@phdthesis{Kurzai2001,
  author    = {Kurzai, Oliver},
  title     = {Molekulare Charakterisierung pH-regulierter Gene bei der humanpathogenen Hefespezies Candida dubliniensis und ihr Nutzen f{\"u}r die epidemiologische Diagnostik},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-1182281},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2001},
  abstract  = {Candida dubliniensis ist eine 1995 erstmals beschriebene pathogene Hefespezies mit enger phylogenetischer Verwandtschaft zu Candida albicans. Sie wird mittels routinem{\"a}ßig angewendeter Verfahren nicht von C. albicans unterschieden, weil sie als einzige Spezies im Genus Candida neben C. albicans Chlamydosporen ausbilden kann. C. dubliniensis ist bisher vor allem aus dem Oropharynx HIV-positiver Patienten isoliert worden. PHR1 und PHR2 sind funktionell homologe, pH-abh{\"a}ngig exprimierte Gene von C. albicans, deren Produkte essentiell f{\"u}r die Verkn{\"u}pfung von b-1,3- und b-1,6-Glukan in der Zellwand sind. Die Deletion jedes dieser Gene f{\"u}hrt zu einem pH-abh{\"a}ngigen Ph{\"a}notyp mit aberranter Morphogenese in vitro und reduzierter Virulenz im Tiermodell. In dieser Arbeit werden PHR homologe Gene im Genom von C. dubliniensis charakterisiert. CdPHR1 weist eine Homologie von 90,5 Prozent zu PHR1 und CdPHR2 eine Homologie von 91,7 Prozent zu PHR2 auf. Wie PHR1 wird auch CdPHR1 nur unter neutralen und alkalischen Bedingungen exprimiert, w{\"a}hrend sich CdPHR2 Transkript, wie das von PHR2, nur unter sauren Bedingungen nachweisen l{\"a}sst. Die funktionelle Homologie von CdPHR1 zu PHR1 wird durch Komplementation des Ph{\"a}notyps einer C. albicans phr1 Mutante mit CdPHR1 gezeigt. Dabei erweist sich der native Promoter von CdPHR1 als funktional in C. albicans. Im Modellorganismus Saccharomyces cerevisiae wird CdPHR1 unter Kontrolle seines nativen Promotors dagegen pH-unabh{\"a}ngig exprimiert. Auch die zus{\"a}tzliche Einf{\"u}hrung eines mutierten, dominant aktiven Allels von RIM101, das in C. albicans f{\"u}r die pH-abh{\"a}ngige Genexpression verantwortlich ist, hat darauf keinen Einfluss. In C. glabrata und Aspergillus nidulans findet sich keine Expression von CdPHR1. Basierend auf Sequenzunterschieden zwischen PHR1 und CdPHR1 wird ein PCR-Schnelltest zur Speziesunterscheidung entwickelt. Dieser wird in einer epidemiologischen Studie mit 133 chlamydosporenpositiven klinischen Isolaten evaluiert. 21 oropharyngeale Isolate von 14 HIV-positiven Patienten k{\"o}nnen so retrospektiv als C. dubliniensis klassifiziert werden, dies entspricht einer Pr{\"a}valenz von C. dubliniensis in diesem Kollektiv von 30 Prozent. Die Ergebnisse der PCR werden durch Sequenzierung ribosomaler Gene (V3, ITS1, ITS2) best{\"a}tigt. Parallel werden ph{\"a}notypische Tests zur Identifizierung von C. dubliniensis auf ihre diagnostische Validit{\"a}t getestet. W{\"a}hrend sich die Chlamydosporenmorphologie der Isolate und die Kolonief{\"a}rbung auf dem Farbindikatormedium CHROMagar Candida als unzul{\"a}nglich f{\"u}r die Unterscheidung erweisen und das f{\"u}r C. dubliniensis beschriebene Wachstumsdefizit bei 45°C zwar sensitiv, nicht aber spezifisch f{\"u}r die Identifizierung dieser Spezies ist, korreliert die Koloniemorphologie auf Staib-Agar zu 100 Prozent mit den molekularen Daten. Alle C. dubliniensis Isolate werden in einem biochemischen Assay (Micronaut RC) untersucht, dabei zeigt der Test auf b-Glukosidase Aktivit{\"a}t hohes diskriminatorisches Potenzial. In Resistenztestungen zeigen sich die C. dubliniensis Isolate sensibler als die oropharyngealen C. albicans Isolate gegen gebr{\"a}uchliche Antimykotika. In dieser Studie kann gezeigt werden, dass C. dubliniensis und C. albicans auf teilweise austauschbare Mechanismen zur Reaktion auf Alterationen des pH-Milieus verf{\"u}gen. Die pH-abh{\"a}ngige Regulation zellwandassoziierter Gene ist dabei eng mit morphogenetischen Prozessen verbunden. Trotz dieser {\"A}hnlichkeit ist C. dubliniensis nicht nur weniger virulent als C. albicans, sondern zeigt auch ein unterschiedliches epidemiologisches Spektrum, das durch eine Spezialisierung auf oropharyngeale Kolonisation und Infektion bei HIV-positiven Patienten gekennzeichnet ist. Um die Gr{\"u}nde f{\"u}r diese Unterschiede aufzeigen zu k{\"o}nnen, ist eine verl{\"a}ssliche Identifizierung von C. dubliniensis notwendig. Dazu stellen die pr{\"a}sentierten Daten einerseits einen schnellen und verl{\"a}sslichen PCR Test, andererseits eine sorgf{\"a}ltige Evaluierung derzeit gebr{\"a}uchlicher ph{\"a}notypischer Verfahren vor. Ph{\"a}notypisch und genotypisch exzellent charakterisierte Isolate beider Spezies stehen f{\"u}r weitere Untersuchungen zur Verf{\"u}gung.},
