Study of ligand-based virtual screening tools in computer-aided drug design

Virtual screening is a central technique in drug discovery today. Millions of molecules can be tested in silico with the aim to only select the most promising and test them experimentally. The topic of this thesis is ligand-based virtual screening tools which take existing active molecules as starting point for finding new drug candidates. One goal of this thesis was to build a model that gives the probability that two molecules are biologically similar as function of one or more chemical similarity scores. Another important goal was to evaluate how well different ligand-based virtual screening tools are able to distinguish active molecules from inactives. One more criterion set for the virtual screening tools was their applicability in scaffold-hopping, i.e. finding new active chemotypes. In the first part of the work, a link was defined between the abstract chemical similarity score given by a screening tool and the probability that the two molecules are biologically similar. These results help to decide objectively which virtual screening hits to test experimentally. The work also resulted in a new type of data fusion method when using two or more tools. In the second part, five ligand-based virtual screening tools were evaluated and their performance was found to be generally poor. Three reasons for this were proposed: false negatives in the benchmark sets, active molecules that do not share the binding mode, and activity cliffs. In the third part of the study, a novel visualization and quantification method is presented for evaluation of the scaffold-hopping ability of virtual screening tools.

Utilization of Meat and bone meal for energy production

At the end of the 1990s the stock breeding in the Europe was suffering from the animal disease epidemics such as Bovine spongiform encephalopathy (BSE) and foot –and mouth disease. The European Union (EU) tackled to this problem by tightening the legislation of animal by-products. At this point, rendering and fat producing industries faces new challenges, which they have to cope with in a way of trying to find alternatives to their products (animal fats and meat and bone meal). One of the most promising alternatives to utilize these products was to use them in energy production purposes. The purpose of the Thesis was to examine the utilization possibilities of Meat and bone meal (MBM) for energy production. The first part of the Thesis consists of theory part. The theory part includes evaluation of basic properties of MBM as a fertilizer and as a fuel, legislative evaluation and evaluation of different burning techniques. The second part of the Thesis consists of burning tests in Energy laboratory of LUT with different mixtures of peat and MBM. The purpose of the burning tests was to identify co-firing possibilities of peat and MBM and emission- and ash properties for peat and MBM.

Luminescence-based assay methods in drug discovery

The drug discovery process is facing new challenges in the evaluation process of the lead compounds as the number of new compounds synthesized is increasing. The potentiality of test compounds is most frequently assayed through the binding of the test compound to the target molecule or receptor, or measuring functional secondary effects caused by the test compound in the target model cells, tissues or organism. Modern homogeneous high-throughput-screening (HTS) assays for purified estrogen receptors (ER) utilize various luminescence based detection methods. Fluorescence polarization (FP) is a standard method for ER ligand binding assay. It was used to demonstrate the performance of two-photon excitation of fluorescence (TPFE) vs. the conventional one-photon excitation method. As result, the TPFE method showed improved dynamics and was found to be comparable with the conventional method. It also held potential for efficient miniaturization. Other luminescence based ER assays utilize energy transfer from a long-lifetime luminescent label e.g. lanthanide chelates (Eu, Tb) to a prompt luminescent label, the signal being read in a time-resolved mode. As an alternative to this method, a new single-label (Eu) time-resolved detection method was developed, based on the quenching of the label by a soluble quencher molecule when displaced from the receptor to the solution phase by an unlabeled competing ligand. The new method was paralleled with the standard FP method. It was shown to yield comparable results with the FP method and found to hold a significantly higher signal-tobackground ratio than FP. Cell-based functional assays for determining the extent of cell surface adhesion molecule (CAM) expression combined with microscopy analysis of the target molecules would provide improved information content, compared to an expression level assay alone. In this work, immune response was simulated by exposing endothelial cells to cytokine stimulation and the resulting increase in the level of adhesion molecule expression was analyzed on fixed cells by means of immunocytochemistry utilizing specific long-lifetime luminophore labeled antibodies against chosen adhesion molecules. Results showed that the method was capable of use in amulti-parametric assay for protein expression levels of several CAMs simultaneously, combined with analysis of the cellular localization of the chosen adhesion molecules through time-resolved luminescence microscopy inspection.

Utilization of Particle Image velocimetry in PPOOLEX condensation experiments

Particle Image Velocimetry, PIV, is an optical measuring technique to obtain velocity information of a flow in interest. With PIV it is possible to achieve two or three dimensional velocity vector fields from a measurement area instead of a single point in a flow. Measured flow can be either in liquid or in gas form. PIV is nowadays widely applied to flow field studies. The need for PIV is to obtain validation data for Computational Fluid Dynamics calculation programs that has been used to model blow down experiments in PPOOLEX test facility in the Lappeenranta University of Technology. In this thesis PIV and its theoretical background are presented. All the subsystems that can be considered to be part of a PIV system are presented as well with detail. Emphasis is also put to the mathematics behind the image evaluation. The work also included selection and successful testing of a PIV system, as well as the planning of the installation to the PPOOLEX facility. Already in the preliminary testing PIV was found to be good addition to the measuring equipment for Nuclear Safety Research Unit of LUT. The installation to PPOOLEX facility was successful even though there were many restrictions considering it. All parts of the PIV system worked and they were found out to be appropriate for the planned use. Results and observations presented in this thesis are a good background to further PIV use.

