Vývoj protokolu využívajícího farmakoforové a dokovací přístupy pro vývoj inhibitorů hlavní proteasy viru SARS-CoV-2

Klenor, Mikuláš

Covid-19 is a highly contagious potentially life-threatening disease caused by the SARS-CoV-2 coronavirus. The virus is responsible for a global pandemic and has claimed over 6 million human lives between years 2020 and 2022. To limit the spread of SARS-CoV-2, numerous vaccines have been developed and applied. For already infected individuals, antiviral drugs are applied. An important validated target is the main protease of SARS-CoV-2 (Mpro ). Although thousands of inhibitors have been prepared and one is used in clinical practice (sold under the name of Paxlovid), improved computational protocols to design new active compounds are needed. The computational approach used here is based on pharmacophores. By curating and inspecting 298 structures of Mpro /inhibitors complexes retrieved from the Protein Data Bank (PDB), we have generated six distinct pharmacophores featuring different binding modes. With their aid, we have carried out molecular docking, whose effectiveness was evaluated by measuring root-mean-square deviation (RMSD) of the generated poses with respect to the native conformations. The routine captured 177 out of 213 ligands naturally binding to the active site of the protein with 127 (72% of the captured) generated with RMSD within 2 Å relative to the native conformation....

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