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.

Design, Synthesis, and Evaluation of New Hybrid Derivatives of 5,6-Dihydro-4H-pyrrolo[3,2,1-ij]quinolin-2(1H)-one as Potential Dual Inhibitors of Blood Coagulation Factors Xa and XIa

Cardiovascular diseases caused by blood coagulation system disorders are one of the leading causes of morbidity and mortality in the world. Research shows that blood clotting factors are involved in these thrombotic processes. Among them, factor Xa occupies a key position in the blood coagulation cascade. Another coagulation factor, XIa, is also a promising target because its inhibition can suppress thrombosis with a limited contribution to normal hemostasis. In this regard, the development of dual inhibitors as new generation anticoagulants is an urgent problem. Here we report the synthesis and evaluation of novel potential dual inhibitors of coagulation factors Xa and XIa. Based on the principles of molecular design, we selected a series of compounds that combine in their structure fragments of pyrrolo[3,2,1-ij]quinolin-2-one and thiazole, connected through a hydrazine linker. The production of new hybrid molecules was carried out using a two-stage method. The reaction of 5,6-dihydropyrrolo[3,2,1-ij]quinoline-1,2-diones with thiosemicarbazide gave the corresponding hydrazinocarbothioamides. The reaction of the latter with DMAD led to the target methyl 2-(4-oxo-2-(2-(2-oxo-5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-1(2H)-ylidene)hydrazineyl)thiazol-5(4H)-ylidene)acetates in high yields. In vitro testing of the synthesized molecules revealed that ten of them showed high inhibition values for both the coagulation factors Xa and XIa, and the IC50 value for some compounds was also assessed. The resulting structures were also tested for their ability to inhibit thrombin.

New Hybrid Tetrahydropyrrolo[3,2,1-ij]quinolin-1-ylidene-2-thioxothiazolidin-4-ones as New Inhibitors of Factor Xa and Factor XIa: Design, Synthesis, and In Silico and Experimental Evaluation

Despite extensive research in the field of thrombotic diseases, the prevention of blood clots remains an important area of study. Therefore, the development of new anticoagulant drugs with better therapeutic profiles and fewer side effects to combat thrombus formation is still needed. Herein, we report the synthesis and evaluation of novel pyrroloquinolinedione-based rhodanine derivatives, which were chosen from 24 developed derivatives by docking as potential molecules to inhibit the clotting factors Xa and XIa. For the synthesis of new hybrid derivatives of pyrrolo[3,2,1-ij]quinoline-2-one, we used a convenient structural modification of the tetrahydroquinoline fragment by varying the substituents in positions 2, 4, and 6. In addition, the design of target molecules was achieved by alkylating the amino group of the rhodanine fragment with propargyl bromide or by replacing the rhodanine fragment with 2-thioxoimidazolidin-4-one. The in vitro testing showed that eight derivatives are capable of inhibiting both coagulation factors, two compounds are selective inhibitors of factor Xa, and two compounds are selective inhibitors of factor XIa. Overall, these data indicate the potential anticoagulant activity of these molecules through the inhibition of the coagulation factors Xa and XIa.

[Development of antiviral drugs based on inhibitors of the SARS-COV-2 main protease]

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.

Docking Paradigm in Drug Design

Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.

Advances in Docking

BACKGROUND

Design of small molecules which are able to bind to the protein responsible for a disease is the key step of the entire process of the new medicine discovery. Atomistic computer modeling can significantly improve effectiveness of such design. The accurate calculation of the free energy of binding a small molecule (a ligand) to the target protein is the most important problem of such modeling. Docking is one of the most popular molecular modeling methods for finding ligand binding poses in the target protein and calculating the protein-ligand binding energy. This energy is used for finding the most active compounds for the given target protein. This short review aims to give a concise description of distinctive features of docking programs focusing on computation methods and approximations influencing their accuracy.

METHODS

This review is based on the peer-reviewed research literature including author's own publications. The main features of several representative docking programs are briefly described focusing on their characteristics influencing docking accuracy: force fields, energy calculations, solvent models, algorithms of the best ligand pose search, global and local optimizations, ligand and target protein flexibility, and the simplifications made for the docking accelerating. Apart from other recent reviews focused mainly on the performance of different docking programs, in this work, an attempt is made to extract the most important functional characteristics defining the docking accuracy. Also a roadmap for increasing the docking accuracy is proposed. This is based on the new generation of docking programs which have been realized recently. These programs and respective new global optimization algorithms are described shortly.

RESULTS

Several popular conventional docking programs are considered. Their search of the best ligand pose is based explicitly or implicitly on the global optimization problem. Several algorithms are used to solve this problem, and among them, the heuristic genetic algorithm is distinguished by its popularity and an elaborate design. All conventional docking programs for their acceleration use the preliminary calculated grids of protein-ligand interaction potentials or preferable points of protein and ligand conjugation. These approaches and commonly used fitting parameters restrict strongly the docking accuracy. Solvent is considered in exceedingly simplified approaches in the course of the global optimization and the search for the best ligand poses. More accurate approaches on the base of implicit solvent models are used frequently for more careful binding energy calculations after docking. The new generation of docking programs are developed recently. They find the spectrum of low energy minima of a protein-ligand complex including the global minimum. These programs should be more accurate because they do not use a preliminary calculated grid of protein-ligand interaction potentials and other simplifications, the energy of any conformation of the molecular system is calculated in the frame of a given force field and there are no fitting parameters. A new docking algorithm is developed and fulfilled specially for the new docking programs. This algorithm allows docking a flexible ligand into a flexible protein with several dozen mobile atoms on the base of the global energy minimum search. Such docking results in improving the accuracy of ligand positioning in the docking process. The adequate choice of the method of molecular energy calculations also results in the better docking positioning accuracy. An advancement in the application of quantum chemistry methods to docking and scoring is revealed.

