The investigations described in this thesis lay out strategies aimed at advancing antibiotic research and development. The examples presented revolve around two main approaches: understanding drug... Show moreThe investigations described in this thesis lay out strategies aimed at advancing antibiotic research and development. The examples presented revolve around two main approaches: understanding drug-target interactions and target identification.Applications of microcalorimetry provide insights into the binding mechanism of known antibiotics and their target within the bacterial membranes. These studies provided the thermodynamic characterization of cell-wall active compounds and their cell-wall precursor or phospholipid targets.Furthermore, by repurposing a small molecule library in a microbial susceptibility screen, the discovery of two new antibiotic leads is described. A suite of target identification methods, including whole genome sequencing and MS-based chemical proteomics, led to the characterization of their mode of action. Structure activity optimization of the leads led to the discovery of a new class of DNA gyrase inhibitors, acting on a so-far unexploited site of this validated bacterial target, as well as the identification of previously unmapped pathways in S. aureus, orchestrated by series of known and unknown enzymes. Show less
Antimicrobial resistance of bacteria is a worldwide and ever-growing problem, directly linked to the use of antimicrobial drugs. Resistant bacteria emerge under the selective pressure of... Show moreAntimicrobial resistance of bacteria is a worldwide and ever-growing problem, directly linked to the use of antimicrobial drugs. Resistant bacteria emerge under the selective pressure of antibiotics. In hospitals, where large-scale usage of antibiotics is common, bacteria frequently become resistant to several antibiotics which causes serious problems for the treatment of patients with infections by these microorganisms. Well-known (multi)-resistant bacteria causing problems in many countries all over the world are methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, penicillin-resistant pneumococci, extended-spectrum betalactamase-producing Klebsiella pneumoniae, carbapenem-resistant Acinetobacter baumannii, and multiresistant Mycobacterium tuberculosis Show less
Since a decade, Clostridium difficile infection (CDI) has increased progressively in incidence and severity of disease. Currently, CDI is considered the leading cause of nosocomial diarrhoea,... Show moreSince a decade, Clostridium difficile infection (CDI) has increased progressively in incidence and severity of disease. Currently, CDI is considered the leading cause of nosocomial diarrhoea, associated with an increased duration of hospitalization, healthcare expenses, morbidity and mortality. This thesis describes our findings with outbreak control, diagnosis, identification of specific risk factors and treatment of CDI after the discovery of the emergence of C. difficile PCR-ribotype 027 in the Netherlands. The studies illustrate the role of antibiotics in relation to persistence, severeness and spreading of CDI. Antibiotics are shown to be a primary risk factor for the development of (ribotype-specific) CDI and an essential part of the outbreak control measures (__bundle-approach__), namely antibiotic stewardship. The use of antibacterials is a risk for selection of novel endemic C. difficile strains in e.g. animals, which introduce an increasing risk of alternative zoonotic transmission routes. Except for very mild CDI, which is clearly induced by usage of specific antibiotics, antibacterial treatment is advised. This thesis reviews the comparative effectiveness of the currently available treatment modalities, thereby providing evidence-based recommendations for CDI remedies. Treatment options include: oral and non-oral antibiotics, toxin-binding resins and polymers, immunotherapy, probiotics, faecal or bacterial intestinal transplantation. Show less
Global healthcare is on the verge of an antibiotic availability crisis as bacteria have evolved resistance to nearly all known antibacterials. Identifying new antibiotics that operate via novel... Show moreGlobal healthcare is on the verge of an antibiotic availability crisis as bacteria have evolved resistance to nearly all known antibacterials. Identifying new antibiotics that operate via novel modes-of-action is therefore of high priority.This thesis contains two drug discovery projects, originating from a antibacterial screen of a compound library. In both projects chemical hits are first structurally optimized, after which their mode-of-action is determined.The first project entails optimizing a hit with potency against MRSA into a submicromolar active antibiotic. By using a chemical proteomics approach, the targets of this compound were elucidated, along with the targets that are most important in its antibacterial activity.The second project concerns Gram-negative bacteria, where a hit molecule is optimized into the conformationally restricted LEI-800. The target of LEI-800 is found to be DNA gyrase, a common antibiotic target. However, it is that LEI-800 inhibits DNA gyrase differently, and more potently, than the status quo. Show less
