Synthesis and evaluation of glycomimetics : tool compounds binding to the FimH adhesin for analytical applications and new antagonists of the PapG-II adhesin

The spreading of bacterial resistance is promoting global research efforts toward the development of new therapeutic alternatives. Antivirulence therapy seems to be a valid, new avenue for discovering innovative medicines. In this context, anti-adhesive drugs, which block the first step of bacterial colonization of the host’s tissues are particularly attractive, as they do not kill the pathogens, and thus do not contribute to the selection of resistant strains. Urinary tract infections (UTIs) are among the most frequent reasons for antibiotic intake, thus playing a pivotal role in spreading bacterial resistance. Moreover, their recurrent nature reduces consistently patient’s quality of life. As the most common pathogen involved in UTIs is E. coli (about 80% in otherwise healthy patients), an anti-adhesive therapy against it would be highly valuable. E. coli uses filamentous structures called pili to adhere to the host’s tissues. In UTIs concerning the lower urinary tract (cystitis), type 1 pili are mainly involved. At the tip of type 1 pili, the lectin FimH is expressed, which recognizes mannosylated glycoproteins, abundant in the urinary bladder. A large body of literature is dedicated to antagonizing FimH. Despite nanomolar antagonists have been long discovered, suitable clinical candidates are lacking. One important determinant for a successful drug is the target occupancy time. Using surface plasmon resonance, we demonstrated that our lead structures have excellent kinetic profiles, when tested against the FimH lectin domain (paper 1). However, one crucial limiting factor was the poor pharmacokinetic profile of these antagonists. We therefore successfully tailored the physicochemical properties of a set of promising lead structures (paper 2). In order to support therapy, a detection system for FimH-expressing E. coli is of great importance. Biosensors offer several advantages, including reliability, low cost, and ease of use. Using a FimH antagonist as recognition element and FimH as analyte, we developed a FimH sensitive biosensor, providing the first proof of concept of label-free detection of a pathologically relevant protein, by field-effect, silicon nanoribbons-based sensors (SiNR-BioFET, paper 4). However, most research efforts have until very recently focused on the isolated lectin domain of FimH, which exists in a high-affinity state. To finally clarify if the high-affinity state is the appropriate therapeutic target, a study based on crystallography, molecular dynamics, and kinetics was undertaken on the full-length FimH protein, which exists prevalently in a low-affinity state (paper 3). The results support the use of the full-length protein as the most appropriate model for anti-adhesive therapy, thus opening a completely new research path for medicinal chemistry studies. In UTIs involving the human upper urinary tract (pyelonephritis), E. coli type P pili have been shown to play an important role. The adhesive properties of these pili arise from the PapG-II adhesin, which recognizes the tetrasaccharide epitope of tetraosyl galactosyl globosides (GbO4). Although the incidence of upper UTIs as compared to cystitis is rather low, the risk of serious organ damage is high. Moreover, the increasing frequency of resistant strains requires new therapeutic alternatives. Medicinal chemistry has so far focused on the modification of the minimal binding epitope, i.e. Galα(14)Gal. However, the best published lead compound exhibits affinity only in the mid-micromolar range. Based on a critical analysis of the present literature on antagonists of PapG-II and of the closely related PapG-I, a new, not yet explored sub-binding site was identified and explored. Disappointingly, no improvement in affinity could be achieved (chapter 3.2.2), confirming the challenging nature of the target. Fragment-based approaches have been shown to have a great potential for hard-to-drug targets. In our group, second-site ligand search using fragments had been successfully applied on other lectin targets. The same strategy was applied to PapG-II, albeit with scarce success (manuscript 1). The observation that the hexasaccharide epitope of the sialosyl galactosyl globoside shows 5-fold increased affinity for PapG-II as compared to the epitope of GbO4, from which it differs by an added disaccharid units at the non-reducing end, led us to study the details of the interaction. Crystallographic and thermodynamic investigations suggested that the improvement in affinity arises from an entropic contribution, due to the non-binding, terminal saccharidic units (paper 5). The data collected during the development of this thesis added important information on PapG-II and will assist further medicinal chemistry research toward the development of high-affinity antagonists

Harnessing AI and computing to advance climate modelling and prediction

There are contrasting views on how to produce the accurate predictions that are needed to guide climate change adaptation. Here, we argue for harnessing artificial intelligence, building on domain-specific knowledge and generating ensembles of moderately high-resolution (10–50 km) climate simulations as anchors for detailed hazard models

Anisotropy studies around the galactic centre at EeV energies with the Auger Observatory

