Adamcová, M.: Study of biological activity of alkaloids isolated from Argemone grandiflora (Papaveraceae) I. Diploma thesis, Charles University in Prague, Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Botany and Ecology, Hradec Králové 2015. The aim of this study was isolation of substances from total diethyl ether alkaloid extract of Argemone grandiflora Sweet, their identification and assessment of their inhibition activity towards acetylcholinesterase, butyrylcholinesterase and prolyl oligopeptidase. Using common chromatografic methods, four alkaloids were isolated, that was identified as (+)-laudanosine, protopine, (-)-argemonine a (-)-platycerine. These substances was tested for their inhibition activity IC50: (+)-laudanosine (IC50 AChE = 617,00 ± 46,55 μM, IC50 BuChE = 644,77 ± 55,52 μM, IC50 POP = not mesured yet); protopine (IC50 AChE = 229,98 ± 21,02 μM, IC50 BuChE = 208,87 ± 17,67 μM, IC50 POP ˃ 1000 μM); (-)-argemonine (IC50 AChE = 4677,75 ± 1241,08 μM, IC50 BuChE = 885,45 ± 119,50 μM, IC50 POP = 337 ± 83,1 μM); (-)-platycerine (IC50 AChE = 223,65 ± 19,61 μM, IC50 BuChE = 1651,25 ± 327,7 μM, IC50 POP = 687 ± 74 μM). In comparison with the standards galanthamine (IC50 AChE = 1,710 ± 0,065 μM, IC50 BuChE = 42,30 ± 1,30 μM) and huperzine A (IC50 AChE = 0,033 ± 0,001...

Dvořáková Zdeňka: Alkaloids of Narcissus 'Dutch Master' (Amaryllidaceae) and their biological activity II. Diploma thesis 2016, Charles University in Prague, Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Botany and Ecology. The content of this work was isolation of compounds from the selected fraction ND-6 obtained by column chromatography of Narcissus 'Dutch Master' alkaloid extract. Preparation of extract and its column chromatography was performed by Mrg. Daniela Hulcová as part of her doctoral studies. By the means preparative TLC was from fraction ND- 6 homolycorine type alkaloid (+)-O-methyllycorenine gained. Its structure was determined on the basis NMR, GC-MS analysis and optical rotation. The obtained data were compared with facts in known literature. By the isolated alkaloid was determined its cholinesterase inhibitory activity against acetylcholinesterase and butyrylcholinesterase. Its inhibitory activity was expressed as IC50 (M) and compared with known standards galanthamine, physostigmine, and Huperzine A. This alkaloid is inactive against cholinesterase (IC50 AChE > 1000 M, IC50 BChE > 1000 M). On the basis of gained results, we can evaluate this alkaloid from the point of view of cholinesterase inhibition as potentially unusable in the treatment of AD. Key...

Vacková, L.: Alkaloids Narcissus 'Dutch Master' (Amaryllidaceae) and their biological activity. I. Diploma thesis, Charles University in Prague, Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Botany and Ecology, Hradec Králové 2016. From a selected fraction ND-6, which was obtained by column chromatography of an alkaloid extract of Narcissus 'Dutch Master' (preparation of the alkaloid extract and column chromatography was performed by Mgr. Daniela Hulcová within her doctoral thesis), lycorine alakloid O-acetylpluviin was isolated using preparative TLC. Its structure was determined on the basis of MS, NMR analysis, and optical rotation, the obtained data were compared with the literature. The isolated alkaloid was tested on its possibility to inhibit human acetylcholinesterase and butyrylcholinesterase. The activity was expressed as IC 50 values (IC50 AChE = 648.03 ± 53.95 μM, IC50 BChE = 602.50 ± 48.50 μM) and compared with IC50 values of galanthamine, huperzine A and physostigmine. O-acetylpluviine showed a very low inhibitory cholinesterase activity, and so, the alkaloid does not seem to be a suitable cholinesterase inhibitor for potential use in the treatment of Alzheimer's disease. Keywords: Narcissus 'Dutch Master', Amaryllidaceae, lycorine alkaloids, Alzheimer's disease,...

