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The methylation of arginine residues in numerous protein targets is a post-translational modification that has gained increased interest in the scientific community over the past two decades. Arginine methylation is performed by the dedicated family of protein arginine methyltransferases and is known to be involved in a plethora of cellular pathways and biochemical mechanisms in both healthy and disease states. The development of inhibitors for these enzymes for use as biological tools can lead to a more detailed understanding of the functions of the different members of the PRMT family. In addition, a number of recent studies point towards PRMTs as therapeutic targets for a number of diseases and the first clinical trials with compounds inhibiting PRMTs are now underway. We here provide a broad overview of the current status of the inhibitors that have been developed against PRMTs using both high-throughput screening and rational design approaches.

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-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.

Glucocorticoids are potent anti-inflammatory drugs widely used clinically to treat various inflammatory and immune conditions. However, two main clinical problems limit their use. GCs trigger severe side effects and they induce acquired glucocorticoid resistance, especially during chronic systemic treatment [6-11]. Therefore, developing novel strategies to improve the treatment inflammatory and immune conditions becomes urgent. Here, we present evidence that ginsenosides act as selective GR agonists, antagonists, and prodrugs. Moreover, our data illustrate that the number and positions of glucose groups bound to the steroid backbone of ginsenosides and different chemical structures are essential factors underlying the differential mechanistic effects of ginsenosides. Understanding the molecular mechanisms and the effects of natural compound (ginsenosides) opens a novel road towards developing improved anti-inflammatory GCs. Attaching one glucose group to classical GCs produced selective Gr agonists, such as GDex and GPdn, which exert anti-inflammatory effects without triggering side effects due to the absence of GR transactivation activities. Attaching two glucose groups to classical GCs resulted in the creation of GC prodrugs, such as GbPdn, which mediates its action locally at the site of inflammation, dependent on GBA2 activity, without triggering side effects.

Streptomycetes are soil-dwelling Gram-positive bacteria and can produce clinical drugs and adapt to environmental fluctuations through diverse morphological changes. The morphological development of streptomycetes features apical growth, which is determined by a tip-organizing center containing machinery for the synthesis of a cellulose-like glycan deposited at the cell surface. This thesis demonstrated that the cellulose-like glycan likely cellulose and the related synthesis machinery are unique in comparison with other Gram-negative cellulose synthesis systems. It showed that the synthesis of this glycan is performed by the glycosyltransferase ClsA and matured galactose-oxidase protein GlxA. Subsequently, the lytic polysaccharides monooxygenase LpmP and the glucanase ClsZ, adjacent to CslA/GlxA, cooperatively cleave peptidoglycan and create a passage to assist the exposure of this glycan on cell surface. In addition, this thesis also revealed coordination of polar growth determinants is performed by a stomatin-like protein StlP, which locates in the same gene cluster with CslA/GlxA/CslZ/LpmP. Oligomerization of StlP forms a fluid microdomain at hyphal tips, which spatially confines the whole tip organizing center. Furthermore, this thesis further showed that the cellulose-like glycan of Streptomyces coelicolor is responsible for the aggregation of clumps, which is distinct from Streptomyces lividans where this glycan mediates germlings’ aggregation.

This thesis has described novel synthetic methods to produce a variety of (glyco)peptides and their application in the study of various immunological processes. The first part of the thesis describes novel insights into the pathogenesis of multiple sclerosis, in the form of new findings in the areas of lectin-driven immunotolerance and a biochemical comparison between human and animal model antigen. The next part describes novel multivalently glycosylated peptides, that can be used to study lectin binding and lectin mediated antigen uptake. The final part of the thesis describes a novel method to produce trans-cyclooctene protected peptides, an exciting new category of molecular tools within chemical biology that have recently been developed.

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 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.

