DATABASE ENRICHMENTS OF MAO-B THROUGH ENSEMBLE DOCKING

Objective: The recent growth of highly resoluted crystallographic structures, together with the continuous improvements of the computing power, has established molecular docking as a leading drug design technique. However, the problems concerning the receptor flexibility and the lowered ability of docking software to correctly score the occurred interactions in some receptors are still relevant. Methods: Recently, several research groups have reported an enhancement in enrichment values when ensemble docking has been applied. Therefore, we utilized the latest technique for a dataset of Monoamine Oxidase–B (MAO-B) inhibitors. The docking program GOLD 5.3 was used in our study. Several docking parameters (grid space, scoring functions and ligand flexibility) were altered in order to achieve the optimal docking protocol. Results: The results of 200 000+docking simulations are represented in a modest table. The ensembled simulations demonstrated low ability of the docking software to correctly score the actives seeded in the dataset. However, the superimposed complex-1S3B-1OJA-1OJC, achieved a moderate enrichment value equaled to 9. No significant improvements were noted when five complexed receptors were employed. Conclusion: As a conclusion, it should be noted that in some cases the ensemble docking enhanced the database enrichments, however overall the value is not suitable for future virtual screening. Further investigations in that area should be considered

Sinteza i antihipoksično djelovanje alifatskih i arilalifatskih amida kofein-8-tioglikolne kiseline

The synthesis of some aliphatic and arylaliphatic amides of caffeine-8-thioglycolic acid was studied. The structures of synthesized compounds were proved by microanalyses, IR- and 1H NMR data. Values of acute p.o. and i.p. toxicity in mice show lower toxicity compared to caffeine. Declines in spontaneous locomotor activity support the idea of depressive CNS activity of the compounds. Two compounds exhibited brain antihypoxic activity (5a and 5b against haemic and circulatory hypoxia, respectively).U radu je opisana sinteza alifatskih i arilalifatskih amida kofein-8-tioglikolne kiseline i njihova karakterizacija elementarnom analizom, IR- i 1H NMR spektroskopijom. Testiranja na miševima pokazuju da su sintetizirani spojevi primijenjeni p.o. i i.p. manje toksični od kofeina. Smanjenje lokomotoričke aktivnosti podupire ideju o njihovom depresivnom djelovanju na SŽS. Spojevi 5a i 5b djeluju antihipoksički u uvjetima krvne i cirkulacijske hipoksije u mozgu

Suitable Docking Protocol for the Design of Novel Coumarin Derivatives with Selective MAO-B Effects

Recently, the application of molecular docking is drastically increasing due to the rapid growth of resolved crystallographic receptors with co-crystallized ligands. However, the inability of docking softwares to correctly score the occurred interactions between ligands and receptors is still a relevant issue. This study examined the Pearson’s correlation coefficient between the experimental monoamine oxidase-B (MAO-B) inhibitory activity of 44 novel coumarins and the obtained GOLD 5.3 docking scores. Subsequently, optimization of the docking protocol was carried out to achieve the best possible pairwise correlation. Numerous modifications in the docking settings such as alteration in the scoring functions, size of the grid space, presence of active waters, and side-chain flexibility were conducted. Furthermore, ensemble docking simulations into two superimposed complexes were performed. The model was validated with a test set. A significant Pearson’s correlation coefficient of 0.8217 was obtained for the latter. In the final stage of our work, we observed the major interactions between the top-scored ligands and the active site of 1S3B

The Solverational Grammar and a Set of Evaluation Results

We provide the Solverational grammar for reference on a technical level. All syntax are presented: abstract, textual and graphical. Additionally we provide a set of evaluation results including a deductive comparison with the spatial relations from SGGs as well as a long list of guidelines which have been evaluated whether they can be implemented using Solverational

Design, microwave-assisted synthesis, biological evaluation, molecular docking and ADME studies of pyrrole-based hydrazide-hydrazones as potential antioxidant agents

In this study, one novel N-pyrrolyl carboxylic acid (3), the corresponding N-pyrrolyl hydrazide (5), and four new hydrazide-hydrazones (5a-d) bearing electron donating moieties were designed, synthesized, and fully elucidated by 1H NMR, FT-IR, and HRMS. The hydrazide-hydrazones were produced in five steps, which were optimized by applying microwave heating. The microwave-assisted synthesis significantly decreased the reaction times and increased the yields of the title molecules. In addition, all novel compounds were assessed for their radical scavenging properties by employing DPPH and ABTS assays. The most promising agent was obtained after condensation of the title hydrazide (5) with a 3,5-dimetoxy-4-hydroxybenzaldehyde (5d). The latter compound showed better antioxidant properties than Trolox (6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid) and could serve as a prominent lead structure for future optimization as an antioxidant agent. A possible binding conformation of 5d in the active site of NADPH oxidase was also identified through molecular docking simulations. Analysis of the major interactions showed the importance of the hydroxyl moiety for the antioxidant activity. Finally, the virtual calculations of the ADME properties of the synthesized compounds displayed good drug-like properties. Overall, an optimized synthetic protocol through MW irradiation was employed. The newly synthesized ethyl (E)-5-(4-bromophenyl)-1-(1-(2-(4-hydroxy-3,5-dimethoxybenzylidene)hydrazineyl)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-2-methyl-1H-pyrrole-3-carboxylate (5d) was found to possess the most prominent radical-scavenging capacity, which identifies it as a promising lead compound for the development of novel antioxidants

