Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.
Byl proveden virtual'nyĭ skrining s ispol'zovaniem dokinga i metodov kvantovoĭ khimii lekarstvenno-podobnykh soedineniĭ bazy dannykh Voronezhskogo universiteta protiv glavnoĭ proteazy koronavirusa SARS-CoV-2, vyzvavshego pandemiiu COVID-19. Snachala byl vypolnen doking bolee 42 tysiach trekhmernykh struktur ligandov s pomoshch'iu programmy SOL. Dalee, na osnovanii otsenki svobodnoĭ énergii sviazyvaniia, vychisliaemoĭ s pomoshch'iu programmy dokinga SOL, bylo otobrano bolee tysiachi ligandov dlia vychisleniia éntal'pii sviazyvaniia belok-ligand s pomoshch'iu kvantovo-khimicheskogo poluémpiricheskogo metoda PM7 s uchetom rastvoritelia (vody) v neiavnoĭ modeli COSMO. V rezul'tate dlia éksperimental'nogo testirovaniia bylo otobrano 20 ligandov, pokazavshikh luchshie znacheniia funktsii otsenki svobodnoĭ énergii sviazyvaniia, vychislennoĭ programmoĭ SOL, i éntal'pii sviazyvaniia, vychislennoĭ kvantovo-khimicheskim metodom. V khode éksperimental'nogo testirovaniia izmeriali ingibiruiushchuiu aktivnost' soedineniĭ protiv glavnoĭ proteazy SARS-CoV-2 i podavlenie replikatsii étogo koronavirusa v kul'ture kletok. Ingibirovanie opredeliali s ispol'zovaniem peptidnogo substrata s fluorestsentnoĭ metkoĭ, vkliuchaiushcheĭ saĭt proteoliza glavnoĭ proteazy. Antivirusnuiu aktivnost' testirovali v kul'ture kletok Vero. V rezul'tate éksperimental'nogo testirovaniia 8 molekul pokazali aktivnost' po ingibirovaniiu glavnoĭ proteazy SARS-CoV-2 v submikromoliarnom i mikromoliarnom diapazonakh IC50, i 3 iz nikh podavliali replikatsiiu SARS-CoV-2 v kul'ture kletok na urovne mikromoliarnykh znacheniĭ EC50 i imeli nizkuiu tsitotoksichnost'. Naĭdennye khimicheski raznoobraznye ingibitory mogut byt' ispol'zovany dlia optimizatsii s tsel'iu polucheniia soedineniia-lidera — osnovy novykh antivirusnykh preparatov priamogo deĭstviia na koronavirus SARS-CoV-2.
Keywords: CADD; COVID-19; Mpro; SARS-CoV-2; antiviral drugs; docking; drug discovery; inhibitors; quantum chemistry.