Doctor of Philosophy (PhD)


Biological Sciences

Document Type



The PFKFB enzymes control the primary checkpoint in the glycolytic pathway and are implicated in a multitude of diseases: from cancer, to schizophrenia, to diabetes, and heart disease. The inducible isoform, PFKFB3, is known to be associated with the upregulation of glycolysis in many cancers. The first study within this work investigates the potential for using tier-based approaches of virtual screening to target small molecule kinases, with PFKFB3 serving as a case study. For this investigation, bioactive compounds for PFKFB3 were identified from a compound library of 1364 compounds via high-throughput screening, with bioactive compounds being further characterized as either competitive or non-competitive for F6P. Using the F6P-competitive compounds, several structure based docking programs were assessed individually and in conjunction with a pharmacophore screening. The results showed that the tiered virtual screening approach, using pharmacophore screening in addition to structure-based docking, improved enrichments rates in 80% of cases, reduced CPU costs up to 7-fold, and lessened variability among different structure-based docking methods. The second study investigates the structural and kinetic characteristics of citrate inhibition on the heart PFKFB isoenzyme, PFKFB2. High levels of citrate, an intermediate of the TCA cycle, signify an abundance of biosynthetic precursors and that additional glucose need not be degraded for this purpose. Previous studies have noted that citrate acts as an important negative feed-back mechanism to limit glycolytic activity by inhibiting PFKFB enzymes, yet the structural and mechanistic details of citrate’s inhibition had not been determined. To study the molecular basis for citrate inhibition, the three-dimensional structures of the human and bovine PFKFB2 orthologues were solved, each in complex with citrate. For both cases, citrate primarily occupied the binding site of Fructose-6-phosphate (F6P), competitively blocking F6P from binding. Additionally, a carboxy arm of citrate extended into the γ-phosphate binding site of ATP, sterically and electrostatically blocking the catalytic binding mode for ATP. In the human orthologue, which utilized AMPPNP as an ATP analogue, conformational changes were observed in the 2-kinase domain as well as the binding mode for AMPPNP. This study gives new insights as to how the citrate-mediate negative feedback loop influences glycolytic flux through PFKFB enzymes.



Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Lee, Yong-Hwan