Vol 43, No 4 (2017)

It is known that albumin can break the ester bonds in organophosphorus compounds (OPs). Amino acids responsible for esterase and pseudoesterase activity of albumin towards OPs are still not determined. It is assumed that Sudlow’s site I with residue Tyr150 exhibits the “true” esterase activity; and Sudlow’s site II containing residue Tyr411, a pseudoesterase one. Binding of fatty acids to albumin affects the efficiency of its interaction with xenobiotics; however, the effect of fatty acids on the interaction of albumin with OPs was not studied. The purpose of this work was to study the interaction of OPs with potential sites of albumin enzymatic activity and to examine the effect of fatty acids on the efficiency of such interaction using the molecular modeling methods by the example of paraoxon, a known inhibitor of acetylcholinesterase, and oleic acid. The structures of the protein complexes with paraoxon and oleic acid were determined by the molecular docking procedure; the conformational changes were calculated by the molecular dynamics method. It has been shown that sorption of oleic acid in one of the fatty acid-binding sites leads to the conformational changes in Sudlow’s sites I and II due to a “reversal” of the side chains of Arg410 and Arg257 residues by 90°. It has been found that this change in geometry reduces the affinity of Sudlow’s site I and increases the Sudlow’s site II affinity to paraoxon. The amino acid residue Ser193, which was previously identified as a site of possible albumin esterase activity, is not able to bind paraoxon efficiently. It is assumed that its activity can be affected by the interaction of the oleic acid molecules with other fatty acid-binding sites. It is hypothesized that the lesser toxicity of paraoxon compared to soman may be associated not only with its lower inhibitory activity against cholinesterases, but also with the increased affinity of paraoxon to albumin. It was concluded that albumin may serve as an alternative means of OP detoxification.

Eu(III) chelate-bonded polymer nanoparticles were used as phosphorescent labels to develop a highly sensitive phosphorescence analysis (PHOSPHAN^TM) for detection of human thyroid stimulating hormone (TSH). The phosphorescence was recorded in a time-resolved mode from microzones (microarrays) that were printed on the bottoms of the wells of standard polystyrene microplates. TSH was detected in paper discs (3.2 mm in diameter) that were punched from capillary blood that was dried on filter paper. The basic analytical and functional characteristics of this new method were similar to those of the commercial reagent kit for TSH detection in dried blood spots from newborns. Both methods made it possible to correctly detect the hormone concentration in the range of 0–250 μIU/mL blood. The analytical sensitivity of the Eu(III) nanoparticle label was 0.46 ± 0.1 μIU/mL (corresponded to approximately 17 fmol/L), which was comparable with the most sensitive assays. The matrix effect was insignificant. The coefficient of the variation of the results (up to 20%) was higher than in the commercial kit. This highly sensitive new test system could be integrated into PHOSPHAN-based multiplex tests to aid in simultaneous detection of markers for several congenital disorders in newborns.

MicroRNAs (miRNAs), approximately 22 nucleotides (nt) long, are small, non-coding RNA molecules with important regulatory functions in gene expression. They are mostly conserved among the organisms and this conservation makes them a good source for the identification of novel miRNAs by computational genomic homology. The miRNA repertoire of a major aquaculture species, Boleophthalmus pectinirostris, has been unknown until recently. Currently, the B. pectinirostris whole-genome sequences have been completed, making it more convenient for us to focus on computational prediction for novel miRNA homologs. Following a range of strict filtering criteria, a total of 62 potential miRNAs were identified for the first time; they belong to 39 different miRNA families. All these miRNAs were observed in the stem portion of the stable stem–loop structures. The minimum free energy (MFE) of the predicted miRNAs ranged from −21.6 to −62.7 kcal/mol with an average of −39.2 kcal/mol. The A + U ranged from 32.5 to 69.1% with an average value of 52.2%. The phylogenetic analysis of predicted miRNAs revealed that miR-23a-3p, miR-184-3p, miR-214-5p, and miR-338-3p from B. pectinirostris are evolutionary highly conserved showing more similarity with other fish species. To verify the predicted miRNAs, selected miRNAs representing 16 of the 39 families were confirmed by stem–loop RT-PCR, indicating that the computational approach that we used to identify the miRNAs is a highly efficient and affordable alternative method. Taken together, these findings provide a reference point for further research on miRNAs identification in fish species, meanwhile, our study also will be useful for further insight into biological functions of miRNAs and improved understanding of genome in B. pectinirostris.

Promising 6-nitro-1,2,4-triazolo[1,5-a]pyrimidine analogues, structural analogues of synthetic inhibitors of adenosine receptors, were sorted out on the basis of quantum-chemical calculations. The compounds were synthesized by nitration and chlorodeoxygenation reactions. The in vivo activity of 6-nitroheterocycles was studied and the affinity to adenosine receptor A_2A was demonstrated in regard to septic conditions.

DNA binding position and binding affinity of drugs are important information that helps medicinal chemists in synthesis of new drugs. We used molecular docking and molecular dynamics simulation to reveal binding strength of thieno[2,3-b]benzo[1,8]naphthyridine derivatives to DNA. Molecular docking showed that molecules with more steric hindrance select groove position in DNA structure. Other molecules are intercalated between base pairs of GC and AT. Restrained electrostatic potential (RESP) charges, root mean square deviation (RMSD), and total potential analyses were performed. RMSD and total potential analyses showed that all simulations have stability for MMGBSA analysis. Binding affinity of all drugs was derived via MMGBSA analysis. Thermodynamics analysis showed that binding affinity of groove binding drugs is less than that of intercalating ones. Also, it was found that a linear relationship exists between RESP charges and ΔG_pred. Additionally, our results demonstrated the highest affinity for molecules carrying substituent groups of–OCH₃ and–CH₃.

Fifteen adamantane derivatives were synthesized. Preliminary evaluation of their potential as dipeptidyl peptidase 4 (DPP-4) inhibitors was performed in silico by the Microcosm informational technology, PASS system, and docking in AutoDock Vina. The DPP-4 inhibition was studied in vitro. The selectivity of action of the most active compounds was studied by the direct inhibition of human plasma DPP-4 and recombinant human DPP-8. The highest activity was found for the compounds containing a nitrogen atom in the β-position of the side chain, namely, derivatives of adamantane carboxylic acid and N-(3-adamantyl-allyl) thiourea. We demonstrated that the most active compound of the series, 3,5-dimethyladamantane 1-carboxamide, was a selective DPP-4 inhibitor with IC₅₀ 53.94 μM.

The interaction of two structurally close flavanones: taxifolin and naringenin with copper(I) ions and its effect on the distribution of flavonoids and the corresponding ions in a biphasic system octanol–water have been studied. It has been shown that these polyphenols form complexes with copper ions of different stoichiometric ratio depending on the pH of medium (5.4, 7.4, and 9.0). The interaction of the flavonoids with copper ions leads to an increase in the fraction of polyphenols in the water phase at all pH values examined. The fraction of metal ions in octanol in the presence of both taxifolin and naringenin is maximal in the range of neutral pH values. The parameters obtained in the study, such as the partition coefficient and the coefficient of distribution in a biphasic system octanol–water (logP and logD) form the physicochemical basis necessary for the estimation of the bioavailability of flavonoids and the corresponding metal ions upon their combined consumption.