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Browsing by study line "Farmaseuttinen kemia"

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  • Sinisalo, Jade (2021)
    Pharmaceutical contaminants in waste and surface waters have been recognized as an emerging risk to environmental health. Bioaccumulation of pharmaceuticals increases the risk of adverse effects in off-target species, as the chemical concentration within the organism exceeds the concentration of the surrounding environment. An organism’s ability to metabolize foreign organic compounds influences the likelihood of bioaccumulation. Current methods for predicting bioaccumulation in aquatic organisms are labour intensive or too simplistic to cover the variety of chemical and physiological processes involved and may lead to over or underestimations of environmental risk. A promising approach to improve bioaccumulation predictions, without the need of excessive animal testing, is to incorporate in vitro biotransformation data into computational models. The primary aim of this study was to assess whether selected pharmaceuticals (diclofenac, gemfibrozil, haloperidol, levomepromazine, levonorgestrel, sertraline and risperidone), that are well metabolized in humans through key biotransformation pathways, are metabolized by rainbow trout (Oncorhynchus mykiss) liver enzymes under physiologically relevant conditions (11°C, pH 7.8). A secondary aim was to produce fish in vitro intrinsic clearance (CLint, in vitro) data, that could potentially be used as input in computational models to predict bioaccumulation. In vitro biotransformation was studied using a single vial approach according to the Organisation for Economic Co-operation and Development (OECD) Test Guideline 319B: Determination of in vitro intrinsic clearance using rainbow trout liver S9 sub-cellular fraction (RT-S9). Depletion of the test compounds were measured during a 3-hour incubation period. High-performance liquid chromatography with ultraviolet detection (HPLC–UV) was used for qualitative and quantitative analysis of the samples. Levomepromazine, levonorgestrel and sertraline showed significant substrate depletion compared to negative controls while gemfibrozil, haloperidol, and risperidone did not seem to be metabolized. The results for verapamil were inconclusive. Levomepromazine displayed a higher in vitro intrinsic clearance rate (26 ml/h/g liver) than diclofenac (6.2 ml/h/g liver). These results are in accordance with previous studies and support the notion that a direct comparability between fish and human metabolism cannot be assumed, highlighting the need of fish in vitro biotransformation studies. The apparent lack of in vitro metabolism of risperidone, haloperidol, and gemfibrozil combined with their lipophilicity suggest that they are more likely to accumulate within rainbow trout, compared with the compounds that showed depletion during the assays, although repetitions and additional studies are needed to confirm this.
  • Grazhdankin, Evgeni (2018)
    We have developed a software for homology modelling by satisfaction of distance restraints using MODELLER back-end. The protocols used extend exploration of distance restraints and conformational space. We drive the models in optimization cycle towards better structures as assessed by the used metrics on DOPE score, retrospective distance restraint realization and others. Hydrogen bond networks are optimized for their size and connectivity density. The performance of the method is evaluated for its ability to reconstruct GPCR structures and an extracellular loop 2. The software is written in object-oriented Python (v.2.7) and supports easy extension with additional modules. We built a relational PostgreSQL database for the restraints to allow for data-driven machine and deep learning applications. An important part of the work was the visualization of the distance restraints with custom PyMOL scripts for three-dimensional viewing. Additionally, we automatically generate a plethora of diagnostic plots for assessing the performance of the modelling protocols. The software utilizes parallelism and is computationally practical with compute requirements on an order of magnitude lower than those typically seen in molecular dynamics simulations. The main challenges left to be solved is the evaluation of restraint goodness, assigning secondary structures, restraint interconditioning, and water and ligand placement.
  • Jalonen, Daniel (2023)
    Orexin receptors have gained more attention due to increased knowledge of their physiological significance. The successful development of orexin receptor antagonists treating insomnia has enlarged the scope of research leading to an interest in developing small molecule agonists that have drug-like properties and induce activation in the orexinergic system. Transforming this idea into reality has remained an unaccomplished challenge. In this work, molecular mechanism of activation in orexin receptor type 2 is studied by conducting molecular dynamics simulations after capturing coordinates of active and inactive state crystal structures. The crystal structure coordinates define the starting pose for the protein and the ligand in the simulations. Preliminary steps prior to simulation include building the surrounding system and model building in which homology modeling is employed to reconstruct missing loops. A 100-nanosecond simulation is executed for both models. Active and inactive state models display stable binding event characteristics when examining the coordinate changes of every atom during the simulation. No major conformational changes are observed. The most congruent feature relative to the literature is the difference in the interactive role of residue Q3x32 between the simulations. The agonist forms two consistent hydrogen bonds with the upward-shifted Q3x32 while an inactive downward-facing version is observed in the antagonist model. Some residues present unexpected features omitting comparative functions of literature, which along with general inconsistency of protein-ligand contacts undermine the reliability of models heavily. The simulations conducted need to be extended to produce a hypothesis for the activation mechanism because of the defects around simulation protocols and the low quantity of simulation runs.
