Docking and other computing tools in drug design against SARS-CoV-2.

The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.

Atomistic Simulation of the Ion-Assisted Deposition of Silicon Dioxide Thin Films.

A systematic study of the most significant parameters of the ion-assisted deposited silicon dioxide films is carried out using the classical molecular dynamics method. The energy of the deposited silicon and oxygen atoms corresponds to the thermal evaporation of the target; the energy of the assisting oxygen ions is 100 eV. It is found that an increase in the flow of assisting ions to approximately 10% of the flow of deposited atoms leads to an increase in density and refractive index by 0.5 g/cm3 and 0.1, respectively. A further increase in the flux of assisting ions slightly affects the film density and density profile. The concentration of point defects, which affect the optical properties of the films, and stressed structural rings with two or three silicon atoms noticeably decrease with an increase in the flux of assisting ions. The film growth rate somewhat decreases with an increase in the assisting ions flux. The dependence of the surface roughness on the assisting ions flux is investigated. The anisotropy of the deposited films, due to the difference in the directions of motion of the deposited atoms and assisting ions, is estimated using the effective medium approach.

[Development of antiviral drugs based on inhibitors of the SARS-COV-2 main protease]. / Razrabotka protivovirusnykh lekarstv na osnove ingibitorov glavnoi proteazy SARS-CoV-2.

Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.

Supercomputer docking with a large number of degrees of freedom.

Docking represents one of the most popular computational approaches in drug design. It has reached popularity owing to capability of identifying correct conformations of a ligand within an active site of the target-protein and of estimating the binding affinity of a ligand that is immensely helpful in prediction of compound activity. Despite many success stories, there are challenges, in particular, handling with a large number of degrees of freedom in solving the docking problem. Here, we show that SOL-P, the docking program based on the new Tensor Train algorithm, is capable to dock successfully oligopeptides having up to 25 torsions. To make the study comparative we have performed docking of the same oligopeptides with the SOL program which uses the same force field as that utilized by SOL-P and has common features of many docking programs: the genetic algorithm of the global optimization and the grid approximation. SOL has managed to dock only one oligopeptide. Moreover, we present the results of docking with SOL-P ligands into proteins with moveable atoms. Relying on visual observations we have determined the common protein atom groups displaced after docking which seem to be crucial for successful prediction of experimental conformations of ligands.

Prediction of features of the course of chronic hepatitis C using Bayesian networks.

MATERIALS AND METHODS: 253 patients with chronic hepatitis C (CHC) and liver cirrhosis were included in the study. Assessment of gene polymorphisms of genes involved in inflammatory reactions and antiviral immunity (IL-1ß-511C/T, IL-10 -1082G/A, IL28B C/T, IL28B T/G, TNF-α -238G/A, TGF-ß -915G/C, IL-6 -174G/C), activators of local hepatic fibrosis (AGT G-6A, AGT 235 M/T, ATR1 1166 A/C), hemochromatosis (HFE C282Y, HFE H63D), platelet receptors (ITGA2 807 C/T, ITGB3 1565 T/C), coagulation proteins and endothelial dysfunction (FII 20210 G/A, FV 1691G/A, FVII 10976 G/A, FXIII 103 G/T, eNOS 894 G/T, CYBA 242 C/T, FBG -455 G/A, PAI-675 5G/4G, MTHFR 677 C/T) was carried. Using Bayesian networks we studied the predictor value of clinical and laboratory factors for the following conditions - end points (EP): development of cirrhosis (EP1), fibrosis rate (EP2), presence of portal hypertension (EP3) and cryoglobulins (EP4). RESULTS AND DISCUSSION: In addition to traditional factors we have shown the contribution of the following mutations. Predicting EP1- liver cirrhosis - HFE H63D, C282Y, CYBA 242 C/T, AGT G-6G, ITGB31565 T/C gene mutations were significant. We also found a link between the rate of progression of liver fibrosis and gene polymorphisms of AGT G-6G, AGT M235T, FV 1691G/A, ITGB31565 T/C. Among the genetic factors associated with portal hypertension there are gene polymorphisms of PAI-I-675 5G/4G, FII 20210 G/A, CYBA 242 C/T, HFE H63D and Il-6 174GC. Cryoglobulins and cryoglobuliemic vasculitis (EP4) are associated with gene mutations MTHFR C677T, ATR A1166C and HFE H63D. CONCLUSION: The results obtained allow to detect the major pathophysiological and genetic factors which determine the status of the patient and the outcome of the disease, to clarify their contribution, and to reveal the significance of point mutations of genes that control the main routes of HCV course and progression.