  language  = {de}
}
@phdthesis{Huenten2005,
  author    = {H{\"u}nten, Peter},
  title     = {Channel-forming proteins in the cell wall of amino acid-producing Corynebacteria},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13890},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Corynebacterium glutamicum is together with C. callunae and C. efficiens a member of the diverse group of mycolic-acid containing actinomycetes, the mycolata. These bacteria are potent producer of glutamate, lysine and other amino acids on industrial scale. The cell walls of most actinomycetes contain besides an arabinogalactan-peptidoglycan complex large amounts of mycolic acids. This three-layer envelope is called MAP (mycolyl-arabinogalactan-peptidoglycan) complex and it represents a second permeability barrier beside the cytoplasmic membrane similar to the outer membrane of Gram-negative bacteria. In analogy to the situation in the outer membrane of Gram-negative bacteria, channels are present in the mycolic acid layer of the mycobacterial cell wall for the passage of hydrophilic solutes. Molecular studies have provided far-reaching findings on the amino acid flux and its balance in C. glutamicum in general, but the L-glutamate export still remains unknown. The properties of the outer layers, typical of mycolata, seem to be of major importance in this process, and diffusion seems to play a key role for this part of the cell wall. The major aim of this thesis was to identify and study novel channel-forming proteins of the amino acid producers C. glutamicum, C. callunae and C. efficiens. Cell wall extracts of the organisms were investigated and a novel pore-forming protein, named PorH, that is homologue in all three organisms, was detected and characterized. PorHC.glut was isolated from C. glutamicum cells cultivated in minimal medium. The protein was identified in lipid bilayer experiments and purified to homogeneity by fast-protein liquid chromatography across a HiTrap-Q column. The purified protein forms cation-selective channels with a diameter of about 2.2 nm and an average single-channel conductance of about 2.5 nS in 1 M KCl in the lipid bilayer assay. Organic solvent extracts were used to study the permeability properties of the cell wall of C. callunae and C.efficiens. The cell extracts contained channel-forming activity, the corresponding proteins were purified to homogeneity by fast-protein liquid chromatography across a HiTrap-Q column and named PorHC.call and PorHC.eff. Channels formed by PorHC.call are cation-selective with a diameter of about 2.2 nm and an average single-channel conductance of 3 nS, whereas PorHC.eff forms slightly anion selective channels with an average single-channel conductance of 2.3 nS in 1 M KCl in the lipid bilayer assay. The PorH proteins were partially sequenced and the corresponding genes, which were designated as porH, were identified in the published genome sequence of C. glutamicum and C. efficiens. The chromosome of C. callunae is not sequenced, but PorHC.call shows a high homology to PorHC.eff and PorHC.glut. The proteins have no N-terminal extension, only the inducer methionine, which suggests that secretion of the proteins could be very similar to that of PorAC.glut of C. glutamicum. PorHC.glut is coded in the bacterial chromosome by a gene that is localized in the vincinity of the porAC.glut gene, within a putative operon formed by 13 genes that are encoded by the minus strand. Both porins are cotranscribed and coexist in the cell wall, which was demonstrated in RT-PCR and immunological detection experiments. The arrangement of porHC.glut and porAC.glut on the chromosome is similar to that of porBC.glut and porCC.glut and it was found that PorAC.glut, PorHC.glut, PorBC.glut and PorCC.glut coexist in the cell wall of C. glutamicum. The molecular mass of about 6 kDa of the PorH channel forming proteins is rather small and suggests that the cell wall channels are formed by oligomers. A possibly hexameric form was demonstrated for PorHC.glut in Western blot analysis with anti- PorHC.glut antibodies. Secondary structure