Structural and Biochemical Studies of Enzymes in Bacterial Glycobiology

The speed that bacterial pathogens gain resistance to antibiotics is alarming. Designing new antibacterial agents is urgent, but it requires understanding their bacterial targets at the molecular level to achieve high specificity and potency. In this thesis, I discuss the structural and biochemical investigations of three potential protein targets for antibiotics. The first is a UDP-Glc/GlcNAc 4-epimerase, called Gne, from the human pathogen Campylobacter jejuni. This enzyme is the sole source of N-acetylgalactosamine (GalNAc) in C. jejuni, which is a common component in three major glycoconjugates decorating the cell surface and is critical for pathogenesis. The second target protein is an integral membrane protein, called MraY, which catalyzes the transfer of phospho-N-acetylmuramyl (MurNAc) pentapeptide to a lipid carrier, undecaprenyl phosphate (C55-P), producing Lipid I in the peptidoglycan biosynthesis pathway. In the following step, a peripheral protein called MurG catalyzes transferring N-acetylglucosamine (GlcNAc) to Lipid I and produces Lipid II, which provides the first building block of the peptidoglycan layer. Peptidoglycan is uniquely bacterial, with MraY and MurG both being essential for cell viability; therefore, they are attractive targets for the development of antibacterial agents and work toward their structures is presented. Finally, MraY from Escherichia coli is the target for the lysis protein E from phage ΦX174.Efforts toward elucidating the EcMraY-E complexstructure are demonstrated here. In total, this thesis provides important data toward a full mechanistic understanding of these important antibacterial targets

The structure of the UDP-Glc/GlcNAc 4-epimerase from the human pathogen Campylobacter jejuni

Worldwide, the food-born pathogen Campylobacter jejuni is the leading bacterial source of human gastroenteritis. C. jejuni produces a variety of diverse cell-surface carbohydrates that are essential for pathogenicity. A critical component of these oligo- and polysaccharides is the sugar N-acetylgalactosamine (GalNAc). The sole source of this sugar is the epimerization of UDP-N-acetylglucosamine (GlcNAc), a reaction catalyzed by the enzyme UDP-GlcNAc 4-epimerase (Gne). This enzyme is unique among known bacterial epimerases in that it also catalyzes the equivalent reaction with the non-N-acetylated sugars. Understanding how CjGne catalyzes these various interconversions is critical to designing novel inhibitors of this enzyme. Here, to further the mechanistic understanding we present a 2.0Å structure of CjGne with its NAD⁺ co-factor bound. Based on novel features found in the structure we perform a variety of biochemical studies to probe the mechanism and compare these results to another bifunctional epimerase, human GalE. We further show that ebselen, previously identified for inhibition of HsGalE, is active against CjGne, suggesting a route for antibiotic development

A practical synthesis of a novel DPAGT1 inhibitor, aminouridyl phenoxypiperidinbenzyl butanamide (APPB) for in vivo studies

Immunotherapy that targets N-linked glycans has not yet been developed due in large part to the lack of specificity of N-linked glycans between normal and malignant cells. N-Glycan chains are synthesized by the sequential action of glycosyl transferases in the Golgi apparatus. It is an overwhelming task to discover drug-like inhibitors of glycosyl transferases that block the synthesis of specific branching processes in cancer cells, killing tumor cells selectively. It has long been known that N-glycan biosynthesis can be inhibited by disruption of the first committed enzyme, dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 (DPAGT1). Selective DPAGT1 inhibitors have the promising therapeutic potential for certain solid cancers that require increased branching of N-linked glycans in their growth progressions. Recently, we discovered that an anti-Clostridium difficile molecule, aminouridyl phenoxypiperidinbenzyl butanamide (APPB) showed DPAGT1 inhibitory activity with the IC_(50) value of 0.25 μM. It was confirmed that APPB inhibits N-glycosylation of β-catenin at 2.5 nM concentration. A sharp difference between APPB and tunicamycin was that the hemolytic activity of APPB is significantly attenuated (IC_(50) > 200 μM RBC). Water solubility of APPB is >350-times greater than that of tunicamycin (78.8 mg/mL for APPB, 60 min) for in vivo studies (PK/PD, safety profiles, and in vivo efficacy) using animal models. We have refined all steps in the previously reported synthesis for APPB for larger-scale. This article summarizes protocols of gram-scale synthesis of APPB and its physicochemical data, and a convenient DPAGT1 assay