The explosive increase in infections by pathogens is a major problem in the clinic today. The theme of this thesis was to find novel antibiotics from actinomycetes. Next-generation... Show more The explosive increase in infections by pathogens is a major problem in the clinic today. The theme of this thesis was to find novel antibiotics from actinomycetes. Next-generation sequencing revealed that the biosynthetic potential of actinomycetes had been grossly underestimated. In this thesis, different antibiotics-eliciting strategies, including microbial cocultivation, streptomycin-resistant mutation, overexpression of pathway-specific activator, variation of culture conditions, were utilized to enforce fluctuations in the production of bioactive compounds in actinomycetes, after which, NMR-based metabolic profiling was used to facilitate uncovering those elicited molecules. This pipeline allowed the discovery of new antibiotics involving various chemical skeletons, such as 7-prenylisatin, methoxylated isocoumarins, endophenazines, and C-glycosylpyranonaphthoquinones. On the other hand, genome-mining methodology enabled the discovery of a group of endophenasides and leucanicidin in Kitasatospora sp. MBT66, whereby the rhamnosylation of both scaffold are executed by a same promiscuous glycosyltransferase. Last but not least, a novel antibiotic termed lugdunomycin with unprecedented chemical scaffold, as well as a number of new angucycline-type antibiotics, were characterized from Streptomyces sp. QL37. The biosynthetic pathway of lugdunomycin was deciphered by genetic knockout and OSMAC (One Strain MAny Compound) strategy. In summary, this thesis explores an interface of genomics and metabolomics to accelerate new antibiotics discovery. Show less
The soil-dwelling, filamentous bacteria of the genus Streptomyces are renowned for their production of useful secondary metabolites including antibiotics. The work described in this thesis provides... Show moreThe soil-dwelling, filamentous bacteria of the genus Streptomyces are renowned for their production of useful secondary metabolites including antibiotics. The work described in this thesis provides new insights on the role and regulation of antibiotic production and resistance in these bacteria. It shows that antibiotic resistance is already beneficial at sub-inhibitory antibiotic concentrations. Resistance can even readily evolve at such low concentrations, thereby possibly explaining the level of resistance seen in pristine environments. Antibiotic producers can benefit from spatial structure, as present in the soil, through the preferential allocation of resources and this enables invasion from low frequencies. Streptomyces do not produce all antibiotics continuously, but antibiotic production is instead tightly regulated in response to environmental cues, including those produced by competitors. Streptomyces are most likely to induce antibiotic production in response to a competitor that shares similar secondary metabolite clusters, indicating a possible role for shared signalling. Besides changes in antibiotic production, other responses to competition are revealed on a transcriptomic level, including an increased expression of developmental genes, suggesting earlier sporulation. Show less
Streptomyces are multicellular bacteria that grow as branched filaments and are best known for producing the majority of our antibiotics, many immunosuppressant and anticancer compounds.... Show moreStreptomyces are multicellular bacteria that grow as branched filaments and are best known for producing the majority of our antibiotics, many immunosuppressant and anticancer compounds. Unfortunately their multicellular life style creates many problems for efficient industrial production. In a bioreactor, depending on the environment and the genetics, it can grow quickly as dispersed mycelia or aggregate in slow growing pellets. Either morphology has advantages and disadvantages, which can be product specific. For my thesis I studied the mechanism by which these filaments can aggregate into dense pellets. I found a small gene cluster that produces poly-1,6-N-acetylglucosamine, a bacterial glue which binds neighboring cells and required for pellet formation in S. coelicolor. Subsequently we can use these genes to control the morphology of streptomycetes in a liquid environment, tailoring it for production. My work has given us new insights in the mechanims through which streptomycetes aggregate, but also has the potential to make streptomycetes a more favorable host for industial production. Show less
