Integração das técnicas de triagem virtual e triagem biológica automatizada em alta escala: oportunidades e desafios em P&D de fármacos

High-throughput screening (HTS) and virtual screening (VS) are useful methods employed in drug discovery, allowing the identification of promising hits for lead optimization. The efficiency of these approaches depends on a number of factors, such as the organization of high quality databases of compounds and the parameterization of essential components of the screen process. This brief review presents the basic principles of the HTS and VS methods, as well as a perspective of the utility and integration of these drug design approaches, highlighting current opportunities and future challenges in medicinal chemistry.

Desenvolvimento e aplicação de métodos para a determinação de ivermectina em medicamentos de uso veterinário

Two methods for the determination of Ivermectin in veterinarian medications were developed and compared. One of the methods was based on UV spectrometry and the other on HPLC-UV. The former method was shown to be positively biased regarding the nominal concentrations of Ivermectin in different medications. The method of standard addition was unable to correct this bias, indicating significant matrix effects. The HPLC-UV method showed good linearity, throughput, recovery and limits of detection and quantitation adequate for its application in the evaluation of Ivermectin in medications. Several medications were evaluated and good agreement between our results and their nominal concentrations was found.

Simultaneous analysis of saturated and unsaturated fatty acids present in pequi fruits by capillary electrophoresis

In the current study, an alternative method has been proposed for simultaneous analysis of palmitic, stearic, oleic, linoleic, and linolenic acids by capillary zone electrophoresis (CZE) using indirect detection. The background electrolyte (BGE) used for the analysis of these fatty acids (FAs) consisted of 15.0 mmol L−1 NaH2PO4/Na2HPO4 at pH 6.86, 4.0 mmol L−1 SDBS, 8.3 mmol L−1 Brij 35, 45% v/v acetonitrile (can), and 2.1% n-octanol. The FAs quantification of FAs was performed using a response factor approach, which provided a high analytical throughput for the real sample. The CZE method, which was applied successfully for the analysis of pequi pulp, has advantages such as short analysis time, absence of lipid fraction extraction and derivatization steps, and no significant difference in the 95% confidence intervals for FA quantification results, compared to the gas chromatography official method (AOCS Ce 1h-05).

Koneinvestoinnin suunnittelu valmistavaan teollisuuteen

Tämän diplomityön tavoitteena oli tutustua ohutlevyjen nykyaikaisiin koneellisiin leikkausmenetelmiin ja tutkia niiden soveltuvuutta yrityksen tarpeisiin. Kohdeyrityksessä investoinnin tarve jakautui tuottavuusinvestoinnin, korvausinvestoinnin ja strategisen investoinnin kesken. Tavoitteena oli luoda investointipolku, jonka avulla poissuljettiin menetelmät, jotka eivät soveltuneet yrityksen tuotantoon. Työn kirjallisuusosuudessa tarkastellaan teoriatietoja, jotka liittyvät yleisesti nykyaikaisiin ohutlevyjen leikkausmenetelmiin sekä investointiprojektin suunnitteluun ja toteutuksen teoriaan. Lisäksi käsitellään investointeihin liittyviä kannattavuus- ja kustannuslaskennan perusperiaatteita. Työn empiirisessä osassa selvitettiin yrityksen ohutlevyosien valmistuksen periaatteita nykytila-analyysin avulla. Tämän perusteella määritettiin nykyaikaisista markkinoilla olevista menetelmistä yritykselle soveltuvin. Tutkimuksen perusteella laserleikkaus oli menetelmistä soveltuvin. Perusinvestoinniltaan laser oli vaihtoehtoisista menetelmistä kallein, mutta se soveltui käytettävyyden, tehokkuuden, joustavuuden ja muiden ominaisuuksiensa perusteella parhaiten tuotannon tarpeisiin. Työn merkittävimmät tulokset osoittivat, että investoinnin kannattavuus riippui koneelle saatavasta käyttösuhteesta. Uusien koneiden tehokkuus lyhentäisi tuotannon läpimenoaikoja, mutta ilman riittävää kapasiteetin käyttöastetta kappaleiden omakustannusarvo nousisi. Lopputulokset ja suositukset on esitetty työn lopussa.