Background-Previously we found that smooth muscle cell (SMC)-specific knockout of miR-17 similar to 92 attenuates hypoxia-induced pulmonary hypertension. However, the mechanism underlying miR-17 similar to 92-mediated pulmonary artery SMC (PASMC) proliferation remains unclear. We sought to investigate whether miR-17 similar to 92 regulates hypoxia-inducible factor (HIF) activity and PASMC proliferation via prolyl hydroxylases (PHDs). Methods and Results-We show that hypoxic sm-17 similar to 92(-/-) mice have decreased hematocrit, red blood cell counts, and hemoglobin contents. The sm-17 similar to 92 (-/-) mouse lungs express decreased mRNA levels of HIF targets and increased levels of PHD2. miR-17 similar to 92 inhibitors suppress hypoxia-induced levels of HIF1 alpha, VEGF, Glut1, HK2, and PDK1 but not HIF2 alpha in vitro in PASMC. Overexpression of miR-17 in PASMC represses PHD2 expression, whereas miR-17/20a inhibitors induce PHD2 expression. The 3'-UTR of PHD2 contains a functional miR-17/20a seed sequence. Silencing of PHD2 induces HIF1a and PCNA protein levels, whereas overexpression of PHD2 decreases HIF1 alpha and cell proliferation. SMC-specific knockout of PHD2 enhances hypoxia-induced vascular remodeling and exacerbates established pulmonary hypertension in mice. PHD2 activator R59949 reverses vessel remodeling in existing hypertensive mice. PHDs are dysregulated in PASMC isolated from pulmonary arterial hypertension patients. Conclusions-Our results suggest that PHD2 is a direct target of miR-17/20a and that miR-17 similar to 92 contributes to PASMC proliferation and polycythemia by suppression of PHD2 and induction of HIF1 alpha.

