Vol. 18 No. 2(70) (2020)
Published:
2020-06-18
Original Researches
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The virtual screening application for searching potential antiviral agents to treat COVID-19 disease
Aim. To provide a brief literature review regarding the structure of the human coronavirus SARS-CoV-2, the mechanism of its replication and the role of viral proteases in this process; to analyze the ability of the known antiviral agents and compounds synthesized de novo in order to bind and inhibit the coronavirus main protease using computer simulation tools.
Results and discussion. COVID-19 coronavirus has become a worldwide challenge in recent months. Taking into account the rapid spread and severity of COVID-19 among a significant part of the population there is an urgent need to develop effective medicines and appropriate treatment protocols, which, unfortunately, are not yet available. Currently, the search for molecules with an acceptable toxicity profile that are able to inhibit and/or stop coronavirus SARS-CoV-2 replication in the human body is very relevant. In this study, the virtual screening and molecular docking of both antiviral agents known and new compounds synthesized have been performed based on the structure of the main protease Mpro of SARS-CoV-2. The regularities identified during our study can be useful for searching and developing new antiviral drugs to control COVID-19 and other coronavirus infections. The analysis of the results of calculations of physicochemical characteristics of antiviral agents, as well as the determination of their binding sites with the main viral protease Mpro gives an optimistic assessment of the possibility to develop new drugs based on the structures of the known antiviral drugs or their modified analogs.
Experimental part. Based on recent studies of the crystal structure of the virus main protease Mpro in the complex with various inhibitors (Protein Data Bank http://www.rcsb.org/pdb, the structure code – 6LU7) the virtual screening and molecular docking of 100 known antiviral agents and 50 novel compounds synthesized were performed. The screening data for the in vitro antimalarial activity of the compounds synthesized were presented. The following binding and physicochemical parameters of the ligand–protein interaction for all virus main protease potential inhibitors were calculated: binding affinity score (BAS), binding energy, lipophilicity (clogP) and topological polar surface area (TPSA). The protein and ligand structures were studied using Jmol, PyMol, and Avogadro graphics software packages. The virtual screening and molecular docking, as well as the analysis of the results were performed using a LigandScout 4.4 software package. Data on the antimalarial activity of 50 compounds synthesized were obtained from the Laboratory of Microbiology, Parasitology and Hygiene of theUniversity ofAntwerp (Belgium).
Conclusions. According to the results of the virtual screening and molecular docking with protein 6LU7 it has been found that a number of the known antiviral drugs have a certain potential for their use as inhibitors of SARS-CoV-2 coronavirus main protease. Remdesivir and ritonavir substances have shown higher activity than the reference compound of the 6LU7 complex. The molecular docking of a series of compounds recently synthesized with the proven in vitro antimalarial activity has revealed that L1 – L6 compounds are promising candidates for further modification and development of new antiviral drugs to control coronavirus infection.
Received: 02.04.2020
Revised: 23.05.2020
Accepted: 29.05.2020 -
Functionalizations of Diamantane Dimers
Aim. To develop preparative methods for functionalization of diamantane dimers.
Results and discussion. The reaction of 1,1′-bisdiamantane with bromine and the subsequent hydrolysis gives 6-hydroxy-1,1′-bіsdіamantane with a yield of 56 %. The reactions of 4,4′-bisdiamantane with nitric acid or liquid bromine followed by hydrolysis leads to a mixture of hydroxy derivatives and 1,1′-dihydroxy-4,4′-bisdiamantane after isomerization in sulfuric acid (with a yield of 73 %). Thus, the reactivity of bisdiamantanes with electrophiles is determined by the higher stability of the carbocations in the medial positions of the cages as shown by DFT computations. Whereas medial bridgehead substitutions dominate in reactions of 4,4′-bisdiamantane with electrophiles, the arylation with benzene in the presence of tert-butyl bromide and aluminum chloride gives bis-apical derivative – 9,9’-diphenyl-4,4’-bisdiamantane.