Parallel-Operating Three-Phase Voltage Source Inverters – Circulating CurrentModeling, Analysis and Mitigation

The maximum realizable power throughput of power electronic converters may be limited or constrained by technical or economical considerations. One solution to this problemis to connect several power converter units in parallel. The parallel connection can be used to increase the current carrying capacity of the overall system beyond the ratings of individual power converter units. Thus, it is possible to use several lower-power converter units, produced in large quantities, as building blocks to construct high-power converters in a modular manner. High-power converters realized by using parallel connection are needed for example in multimegawatt wind power generation systems. Parallel connection of power converter units is also required in emerging applications such as photovoltaic and fuel cell power conversion. The parallel operation of power converter units is not, however, problem free. This is because parallel-operating units are subject to overcurrent stresses, which are caused by unequal load current sharing or currents that flow between the units. Commonly, the term ’circulatingcurrent’ is used to describe both the unequal load current sharing and the currents flowing between the units. Circulating currents, again, are caused by component tolerances and asynchronous operation of the parallel units. Parallel-operating units are also subject to stresses caused by unequal thermal stress distribution. Both of these problemscan, nevertheless, be handled with a proper circulating current control. To design an effective circulating current control system, we need information about circulating current dynamics. The dynamics of the circulating currents can be investigated by developing appropriate mathematical models. In this dissertation, circulating current models aredeveloped for two different types of parallel two-level three-phase inverter configurations. Themodels, which are developed for an arbitrary number of parallel units, provide a framework for analyzing circulating current generation mechanisms and developing circulating current control systems. In addition to developing circulating current models, modulation of parallel inverters is considered. It is illustrated that depending on the parallel inverter configuration and the modulation method applied, common-mode circulating currents may be excited as a consequence of the differential-mode circulating current control. To prevent the common-mode circulating currents that are caused by the modulation, a dual modulator method is introduced. The dual modulator basically consists of two independently operating modulators, the outputs of which eventually constitute the switching commands of the inverter. The two independently operating modulators are referred to as primary and secondary modulators. In its intended usage, the same voltage vector is fed to the primary modulators of each parallel unit, and the inputs of the secondary modulators are obtained from the circulating current controllers. To ensure that voltage commands obtained from the circulating current controllers are realizable, it must be guaranteed that the inverter is not driven into saturation by the primary modulator. The inverter saturation can be prevented by limiting the inputs of the primary and secondary modulators. Because of this, also a limitation algorithm is proposed. The operation of both the proposed dual modulator and the limitation algorithm is verified experimentally.

Direct determination of calcium in milk by atomic absorption spectrometry using flow-injection analysis

A flow-injection system with sample and reagent addition by the synchronous merging zones approach for calcium determination in milk by flame AAS is proposed. Main parameters were optimized using a factorial design with central point. The optimum conditions were 2.5% (m/v) for La concentration, 8 mL min-1 for the carrier flow-rate, 20 cm for coiled reactor and 250 ìL for sample volume. Different sample preparation procedures were evaluated such as dilution in water or acid and microwave-assisted decomposition using concentrated or diluted acids. The optimized flow system was applied to determine Ca in eleven commercial milk samples and two standard reference materials diluted in water. Similar calcium levels were encountered comparing the results obtained by the proposed method (dilution in water) with those obtained using microwave-oven digestion. Results obtained in two standard reference materials were in agreement at 95% confidence level with those certified. Recoveries of spiked samples were in the 93% - 116% range. Relative standard deviation (n = 12) was < 5.4% and the sample throughput was 150 measurements per hour, corresponding to a consumption of 250 µL of sample and 6.25 mg La per determination.

