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Hospitals worldwide are becoming increasingly plagued by antibiotic-resistant pathogens; concomitantly, the number of patients who die from antibiotic-resistant pathogens is increasing. The rise of multi-drug resistant (MDR) pathogens has rendered many antibiotics obsolete. The streptogramin and aminoglycoside antibiotics are drugs of last resort against life-threatening, MDR Gram-positive (e.g., methicillin resistant Staphylococcus aureus (MRSA)) and -negative (e.g., Pseudomonas aeruginosa) pathogens, respectively; however, as microbial drug resistance continues to emerge, the efficacy of these two important drug classes is decreasing. One of the most common mechanisms by which pathogens become resistant to streptogramin and aminoglycoside antibiotics is enzymatic inactivation: the Vat and AAC(3) acetyltransferases are employed by pathogens to inactivate streptogramin and aminoglycoside antibiotics, respectively. There currently is a dire need to not only develop new antibiotics, but to find new, creative strategies to outwit microbial resistance mechanisms. One of these strategies is to rescue the activity of antibiotics through the discovery of antibiotic adjuvants. In the current study, adjuvants which rescue the activity of streptogramin and aminoglycoside antibiotics through inhibition of the resistance acetyltransferases, VatD and AAC(3)-Ia, have been discovered—through the development of a cell-based screening method, we have found the first inhibitors of VatD, as well as of AAC(3)-Ia and its homologues, AAC(3)-Ib, AAC(3)-Ic, and AAC(3)-Id. We have demonstrated that streptogramin and aminoglycoside resistance can be reversed both in vitro and in vivo by the protein kinase inhibitors, GW5074 and rottlerin. Steady state kinetics revealed these compounds to inhibit VatD and AAC(3) enzymes mainly through noncompetitive or mixed mechanisms. This study has also demonstrated that eukaryotic kinase inhibitor libraries may be repurposed for the discovery of not only new antibiotic adjuvants, but also new antimicrobial targets. The inhibitors described herein may someday serve as effective adjuvants of streptogramin and aminoglycoside antibiotics. / Thesis / Doctor of Philosophy (PhD)

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L'émergence de bactéries résistantes aux antibiotiques constitue un problème majeur de santé publique responsable d'un nombre croissant de décès, surtout dans les hôpitaux. La résistance aux aminoglycosides est principalement due à l'expression d'enzymes capables de les modifier, comme les aminoglycosides phosphotransférases (APH).Le premier volet de ce travail de thèse vise à mieux comprendre les bases moléculaires des interactions protéine-ligands et de la catalyse enzymatique d'une de ces enzymes, l'APH(2”)-IVa. La spécificité de substrats a été caractérisée en détails pour différents aminoglycosides par des méthodes thermodynamiques, de mesures cinétiques à l'état stationnaire et transitoire, par amarrage moléculaire et cristallographie aux rayons X. La seconde partie de cette étude consiste à développer et optimiser des inhibiteurs allostériques de ces enzymes capables de restaurer l'efficacité des aminoglycosides. Pour cela, une cavité, potentiellement impliquée dans la dynamique de l'APH(2”)-IVa, a été identifiée à partir de simulations de dynamique moléculaire. Celle-ci a servi de cible pour cribler, in silico, 12 000 composés issus de la banque de données Zinc. Ainsi, 14 composés ont été testés in vitro pour leur capacité à diminuer l'activité enzymatique d'APH. Parmi ces derniers, une molécule s'est révélée être un inhibiteur non-compétitif de l'APH(2”)-IVa. Une étude des relations structure-fonction a permis de déterminer les groupements les plus favorables à l'inhibition et d'identifier un composé plus efficace. L'utilisation de ces deux molécules permet de restaurer, par exemple, la sensibilité à la sisomicine d'une souche d'E. faecium exprimant cette enzyme. Cette étude fournit des bases au développement de thérapies combinant un aminoglycoside et un inhibiteur des enzymes d'inactivation constituant une stratégie pour lutter contre la résistance aux antibiotiques dans un contexte thérapeutique. / Emergence of multi-drug resistant bacteria leads to increasing fatal issues especially in hospitals. Resistance to aminoglycoside antibiotics is mainly due to the expression of modifying enzymes, such as aminoglycoside phosphotransferases (APH). The first aim of this project was to elucidate the molecular basis of protein-ligand interactions and catalysis of one of these enzymes, the APH(2”)-IVa. Promiscuity of aminoglycoside substrates has thus been characterized in details using thermodynamics, transient and steady state kinetics, molecular docking and X-ray crystallography techniques.The second part aimed to develop and optimize allosteric inhibitors of these enzymes able to counterbalance aminoglycoside resistance. For this purpose, a small cavity, potentially involved in APH dynamics, was identified from molecular dynamic simulations. This cavity was used as a target to virtually screen 12 000 compounds of the Zinc database. The efficiency of the 14 high-ranked molecules to inhibit APH was evaluated in vitro and lead to the identification of a non-competitive inhibitor of APH(2”)-IVa. Structure-activity relationships highlighted the most favourable substituents for APH inhibition and permitted to obtain a more potent compound. The two molecules were able to restore, for example, sisomicin susceptibility of an E. faecium strain, expressing this enzyme.This study provides a basis for the development of combined chemotherapies (antibiotic with enzyme inhibitor) which may overcome antibiotic resistance in a clinical context.