[Docking with combined use of a force field and a quantum-chemical method]. / Doking s kombinirovannym primeneniem silovogo polia i kvantovo-khimicheskogo metoda.

The paper presents the results concerning the application of docking programs FLM to combined use of the MMFF94 force field and the semiempirical quantum-chemical method PM7 in the docking procedure. At the first step of this procedure a fairly wide range of low-energy minima of the protein-ligand complex is found in the frame of the MMFF94 force field using the FLM program. The energies of all these minima are recalculated using the PM7 method and the COSMO solvent continuum model at the second step. On the basis of these calculations the deepest minimum of the protein-ligand energy, calculated by the PM7 method with COSMO solvent, is determined, which gives the position of the ligand closest to its position in the crystal of the protein-ligand complex. It is shown that the first step of the combined procedure is performed more quickly and more efficiently in vacuum, rather than with a solvent model.

Short-range combined water model.

The short-range combined water model (SRCW model) for the calculation of the hydration free energy of the non-polar solutes is presented. A mixed explicit/implicit representation of the solvent is used in the model. A thermodynamic basis for the boundary potential between explicit and implicit parts of the simulation area is derived. A simple functional form for the boundary potential minimizing the water density fluctuations in the explicit part is found. Hydration free energies of the model solutes are calculated in the frame of the developed model. Obtained values are in the good agreement with results of the Monte Carlo simulation using the periodic boundary conditions.

[The Activities of the Ministry of Public Education Related to Amelioration of School Sanitary Hygienic Standards in Beginning of XX Century].

The article considers the role of the Ministry of National Education in development of the legislation of sanitary hygienic standards in worldly schools. In the beginning of XX century, in educational institutions of the Western Siberia the process of application of the mentioned legislative acts was in progress. The actual legal base promoted organization of more efficient activity of the administration of the Western Siberian educational okrug related to prevention of diseases among school pupils, activization of activities of physicians related to sanitary educational propaganda among schoolchildren, their parents and whole population of the region. During the studied period the Ministry of National Education was headed by V. G. Glazov. During his administration, an increasing of attention to prevention of epidemics in educational institutions was noted. Also, a whole complex of measures concerning development of health preserving technologies among students and pedagogic personnel was implemented for the first time.

[Increased myocardial expression of Toll-like receptors 2 and 9 as a marker of active myocarditis and a possible predictor of therapeutic effectiveness]. / Povyshennaia ékspressiia toll-like-retseptorov 2-go i 9-go tipov v miokarde kak marker aktivnogo miokardita i vozmozhnyi prediktor éffektivnosti lecheniia.

AIM: to investigate the myocardial expression of some structural proteins and markers of cellular proliferation and innate immunity for assessing their possible diagnostic and prognostic role in patients with chronic myocarditis. SUBJECTS AND METHODS: The investigation enrolled 23 patients (16 men; mean age, 52.0±12.4 years (range, 27 to 73) with various forms of noncoronarogenic myocardial injury who underwent right ventricular endomyocardial biopsy (n=4), intraoperative left ventricular biopsy (n=17) or autopsy (n=2). Prior to their morphological examination, the patients were divided into two groups: 1) 10 patients with dilated cardiomyopathy and presumptive myocarditis; 2) 13 patients with valvular heart disease, hypertrophic cardiomyopathy, myxoma, and chronic pulmonary thromboembolism, presumptively without myocarditis. Along with myocardial histological and immunohistochemical (IHC) examinations, the expression of vimentin, desmin, c-kit, Ki-67, and Toll-like receptors (TLR) 2 and 9 was determined. Polymerase chain reaction was used to identify whether herpes viruses of and parvovirus B19 genomes were present in the blood and myocardial samples; indirect ELISA was applied to estimate the blood level of antibodies against various cardiac antigens. RESULTS: According to the histological findings, active/borderline lymphocytic myocarditis was diagnosed in all the patients (Group 1) and in 6 patients (Group 2) in conjunction with the underlying disease (only in 9 and 7 patients, respectively), viral genome was detected in the myocardium of 15 patients, including in 5 without morphological signs of myocarditis (parvovirus B19 (n=11), herpesvirus 6 (n=4), herpes simplex virus types 1 and 2 (n=1), Epstein-Barr virus (n=2), and cytomegalovirus (n=1)), and in the blood (n=4). A marked correlation was found between TLR2 and TLR9 expressions and the morphological pattern of active myocarditis in the absence of this correlation with the expression level of other studied markers. The expression level of TLR2 in patients with and without borderline myocarditis was 0 [0; 0,75] and in those with active myocarditis was 1.5 [1; 1,5] points; that of TLR9 was 2 [2; 2] and 4 [3; 4] points, respectively (p<0.001). The expression of TLR2 and TLR9 in patients with borderline myocarditis was lower than in those without myocarditis (0 [0; 0] versus 0 [0; 1] and 2 [1,5; 2] versus 2 [2; 3] points), which can reflect cardiomyocyte destruction/depletion at later stages of the disease. There was also a close correlation between the expression level of TLR2 and that of TLR9 (r=0.824; p<0.001) and with Ki-67 levels (r=-0.531 and r=-0.702; p<0.01). There was also a correlation of the expression of the studied markers with viral persistence (desmin), the degree of myocardial dysfunction and cardiosclerosis (c-kit), which calls for further investigations. CONCLUSION: Determination of the myocardial expression level of TLR2 and TLR9 may serve as an immunohistochemical marker for myocarditis and preservation of its activity, which is especially valuable in patients with borderline forms. The marked expression of these markers for innate immunity may reflect both one of the mechanisms of genetic predisposition to myocarditis and its severe course and their secondary activation in the pathogenesis of the disease and is a potential target of therapy.