The application of cDNA and tissue microarray methods in the study of human carcinomas

Currently, numerous high-throughput technologies are available for the study of human carcinomas. In literature, many variations of these techniques have been described. The common denominator for these methodologies is the high amount of data obtained in a single experiment, in a short time period, and at a fairly low cost. However, these methods have also been described with several problems and limitations. The purpose of this study was to test the applicability of two selected high-throughput methods, cDNA and tissue microarrays (TMA), in cancer research. Two common human malignancies, breast and colorectal cancer, were used as examples. This thesis aims to present some practical considerations that need to be addressed when applying these techniques. cDNA microarrays were applied to screen aberrant gene expression in breast and colon cancers. Immunohistochemistry was used to validate the results and to evaluate the association of selected novel tumour markers with the outcome of the patients. The type of histological material used in immunohistochemistry was evaluated especially considering the applicability of whole tissue sections and different types of TMAs. Special attention was put on the methodological details in the cDNA microarray and TMA experiments. In conclusion, many potential tumour markers were identified in the cDNA microarray analyses. Immunohistochemistry could be applied to validate the observed gene expression changes of selected markers and to associate their expression change with patient outcome. In the current experiments, both TMAs and whole tissue sections could be used for this purpose. This study showed for the first time that securin and p120 catenin protein expression predict breast cancer outcome and the immunopositivity of carbonic anhydrase IX associates with the outcome of rectal cancer. The predictive value of these proteins was statistically evident also in multivariate analyses with up to a 13.1- fold risk for cancer specific death in a specific subgroup of patients.

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.

Modeling and Analysis of Noise and Interconnects for On-Chip Communication Link Design

This thesis considers modeling and analysis of noise and interconnects in onchip communication. Besides transistor count and speed, the capabilities of a modern design are often limited by on-chip communication links. These links typically consist of multiple interconnects that run parallel to each other for long distances between functional or memory blocks. Due to the scaling of technology, the interconnects have considerable electrical parasitics that affect their performance, power dissipation and signal integrity. Furthermore, because of electromagnetic coupling, the interconnects in the link need to be considered as an interacting group instead of as isolated signal paths. There is a need for accurate and computationally effective models in the early stages of the chip design process to assess or optimize issues affecting these interconnects. For this purpose, a set of analytical models is developed for on-chip data links in this thesis. First, a model is proposed for modeling crosstalk and intersymbol interference. The model takes into account the effects of inductance, initial states and bit sequences. Intersymbol interference is shown to affect crosstalk voltage and propagation delay depending on bus throughput and the amount of inductance. Next, a model is proposed for the switching current of a coupled bus. The model is combined with an existing model to evaluate power supply noise. The model is then applied to reduce both functional crosstalk and power supply noise caused by a bus as a trade-off with time. The proposed reduction method is shown to be effective in reducing long-range crosstalk noise. The effects of process variation on encoded signaling are then modeled. In encoded signaling, the input signals to a bus are encoded using additional signaling circuitry. The proposed model includes variation in both the signaling circuitry and in the wires to calculate the total delay variation of a bus. The model is applied to study level-encoded dual-rail and 1-of-4 signaling. In addition to regular voltage-mode and encoded voltage-mode signaling, current-mode signaling is a promising technique for global communication. A model for energy dissipation in RLC current-mode signaling is proposed in the thesis. The energy is derived separately for the driver, wire and receiver termination.

