Chemical activity of anticancer compounds : computational studies on the mechanism of bleomycin and the recognition of flavonoids

The thesis is focused on the DNA-cleaving antibiotic bleomycin that is successfully used in the chemotherapy against several types of cancer like head and neck cancer or certain lymphomas and testicular cancer. Although it has been in use for more than two decades, the mechanism of its action is not known. Thus the harmful side effects are difficult to eliminate. On the other hand the process of design or improvement of pharmaceuticals is extremely complex and expensive. Therefore a new trend within drug discovery is emerging with the application of clean chemistry, by performing molecular modeling of new compounds and by running virtual tests to assess their suitability before an expensive synthesis attempt is made. In the thesis, the contribution of different computational methods into this field is discussed, emphasizing the growing role played by quantum mechanical methods. Using state-of-the-art methods, an insight into the mechanism of bleomycin action was gained. The possible reaction pathways of the active bleomycin-Fe(III)-OOH complex with the deoxyribose sugar of DNA were investigated. The simulations show that a facile decaying process involves a homolytic O-O bond cleavage with an almost simultaneous hydrogen atom abstraction. The formation of a hydrogen bond appears to be crucial for the O-O bond cleavage in the Fe(III)-OOH species. The highly selective reaction between the bleomycin drug and the genetic material comes from the selectivity of the created hydrogen bondLEI Universiteit LeidenLIC projectLIO

The metal bonding domain of the antitumor drug Fe(II)-bleomycin: a DFT investigation

Solid state NMR/Biophysical Organic Chemistr

The SULSA Assay Development Fund:accelerating translation of new biology from academia to pharma

With industry increasingly sourcing preclinical drug discovery projects from academia it is important that new academic discoveries are enabled through translation with HTS-ready assays. However, many scientifically interesting, novel molecular targets lack associated high-quality, robust assays suitable for hit finding and development. To bridge this gap, the Scottish Universities Life Sciences Alliance (SULSA) established a fund to develop assays to meet quality criteria such as those of the European Lead Factory. A diverse project portfolio was quickly assembled, and a review of the learnings and successful outcomes showed this fund as a new highly cost-effective model for leveraging significant follow-on resources, training early-career scientists and establishing a culture of translational drug discovery in the academic community

Lasing without inversion in three-level systems : self-pulsing in the cascade schemes

Lasing without inversion (LWI) in specific models of closed three-level systems is analyzed in terms of nonlinear dynamics. From a linear stability analysis of the trivial nonlasing solution of the homogeneously broadened systems with on-resonance driving and laser fields, we find that, near lasing threshold, resonant closed Λ and V schemes yield continuous-wave LWI while resonant cascade schemes can give rise to self-pulsing LWI. The origin of this different behavior is discussed. For parameters of a real cascade system in atomic 138Ba we check numerically that the self-pulsing solution is stable in a broad range of nonzero detunings. It is shown that the self-pulsing emission can still be observed when the typical residual Doppler broadening of an atomic beam is taken into account

NON-DESTRUCTIVE TESTING OF THE HISTORIC TIMBER ROOF STRUCTURES OF THE NATIONAL MUSEUM IN STOCKHOLM, SWEDEN

The National Museum in Stockholm is Sweden’s leading museum of art and design. Behind the now closed doors of the National Museum and its construction coverings a renovation project is taking place, which began in 2014 and will be completed in 2018. The renovation project will create a modern museum, a brighter atmosphere for the arts and for its visitors. Part of the renovation project was to de-sign and upgrade the timber roof structure for new loads according to Eurocode 5. As the roof structure was originally built in 1860, it was important to evaluate the condition and mechanical properties of the original load-bearing timber members. The roof structure, which is of main interest, comprises roof trusses and lantern structures.The main aim of the project regarding the timber roof structure in the National Museum was a safety verification in both the ultimate state (ULS) and the serviceability limit state (SLS). The preliminary capacity calculations for the roof structure showed that the roof members were under the new load conditions (with increased loads due to security and environmental requirements) utilized above 100%. Therefore, an investigation into the properties of the old timber members and connections was of vital importance. The need for non-destructive testing (NDT) of structural timber is well known under the name of strength grading and the concept has been used for many years to classify timber with respect to mechanical performance. The stress wave technique used in the project was based on commercial instruments such as FAKOPP\uae. The timber quality investigation for the attic roof structures showed that the material was generally in very good condition. As a result, according to SS-EN 338-2009, the timber strength could be assigned strength class C27–C30. Based on the results of the investigation, further design of strengthening works and refurbishment of the roof structure were being undertake

Triazole Fungicides Can Induce Cross-Resistance to Medical Triazoles in Aspergillus fumigatus

