Defense Date


Document Type


Degree Name

Master of Science


Medicinal Chemistry

First Advisor

Dr. Donald J. Abraham


Erythrocyte pyruvate kinase (R-PK) is a key glycolytic enzyme catalyzing the transphosphorylation of phosphoenolpyruvate (PEP) and ADP to pyruvate and ATP respectively3,4. The substrate PEP and product pyruvate of this reaction are involved in a number of energetic and biosynthetic pathways; hence a tight regulation of R-PK activity is crucial not only for glycolysis, but also for the entire cellular metabolism. Deficiency of R-PK is one of the most common enzymatic defects of RBC, and may be caused by mutations of the PK-LR (pyruvate kinase liver red blood cell) gene31, 32. Clinically, R-PK deficiency manifests itself as a chronic life-long hemolysis ranging from very mild or fully compensated anemia to life-threatening neonatal anemia and pronounced jaundice. Current treatment options are limited to continuous blood transfusions and splenectomy. Thus, there is an urgent need for medications to counter R-PK deficiency without resorting to these complicated procedures. Our aim is to identify novel allosteric modifiers of R-PK using a combination of computational studies and enzyme activity assays. Such compounds could be of medical interest. Human R-PK was expressed in DH-5α cells and was purified by the procedure reported by Wang et al57. However, this method gave a very low yield of R-PIS (5mg/L). In an attempt to increase the yield, we expressed R-PK in Rosetta strain cells. Further, addition of His-tag to the protein's N-terminus simplified purification to a one step Ni-NTA (Nickel- nitrilotriacetic acid) column resulting in a 6-fold increase in the yield. Computational methods were applied to identify small molecules that bind to the allosteric activator fructose 1,6-bisphosphate (FBP) binding site of R-PK to identify compounds that could interact with the protein. The software UNITY, as present in the molecular modeling software Sybyl was used to perform 3D searches against the National Cancer Institute (NCI) chemical database. From these searches we obtained 29 hits that were subjected to further computational analysis. The small molecules were docked into the FBP binding site of R-PK with different docking methods includingFlexX, GOLD and energy minimization. The energy scoring function of HINT was then applied to analyze the interactions between the docked molecules and R-PK. Compounds with highest HINT score were requested fiom NCI and were subjected to further kinetic analysis to identify possible allosteric effectors of R-PK.In the kinetic analysis, we employed a lactate dehydrogenase (LDH) coupled spectrophotometric assay to determine the activity of R-PK in the presence of these compounds. The steady state kinetics of R-PK gave a typical S-shaped curve that fitted a signloidal function indicative of allosterism. All the kinetic parameters of our enzyme were in excellent agreement with native R-PK activity as previously reported5, 57. R-PK activity in the presence of the analyzed compounds revealed both activators and inhibitors of R-PK. X-ray crystallographic analysis of R-PK in the presence of FBP and the identified small molecule effectors are currently in progress. These experiments were initiated to reveal the binding site of the compounds in R-PK, allowing for further optimization of the starting phannacophores and syntheses of new molecular entities for enhanced allosteric activity.In conclusion, we have developed a simple and efficient method for the expression and purification of R-PK. Using computational screening and HINT analysis we have also identified several compounds that interact with R-PK and kinetic analysis revealed both activators and inhibitors of the protein. Crystals of R-PK in the presence of effectors have been obtained and identification of the binding site on R-PK is under investigation. R-PK effectors discovered in this study could prove to be lead compounds for developing medications for the treatment of anemia and other disorders arising from R-PK malfunction.


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Date of Submission

June 2008