Chemical Biology Screen for Prostate Cancer Therapeutics

Prostate cancer initially responds to hormone-based therapeutics such as anti-androgen treatment or chemotherapeutics but eventually becomes resistant. Novel treatment options are therefore urgently needed. This thesis study applied a high-throughput screen of 4910 known drugs and drug-like small molecules to identify compounds that selectively inhibit growth of prostate cancer cells. In addition, the mechanisms underlying the cellular sensitivity to potent cancer selective compounds were addressed. Surprisingly, many of the compounds currently used in the clinics or studied in clinical trials were not cancer-selective. Only four drugs, aldehyde dehydrogenase inhibitor disulfiram (Antabus), antibiotic ionophore monensin, histone deacetylase inhibitor tricostatin A and fungicide thiram inhibited prostate cancer cell growth at nanomolar concentrations without major effects on non-malignant prostate epithelial cells. Disulfiram, monensin and a structurally similar compound to monensin, salinomycin, induced oxidative stress and inhibited aldehyde dehydrogenase activity. Moreover, monensin and salinomycin reduced androgen receptor signalling and steroidogenesis, enforced cell differentiation and reduced the overall levels of cancer stem cells. Taken together, novel and potentially prostate cancer-selective therapeutic agents were identified in this study, including the description of a multitude of intoxicating mechanisms such as those relating to oxidative stress. The results provide novel insights into prostate cancer biology and exemplify useful means of considering novel approaches to cancer treatment.

Welding development of crane main girder

Konecranes Corporation manufactures huge steel structures in 16 factories worldwide, in which the environment and quality varies. The company has a desire to achieve the same weld quality in each factory, regardless of the manufacturing place. The main subject of this master’s thesis was to develop the present box girder crane welding process, submerged arc welding and especially the fillet welding. Throughput time and manufacturing costs can be decreased by welding the full penetration fillet weld without a bevel, changing present groove types for more appropriate ones and by achieving the desired weld quality on the first time. Welding experiments of longitudinal fillet welding were made according to the present challenges, which the manufacturing process is facing. In longitudinal fillet welding tests the main focus was to achieve full penetration fillet weld for 6, 8 and 10 millimeters thick web plates with single and twin wire submerged arc welding. Full penetration was achieved with all the material thicknesses, both with single and twin wire submerged arc welding processes. The main problem concerning the weld was undercutting and shape of the weld bead. The question about insufficiency of presently used power sources with twin wire was risen up during testing, due to the thicknesses that require high welding current. Bigger power source is required when box girders are welded nonstop, if twin wire is used. For single wire process the penetration was achieved with significantly less amperage than with twin wire.

A Farewell to Flat Biology. Three-dimensional Cell Culture Models in Cancer Drug Target Identification and Validation

Cells of epithelial origin, e.g. from breast and prostate cancers, effectively differentiate into complex multicellular structures when cultured in three-dimensions (3D) instead of conventional two-dimensional (2D) adherent surfaces. The spectrum of different organotypic morphologies is highly dependent on the culture environment that can be either non-adherent or scaffold-based. When embedded in physiological extracellular matrices (ECMs), such as laminin-rich basement membrane extracts, normal epithelial cells differentiate into acinar spheroids reminiscent of glandular ductal structures. Transformed cancer cells, in contrast, typically fail to undergo acinar morphogenic patterns, forming poorly differentiated or invasive multicellular structures. The 3D cancer spheroids are widely accepted to better recapitulate various tumorigenic processes and drug responses. So far, however, 3D models have been employed predominantly in the Academia, whereas the pharmaceutical industry has yet to adopt a more widely and routine use. This is mainly due to poor characterisation of cell models, lack of standardised workflows and high throughput cell culture platforms, and the availability of proper readout and quantification tools. In this thesis, a complete workflow has been established entailing well-characterised 3D cell culture models for prostate cancer, a standardised 3D cell culture routine based on high-throughput-ready platform, automated image acquisition with concomitant morphometric image analysis, and data visualisation, in order to enable large-scale high-content screens. Our integrated suite of software and statistical analysis tools were optimised and validated using a comprehensive panel of prostate cancer cell lines and 3D models. The tools quantify multiple key cancer-relevant morphological features, ranging from cancer cell invasion through multicellular differentiation to growth, and detect dynamic changes both in morphology and function, such as cell death and apoptosis, in response to experimental perturbations including RNA interference and small molecule inhibitors. Our panel of cell lines included many non-transformed and most currently available classic prostate cancer cell lines, which were characterised for their morphogenetic properties in 3D laminin-rich ECM. The phenotypes and gene expression profiles were evaluated concerning their relevance for pre-clinical drug discovery, disease modelling and basic research. In addition, a spontaneous model for invasive transformation was discovered, displaying a highdegree of epithelial plasticity. This plasticity is mediated by an abundant bioactive serum lipid, lysophosphatidic acid (LPA), and its receptor LPAR1. The invasive transformation was caused by abrupt cytoskeletal rearrangement through impaired G protein alpha 12/13 and RhoA/ROCK, and mediated by upregulated adenylyl cyclase/cyclic AMP (cAMP)/protein kinase A, and Rac/ PAK pathways. The spontaneous invasion model tangibly exemplifies the biological relevance of organotypic cell culture models. Overall, this thesis work underlines the power of novel morphometric screening tools in drug discovery.

