[Molecular modeling of interaction of 17(20)Z- and 17(20)E-pregna-5,17(20)-dien-21-oyl amides with the nuclear receptor LXRbeta].

Aiming the search of novel regulators of lipid metabolism and their potential targets, in this study we performed molecular modeling of eight isomeric 17(20)Z- and 17(20)E-pregna-5,17(20)-dien-21-oyl amides differing in structure of the amide moiety. Analysis of the low energy conformers revealed that all 17(20)E-isomers had three main energy minima (corresponding to values of the dihedral angle theta20,21 (C17 = C20-C21 = 0) to approximately 0 degrees, to approximately 120 degrees and to approximately 240 degrees), the most occupied minimum was found to correspond to theta20,21 to approximately 0 degrees; while 17(20)Z-isomers had either one or two pools of low energy conformations. Molecular docking of these compounds to the ligand-binding site of the nuclear receptor LXRbeta (a potential target) indicates high probability of binding for E-isomers and the absence of that for Z-isomers. Results of the molecular modeling were confirmed by an experiment in which stimulation of triglyceride biosynthesis in Hep G2 cells in the presence of 17(20)E-3beta-hydroxypregna-5,17(20)-dien-21-oyl (hydroxyethyl)amide was demonstrated.

[Computer-based substrate specifity prediction for cytochrome P450].

Cytochrome P450 is important class of enzymes metabolizing numerous drugs. The composition and activity of these enzymes are determined the drug distribution in organism, its pharmacological and toxic effect. Thus the prediction of the behaviour of compounds in organism is essential for discovery and development of new drugs in the early stages of this process. The different isoforms of cytochrome P450 can oxidized wide range of chemical compounds and their substrate specifity do not correlate with their taxonomical classification. The main methods of cytochrome P450 substrate specifity prediction is reviewed. These methods divided based on primary informations that used: prediction based on amino acid sequences, ligand-based (pharmacophore and QSAR models) and structure-based (molecular docking, affinity prediction) methods. The common problem of cytochrome P450 substrate prediction and advantage and disadvantages of these methods are discussed.

[Analysis of contact interfaces of HIV reverse transcriptase subunits].

Analysis of structure and features of subunit contact areas of reverse transcriptase (RT) HIV was done. The amino acid residues from contact areas of RT subunits are more conservative than the rest residues of the protein. Estimation of contribution of the amino acid residues from contact areas in binding energy of subunits showed that binding energy is mostly localized on the several amino acid residues of the dimer interface (hot spots). The majority of these hot spots form several clusters on contact surfaces. Analysis of these clusters allows to predict the region on the contact area of protein dimer that can be useful for design the inhibitors of dimerization of RT HIV.

[Methods of experimental validation of potential target proteins for creation of new drugs].

Review is devoted to the description of the main existing and developing technologies for experimental validation of potential targets predicted in silico by comparative genomics and bioinformatics methods. Since this problem has not been solved yet, the description of a wide set of methods, suitable for the validation of potential targets, is given. The following questions have been considered: (1) applications of proteomic technologies (control of potential targets expression and their variability, analysis of protein-protein interactions); (2) use of genomics technologies in experimental validation of targets (inactivation of the target genes, suppression of transcription, inactivation of the target mRNA, suppression of translation); (3) methods of direct inactivation of target proteins (monoclonal antibodies, light-inactivation, one-chain antibodies, intrabodies, aptamers); (4) high-throughput technologies; (5) targets validations in vivo.

[Full atomic computer model of a bilayer membrane with MAO A]. / Polnoatomnaia komp'iuternaia model' bisloinoi membrany s MAO A.

The present paper describes computer simulations of dipalmitoylphosphatidylcholine (DPPC) bilayer. DPPC model was constructed from the crystal structures of choline, glycerophosphate and two fatty acid residues. DPPC structure was cloned and the model of lipid bilayer containing 338 DPPC molecules was designed. The molecular dynamics simulation of mixed system composed of DPPC bilayer and 30715 water molecules was performed during 3.5 ns. Some structural parameters like volume and area of bilayer, occupied by one lipid molecule, order parameter of the fatty acyl carbons and density profiles generated by the molecular dynamic simulation were in good agreement with known experimental data. The usefulness of the obtained membrane system for further modelling of membrane proteins topology was tested with monoamine oxidase A (MAO A) membrane topology simulation. Molecular dynamics simulation of lipid bilayer, MAO A and two water phases was carried out during 3.0 ns. Comparative analysis of the equilibrium model and membrane topology of MAO A with known the crystal structure has shown good agreement.

[The role of reactive oxygen species in copper-induced permeability of plasma membranes in Escherichia coli]. / Rol' aktivnykh form kisloroda v med'-indutsirovannoi pronitsaemosti plazmaticheskoi membrany bakterii Escherichia coli.

The role of active oxygen species in the induction of nonselective cationic permeability of the plasma membrane of bacteria Escherichia coli B by the action of Cu2+ ions was studied. It was found that the increase in the amount of active oxygen species in the suspension after treating cells with copper occurred synchronously with the leakage of K+ cations from them. Evidence is presented that active oxygen species formed during the interaction of copper ions with bacteria under aerobic conditions are not involved in the induction of channel conductivity in the membrane. Moreover, the ability of oxygen to protect the membrane from the toxic action of copper was shown, and the activation of membrane damage by external reductants was confirmed. These data suggest that the barrier properties of the membrane are disturbed during the interaction of Cu+ ions with critical targets on the surface, the concentration of Cu+ being determined by all redox processes in the near-membrane space.