The ongoing increase in antimicrobial resistance combined with the low discovery of novel antibiotics is a serious threat to our health care. Genome mining has given new potential to the field of... Show moreThe ongoing increase in antimicrobial resistance combined with the low discovery of novel antibiotics is a serious threat to our health care. Genome mining has given new potential to the field of natural product discovery, as thousands of biosynthetic gene clusters (BGCs) are discovered for which the natural product is not known.Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a highly diverse class of natural products. The large number of different modifications that can be applied to a RiPP results in a large variety of chemical structures, but also stems from a large genetic variety in BGCs. As a result, no single method can effectively mine for all RiPP BGCs, making it an interesting source for new molecules.In this thesis, new methods are explored to mine genomes for the BGCs of novel RiPP variants, with a focus on discovering RiPPs that have new modifications. RRE-Finder is a new tool for the detection of RiPP Recognition Elements, domains that are often found in RiPP BGCs. DecRiPPter is another tool that employs machine learning models to discover new RiPP precursor genes encoded in the genomes. Both tools can be used to prioritize novel RiPP BGCs. Two candidate BGCs are characterized, one of which could be shown to specify a new RiPP, validating the approach. Show less
This PhD thesis describes several studies into the structure and function of Escherichia coli Elongation Factor Tu (EF-Tu). EF-Tu plays a central role in the bacterial protein synthesis machinery... Show moreThis PhD thesis describes several studies into the structure and function of Escherichia coli Elongation Factor Tu (EF-Tu). EF-Tu plays a central role in the bacterial protein synthesis machinery as the carrier of "coded building blocks" for protein synthesis, aminoacylated tRNA (aa-tRNA). Without EF-Tu, fast and accurate protein synthesis would be impossible. It not only binds and carries the aa-tRNA to the ribosome, it also plays a role in the selection of the correct aa-tRNA for the codon of the messenger RNA (mRNA) currently being decoded. This selection process, which takes place on the ribosome, is supported by hydrolysis of a GTP molecule bound to the EF-Tu-aa-tRNA complex. Once the GTP is hydrolyzed to GDP, the EF-Tu changes conformation and detaches from both the aa-tRNA and the ribosome. The aa-tRNA, if it matches the anticodon on the mRNA, will progress to the incorporation of its activated amino acid into the growing protein chain. If the anticodon does not match, however, proofreading will (r)eject it from the ribosome. There are indications that a second EF-Tu, or at least GTP hydrolysis by a second EF-Tu is involved in this process, but it is not understood how. The work in this thesis is mostly centered on understanding the role of several amino acid residues of EF-Tu in the interaction with the GTP or GDP nucleotide, the catalysis of GTP hydrolysis but EF-Tu and the mechanism by which this only accelerated five orders of magnitude on the ribosome. It leads to a number of interesting conclusions that shed light on the problem, but cannot explain the "triggered catalysis" mechanism. Show less
Group B Streptococcus (GBS, Streptococcus agalactiae) has been recognized as an important cause of perinatal morbidity and mortality. The frequency of GBS colonization ranges from 10% to 35% in... Show moreGroup B Streptococcus (GBS, Streptococcus agalactiae) has been recognized as an important cause of perinatal morbidity and mortality. The frequency of GBS colonization ranges from 10% to 35% in women of reproductive age. GBS colonization can be transient, intermittent or persistent. Vertical transmission of GBS from mother to child occurs during labor. Studies on vertical GBS transmission in colonized mothers during labor report incidences of colonization of the infant between 16 and 69%. Early-onset group B streptococcal disease (GBS-EOD) occurs in approximately 1% of newborns who are colonized with GBS. Established risk factors for acquiring GBS-EOD are prolonged rupture of membranes, preterm labor, intrapartum fever, GBS bacteriuria during pregnancy or a previous child with GBS-EOD. Intrapartum antibiotic prophylaxis (IAP) given to women at risk of transmitting GBS to their baby may prevent GBS-EOD. Identification of mothers at risk may be performed by screening (taking a culture during pregnancy to detect maternal colonization) and/ or by identifying pregnancies with one or more of the established risk factors for GBS-EOD. Since the overall effect of the Dutch guideline on the incidence of GBS-EOD is disappointing, adaptation of the Dutch guidelines should be reconsidered. The aim of this thesis is to contribute to the information needed for the establishment of an optimal prevention strategy for GBS-EOD. In this thesis, studies on prevalence of GBS carriage, risk factors for GBS-sepsis in relation to GBS carriage, timing of GBS cultures, association of GBS carriage and preterm labor and resistance of GBS for antibiotics are combined. Show less
