[Full atomic computer model of a bilayer membrane with 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.

Nonselective inhibition of monoamine oxidases A and B by activators of soluble guanylate cyclase

Several activators of soluble guanylate cyclase were investigated as potential inhibitors of rat liver mitochondrial monoamine oxidases (MAO) A and B. They all fitted into the previously designed "molds" of substrate-inhibitor binding sites of these enzymes. However, only two of them, NO donors (7-nitro-benzotetrazine-1,3-dioxide (7-NBTDO) and benzodifuroxan), caused nonselective inhibition of MAO A and MAO B with IC(50) values of 1.3-1.6 and 6.8-6.3 microM, respectively. The inhibitory effect on both MAO A and MAO B was reduced by mitochondria wash suggesting reversible mode of the enzyme inhibition. There was no correlation between potency of MAO inhibition and activation of human platelet soluble guanylate cyclase. The NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (carboxy-PTIO) had no effect on the manifestation of MAO inhibition by benzodifuroxan and 7-NBTDO; however, at 50 microM concentration carboxy-PTIO caused potent inhibition of MAO A with minor effect on MAO B activity. The data suggest that nonselective inhibition of MAO A and MAO B by benzodifuroxan and 7-NBTDO can be attributed to the properties of the chemical structures of these compounds. The results of the present study demonstrate a real possibility for the development of a new generation of effective reversible nonselective MAO inhibitors exhibiting equal inhibitory activity with respect to both MAO A and MAO B.

[Double disposition of the major vessels from the right ventricle of the Fallot tetralogy type]

Forty-six patients with double disposition of the major vessels from the right ventricle in combination with stenosis of the pulmonary artery, in sub-aortal and bi-committed defects of the interventricular septum have undergone biventricular intraventricular correction. The most specific and accurate anatomic characteristics were: 1) position of the major vessels (particularly side-to-side); 2) location of two and a part of the third aortal sinuses above the right ventricle; 3) bilateral cone; 4) absence of aorto-mitral contact; 5) location of valves of aorta and pulmonary artery on the same level. One (2,2%) patient died during surgery due to progressed cardiac insufficiency. One (2,5%) patient died 2 years after radical correction of the defect due to progressive dysfunction of the right ventricle.

Computer visualisation of the active site of monoamine oxidase-A by means of selective inhibitors

Computer visualisation of the active site of monoamine oxidase (MAO) is based on an assumption that the specific and reversible interaction of a ligand (substrate or inhibitor) with the substrate-binding region of the active site requires shape complementarity. The size of the ligand must allow its accommodation at the substrate-binding region. Analysis of the MAO-inhibitory activity of rigid analogues of isatin and pirlindole revealed a dependence between three-dimensional linear sizes of these molecules and the efficacy of inhibition of both MAO-A and MAO-B. However, flexible molecules did not exhibit any dependence between linear sizes and MAO-B inhibitory potency, possibly because they folded into compact structures could fit into the substrate-binding pocket of MAO-B. 'Moulding' of the substrate/inhibitor binding region by superposition of effective MAO-A inhibitors from various groups of chemicals allowed the shape of substrate/inhibitor binding region to be visualised. 'Removal of contents' from this mould yielded a cavity, which corresponded to the shape of substrate/inhibitor binding region. Such cavity can be used to evaluate the most probable positions known inhibitors take in binding to it. The docking procedure can also be used for searching molecular databases for new inhibitors. Pilot experiments revealed that relatively rigid compounds, which did not fit to this cavity, were poor inhibitors of MAO-A.

[Computer modeling the cytochrome P450 three-dimensional structure: problems and prospects]

The review is devoted to the description of basic approaches, problems and prospects of computer modelling of 3D structures of cytochromes P450 (P450s). The following questions have been are considered in the review: (1) the role of computer molecular modelling in P450s research; (2) basic stages of homology modelling of protein 3D structures; (3) purposes and tasks of molecular modelling; (4) problems of P450s homology modelling; (5) criteria for successful P450s homology modelling; (6) methods of P450s models refinement, verification of correctness and reliability.

