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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.
  • Jämsä, Antti (2023)
    Prolyl oligopeptidase (PREP) is endopeptidase which cleaves short proline containing peptides. Abnormalities in brain PREP activity has been connected to neurodegenerative diseases. Recently it has been detected that besides its proteolytic activity PREP interacts directly with other proteins which might contribute to generation of neurodegenerative diseases. Further it has been discovered that certain small molecular PREP inhibitors are able to modify these protein-protein interactions (PPIs) and thus have a potential to alleviate the progression of neurodegenerative diseases. This has led to the development of novel second generation PREP ligands which lack the strong inhibitory activity but are potent compounds on modifying the PPIs. Thiazole structure containing PREP modulators has provided most promising class of compounds. It has been detected that these compounds mediate their effects via novel binding site on the enzyme and these effects are not connected to the inhibition of the enzymatic activity. The synthesis of these thiazole containing PREP modulators has proven to be demanding since it have involved a usage of laborious synthesis route and provided low yields. The aim of this research was to examine the synthesis of 2-(2-benzimidazol-1-yl)ethyl)- 4-methyl thiazole containing PREP modulators via previously reported synthesis route. Another aim was to design and develop a synthesis route for 2-(2-(benzimidazol-1- yl)ethyl)-5-bromo-4-methylthiazole, a molecule which serves as valuable intermediate for the lead optimization and generation of second-generation PREP modulators. A synthetic route for 2-(2-(benzimidazol-1-yl)ethyl)-5-bromo-4-methylthiazole was successfully developed. Despite that the total yield of the route remained low. When searching the reasons for the low obtained yield the chemistry behind a thiazole creating cycloaddition reaction and an aromatic halogenation was examined. This led to the discovery of a rare cationic compound which was found to be synthesized from previously undescribed starting materials.
  • Tiainen, Elina (2024)
    New drugs against malaria are required, as millions of people are still affected yearly by this deadly disease. The development of drug resistance to current antimalarials is an ongoing process. Membrane-bound pyrophosphatases (mPPases) are potential new drug targets against malaria and other protozoan diseases. mPPases play a crucial role in the survival of the malaria parasite, they couple the energy released from the hydrolysis of pyrophosphate into the transport of protons or ions against an electrochemical gradient. The aim of this study was to identify potential mPPase inhibitors through a docking-based virtual screen of the Tres Cantos Antimalarial Compound Set, which consists of over 13500 malaria-active compounds. The virtual screen against a Thermotoga maritima mPPase protein structure identified a 2,4-diamino-1,6-dihydrotriazine among the top-ranking scaffolds. Four compounds found among the docking results containing this scaffold were synthesised: three with a halophenyl substituent, and one with a hydroxyl substituent. The compounds in their hydrochloride salt forms were synthesised using a three-component method for the synthesis of 2,4-diamino-1,6-dihydrotriazines. The compounds were also freed from the hydrochloride salts into their corresponding molecular forms. The structural characterisation of the compounds, especially the molecular forms, presented challenges. The docking results were also searched to identify compounds containing previously identified mPPase-active substructures. From the docking results, several other interesting compounds were identified in addition to the synthesised compounds. The knowledge and results obtained from this study can be used as openings for potential future docking and synthesis projects in the development of mPPase inhibitors. The activity of the compounds synthesised in the project remains to be evaluated in subsequent investigations.
  • 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.
  • Rahikainen, Otto (2023)