Abstract Oxygen is vital for human survival. To ensure its sufficient supply, the body has an intricate system, which involves the circulatory, respiratory and neuroendocrine systems. When oxygen is lacking, a state of hypoxia occurs, and adaptive changes in gene expression increase oxygen delivery to promote survival. The key regulator of the transcriptional hypoxia response is hypoxia-inducible factor (HIF) which targets over 1000 genes. The HIF prolyl 4-hydroxylases (HIF-P4Hs) govern the stability of HIF in an oxygen-dependent fashion. In our studies we investigated whether activation of the hypoxia response through inhibition of either of two distinct HIF-P4Hs, HIF-P4H-2 or P4H-TM would reduce atherosclerosis in mice. We found that inhibition of HIF-P4H-2 led to reductions in numbers of atherosclerotic plaques, and levels of serum cholesterol and inflammation in white adipose tissue and aortic plaques. In addition, HIF-P4H-2 deficient mice had elevated levels of modified LDL-targeting, atheroprotective circulating autoantibodies. The P4H-TM knockout mice also had reduced numbers of atherosclerotic plaques and increased levels of atheroprotective autoantibodies in their sera, but in contrast to the HIF-P4H-2 deficient mice, they also showed a reduction in serum triglyceride levels. To determine how hypoxia alters maternal glucose and lipid metabolism in pregnancy, we studied pregnant mice that were predisposed to a hypoxic condition (15% ambient O2). We found that they had enhanced glucose metabolism due to reduced insulin resistance and an increased flux of glucose to maternal tissues. The hypoxic dams also failed to gain weight and store adipose tissue in the anabolic phase to the same extent as normoxic control dams. These results implicate HIF-P4H inhibition as a novel therapeutic mechanism for atherosclerosis, and suggest that the small molecule HIF-P4H inhibitors currently in clinical trials for renal anemia may have further possible therapeutic applications. In addition, greater understanding of the changes in maternal metabolism that underly reduced fetal growth in hypoxic conditions, and the development of targeted interventions may allow the preservation of fetal growth in cases of maternal hypoxia. / Tiivistelmä Happi on ihmiselle elintärkeää. Tämän vuoksi meille on kehittynyt pitkälle jalostunut verenkierto-, hengitys- ja neuroendokriininen järjestelmä sekä sellaisten geenien ilmentymisen muutoksia, jotka joko lisäävät hapen kuljetusta tai auttavat selviytymään hypoksisissa oloissa, jotta taataan riittävä hapen saanti. Hapen puutteessa hypoksiavaste, jonka tärkein säätelijä on hypoksiassa indusoituva transkriptiotekijä (HIF), aktivoituu. HIF:lla on yli 1000 kohdegeeniä joiden kautta sen vaikutukset välittyvät. HIF-prolyyli-4-hydroksylaasit (HIF-P4H:t) säätelevät HIF:n stabiilisuutta hapesta riippuvaisesti. Tutkimuksessamme selvitimme, vähentääkö hypoksiavasteen aktivointi HIF-P4H-2:n tai P4H-TM:n inhibition kautta ateroskleroosia hiirillä. Tuloksena oli, että HIF-P4H-2:n inhibitio vähensi ateroskleroottisia plakkeja, seerumin kolesterolia ja inflammaatiota valkoisessa rasvakudoksessa sekä plakeissa. Lisäksi hiirillä, joilta puuttui HIF-P4H-2, oli lisääntynyt määrä ateroskleroosilta suojaavia muokattua LDL:ää sitovia autovasta-aineita seerumissa. P4H-TM-poistogeenisillä hiirillä todettiin vastaavasti vähemmän ateroskleroottisia plakkeja ja lisääntynyt määrä ateroskleroosilta suojaavia autovasta-aineita seerumissa. Poiketen HIF-P4H-2-puutteisista hiiristä, niillä oli matalammat seerumin triglyseridi-tasot. Tutkimme raskaina olevia hiiriä, jotka altistimme hypoksisille olosuhteille (15% O2), jotta pystyisimme määrittämään, kuinka hypoksia vaikuttaa äidin sokeri- ja rasva-aineenvaihduntaan. Hypoksiassa raskaana olevilla hiirillä todettiin tehostunut sokeriaineenvaihdunta, joka oli seurausta alentuneesta insuliiniresistenssistä sekä lisääntyneestä sokerin sisäänotosta äidin kudoksiin. Hypoksiassa eivät raskaana olevien hiirten paino eivätkä rasvavarastot lisääntyneet samassa suhteessa normoksiassa raskaana olevien hiirten kanssa. Nämä tulokset tarjoavat uusia mahdollisuuksia HIF-P4H-inhibition käyttämiseen terapeuttisena vaihtoehtona ateroskleroosin hoidossa ja ehkäisemisessä. Kliinisissä kokeissa munuaisperäisen anemian hoidossa olevat HIF-P4H-estäjät voisivat näin ollen saada lisää indikaatioita. Lisäksi korkean ilmanalan aiheuttaman pienipainoisuuden takana olevien aineenvaihdunnan muutoksien ymmärtäminen voi mahdollistaa sikiön kasvun turvaamisen spesifein interventioin.

1 9 ABSTRACT Jurkaninová, M.: Vinca minor L. alkaloids and their biological activity I. Diploma thesis, Charles University, Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Botany, Hradec Králové, 2019 The aim of this thesis was the isolation of alkaloids from selected fraction 3 (joined fractions (15 - 36), which was a sub-fraction of the fraction VM 323 - 327. It was obtained from the previous processing of an alkaloidal extract from the Vinca minor L at the Department of Pharmaceutical Botany as a part of elaboration of diploma thesis of Aneta Vítavcová.[78] The fraction VM 323-327 was separated by column chromatography on silica gel and a totally, of 7 subfractions were obtained. Subsequent repeated processing of the selected sub-fraction 3 (15 - 36) by preparative TLC on silica gel resulted in the isolation of (-)-vinoxine and its racemate (±)-vinoxine. Identification of their structure was determined based on MS, NMR and optical rotation. The inhibitory activity against acetylcholinesterase, butyrylcholiesterase and prolyl oligopeptidase were determined for the isolated substances. Inhibitory activity against selected enzymes was measured by spectrophotometric methods. Isolated alkaloids were required to be inactive against AChE and POP (IC50 >1000 μM), against to BChE showed a...

