Synthesis, characterization and identification of inhibitory activity on the main protease of COVID-19 by molecular docking strategy of (4-oxo-piperidinium ethylene acetal) trioxonitrate

Sofian Gatfaoui; Noureddine Issaoui; Aleksandr S Kazachenko; Omar M Al-Dossary; Thierry Roisnel; Houda Marouani

doi:10.1016/j.jksus.2023.102758

Synthesis, characterization and identification of inhibitory activity on the main protease of COVID-19 by molecular docking strategy of (4-oxo-piperidinium ethylene acetal) trioxonitrate

J King Saud Univ Sci. 2023 Aug;35(6):102758. doi: 10.1016/j.jksus.2023.102758. Epub 2023 Jun 13.

Authors

Sofian Gatfaoui¹, Noureddine Issaoui², Aleksandr S Kazachenko^{3

4}, Omar M Al-Dossary⁵, Thierry Roisnel⁶, Houda Marouani¹

Affiliations

¹ Materials Chemistry Laboratory, Faculty of Sciences of Bizerte, Carthage University, 7021 Zarzouna, Tunisia.
² Laboratory of Quantum and Statistical Physics, Faculty of Sciences, University of Monastir, Monastir 5079, Tunisia.
³ Siberian Federal University, pr. Svobodny 79, Krasnoyarsk 660041, Russia.
⁴ Institute of Chemistry and Chemical Technology, Krasnoyarsk Scientific Center, Siberian Branch, Rus-sian Academy of Sciences, Akademgorodok 50, bld. 24, Krasnoyarsk 660036, Russia.
⁵ Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia.
⁶ X-Ray Diffractometry Center, UMR 6226 CNRS, Rennes Chemical Sciences Unit, Rennes I University, 263 General Leclerc Avenue, 35042 Rennes, France.

Abstract

In this investigation a single crystal of (4-oxo-piperidinium ethylene acetal) trioxonitrate (4-OPEAN) was synthesized by modifying the mechanism of gradual evaporation at ambient temperature. The operational groupings are found in the complex material in the elaborate substance, according to the infrared spectrum. Single crystal X-ray diffraction suggests, (4-OPEAN) with the chemical formula (C₇H₁₂NO₂)NO₃ belongs to the orthorhombic space group Pnma and is centrosymmetric in three dimensions with the aforementioned network configurations, a = 11.7185(8) Å, b = 7.2729(6) Å, c = 11.0163(8) Å, Z = 4, V = 938.89(12) Å³, R = 0.0725 and wR = 0.1762. Many N-H…O and C-H…O hydrogen bridges, both bifurcated and non-bifurcated, link the 4-oxo-piperidinium ethylene acetal cations to the trigonal (NO₃^-) anions. Molecular geometry and optimal parameters of (4-OPEAN) have been determined via DFT computations at the theory-level B3LYP/6-311 ++ G(d, p), these have been contrasted with the X-ray data already available. Hirshfeld surface analysis has made it possible for the visualization and quantification of relationships between molecules in the crystal composition. Quantum theory atoms in molecules, electron location function, decreased density gradient, and localized orbital locator research have all been used to explore non-covalent interactions in crystal structure. In order to pinpoint both the nucleophilic and electrophilic locations that support hydrogen bond formation, the molecule electrostatic potential was determined. The greatest and lowest energies of occupied and unfilled molecular orbitals, together with additional derived atomic characteristics, show the material to be extremely stable and hard. According to a molecular docking study, 4-OPEAN may exhibit inhibiting effects on the 6Y84 and 7EJY virus proteins from corona (COVID-19).

Keywords: COVID-19; Chemical docking; DFT; Hirshfeld surface; Synthesis; X-ray diffraction.