Renal denervation with a resistant arterial hypertension: the results of a five-year follow-up.

AIM: To evaluate the 5-year results of renal denervation (RDN) in patients with resistant arterial hypertension (AH). MATERIALS AND METHODS: The study included 14 patients to whom, during the 2011-2013 period RDN has been completed. Before and after the intervention, office blood pressure, quality of life indicators according to the EQ-5D questionnaire, mass index bodies, indicators of kidney function were duly assessed. RESULTS: Five years after RDN, office BP decreased from 165/110 to 139/95 mm Hg. Art. (p<0.05), with the average number of of drugs decreased from 4.6 to 3.1. 12 months after the RDA, the quality of Life, based on the questionnaire EQ-5D has increased from 60 to 80 points, by the fifth year the indicator fell to 74 points. Body mass index during 5 years decreased from 33.8 ± 3.5 to 30.9 ± 3.0 kg/m2. Mean plasma creatinine initially and after 5 years remained within the normal range, the mean the GFR score after 5 years being decreased by 9.5 ml/min/1.73 m2. CONCLUSION: RDN can be regarded as effective and safe method of additional treatment of patients with resistant hypertension.

[Clinical, laboratory and instrumental criteria for myocarditis, established in comparison with myocardial biopsy: A non-invasive diagnostic algorithm]. / Klinicheskie, laboratornye i instrumental'nye kriterii miokardita, ustanovlennye v sopostavlenii s biopsiinym issledovaniem miokarda (algoritm neinvazivnoi diagnostiki).