    Ramansironta on sähkömagneettisen säteilyn ilmiö, jonka avulla voidaan havaita molekyylivärähdyksiä niistä sironneen valon avulla. Kun sähkömagneettinen säteily kohtaa molekyylin se voi häiritä elektronipilveä ytimen ympärillä ja prosessin lopputuloksena energiaa vapautuu sironneen säteilyn muodossa. Tätä kutsutaan epäelastiseksi sironnaksi. Mikäli sironnassa ei tapahdu fotonin energiassa muutosta kyseessä on elastinen siroaminen. Mikäli näytteeseen menevän ja sironneen fotonin välillä havaitaan energian muutos, käytetään ilmiöstä nimeä epäelastinen Raman sironta. Energian muutosta voidaan mitata, ja saatu spektri antaa tietoa kohdemolekyylistä. Tämän työn tarkoituksena oli tutkia eri Raman-spektroskopiatekniikoiden, lähinnä spontaani-Raman spektroskopian sekä koherentti anti-Stokes Ramanspektroskopian ja mikroskopian soveltuvuutta lääkemolekyylien havaitsemiseen sekä nanopartikkeleiden karakterisoinnissa ja nanopartikkeleiden ja solujen välisten interaktioiden tutkimisessa. Tekniikan vahvuuksiin kuuluu käytön suhteellinen helppous ja CARS-mikroskopian nopeus sekä korkea erotuskyky, mahdollisuus havainnoida solunäytteitä, ja epätodennäköisyys vaurioittaa tutkittavaa kohdetta. Haasteisiin lukeutuu fluoresenssin taipumus häiritä signaalia, spontaani-Raman mikroskopian heikompi erottelukyky, analyysin hitaus sekä tarve valikoida molekyyli, jonka rakenne antaisi vahvan Raman-signaalin. Tutkimuksen alatavoitteina oli sopivan lääkemolekyylin valitseminen nanopartikkeliformulaatioon, nanopartikkeleiden formulointi, niiden karakterisointi Raman-spektroskopiatekniikoilla, ja lopulta tutkia Raman spektroskopian soveltuvuutta nanopartikkeleiden ja lääkeaineen sekä solujen interaktioiden tutkimisessa ja lääkeaineen havaitsemisessa solujen sisältä. Tutkimuksessa uutta on se, että ensimmäistä kertaa polymeerinanopartikkeleiden ja niihin ladattujen lääkeaineiden soluunkulkeutumisen tutkiminen pelkällä Raman-spektroskopialla ilman esim. fluoresoivia merkkiaineita. Tutkimuksen tavoitteen pääasiallisesti täyttyivät. Valitsimme kohdemolekyyliksi klorotaloniilin, fungisidin joka on edullinen ja antaa selvästi tunnistettavan Raman-signaalin. Klorotaloniilille suoritettiin normaalit sytotoksisuuskokeet sekä vapaana lääkeaineena että formuloituina nanopartikkeleina. Nanopartikkelien formulointi onnistui ja molemmat Raman-spektroskopiatekniikat näyttivät selvästi sekä lääkemolekyylin että polymeerin kemikaalispesifiset Raman signaalit. Lääkemolekyylin havaitsemin solujen sisältä onnistui. Polymeerimolekyylit eivät missään vaiheessa kulkeutuneet solujen sisälle. Tämä oli ehkä yllättävää koska käytimme makrofageja, mutta toisaalta myös johdonmukainen muiden tutkimusten kanssa. Raman-tekniikat osoittautuivat hyviksi tutkimusmenetelmiksi, ja erityisesti CARS-mikroskoopin suuri erotuskyky osoittautui hyödylliseksi soluunkulkeutumisen kuvantamisessa.
  • 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.
  • Vartiainen, Pyry (2023)
    Orexins (hypocretins) are two neuropeptides, orexin-A (OX-A) and orexin-B (OX-B), produced by a neuron subpopulation in the mammalian hypothalamus. They are natural substrates of two G-protein-coupled receptors (GPCRs), orexin receptor 1 (OX1R) and orexin receptor 2 (OX2R), respectively. Orexin receptors are expressed widely in the central nervous system. Orexin peptides and receptors were originally discovered in 1998 and have been extensively researched ever since. Maintaining a steady state of wakefulness has been identified as one main physiological function of orexinergic signalling, and loss of orexinergic neurons in the hypothalamus has been linked to narcolepsy. Over the past decade orexin receptor antagonists have been developed for treatment of insomnia – suvorexant as the first one, approved for clinical use in 2014. Orexin receptor agonists remain under development for treatment of narcolepsy as one potential therapeutical indication, with no clinical applications yet approved. Orexin receptor activation by small-molecule agonists has proven a challenge not yet conclusively resolved. The aim of this study was to validate a novel scaffold for orexin receptor agonists from compounds identified as orexin receptor agonists in previous studies. Total of ten compounds were designed for synthesis, three of which were successfully synthesized. These three compounds exhibited very low orexinergic activity (0.06–1.36% and 2.33–5.19% response of full activation for OX1R and OX2R, respectively). After activity testing retrospective modelling of the receptor binding of the synthesized and designed compounds was implemented computationally by structure-based molecular docking to the recently discovered (2021) crystal structure of OX2R in complex with bound small-molecule agonist 3′-(N-(3-(2-(2-(2H-1,2,3-triazol-2-yl)benzamido)ethyl)phenyl)sulfamoyl)-4′-methoxy-N,N-dimethyl-[1,1′-biphenyl]-3-carboxamide. Some of the key interactions known as crucial for receptor activation, such as hydrogen bonds with glutamine Q1343.32, were found possible for some of the synthesized and designed compounds. This may in part explain the orexinergic activity, however very low, measured for the synthesized compounds. Low activity of the synthesized compounds may be a result of low binding since their binding was not tested in this study. Interactions between the synthesized compounds and OX2R predicted by molecular modelling are consistent with the low measured activity of the compounds, and alternative, more optimal chemical scaffolds for orexin receptor activation could be searched in future studies.
  • 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.