predictions for PorHC.glut, PorHC.call and PorHC.eff predict that a stretch of about 42 amino acids of PorHC.glut and 28 amino acids of PorHC.call and PorHC.eff forms amphipathic \&\#61537;-helices with a total length of 6.3 nm and 4.2 nm respectively. This should be sufficient to cross the mycolic acid layer. Another objective of this work was to establish an heterologous expression system for corynebacterial channel-forming proteins, to investigate the channel-forming properties of the up to now only hypothetical porins PorA, PorB, PorC from C. efficiens and PorC from C. glutamicum. We could demonstrate with recombinant expression experiments in E. coli that porBC.eff and porCC.eff encode for channel-forming proteins. They are, like PorBC.glut, anion-selective with a similar single-channel conductance of 1 nS in 1 M KCl.},
  subject      = {Corynebacterium callunae},
  language  = {en}
}
@phdthesis{Denker2006,
  author    = {Denker, Katrin},
  title     = {Isolation and characterization of channel-forming proteins in the outer membrane of E. coli and Borrelia species},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-16955},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2006},
  abstract  = {In this study pore forming proteins of the gram-negative bacteria B. burgdorferi, B. duttonii and E.coli were investigated. Therefore the study is subdivided into three parts. In the first part outer membrane preparation of three relapsing fever Borrelia were investigated. In the second part the putative TolC homologue BB0124 of B. burgdorferi, the Lyme borreliosis agent, was studied. In the last part the influence of point mutants within the greasy slide of the maltose specific porin (LamB) of E. coli were shown. In the first part of this study outer membrane preparations of three Borrelia relapsing fever strains have been studied for pore-forming activity in the black lipid bilayer assay. Histograms of conductance fluctuations were obtained from single-channel experiments with outer membrane preparations of B. hermsii, B. recurentis and B. duttonii. All strains had a different conductance fluctuation pattern with a broad range of single-channel conductance values varying from 0.5 nS - 11 nS. Common for all three strains was a high pore-forming activity at around 0.5 nS. Furthermore the proteins of the outer membrane of B. duttonii were separated by chromatographic methods. Some eluate fractions contained a channel-forming protein, which was forming stable channels with a single-channel conductance of 80 pS in 1 M KCl. Characterization of this channel showed that it is slightly anionic selective and voltage independent. The small single-channel conductance suggests that it is a specific pore. However, a substrate specificity could not be determined. In the second part, for the B. burgdorferi HB19 and p66 knock out strain HB19/K02, their outer membrane preparations were characterized in the black lipid bilayer assay. Comparing the histograms of single-channel conductions fluctuations of both strains showed no single-channel activity at 11.5 nS for the p66 knock out strain. This verifies earlier studies that P66 is a pore-forming protein in B. burgdorferi. Furthermore, one fraction obtained by anion exchange chromatography of the p66 knock out outer membrane protein preparation showed a uniform channel-forming activity with a single channel conductance of 300 pS. The electrophysically characterization of the 300 pS channel showed that it is not ionselective or voltage dependent. By mass spectrometry using peptide mass finger prints, BB0142 could be identified as the sole channel forming candidate in the active fraction. A BLAST search and a conserved domain search showed that BB0142 is a putative TolC homologue in B. burgdorferi. Furthermore the location of the bb0142 gene within the chromosome is in an operon encoding a multidrug efflux pump. In this study the expression of an outer membrane component of a putative drug efflux system of B. burgdorferi was shown for the first time. In the third part functional studies of the maltooligosaccharide-specific LamB channel were performed. The 3D-structure of LamB suggests that a number of aromatic residues (Y6, Y41, W74, F229, W358 and W420) within the channel lumen is involved in carbohydrate and ion transport. All aromatic residues were replaced by alanine (A) scanning