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A Novel Ambroxol-Derived Tetrahydroquinazoline with a Potency against SARS-CoV-2 Proteins. Int J Mol Sci 2023; 24:ijms24054660. [PMID: 36902093 PMCID: PMC10002583 DOI: 10.3390/ijms24054660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
We report synthesis of a novel 1,2,3,4-tetrahydroquinazoline derivative, named 2-(6,8-dibromo-3-(4-hydroxycyclohexyl)-1,2,3,4-tetrahydroquinazolin-2-yl)phenol (1), which was obtained from the hydrochloride of 4-((2-amino-3,5-dibromobenzyl)amino)cyclohexan-1-ol (ambroxol hydrochloride) and salicylaldehyde in EtOH. The resulting compound was produced in the form of colorless crystals of the composition 1∙0.5EtOH. The formation of the single product was confirmed by the IR and 1H spectroscopy, single-crystal and powder X-ray diffraction, and elemental analysis. The molecule of 1 contains a chiral tertiary carbon of the 1,2,3,4-tetrahydropyrimidine fragment and the crystal structure of 1∙0.5EtOH is a racemate. Optical properties of 1∙0.5EtOH were revealed by UV-vis spectroscopy in MeOH and it was established that the compound absorbs exclusively in the UV region up to about 350 nm. 1∙0.5EtOH in MeOH exhibits dual emission and the emission spectra contains bands at about 340 and 446 nm upon excitation at 300 and 360 nm, respectively. The DFT calculations were performed to verify the structure as well as electronic and optical properties of 1. ADMET properties of the R-isomer of 1 were evaluated using the SwissADME, BOILED-Egg, and ProTox-II tools. As evidenced from the blue dot position in the BOILED-Egg plot, both human blood-brain barrier penetration and gastrointestinal absorption properties are positive with the positive PGP effect on the molecule. Molecular docking was applied to examine the influence of the structures of both R-isomer and S-isomer of 1 on a series of the SARS-CoV-2 proteins. According to the docking analysis results, both isomers of 1 were found to be active against all the applied SARS-CoV-2 proteins with the best binding affinities with Papain-like protease (PLpro) and nonstructural protein 3 (Nsp3_range 207-379-AMP). Ligand efficiency scores for both isomers of 1 inside the binding sites of the applied proteins were also revealed and compared with the initial ligands. Molecular dynamics simulations were also applied to evaluate the stability of complexes of both isomers with Papain-like protease (PLpro) and nonstructural protein 3 (Nsp3_range 207-379-AMP). The complex of the S-isomer with Papain-like protease (PLpro) was found to be highly unstable, while the other complexes are stable.
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Garkusha NA, Anikeeva OP, Bayıl I, Taskin-Tok T, Safin DA. DFT, ADMET, molecular docking and molecular dynamics studies of pyridoxal. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Omar RA, Koparir P, Sarac K, Koparir M, Safin DA. A novel coumarin-triazole-thiophene hybrid: synthesis, characterization, ADMET prediction, molecular docking and molecular dynamics studies with a series of SARS-CoV-2 proteins. J CHEM SCI 2023; 135:6. [PMID: 36686402 PMCID: PMC9845830 DOI: 10.1007/s12039-022-02127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023]
Abstract
Synthesis, characterization and theoretical studies of a novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1), which was fabricated from 4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazole-3-thiol and 4-(chloromethyl)-6,7-dimethyl-2H-chromen-2-one, are reported. The resulting compound was characterized by microanalysis, IR, 1H, and 13C APT NMR spectroscopy. The DFT calculations examined the structure and electronic properties of 1 in gas phase. Its reactivity descriptors and molecular electrostatic potential revealed the reactivity and the reactive centers of 1. ADMET properties of 1 were evaluated using the respective online tools. It was established that 1 exhibit positive gastrointestinal absorption properties and negative human blood-brain barrier penetration. The Toxicity Model Report revealed that 1 belongs to toxicity class 4. Molecular docking was additionally applied to study the interaction of 1 with some SARS-CoV-2 proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with Papain-like protease (PLpro). The interaction of 1 with the applied proteins was also studied using molecular dynamics simulations. Graphical abstract A novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1) is reported. The structure and electronic properties of 1 were examined by the DFT calculations. ADMET properties of 1 were also evaluated. Molecular docking and molecular dynamics simulations were applied to study interactions of 1 with a series of the SARS-CoV-2 proteins. Supplementary Information The online version contains supplementary material available at 10.1007/s12039-022-02127-0.