Micro-Segregated Liquid Crystal Haze Films for Photovoltaic Applications: A Novel Strategy to Fabricate Haze Films Employing Liquid Crystal Technology

Herein, a novel strategy to fabricate haze films employing liquid crystal (LC) technology for photovoltaic (PV) applications is reported. We fabricated a high optical haze film composed of low-molecular LCs and polymer and applied the film to improve the energy conversion efficiency of PV module. The technique utilized to fabricate our haze film is based on spontaneous polymerization-induced phase separation between LCs and polymers. With optimized fabrication conditions, the haze film exhibited an optical haze value over 95% at 550 nm. By simply attaching our haze film onto the front surface of a silicon-based PV module, an overall average enhancement of 2.8% in power conversion efficiency was achieved in comparison with a PV module without our haze film

Substrate Tolerance of Bacterial Glycosyltransferase MurG: Novel Fluorescence-based Assays

MurG (uridine diphosphate-N-acetylglucosamine/N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase) is an essential bacterial glycosyltransferase that catalyzes the N-acetylglucosamine (GlcNAc) transformation of lipid I to lipid II during peptidoglycan biosynthesis. Park’s nucleotide has been a convenient biochemical tool to study the function of MraY (phospho-MurNAc-(pentapeptide) translocase) and MurG; however, no fluorescent probe has been developed to differentiate individual processes in the biotransformation of Park’s nucleotide to lipid II via lipid I. Herein, we report a robust assay of MurG using either the membrane fraction of a M. smegmatis strain or a thermostable MraY and MurG of Hydrogenivirga sp. as enzyme sources, along with Park’s nucleotide or Park’s nucleotide-Nε-C6-dansylthiourea and uridine diphosphate (UDP)-GlcN-C6-FITC as acceptor and donor substrates. Identification of both the MraY and MurG products can be performed simultaneously by HPLC in dual UV mode. Conveniently, the generated lipid II fluorescent analogue can also be quantitated via UV–Vis spectrometry without the separation of the unreacted lipid I derivative. The microplate-based assay reported here is amenable to high-throughput MurG screening. A preliminary screening of a collection of small molecules has demonstrated the robustness of the assays and resulted in rediscovery of ristocetin A as a strong antimycobacterial MurG and MraY inhibitor

Novel FR-900493 Analogues That Inhibit the Outgrowth of Clostridium difficile Spores

The spectrum of antibacterial activity for the nucleoside antibiotic FR-900493 (1) can be extended by chemical modifications. We have generated a small focused library based on the structure of 1 and identified UT-17415 (9), UT-17455 (10), UT-17460 (11), and UT-17465 (12), which exhibit anti-Clostridium difficile growth inhibitory activity. These analogues also inhibit the outgrowth of C. difficile spores at 2× minimum inhibitory concentration. One of these analogues, 11, relative to 1 exhibits over 180-fold and 15-fold greater activity against the enzymes, phospho-MurNAc-pentapeptide translocase (MraY) and polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA), respectively. The phosphotransferase inhibitor 11 displays antimicrobial activity against several tested bacteria including Bacillus subtilis, Clostridium spp., and Mycobacterium smegmatis, but no growth inhibitory activity is observed against the other Gram-positive and Gram-negative bacteria. The selectivity index (Vero cell cytotoxicity/C. difficileantimicrobial activity) of 11 is approximately 17, and 11 does not induce hemolysis even at a 100 μM concentration

A practical synthesis of a novel DPAGT1 inhibitor, aminouridyl phenoxypiperidinbenzyl butanamide (APPB) for in vivo studies