mutagenesis. Furthermore, LamB mutants were created in which one, two, three, four and five aromatic residues were replaced to study their effects on ion and maltopentaose transport through LamB. The purified mutant proteins were reconstituted into lipid bilayer membranes and the single-channel conductance was studied. The results suggest that all aromatic residues provide some steric hindrance for ion transport through LamB. Highest impact is provided by Y6 and Y41, which are localized opposite to Y118, which forms the central constriction of the LamB channel. Stability constants for binding of maltopentaose to the mutant channels were measured using titration experiments with the carbohydrate. The mutation of one or several aromatic amino acids led to a substantial decrease of the stability constant of binding. The highest effect was observed when all aromatic amino acids were replaced by alanine because no binding of maltopentaose could be detected in this case. However, binding was again possible when Y118 was replaced by tryptophane (W). The carbohydrate-induced block of the channel function could also be used for the study of current noise through the different mutant LamB-channels. The analysis of the power density spectra of some of the mutants allowed the evaluation of the on- and off-rate constants (k1 and k-1) of carbohydrate binding to the binding-site inside the channels. The results suggest that both on- and off-rate constants were affected by the mutations. For most mutants k1 decreased and k-1 increased.},
  subject      = {Escherichia coli},
  language  = {en}
}
@phdthesis{Barth2008,
  author    = {Barth, Enrico},
  title     = {Study of the properties of channel-forming proteins of the cell walls of different Corynebacteriae},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-36325},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {Die Gattung Corynebacterium geh{\"o}rt, neben Mycobacterium, Nocardia, Rhodococcus und weiteren nahverwandten Gattungen, dem unverwechselbaren, gattungs{\"u}bergreifenden Taxon Mycolata an. Viele Spezies aus dieser heterogenen Gruppe Mycols{\"a}ure-haltiger Actinomyceten sind entweder aufgrund ihrer medizinischen oder ihrer biotechnologischen Bedeutung bekannt. Beispielsweise z{\"a}hlen Mycobacterium tuberculosis, Mycobacterium leprae, Corynebacterium diphtheriae und Nocardia farcinica, welche weltweit Verursacher besonders gef{\"a}hrlicher bakterieller Infektionskrankheiten sind, zu dieser ungew{\"o}hnlichen Gruppe Gram-positiver Bakterien. Ebenso bedeutsam sind einige apathogene Mycolata-Arten, die industrielle Anwendung finden. Corynebacterium glutamicum und Corynebacterium efficiens sind leistungsf{\"a}hige Bakterien, die zum Beispiel in der Produktion des Geschmacksverst{\"a}rkers Glutamat und des Tierfuttermittelzusatzes Lysin eingesetzt werden, w{\"a}hrend verschiedene Rhodococcus Spezies Anwendung bei der Herstellung von Acryls{\"a}uren finden. Die Zellwand der Mycolata zeigt, verglichen mit der klassischer Gram-positiver Bakterien, eine außergew{\"o}hnliche Zusammensetzung und Struktur auf. Abgesehen von einem Arabinogalactan-Peptidoglycan-Komplex enth{\"a}lt die Zellwand der meisten Actinomyceten einen hohen Anteil an Mycols{\"a}uren. Diese langkettigen, verzweigten Fetts{\"a}uren formen eine, mit der {\"a}ußeren Membran Gram-negativer Bakterien vergleichbare, stark undurchl{\"a}ssige, hydrophobe {\"a}ußere H{\"u}lle, welche die Grundlage der außergew{\"o}hnlichen Medikamentenresistenz bei den Mycolata bildet. Wie die {\"a}ußere Membran Gram-negativer Bakterien enth{\"a}lt die Zellwand der Mycolata porenformende Proteine, die den Durchlass hydrophiler Substanzen gestatten. Indem sie eine Verbindung zwischen dem Zellinneren und der Umwelt, in der das Bakterium lebt, schaffen und einen kontrollierten Austausch zwischen beiden erm{\"o}glichen, tragen die Kanalproteine entscheidend zur Funktion der bakteriellen Zellh{\"u}lle bei. Das Ziel dieser Arbeit war das Wissen {\"u}ber Zellwandkan{\"a}le in Corynebakterien zu erweitern. Deshalb untersuchten wir PorA und PorH Proteine, die basierend auf fr{\"u}heren Studien Zellwandkan{\"a}len in C. glutamicum, C. efficiens und Corynebacterium callunae zugeordnet werden, um ungekl{\"a}rten Fragen nachzugehen und um Wissen {\"u}ber deren Struktur zu erlangen. Ferner inspizierten wir Zellw{\"a}nde pathogener Corynebakterien, genauer gesagt von