Poster abstracts

Poster number 37 submitted by Stephanie Kim

Identification of novel cyclin A2 binding site and nanomolar inhibitors of cyclin A2-CDK2 complex

Stephanie S. Kim (Biophysics), Michele Joana Alves (Department of Pathology, Ohio State University), Patrick Gygli (Department of Pathology, Ohio State University), Jose Javier Otero (Department of Pathology, Ohio State University), Steffen Lindert (Department of Chemistry and Biochemistry, Ohio State University)

Abstract:
Cyclin A2 is the main mammalian S-phase cyclin and has been shown to have diverse roles in cell cycle regulation and DNA damage response. Thus, identifying small molecule regulators of cyclin A2 activity carries significant potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer. No functional modulators of cyclin A2 are known to date. Here, we identified a potential allosteric cyclin A2 ligand binding pocket based on high-resolution structural data. Molecular dynamics simulations were used to generate diverse binding pocket conformations for application of the relaxed complex scheme (1-3). We then used structure-based virtual screening to find potential dual cyclin A2 and CDK2 inhibitors. Based on a consensus score of docked poses from Glide and AutoDock Vina, we identified about 40 promising hit compounds, where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay of cyclin A2-CDK2 function was used for experimental verification and we identified two nanomolar and two micromolar inhibitors that were predicted to target both cyclin A2 and CDK2. The four cyclin A2-CDK2 complex inhibitors are the first reported inhibitors that were specifically designed not to target the cyclin A2-CDK2 protein-protein interface.

References:
1. Amaro, R. E., R. Baron, and J. A. McCammon. 2008. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des 22(9):693-705.
2. Lin, J. H., A. L. Perryman, J. R. Schames, and J. A. McCammon. 2003. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68(1):47-62.
3. Lin, J.-H., A. L. Perryman, J. R. Schames, and J. A. McCammon. 2002. Computational Drug Design Accommodating Receptor Flexibility:  The Relaxed Complex Scheme. Journal of the American Chemical Society 124(20):5632-5633.

Keywords: computational drug discovery, structure-based drug discovery, polypharmacology