Vancomycin is a last-resort antibiotic for the treatment of many Gram-positive bacterial infections, while remaining inactive against Gram-negative strains. Resistance to vancomycin in Gram-positive stains continues to develop. This thesis describes the recent developments in semisynthetically modifying glycopeptide antibiotics to improve their antibacterial activity. Furthermore, the development of several semisynthetic glycopeptide antibiotics are described including the guanidino lipoglycopeptides, the vancomyxins, and the vancomycin-sideromycins. The guanidino lipoglycopeptides are readily synthesized from vancomycin and display potent in vitro and in vivo activity against Gram-positive bacteria, including vancomycin-resistant strains. Assessment of the activity, properties, and mechanism of action of the guanidino lipoglycopeptides shows the potential of these novel glycopeptides to become best-in class. The vancomyxins, which consist of covalently conjugated vancomycin and outer membrane disruptor polymyxin nonapeptide, display enhanced activity against Gram-negative bacterial strains compared to vancomycin monotherapy or co-administration of the two components. The vancomycin-sideromycins are also aimed at conferring antibacterial activity against Gram-negative bacteria by exploiting an iron-uptake system. Overall, a variety of semisynthetic vancomycin derivatives, aimed at overcoming vancomycin resistance or sensitizing Gram-negative strains, are developed and assessed on their activity in this work.

Extending our current arsenal of antibiotics is key to staying ahead in the arms race between humans and resistant bacteria. Classes of antibiotics otherwise limited to the treatment of Gram-positive pathogens may be potentiated against Gram-negative bacteria by disruption of their outer membrane. The work described in this thesis focuses on the development of novel synergists designed to selectively disrupt the outer membrane and in doing potentiate the activity of antibiotics that are otherwise inactive against Gram-negative bacteria.

The work described in this thesis focuses on the development of linear or cyclized peptide probes against protein N-methyltransferases to characterize their specific binding behavior, providing further binding details for inhibitory activity study. The thesis not only describes the extended application to produce peptide-based transition states mimicking PRMT inhibitors but builds an LC-MS/MS method to evaluate CARM1 inhibition and activity.

Monoacylglycerol lipase (MAGL) is the principal enzyme responsible for hydrolysis of the endocannabinoid 2-arachidonoylglycerol (2-AG). MAGL inhibition provides several potential therapeutic opportunities, including anti-nociceptive, anti-inflammatory and anti-cancer activity. This thesis describes the discovery of LEI-515 as peripherally restricted, reversible MAGL inhibitor. A library of 233.820 compounds was screened at the Pivot Park Screening Center and 7 hits were confirmed. Over 100 analogues of the most promising hit were designed, synthesized and evaluated in a natural substrate assay and activity-based protein profiling. This resulted in the identification of LEI-515, which has subnanomolar inhibitory potency, high selectivity and good metabolic stability. LEI-515 is a reversible inhibitor that forms a hemiketal with catalytic Ser122, stabilized by hydrogen bonds with Ala53 and Met123. LEI-515 is > 100-fold selective over a panel of 44 ion channels, receptors and enzymes, including the cannabinoid CB1 and CB2 receptor, hERG and cyclooxygenases. Targeted lipidomics revealed that LEI-515 increased cellular 2-AG levels in a concentration and time-dependent manner. Pharmacokinetic studies indicated that LEI-515 has excellent oral bioavailability, but does not penetrate the brain.