Corynebacterium diphtheriae und Corynebacterium jeikeium, um herauszufinden, ob diese Spezies wie ihre harmlosen Verwandten Kanalproteine besitzen. In dieser Arbeit wiesen wir mit C. diphtheriae und C. jeikeium in zwei weiteren Corynebacterium-Arten offene, mit Wasser gef{\"u}llte Zellwandkan{\"a}le nach. Des Weiteren stellten wir fest, dass sich die Zellwandkan{\"a}le von C. glutamicum, C. efficiens und C. diphtheriae aus zwei Proteinen zusammensetzen, einem zugeh{\"o}rig zu der Gruppe der PorH Proteine und einem weiteren aus der Gruppe der PorA Proteine. Diese heteromere Struktur von Zellwandkan{\"a}len bei Corynebakterien stellt ein Novum f{\"u}r Zellwandkan{\"a}le bei den Mycolata dar. Indessen besteht der Zellwandkanal von C. jeikeium aus nur einem Protein, CjPorA, angeordnet zu einem Oligomer. Obgleich das Molekulargewicht dieses Proteins (4 kDa) mit dem von PorH und PorA Proteinen vergleichbar ist (5-7 kDa), weißt seine Prim{\"a}rsequenz keine eindeutige Homologie zu diesen auf. Dennoch deutet vieles auf eine Verwandtschaft zwischen CjPorA und PorH/PorA Proteinen hin, da das Gen jk0268, welches f{\"u}r CjPorA kodiert, sich in einer Region des C. jeikeium Chromosoms befindet, die der Genomregion entspricht in welcher die porH/porA Gene der anderen Corynebakterien lokalisiert sind. Dies l{\"a}sst vermuten, dass jk0268 (welches f{\"u}r den homomeren Zellwandkanal in C. jeikeium kodiert) und die porH/porA Gene von C. glutamicum, C. efficiens und C. diphtheriae (die einen heteromeren Zellwandkanal kodieren) wahrscheinlich Nachkommen eines gemeinsamen Vorl{\"a}ufergens sind. Phylogenetische Analysen der Gattung Corynebacterium unterst{\"u}tzen diese Annahme. Desweitern legen sie nahe, dass die hier untersuchten Zellwandkan{\"a}le innerhalb dieser Gattung wahrscheinlich weit verbreitet sind. Ein umfassendes Wissen {\"u}ber Zellwandkan{\"a}le, denen beim Transport gel{\"o}ster Stoffe {\"u}ber die {\"a}ußere Membran in Corynebakterien und anderen Mitgliedern der Mycolata eine entscheidende Rolle zukommt, k{\"o}nnte von großem wirtschaftlichem und medizinischem Nutzen sein.},
  subject      = {Zellwand},
  language  = {en}
}
@phdthesis{Luckner2009,
  author    = {Luckner, Sylvia},
  title     = {Towards the development of high affinity InhA and KasA inhibitors with activity against drug-resistant strains of Mycobacterium tuberculosis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-43621},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Mycobacterium tuberculosis is the causative agent of tuberculosis and responsible for more than eight million new infections and about two million deaths each year. Novel chemotherapeutics are urgently needed to treat the emerging threat of multi drug resistant and extensively drug resistant strains. Cell wall biosynthesis is a widely used target for chemotherapeutic intervention in bacterial infections. In mycobacteria, the cell wall is comprised of mycolic acids, very long chain fatty acids that provide protection and allow the bacteria to persist in the human macrophage. The type II fatty acid biosynthesis pathway in Mycobacterium tuberculosis synthesizes fatty acids with a length of up to 56 carbon atoms that are the precursors of the critical mycobacterial cell wall components mycolic acids. KasA, the mycobacterial ß-ketoacyl synthase and InhA, the mycobacterial enoyl reductase, are essential enzymes in the fatty acid biosynthesis pathway and validated drug targets. In this work, KasA was expressed in Mycobacterium smegmatis, purified and co-crystallized in complex with the natural thiolactone antibiotic thiolactomycin (TLM). High-resolution crystal structures of KasA and the C171Q KasA variant, which mimics the acyl enzyme intermediate of the enzyme, were solved in absence and presence of bound TLM. The crystal structures reveal how the inhibitor is coordinated by the enzyme and thus specifically pinpoint towards possible modifications to increase the affinity of the compound and develop potent new drugs against tuberculosis. Comparisons between the TLM bound crystal structures explain the preferential binding of TLM to the acylated form of KasA. Furthermore, long polyethylene glycol molecules are bound to KasA that mimic a fatty acid substrate of approximately 40 carbon atoms length. These structures thus provide the first insights into the molecular mechanism of substrate recognition and