The Design of Novel DCB-3503 Analogues: Ligand-Based and Structure-Based Approaches

Author

Yundi Gan, University of Tennessee - KnoxvilleFollow

Date of Award

12-2015

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Chemistry

Major Professor

David C. Baker

Committee Members

John Bartmess, Brian Long, Jerome Baudry

Abstract

This research centers around a tylophorine analogue, DCB-3503, a lead compound that possesses potent growth inhibitory activities against all 60 human-derived cell lines screened by the National Cancer Institute (NCI). In comparison with other known antitumor compounds using the NCI’s COMPARE analysis, it is apparent that the compound is acting through a unique mechanism—one decidedly different from that of other known anticancer drugs. Additionally DCB-3503 has shown inhibitory activities against HepG2 (human hepatocellular cancer, HCC), PANC-1 (human pancreatic ductal carcinoma) and chemotherapeutic-resistant KB cell lines in the hands of our collaborator, Dr. Yung-Chi Cheng of Yale University School of Medicine. In order to predict structure–activity relationships, a Comparative Molecular Field Analysis (CoMFA) model was constructed, and several DCB-3503 analogues with higher projected antitumor activities were designed. These analogues included those with modifications at positions 3 and 7, with CoMFA indicating greatest tolerance at the 3-position. Results from biological studies suggested that a more complicated mechanism with different pathways for different analogues was operative. A biotinylated DCB-3503 analogue that was designed and synthesized previously in Dr. David Baker’s lab was utilized by our Yale collaborators to snare a protein targeted by DCB-3503 type compounds. A cellular heat shock cognate protein 70 (Hsc70) was identified as one of the target proteins of DCB-3503 in an anti-hepatitis C virus (HCV) study. The target protein was then synthesized without and with ¹⁵N [nitrogen-15] labeling in our lab, and the thermodynamic and NMR studies of its interactions with DCB-3503 were carried out. However, failure to elucidate the specific DCB-3503 and Hsc70 interactions by NMR studies prompted us to turn to computational simulations, where two docking models, including the one based on DCB-3503 and the ATP-state Hsc70 nucleotide binding domain (NBD), and another based on DCB-3503 and the apo-state Hsc70 NBD, were constructed. The most reasonable docking pose of DCB-3503 was generated in the ATP-state protein based on the analysis of both the experimental observations and the docking scores. Design of more promising active candidates can likely be realized in the future through the study of the aforementioned docking pose.

Recommended Citation

Gan, Yundi, "The Design of Novel DCB-3503 Analogues: Ligand-Based and Structure-Based Approaches. " PhD diss., University of Tennessee, 2015.
https://trace.tennessee.edu/utk_graddiss/3546