions. Further exemplification of the REPLACE strategy for generating inhibitors of protein-protein interactions demonstrated that it can be used to optimize fragment alternatives of key determinants, to combine these in an effective way and was achieved for compounds targeting the CDK2 substrate recruitment site on the cyclin regulatory subunit. Phenylheterocyclic isosteres replacing a critical charge-charge interaction provided new structural insights for binding to the cyclin groove. In particular, these results shed light onto the key contributions of a H-bond observed in crystal structures of N-terminally capped peptides. Furthermore the structure-activity relationship of a bisarylether C-terminal capping group mimicking dipeptide interactions, was probed through ring substitutions, allowing increased complementarity with the primary hydrophobic pocket. This study further validates REPLACE as an effective strategy for converting peptidic compounds to more pharmaceutically relevant compounds.

Cyclin dependent kinase (CDK) inhibitors as anticancer drugs

“…McInnes et al applied the REPLACE-mediated conversion of the known octapeptide cyclin groove inhibitor (HAKRRLIF) into N-and C-terminal di-capped or Nterminal mono-capped peptides to develop non-ATP competitive CDK2/cyclin A inhibitors. 37,38 Some recent examples are exemplified in Figure 3A.…”

Efficient soluble expression of active recombinant human cyclin A2 mediated by E. coli molecular chaperones

“…Non-ATP competitive inhibition through the cyclin groove is required for next generation inhibitors that specifically block the cell cycle CDKs and avoid activities on transcriptional regulating CDKs that contribute to toxicities of clinically evaluated compounds[4–6]. In our previous work, the REPLACE strategy has been validated and used for ligand optimization in designing fragment and non-peptidic alternatives, in the context of the binding peptide [7, 8]. In application to CDK2/cyclin A, fragment alternatives for both the N-terminal tetrapeptide and the C-terminal dipeptide of an optimized p21WAF peptide (HAKKRLIF) have been identified [9].…”

“…More drug-like ligands obtained through REPLACE and their resulting affinity to the CDK2/cyclin A (174–432 fragment) complex have been previously characterized through fluorescence polarization binding and kinase assays, while further verified by co-crystallization of the protein-ligand complexes [9]. Further to this initial N-cap series [8], an additional class of ligand alternatives for the N-terminus was identified. These include 4-substituted benzoic acids and the optimized N-capped peptide: 4-((4-methylpiperazin-1-yl)methyl)benzoic acid ligated to the p21 C-terminus, RLIF (SCCP5921, this study).…”

Targeting the cyclin-binding groove site to inhibit the catalytic activity of CDK2/cyclin A complex using p27KIP1-derived peptidomimetic inhibitors

“…Disrupting the conserved cyclin-binding groove (CBG) of cyclin A is one of the possible ways to specifically inactivate the G1 to S phase transition of CDK2 complex [2]. Designing of peptide-based inhibitors that target the CBG site is a revolutionary approach to block the malignant cellular proliferation [9,26,27].…”