Small molecule screening compounds for coronavirus / SARS-CoV-2 / COVID-19 drug discovery
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of June 2020, more than 6 months into the outbreak, there were no approved vaccines or small-molecule drugs available which were specifically developed for COVID-19. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics.
In August 2020, ChemBridge released the new Coronavirus Library, which offers more than 15,000 compounds with potential to interact with SARS-CoV-2 viral targets or the host target ACE2. Compounds in the Coronavirus Library were selected in collaboration with the Wagner Lab at Harvard using the Virtual Flow methodology developed and published by the Wagner Lab. Details on the Virtual Flow methodology are published in Gorgulla, C., Boeszoermenyi, A., Wang, Z. et al. "An open-source drug discovery platform enables ultra-large virtual screens" Nature 580, 663–668 (2020). This SARS-CoV-2 / COVID-19 small molecule library may also have application in other coronavirus research programs.
to download a copy of the Coronavirus Library product sheet.
ChemBridge’s stock of more than 1.3 million compounds were prepared and docked against each of 40 different target sites on 17 different potential viral and host targets using the Virtual Flow screening platform. Top ranked compounds were further filtered to ensure that the Coronavirus Library included only high quality, lead-like or drug-like compounds free of undesirable chemical functionalities and free of PAINS structural alerts. The compound count per target ranges from 1,000 to 5,000 with 1,000 to 2,000 compounds per site screened.
Structures from ChemBridge stock were prepared with VirtualFlow for Ligand Preparation (VFLP)1. For each virtual screen a single target structure was used, and the protein was held rigid. QuickVina-W2 was used to perform a blind docking procedure for the HR1 domain of the spike protein, the RNA binding interface of the nucleoprotein, the RNA binding site of nsp12, as well as for nsp7 and ORF7a. For all the other site specific docking routines, QuickVina 23 was used. Both docking programs are based on AutoDock Vina4. The receptor structures were prepared with AutoDockTools5 from the PDB format to the PDBQT format.
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