Strategy of computer-aided drug design

Modern strategies of computer-aided drug design (CADD) are reviewed. The task of CADD in the pipeline of drug discovery is accelerating of finding the new lead compounds and their structure optimization for the following pharmacological tests. The main directions in CADD are based on the availability of the experimentally determined three-dimensional structure of the target macromolecule. If spatial structure is known the methods of structure-based drug design are used. In the opposite case the indirect methods of CADD based on the structures of known ligands (ligand-based drug design) are used. The interrelationship between the main directions of CADD is reviewed. The main CADD approaches of molecule de novo design and database mining are described. They include methods of molecular docking, de novo design, design of pharmacophore and quantity structure-activity relationship models. New ways and perspectives of CADD are discussed.

[Principles of enzymatic analysis of lipids]

The review described principles of modern methods of enzymatic analysis of lipids. Many of these methods of determination of cholesterol, cholesterol ethers, triglycerides, free fatty acids, various types of phospholipids and oxisterols may be employed or are employed in clinical diagnostic laboratories.

Protein-protein interactions: mechanisms and modification by drugs

Protein-protein interactions form the proteinaceous network, which plays a central role in numerous processes in the cell. This review highlights the main structures, properties of contact surfaces, and forces involved in protein-protein interactions. The properties of protein contact surfaces depend on their functions. The characteristics of contact surfaces of short-lived protein complexes share some similarities with the active sites of enzymes. The contact surfaces of permanent complexes resemble domain contacts or the protein core. It is reasonable to consider protein-protein complex formation as a continuation of protein folding. The contact surfaces of the protein complexes have unique structure and properties, so they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations have been undertaken to find or design small molecules that block protein dimerization or protein(peptide)-receptor interaction, or on the other hand, induce protein dimerization.

[Computer model of 3D structure of cytochrome P450 2B4]

Cytochromes P450 (CYPs) play an important role in the oxidative metabolism of xenobiotics. Three-dimensional structures of CYPs are needed to study structure-function relationships in their molecules and interaction with partner proteins. Experimental determination of eucaryotic CYPs 3D structures is difficult because of hydrophobic membrane anchors and surface hydrophobic regions that prevent their crystallization. Replacement of surface hydrophobic amino acids by hydrophilic residues without any changes in protein structure and function can help to solve this problem. Such modification can be proposed using the analysis of 3D model of protein. In this work computer aided 3D structure of microsomal P450 2B4 (CYP2B4) was modeled for the further prediction of surface mutations for hydrophilization of the protein surface. The model of 3D structure of CYP2B4 was constructed by homology with CYP2C5 Model optimization was made by energy minimization and molecular dynamics simulation of protein molecule in water environment. The model was verified by using special statistic software and by comparison with the experimental data on the substrate recognition site, redox-partner binding sites and chemical modification of the protein surface.

[Computer drug design based on analysis of a target macromolecule structure. I. Search and description of a ligand binding site in a target molecule]

The applicability of molecular docking method for finding of ligand binding site in a target protein was tested. The basic principle of tested approach consists in generation of hypotheses of protein-ligand complexes by molecular docking of small ligand to all surface of protein. The subsequent scoring of these hypotheses utilizes the values of contact surfaces and complex formation energy. The docking procedure was executed using the original software DockSearch running on PC Pentium or SGI computers. A set of hypotheses of probable ligand positions on the protein surface was created and evaluated with the help of DockSearch. Energy minimization of molecular complexes was done using Sybyl 6.5 (Tripos Inc.) running on SGI server Origin 200. The final set of the best hypotheses of complexes were selected by the values of contact surfaces and complex formation energy. The applicability and the limits of this approach was tested using known 3D structures of different proteins in free state and in complexes with ligands. For most target proteins the method allows to find the ligand binding site correctly. The accuracy of description of ligand binding site is adequate for subsequent searching of lead compounds by database mining. The reasons of some negative results obtained in testing of this approach are also discussed.

Modelling of three-dimensional structures of cytochromes P450 11B1 and 11B2

The final steps of the biosynthesis of glucocorticoids and mineralocorticoids in the adrenal cortex require the action of two different cytochromes P450--CYP11B1 and CYP11B2. Homology modelling of the three-dimensional structures of these cytochromes was performed based on crystallographic coordinates of two bacterial P450s, CYP102 (P450BM-3) and CYP108 (P450terp). Principal attention was given to the modelling of the active sites and a comparison of the active site structures of CYP11B1 and CYP11B2 was performed. It can be demonstrated that key residue contacts within the active site appear to depend on the orientation of the heme. The obtained 3D structures of CYP11B1 and CYP11B2 were used for investigation of structure-function relationships of these enzymes. Previously obtained results on naturally occurring mutants and on mutants obtained by site-directed mutagenesis are discussed.