Mycobacterium tuberculosis, the causative pathogen of tuberculosis, currently infects one-third of the world’s population, resulting in two million deaths annually. This clearly shows that tuberculosis is one of the most serious diseases of our times. The often unpleasant side effects from the current drugs, combined with the difficulty of ensuring patient compliance, and the emergence of drug-resistant and multidrug-resistant strains, makes the need for new and better drugs urgent. In this thesis, all the steps, from cloning, purification, crystallization, to activity determination, and structure determination are presented for two different M. tuberculosis enzymes. The structures, which were modeled from X-ray crystallographic data, provide the framework for structure-based drug design. Here, new potential inhibitors can be tailor-made based on the specific interactions in the enzyme’s active site. The bacteria have two different peptidyl-prolyl cis-trans isomerases that catalyze the isomerization of peptide bonds preceding proline residues, a process of high importance for correct folding. Here we present the structure of peptidyl-prolyl cis-trans isomerase A, an enzyme present inside the bacteria, and distinguish it from the B form of the enzyme, which is membrane bound, placing its active site outside the bacteria. The enzyme 1-deoxy-D-xylulose-5-phosphate reductoisomerase catalyzes the second step within the non-mevalonate pathway, which leads to the production of isopentenyl diphosphate. This compound is the precursor of various isoprenoids, vital to all living organisms. In humans, isopentenyl diphosphate is produced via a different pathway, indicating that all the enzymes within the non-mevalonate pathway may be suitable drug targets in M. tuberculosis. Several structures of both wild type and mutant 1-deoxy-D-xylulose-5-phosphate reductoisomerase in complex with different substrates, and also with the known inhibitor fosmidomycin, provide valuable information not only to the field of drug design, but also, in this case, into the catalysis.

In eukaryotes, the first step of interpreting the genetic information is the transcription of DNA into RNA. For protein-coding genes, such transcription is carried out by RNA polymerase II. A special domain of RNA polymerase II, called the C-terminal domain (CTD), functions as a master controller for the transcription process by providing a platform to recruit regulatory proteins to nascent mRNA (Chapter 1-2). The modifications and conformational states of the CTD, termed the 'CTD code', represent a critical regulatory checkpoint for transcription. The CTD, found only in eukaryotes, consists of 26--52 tandem heptapeptide repeats with the consensus sequence, Tyr₁Ser₂Pro₃Thr₄Ser₅Pro₆Ser₇. Phosphorylation of the serines and prolyl isomerization of the prolines represent two major regulatory mechanisms of the CTD. Interestingly, the phosphorylation sites are typically close to prolines, thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Understanding how those modifying enzymes recognize and regulate the CTD is important for expanding our knowledge on the transcription regulation and deciphering the 'CTD code'. During my PhD study, I studied the function of CTD phosphatases and prolyl isomerase in the CTD regulation using Scp1, Ssu72 and Pin1 as model regulators. Scp1 and Ssu72 are both Ser5 phosphatases. However, Ssu72 is an essential protein and regulates the global transcription while Scp1 epigenetically silences the expression of specific neuronal genes. Pin1 is a highly conserved phosphorylation-specific prolyl isomerase that recognizes the phospho-Ser/Thr-Pro motif within the CTD as one of its primary substrates in vivo. Among these enzymes, Scp1 is the focal point of this dissertation, as it was studied from different angles, such as enzymatic mechanism (Chapter 3 describes the capture of phospho-aspartyl intermediate of Scp1 as a direct evidence for the proposed two-step mechanism), specific inhibition (Chapter 4 describes the identification and characterization of the first specific inhibitor of Scp1), and its non-active-site contact with the CTD (Chapter 5 describes the structural basis of this contact). These studies are of great importance towards understanding the molecular mechanism of the dephosphorylation process of the CTD by Scp1. / text