[Modeling of monoamine oxidase B active site by computer moulding]. / Modelirovanie aktivnogo tsentra monoaminoksidazy tipa B metodom postroeniia slepka.

Using previously developed approach for active site modelling of enzymes with unknown spatial structure (Veselovsky et al., Biochemistry (Moscow), 65, 1072-1079) substrate/inhibitor binding site of monoamine oxidase B was designed by means of computer moulding. This mould corresponds to the shape and volume size of selective substrates and inhibitors of this enzyme. Active site moulds of monoamine oxidases A and B exhibit significant differences in these parameters. The correctness of the resultant model of monoamine oxiadse B active site was validated by using three compounds which were not employed in the training sets. Weak inhibitors were not accommodated in the mould whereas their "flexible" analogues exhibitng rather potent inhibition are readily accommodated in this mould. This suggests that our mould reflects some important spatial features of monoamine oxidase B active site. This mould can be employed for screening of new perspective inhibitior of monoamine oxidase B and pilot evaluation of their monoamine oxidase B inhibitory activity.

[Reducing centers on the surface of Escherichia coli bacteria and their role in copper-induced plasma membrane permeability]. / Vosstanavlivaiushchie tsentry na poverkhnosti bakterii Escherichia coli i ikh rol' v med'indutsirovannoi pronitsaemosti plazmaticheskoi membrany.

The reducing properties of Escherichia coli and their role in the induction of nonselective cationic permeability of plasma membrane by the action of Cu2+ ions were studied. The ability of cells to reduce exogenous dithiopyridine was shown to be maximal in freshly collected culture and to decrease upon starvation or exhaustion of bacteria by dinitrophenol, in the presence of other oxidants of cell thiols in the medium, and after the disturbance of the barrier properties of membrane by tetrachloracetic acid or butanol. The alkylation of cell thiols accessible for N-ethyl maleimide completely disrupted the reducing activity of bacteria. These data are consistent with the conception that the reduction of dithiopyridine and Cu2+ ions by bacteria occurs on the thiol-containing centers of the cell surface, which are continuously reduced by the transfer of cell reducing equivalents from the inner to the outer surface of plasma membrane. The analysis of data on the effect of external oxidizing and reducing agents on the copper-induced plasmolysis of bacteria showed that the induction of membrane permeability by the action of copper can occur upon interaction with critical targets on the surface of Cu+ ions formed in the periplasmic space in the reaction of Cu2+ ions with reducing centers.

[Computer modeling in the study of mechanism of catalytic activity and the structure of active site of glutamine(asparagine)ase. I. Pharmacophore models of glutamine(asparagine)ase substrates]. / Issledovanie mekhanizma kataliticheskogo deistviia i struktury aktivnogo tsentra glutamin(asparagin)azy metodom komp'iuternogo modelirovaniia. I. Modeli farmakoforov substratov glutamin(asparagin)azy.

Glutamine(asparagine)ase catalyses desamidation of both L-glutamine and L-asparagine, and their D-isomers. In this study the two-pharmacophore models of main enzyme substrates and their hydrolysed analogues were design. The received models reflect two stage of substrate interaction with the enzyme active site. These models allow to explain the wide substrate specificity of glutamine(asparagine)ase.

[Use of selective inhibitors for computer modeling of the monoamine oxidase active site]. / Ispol'zovanie selektivnykh ingibitorov dlia komp'iuternogo modelirovaniia aktivnogo tsentra monoaminoksidaz.

Monoamine oxidase (MAO) is an integral protein of the outer mitochondrial membrane, catalysing the reaction of oxidative deamination of monoamines in the central nervous system and peripheral tissues. The present paper reviews data on the structure of MAO, approaches and methods of computer modeling of active site structure, based on the analysis of MAO inhibition by selective inhibitors Flexible molecules, possessing many conformers are useless for computer modeling. Competitive fully reversible MAO inhibitors with rigid structure and limited number of conformers are preferential compounds for these studies.

[The role of oxygen in the inhibition of Escherichia coli respiration by copper ions]. / Rol' kisloroda v ingibirovanii dykhaniia Escherichia coli ionami medi.

Effect of Cu2+ on E. coli respiration and the role of oxygen in toxic action of copper has been studied. Stimulation of respiration is observed at initial time after introduction of Cu2+. It is based on a nonspecific cell response to membrane damage. After finishing of transitory processes, Cu2+ influenced respiration by noncompetitive inhibition, i.e. copper-sensitive enzyme can be oxygenated or nonoxygenated, and only the latter form of the enzyme is inhibited.

[The effect of CuCl2 on the efflux of inorganic phosphate from Escherichia coli]. / Vliianie CuCl2 na utechku neorganicheskogo fosfata iz Escherichia coli.

The influence of CuCl2 on inorganic phosphate efflux from resting E. coli and those treated with glucose has been studied. Maintaining of high phosphate gradient on the membrane is possibly only in case of continuous supply of external metabolic energy. Treatment with CuCl2 does not lead to the increase in permeability of the resting cell membrane for phosphates, but it causes the efflux of phosphates in glucose-treated cells. The above data suggest that the efflux is determined by inhibition of energy influx into cell by CuCl2, not by damaging the cytoplasmic membrane.