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.

[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.

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.

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.

[Predictors of epilepsy in children after ischemic stroke]. / Prediktory formirovaniya epilepsii u perenesshikh ishemicheskii insul't detei.

AIM: To determine clinical/instrumental predictors of symptomatic epilepsy after ischemic stroke in children. MATERIAL AND METHODS: One hundred and thirty-six patients, aged 0-15 years, with the diagnosis of ischemic stroke (ICD-10 I63.0-I63.9) were examined. The duration of the study was 18 months - 12 years. Patients were stratified into post-stroke (n=22) and control (n=114) groups, the latter included patients without epilepsy regardless of the presence of convulsive seizures in the acute stage of stroke. Predictors were determined based on EEG and characteristics of convulsive syndrome in the acute stage of stroke. RESULTS AND CONCLUSION: The following prognostic criteria were found: generalized type of seizures, focal type of seizures with secondary generalization, epileptiform (peak and/or peak-wave) activity, focal character of epileptiform activity, generalized type of seizures in the combination with slow wave background activity on EEG, generalized type of seizures in the combination with slow wave activity and disorganized activity on EEG.

[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.

[Chondroprotectors in complex treatment of internal TMJ disorders].

The article presents a detailed analysis of the clinical studies on the use of chondroprotector (Alflutop) in patients with persistent displacement of the articular disk of the temporomandibular joint in order to prevent the development of secondary osteoarthrosis. The study showed that the inclusion in the therapy chondroprotective action agents allows achieving short-term positive outcomes in most cases, relief of inflammation and pain, as well as improving joint function and stabilization of the thickness of the articular cartilage that provides cushioning function.

[Screening of the atypical oral mucosa lesions].

ViziLite system was used for mucosal lesions screening in 55 patients 22 of whom showed visible changes in the oral mucosa. Diagnoses were confirmed morphologically. Authors diagnostic algorithm for precancerous lesions of the oral mucosa is presented in the paper.

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.

[Role of total systems' connective tissue disease in the development of posttraumatic changes in the temporomandibular joint]. / Rol' sistemnoi patologii soedinitel'noi tkani v razvitii posttravmaticheskikh izmenenii v visochno-nizhnecheliustnom sustave.

The aim of our work was to ascertain the relationship between temporomandibular joint (TMJ) complications of jaw fractures and displasia of connective tissue (DCT). The results of this investigation suggest, that DCT is an important factor of risk for joint disturbance such as arthritis and osteoarthrosis of TMJ.

[EEG coherence analysis in music listening]. / Analiz kogerentnosti EEG pri proslushivanii muziki.

Changes in EEG coherence were studied in subjects without special musical education when they were listening to low classic music (below 30 dB). The numbers of significant changes in coherence function in the left and right hemispheres were different. Predominant increase in coherence in the alpha 2, beta 1, and beta 2 frequency ranges was observed in the right temporal-central and parietal-occipital cortical areas. The left-hemispheric coherence was predominantly, decreased on the account of its decrease in the alpha range.

[Lengthy unilateral EEG changes in alert rabbits after a spreading single depressed wave]. / Dlitel'noe odnostoronnee izmenenie élektrokortikogrammy bodrstvuiushchego krolika posle odinochnoi volny rasprostraniaiushcheisia depressii.

Effects of a single wave of the cortical spreading depression (SD) on the ECoG of a waking rabbit was studied with chronically implanted intracortical calomel and silverball epidural electrodes. DC potential shifts and integral electrical activity were recorded monopolary in reference to a nasal-bone electrode. ECoG spectral analysis (FFT) showed that an SD wave was accompanied by a suppression of the neocortical activity in a broad frequency range (0.25-80 Hz). However, the SD-related ECoG depression was a rather short phenomenon (5-7 min) as compared to a following rebound effect, i.e., persistent (1.5-2 h) unilateral exaltation of bioelectrical activity. The spectral power in the delta (6-14 fold) and beta bands (2-6-fold) increased, whereas the high-frequency activity (40-80 Hz) remained suppressed. Similar changes in the contralateral neocortex were poorly pronounced or absent; this resulted in a strong interhemispheric asymmetry. It is suggested that (1) exaltation of the delta activity after SD wave is related not only to a dendrite swelling and changes in the extracellular space structure but to increase in synaptic transmission efficiency, probably, by the type of anoxic potentiation, (2) activation of some subcortical structures by the mechanism of their release from the inhibitory neocortical control is an additional factor of the augmentation of the delta and spindle-like beta activity after an SD wave, and (3) the long-term attenuation of the high-frequency gamma activity is a result of its strong suppression during the SD and its reciprocal relations with the exalted delta activity.