Immunotherapy that targets N-linked glycans has not yet been developed due in large part to the lack of specificity of N-linked glycans between normal and malignant cells. N-Glycan chains are synthesized by the sequential action of glycosyl transferases in the Golgi apparatus. It is an overwhelming task to discover drug-like inhibitors of glycosyl transferases that block the synthesis of specific branching processes in cancer cells, killing tumor cells selectively. It has long been known that N-glycan biosynthesis can be inhibited by disruption of the first committed enzyme, dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 (DPAGT1). Selective DPAGT1 inhibitors have the promising therapeutic potential for certain solid cancers that require increased branching of N-linked glycans in their growth progressions. Recently, we discovered that an anti-Clostridium difficile molecule, aminouridyl phenoxypiperidinbenzyl butanamide (APPB) showed DPAGT1 inhibitory activity with the IC_(50) value of 0.25 μM. It was confirmed that APPB inhibits N-glycosylation of β-catenin at 2.5 nM concentration. A sharp difference between APPB and tunicamycin was that the hemolytic activity of APPB is significantly attenuated (IC_(50) > 200 μM RBC). Water solubility of APPB is >350-times greater than that of tunicamycin (78.8 mg/mL for APPB, 60 min) for in vivo studies (PK/PD, safety profiles, and in vivo efficacy) using animal models. We have refined all steps in the previously reported synthesis for APPB for larger-scale. This article summarizes protocols of gram-scale synthesis of APPB and its physicochemical data, and a convenient DPAGT1 assay

Pulmonary nodular ground-glass opacities in patients with extrapulmonary cancers: what is their clinical significance and how can we determine whether they are malignant or benign lesions?

BACKGROUND: The clinical significance of pulmonary nodular ground-glass opacities (NGGOs) in patients with extrapulmonary cancers is not known, although there is an urgent need for study on this topic. The purpose of this study, therefore, was to investigate the clinical significance of pulmonary NGGOs in these patients, and to develop a computerized scheme to distinguish malignant from benign NGGOs. METHODS: Fifty-nine pathologically proven pulmonary NGGOs in 34 patients with a history of extrapulmonary cancer were studied. We reviewed the CT scan characteristics of NGGOs and the clinical features of these patients. Artificial neural networks (ANNs) were constructed and tested as a classifier distinguishing malignant from benign NGGOs. The performance of ANNs was evaluated with receiver operating characteristic analysis. RESULTS: Twenty-eight patients (82.4%) were determined to have malignancies. Forty NGGOs (67.8%) were diagnosed as malignancies (adenocarcinomas, 24; bronchioloalveolar carcinomas, 16). Among the rest of the NGGOs, 14 were atypical adenomatous hyperplasias, 4 were focal fibrosis, and 1 was an inflammatory nodule. There were no cases of metastasis appearing as NGGOs. Between malignant and benign NGGOs, there were significant differences in lesion size; the presence of internal solid portion; the size and proportion of the internal solid portion; the lesion margin; and the presence of bubble lucency, air bronchogram, or pleural retraction (p < 0.05). Using these characteristics, ANNs showed excellent accuracy (z value, 0.973) in discriminating malignant from benign NGGOs. CONCLUSIONS: Pulmonary NGGOs in patients with extrapulmonary cancers tend to have high malignancy rates and are very often primary lung cancers. ANNs might be a useful tool in distinguishing malignant from benign NGGOs

Tetraarsenic Hexoxide Induces Beclin-1-Induced Autophagic Cell Death as well as Caspase-Dependent Apoptosis in U937 Human Leukemic Cells

Tetraarsenic hexaoxide (As4O6) has been used in Korean folk remedy for the treatment of cancer since the late 1980s, and arsenic trioxide (As2O3) is currently used as a chemotherapeutic agent. However, evidence suggests that As4O6-induced cell death pathway was different from that of As2O3. Besides, the anticancer effects and mechanisms of As4O6 are not fully understood. Therefore, we investigated the anticancer activities of As4O6 on apoptosis and autophagy in U937 human leukemic cells. The growth of U937 cells was inhibited by As4O6 treatment in a dose- and a time-dependent manner, and IC50 for As4O6 was less than 2 μM. As4O6 induced caspase-dependent apoptosis and Beclin-1-induced autophagy, both of which were significantly attenuated by Bcl-2 augmentation and N-acetylcysteine (NAC) treatment. This study suggests that As4O6 should induce Beclin-1-induced autophagic cell death as well as caspase-dependent apoptosis and that it might be a promising agent for the treatment of leukemia