The spindle assembly checkpoint as a drug target - Novel small-molecule inhibitors of Aurora kinases

Cell division (mitosis) is a fundamental process in the life cycle of a cell. Equal distribution of chromosomes between the daughter cells is essential for the viability and well-being of an organism: loss of fidelity of cell division is a contributing factor in human cancer and also gives rise to miscarriages and genetic birth defects. For maintaining the proper chromosome number, a cell must carefully monitor cell division in order to detect and correct mistakes before they are translated into chromosomal imbalance. For this purpose an evolutionarily conserved mechanism termed the spindle assembly checkpoint (SAC) has evolved. The SAC comprises a complex network of proteins that relay and amplify mitosis-regulating signals created by assemblages called kinetochores (KTs). Importantly, minor defects in SAC signaling can cause loss or gain of individual chromosomes (aneuploidy) which promotes tumorigenesis while complete failure of SAC results in cell death. The latter event has raised interest in discovery of low molecular weight (LMW) compounds targeting the SAC that could be developed into new anti-cancer therapeutics. In this study, we performed a cell-based, phenotypic high-throughput screen (HTS) to identify novel LMW compounds that inhibit SAC function and result in loss of cancer cell viability. Altogether, we screened 65 000 compounds and identified eight that forced the cells prematurely out of mitosis. The flavonoids fisetin and eupatorin, as well as the synthetic compounds termed SACi2 and SACi4, were characterized in more detail utilizing versatile cell-based and biochemical assays. To identify the molecular targets of these SAC-suppressing compounds, we investigated the conditions in which SAC activity became abrogated. Eupatorin, SACi2 and SACi4 preferentially abolished the tensionsensitive arm of the SAC, whereas fisetin lowered also the SAC activity evoked by lack of attachments between microtubules (MTs) and KTs. Consistent with the abrogation of SAC in response to low tension, our data indicate that all four compounds inhibited the activity of Aurora B kinase. This essential mitotic protein is required for correction of erratic MT-KT attachments, normal SAC signaling and execution of cytokinesis. Furthermore, eupatorin, SACi2 and SACi4 also inhibited Aurora A kinase that controls the centrosome maturation and separation and formation of the mitotic spindle apparatus. In line with the established profound mitotic roles of Aurora kinases, these small compounds perturbed SAC function, caused spindle abnormalities, such as multi- and monopolarity and fragmentation of centrosomes, and resulted in polyploidy due to defects in cytokinesis. Moreover, the compounds dramatically reduced viability of cancer cells. Taken together, using a cell-based HTS we were able to identify new LMW compounds targeting the SAC. We demonstrated for the first time a novel function for flavonoids as cellular inhibitors of Aurora kinases. Collectively, our data support the concept that loss of mitotic fidelity due to a non-functional SAC can reduce the viability of cancer cells, a phenomenon that may possess therapeutic value and fuel development of new anti-cancer drugs.

