Electronic Theses and Dissertations

Date of Award


Document Type


Degree Name

Ph.D. in Pharmaceutical Sciences


Biomolecular Sciences

First Advisor

Stephen J. Cutler

Second Advisor

Ikhlas A. Khan

Third Advisor

Robert J. Doerksen

Relational Format



Alzheimer's disease (AD) is one of the most dreaded forms of progressive neurodegenerative diseases. The two main hallmarks of AD are the formation of amyloid senile plaques and neurofibrillary tangles. Cyclin dependent kinase 5 (CDK5) is a proline directed serine/threonine kinase, which expressed primarily in the central nervous system. In the biochemical process the CDK5-natural activator, p35 is cleaved by calpain to a shorter protein p25, which in turn hyperphosphorylates Tau, forms neurofibrillary tangles and causes AD. CDK5 deregulation is also indicated in other neurodegenerative diseases, such as Huntington's chorea, stroke, Parkinson's disease, amyotrophic lateral sclerosis, major depression and substance abuse.

We chose to design CDK5/p25 inhibitors as a target against neurodegeneration leading to Alzheimer's disease. One of our major goals was to design CDK5/p25 inhibitors selective over CDK2. Since we were targeting neurodegeneration we wanted to avoid any undesired cell cycle mediated apoptotic effects of CDK2 inhibition. The task was very challenging, because the two kinases possessed very high levels of sequence homology. In our approach we decided to achieve selectivity through structure based virtual screening strategy, validate the hits through biological screening and explore structure activity relationship (SAR) modifications around the lead structure.

To identify de-novo templates, we decided to use the structure based E-pharmacophore models coupled with docking based virtual screening workflow to screen a commercially available database containing 2.84 million compounds. The biological screening was performed using radiometric filter binding assays with full length hCDK5/p25 and hCDK2/E kinases. An ATP non-competitive and selective inhibitor with ligand efficiency of 0.3 was identified as the lead molecule.

We developed an efficient six-step synthesis of a key intermediate starting from aniline utilizing a sequence of Friedel-Crafts, Vilsmeier-Haack, nucleophilic aromatic substitution and cyclization reactions. We also developed an easy derivatization approach utilizing convergent analog synthesis to study SAR around the lead structure.

Further SAR optimization led to the discovery of several low micromolar ATP non-competitive CDK5/p25 inhibitors with much greater CDK2/E selectivity. This new series of compounds can be further evaluated in in-vitro and in-vivo AD models to develop future drug candidates.


Emphasis: Medicinal Chemistry



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