Application of molecular modeling to urokinase inhibitors development.

Urokinase-type plasminogen activator (uPA) plays an important role in the regulation of diverse physiologic and pathologic processes. Experimental research has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients, whereas suppression of proteolytic activity of uPA leads to evident decrease of metastasis. Therefore, uPA has been considered as a promising molecular target for development of anticancer drugs. The present study sets out to develop the new selective uPA inhibitors using computer-aided structural based drug design methods. Investigation involves the following stages: computer modeling of the protein active site, development and validation of computer molecular modeling methods: docking (SOL program), postprocessing (DISCORE program), direct generalized docking (FLM program), and the application of the quantum chemical calculations (MOPAC package), search of uPA inhibitors among molecules from databases of ready-made compounds to find new uPA inhibitors, and design of new chemical structures and their optimization and experimental examination. On the basis of known uPA inhibitors and modeling results, 18 new compounds have been designed, calculated using programs mentioned above, synthesized, and tested in vitro. Eight of them display inhibitory activity and two of them display activity about 10 µM.

[Dielectric parameters of ascitic and pleural fluids in the microwave range in different nosologies].

The dielectric parameters of ascitic and pleural fluids formed in the human body in oncological and nononcological diseases of different nosology have been estimated in the range between 400 MHz and 1.2 GHZ. The dependence of refractive and absorption indices of ascitic and pleural liquids on the signal frequency and mass concentration of dissolved substances was found. Common regularities and distinctions in the behavior of their dielectric properties were revealed.

[Dielectric properties of human sweat fluid in the microwave range].

The dielectric properties of sweat fluid gathered from different zones of the human body have been studied in the frequency range from 300 MHz to 3 GHz. It has been shown that the dielectric properties of sweat of different zones differ. The dependence of refraction and absorption indices on the frequency of the signal and the mass concentration of substances dissolved in sweat liquid has been determined.

[Changes in the dielectric properties of water in yeast cells during their death].

The dielectric properties of living and dead unicellular microorganisms (yeast) were studied in the microwave range, and the general regularities and differences were revealed. The effect of temperature on the dielectric properties of yeast cells has been studied. The dielectric parameters of water fractions contained in yeast cells were estimated using the refraction model.

Computation of the contribution from the cavity effect to protein-ligand binding free energy.

We present results of the investigation of the cavity creation/annihilation effect in view of formation of the protein-ligand (PL) complexes. The protein and ligand were considered as rigid structures. The change of the cavity creation/annihilation free energy DeltaG(cav) was calculated for three PL complexes using the thermodynamic integration procedure with the original algorithm for growing the interaction potential between the cavity and the water molecules. The thermodynamic cycle consists of two stages, annihilation of the cavity of the ligand for the unbound state and its creation at the active site of the protein (bound state). It was revealed that for all complexes under investigation, the values of DeltaG(cav) are negative and favorable for binding. The main contribution to DeltaG(cav) appears due to the annihilation of the cavity of the ligand. All computations were made using the parallel version of CAVE code, elaborated in our preceding work.

Cavitation free energy for organic molecules having various sizes and shapes.

Cavitation free energy DeltaG(cav), corresponding to the formation of an excluded volume cavity in water, is calculated for a large set of organic molecules employing the thermodynamic integration procedure, which is realized as the original two-step algorithm for growing the interaction potential between the hard cavity wall and the water molecules. A large variety of solute systems is considered. Their characteristic radii change in the range 3-7 A; spherical cavities with radii 3-6 A are also studied. The interaction between water molecules is described by the four-site nonpolarizable TIP4P model. The diversity of the trial molecular set is provided by using a specially formulated nonspherical criterion classifying the cavity shapes according to their deviation from a sphere. Molecular objects were partly taken from the data base NCI Diversity with the aid of this criterion. The so-computed free energies are approximated by the linear volume dependence DeltaG(cav)V = XiV, where V is the cavity volume. This relation works fairly well until the cavity size becomes very large (the effective radius larger than 7 A). The volume dependence valid for solutes of arbitrary shapes can be included in a calculation of the nonpolar free energy component as required in the implicit water model.

Computation of entropy contribution to protein-ligand binding free energy.

The entropy contribution DeltaS to protein-ligand binding free energy is studied for nine protein-lipid complexes. The entropy effect from the loss of the translational/rotational degrees of freedom (DeltaStr) is calculated using the ideal gas approach. The change in the vibrational entropy (DeltaSvib) is calculated using the effective quantum oscillator approach with frequencies derived from the coordinate covariance matrix, so the inharmonic effects are taken into account. The change in the entropy of solvation (DeltaSsolv) is considered using the binomial cell model (developed by the authors) for the hydrophobic effect. The entropy contribution from loss of conformations that are available for the free ligand (DeltaSconf) is also estimated. It is revealed that the negative in view of binding term DeltaStr is only partly compensated by increasing of DeltaSvib, so T(DeltaStr+DeltaSvib+DeltaSconf)<0 for all complexes under investigation, but taking into account DeltaSsolv leads to significantly increased DeltaS. For all complexes except biotin-streptavidin, the results are found to be in reasonable agreement with experimental data.

