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Title:Targeting isoprenoid biosynthesis for drug discovery
Author(s):Zhu, Wei
Director of Research:Oldfield, Eric
Doctoral Committee Chair(s):Oldfield, Eric
Doctoral Committee Member(s):Gennis, Robert B.; Nair, Satish K.; Mitchell, Douglas A.
Department / Program:School of Molecular & Cell Bio
Discipline:Biophysics & Computnl Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):drug discovery
in silico high-throughput screening
peptidoglycan
protein structure
undecaprenyl diphosphate synthase (UPPS)
farnesyl diphosphate synthase (FPPS)
Deoxyribonucleic acid (DNA)
Abstract:Cancer and infectious diseases are huge threats to human beings. With the rapid rise in drug resistance, there is a need for new drugs, and isoprenoid biosynthesis is an attractive target for drug discovery. In chapter 1, I briefly introduce the isoprenoid biosynthesis pathway and two important drug targets: a trans-prenyl transferase farnesyl diphosphate synthase (FPPS), and a cis-prenyl transferase undecaprenyl diphosphate synthase (UPPS). In chapter 2, I report the discovery and x-ray crystallographic structures of 10 structurally diverse compounds (benzoic/diketo/phosphonic acids, bisamidine, and bisamine) that inhibit UPPS, an essential enzyme involved in cell wall biosynthesis. The inhibitors bind to one or more of the four inhibitor-binding sites with the most active leads binding to site-4, not the substrate-binding sites. The most potent leads are active against Staphylococcus aureus and one potently synergizes with methicillin. These results provide numerous new leads for anti-bacterial development and open up the possibility of multi-site targeting of cell wall biosynthesis, as well as of restoring sensitivity to drugs such as methicillin and vancomycin, using combination therapies. In chapter 3, I report the mechanisms of action and inhibition of antibacterial leads, keto and diketo acids, targeting dehydrosqualene synthase (CrtM) in addition to UPPS. The x-ray structures of CrtM and UPPS with inhibitors bound are also reported. In all cases, the inhibitors bind to a farnesyl diphosphate substrate-binding site. Some of the compounds have potent activity against a variety of bacteria but very little activity against human cell lines. In chapter 4, I report the additional targets of bisamidine inhibitors, besides UPPS. The enzyme inhibition results show that bisamidines also inhibit FPPS. In addition, the differential scanning calorimetry (DSC) results show that these compounds bind to DNA, shifting the melting temperature (Tm) by more than 10 degrees. And a crystallographic investigation reveals that the inhibitor binds to the central AATT site located in the minor groove of the DNA dodecamer d(CGCGAATTCGCG)2 duplex. These results provide new leads for antibacterial development based on a poly-pharmaceutical approach targeting DNA and isoprenoid biosynthesis. In chapter 5, I report the possibility of bisphosphonates as chemo-immunotherapeutic anti-malarials, acting by killing malaria parasites directly via FPPS/GGPPS enzyme inhibition, as well as activation of human γδ T cells to kill extracellular parasites in an indirect manner. In chapter 6, I report the synthesis and characterization of novel Mo, W or V-containing polyoxometalate (POM) bisphosphonate complexes with metal nuclearities ranging from 1 to 6 and their potent activities against human cell lines, opening up the possibility of the development of novel drug leads based on polyoxometalate-bisphosphonate clusters.
Issue Date:2013-08-22
URI:http://hdl.handle.net/2142/45658
Rights Information:Copyright 2013 Wei Zhu
Date Available in IDEALS:2013-08-22
2015-08-22
Date Deposited:2013-08


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