Data from the Pierre Auger Observatory are analyzed to search for anisotropies near the direction of the Galactic Centre at EeV energies. The exposure of the surface array in this part of the sky is already significantly larger than that of the fore-runner experiments. Our results do not support previous findings of localized excesses in the AGASA and SUGAR data. We set an upper bound on a point-like flux of cosmic rays arriving from the Galactic Centre which excludes several scenarios predicting sources of EeV neutrons from Sagittarius $A$. Also the events detected simultaneously by the surface and fluorescence detectors (the `hybrid' data set), which have better pointing accuracy but are less numerous than those of the surface array alone, do not show any significant localized excess from this direction.Comment: Matches published versio

Highlights from the Pierre Auger Observatory

The Pierre Auger Observatory is the world's largest cosmic ray observatory. Our current exposure reaches nearly 40,000 km$^2$ str and provides us with an unprecedented quality data set. The performance and stability of the detectors and their enhancements are described. Data analyses have led to a number of major breakthroughs. Among these we discuss the energy spectrum and the searches for large-scale anisotropies. We present analyses of our X$_{max}$ data and show how it can be interpreted in terms of mass composition. We also describe some new analyses that extract mass sensitive parameters from the 100% duty cycle SD data. A coherent interpretation of all these recent results opens new directions. The consequences regarding the cosmic ray composition and the properties of UHECR sources are briefly discussed.Comment: 9 pages, 12 figures, talk given at the 33rd International Cosmic Ray Conference, Rio de Janeiro 201

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

Atmospheric effects on extensive air showers observed with the Surface Detector of the Pierre Auger Observatory

Atmospheric parameters, such as pressure (P), temperature (T) and density, affect the development of extensive air showers initiated by energetic cosmic rays. We have studied the impact of atmospheric variations on extensive air showers by means of the surface detector of the Pierre Auger Observatory. The rate of events shows a ~10% seasonal modulation and ~2% diurnal one. We find that the observed behaviour is explained by a model including the effects associated with the variations of pressure and density. The former affects the longitudinal development of air showers while the latter influences the Moliere radius and hence the lateral distribution of the shower particles. The model is validated with full simulations of extensive air showers using atmospheric profiles measured at the site of the Pierre Auger Observatory.Comment: 24 pages, 9 figures, accepted for publication in Astroparticle Physic

A search for point sources of EeV photons

Measurements of air showers made using the hybrid technique developed with the fluorescence and surface detectors of the Pierre Auger Observatory allow a sensitive search for point sources of EeV photons anywhere in the exposed sky. A multivariate analysis reduces the background of hadronic cosmic rays. The search is sensitive to a declination band from -85{\deg} to +20{\deg}, in an energy range from 10^17.3 eV to 10^18.5 eV. No photon point source has been detected. An upper limit on the photon flux has been derived for every direction. The mean value of the energy flux limit that results from this, assuming a photon spectral index of -2, is 0.06 eV cm^-2 s^-1, and no celestial direction exceeds 0.25 eV cm^-2 s^-1. These upper limits constrain scenarios in which EeV cosmic ray protons are emitted by non-transient sources in the Galaxy.Comment: 28 pages, 10 figures, accepted for publication in The Astrophysical Journa

Update on the correlation of the highest energy cosmic rays with nearby extragalactic matter

Data collected by the Pierre Auger Observatory through 31 August 2007 showed evidence for anisotropy in the arrival directions of cosmic rays above the Greisen-Zatsepin-Kuz'min energy threshold, \nobreak{$6\times 10^{19}$eV}. The anisotropy was measured by the fraction of arrival directions that are less than $3.1^\circ$ from the position of an active galactic nucleus within 75 Mpc (using the V\'eron-Cetty and V\'eron $12^{\rm th}$ catalog). An updated measurement of this fraction is reported here using the arrival directions of cosmic rays recorded above the same energy threshold through 31 December 2009. The number of arrival directions has increased from 27 to 69, allowing a more precise measurement. The correlating fraction is $(38^{+7}_{-6})$, compared with $21$ expected for isotropic cosmic rays. This is down from the early estimate of $(69^{+11}_{-13})$. The enlarged set of arrival directions is examined also in relation to other populations of nearby extragalactic objects: galaxies in the 2 Microns All Sky Survey and active galactic nuclei detected in hard X-rays by the Swift Burst Alert Telescope. A celestial region around the position of the radiogalaxy Cen A has the largest excess of arrival directions relative to isotropic expectations. The 2-point autocorrelation function is shown for the enlarged set of arrival directions and compared to the isotropic expectation.Comment: Accepted for publication in Astroparticle Physics on 31 August 201