We have examined sequences from the ligand-binding domain of the nicotinic acetyl choline receptor (nAChR) in 148 vertebrate species. We are in interested in this receptor because the α-neurotoxins of many venomous snakes binds to this receptor in its location at the neuromuscular junction in all vertebrates. Furthermore, some animals have evolved resistance to snake venoms and show modifications in the ligand binding domain of the nAChR which inhibit the binding of snake α-neurotoxins. Our analysis has shown that numerous vertebrate species, most of which were not previously known to possess α-neurotoxin resistance, do actually contain resistance-related modifications. These modifications are present in most of the taxa in our dataset, with the unexpected exclusion of the birds. It was particularly surprising to us that the snake-specialist predatory birds Circaetus pectoralis (black-chested snake eagle) and Sagittarius serpentarius (secretary bird) did not possess resistance modifications. There were also relatively few resistance-related mutations within the mammals. By contrast, there were multiple convergent evolutions of the well-characterised N-glycosylation motif within the squamate reptiles—particularly the snakes. We also identified a number of sites under positive selection, such as mutations to the proline subsite. Future functional testing will be needed to validate that these modifications do indeed confer resistance. To provide functional confirmation that resistance-related modifications do indeed reduce susceptibility to toxins, we used developmental bioassays. These assays showed that two species possessing resistance-related modifications of the nAChR (stickleback and bearded dragon) were less susceptible to the toxic effects of cobra venom than two species that lacked such modifications (zebrafish and chicken). In summary, we demonstrate that the range of mechanisms along with the phylogenetic distribution of resistance to snake α-neurotoxin appears to be more extensive than was previously appreciated. It also shows strong evidence of the convergent evolution of the same resistance mutations in independent linages. Our findings also support the notion that the mutations we have identified in this thesis may represent adaptive change in response to selective pressures exerted by α-neurotoxic snake venoms in an evolutionary arms race. Thus, we conclude that the evolutionary arms race between predator and prey appears to be a pervasive feature of the trophic interactions surrounding venomous snakes, which is shaping the molecular evolution of the nAChR in the vertebrates.

This thesis describes research concerned with the design, synthesis and biological evaluation of cyclic peptides that target infectious diseases. Chapter 2 describes the design and synthesis of cyclic peptides related to Laspartomycin C. A small library of lipopeptides were synthesized and tested for their activity. In collaboration with the group of Bert Janssen (Utrecht University) high-resolution crystal structures were obtained for two compounds. Interestingly, the results show that a high-ordered crystal arrangement is formed, this higher-ordered arrangement is driven by various amino acids not present in the parent compound but found in the amphomycin/friulimicin class. Chapter 3 builds upon the results described in Chapter 2. To further understand the amino acids that play a key role in the activity of Laspartomycin C three achiral amino acids (Gly) were substituted with the bulkier 2-aminoisobutyric acid (Aib) counterpart. These findings led to the discovery that position eight in Laspartomycin is crucial for activity as it is part of the calcium binding motif. The other two positions were much more amenable to change and further substituted for either a L- or D-Alanine. While overall activity increased when going from Aib to either L- or D-alanine it was found that there was an eight-fold difference in activity between L- and D-alanine at position six (with D-alanine being more active). Position six is always a D-amino acid in the broader CDA family, with Laspartomycin C being the only one that contains a Gly at that position. Chapter 4 reports a fast and convenient synthetic route to obtaining bicyclic peptides that are active against Gram-negative pathogens. Specifically, this synthesis route uses a chemoenzymatic approach to generate large quantities of polymyxin E nona-peptide (PMEN). This PMEN can be covalently linked to the second β-hairpin peptide macrocycle. These peptides bind to the newly reported BamA complex in Gram-negative pathogens and even demonstrate potent activity against MCR-1 pathogens. Chapter 5 focuses on the design and synthesis of β-hairpin peptide macrocycles that can be recognized by the newly discovered bacterial enzyme EarP. EarP transfers a rhamnose to a specific arginine residue in its acceptor protein EF-P. The in vitro rhamnosyltransferase activity of EF-P is abolished when presented with linear substrate peptide (derived from EF-P). However, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. This was done in collaboration with the group of Marthe Walvoort (University of Groningen). Using detailed NMR studies, it was established that the active peptide substrates all share some degree of β-hairpin formation.

This thesis describes the antimicrobial discovery strategy developed in our group, the den Hertog Group at the Hubrecht Institute. It includes a cultivation-based screening approach for novel antimicrobial agents from the source of fungi, and a bacterial time-lapse imaging approach for antimicrobial mechanism of action (MoA) identification. With this strategy, we have discovered several interesting antimicrobial agents and have demonstrated the detailed antimicrobial property of two of them, berkchaetoazaphilone B (BAB) and harzianic acid (HA).