[The epidemiological characteristics of fatal subdural hematomas in forensic medical practice]. / Epidemiologicheskie osobennosti smertel'nykh subdural'nykh gematom v sudebno-meditsindskoi praktike.

A retrospective analysis of subdural hematomas is carried out: 493 in subjects dead from mechanical injuries (from files of forensic medical morgues in Tver', 1992-1994), and 37 cases with chronic subdural hematomas (from files of forensic medical morgues No. 2 and 6 in Moscow, 1995-1997). Age and sex of victims, time and circumstances of injuries, topographic and morphological features of subdural hemorrhages and their relation to concomitant injuries, and presence of ethyl alcohol in the organism are studied. The data on chronic subdural hematomas are presented. The authors emphasize the need in forensic medical studies of this condition.

[The morphological characteristics of chronic subdural hematomas]. / Morfologicheskaia kharakteristika khronicheskikh subdural'nykh gematom.

Preparations of chronic subdural hematomas (CSH) obtained during surgery from 29 patients aged 19-50 years are studied. Histological sections were stained with hematoxylin-eosin after van Gieson. Morphological criteria of CSH variants are defined, permitting forensic medical experts to make well-based conclusions on the nature (traumatic or not) of CSH (two types of capsules) and the time when it occurred.

Scanning tunneling microscopy study of cytochrome P450 2B4 incorporated in proteoliposomes.

In the present paper, the application of scanning tunneling microscopy in cytochrome P450s membrane topology is discussed. The method enables visualization of heme location in the lipid-bilayer-incorporated protein. It is supposed that the membrane-bound cytochrome P450 on the tunneling microscope substrate should behave as 'molecular diode'. A model explaining the liposome and the proteoliposome images observed is proposed.

[The effect of hypothermia and oxygenation on the cardiorespiratory system in man exposed to experimental weightlessness]. / Vliianie okhlazhdeniia i oksigenatsii na kardiorespiratornuiu sistemu cheloveka, nakhodiashchegosia v usloviiakh vozdeistviia faktorov modelirovannoi nevesomosti.

It has been established that hypothermia in experimental weightlessness, as compared to normal conditions, was characterized by a considerably smaller deficit of erythrocytes in the energy balance and reduced gas exchange level, despite unidirectional changes in hemodynamic parameters. Unlike in hypothermia, an increase in oxygen concentration in the inhaled gas mixture had no noticeable effect on the parameters of the cardiorespiratory system studied.

[Paramecium test for toxic substances in the blood of humans exposed to conditions simulating weightlessness]. / Parametsiinyi test na toksicheskie veshchestva v krovi cheloveka, nakhodiashchegosia v usloviiakh, modeliruiushchikh nevesomost'.

The Paramecium test was for the first time used to measure the build-up of toxic substances in the healthy man exposed to simulated weightlessness. The most distinct changes were seen on bed rest days 3 and 7-8 in all test subjects (41 subjects). After bed rest day 8 the parameter reached a plateau, the toxicity level stopped to increase, but the Paramecium test time remained shorter than normal. It can therefore be suggested that the prognosis of any disease that may develop in this situation will be worse. In view of this it is important to improve the prophylaxis and treatment of endogenous and exogenous intoxications during space flight and to provide active detoxication based on the purification of biological fluids by sorption.

[Oncological characteristics of CC57BR mice]. / Onkologicheskaia kharakteristika myshei linii CC57BR.

The oncologic and non-oncologic morbidity in intact CC57BR mice was studied over a period of 1978-1980. Tumors occurred in 23.5%, while malignant tumors were in 14.3% of mice. Benign adenomas of lung were the most frequent 10.9%. Malignant tumors included generalized reticulosarcomatosis and leukemia 6.8%, cancer of the skin 3.4% and single different tumors. Pneumonia and enteritis were the most frequent among non-oncologic diseases. Since CC57BR mice belong to a low cancer line, they should be used for various long-term cancer and non-cancer experiments.

[Oncologic properties of non-inbred white rats raised at the Petrov Research Institute of the Ministry of Health of the USSR]. / Onkologicheskaia kharakteristika belykh besporodnykh krys razvodki NII onkologii im. prof. N.N. Petrova Minzdrava SSSR.

The paper discusses the incidence of spontaneous tumors and general morbidity in albino noninbred rats raised at the N. N. Petrov Research Institute of Oncology of the USSR Ministry of Health and used in different chronic experiments. It was found that spontaneous tumors occur, on the average, in 25.7 and malignancies--in 6.2%. Infectious hemorrhagic pneumonia and gastroenteritis (acute capillary toxicosis) are relatively infrequent. The general morbidity patterns in these rats are similar to those in Wistar line, the essential difference being a lower frequency of tumors of the medullar layer of adrenals. Hence, the rats bred at the Institute may be successfully used in various chronic experiments, including those associated with carcinogenic studies.