AIM: To determine the diagnostic value of different clinical, laboratory, and instrumental signs in the diagnosis of myocarditis in patients with the picture of idiopathic arrhythmias, dilated cardiomyopathy (DCM) and in a comparison group when comparing with myocardial morphological examination. SUBJECTS AND METHODS: A study group included 100 patients (35 women; mean age, 44.7±12.5 years) with idiopathic arrhythmias (n=20) and DCM as a syndrome (n=100). All underwent myocardial morphological examination: endomyocardial biopsy (EMB) (n=71), intraoperative biopsy (n=13), study of the explanted heart (n=6), and autopsy (n=11). A comparison group consisted of 50 patients (25 women; mean age, 53.7±11.7 years) with non-inflammatory diseases of the heart (left ventricular end-diastolic dimension <6.0 cm, ejection fraction >50%) who underwent open-heart surgery (n=47), EMB (n=2), or autopsy (n=1). The investigators also performed polymerase chain reaction for cardiotropic viral DNA in the blood and myocardium, anticardiac antibody (ACA) identification, myocardial scintigraphy (n=26), coronary angiography (n=47), magnetic resonance imaging (MRI) (n=25), and multislice computed tomography of the heart (n=45). The diagnostic value of the extended spectrum of clinical, laboratory, and instrumental markers for myocarditis was estimated. RESULTS: Active/borderline myocarditis was diagnosed in 76% of the patients in the study group (75.5% in the arrhythmia subgroup and 76.3% in the DCM one) and in 24.3% of those in the comparison group (p<0.001). A viral genome in the myocardium was detected statistically significantly less frequently in the study group than that in the comparison one (40.2 and 65%, respectively; p<0.01): in 46.6% in the DCM subgroup and 15.8% in the arrhythmia one. An ACA set (sensitivity, specificity, and predictive value of positive and negative test results (45.7, 80, 80.4, and 45%, respectively)) was of the greatest diagnostic importance in identifying myocarditis; antibodies to cardiomyocyte nuclei in a titer of 1:160-1:320 had the highest specificity (93.3%). A specificity above 70% was seen for a full medical history triad (acute onset, an association between onset and infection, a symptom duration of less than one year), systemic immune manifestations, anginas in the history and elevated anti-O-streptolysin levels, systemic blood changes, Q waves/QS complexes on ECGs, local hypokinesias, pericardial effusion, atriomegalia (in arrhythmias), angina/ischemia with intact coronary arteries, and focal perfusion defects during myocardial scintigraphy. A sensitivity higher than 50% was observed for age over 40 years (differential diagnosis with genetic forms), acute onset, a correlation with infection, and delayed contrast agent accumulation, as evidenced by MSCT/MRI. CONCLUSION: When the incidence of myocarditis is similar in the arrhythmia and DCM subgroups, the viral genome detection rate is statistically significantly higher in DCM. Among the non-invasive markers, an ACA set (high sensitivity and specificity) is of the greatest diagnostic value in the diagnosis of myocarditis. The diagnostic rule based on counting the number of scores has been developed, which makes it possible to individually establish the risk of myocarditis in patients with idiopathic arrhythmias and DCM for both the determination of indications for biopsy and the lack of the possibility of its performance. The risk of myocarditis is high if there are 5-7 scores; that is close to 100% if there are 8 scores or more.

[Efficiency of immunosuppressive therapy in virus-negative and virus-positive patients with morphologically verified lymphocytic myocarditis]. / Éffektivnost' immunosupressivnoi terapii u virus-negativnykh i viruspozitivnykh bol'nykh s morfologicheski verifitsirovannym limfotsitarnym miokarditom.

AIM: To evaluate the efficiency of immunosuppressive therapy (IST) in virus-negative (V-) and virus-positive (V+) patients with lymphocytic myocarditis (LM). SUBJECTS AND METHODS: 60 patients (45 males) (mean age 46.7±11.8 years) with dilated cardiomyopathy (mean left ventricular (LV) end diastolic size (EDS) 6.7±0.7 cm; ejection fraction (EF) 26.2±9.1%) were examined. The diagnosis of active/borderline LM was verified by right ventricular endomyocardial biopsy in 38 patients, by intraoperative LV biopsy in 10, in the study of explanted hearts from 3 patients and at autopsy in 9. The investigators determined the genomes of parvovirus B19, herpes viruses types 1, 2 and 6, Epstein-Barr (EBV), zoster, and cytomegalovirus in the blood and myocardium and, if antibodies were present in the blood, hepatitis B and C viruses, as well as antibodies against antigens in the endothelium, cardiomyocytes and their nuclei, smooth muscles, fibers of the conducting system. IST was used in terms of histological, immune, and viral activities. IST was performed in 22 V+ patients (Group 1) and in 24 V- patients (Group 2); this was not done in 10 V+ patients (Group 3) and V- patients (Group 4). IST comprised methylprednisolone at a mean dose of 24 mg/day (n=40), hydroxychloroquine 200 mg/day (n=20), azathioprine at a mean dose of 150 mg/day (n=21); antiviral therapy included acyclovir, ganciclovir, intravenous immunoglobulin (n=24). The follow-up period was 19 (7.3-40.3) months. RESULTS: The viral genome was detected in the myocardium of 32 patients who made up a V+ group. The degree of histological activity did not differ in relation to the presence of viral genome in the myocardium. The degree of immune activity (anticardiolipin antibody titers) in the V+ patients was as high as that in V- ones. At baseline, the V+ patients had a significantly higher LV EDS and a lower EF than the V- patients. Overall, IST only could lead to a significant increase in EF (from 26.5±0.9 to 36.0±10.8%; p<0.001) and reductions in NYHA functional class from III to II (p<0.001), LV EDS (from 6.7±0.7 to 6.4±0.8 cm; p<0.01), pulmonary artery systolic pressure (from 48.9±15.5 to 39.4±11.5 mm Hg (p<0.01); the IST group had significantly lower mortality rates than the non-IST group (23.9 and 64.3%; p<0.01). At the same time, a significant trend was seen in both V- and V+ patients. The mortality rate in the V+ patients, as a whole, was higher (46.9 and 17.9%; p<0.05). CONCLUSION: IST leads to a significant improvement of functional indices and it is associated with lower mortality rates in both myocardial V- and V+ patients with LM. A more than 10% EF increase in the first 2 months is associated with a good prognosis. The presence of viral genome in the myocardium (primarily herpesviruses rather than parvovirus-19) is accompanied by more severe initial dysfunction, a less pronounced effect of IST, and higher mortality rates. However, the positive effect of IST also persists in V+ patients. No positive changes (a decrease in EF was observed) were absent only in IST-naïve V+ patients.

Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

Computational experiments on atomistic modeling of thin-film deposition.

The molecular dynamic algorithm for simulation of thin-film growth is reported. The achieved performance of this algorithm is sufficient for detailed investigations of structural effects in thin films with practically meaningful dimensions.

Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused more by different parameterization and less by methods and indicates the need for further improvement of implicit solvent models parameterization. Within the same parameterization, various implicit methods give practically the same correlation with results obtained in explicit solvent model for ligands and proteins: e.g. correlation values of polar ligand solvation energies and the corresponding energies in the frame of explicit solvent were 0.953-0.966 for the APBS program, the GBNSR6 program and all models used in the DISOLV program. The DISOLV program proved to be on a par with the other used programs in the case of proteins and ligands solvation energy calculation. However, the solution of the Poisson-Boltzmann equation (APBS program) and Generalized Born method (implemented in the GBNSR6 program) proved to be the most accurate in calculating the desolvation energies of complexes.

Myocardial Biopsy In "Idiopathic¼ Atrial Fibrillation And Other Arrhythmias: Nosological Diagnosis, Clinical And Morphological Parallels, And Treatment.

BACKGROUND: The nosological nature of "idiopathic" arrhythmias and the effect of etiotropic and pathogenetic treatment are often unknown. METHODS AND RESULTS: 19 patients (42.6±11.3 years, 9 women) with atrial fibrillation (n = 16), supraventricular (n = 10) and ventricular (n = 4) premature beats, supraventricular (n = 2) and ventricular tachycardia (n = 1), left bundle branch block (n= 2), AV block (n = 2) without structural heart changes. Viruses were identified (polymerase chain reaction, PCR) along with measurement of anti-heart antibodies (AHA) and endomyocardial biopsy (EMB). EMB allowed to establish diagnosis in all patients: infectious-immune myocarditis (n = 11, parvovirus-positive in 1),parvovirus-positive endomyocarditis (n = 1),systemic (n = 2) and myocardial (n = 1) vasculitis,Fabry's disease (n = 1), arrhythmogenic right ventricular dysplasia (n = 1),unspecified genetic cardiomyopathy (n = 2, herpes virus 6 one positive). Level of AHA had the greatest significance for myocarditis diagnostics. All patients with myocarditis/vasculitis had background therapy: acyclovir (n = 10), IV immunoglobulin (n = 2), meloxicam (n = 12), hydroxychloroquine (n = 15), steroids (n = 14, 31.1±12.5 mg/day), azathioprine 150 mg/day (n = 2). Median follow-up was 4 years. Treatment significantly reduced the rate of arrhythmias (8 [5;8] to 3 [1.25;7.75] points); disappearance of bundle branch block was noted. CONCLUSION: EMB allowed to diagnose immune-mediated inflammatory diseases in 78.9% patients with 'idiopathic' arrhythmias and genetic diseases in 21.1%. Background therapy of myocarditis improved the antiarrhythmic efficiency, and allowed the best premed for interventional treatment.

[Supercomputer investigation of the protein-ligand system low-energy minima].

The accuracy of the protein-ligand binding energy calculations and ligand positioning is strongly influenced by the choice of the docking target function. This work demonstrates the evaluation of the five different target functions used in docking: functions based on MMFF94 force field and functions based on PM7 quantum-chemical method accounting or without accounting the implicit solvent model (PCM, COSMO or SGB). For these purposes the ligand positions corresponding to the minima of the target function and the experimentally known ligand positions in the protein active site (crystal ligand positions) were compared. Each function was examined on the same test-set of 16 protein-ligand complexes. The new parallelized docking program FLM based on Monte Carlo search algorithm was developed to perform the comprehensive low-energy minima search and to calculate the protein-ligand binding energy. This study demonstrates that the docking target function based on the MMFF94 force field can be used to detect the crystal or near crystal positions of the ligand by the finding the low-energy local minima spectrum of the target function. The importance of solvent accounting in the docking process for the accurate ligand positioning is also shown. The accuracy of the ligand positioning as well as the correlation between the calculated and experimentally determined protein-ligand binding energies are improved when the MMFF94 force field is substituted by the new PM7 method with implicit solvent accounting.