[Modeling of monoamine oxidase B active site by computer moulding]

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.

[Clinical, diagnostic and therapeutic features of tricuspid infectious endocarditis]

From 1987 to 1998, examination and treatment were conducted of 12 patients with infectious endocarditis of the tricuspid valve (TIE). 11 of them were operated. TIE was clinically characterized by lesser circulation thromboembolism and marked right ventricular failure. TIE was successfully diagnosed by echo-CG (diagnostic sensitivity 83.3%). Serious disturbances of cellular immunity demanded immunocorrection. Indications for surgical treatment are listed.

[Computer searching of new targets for antimicrobial drugs based on comparative analysis of genomes]

The progress in genome research allows to use genomic databases for drug discovery. The major interest consists in their usage for searching of new molecular targets for new drugs. It is especially important in the area of new antimicrobial drugs creation. In recent years, the applicability of genome analysis for solution of this problem was shown by different authors. We propose an approach for searching new targets for antimicrobial drugs based upon comparative analysis of genomes and samples from molecular databases. For each protein encoded by the target microorganism genome the conformance to a number of medico-biological and technological requirements was tested. The obtained evaluations were used for selection of potential targets. The approach was implemented in the original software GenMesh. It was successfully tested with known targets of drugs against tuberculosis when correct valuations were obtained. The attempt of new targets selection for design of new drugs against tuberculosis was done with reliable results.

Selective inhibitors and computer modelling of the active site of monoamine oxidase

MAO inhibitors can be employed for computer modelling of the active site of MAO A and B. Competitive fully reversible MAO inhibitors with rigid structure and limited number of conformers are preferential compounds for these studies. Among various isatin analogues with nearllanar structure selective MAO B inhibitors fit to 3D box of 8.5x5.1x1.8 A, whereas 3D box of 14.2x5.6x1.8 A accommodates selective MAO A inhibitors. Validity of these data was tested using a series of pyrazinocarbazoles, analogues of short-acting antidepressant pirlindole. Rigid analogues exhibiting potent and selective inhibition of MAO A have 3D size limits of 13x7x4.4 A. Flexible analogues also demonstrated potent inhibition of MAO B and in contrast to rigid analogues their inhibitory activity did not show any dependence on 3D sizes. 3D-QSAR with CoMFA of isatin and pirlindole analogues of MAO A and B revealed differences in the models of MAO A and B.

[Surgical correction of incomplete form of open atrioventricular canal in adults]

Clinical and anatomo-hemodynamic features of adult patients with incomplete form of the open atrioventricular canal are presented, policy of surgical treatment and optimal degree of surgical intervention on mitral valve are determined. The study of variant anatomy of the defect, revealed two variants of left atrioventricular valve formation (with "functional" and with "anatomical" septal commissure). In the first anatomic variant the mitral insufficiency was hemodynamically important and required surgical correction. In the second variant, the mitral valve had good closure function, that permitted to avoid the routine suturing of anterior velum's splitting.

An approach for visualization of the active site of enzymes with unknown three-dimensional structures

A new approach for virtual characterization of the active site structure of enzymes with unknown three-dimensional (3D) structure has been proposed. It includes analysis of data on enzyme interaction with reversible competitive inhibitors, their 3D structures and moulding of the substrate-binding region. The superposition of ligands in biologically active conformations allows to determine the shape and dimension of the active site cavity accommodating these compounds. Monoamine oxidase A (MAO-A), a "typical" enzyme with unknown spatial organisation, was used to test this method. The correctness of such approach was validated by the analysis of HIV protease interaction with its inhibitors using 3D structures of their complexes. Mould of the substrate/inhibitor binding site can be used for the visualization of this binding site and for searching new ligands in molecular databases.

