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One-pot synthesis, X-ray crystal structure, and identification of potential molecules against COVID-19 main protease through structure-guided modeling and simulation approach.
El Bakri, Youness; Musrat Kurbanova, Malahat; Ali Siddique, Sabir; Ahmad, Sajjad; Goumri-Said, Souraya.
  • El Bakri Y; Department of Theoretical and Applied Chemistry, South Ural State University, Lenin prospect 76, Chelyabinsk 454080, Russian Federation.
  • Musrat Kurbanova M; Baku State University, Organic Chemistry Department, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan.
  • Ali Siddique S; Center for Organic Chemistry, School of Chemistry, University of the Punjab, Lahore 54590, Pakistan.
  • Ahmad S; Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan.
  • Goumri-Said S; College of Science, Physics department, Alfaisal University, Riyadh 11533, Saudi Arabia.
Arab J Chem ; 15(11): 104230, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2031134
ABSTRACT
Although antimicrobial resistance before the Covid-19 pandemic is a top priority for global public health, research is already ongoing on novel organic compounds with antimicrobial and antiviral properties in changing medical environments in connection with Covid 19. Thanks to the Biginelli reaction, which allows the synthesis of pyrimidine compounds, blockers of calcium channels, antibodies, antiviral, antimicrobial, anti-inflammatory, or antioxidant therapeutic compounds were investigated. In this paper, we aim to present Biginelli's synthesis, its therapeutic properties, and the structural-functional relationship in the test compounds that allows the synthesis of antimicrobial compounds. Both the DFT and TD-DFT computations of spectral data, molecular orbitals (HOMO, LUMO) analysis, and electrostatic potential (MEP) surfaces are carried out as an add-on to synthetic research. Hirshfeld surface analysis was also used to segregate the different intermolecular hydrogen bonds involved in the molecular packing strength. Natural Bond Orbital (NBO) investigation endorses the existence of intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. The dipole moment, linear polarizability, and first hyperpolarizabilities have been explored as molecular parameters. All findings based on DFT exhibit the best consistency with experimental findings, implying that synthesized molecules are highly stable. To better understand the binding mechanism of the SARS-CoV-2 Mpro, we performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations.
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Full text: Available Collection: International databases Database: MEDLINE Language: English Journal: Arab J Chem Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Language: English Journal: Arab J Chem Year: 2022 Document Type: Article