Experimental part. The structure of 6-hydroxy-1,1′-bіsdіamantane was confirmed by X-ray diffraction analysis. The substitution pattern in 1,1′-dihydroxy-4,4′-bisdamantane was confirmed by 2D-NMR spectra. The arylation of 4,4′-bisdiamantane with benzene proceeds as bis-apical substitution to give highly symmetric 9,9’-diphenyl-4,4’-bisdiamantane in 47 %.
Conclusions. It has been shown that the medial bridgehead substitution dominates in the reactions of bisdiamantanes with strong electrophiles, and only the arylation of 4,4′-bisdiamantane proceeds as a bis-apical substitution.
Received: 31.03.2020
Revised: 05.05.2020
Accepted: 29.05.2020 -
The synthesis of polyfluoroalkyl substituted pyrroles as building blocks for obtaining fluorinated pyrrolidine-containing alkaloids
Aim. To study the synthetic potential of cyclization of N-(β-polyfluoroacyl)vinyl derivatives of proline and N-substituted glycines into polyfluoroalkyl pyrroles, which are useful intermediates to fluorinated pyrrolidine alkaloids.
Results and discussion. N-(β-Polyfluoroacyl)vinyl derivatives of proline and N-substituted glycines have been obtained and transformed to polyfluoroalkyl-containing pyrroles using acetic or trifluoroacetic anhydride.
Experimental part. N-(β-Polyfluoroacyl)vinyl derivatives of proline and N-substituted glycines were obtained from β-alkoxyvinyl polyfluoroalkyl ketones and the corresponding amino acids. The enaminones so obtained were transformed to polyfluoroalkyl-containing pyrroles with acetic or trifluoroacetic anhydride. The structure and composition of the compounds synthesized were proven by the data of 1Н and 19F NMR spectroscopy and elemental analysis.
Conclusions. It has been shown that an increase of steric hindrance in N-(β-polyfluoroacyl)vinyl derivatives of proline (the perfluoroethyl group instead of the trifluoromethyl group) and N-substituted glycines (replacement of the N-methyl group with the N-benzyl group) gives mainly polyfluoroacyl pyrrolyl acetates when heating in acetic anhydride. Polyfluoroalkyl-containing pyrroles have been obtained by treatment of N-(β-polyfluoroacyl)vinyl derivatives of proline and glycine with trifluoroacetic anhydride.
Received: 01.04.2020
Revised: 05.05.2020
Accepted: 29.05.2020 -
The synthesis, analgesic and anti-inflammatory activity of 3-aryl(heteryl)-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)-acrylonitrile derivatives.
Aim. To synthesize, prove the structure and study the analgesic and anti-inflammatory activities of 3-(het)-aryl-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitrile derivatives.
Results and discussion. Condensation of 2-methoxy-3,4,5,6-tetrahydro-7H-azepine with cyanoacetic acid hydrazide leads to formation of 2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acetonitrile. The latter readily reacts with the corresponding (het)arenecarbaldehydes in refluxing ethanol in the presence of catalytic amount of piperidine yielding a series of new 3-(het)aryl-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitrile derivatives. Further functionalization of 3-(4-hydroxy-3-R-phenyl)-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitriles has been done by modification of the OH group. One of the compounds synthesized, namely 3-(4-hydroxyphenyl)-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitrile, exhibits a high level of the analgesic activity on the “hot plate” model, and a similar level of the activity on the model of “acetic acid-induced writhings” as compared to ketorolac. The results obtained indicate the pronounced antinociceptive activity for the test compound.
Experimental part. 1H NMR spectra of the compounds synthesized were recorded on a Bruker VXR-300 spectrometer (Germany) operating at a frequency of 299.945 MHz, in DMSO-d6, using tetramethylsilane (TMS) as an internal standard. Melting points were measured using a RNMK 05 device (VEB Analytik,Dresden). The elemental analysis was performed on a EuroEA 3000 elemental analyzer. The analgesic and anti-inflammatory activities of 3-(4-hydroxyphenyl)-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitrile were determined using models of “carrageenan induced paw edema”, ”hot plate” and “acetic acid-induced writhings”, and compared to the reference drug ketorolac.