[Sleep EEG as a nonlinear dynamic process: a comparison of global correlation dimension of human EEG and measures of linear interdependence between channels]. / Izuchenie EEG sna kak nelineinogo dinamicheskogo protsessa: sravnenie global'noi korreliatsionnoi razmernosti EEG cheloveka i mer lineinoi zavisimosti mezhdu kanalami.

The goal of this work was to study (1) whether the estimation of correlation dimension (D2) using spatial embedding distinguishes between sleep stages and (2) whether information gained from the application of global D2 is redundant to measures of linear interdependence between channels. Twenty one-channel EEG segments of 12 healthy male subjects recorded during waking and sleep stages REM, I, II, and III-IV (according to the Rechtshaffen and Kales criteria) were analyzed with global (multichannel) D2, mean square correlation coefficients (MS) and proportion of variance accounted for by the first principal component (PC1). D2 was found to decrease progressively from stage I to stage III-IV with D2 values of waking and REM being close to those of stages I and II. MS and PC1 did not distinguish among sleep stages but yielded significant differences between waking and sleep. The results suggest that global D2 extracts information from human EEG. That sort of evidence cannot be obtained with measures of linear interdependence between channels.

Investigation of brain potentials in sleeping humans exposed to the electromagnetic field of mobile phones.

An investigation was made of 8-hour EEG tracings of sleeping humans exposed to the electromagnetic field of a GSM-standard mobile phone. To analyze the EEG-patterns, manual scoring, nonlinear dynamics, and spectral analysis were employed. It was found that, when human beings were exposed to the electromagnetic field of a cellular phone, their cerebral cortex biopotentials revealed an increase in the alpha-range power density as compared to the placebo experiment. It was also found that the dimension of EEG correlation dynamics and the relation of sleep stages changed under the influence of the electromagnetic field of a mobile phone.

Cellular phone electromagnetic field effects on bioelectric activity of human brain.

24 volunteers participated in the experiments. The investigation of EEG reactions to cellular phone (EMF frequency 902.4 MHz and intensity 0.06 mW/cm2) was conducted. Two experiments were performed with each subject--cellular phone exposure and Placebo Duration of the experiment was 60 min: 15 min--background; 15 min--EMF exposure or Placebo; 30 min--afterexposure. EEG was recorded in 16 standard leads with "eyes open" and "eyes closed". Special software with non-linear dynamics was developed for EEG analyses. One parameter, multichannel (global) correlation dimension, was calculated. The changes of these parameters can be evidence of brain functional state changes. As a result of EEG record processing, a significant increase of global correlation dimension during the exposure and afterexposure period was discovered, more pronounced in the case of "eyes closed". That can be viewed as the manifestation of cortex activation under phone EMF exposure.

[Spectral analysis of the human EEG while listening to music]. / Spektral'nyi analiz EEG chelovbeka pri proslushivanii muzyki.

EEG was recorded from 16 electrodes (International 10-20 System) in 14 healthy volunteers aged from 18 to 45 in the state of rest and during listening to music (popular classical symphonic pieces). The EEG spectral analysis was carried out. Presentation of musical pieces increased the EEG spectral power in the alpha-range in the parietal and occipital areas of both hemispheres. During repeated listening of the same musical fragment there was a tendency for attenuation of these changes. A significant decrease in the peak frequency of the alpha-band was found in the process of listening. The spectral values did not significantly differ between the left and right hemispheres. The findings suggest a decrease in the level of CNS activation under the influence of music.