Synthesis and preliminary hepatotoxicity evaluation of new caffeine-8-(2-thio)-propanoic hydrazid-hydrazone derivatives

New series of caffeine-8-(2-thio)-propanoic hydrazid-hydrazone derivatives were designed and synthesized. The targed compounds were obtained in yields of 51 to 96% and their structures were elucidated by FTIR, 1H NMR, 13C NMR, MS and microanalyses. All of the compounds were found to be “drug-like” as they fulfill the criteria of drug-likeness, which includes the MDDR-like rule. The tested compounds were subjected to in silico prediction of substrate/metabolite specificity and Drug Induced Liver Injury (DILI). The prediction for indicated that the evaluated compounds would most probably act as CYP1A2 substrates. The performed in vitro studies didn’t reveal statistically significant hepatotoxicity of the tested compounds, probably due to the pro-oxidant effects expressed on sub-cellular (isolated rat liver microsomes) level. The obtained experimental results confirmed the predicted low hepatotoxicity for the tested structures. Based on these results the compounds may be considered as promising structures for design of future molecules with low hepatotoxicity

Neuroprotective and MAOB inhibitory effects of a series of caffeine-8-thioglycolic acid amides

The effects of new derivatives of caffeine-8-thioglycolic acid (100 μM) on isolated rat brain synaptosomes, human neuroblastoma cell line SH-SY5Y and human recombinant MAOB enzyme (hMAOB) (1 μM) were evaluated. Most of the compounds, administered alone, didn’t show statistically significant neurotoxic effects on SH-SY5Y, when compared to the control (non-treated cells). Of all studied structures JTA-2Ox, JTA-11, JTA-12 and JTA-13 decreased cell viability. In combination with 6-hydroxydopamine (6-OHDA) (100 μM), only JTA-1 and JTA-2 revealed neuroprotective effects, stronger than those of caffeine. All compounds administered alone revealed, neurotoxic effects on synaptosomes, as compared to nontreated synaptosomes. JTA-1, JTA-2 and JTA-3 showed lowest neurotoxic effects and were investigated in a model of 6-OHDA-induced oxidative stress. In this model of neurotoxicity, only JTA-1 and JTA-2 showed statistically significant neuroprotective effect, by preserving the synaptosomal viability and the level of reduced glutathione. Inhibition of hMAOB, was revealed by JTA-1 and JTA-2. They inhibited the enzyme by 23% and 25% respectively, thus approaching the selegiline activity, which was 42%. The possible mechanisms of neuroprotection of JTA-1 and JTA-2 might be a result from the inhibition of hMAOB, which catalyze the production of neurotoxic p-quinone from 6-OHDA

Synthesis, in silico prediction of sites of metabolism and in-vitro hepatotoxicity evaluationofnew seriesN’-substituted 3-(1,3,7-trimethyl-xanthin-8-ylthio)propanehydrazides

New series of 3-(1,3,7-trimethyl-xanthin-8-ylthio)propanehydrazide derivatives were designed and synthesized. The targed compounds were obtained in yields of 54 to 100% and their structures were elucidated by FTIR,1H NMR,13C NMR, MS and microanalyses. The tested compounds were subjected to in silico prediction of sites of metabolism (SOMs). The predictions show thatthe main metabolic changes will be primarily related to oxidation of the sulfur atom in the side chain, carried out under the action of CYP2C19, as well as O-demethylation of compounds containing methoxy groups.The N-demethylation of the xanthine fragment was determined to be regulated by CYP1A2, CYP2C9, CYP2D6 and CYP3A4. Theperformed in vitro studies confirmed for two of the tested compounds to be low hepatotoxic, due to the presented prooxidant effects at subcellular level (isolated rat liver microsomes). These results highlight these molecules as promising hydrazide-hydrazone structures for the design of compounds with low hepatotoxicity

Development of a chiral RP-HPLC method for identification of stereomers of newly synthesised xanthine-based hydrazide-hydrazone compound

A reverse phase enantio-selective high performance liquid chromatographic method was developed for enantiomeric separation of 2-(1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purine-7(6H)-yl)-N’-(3-fluorobenzylidene)-propanehydrazide isomers. The enantiomers of 2-(1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purine-7(6H)-yl)-N’-(3-fluorobenzylidene)propanehydrazide were resolved on a ACE®Equivalence™ С18 (250 × 4.6 mm, 5 μm) column using a mobile phase system containing methanol, water, phosphate buffer рН 7.4 (50:46:4 v/v/v). The resolution between enantiomers was found to be more than 2.0. The sample solution and mobile phase were found to be stable for at least 48 h. The final optimised method was successfully applied to separate the (R)- and the (S)-enantiomers of 2-(1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purine-7(6H)-yl)-N’-(3-fluorobenzylidene)-propanehydrazide and was proven to be reproducible and accurate

Modeling Usability in Model-Transformations

Developers of transformation rules for user interface models should have the option to support usability in their transformations. As different aspects of usability highly depend on each other, transformation rules should be able to model these dependencies. We provide an example how this can be done in a transformation language through a QVT Relations dialect