Widespread antibiotic resistance is a major public health concern, and plants represent an emerging antibiotic exposure route. Recent studies indicate that crop plants fertilized with antibiotic-laden animal manure accumulate antibiotics, however, the molecular mechanisms of antibiotic entry and subcellular partitioning within plant cells remain unknown. Here we report that mutations in the Arabidopsis locus Multiple Antibiotic Resistance (MAR1) confer resistance, while MAR1 overexpression causes hypersensitivity to multiple aminoglycoside antibiotics. Resistance is highly specific for aminoglycosides and does not extend to antibiotics of other classes, including the aminocyclitol, spectinomycin. Yeast expressing MAR1 are hypersensitive to the aminoglycoside, G418, but not to chloramphenicol or cycloheximide. MAR1 encodes a protein with 11 putative transmembrane domains with low similarity to ferroportin1 from Danio rerio. A MAR1:YFP fusion protein localizes to the chloroplast, and chloroplasts from plants overexpressing MAR1 accumulate more of the aminoglycoside, gentamicin, while mar1-1 mutant chloroplasts accumulate less than wild type. MAR1 overexpression lines are slightly chlorotic, and this chlorosis is rescued by application of exogenous iron. MAR1 expression is also downregulated by low iron. Taken together, these data suggest that MAR1 is a plastid transporter that is likely to be involved in cellular iron homeostasis, and allows opportunistic entry of multiple antibiotics into the chloroplast. mar1 mutants represent an interesting example of plant antibiotic resistance that is based on the restriction of antibiotic entry into a subcellular compartment. Knowledge about this process – and other processes of antibiotic entry – could enable the production of crop plants that are incapable of antibiotic accumulation, aid in development of phytoremediation strategies for decontamination of water and soils polluted with antibiotics, and further the development of new plant-based molecular markers. The work described here also contributes to our understanding of how plants interact with the antibiotics they encounter, both in the laboratory (where aminoglycosides such as kanamycin are used heavily to select for transgenics) and in the natural environment. / text

Protein synthesis, translation, performed by the ribosome, is a fundamental process of life and one of the main targets of antibacterial drugs. This thesis provides structural and biochemical understanding of three aspects of bacterial translation. Elongation factor G (EF-G) is the target for the antibiotic fusidic acid (FA). FA binds to EF-G only on the ribosome after GTP hydrolysis and prevents EF-G dissociation from the ribosome. Point mutations in EF-G can lead to FA resistance but are often accompanied by a fitness cost in terms of slower growth of the bacteria. Secondary mutations can compensate for this fitness cost while resistance is maintained. Here we present the crystal structure of the clinical FA drug target, Staphylococcus aureus EF-G, together with the mapping and analysis of all known FA-resistance mutations in EF-G. We also present crystal structures of the FA-resistant mutant F88L, the FA-hypersensitive mutant M16I and the FA-resistant but fitness-compensated double mutant F88L/M16I. Analysis of mutant structures together with biochemical data allowed us to propose that fitness loss and compensation are caused by effects on the conformational dynamics of EF-G on the ribosome. Aminoglycosides are another group of antibiotics that target the decoding region of the 30S ribosomal subunit. Resistance to aminoglycosides can be acquired by inactivation of the drugs via enzymatic modification. Here, we present the first crystal structure an aminoglycoside 3’’ adenyltransferase, AadA from Salmonella enterica. AadA displays two domains and unlike related structures most likely functions as a monomer. Frameshifts are deviations the standard three-base reading frame of translation. -1 frameshifting can be caused by normal tRNASer3 at GCA alanine codons and tRNAThr3 at CCA/CCG proline codons. This process has been proposed to involve doublet decoding using non-standard codon-anticodon interactions. In our study, we showed by equilibrium binding that these tRNAs bind with low micromolar Kd to the frameshift codons. Our results support the doublet-decoding model and show that non-standard anticodon loop structures need to be adopted for the frameshifts to happen. These findings provide new insights in antibiotic resistance and reading-frame maintenance and will contribute to a better understanding of the translation elongation process.