Antibiotic resistance is an increasing problem in the battle against (bacterial) infectious diseases. The emergence of drug-resistant Mycobacterium tuberculosis (Mtb) threatens to render... Show moreAntibiotic resistance is an increasing problem in the battle against (bacterial) infectious diseases. The emergence of drug-resistant Mycobacterium tuberculosis (Mtb) threatens to render tuberculosis (TB) untreatable. Efforts to develop novel antibiotics have so far been unsuccessful, calling for additional approaches for treatment of bacterial infections. Intracellular pathogens like Mtb and Salmonella can survive in the host by manipulating host cell signaling. This provides opportunities for novel therapeutic strategies by targeting the host, rather than the bacterium (host-directed therapy). In this thesis we report the development and application of novel (in vitro and in vivo) methods for identifying host genes and proteins involved in host control of intracellular bacteria, as well as chemical compounds that target host molecules as a basis for drug development for host-directed therapies. As a result, we report the identification of RTK inhibitors, the novel kinase inhibitor 97i, the human kinase family PCTAIRE and the host protein DRAM1 as promising leads for further drug development for host-directed therapeutic strategies for intracellular bacterial infections. Show less
The work described in this thesis focussed on the modes of action of maggot therapy in chronic wounds, especially related to the inflammatory phase of wound healing. For this purpose, the effect of... Show moreThe work described in this thesis focussed on the modes of action of maggot therapy in chronic wounds, especially related to the inflammatory phase of wound healing. For this purpose, the effect of maggot excretions and/or secretions on microbiological, haematological and immunological processes was investigated. The results showed that maggot excretions/secretions breakdown biofilms of both Gram-positive and Gram-negative bacteria, exposing them to the immune system, antibiotics, and ingestion and subsequent degradation by the maggots. Furthermore, proteases in maggot secretions enhance debridement by increasing the fibrinolytic activity of wound components and by degrading matrix components directly. Additionally, maggot secretions inhibit the pro-inflammatory responses of phagocytes but do not affect their ability to ingest and intracellularly kill micro-organisms. Finally, secretions induce the production of growth factors essential for angiogenesis. In conclusion, the results described in this thesis provide new insights into the modes of action of maggot therapy in chronic wounds. The success of maggot therapy may be explained by the broad spectrum of processes that are modulated by maggot secretions. Show less
Polymyxins are clinically used antibiotics, discovered in mid-20th century. Once abandoned due to excessive nephrotoxicity, they are now used increasingly to address infections caused by multi-drug... Show morePolymyxins are clinically used antibiotics, discovered in mid-20th century. Once abandoned due to excessive nephrotoxicity, they are now used increasingly to address infections caused by multi-drug resistant Gram-negative bacteria.In this thesis, we describe the development and synthesis of analogues of polymyxin, aimed at reducing its associated nephrotoxicity. Analogues were made by semisynthesis, with modifications introduced mostly in the exocyclic portion of the molecule. Especially the introduction of a disulfide bond within the linked lipid helped in reducing the toxicity of the molecules, as evidenced by testing on proximal tubule epithelial cells. For most potent analogues, the antimicrobial activity was completely retained.In addition, this thesis describes studies on the mechanism of action of polymyxin, mostly based on the full stereoisomer of polymyxin B4. This analogue lacks antimicrobial activity, indicating its original stereochemistry to be of utmost importance for its use as an antibiotic.Hybrids based on polymyxin B derivatives are described, addressing non-conventional targets. A hybrid with vancomycin (typically active on Gram-positive bacteria only) shows activity on Gram-negative bacteria. A polymyxin-based hybrid coupled to a peptide with a beta-hairpin motif addresses Gram-negative bacteria, presumably by binding to outer membrane protein BamA. Show less