This thesis describes the antimicrobial discovery strategy developed in our group, the den Hertog Group at the Hubrecht Institute. It includes a cultivation-based screening approach for novel antimicrobial agents from the source of fungi, and a bacterial time-lapse imaging approach for antimicrobial mechanism of action (MoA) identification. With this strategy, we have discovered several interesting antimicrobial agents and have demonstrated the detailed antimicrobial property of two of them, berkchaetoazaphilone B (BAB) and harzianic acid (HA).

NNMT wordt beschouwd als een nieuw potentieel farmacologisch doelwit in de behandeling van een verscheidenheid van kankers, stofwisselingsziekten en andere pathologieën. Het toenemend aantal publicaties waarin de rol van NNMT bij ziekten wordt opgehelderd, heeft op zijn beurt de ontwikkeling van krachtige en selectieve remmers van NNMT gestimuleerd, waarbij in de afgelopen vijf jaar een toenemend aantal verbindingen is onthuld. Hoofdstuk 1 geeft een uitgebreid overzicht van de huidige status van de ontwikkeling van NNMT remmers, relevante in vitro en in vivo studies, en een bespreking van de uitdagingen waar men bij de ontwikkeling van NNMT remmers voor staat. In hoofdstuk 2 werd een gevarieerde bibliotheek van remmers geprepareerd om de verschillende gebieden van de NNMT bindingsplaats te onderzoeken. In hoofdstuk 3 wordt verslag gedaan van een scaffold-hopping strategie om nieuwe en krachtige bisubstraat NNMT remmers te genereren. In hoofdstuk 4 wordt een prodrug strategie beschreven om de polariteit van verbinding 17u te verlagen en de cellulaire activiteit te verbeteren. In hoofdstuk 5 wordt het ontwerp en de synthese beschreven van een bibliotheek van verbindingen die zich richten op de covalente interactie met actieve site cysteïne en serine residuen met behulp van verschillende functionele groepen.

Synthesis and application of chemical biology tools to study immunomodulatory signaling lipids.

The main focus of the thesis is the discovery and development of novel inhibitors of bacterial metallo-β-lactamases (MBLs). Chapter 1 provides an overview of FDA-approved β-lactamase inhibitors as well as those currently being evaluated in clinical trials. Chapters 2 and 3 describe our evaluation of small-molecule aminocarboxylic acids either commercially available or prepared via chemoenzymatic approaches for their activity against clinically important MBLs. We found that nitrilotriacetic acid and its phosphonic acid isostere, as well as ethylenediamine-N,N′-disuccinic acid (EDDS), are potent inhibitors of New-Delhi metallo-beta-lactamase (NDM-1). Focusing on another class of MBL inhibitors, chapter 4 describes our study of selected thiol-containing compounds. Among them, thiomandelic acid showed the most potent and broad-spectrum synergistic activity when combined with meropenem against MBL-producing gram-negative bacteria. Stability studies, however, showed that thiomandelic acid is oxidized to its corresponding disulfide with the half-life of ca. 5 h. To address the stability and selectivity issue associated with thiols, in chapter 5 we describe a prodrug approach where we synthesized and evaluated a series of thiol conjugates of cephalosporins. Some of these cephalosporin conjugates exhibit potent inhibition of IMP class of MBLs. Finally, chapter 6 describes our biochemical evaluation of a newly identified class A carbapenemase.

