Browsing by Subject "COMT"

The aims of this work were (1) to compare the three dimensional structures of different S- adenosylmethionine (SAM)-dependent methyltrasferases and (2) to screen in silico a commercial library for potential methyltransferase inhibitors. In this work we decided to focus on DNA methyltransferase-like enzyme (DNMT2) and catechol-O-methyltransferase(COMT). There were two different parts in my work. The first part was to analyze the 3Dstructures of DNMT2 and COMT in relation with their amino acid sequences. The structures of DNMT2 and COMT were compared together by means of superimposition with Sybyl 8. The ligand binding properties were studied by manual and automatic docking of known inhibitors in order to understand the binding specificity of these methyltransferases. The softwares I used for docking were Autodock 4.2 and Gold 4.0. The sequence alignments and superimposition of the known crystal structures showed that the structures of DNMT2 and COMT share a similar fold. Furthermore the main similarities between the structures of these enzymes are in the co-enzyme binding sites. The only significant difference in the binding sites is the place of one tyrosine residue, which causes a slight change in the conformation of the bound co-enzyme. Unlike co- enzyme binding sites, the substrate binding sites of DNMT2 and COMT are different. There is indeed a bound magnesium ion in the substrate binding site of COMT but not in the substrate binding site of DNMT2. Because the substrate binding sites are more different than the co-enzyme binding sites, we decided to screen the potential active ligands only at the substrate binding sites. The second part of the work was virtual screening. I used a subset of 20.000 molecules of ChemBridge DIVER Set that can be purchased commercially. The softwares I used for library preparation were CONCORD and Balloon, from which Balloon created more reasonable 3D structures for the docking. I did two parallel screenings to the crystal structure of COMT (PDB code 3BWM) with docking program GOLD 4.0, which is the only program that can take account metal coordination. To DNMT2 I did two sets of screenings, one with GOLD 4.0 and another with Autodock 4.2. I used known COMT inhibitors as control in the COMT run and known DNA methyltransferase inhibitors as control in DNMT2 run. Before docking to the three dimensional structure of DNMT2, one loop near the substrate binding site had to be modeled. I used Swiss-Modeler and Modeller softwares for that. Docking to COMT was successful according to the rank of the known COMT inhibitors compared to the subset of the FIMM library that was screened. I created the hitlist of 60 compounds based on the scores of these compounds, pharmacophore search and visual examination. 30 of these compounds were purchased and are currently being tested. The results of the DNMT2 run were not as reliable as the results of COMT run mentioned before, since the DNMT2 run was unable to retrieve known inhibitors better than random. The reason for that can be the quality of the model of the missing loop or the chosen controls. Furthermore only one of the ten small molecules that we used as controls is proved to be DNMT2 inhibitor, the others are DNMT1 and DNMT3 inhibitors and while the binding sites of DNMT1, DNMT2 and DNMT3 are very similar, they are, however, not completely identical.

Parkinson's disease is characterized primarily as a bradykinetic disorder with severe nigral cell loss. In addition to motor symptoms, up to 85 % of patients with Parkinson's disease experience pain and in about 60 % of cases pain is related to Parkinson's disease. Most of it is classified as musculoskeletal pain. Bradykinesia and muscle cramps lead to pain by causing malpositions of joints and trunk. Up to 40 % of parkinson patients experience pain caused by dystonia. Neuritic or radicular pain is also related to Parkinson's disease. Less than 10 % of patients have primary central pain. Pain threshold and nociceptive flexon reflex threshold are lower among patients with Parkinson's disease than in healthy subjects. Common comorbidities, namely restless legs syndrome and depression can also exacerbate pain. The pathology of pain in patients is not well understood. It is known that basal ganglia take part in pain perception and modulation. Lesions in basal ganglia can interfere pain perception and cause the exacerbation of pain. The modulation of pain in central nervous system is altered and descending inhibitory tracts are thought to work insufficiently. Levodopa alleviates the pain in about 60 % of patients with Parkinson's disease suffering from pain. Levodopa normalizes dopamine function at least partly in basal ganglia and that way alleviates the pain caused by dysfunction of dopamine tracts. Levodopa relieves motor symptoms and so alleviates the secondary pain caused by muscle cramps and stiffness. Levodopa raises the pain thresholds of patients to normal level. Levodopa may have also a direct analgesic effect via dopamine D2 receptor activation. The mutations of the gene that codes catechol-O-methyltransferase (COMT) change its activity and are related to pain perception. Low COMT activity is related to several functional differences including increased sensitivity to pain and increased response to opioids. Also COMT inhibitors sensitize mice and rats to pain. The mechanism underlying the sensitization is not well understood. We examined the effects of COMT gene disruption and COMT inhibition in acute pain models. In the first part of our study, we examined the effect of COMT inhibitor OR-486 in COMT deficient mice. We tried to clarify wether sensitization to pain is caused by COMT inhibition or some other mechanism. We also tested the effects of endogenous opioids (swim stress) and exogenous opioid (morphine) in COMT deficient mice. In the second part, we tested the effects of an atypical COMT inhibitor CGP 28014 in acute pain models. CGP 28014 does not inhibit COMT in vitro but it inhibits the Omethylation of catecholamines in vivo. The main finding of our study was the sensitization to pain caused by CGP 28014. The result gives support to hypothesis claiming that sensitization to pain is caused by O-methylation of catecholamines. The results of our study are also in line with the theory that low COMT activity is related to pain sensitization and increased response to opioids.