reveal how a wax-like substance can be accommodated in a cytosolic environment. InhA was purified and co-crystallized in complex with the slow, tight binding inhibitor 2-(o-tolyloxy)-5-hexylphenol (PT70). Two crystal structures of the ternary InhA-NAD+-PT70 were solved and reveal how the inhibitor is bound to the substrate binding pocket. Both structures display an ordered substrate binding loop and corroborate the hypothesis that slow onset inhibition is coupled to loop ordering. Upon loop ordering, the active site entrance is more restricted and the inhibitor is kept inside more tightly. These studies provide additional information on the mechanistic imperatives for slow onset inhibition of enoyl ACP reductases.},
  subject      = {Tuberkelbakterium},
  language  = {en}
}
@phdthesis{Kesetovic2016,
  author    = {Kesetovic, Diana},
  title     = {Synthesis and biological testing of potential anti-tuberculosis drugs targeting the β-ketoacyl ACP synthase},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131301},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {With 9.6 million new cases and 1.5 million deaths in 2014, tuberculosis (TB) is alongside with AIDS the most deadly infection.‎ Foremost, the increased prevalence of resistant strains of M. tuberculosis among the TB-infected population represents a serious thread. Hence, in the last decades, novel drug targets have been investigated worldwide. So far a relatively unexplored target is the cell wall enzyme β-ketoacyl-ACP-synthase "KasA", which plays a crucial role in maintaining the membrane impermeability and hence the cell ability to resist to the immune response and drug therapy. KasA is a key enzyme in the fatty acid synthase "FAS-II" elongation cycle, responsible for the extension of the growing acyl chain within the biosynthesis of precursors for the most hydrophobic constituents of the cell wall - mycolic acids. Design of the novel KasA inhibitors, performed in the research group of Prof. Sotriffer by C. Topf and B. Schaefer, was based on the recently published crystal structure of KasA‎ in complex with its known inhibitor thiolactomycin (TLM). Considering the essential ligand-enzyme interactions, a pharmacophore model was built and applied in the virtual screening of a modified ZINC database. Selected hits with the best in silico affinity data have been reported by Topf‎ and Schaefer‎. In this work, two of the obtained hits were synthesized and their structure was systematically varied. First, a virtual screening hit, chromone-2-carboxamide derivative GS-71, was modified in the amide part. Since the most of the products possessed a very low solubility in the aqueous buffer medium used in biological assays, polar groups (nitro, succinamidyl and trimethyl-amino substituent in position 6 of the chromone ring or hydroxyl group on the benzene ring in the amide part have been inserted to the molecule. Further variations yielded diaryl ketones, diaryl ketone bearing a succinamidyl substituent, carboxamide bearing a methylpiperazinyl-4-oxobutanamido group and methyl-malonyl ester amides. Basically, the essential structural features necessary for the ligand-enzyme interactions have been maintained. The latter virtual screening hit, a pyrimidinone derivative VS-8‎ was synthesized and the structure was modified by substitution in positions 2, 4, 5 and 6 of the pyrimidine ring. Due to autofluorescence, detected in most of the products, this model structure was not further varied. Simultaneously, experiments on solubilization of the first chromone-2-carboxamides with cyclodextrins, cyclic oligosacharides known to form water-soluble inclusion complexes, were performed. Although the assessed solubility of the chromone 3b/DIMEB (1:3) mixture exceeded 14-fold the intrinsic one, the achieved 100 µM solubility was still not sufficient to be used as a stock solution in the binding assay. The experiments with cyclodextrin in combination with DMSO were ineffective. Owing to high material costs necessary for the appropriate cyclodextrin amounts, the aim focused on structural modification of the hydrophobic products. Precise structural data have been obtained from the solved crystal structures of three chromone derivatives: the screening hit GS-71 (3b), its trimethylammonium salt (18) and 6-nitro-substituted N-benzyl-N-methyl-chromone-2-carboxamide (9i). The first two compounds are nearly