  • Auno, Samuli (2019)
    Heart failure is a disease of major social and economic impact. The disease is most commonly onset by extensive cardiomyocyte death following a myocardial infarction. Five-year mortality of heart failure is higher than some cancers. Loss of cardiac muscle tissue leads to pathological thickening and fibrosis of the left ventricular wall, which eventually further diminish cardiac function. Cardiomyocytes hardly proliferate, which also exacerbates the problem. Several cell signalling pathways are indicated in pathological reprogramming of the heart and the exact significance of these pathways remains to be demonstrated. Treatment strategies based on renewing cardiac muscle, such as direct injection of stem cells into the myocardium, have failed to reach clinically significant effects on heart failure patients. Direct inhibition of pathological cardiac reprogramming by using small molecule modulators remains as an auspicious strategy to treat heart failure. GATA4, or GATA binding protein 4, is a transcription factor expressed mainly in heart, lung, intestine, gonad and liver tissues, which regulates tissue renewal and cell proliferation by controlling protein transcription. GATA4 binds to GATA sequences in DNA with two zinc finger moieties and enables transcription of target genes. Interactions of GATA4 and several other transcription factors are in central role of guiding heart development, hypertrophy and fibrosis. One of these transcription factors is NKX2-5, which synergistically interacts with GATA4. Inhibition of this interaction in rat myocardial infarction model has been shown to protect against development of heart failure. A screening campaign against the transcriptional synergy of GATA4 and NKX2-5 found potent small molecule inhibitors of this interaction, but these compounds are characterised with stem cell toxicity. The aim of the study was to design and synthesise novel derivatives of GATA4-NKX2-5 synergy inhibitor hit molecule with reduced stem cell toxicity. Modifications on the phenyl ring of the hit molecule were designed, which either increase electron density of the ring or possibly alter the torsional angle between the phenyl and isoxazole ring moieties. Activity of the compounds was studied on a luciferase reporter gene system in COS-1 cells and toxicity was analysed on IMR90 human induced pluripotent stem cell line. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) bromide and lactate dehydrogenase (LDH) assays were selected to measure toxicity on stem cells. Stem cell toxicity of several previously synthesised compounds was assayed in parallel with the novel derivatives. Ten novel derivatives were designed, synthesised and assayed. Four of the new compounds, a mono-ortho-methyl, a di-ortho-methyl, a di-meta-methoxy and cyclohexyl derivatives were found to be equipotent inhibitors of reporter gene activity compared to the hit compound. Additionally, the mono-ortho-methyl, di-ortho-methyl and di-meta-methoxy derivatives were less toxic to stem cells than the hit molecule in the MTT assay. Several other derivatives were found to be less toxic, but also non-active in the luciferase assay. None of the studied compounds exhibited notable necrotic toxicity on stem cells, as examined by the LDH assay. According to this study it may be concluded that substituents of the hit molecule phenyl ring may be altered to decrease stem cell toxicity of the compound. Some of the alterations, most notably substituents in the para-position of the phenyl ring and substitution of the phenyl ring with smaller saturated hydrocarbon rings, diminish the activity of the hit compound. Remarkable toleration of ortho-substitution reinforces the hypothesis of phenyl-isoxazole torsional angle significance for toxicity. On the other hand, addition of two methoxy groups to both meta positions most likely lacks any substantial effect on the torsional angle, which implies another mechanism of toxicity avoidance. Activity and improved safety of the novel inhibitors should be confirmed in animal models before any decisive conclusions on the effects of structural modifications on the hit molecule can be made. In addition, other mechanisms of toxicity should be studied with relevant cell-based assays.