Lohkovalmistuksen läpimenoaikojen tarkastelu ja kehittäminen työntutkimuksen avulla

Tutkimus tehtiin STX Finlandin Turun telakalle osana suurempaa kehitysohjelmaa, joka tähtää läpimenoaikojen lyhentämiseen ja kilpailukyvyn paranemiseen. Työntutkimuksesta saatujen tietojen avulla toimintaa pyritään kehittämään tuottavammaksi ja läpimenoaikaa lyhyemmäksi. Työssä pyrittiin löytämään valmistusteknillisiä keinoja läpimenoajan lyhentämiseksi käyttäen hyväksi Lean-ajattelutapaa. Mittaustuloksista voidaan nähdä, miten aika jakaantuu lohkonkoonnissa ja mihin aikaa hukataan. Tuloksista huomataan, että lisäarvoa tuottavan työn osuutta työajasta voidaan lisätä. Kasvattamalla jalostavan työn osuutta voidaan tuotannosta tehdä tehokkaampaa ja läpimenoaikaa lyhentää. Tuloksista selviää, minkälaisia Lean-ajattelutavan hukkia työvaiheet sisältävät ja kuinka paljon aikaa niihin kuluu. Tutkimus tehtiin tunnettuja työntutkimuksen keinoja hyväksikäyttäen. Käytössä oli havainnointitutkimus sekä ajankäyttötutkimus. Havainnointitutkimuksen avulla saatiin selville tuotannon epäkohtia. Työntutkimuksen avulla selvisi myös, ettei mekanisointien käyttö hitsauksessa ole riittävällä tasolla. Suuri osa hitsauksesta tehdään manuaalisesti ilman kuljettimia, jolloin paloaikasuhde pysyy matalana. Tuotannossa esiintyvät virheet jäävät liian usein raportoimatta. Tutkimuksessa on esitetty toimintamalli tuotannon epäkohtien raportoinnin toteutukselle. Johtopäätöksinä syntyi kehitysideoita lohkovalmistuksen tehostamiseksi. Tutkimuksen avulla luotiin pohja työntutkimuksen uudelleenkäynnistämiselle. Luotuja työntutkimuskaavioita voidaan käyttää tulevissa työntutkimuksissa. Johtopäätöksinä syntyi kehitysideoita lohkovalmistuksen tehostamiseksi. Menetelmien avulla lohkovalmistuksen läpimenoaikaa saadaan tehostettua.

Identification of novel regulators for tumor progression in breast cancer

Breast cancer is the most frequent solid tumor among women and the leading cause of cancer related death in women worldwide. The prognosis of breast cancer patients is tightly correlated with the degree of spread beyond the primary tumor. In this thesis, the aim was to identify novel regulators of tumor progression in breast cancer as well as to get insights into the molecular mechanisms of breast cancer progression and metastasis. First, the role of phospholipid remodeling genes and enzymes important for breast cancer progression was studied in breast cancer samples as well as in cultured breast cancer cells. Tumor samples displayed increased de novo synthesized fatty acids especially in aggressive breast cancer. Furthermore, RNAi mediated cell based assays implicated several target genes critical for breast cancer cell proliferation and survival. Second, the role of arachidonic acid pathway members 15-hydroxyprostaglandin dehydrogenase (HPGD) and phospholipase A2 group VII (PLA2G7) in tumorigenesis associated processes was explored in metastatic breast cancer cells. Both targets were found to contribute to epithelial-mesenchymal transition related processes. Third, a high-throughput RNAi lysate microarray screen was utilized to identify novel vimentin expression regulating genes. Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) was found to promote cellular features connected with metastatic disease, thus implicating MTHFD2 as a potential drug target to block breast cancer cell migration and invasion. Taken together, this study identified several putative targets for breast cancer therapy. In addition, these results provide novel information about the mechanisms and factors underlying breast cancer progression.