Evaluation of Location Intelligence exploitation in capital-intensive business

As technology has developed it has increased the number of data produced and collected from business environment. Over 80% of that data includes some sort of reference to geographical location. Individuals have used that information by utilizing Google Maps or different GPS devices, however such information has remained unexploited in business. This thesis will study the use and utilization of geographically referenced data in capital-intensive business by first providing theoretical insight into how data and data-driven management enables and enhances the business and how especially geographically referenced data adds value to the company and then examining empirical case evidence how geographical information can truly be exploited in capital-intensive business and what are the value adding elements of geographical information to the business. The study contains semi-structured interviews that are used to scan attitudes and beliefs of an organization towards the geographic information and to discover fields of applications for the use of geographic information system within the case company. Additionally geographical data is tested in order to illustrate how the data could be used in practice. Finally the outcome of the thesis provides understanding from which elements the added value of geographical information in business is consisted of and how such data can be utilized in the case company and in capital-intensive business.

Deinking sludge utilization possibilities: technical, economic, and environmental assessments

This report introduces the ENPI project called “EMIR - Exploitation of Municipal and Industrial Residues” which was executed in a co-operation between Lappeenranta University of Technology (LUT), Saint Petersburg State University of Economics (SPbSUE), Saint Petersburg State Technical University of Plant Polymers (SPbSTUPP) and industrial partners from both Leningrad Region (LR), Russia and Finland. The main targets of the research were to identify the possibilities for deinking sludge management scenarios in co-operation with partner companies, to compare the sustainability of the alternatives, and to provide recommendations for the companies in the Leningrad Region on how to best manage deinking sludge. During the literature review, 24 deinking sludge utilization possibilities were identified, the majority falling under material recovery. Furthermore, 11 potential utilizers of deinking sludge were found within the search area determined by the transportation cost. Each potential utilizer was directly contacted in order to establish cooperation for deinking sludge utilization. Finally, four companies, namely, “Finnsementti” – a cement plant in Finland (S1), “St.Gobian Weber” – a light-weight aggregate plant in Finland (S2), “LSR-Cement” – a cement plant in LR (S3), and “Rockwool” – a stone wool plant in LR (S4) were seen as the most promising partners and were included in the economic and environmental assessments. Economic assessment using cost-benefit analysis (CBA) indicated that substitution of heavy fuel oil with dry deinking sludge in S2 was the most feasible option with a benefit/cost ratio (BCR) of 3.6 when all the sludge was utilized. At the same time, the use of 15% of the total sludge amount (the amount that could potentially be treated in the scenario) resulted in a BCR of only 0.16. The use of dry deinking sludge in the production of cement (S3) is a slightly more feasible option with a BCR of 1.1. The use of sludge in stone wool production is feasible only when all the deinking sludge is used and burned in an existing incineration plant. The least economically feasible utilization possibility is the use of sludge in cement production in Finland (S1) due to the high gate fee charged. Environmental assessment was performed applying internationally recognized life cycle assessment (LCA) methodologies: ISO 14040 and ISO 14044. The results of a consequential LCA stated that only S1 and S2 lead to a reduction of all environmental impacts within the impact categories chosen compared to the baseline scenario where deinking sludge is landfilled. Considering S1, the largest reduction of 13% was achieved for the global warming potential (GWP), whereas for S2, the largest decrease of abiotic depletion potential (ADP) was by 1.7%, the eutrophication potential (EP) by 1.8%, and a GWP of 2.1% was documented. In S3, the most notable increase of ADP and acidification potential (AP) by 2.6 and 1.5% was indicated, while the GWP was reduced by 12%, the largest out of all the impact categories. In S4, ADP and AP increased by 2.3 and 2.1% respectively, whereas ODP was reduced by 25%. During LCA, it was noticed that substitution of fuels causes a greater reduction of environmental impact (S1 and S2) than substitution of raw materials (S3 and S4). Despite a number of economically and environmentally acceptable deinking sludge utilization methods being assessed in the research, evaluation of bottlenecks and communications with companies’ representatives uncovered the fact that the availability of the raw materials consumed, and the risks associated with technological problems resulting from the sludge utilization, limited the willingness of industrial partners to start deinking sludge utilization. The research results are of high value for decision-makers at already existing paper mills since the result provide insights regarding alternatives to the deinking sludge utilization possibilities already applied. Thus, the research results support the maximum economic and environmental value recovery from waste paper utilization.