  • Pätsi, Henri (2019)
    Prolyl oligopeptidase (POP) is a serine peptidase found at high concentrations in the brain, which cleaves short proline-containing peptides at the carboxyl side of proline. POP activity has been shown to differ between healthy people and ones suffering from certain neurodegenerative diseases. Amongst its other functions, it has been shown to accelerate α-synuclein aggregation. Inhibiting the enzyme prevents this acceleration. Many highly potent peptidic POP inhibitors, based on the enzyme’s natural substrates, have been synthesized. One of the problems with many of these peptide-like inhibitors is their inability to penetrate the blood-brain barrier efficiently. Recently, a new surprisingly potent non-peptidic inhibitor based on a novel heteroaromatic scaffold was discovered. There was a need to synthesize analogues of this inhibitor in order to gain a better understanding of the structure-activity relationship for compounds based on the new scaffold. Unfortunately, the heteroaromatic scaffold is relatively unstable without a stabilizing substituent. The aim of this research was synthesizing stable analogues, primarily by replacing the original heteroaromatic ring with other, more stable heteroaromatic rings. It was hypothesized that the activity of the original compound could be retained, as heteroaromatics can often act as bioisosteres of each other. Multiple close analogues containing the new heteroaromatic rings were successfully synthesized and tested. Although they were considerable more stable compared to the original compound, there was a significant decrease in potency. However, the new compounds were not completely inactive, and they provided useful information on the viability and importance of several different substituents. Furthermore, measuring the IC50 value is not enough to evaluate their overall effect on POP, since the inhibition of the proteolytic activity of POP does not seem to correlate with the inhibition of its other functions. Further investigation and development of the new compound series is needed.
  • Häiväläinen, Heidi (2023)
    Inhibition of the cytochrome P450 enzymes is one of the most significant factors causing drug-drug-interactions, and thus one of the most important objects of study at preclinical drug development. CYP-inhibition can be either reversible or irreversible. Although different inhibition mechanisms are well known, their evaluation in vitro is still challenging. Thus, the development of more accurate and efficient in vitro methods is important and as a continuous target of interest. Immobilized enzyme microreactors (IMER) have presumably several advantages over traditional in vitro methods and have been presented as a promising tool for drug metabolism studies in vitro. The purpose of this work was to evaluate the suitability of a novel flow-through based immobilized enzyme microreactor in determining the CYP enzyme kinetic parameters. The developed immobilization protocol is based on attaching biotinylated human liver microsomes to a thiolene-based microreactor coated with Streptavidin. To validate the developed method, the activity of the CYP2C9 enzyme was assessed using the recommended model reaction by authorities, that is 4-hydroxylation of diclofenac. The enzyme kinetic parameters i.e., enzyme affinity (Km) and activity (Vmax), determined with the developed IMER were comparable to the values previously published in the literature and determined in static in vitro conditions. In addition, the inhibition of CYP2C9 enzyme by four model inhibitors (fluconazole, nicardipine, sulfaphenazole and miconazole), was examined by determining the IC50 (half-maximal inhibitory constant) values for each compound and by monitoring the reversibility of the CYP2C9 enzyme for 90 minutes after the inhibitor was removed from the feed solution. The IC50 values determined with the developed method for all inhibitors were well in line with previous publications, showing fluconazole (IC50 22 µM) to be the weakest inhibitor of CYP2C9 enzyme and the other examined inhibitors caused more potent inhibition (IC50 for sulfaphenazole 1.3 µM; IC50 for miconazole 1.3 µM; IC50 for nicardipine 0.67-1.1 µM). The reversibility of the CYP2C9 enzyme was examined by removing the inhibitor from the feed solution and monitoring the recovery of the enzyme activity via diclofenac 4-hydroxylation. Based on the results obtained with developed IMER, the inhibition of fluconazole and sulfaphenazole was reversible and thus well in line with previous studies. In contrast, on account of data obtained with IMER, inhibition by miconazole and nicardipine was not reversible, although these compounds have previously been reported to be reversible CYP2C9 inhibitors in vitro, which may be due to the strong aggregation tendency of these compounds. The study shows that the developed flow-through based IMER is well suited for studying inhibition of CYP enzymes However, to utilize the developed technology in CYP enzyme inhibition research, it’s applicability in determining enzyme inhibition should still be evaluated with more comprehensively with several CYP isoenzymes.
  • 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.
  • Saharinen, Janne (2020)
    Prolyloligopeptidase (PREP) and alphasynuclein are linked to various neurological and psychiatric conditions of which the most relevant considering this study is parkinsonism. PREP cleaves small peptides after a proline residue. It has also protein-protein ineractions with alphatubulin, GAP-43 and alphasynuclein. PREP inhibitors have been shown to have an effect to elimination of alphasyuclein via autophagy. Thiazole is a heteroaromatic compound with two heteroatoms (sulphur and nitrogen). Thiazole can be found as a structural component among various active pharmaceutical ingredients with wide array of indications. Synthetic route for thiazole was published in 1887 and a considerable amount of literature regarding the use of thiazole in medicinal and synthetic chemistry has been published. The aim of the study was to extend the the scope of research done in the research group on small-molecular thiazole-based PREP inhibitors. The goal was to develop a synthetic route to access a series of molecules and gain information of the possible biological activities of the produced compounds by determining their IC50-values in vitro, effect on dimerization of alphasynuclein and removal of alphasynuclein via autophagy in a cell culture. Optimization of the synthetic route and search of alternative reactions were among the aims to some extent. During the course of study yields of some steps of the synthesis were improved and some new molecules had biological activity.
  • 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.