Segundo a Organização Mundial de Saúde (OMS), mais de um bilhão de pessoas estão infectadas com uma ou mais doenças tropicais endêmicas encontradas especialmente entre as populações pobres da África, Ásia e América Latina. Nos últimos 25 anos, apenas 1% de todos os medicamentos desenvolvidos no mundo foram destinados ao tratamento de doenças tropicais, como a doença de Chagas. A doença de Chagas é causada por um protozoário intracelular, o Trypanosoma cruzi, e atualmente apenas dois compostos tem sido empregados para tratamento etiológico da doença de Chagas: nifurtimox e benznidazol. Entretanto, ambos os compostos apresentam considerável toxicidade sistêmica. Nesse contexto, o objetivo do presente trabalho foi desenvolver complexos híbridos de rutênio, com potencial atividade tripanocida, que possam atuar com maior eficácia em sítios biológicos específicos do Trypanosoma cruzi e com reduzida toxicidade sistêmica. Para tal efeito, moléculas com conhecida atividade microbicida como derivados aminoglicosídeos, óxido nítrico e benznidazol foram coordenados a complexos de rutênio originando as espécies Ru(desoxiestreptamina), Ru(neamina), cis-[Ru(bpy)2(Bz)(NO)](PF6)3 e cis-[Ru(NO2)(bpy)2(Bz)]PF6. Os complexos foram caracterizados por espectroscopia de absorção no UV-vis e FTIR, espectrometria de massa, análise elementar, voltametria cíclica e voltametria de pulso diferencial. Nossos estudos sugerem que os complexos Ru(desoxiestreptamina), Ru(neamina), cis-[Ru(bpy)2(Bz)(NO)](PF6)3 e cis-[Ru(NO2)(bpy)2(Bz)]PF6 apresentam propriedades químicas que suportam o sucesso da coordenação dos ligantes ao íon metálico rutênio(II) ou (III). Dentre todos os compostos estudados, cis-[Ru(NO2)(bpy)2(Bz)]PF6, apresentou maior potência tripanocida desprovida de citotoxicidade, a julgar pelos estudos in vitro. IC50 foi ao redor de 0,24 ?mol.L-1, o que é 47 vezes menor do que a droga comumente usada em tratamento de Doença de Chagas. Isto determinou avaliação in vivo, no que foi observado aumento da sobrevida dos animais infectados com tripomastigotas, para 60 dias. Os estudos desenvolvidos com complexos de rutênio no presente trabalho reafirmam o sucesso na obtenção de tais complexos inicialmente propostos, implementando importantes informações e perspectivas no que diz respeito a complexos nitrosilos de rutênio e seus potenciais terapêuticos na doença de Chagas. / Ru(bpy)2(Bz)(NO)](PF6)3 and cis-[Ru(NO2)(bpy)2(Bz)]PF6 complexes. The compounds were characterized by UV-vis absorption spectroscopy, FTIR, mass spectrometry, elemental analysis, and cyclic voltammetry and differential pulse voltammogram. The chemical characterization presented in this work gave evidencie that support the coordination of biological ligand in ruthenium ion such as in Ru(desoxiestreptamina), Ru(neamina), cis-[Ru(bpy)2(Bz)(NO)](PF6)3 and cis-[Ru(NO2)(bpy)2(Bz)]PF6 complexes. Subsequently, in vitro and in vivo studies have been conducted evaluating the cytotoxicity and trypanocidal activity of the ligands and ruthenium complexes. In vitro analysis suggested us that ruthenium complexes are greatly effective against T. cruzi. Among all complexes synthesized cis-[Ru(NO2)(bpy)2(Bz)]PF6 showed higher in vitro trypanocidal activity, which has determined the in vivo assays with this compound. IC50 was around 0,24 ?mol.L-1, which is 47 times less than usual drugs used in Chagas diseases treatment. This was performed using animals infected with T. cruzi in trypomastigote form, animal survivals until 60 days. The studies developed for ruthenium complexes reaffirm the success in obtaining of the complexes originally proposed, implementing important information and perspectives regarding the nitrosyl ruthenium complex and its therapeutic potential in Chagas disease.