Conclusions. A series of new 3-(het)aryl-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitrile derivatives can be easily synthesized by the interaction of 2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acetonitrile with (het)arenecarbaldehydes. The hydroxy group in 3-(4-hydroxy-3-R-phenyl)-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitriles can be modified to obtain phenyl esters of aliphatic and aromatic carboxylic acids. The high level of the analgesic activity for 3-(4-hydroxyphenyl)-2-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)acrylonitrile has been determined.
Received: 30.01.2020
Revised: 17.05.2020
Accepted: 29.05.2020 -
The synthesis of 3-methyl-6-R-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives
Aim. To conduct the synthesis and confirm the structure of 3-methyl-6-R-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole derivatives as potential biologically active compounds.
Results and discussion. It has been shown that the heterocyclization reaction of 4-amino-5-methyl-4H-1,2,4-triazole-3-thiol with carboxylic acids in the excess of phosphorus oxychloride yields 3-methyl-6-R-[1,2,4]-triazolo[3,4-b][1,3,4]thiadiazoles.
Experimental part. The reaction of 4-amino-5-methyl-4H-1,2,4-triazole-3-thiol with the corresponding carboxylic acids was carried out in the excess of phosphorus oxychloride. The mixture was heated for 5 h with subsequent cooling and neutralization to pH 7 using ammonia solution. 1H NMR spectra of the compounds synthesized were recorded on a Varian Mercury VX-200 spectrometer operating at a frequency of 200 MHz, in DMSO-d6, using tetramethylsilane (TMS) as an internal standard. Melting points were measured using a MPA100 device. The elemental analysis was performed on a Elementar Vario EL Cube elemental analyzer. Agilent 1260 Infinity HPLC System equipped with Agilent 6120 mass spectrometer were used for registering LC-MS data.
Conclusions.As a result of this study 10 new compounds of the 3-methyl-6-R-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole series have been obtained. The structure and purity of the products have been confirmed using 1Н NMR spectroscopy, LC-MS and elemental analysis.Received: 18.02.2020
Revised: 29.04.2020
Accepted: 29.05.2020 -
Optimization of the process of dissolution of phosphate calculi of the human kidney in vitro
Aim. To study the influence of physicochemical parameters of litholytic compositions on the degree of dissolution of phosphate calculi.
Results and discussion. A number of factors affecting the effectiveness of litholytic compositions on dissolution of phosphate renal calculi have been studied. It has been shown that with increasing the temperature of the solution above 38.5°C the increase of the dissolution rate of the mineral component and denaturation of the protein matrix of the calculi are competitive processes. It has been determined that the degree of litholysis while increasing the speed of the calculus washing increases linearly. The optimal values of temperature, solution feed rate and complexon concentration for dissolution of renal calculi in vivo have been determined taking into account the physiological capabilities of the kidney.
Experimental part. 73 native, surgically removed calculi were used in the experiment. The stratification of the calculus was visualized by staining with Kumassi R-250. The chemical and structural homogeneity of phosphate calculi was determined by analyzing their infrared spectra. IR spectra were obtained on a Specord M-80 spectrophotometer in KBr tablets. An ION 700 instrument (Eutec Instruments) was used to control the pH of the medium.
Conclusions. It has been shown that taking into account the physiological capabilities of the kidney the temperature of litholysis solutions should not exceed 37.5°C, the optimum feed rate of the solution is 5 mL/min, and the effective complexon concentration is 0.02 – 0.20 mol/L.