Groep B streptokokken (GBS) zijn belangrijke veroorzakers van ernstige infecties rondom de bevalling. Ter preventie van GBS-ziekte bij het kind worden antibiotica aan ongeveer 20% van alle... Show moreGroep B streptokokken (GBS) zijn belangrijke veroorzakers van ernstige infecties rondom de bevalling. Ter preventie van GBS-ziekte bij het kind worden antibiotica aan ongeveer 20% van alle zwangeren toegediend. Ondanks de toediening van antibiotica worden er soms kinderen ziek. Onderzoek naar de farmacokinetiek (lotgevallen van geneesmiddelen in het lichaam) en de huidige dosering van deze antibiotica tijdens de bevalling werd nog niet eerder verricht. Antibiotica zoals amoxicilline en clindamycine, die tijdens de bevalling worden toegediend, moeten bij de moeder een voldoende tijd een werkzame bloedspiegel hebben, de moederkoek passeren en ook bij het kind een voldoende tijd een werkzame bloedspiegel bereiken. Uit ons onderzoek blijkt, dat voor amoxicilline de farmacokinetiek bij vrouwen met gebroken vliezen voor aanvang van de bevalling vergelijkbaar is met die bij niet-zwangeren. Verschillende situaties bleken geen invloed te hebben op de farmacokinetiek van amoxicilline. Wanneer gebruik wordt gemaakt van een farmacokinetisch computermodel, waarin de bloedspiegels van amoxicilline van moeder, de navelstreng en het kind verwerkt zijn, lijkt de begin dosis van 2 gram amoxicilline afdoende voor het voorkomen van GBS-ziekte. Doseringen penicilline G die gebruikt worden voor de behandeling van GBS-ziekte bij vroegtijdig geboren kinderen zijn ook afdoende. Over clindamycine kunnen geen definitieve conclusies getrokken worden. Show less
The aim of this thesis was to stimulate rational and effective use of antimicrobials, by addressing the first two cornerstones: (1) refining stewardship of existing antimicrobials and (2) re... Show moreThe aim of this thesis was to stimulate rational and effective use of antimicrobials, by addressing the first two cornerstones: (1) refining stewardship of existing antimicrobials and (2) re-introducing old antibiotics within the framework of antimicrobial stewardship. The overall aim is to contribute to antimicrobial stewardship and to explore the value of the re-introduction of old antibiotics that are currently scarcely used. The basic step is the in vitro relationship expressed as minimal inhibitory concentration (MIC) for a given bacteria for a given antibiotic. The next step is the in vivo situation. This thesis concentrates on the in vivo situation. Show less
Renal clearance is responsible for the elimination of a large number of water-soluble drugs and metabolites and is therefore of large importance when characterizing the pharmacokinetics of drugs.... Show moreRenal clearance is responsible for the elimination of a large number of water-soluble drugs and metabolites and is therefore of large importance when characterizing the pharmacokinetics of drugs. Renal clearance includes glomerular filtration, tubular secretion and reabsorption and each of these processes is subject to different developmental changes. To estimate the renal clearance of drugs in children, a thorough understanding of these developmental changes in the different subprocesses contributing to renal function is needed. Therefore the aim of the research described in this thesis was to characterize the developmental changes in renal function over the entire pediatric age range. To this end, a system-based pharmacology approach was applied implicating that within the models for the different subprocesses contributing to renal function a distinction was made between system-specific and drug-specific properties. The transition to a more system-based pharmacology approach and the combination of different strategies (extrapolation to other drugs, adult data or non-clinical data) will result in an approach focusing on the underlying system instead of focusing on the drugs and may facilitate development of pharmacokinetic models and evidence-based dosing regimens in the pediatric population. Show less
This Thesis deals with the design, synthesis and biological evaluation of peptide-based drugs. In chapters 1-4, the development of peptides derived from natural gluten which can serve as drugs to... Show moreThis Thesis deals with the design, synthesis and biological evaluation of peptide-based drugs. In chapters 1-4, the development of peptides derived from natural gluten which can serve as drugs to combat the symptoms of celiac disease is described. These symptoms are caused by a misdirected immune response towards dietary gluten in genetically predisposed individuals. Peptides which can inhibit this immune response possibly can be used as an addition to the gluten-free diet, which is the only therapy available today. In Chapters 5 and 6, the synthesis and biological evaluation analogs of the antibiotic peptide Gramicidin S is described. Gramicidin S is a naturally occurring antibiotic peptide. It is very effective against bacteria, but also exhibits toxicity towards human red blood cells which limits its use to topical applications. Analogs of this natural peptide may lead to efficient antibiotics which are broadly applicable. Show less