  • Dillemuth, Pyry (2021)
    Prolyl oligopeptidase (PREP) is a serine protease that is widely found throughout the human body and especially in the brain. The primary function of PREP is thought to be the hydrolysis of the carboxyl side bond of proline residues in oligopeptides. PREP is also shown to increase the dimerization and aggregation of α-synuclein and downregulate the protein phosphatase 2A mediated autophagy in the cell via direct protein-protein interactions (PPI). The accumulation of α-synuclein aggregates in cell is known to cause α-synucleinopathies such as Parkinson’s disease. This makes the PPIs of PREP an attractive target for drug research. The mechanisms of the PPIs of PREP are still poorly understood. Recent studies have shown that these PPIs can be modulated with ligands lacking high inhibitory activity for the proteolytic activity. These studies show that the IC50-value of the ligand does not correlate with ligands ability to affect the PPIs of PREP. Ligands that could selectively modulate the PPIs of PREP without inhibiting the proteolytic activity of PREP could give valuable information on the mechanisms of the PPIs and on how to modulate them. It is hypothesized that the ligands could bind to PREP at a site that does not interfere with its proteolytic activity, and ligand binding is assumed to restrict the dynamic structure of PREP and thereby also modulating the PPIs of PREP. The aim of this study was to synthetize novel peptidic PREP ligands and study their effects on the proteolytic activity of PREP and the PPIs of PREP. The aim was to find and identify ligands and structures that would modulate the PPIs of PREP and observe how the IC50-values of the ligands would correlate. L-Alanyl-pyrrolidine was selected as the scaffold for the compound series and the five-membered heteroaromatics, imidazole, triazole and tetrazole, were added to the 2-position of the pyrrolidine ring. In this position there is an electrophilic group in many PREP inhibitors, although these heteroaromatics are not electrophiles. The scaffold was also expanded by adding phenyalkyl groups with different linker lengths were added to the N-terminal side of the alanine. The ligands were synthesized using four synthesis routes which were based on synthesis methods found in literature. The IC50-values and the effects on α-synuclein dimerization and autophagic flux were determined for five synthetized compounds. The tested compounds were all weak PREP inhibitors and showed no strong activity in the α-synuclein dimerization and autophagy assays. Despite the weak activities in the assays, the importance of the linker length in the phenyalkyl group was shown. Changing the linker by one methylene group had noticeable effect on the overall activity. The results also demonstrate a lack of correlation between the IC50-values and the effects on α-synuclein dimerization and autophagic flux, which further confirms the lack of correlation between the proteolytic function and the PPIs of PREP which was observed also in previous studies.
  • Zwiers, Harry (2021)
    Membraanipyrofosfataasit eli mPPaasit katalysoivat pyrofosfaatin hydrolyysiä kahdeksi ortofosfaattimolekyyliksi vapauttaen samalla energiaa. mPPaasit ovat merkittävässä roolissa useiden patogeenisten alkueläinloisten mahdollisuudessa selvitä ulkoisesta osmoottisesta stressistä ja pH:n vaihteluista, joiden lisäksi mPPaasit vaikuttavat niiden kasvuun ja virulenssiin. mPPaaseja ei toistaiseksi ole löydetty ihmisistä eikä eläimistä, jonka vuoksi ne ovat mielenkiintoisia lääkevaikutuksen kohteita. Tässä työssä syntetisoitiin 9 uutta yhdistettä, joita ei ole aiemmin raportoitu kirjallisuudessa. Johtomolekyyleinä käytettiin aiemmassa tutkimuksessa löydettyjä isoksatsolijohdannaisa, jotka inhiboivat T. maritiman mPPaasia IC50-arvoilla 6‒7 μM (Johansson ym. 2020). Uusiin yhdisteisiin liitettiin formyyliryhmiä useaan eri kohtaan, joiden avulla toivotaan saavan lisää tietoa niiden sitoutumisesta mPPaasiin ja niiden rakenne-aktiivisuussuhteista. Uudet yhdisteet tullaan testaamaan aktiivisuuden varalta in vitro T. maritiman mPPaasissa ja tarvittaessa myös P. falciparumissa. Formyyliryhmät liitettiin isoksatsolirenkaiden 3-, 4- ja 5-asemiin erilaisten substituenttien välityksellä. Isoksatsolirenkaan 3-aseman karboksylaattiryhmään esteröitiin kolme eri bromiformyylifenolia formyyliryhmän paikkaa vaihdellen. Isoksatsolirenkaan 4-asema halogenoitiin mikroaaltoavusteisesti, jonka jälkeen liitettiin formyyliryhmiä sisältäviä heterosyklisiä booriyhdisteitä Suzuki-reaktioilla. Myös isoksatsolirenkaan 5-asemaan sitoutuneeseen fenyylirenkaaseen liitettiin formyyliryhmän sisältävän yhdisteen Suzuki-reaktiolla. Uusien yhdisteiden aktiivisuuskokeiden tulokset julkaistaan myöhemmin. Yhdisteiden rakenne-aktiivisuussuhteisiin tai tehokkuuksiin ei ole tässä työssä vielä mahdollista ottaa kantaa.