planar with an anti-/trans-rotamer configuration. In the latter structure, the carboxamide bridge is bent out of the chromone plane, showing an anti-rotamer, too. Considering the relatively low partition coefficient of compound 3b (cLogP = 2.32), the compound planarity and correlating tight molecular packing might be the factors significantly affecting its poor solubility. Regarding the biological results of the chromone-based compounds, similar structure-activity correlations could be drawn from the binding assay and the whole cell activity testing on M. tuberculosis. In both cases, the introduction of a nitro group to position 6 of the chromone ring and the presence of a flexible substituent in the amide part showed a positive effect. In the binding study, the nitro group at position 4 on the N-benzyl residue was of advantage, too. The highest enzyme affinity was observed for N-(4-nitrobenzyl)-chromone-2-carboxamide 4c (KD = 34 µM), 6-nitro substituted N-benzyl-chromone-2-carboxamide 9g (KD = 40 µM) and 6‑nitro-substituted N-(4-nitrobenzyl)-chromone-2-carboxamide 9j (KD = 31 µM), which could not be attributed to the fluorescence quenching potential of the nitro group. The assay interference potential of chromones, due to a covalent binding on the enzyme sulfhydryl groups, was found to be negligible at the assay conditions. Moderate in vivo activity was detected for 6‑nitro-substituted N-benzyl-chromone-2-carboxamide 9g and its N-benzyl-N-methyl-, N‑furylmethyl-, N-cyclohexyl- and N-cyclohexylmethyl derivatives 9i, 9d, 9e, 9f, for which MIC values 20 - 40 µM were assessed. Cytotoxicity was increased in the N‑cyclohexylmethyl derivative only. None of the pyrimidine-based compounds showed activity in vivo. The affinity of the model structure, VS-8, surpassed with KD = 97 µM the assessed affinity of TLM (KD = 142 µM). Since for the model chromone compound GS-71 no reliable KasA binding data could be obtained, a newly synthesized chromone derivative 9i was docked into the KasA binding site, in order to derive correlation between the in silico and in vitro assessed affinity. For the 6‑nitro-derivative 9i a moderate in vivo activity on M. tuberculosis was obtained. The in silico predicted pKi values for TLM and 9i were higher than the corresponding in vitro results, maintaining though a similar tendency, i.e., the both affinity values for compound 9i (pKi predicted = 6.64, pKD experimental = 4.02) surpassed those obtained for TLM (pKi predicted = 5.27, pKD experimental = 3.84). Nevertheless, the experimental pKD values are considered preliminary results. The binding assay method has been improved in order to acquire more accurate data. Owing to the method development, limited enzyme batches and solubility issues, only selected compounds could be evaluated. The best hits, together with the compounds active on the whole cells of M. tuberculosis, will be submitted to the kinetic enzyme assay, in order to confirm the TLM-like binding mechanism. Regarding the in vivo testing results, no correlations could be drawn between the predicted membrane permeability values and the experimental data, as for the most active compounds 9e and 9f, a very low permeability was anticipated (0.4 and 0.7 \%, respectively). Further biological tests would be required to investigate the action- or transport mode.},
  subject      = {Tuberkelbakterium},
  language  = {en}
}
@phdthesis{Jarick2020,
  author    = {Jarick, Marcel},
  title     = {Molekulare und funktionelle Charakterisierung der Serin/Threonin-Proteinkinase Stk und -Proteinphosphatase Stp von \(Staphylococcus\) \(aureus\)},
  doi       = {10.25972/OPUS-17654},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176542},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Staphylococcus aureus ist ein Kommensale, der die menschliche Haut und Schleimhaut der Nase und des Rachens besiedelt. Der Keim verursacht aufgrund zahlreicher Virulenzfaktoren leichte aber auch schwere Infektionen wie Pneumonie, Endokarditis oder Sepsis. Die Behandlung von S. aureus-Infektionen gestaltet sich heutzutage schwierig, da der Keim Resistenzen gegen verschiedenste Antibiotika ausgebildet hat. Zur Bek{\"a}mpfung dieser Resistenzen werden neue Antibiotika ben{\"o}tigt, die u.a. mit der Zellphysiologie und der Zellwandwandsynthese der Bakterien interferieren. Die Zellphysiologie und Zellwandsynthese wird abh{\"a}ngig von