La flexibilité est une caractéristique intrinsèque des protéines qui doivent, dès le mo- ment de leur synthèse, passer d’un état de chaîne linéaire à un état de structure tridimen- sionnelle repliée et enzymatiquement active. Certaines protéines restent flexibles une fois repliées et subissent des changements de conformation de grande amplitude lors de leur cycle enzymatique. D’autres contiennent des segments si flexibles que leur structure ne peut être résolue par des méthodes expérimentales. Dans cette thèse, nous présentons notre application de méthodes in silico d’analyse de la flexibilité des protéines : • À l’aide des méthodes de dynamique moléculaire dirigée et d’échantillonnage pa- rapluie, nous avons caractérisé les trajectoires de liaison de l’inhibiteur Z-pro- prolinal à la protéine Prolyl oligopeptidase et identifié la trajectoire la plus pro- bable. Nos simulations ont aussi identifié un mode probable de recrutement des ligands utilisant une boucle flexible de 19 acides aminés à l’interface des deux domaines de la protéine. • En utilisant les méthodes de dynamique moléculaire traditionnelle et dirigée, nous avons examiné la stabilité de la protéine SAV1866 dans sa forme fermée insérée dans une membrane lipidique et étudié un des modes d’ouverture possibles par la séparation de ses domaines liant le nucléotide. • Nous avons adapté auproblème de la prédiction de la structure des longues boucles flexibles la méthode d’activation et de relaxation ART-nouveau précédemment uti- lisée dans l’étude du repliement et de l’agrégation de protéines. Appliqué au replie- ment de boucles de 8 à 20 acides aminés, la méthode démontre une dépendance quadratique du temps d’exécution sur la longueur des boucles, rendant possible l’étude de boucles encore plus longues. / Flexibility is an intrinsic characteristic of proteins who from the moment of synthesis into a linear chain of amino acids, have to adopt an enzymatically active tridimensionnel structure. Some proteins stay flexible once folded and display large amplitude confor- mational changes during their enzymatic cycles. Others contain parts that are so flexible that their structure can’t be resolved using experimental methods. In this thesis, we present our application of in silico methods to the study of protein flexibility. • Using steered molecular dynamics and umbrella sampling, we characterized the binding trajectories of the Z-pro-prolinal inhibiter to the Prolyl oligopeptidase pro- tein and we identified the most probable trajectory. Our simulations also found a possible ligand recrutement mechanism that involves a 19 amino acids flexible loop at the interface of the two domains of the protein. • Using traditional and steered molecular dynamics, we examined the stability of the SAV1866 protein in its closed conformation in a lipid membrane and we studied one of its proposed opening modes by separating its nucleotide binding domains. • We also adapted the activation-relaxation technique ART-nouveau which was pre- viously used to study protein folding and aggregation to the problem of structure prediction of large flexible loops. When tested on loops of 8 to 20 amino acids, the method demonstrate a quadratic execution time dependance on the loop length, which makes it possible to use the method on even larger loops.

Michal, Vojtěch: STUDY OF BIOLOGICAL ACTIVITY OF ISOLATED ALKALOIDS FROM ARGEMONE GRANDIFLORA (PAPAVERACEAE) II. Diploma thesis 2015. Charles University in Prague, Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Botany and Ecology. Supervisor: PharmDr. Jakub Chlebek, PhD. Key words: Argemone grandiflora Sweet, Papaveraceae, alkaloids, isolation, acetylcholinesterase, butyrylcholinesterase, prolyloligopeptidase, Alzheimerʼs disease, in vitro assay. Diethylether alkaloid extract obtained from stem and roots of Argemone grandiflora Sweet was chromatografically analyzed. Using common chromatografic methods, three alkaloids were isolated in clean form. These substances were identified as allocryptopine, (-)-munitagine and (-)-norargemonine by structural analysis (MS, NMR). These obtained alkaloids were tested for their inhibitory activity against human erythrocyte acetylcholinesterase (AChE) and human plasma butyrylcholinestrase (BuChE) by Ellman's method. The results were represented as IC50 values (allocryptopine: IC50 AChE = 250,0 ± 2,52 μM, IC50 BuChE = 530 ± 28,2 μM; (-)-munitagine: IC50 AChE = 62,29 ± 5,81 μM, IC50 BuChE = 837,4 ± 23,03 μM; (-)-norargemonine: IC50 AChE = 205,17 ± 11,6 μM, IC50 BuChE = 4158,20 ± 495,78 μM). Inhibition against prolyloligopeptidase was tested for...