Published August 15, 2023 | Version v1
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Modeling and Study of Anti-coronavirus Activity of 6,7-Dimethoxyquinazoline-4(3H)-one Derivatives in Relation to SARS-COV-2 by in silico and in vitro Methods

  • 1. Volgograd Medical State University

Description

The pandemic of the new coronavirus infection SARS-CoV-2 (COVID-19) has put a significant strain on the healthcare system and revealed the need to develop effective medicines for the treatment of this disease. The research results presented in the article are devoted to the development of new compounds with anti-coronavirus action against SARS-CoV-2, which are derivatives of 6,7-dimethoxykinazoline-4(3H)-one. In silico, the research was carried out by the molecular docking method in the freely distributed Autodock 4.0 program. The virtual structures of the simulated compounds were constructed in the HyperChem 8.0.4 program, and the final optimization of the geometry of virtual structures was calculated in the ORCA 4.1 program using the density functional theory (UB3LYP) method and the base set 6-311G**. The main protease (identification number 7K6D) and papain-like (identification number 7LBR) protease SARS-Cov-2 were used to predict antiviral activity. In vitro studies were carried out by multiple dilutions of the analyzed compounds using a chromogenic substrate. It follows from the results that the newly synthesized derivatives of 6,7-dimethoxyquinazoline-4(3H)-one should be considered as promising candidates for the development of new antiviral drugs. The most pronounced antiviral activity is observed in substance 8c containing a glycyltryptophan residue. It is worth noting that the proposed algorithm for searching for innovative antiviral drugs in silico agrees quite well with the results of the in vitro experiment.

Notes

The reported study was funded by RFBR, project no. 20-315-90060

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References

  • Wu, D., Wu, T., Liu, Q., & Yang, Z. (2020). The SARS-CoV-2 outbreak: what we know. International journal of infectious diseases, 94, 44-48. https://doi.org/10.1016/j.ijid.2020.03.004
  • Pozzi, C., Vanet, A., Francesconi, V., Tagliazucchi, L., Tassone, G., Venturelli, A., ... & Tonelli, M. (2023). Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery - Genetics Alliance Perspective. Journal of Medicinal Chemistry, 66, (6), 3664-3702. https://doi.org/10.1021/acs.jmedchem.2c01229
  • Zolotyh, D. S., Daytona, Zh. V., & Pozdnyakov, D. I. (2022). Antiviral activity of compounds containing a structural fragment of benzopyran-2-one. Problems of biological, medical and pharmaceutical chemistry. 25, (6), 22-27. https://doi.org/10.29296/25877313-2022-06-03
  • Chiriapkin, A. S. (2022). Review of pyrimidine derivatives as pharmacologically active compounds. Juvenis Scientia, 8, (5), 16-30. https://doi.org/10.32415/jscientia_2022_8_5_16-30
  • Verma, V. A., Saundane, A. R., Meti, R. S., & Vennapu, D. R. (2021). Synthesis of novel indolo [3, 2-c] isoquinoline derivatives bearing pyrimidine, piperazine rings and their biological evaluation and docking studies against COVID-19 virus main protease. Journal of Molecular Structure, 1229, 129829. https://doi.org/10.1016/j.molstruc.2020.129829
  • Abu-Zaied, M. A., Elgemeie, G. H., & Mahmoud, N. M. (2021). Anti-covid-19 drug analogues: synthesis of novel pyrimidine thioglycosides as antiviral agents against SARS-COV-2 and avian influenza H5N1 viruses. ACS omega, 6(26), 16890-16904. https://doi.org/10.1021/acsomega.1c01501
  • Alamshany, Z. M., Khattab, R. R., Hassan, N. A., El-Sayed, A. A., Tantawy, M. A., Mostafa, A., & Hassan, A. A. (2023). Synthesis and Molecular Docking Study of Novel Pyrimidine Derivatives against COVID-19. Molecules, 28(2), 739. https://doi.org/10.3390/molecules28020739
  • Khan, S., Kale, M., Siddiqui, F., & Nema, N. (2021). Novel pyrimidine-benzimidazole hybrids with antibacterial and antifungal properties and potential inhibition of SARS-CoV-2 main protease and spike glycoprotein. Digital Chinese Medicine, 4(2), 102-119. https://doi.org/10.1016/j.dcmed.2021.06.004
  • Algethami, F. K., Cherif, M., Jlizi, S., Ben Hamadi, N., Romdhane, A., Elamin, M. R., ... & Ben Jannet, H. (2021). Design, microwave-assisted synthesis and in silico prediction study of novel isoxazole linked pyranopyrimidinone conjugates as new targets for searching potential Anti-SARS-CoV-2 agents. Molecules, 26(20), 6103. https://doi.org/10.3390/molecules26206103
  • Kodonidi, I. P., Chiriapkin, A. S., & Tworowski, D. E. (2021). Molecular design of N-acyl derivatives of 2-(2-oxopyrolidin-1-yl)-acetamide with GABA-ergic and glutamatergic activities. Pharmacy & Pharmacology, 9(1), 84-97. https://doi.org/10.19163/2307-9266-2021-9-1-84-97
  • Chiriapkin, A. S., Kodonidi, I. P., & Pozdnyakov, D. I. (2022). Synthesis and evaluation of cerebroprotective activity of novel 6, 7-dimethoxyquinazolin-4 (3H)-one derivatives containing residues of amino acids and dipeptides. Chimica Techno Acta. 2022. Vol. 9.№ 2, 9(2). https://doi.org/10.15826/chimtech.2022.9.2.12
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, 30(16), 2785-2791. https://doi.org/10.1002/jcc.21256
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., ... & Bourne, P. E. (2000). The protein data bank. Nucleic acids research, 28(1), 235-242. https://doi.org/10.1093/nar/28.1.235
  • Teppen, B. J. (1992). HyperChem, release 2: molecular modeling for the personal computer. Journal of chemical information and computer sciences, 32(6), 757-759. https://doi.org/10.1021/ci00010a025
  • O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics, 3(1), 1-14. https://doi.org/10.1186/1758-2946-3-33
  • Andi, B., Kumaran, D., Kreitler, D. F., Soares, A. S., Keereetaweep, J., Jakoncic, J., ... & McSweeney, S. (2022). Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Scientific reports, 12(1), 12197. https://doi.org/10.1038/s41598-022-15930-z
  • Shen, Z., Ratia, K., Cooper, L., Kong, D., Lee, H., Kwon, Y., ... & Xiong, R. (2021). Design of SARS-CoV-2 PLpro inhibitors for COVID-19 antiviral therapy leveraging binding cooperativity. Journal of medicinal chemistry, 65(4), 2940-2955. https://doi.org/10.1021/acs.jmedchem.1c01307
  • Yang, H., Xie, W., Xue, X., Yang, K., Ma, J., Liang, W., ... & Rao, Z. (2005). Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS biology, 3(10), e324. https://doi.org/10.1371/journal.pbio.0030428
  • Pitsillou, E., Liang, J., Ververis, K., Lim, K. W., Hung, A., & Karagiannis, T. C. (2020). Identification of small molecule inhibitors of the deubiquitinating activity of the SARS-CoV-2 papain-like protease: in silico molecular docking studies and in vitro enzymatic activity assay. Frontiers in chemistry, 8, 623971. https://doi.org/10.3389/fchem.2020.623971
  • Amporndanai, K., Meng, X., Shang, W., Jin, Z., Rogers, M., Zhao, Y., ... & Samar Hasnain, S. (2021). Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nature communications, 12(1), 3061. https://doi.org/10.1038/s41467-021-23313-7