The goal of this project is to provide a collaborative structural hub to promote SBPMDI Cancer Center science, drug discovery, structure-based drug design and inhibitory mechanism. To understand the mechanism of a discovered probe/lead compound and/or to enhance its potency, a co-crystal structure of the probe with a target protein is required. This type of work typically requires troubleshooting and optimization, because compounds obtained by screening often bind with unknown affinity, have solubility issues which complicate co-crystallization and/or bind at unknown allosteric sites. I have already succeeded on six project fronts in collaboration with Principal Investigators at the SBPMDI Cancer Center. Four of these projects have NCI funding (RXR? ligand binding domain, Hif2? PASB domain, PLEKHA7 PH domain, FAS TE domain) and two are part of NCI applications currently under review (TAO3 kinase domain and ALDOA). The RXR? work revealed distinct inhibitory mechanisms between very similar lead compounds. The Hif2? PASB work demonstrated the structural basis of tight inhbition. The PLEKHA7 PH and TAO3 kinase domains are novel crystal structures with bound ligand; in the first case, revealing a structural basis for substrate specificity and in the second case, pointing to a pathway to enhance inhibitor specificity. The ALDOA project has revealed the structural basis of novel allosteric covalent inhibitors, as well as potential S-nitrosylation sites that may determine subcellular localization. All six targets are novel (PLEKHA7, TAO3 and ALDOA), or established (RXR?, Hif2? and FAS TE) cancer targets, and I plan to continue collaborations on their further development from hit-to-lead. I have also added to the list the PH domain of CNK1, a KRas-linked cancer target with unique properties. Based on my varied experiences, I have developed a cost efficient methodology with a high likelihood of success, employing biophysical analysis, NMR, high-throughput crystallization and fine-focus synchrotron radiation. I also encourage and provide training to postdocs, students, staff scientists and technicians, who wish to participate in structural studies. The NCI R50 award will allow me a firm financial basis on which to extend current studies and initiate new collaborations to include investigators with newly discovered targets or probes but who currently lack the funding to support my collaborative work. Understanding structural and mechanistic aspects of new drug candidates is required to move hit compounds toward leads and a clinical testing funnel, and aid Principal Investigators in obtaining funding for their research, thereby expediting the movement of basic science discoveries from bench to bedside.

Public Health Relevance

Atomic resolution structures of novel cancer targets in complex with lead inhibitors provide a powerful platform upon which to build a drug discovery pipeline; however, most Cancer Center Principal Investigators lack the skills necessary to perform this highly technical work. This project seeks to provide a mechanism to shore up this gap and expedite drug discovery in a basic research environment.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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Special Emphasis Panel (ZCA1-SRB-V (A1))
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Knowlton, John R
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Sanford Burnham Prebys Medical Discovery Institute
La Jolla
United States
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Stanford, Stephanie M; Aleshin, Alexander E; Zhang, Vida et al. (2017) Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase. Nat Chem Biol 13:624-632
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