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Title:Mechanism, inhibition and spectroscopy of isoprenoid biosynthesis enzymes
Author(s):Li, Jikun
Director of Research:Oldfield, Eric
Doctoral Committee Chair(s):Oldfield, Eric
Doctoral Committee Member(s):Gruebele, Martin; Rienstra, Chad M.; Imlay, James A.
Department / Program:School of Molecular & Cell Bio
Discipline:Biophysics & Computnl Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Subject(s):isoprenoid biosynthesis
electron paramagnetic resonance (EPR) spectroscopy
drug discovery
Abstract:Isoprenoids (or terpenes) are a large class of compounds with great physiological importance in all kingdoms of life. The research in this work explored the mechanism and inhibition of several enzymes in two important pathways for isoprenoid biosynthesis. The first pair of enzyme are IspG and IspH, which constitute the last two steps in the MEP/DOXP (or non-mevalonate) pathway, which some bacteria, protozoa and plants rely on to produce the basic building blocks of isoprenoids, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). IspG and IspH are both 4Fe-4S cluster-containing proteins with a unique iron whose ligand is not a cysteine residue. Continuous-wave and pulsed electron paramagnetic resonance (EPR) experiments, with the help of isotope-labeled substrates, revealed the electronic structures of reaction intermediates and inhibitors bound to the iron-sulfur clusters. Diverse binding modes of ligands to the clusters were discovered. In addition to IspG and IspH, another 4Fe-4S protein, NadA (in a biosynthetic pathway to NAD) was also mechanistically studied. The second pair of enzymes are FPPS and SQS, the enzymes responsible for the first two steps of the biosynthetic pathway of sterols in animals, bacteria and protozoa. We focused on the inhibition and structure aspects of the FPPS and SQS enzymes of the protozoan pathogen Trypanosoma cruzi. For a series of bisphosphonate inhibitors, structure-activity relationship was explored, as well as their cell-killing capability.
Issue Date:2014-09-16
Rights Information:Copyright 2014 Jikun Li. Figure 1.2 is adapted, with permission, from Eisenreich W, Bacher A, Arigoni D, Rohdich F. Biosynthesis of isoprenoids via the non-mevalonate pathway. Cell Mol Life Sci CMLS. 2004 Jun 1;61(12):1401–26. Copyright 2004, Springer. Figure 1.3 is adapted, with permission, from Gazzaniga F, Stebbins R, Chang SZ, McPeek MA, Brenner C. Microbial NAD Metabolism: Lessons from Comparative Genomics. Microbiol Mol Biol Rev MMBR. 2009 Sep;73(3):529–41. Copyright 2009, American Society for Microbiology. Figure 1.6 is adapted, with permission, from Lin F-Y, Liu Y-L, Li K, Cao R, Zhu W, Axelson J, et al. Head-to-Head Prenyl Tranferases: Anti-Infective Drug Targets. J Med Chem. 2012 May 10;55(9):4367–72. Copyright 2012, American Chemical Society. Chapter 2 is partly adapted, with permission, from the following publications: Wang, W. et al., 2010. Organometallic mechanism of action and inhibition of the 4Fe-4S isoprenoid biosynthesis protein GcpE (IspG). Proceedings of the National Academy of Sciences, 107(25), pp.11189–11193, Copyright 2010, National Academy of Sciences; and Wang, W. et al., 2011. An ENDOR and HYSCORE Investigation of a Reaction Intermediate in IspG (GcpE) Catalysis. Journal of the American Chemical Society, 133(22), pp.8400–8403, Copyright 2011, American Chemical Society. Chapter 3 is is partly adapted, with permission, from the following publications: Wang, W. et al., 2010. Bioorganometallic mechanism of action, and inhibition, of IspH. Proceedings of the National Academy of Sciences, 107(10), pp.4522–4527, Copyright 2010, National Academy of Sciences; and Li, J. et al., 2013. Isoprenoid Biosynthesis: Ferraoxetane or Allyl Anion Mechanism for IspH Catalysis? Angewandte Chemie, 125(25), pp.6650–6653, Copyright 2013 WILEY-VCH Verlag. Chapter 4 is partly adapted, with permission, from the following publications: Wang, W., Li, J., Wang, K., Smirnova, T.I., Oldfield, E., 2011. Pyridine Inhibitor Binding to the 4Fe-4S Protein A. aeolicus IspH (LytB): A HYSCORE Investigation. J. Am. Chem. Soc. 133, 6525–6528. Copyright 2011, American Chemical Society; and Guerra, F., Wang, K., Li, J., Wang, W., Liu, Y.-L., Amin, S., Oldfield, E., 2014. Inhibition of the 4Fe–4S proteins IspG and IspH: an EPR, ENDOR and HYSCORE investigation. Chem. Sci. 5, 1642–1649. Copyright 2014, Royal Society of Chemistry. Chapter 6 is partly adapted, under Creative Commons Attribution 4.0 license, from the following publication: Shang, N. et al., 2014. Squalene Synthase as a Target for Chagas Disease Therapeutics. PLoS Pathog, 10(5), p.e1004114.
Date Available in IDEALS:2014-09-16
Date Deposited:2014-08

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