  • Harju, Elina (2021)
    Extracellular vesicles (EVs) are nano-sized lipid bilayer-delimited particles, released by cells. They take part in intercellular communication by their molecular composition and are part of both physiological and pathophysiological functions. EVs can be extracted from bodily fluids, and they are particularly abundant in blood. The purpose of this thesis was to evaluate the use of Raman spectroscopy in the characterization of EVs. Raman spectroscopy is an analysis method based on the interaction of light and matter, and the inelastic scattering of light, and it is used to get information on the biochemical composition of a substance. Principal component analysis (PCA) was used to investigate if Raman spectroscopy could differentiate two different platelet-derived EV samples, a red blood cell-derived EV-sample and a red blood cell-derived reference material. Evaluation of the characterization also included a stability study of these samples, where it was examined if any temperature dependent changes occurred that could be detected by Raman spectroscopy. Additionally, the applicability of Raman spectroscopy for lipoprotein contamination detection was evaluated by examining if purification of an EV sample decreased the intensity of carotenoid peaks typical for lipoprotein spectra. Raman spectroscopy was able to differentiate all three EV samples and the red blood cell-derived reference material from each other. The most clear differences were found between red blood cell and platelet-derived samples, due to for example the characteristic haemoglobin peaks of red blood cell-derived samples. Differences were also found between the two platelet EV samples, which were thought to implicate difference in protein compositions. The characterization of red blood cell-derived samples proved to be difficult because haemoglobin contained in the samples covered most of the other signal from the samples. Stability studies implicated that during fridge storage the carotenoid peak intensity of platelet-derived EV samples decreases due to the degradation of carotenoids. In the red blood cell-derived samples, no differences assignable to changes in some specific components of the samples were observed. Contamination studies suggested the intensity of the carotenoid peaks may increase due to purification of the sample. This was counter to the assumption and may suggest the carotenoids of the EV samples are not from lipoprotein contamination, but part of the EV composition. In conclusion, Raman spectroscopy proved to be a promising method for characterization and identification of different EV samples.
  • Niemissalo, Sanna (2022)
    The aim of this master’s thesis was to investigate whether drug-induced inhibition of cytochrome P450 enzymes (CYP), especially time-dependent inhibition (TDI), could be the reason for bioaccumulation of the pharmaceuticals present in the aquatic environment in fish and whether the in vitro method could identify pharmaceuticals causing an environmental risk, which should primarily be investigated more closely. The half-maximal inhibitory concentrations (IC50) of seven antimicrobial drugs detected in the environment (erythromycin, clarithromycin, ketoconazole, clotrimazole, miconazole, ciprofloxacin, and sulfamethoxazole) and three known human time-dependent inhibitors (furafylline, diltiazem and verapamil) chosen for the validation of the method, were determined by EROD (7-ethoxy-resorufin-O-deethylase) and BFCOD (7-benzyloxy-4-trifluoromethyl-coumarin-O-debenzyloxylase) activities. The IC50 shift method and commercially available rainbow trout (Oncorhynchus mykiss) liver microsomes were used in determinations. The known human time-dependent inhibitors chosen for the validation of the method, furafylline (EROD) and diltiazem (BFCOD) proved to be possible time-dependent inhibitors also in rainbow trout in vitro, but this was not observed for verapamil (BFCOD). All antimicrobial drugs, except ciprofloxacin, inhibited more selectively BFCOD-reaction, as in human. In the case of sulfamethoxazole, inhibition was not observed at the concentrations used (0–500 µmol/L). Both enzyme activities (EROD and BFCOD) were inhibited in rainbow trout by ketoconazole, clotrimazole and miconazole. Among antimicrobial drugs acting as time-dependent inhibitors in human, erythromycin inhibited BFCOD activity in a time-dependent manner also in rainbow trout, but this was not observed for clarithromycin. Strongest inhibitors for CYP enzymes of rainbow trout in vitro were ketoconazole (EROD, IC50=4,19 µM and BFCOD, IC50=2,31 µM) and clotrimazole (EROD, IC50=33,78 µM and BFCOD, IC50=1,55 µM). The IC50 values of diltiazem, erythromycin, clarithromycin, ciprofloxacin, and verapamil were of the same order of magnitude as in human. The IC50 values of furafylline, ketoconazole, clotrimazole and miconazole were several times higher in rainbow trout than in human. Based on the results of this study, the IC50-shift method is also valid for fish, but there are differences in the inhibition potencies between human and fish, and the inhibition potency of human CYP enzymes cannot therefore directly predict enzyme inhibition of fish or the mechanism of inhibition. The In vitro measured IC50 values of rainbow trout were several orders of magnitude higher than the average concentrations of the pharmaceutical residues measured in the environment. Exposure to pharmaceutical mixtures is long-term, so interactions and bioaccumulation may still be possible due to inhibition of CYP enzymes. Developing a valid in vitro method for environmental risk assessment would be important, as animal experiments are ethically challenging.