Streptomyces present a valuable platform for natural product discovery. Lugdunomycin is a novel angucycline-derived polyketide from Streptomyces sp QL37, with unprecedented skeleton and antimicrobial activity. This dissertation covers the research on the biosynthesis of this novel antibiotic and the developmental biology of Streptomyces. The data in this thesis have provided important new insights into the puzzle of lugdunomycin biosynthesis and the sporulation-specific cell division of Streptomyces. By means of molecular biology, structural biology, biochemical, chemical and bioinformatics approaches, we have uncovered the potential functions of the key enzymes, especially those encoded oxygenases (LugOI-LugOV) in lugdunomycin biosynthesis. Furthermore, we extensively studied the role of SsgB in Streptomyces development, that led us to the discovery of longitudinal cell division that support the predominant role of SsgB in the accurate positioning of the division site and the placement of the Z-ring.

Doxorubicin is one of the Topoisomerase II inhibitors that are used for the treatment of various types of cancer, including leukaemia and non-Hodgkin lymphoma. As effective and popular as this drug is, its usage is hugely limited by the cumulative cardiotoxicity it brings along. Conversely, aclarubicin sees little use in the Western world but is not nearly as cardiotoxic. This thesis describes a flexible methodology that allowed for the preparation of mono-, di- and trisaccharide analogues of doxorubicin and aclarubicin. Structural variation in the target compounds has been achieved by swapping and shuffling of the sugar sequence and varying the alkylation pattern on the amine functionality.

Almost all bacteria are enveloped by a cell wall that provides cellular protection. In this thesis I show that some filamentous actinomycetes have a surprising natural ability to adopt a cell wall-deficient life style. The formation of these newly identified S-cells is a transient morphological adaptation in response to hyperosmotic stress conditions. In contrast, prolonged exposure to cell wall-targeting antibiotics or osmotic stress leads to the formation of so-called L-form cells, which are mutants that can proliferate indefinitely without their cell wall. The exciting properties of L-forms were used to discover a new cell-wall biosynthetic enzyme and to study enzyme secretion in the absence of a cell wall.

The studies presented in the work show the potential of the integrative use of biophysical data in defining the structural basis of protein interactions. Even if the results obtained hold a degree of ambiguity, this approach allows to iteratively refine and validate the model and interpret its meaning for the molecular basis of protein function. Often all three points at the same time. This dynamic nature makes the use of structural models in the design of therapeutic compounds especially useful since the inhibition of a certain protein function might not require a structure to be accurate down to the last atom but rather highlight key interactions or structural features that can be addressed in context of small molecule or peptide inhibitors. Presented are the use of strucutral biochemistry techniques to investigate the mechanism of how the ubiquitine ligase PSIP1 obtains its target specificity. Furthermore, another epigenetic effector protein PSIP1 is investigated with the aim to develop a workflow for the design of potential peptide-based inhibitors.

This thesis describes the structural and biochemical characterization of the β-lactamase BlaC from Mycobacterium tuberculosis (Mtb), and the Alr and YlmE proteins from Streptomyces coelicolor A3(2).Mtb is the main cause of tuberculosis. The inherent production of BlaC by Mtb makes the antibiotic treatment of tuberculosis particularly difficult because BlaC renders Mtb naturally resistant to β-lactam antibiotics. One possible way to circumvent this BlaC-mediated resistance is the co-administration of β-lactamase inhibitors, thus preventing antibiotics’ hydrolysis. The crystal structure of BlaC was determined in complex with the β-lactamase inhibitors clavulanic acid, sulbactam, tazobactam, and avibactam, and new BlaC-inhibitors covalent adducts were visualized. The affinity of BlaC for the inhibitors was further studied using catalytically inactive mutants of the enzyme.In parallel, the Alr and YlmE proteins from S. coelicolor A3(2) were studied. Alr and YlmE are putatively involved in the racemization of L-Ala into D-Ala. The latter is an essential peptidoglycan building block, and ensures cell wall compaction and bacterial survival. The structural and biochemical characterization of the heterologous, purified Alr and YlmE proteins showed that while Alr is indeed involved in Ala racemization, YlmE is not. Our findings revealed a possible new, surprising role for YlmE in nucleic acid binding.