Glycosaminoglycans (GAGs) are sulfated polysaccharides that mediate a variety of extracellular interactions. Heparan sulfate (HS) is one of the most prominent GAGs on human cell surfaces. Both endogenous proteins, such as growth factors, and exogenous proteins, such as pathogen surface proteins, recognize and bind GAGs to gain access to human cells. Oligosaccharides and other structural analogs of HS and GAGs have been evaluated for a variety of therapeutic targets including angiogenesis and infectious diseases. Development of compounds to block HS-protein interactions has primarily focused on optimizing the degree and orientation of anionic substituents on a scaffold, to mimic HS structure, but their utility is diminished by their large size and non-specific interactions with many proteins. To overcome these limitations, it has been demonstrated that replacing N-sulfo groups on heparin with non-anionic N-arylacyl groups increased affinity and selectivity for binding different heparin-binding proteins. However, the heparin-derived compounds in that work were heterogeneous polysaccharides. Strategies to obtain small, structurally-defined and lower charge ligands are needed to ultimately obtain specific bind-and-block antagonists of HS-binding proteins. This study addresses these challenges by synthesizing N-arylacyl O-sulfonated aminoglycosides as small molecule, structurally-defined ligands to identify novel structures that selectively bind to HS-binding proteins. This study details development of new HPLC and LC-MS methods to separate, characterize, and purify amphiphilic oligosaccharides. The development of these methods enabled the synthesis of a panel of N-arylacyl O-sulfonated aminoglycosides. The compounds in this panel were screened for affinity and selectivity in binding with HS-binding proteins. This work demonstrates for the first time the selective binding of small amphiphilic oligosaccharides with HS-binding proteins. Significantly, individual compounds demonstrate heparin-like affinity for binding with select HS-binding proteins. Structural differences between the N-arylacyl O-sulfonated aminoglycosides, including changing the aminoglycoside core or the structure of the N-arylacyl moiety, are shown to impart specificity for these compounds to selectively bind different HS-binding proteins.

Fusarium graminearum is one of the most problematic phytopathogens in US agriculture. This fungus causes head blight, foot rot, and damping off on wheat and barley. The infection lowers the grain yield and causes contamination of the grain product with mycotoxins. Effective control measures are lacking, and new fungicides that kill F. graminearum but remain safe and economical to use are needed. Newly synthesized aminoglycosides (JL22, JL38, JL39, JL40, NEOF004, NEOF005), classic aminoglycosides (amikacin, gentamicin, kanamycin A, kanamycin B, neomycin, and ribostamycin), and a lipopeptide, syringomycin E (SRE), were studied to determine their antifungal potential to control F. graminearum. Aminoglycosides are protein synthesis inhibitors that mainly target bacteria, but a few were recently observed to kill fungi. They consist of an aminocyclitol ring bound with two or more amino sugars. Novel aminoglycosides were recently synthesized using novel glycodiversification synthetic schemes involving the replacement of the original amino sugars with unusual amino sugars. SRE is an antifungal lipodepsinonapeptide produced by Pseudomonas syringae pv. syringae. This bacterium is an opportunistic pathogen in a wide range of plant species and produces several fungicidal lipopeptides. SRE forms pores on fungal plasma membrane and causes ion fluxes. An enhancement of its antifungal activity is reported in the presence of rhamnolipid surfactants. The antifungal activities of various aminoglycosides, SRE, and a SRE-rhamnolipids mixture were determined against F. graminearum by measuring in vitro minimum inhibition concentrations (MICs) and in planta lesion area and chlorosis development using a leaf infection assay protocol. It was determined that using Tween® 20 at 0.2 % (v/v) concentration in the leaf infection assay promotes lesion development by F. graminearum with minimum phytotoxicity. In vitro, SRE, SYRA, and synthetic aminoglycoside JL38 showed the best antifungal activities. With the in planta assay, all three antifungal agents prevented infection by F. graminearum. However, inconsistent phytotoxicities were observed with SRE and SYRA that were influenced by the Tween® 20 surfactant included in the leaf infection assay. How Tween® 20 induces these phytotoxic inconsistencies is not known.