Molecular modeling as a new approach to the development of urokinase inhibitors.

Proteolytic activity of urokinase plays an important role in negative remodeling of blood vessels, restenosis, tumor angiogenesis, and metastasizing, which necessitates the development of selective urokinase inhibitors. Using methods of computer modeling (docking, post processing, and direct docking) and quantum chemistry, we selected substances from the large compound database, analyzed their structures, and experimentally verified their inhibitor activity. New urokinase inhibitor candidates were proposed based on the theoretical predictions and experimental verification of compound activities. The process of modifying urokinase inhibitors based on (benzothiazol-3-yl)guanidine was developed. A new urokinase inhibitor (5-brom-benzothiazol-3-yl)guanidine, that can be effective for regulation of vascular remodeling and tumor angiogenesis, was created.

[Idiopathic arrhythmias: possibilities of complex nosological diagnosis, and differentiated treatment].

AIM: of the study was to elucidate nosological nature of "idiopathic" arrhythmias by means of complex clinical-morphological examination and to assess efficacy of differentiated (including etiotropic and pathogenetic) treatment. MATERIAL AND METHODS: We examined 190 patients (117 women, mean age 45.33 ± 14.84 years) with "idiopathic" arrhythmias: atrial fibrillation (38.9%) (AF,) and flutter (11.1%), supraventricular (44.7%) and ventricular (55.3%) extrasystoles (SVE and VE), bouts of ventricular tachycardia (15.8%), atrioventricular block (22,6%) et al. Mean number of antiarrhythmic drugs per patient was 3 (from 1 to 8). Examination included Holter ECG monitoring, echocardiography, determination of anticardiac antibodies (97.4%) and markers of cardiotropic viruses (87.4%), treadmill test (26.3%), transesophageal cardiac pacing (12.1%), electrophysiological investigation (10%), multispiral computed tomography (22.1%), magnetic resonance tomography (21.6%), scintigraphy (27.4%), coronary angiography (10.0%), endomyocardial biopsy (EMB) (10.0%), DNA diagnostics (8.9%). RESULTS: EMB revealed immune-inflammatory (myo/endocarditis, systemic/myocardial vasculitis) or genetic pathology in 78.9 and 21.1% of cases, respectively. Level of anticardiac antibodies (including specific antinuclear factor) most closely correlated with EMB findings. On the basis of comparison of EMB data with data of complex examination we created algorithm of nosological diagnostics in "idiopathic" arrhythmias. According to nosology all patients were distributed in the following way: 1) chronic infectious-immune myocarditis (n=144, 75.7%), morphologically verified in 14, viral in 27 patients; 2) genetic cardiomyopathy (n=15, 7.9%), morphologically verified in 4, virus positive in 1 (arrhythmogenic right ventricular dysplasia, non-compaction myocardium, Fabri disease, Brugada syndrome, undetermined); in 4 patients mutations in plakophilin 2, desmoglein, desmin, -galactosidase A genes were found; 3) combination of genetic diseases with myocarditis (n=18; 9.5%) including viral (n=3); 4) isolated myocardiodystrophy (tonsillogenic< dyshormonal, n=3, 1.6%); 5) proper idiopathic arrhythmias (n=10, 5.3%). Therapy of myocarditis included antiviral (43.2%) and immunosuppressive (76.3%) drugs. Cardiotropic and antiarrhythmic therapy was also administered. Only in patients with myocarditis it was possible to withdraw effective antiarrhythmic (16.7%) and to improve effect of previously ineffective drugs. Surgical treatment (implantation of pacemaker or cardioverter-defibrillator, radiofrequency ablation) was more frequently used in patients with genetic (39.4%) and idiopathic arrhythmias (53.8%) than in patients with myocarditis (16.0%). CONCLUSION: Etiology of idiopathic arrhythmias can be established in most cases. Their main causes are immune-inflammatory diseases, genetic cardiomyopathies and their combination. Therapy of myocarditis improves antiarrhythmic activity of treatment, in some patients allows to withdraw antiarrhythmic drugs, decrease requirements in surgical treatment and to optimally prepare patients to radiofrequency ablation.

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.