Received: 13.03.2020
Revised: 05.05.2020
Accepted: 29.05.2020 -
The synthesis and study of physicochemical properties of 1,2,4-triazole derivatives containing the phenethyl group in position 5
During the last decade, national and foreign scientists have been constantly examining an example of studying the physicochemical and biological properties of nitrogen containing heterocycles, particularly with the nucleus of 1,2,4-triazole. The main advantage of such substances is to exhibit low levels of acute toxicity with a wide spectrum of pharmacological activity. To date, a large number of medicines on the basis of 1,2,4-triazole has been created, namely fluconazole, voriconazole, anastrozole, itraconazole, and letrozole. Therefore, the creation of new molecules based on 1,2,4-triazole and the search for new biologically active compounds among them is an urgent task of modern synthetic and pharmaceutical chemistry.
Aim. To study some aspects of 5-phenethyl-1H-1,2,4-triazole-3-amine reactivity and investigate the physicochemical properties of synthesized compounds.
Results and discussion. A series of 1-alkyl(aryl)-N-(5-phenethyl-1H-1,2,4-triazolе-3-yl)methanimines has been synthesized and the reaction of their reduction has been studied. The structure and purity of the synthesized compounds have been confirmed by the complex of modern instrumental methods of analysis – elemental analysis, IR, 1H NMR spectroscopy, LC-MS.
Experimental part. The reaction of 5-phenethyl-1H-1,2,4-triazole-3-amine with aldehydes at the ambient temperature in acetic acid medium gave 1-alkyl(aryl)-N-(5-phenethyl-1H-1,2,4-triazolе-3-yl)methanimines. At the next stage, the selective reduction of the exocyclic C=N-group of 1-alkyl(aryl)-N-(5-phenethyl-1H-1,2,4-triazolе-3-yl)methanimines by the action of sodium borohydride in the dimethylformamide was carried out.
Conclusions. 13 new 1,2,4-triazole derivatives, namely 1-alkyl(aryl)-N-(5-phenethyl-1H-1,2,4-triazolе-3-yl)methanimines and arylmethyl-(5-phenethyl-1H-1,2,4-triazolе-3-yl)amines, have been obtained. The both structure and purity of the obtained substances have been confirmed by the complex of modern instrumental methods of analysis.
Received: 12.08.2019
Revised: 18.09.2019
Received after correction: 27.12.2019
Revised: 25.04.2020
Accepted: 29.05.2020 -
Application of thin layer chromatography for the analytical diagnostics of combined prochlorperazine poisonings
The uncontrolled simultaneous application of prochlorperazine with typical phenothiazine derivatives antipsychotics and other drugs leads to fatal poisonings.
Aim. To optimize TLC procedures for the screening examinations in combined poisonings with prochlorperazine and other drugs.
Results and discussion. The chromatographic mobility of prochlorperazine, clorpromazine, ibuprofen, trifluoperazine and quetiapine has been studied on two types of plates (HPTLC and TLC). It has been shown that the TLC-systems used (special – for prochlorperazine, general – for screening of phenothiazine derivatives, as well as drug and narcotic substances of the basic nature recommended by the International Association of Forensic Toxicologists) rather effectively separate the substances analyzed in a thin layer of a sorbent, except for trifluoperazine. To detect the adsorption zones of substances, the Lieberman reagent giving different staining, the Dragendorff reagent and irradiation of chromatograms by UV-light (λ = 254 nm) have been proposed. The detection sensitivity is 0.5 – 1.0 μg in the sample. The validation assessment of the methods developed has been carried out by the chromatographic analysis of prochlorperazine model mixtures with each of the substances studied.
Experimental part. The studies were carried out on HPTLC plates (silica gel 60G, particle size – 5 – 7 μm, substrate type – glass, Estonia) with 10 × 10 cm in size and Merck plates (silica gel 60G F254, particle size – 10 – 15 μm, substrate type – aluminum foil, Germany) with 10 × 10 cm in size.
Conclusions. The TLC-conditions for screening of prochlorperazine, chlorpromazine, ibuprofen, trifluoperazin and quetiapine have been determined; they can be recommended for drugs detection in real samples of biological objects in the case of combined poisoning.
Received: 17.02.2020
Revised: 15.04.2020
Accepted: 29.05.2020