[Computer modeling of the three-dimensional structure of full-length cytochrome B5]

The computer-aided reconstruction of 3D structure of full-length cytochrome b5 was done. Software Sybyl 6.4 from Tripos running on workstation Silicon Graphics Indigo2 (R4400, XZ) was used. The reconstruction was carried out by computer modelling of membrane part of cytochrom b5 with subsequent linking with known structure of water-soluble b5 part (fragment 5-91 of amino acid residues-file 3B5C in the protein data bank, PDB). The obtained structure of full-length cytochrome b5 was refined in the mixture of polar and nonpolar solvents by molecular dynamics simulation and deterministic minimization. Molecular dynamics simulation was performed in periodic box of binary system of solvents with a step of 1 fs during 550 ps at constant number of particles, pressure and temperature. The balance of system was achieved after 400 ps. With period in 5 ps the potential energy was minimized without molecular dynamics interruption. As a result 100 conformations of full-length cytochrome b5 were obtained. Distribution of potential energy was from -2.7 x 10(4) to -4.2 x 10(4) kcal/mol. Conformation of cytochrome b5 with minimal value of potential energy was accepted as the final. Analysis of lipophilic surface of obtained model have shown that membrane bounded part is more hydrophobic and forms a loop structure. This model corresponds to some known experimental data about cytochrome b5 structure.

[The possibilities for preventing adhesive disease after appendectomy]

The authors have developed a method for influencing the altered peritoneum in the area of the inflammation focus by insufflation of medical aerosol at the postoperative period for quicker reestablishment of integrity and physiological function of its mesothelium and fibrinolytic activity which allows the probability of forming commissures in patients after appendectomy to be reduced. Long-term follow-up (up to 3 years) of 61 patients operated upon by the proposed method showed that in 59 of then the results were excellent and good.

Influence of transketolase substrates on its conformation

Dynamics stimulation of the holotransketolase molecule revealed that the enzyme's conformation in crystal was different from that in solution. It was shown also that dissolved holotransketolase can bind aldose (the acceptor substrate) even in the absence of ketose (the donor substrate). The holotransketolase conformation did not change upon aldose binding unlike in the case of ketose binding/cleavage. Therefore the conformation of a catalytic complex of holotransketolase with an intermediate-i.e., a glycolaldehyde residue formed upon binding and subsequent cleavage of ketose-differed, at least in solution, from the conformation of both the free and aldose-complexed holotransketolase. Some structural peculiarities of the holotransketolase with the intermediate were established by means of molecular dynamics stimulation.

[Prediction of binding affinities of protein-ligand complexes using nonlinear models]

A network model for prediction of the free energy changes in protein-ligand complexes has been developed. The 150 complexes of different nature were used as a training set. The computational physics-chemical parameters of these complexes were used as independent variables. Both classical models of multiple linear regression and several network models with one hidden layer were created and the best was chosen. Significant improvement was shown for network model prediction quality in comparison with classical model of multiple linear regression (R2 on training--0.81 and 0.54; R2 on "leave-one-out" procedure--0.74 and 0.52 respectively).

Modeling of substrate-binding region of the active site of monoamine oxidase A

The mold of the substrate-binding region of the active site of monoamine oxidase A (MAO A) was designed using data of the enzyme interaction with reversible competitive inhibitors and the analysis of their three-dimensional structures. The superposition of ligands in biologically active conformations allowed determination of the shape and dimension of the active site cavity accommodating these compounds. The correctness of this approach was validated by the analysis of HIV protease interaction with its inhibitors using three-dimensional structures of HIV protease-inhibitor complexes. The mold of the substrate/inhibitor-binding site can be used for searching for new ligands in molecular databases and the development of a new generation of MAO inhibitors using lead structures that have not been employed for this purpose yet.

[Course of pulmonary hypertension in patients operated for rheumatic mitral heart disease]

AIM

To study changes in pulmonary hypertension in patients with isolated mitral valvular defects of rheumatic etiology after surgical correction and in the early postoperative period.

MATERIALS AND METHODS

Central hemodynamics in heart chamber probing before operation and intraoperatively were measured in 98 patients with rheumatic mitral defects (41 males, 57 females, mean age 39.5 +/- 8.74). Manometry before and after the defect correction, intraoperative catheterization (cath. Swan-Ganz) for hemodynamics 24-h follow-up were made.

RESULTS

After valvular defect correction 90(91%) patients had residual pulmonary hypertension, stage II-III in 41%.

CONCLUSION

Patients operated for rheumatic heart disease complicated by pulmonary hypertension often suffer from residual pulmonary hypertension. This requires pharmacological correction.