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Affiliation(s)
- Rebaz Anwar Omar
- Department of Chemistry, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq Iraq
| | - Pelin Koparir
- Department of Chemistry, Institute of Forensics, Firat University, 23169 Elazig, Turkey
| | - Kamuran Sarac
- Department of Chemistry, Faculty of Art and Sciences, Bitlis Eren University, 13000 Bitlis, Turkey
| | - Metin Koparir
- Department of Chemistry, Faculty of Sciences, Firat University, 23000 Elazığ, Turkey
| | - Damir A Safin
- Scientific and Educational and Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B. N. Yeltsin, Ekaterinburg, 620002 Russian Federation ,University of Tyumen, Volodarskogo Str. 6, 625003 Tyumen, Russian Federation
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Burkhanova TM, Krysantieva AI, Babashkina MG, Konyaeva IA, Monina LN, Goncharenko AN, Safin DA. In silico analyses of betulin: DFT studies, corrosion inhibition properties, ADMET prediction, and molecular docking with a series of SARS-CoV-2 and monkeypox proteins. Struct Chem 2022; 34:1-12. [PMID: 36320318 PMCID: PMC9607775 DOI: 10.1007/s11224-022-02079-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/06/2022] [Indexed: 12/04/2022]
Abstract
We report detailed computational studies of betulin - a pentacyclic naturally occuring triterpene, which is a precursor for a broad family of biologically active derivatives. The structure, electronic, and optical properties of betulin were studied by the density functional theory (DFT) calculations in gas phase. The reactivity and the reactive centers of betulin were revealed through its global reactivity descriptors and molecular electrostatic potential (MEP). The DFT calculations were also applied to probe betulin as a potential corrosion inhibitor for some important metals used in implants. Electron charge transfer from the molecule of betulin to the surface of all the examined metals (Ti, Fe, Zr, Co, Cu, Cr, Ni, Mn, Mo, Zn, Al, W, Ag, Au) was revealed, of which the best results were obtained for Ni, Au and Co. Bioavailability, druggability as well as absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of betulin were evaluated using the SwissADME, BOILED-Egg and ProTox-II tools. Molecular docking was applied to examine the influence of the title compound on a series of the SARS-CoV-2 proteins as well as one of the monkeypox proteins. It was established that betulin is active against all the applied proteins with the best binding affinity with papain-like protease (PLpro) and spike protein (native) of SARS-CoV-2. The title compound is also active against the studied monkeypox protein. Interaction of betulin with papain-like protease (PLpro) was studied using molecular dynamics simulations.
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Affiliation(s)
- Tatyana M. Burkhanova
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
- Scientific and Educational and Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named After the First President of Russia B.N. Yeltsin, Mira Str. 19, Ekaterinburg, 620002 Russian Federation
| | - Alena I. Krysantieva
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
| | - Maria G. Babashkina
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
| | - Irina A. Konyaeva
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
| | - Lyudmila N. Monina
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
| | - Anastasiya N. Goncharenko
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
| | - Damir A. Safin
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, Kurgan, 640020 Russian Federation
- Scientific and Educational and Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named After the First President of Russia B.N. Yeltsin, Mira Str. 19, Ekaterinburg, 620002 Russian Federation
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Babashkina MG, Burkhanova TM, Safin DA. In silico studies of 6-phenyl-3-(pyridin-2-yl)-1,2,4-triazine as a corrosion inhibitor for some important metals used in implants. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Koparir P, Omar RA, Sarac K, Ahmed LO, Karatepe A, Taskin-Tok T, Safin DA. Synthesis, Characterization and Computational Analysis of Thiophene-2,5-Diylbis((3-Mesityl-3-Methylcyclobutyl)Methanone). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2112712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Pelin Koparir
- Institute of Forensic, Department of Chemistry, Firat University, Elazig, Turkey
| | - Rebaz Anwar Omar
- Department of Chemistry, Faculty of Science and Health, Koya University–University Park, Daniel Mitterrand Boulevard, Koya, Kurdistan Region, F. R. Iraq
| | - Kamuran Sarac
- Department of Chemistry, Faculty of Art and Sciences, Bitlis Eren University, Bitlis, Turkey
| | - Lana Omer Ahmed
- Department of physics, Faculty of Science and Health, Koya University – University Park, Daniel Mitterrand Boulevard, Koya, Kurdistan Region, F. R. Iraq
| | - Arzu Karatepe
- Department of Chemistry, Faculty of Sciences, Firat University, Elazığ, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, University of Gaziantep, Gaziantep, Turkey
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, University of Gaziantep, Gaziantep, Turkey
| | - Damir A. Safin
- «Advanced Materials for Industry and Biomedicine» Laboratory, Kurgan State University, Kurgan, Russia Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russia Federation
- University of Tyumen, Tyumen, Russia Federation
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Babashkina MG, Taskin-Tok T, Burkhanova TM, Safin DA. 1-hydroxy-6,6-Dimethyl-3-Phenyl-1,6-Dihydropyridine-2,5-Dione as a Promising Inhibitor of the SARS-CoV-2 Proteins: insight into the Crystal Structure, Hirshfeld Surface Analysis and Computational Study. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2094420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Maria G. Babashkina
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Kurgan, Russian Federation
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, University of Gaziantep, Gaziantep, Turkey
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, University of Gaziantep, Gaziantep, Turkey
| | - Tatyana M. Burkhanova
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Kurgan, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russian Federation
- University of Tyumen, Tyumen, Russian Federation
| | - Damir A. Safin
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Kurgan, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russian Federation
- University of Tyumen, Tyumen, Russian Federation
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