CONCLUSION

The findings of this review confirm the great demand in docking programs for discovery of new medicine substances with the help of molecular modeling. New trends in docking programs design are revealed. These trends are focused on the increase of the docking accuracy at the expense of more accurate molecular energy calculations without any fitting parameters, including quantum-chemical methods and implicit solvent models, and by using new global optimization algorithms which make it possible to treat flexibility of ligands and mobility of protein atoms simultaneously. Finally, it is shown that all the necessary prerequisites for increasing the docking accuracy can be accomplished in practice.

[Docking with combined use of a force field and a quantum-chemical method]

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.

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-1β-511C/T, IL-10 -1082G/A, IL28B C/T, IL28B T/G, TNF-α -238G/A, TGF-β -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.

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms

We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.

[Predictors of epilepsy in children after ischemic stroke]

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.

[Lengthy unilateral EEG changes in alert rabbits after a spreading single depressed wave]

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.

[EEG coherence analysis in music listening]

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.

[Sleep EEG as a nonlinear dynamic process: a comparison of global correlation dimension of human EEG and measures of linear interdependence between channels]

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.

[The characteristics of operator activity in a sensorially enriched environment]

The mechanism of Ukhtomskiĭ's dominant was used to improve operator's performance activity. Recognition of visual images--obscured Arabic numerals--in a sensorially rich environment (classic or rock music records) turned to be more successful: time of the task was reduced and the probability of correct identification increased. A reverse U-shaped dependence between the intensity of music and identification was stated. Repetition of music fragments at a constant value marred the positive effect.

[Spectral analysis of the human EEG while listening to music]

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.

Recognition of visual images in a rich sensory environment: musical accompaniment

Human recognition of visual images in the form of Arabic numerals affected by "noise" showed a reduction in the time needed for recognition and an increase in the probability of making a correct identification in a rich sensory environment (use of classical or rock music). There was no direct relationship between the volume of the music and its positive effect on the recognition of visual images. The greatest changes in the recognition time and quality of correct recognition occurred at specific volume levels for both classical and rock music, and there were individual differences. The efficiency of image recognition decreased when the same musical fragments were used again with the same volume. The data are interpreted as a manifestation of the dominant.

[The recognition of visual images in a sensorially enriched environment: musical accompaniment]

Time of recognition by human subjects of masked Arabic numerals decreased and the probability of correct responses increased under conditions of listening of tape-recordings of classic or rock music. Changes in recognition were most pronounced under the definite music power. The efficiency of recognition decreased during repeated listening of the same music fragments with unchanged power. The obtained data are considered as a manifestation of the dominant regularities.

[A computer program for the support of the treatment-diagnosis process for patients with benign prostatic hyperplasia]

The computer program "Prostate" (Windows, 1.0 version) is designed to assist the urologist in: objective assessment of the lower urinary tract in benign prostatic hyperplasia (BPH), accumulation and storage of information on the patients (data file), comparison (text, graphics) with previous data to control the course of the disease, treatment efficacy, to refer to international recommendations and recent advances in the treatment of both BPH and its complications. The status of the lower urinary tract is to be described basing on the IPSS and QOL tables, PSA findings, rhythm of spontaneous uresis, uroflowmetry, residual urine, prostate size, laboratory and microbiological urinalysis. The program "Prostate" is a new step in medical recording and efficacy of BPH treatment assessment in urology.

[EEG spectral analysis in the hunger dominant in man]

EEG spectral characteristics were studied in the states of satiation, short-term food deprivation, and hunger dominant in 10 healthy right-handed subjects. The dominant of hunger was created at the background of short-term food deprivation by using sensory stimuli. Appearance of the swallowing movements in response to the applied stimuli was a criterion of dominant formation. Both food deprivation and hunger dominant were associated with a decrease of the EEG spectral power in the delta range and its increase in the alpha range. Food deprivation, additionally, was accompanied by an increase of the spectral power in the theta 2 range. Apart from the spectral changes, reduction of the alpha-rhythm frequency was observed in the states of food deprivation. This phenomenon was absent in the dominant state. In the states both of food deprivation and hunger dominant, EEG spectral characteristics, predominantly, changed in the left hemisphere, especially, in the alpha- and delta-ranges.

[The hunger dominant in man and the reactions of the autonomic nervous system]

Formation of hunger dominant takes place in man under the conditions of alimentary deprivation and application of sensory stimuli. Summation reactions, namely, swallowing movements, appear in response to the stimuli. Time of deprivation necessary for dominant formation is different in different subjects. Study of ECG, GSR, and respiration during the dominant formation revealed an increase of vegetative reactivity during application of the testing stimuli and before the summating swallow as well. The obtained data allow to make a conclusion on the active participation of the vegetative component in the formation of dominant constellation. The former joins the summation process earlier than the motor component.