Date of Award


Document Type

Open Access Dissertation


College of Pharmacy

First Advisor

Campbell McInnes


Inhibition of CDK2 activity in G1 and S phases of the cell cycle can promote selective apoptosis of cancer cells through the E2F1 pathway. Currently available CDK inhibitors target the ATP binding pocket and result in lack of specificity for the cell cycle vs. the transcriptional CDKs. It has been shown that a peptide HAKRRLIF derived from the tumor suppressor p21 binds to the cyclin binding groove (CBG) and selectively inhibits cell cycle CDKs (CDK2/Cyclin A, CDK2/Cyclin E and CDK4/Cyclin D). The CBG is unique to cell cycle CDKs hence targeting this site avoids the inhibition of transcriptional CDKs can potentially lead to toxicity. The goal of this project is to iteratively convert potent cyclin groove inhibitory (CGI) peptides into more drug like molecules called FLIPs (Fragment ligated inhibitory peptides) using the REPLACE strategy (Replacement with Partial Ligand Alternatives through Computational Enrichment). FLIPs were constructed by sequentially replacing key peptide binding determinants for RRLIF with fragment like small molecules in order to obtain a non-ATP competitive inhibitor of cell cycle CDKs with improved drug like properties. Fragment alternative capping groups were evaluated by docking, synthesis and testing of FLIPs in competitive binding and cellular viability assays. Partial Ligand Alternatives were identified which interacted with the main subsites of the N-terminal tetrapeptide of HAKRRLIF and were derivatives of phenyl heterocyclic carboxylic acids, furoic, picolinic and benzoic acids. The most effective Ncap was found to be 1-(3,5- dichlorophenyl)-5-methyl-1H-1,2,4-triazole-3-carboxylic acid (35DCPT) ligated to RLIF. In a further iteration of REPLACE, the C-terminal motif was modified with β-homoleucine (βLeu) and N-Methyl Phe or 3-Thienylalanine in order to improve metabolic stability. The lead compound after Ncap and Ccap optimization was found to be 35DCPT-R{βLeu}{3TA}-NH2 (SCCP5964) which has respectable antiproliferative activity and is also capable of inducing a G1 cell cycle arrest. The REPLACE strategy has therefore been further validated in the development of FLIPs molecules as non-ATP competitive CDK inhibitors. These cyclin groove inhibitors represent next generation CDK therapeutics having anti-tumor activity consistent with on target inhibition and demonstrated potential for drug development.


© 2014, Padmavathy Nandha Premnath