Contains fulltext : 103858.pdf (publisher's version ) (Open Access)BACKGROUND: Azoles play an important role in the management of Aspergillus diseases. Azole resistance is an emerging global problem in Aspergillus fumigatus, and may develop through patient therapy. In addition, an environmental route of resistance development has been suggested through exposure to 14alpha-demethylase inhibitors (DMIs). The main resistance mechanism associated with this putative fungicide-driven route is a combination of alterations in the Cyp51A-gene (TR(34)/L98H). We investigated if TR(34)/L98H could have developed through exposure to DMIs. METHODS AND FINDINGS: Thirty-one compounds that have been authorized for use as fungicides, herbicides, herbicide safeners and plant growth regulators in The Netherlands between 1970 and 2005, were investigated for cross-resistance to medical triazoles. Furthermore, CYP51-protein homology modeling and molecule alignment studies were performed to identify similarity in molecule structure and docking modes. Five triazole DMIs, propiconazole, bromuconazole, tebuconazole, epoxiconazole and difenoconazole, showed very similar molecule structures to the medical triazoles and adopted similar poses while docking the protein. These DMIs also showed the greatest cross-resistance and, importantly, were authorized for use between 1990 and 1996, directly preceding the recovery of the first clinical TR(34)/L98H isolate in 1998. Through microsatellite genotyping of TR(34)/L98H isolates we were able to calculate that the first isolate would have arisen in 1997, confirming the results of the abovementioned experiments. Finally, we performed induction experiments to investigate if TR(34)/L98H could be induced under laboratory conditions. One isolate evolved from two copies of the tandem repeat to three, indicating that fungicide pressure can indeed result in these genomic changes. CONCLUSIONS: Our findings support a fungicide-driven route of TR(34)/L98H development in A. fumigatus. Similar molecule structure characteristics of five triazole DMIs and the three medical triazoles appear the underlying mechanism of cross resistance development. Our findings have major implications for the assessment of health risks associated with the use of triazole DMIs

Narrowing of EIT resonance in a Doppler Broadened Medium

We derive an analytic expression for the linewidth of EIT resonance in a Doppler broadened system. It is shown here that for relatively low intensity of the driving field the EIT linewidth is proportional to the square root of intensity and is independent of the Doppler width, similar to the laser induced line narrowing effect by Feld and Javan. In the limit of high intensity we recover the usual power broadening case where EIT linewidth is proportional to the intensity and inversely proportional to the Doppler width.Comment: 4 pages, 2 figure

Modulators of 14-3-3 Protein-Protein Interactions

Direct interactions between proteins are essential for the regulation of their functions in biological pathways. Targeting the complex network of protein-protein interactions (PPIs) has now been widely recognized as an attractive means to therapeutically intervene in disease states. Even though this is a challenging endeavor and PPIs have long been regarded as 'undruggable' targets, the last two decades have seen an increasing number of successful examples of PPI modulators resulting in a growing interest in this field. PPI modulation requires novel approaches and the integrated efforts of multiple disciplines to be a fruitful strategy. This Perspective focuses on the hub protein 14-3-3, which has several hundred identified protein interaction partners and is therefore involved in a wide range of cellular processes and diseases. Here, we aim to provide an integrated overview of the approaches explored for the modulation of 14-3-3 PPIs and review the examples resulting from these efforts in both inhibiting and stabilizing specific 14-3-3 protein complexes by small molecules, peptide-mimetics and natural products

Patients with allergic rhinitis and allergic asthma share the same pattern of eosinophil and neutrophil degranulation after allergen challenge

<p>Abstract</p> <p>Background</p> <p>Patients with allergic rhinitis and allergic asthma demonstrate comparable local and systemic eosinophil inflammation, and yet they present with different clinical pictures. Less is even known about the contribution of neutrophil inflammation in allergic diseases. The aim of the study was to examine the propensity and selectivity of granule release from primed systemic eosinophils and neutrophils in allergic rhinitis and allergic asthma after seasonal and experimental allergen exposure. We hypothesize that the dissimilar clinical manifestations are due to diverse eosinophil and neutrophil degranulation.</p> <p>Methods</p> <p>Nine birch pollen allergic patients with rhinitis, eight with asthma and four controls were studied during pollen season and after nasal and bronchial allergen challenge. Eosinophils and neutrophils were incubated in vitro with assay buffer and opsonized Sephadex particles for spontaneous and C3b-induced granule protein release. The released amount of eosinophil cationic protein (ECP), eosinophil peroxidase (EPO) and myeloperoxidase (MPO) was measured by specific radioimmunoassay.</p> <p>Results</p> <p>C3b-induced degranulation resulted in increased release of ECP and MPO from primed blood eosinophils and neutrophils in both allergic rhinitis and allergic asthma during pollen season and after both nasal and bronchial challenge (p-values 0.008 to 0.043). After bronchial challenge, the ECP release was significantly higher in the rhinitic group compared to the asthmatic group [19.8 vs. 13.2%, (p = 0.010)]. The propensity for EPO release was weak in all challenge models but followed the same pattern in both allergic groups.</p> <p>Conclusions</p> <p>Systemically activated eosinophils and neutrophils have similar patterns of degranulation after allergen exposure in allergic rhinitis and allergic asthma. The released amount of ECP, EPO and MPO was similar in all allergen challenge models in both allergic groups. Our results indicate that other mechanisms than the magnitude of eosinophil and neutrophil inflammation or the degranulation pattern of the inflammatory cells determines whether or not an allergic patient develops asthma.</p