VirtualScreening

Virtual Screening

Target the binding site of the crystal structure SARS-CoV-2 main protease (6LU7 [1], 6YB7 [2]) with potential inhibitors using RxDock.

[1] Zhang, L. et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science (2020) doi:10.1126/science.abb3405.
[2] Main protease structure and XChem fragment screen

Initial work

The Diamond Light Source's XChem team recently completed a successful fragment screen on the SARS-CoV-2 main protease (MPro), which provided crystal structures of the protein in complex with 55 different small molecules (fragment hits). These can be viewed interactively here. In an effort to identify candidate molecules for binding, InformaticsMatters, the XChem group and the European Galaxy team have joined forces to construct and execute a Galaxy workflow for performing and evaluating molecular docking on a massive scale, based on the set of fragment hits which are known experimentally to bind to the protein.

Learn more about this project here: https://covid19.galaxyproject.org/cheminformatics

Communication

• Slack: #htvs
• Jitsi Meet: HTVS

Participants

• Vedran Miletić (coordinator)
• Patrik Nikolić
• Ali Haider Bangash
• Didier Barradas
• Gonzalo Colmenarejo

Ideas

• Pose search parameter tuning
• Workflow automation (e.g. KNIME)
• Applications of machine learning techniques