Lara Scharbert

In response to the global COVID-19 pandemic that emerged in the spring of 2020, we initiated a Computer-Aided Drug Design (CADD) project aimed at contributing to the discovery and development of a prospective drug against SARS-CoV-2. The approach involved screening over one million compounds by docking them against the main protease (3CLpro) of the virus, followed by molecular dynamics (MD) simulations to identify the most promising drug candidates.

Building upon these initial screenings, our current focus is to assess the inhibitory activity of a diverse range of peptides, including D-amino acid containing and cyclic peptides against two SARS-CoV-2 proteases, the main protease and the papain-like protease. We use Molecular Docking and MD simulations to explore the binding mode on a molecular level and to design peptide inhibitors, drawing insights from intermolecular interactions, ligand flexibility and binding free energy calculations. Collaborating closely with researchers at the Forschungszentrum Jülich and the Heinrich-Heine University Düsseldorf, we employ a holistic approach using in silico, in vitro, and in cell techniques to evaluate the ligands for their drug potential.