der Wachstumsphase und Umwelt-einfl{\"u}ssen in den Bakterien streng reguliert. Neben den Zweikomponentensystemen sind Serin/Threonin-Proteinkinasen und -Phosphatasen wesentliche Sensoren und Regulatoren der Bakterien. Durch Phosphorylierung und Dephosphorylierung bewirken diese beiden Systeme eine Hemmung oder Aktivierung der entsprechenden Zielproteine. Dadurch kann sich die Bakterienzelle an innere und {\"a}ußere Reize anpassen. In dieser Arbeit wurde die konservierte Serin/Threonin-Proteinkinase Stk und die Serin/Threonin-Phosphatase Stp von S. aureus untersucht. Die beiden Proteine Stk und Stp haben einen großen Einfluss auf die Signalweiterleitung, den zentralen Metabolismus, die Stressantwort, die Antibiotikaresistenz und die Virulenz von S. aureus. Im ersten Teil dieser Arbeit wird dargelegt, dass Stk und Stp in der bakteriellen Membran lokalisiert sind, dort miteinander interagieren und antagonistisch Zielproteine phosphorylieren bzw. dephospho-rylieren. Die Deletion der Phosphatase Stp bewirkt, dass zahlreiche Proteine in der Zelle permanent phosphoryliert und daher vermutlich nur noch eingeschr{\"a}nkt funktionst{\"u}chtig sind. Die ausbleibende Dephosphorylierung der Proteine in der stp-Mutante hat einen dramatischen Effekt auf die Zellwand-synthese und die Virulenz von S. aureus. So hat die stp-Mutante eine verdickte Zellwand und ist weniger virulent als die stk-Mutante und der Wildtypstamm. Im Rahmen dieser Arbeit wird erstmals eine Erkl{\"a}rung pr{\"a}sentiert, die die strukturellen Besonderheiten von Stk und deren Auswirkung auf die Zellwandsynthese zusammenf{\"u}hrt: In der stp-Mutante akkumulieren Zellwandvorl{\"a}ufer in der Zelle, da vermutlich die entsprechenden Zellwandsyntheseproteine durch Stk-vermittelte Phosphorylierung gehemmt werden. Die Proteine FemXAB nehmen eine zentrale Rolle in der Zellwandsynthese ein, indem sie die Pentaglycin-Interpeptidbr{\"u}cke des Zellwandvorl{\"a}ufers Pentaglycin-Lipid II syntheti-sieren. Stk wird durch die Bindung seiner extrazellul{\"a}ren Dom{\"a}nen an Pentaglycin-Lipid II aktiviert. In der vorliegenden Arbeit konnte FemX als in vitro Substrat von Stk und Stp identifiziert werden. Die permanente Phosphorylierung von FemX in der stp-Mutante f{\"u}hrt zur verminderten Synthese der Pentaglycin-Br{\"u}cken am Lipid II und infolgedessen zum Einbau von unvollst{\"a}ndigen Muropeptiden in den neuen Peptidoglycanstrang. Diese strukturelle Ver{\"a}nderung f{\"u}hrt zur Verdickung der Zellwand und folglich zur verminderten Empfindlichkeit gegen{\"u}ber der Glycyl-Glycinpeptidase Lysostaphin. Neben FemX interagiert Stk mit weiteren Zellwandsyntheseproteinen wie FemAB und einigen Zellteilungsproteinen. Diese Ergebnisse verdeutlichen, dass Stk das Vorkommen seines extrazellul{\"a}ren Liganden Lipid II detektiert und dementsprechend die Zellwandsynthese {\"u}ber FemX reguliert. Im zweiten Teil der Arbeit wurde anhand verschiedener Omics-Techniken die stk-, stp- und stk/stp-Mutante im Vergleich zum S. aureus NewmanHG Wildtyp charakterisiert. Dabei zeigten sich teilweise große Unterschiede zwischen der stp-Mutante und den anderen St{\"a}mmen. Mit diesen Unter-suchungen konnten Ergebnisse aus anderen Studien best{\"a}tigt und mit weiteren Daten untermauert werden. So l{\"a}sst sich die verminderte Virulenz der stp-Mutante mit der reduzierten Expression und Sekretion von Toxinen wie H{\"a}molysinen und Leukozidinen erkl{\"a}ren. Dies f{\"u}hrt zu einer verminderten H{\"a}molyse von Erythrozyten und einer verminderten Immunantwort gegen diese Toxine im Infektions-versuch. Stk und Stp phosphorylieren bzw. dephosphorylieren Transkriptionsfaktoren und Antwort-regulatoren von Zweikomponentensystemen, was zu der ver{\"a}nderten Expression und Sekretion der Virulenzfaktoren f{\"u}hrt. Die Analyse der Mutanten offenbart, dass Stk ein negativer und Stp ein positiver Regulator der Virulenz in S. aureus ist. Außerdem regulieren Stk und Stp zentrale Aspekte des Metabolismus in S. aureus. So ist die Konzentration an Nukleotidtriphosphaten in der stp-Mutante reduziert, was auf eine verminderte Expression der Gene der Pyrimidinsynthese zur{\"u}ckzuf{\"u}hren ist. Anhand dieser Ergebnisse wird deutlich, dass Stk und Stp wesentliche Aspekte der Zellphysiologie wie die Zellwandsynthese, den zentralen Metabolismus und die Virulenz von S. aureus regulieren.},
  subject      = {Kinase},
  language  = {de}
}