Educational Tools for Drug Discovery and Design Focusing on the SARS‐CoV‐2 Main Protease nsp5

Abstract

A new coronavirus causing an acute respiratory syndrome (SARS‐CoV‐2) emerged in late 2019 and has been responsible for the outbreak of coronavirus disease 2019 (COVID‐19). Symptoms of COVID‐19 range from mild to severe, including respiratory symptoms, systemic inflammatory responses, and even death. Currently, remdesivir is the only FDA‐approved therapeutic agent to treat COVID‐19, although it shows limited efficacy. We were interested in learning about the drug design process for a novel virus. We focused on drug research targeting the SARS‐CoV‐2 main protease, known as nsp5 or Mpro. The nsp5 protease is an enzyme critical for viral replication, with ebselen, cinanserin, and N3 being lead compounds identified as possible effective drugs (Jin, 2020). Starting with these chemical drug structures, we used an in silico drug design process to explore how to modify and refine these drugs. Our goal was to make the compounds more drug‐like, according to Lipinski's and Veber's rules. Using the crystal structure file 6YB7 from the Protein Data Bank (PDB), we focused on the protease active site, defined by amino acids His41, Met49, Asn142, Cys145, His164, Met165, Glu166, Pro168, and Gln189. Cys145 is especially important, as it is the target for irreversible covalent inhibitors. Based on this information, we used molecular docking software to first re‐dock these drugs into the nsp5 protease. We then made changes to the structures of the lead compounds, docked those new compounds, and used the energetic information to continue the refinement process. Once we completed our own drug design explorations, we created a three‐dimensional printed model of the full nsp5 protease, with the key amino acids highlighted. We also created a three‐dimensional model zoomed in on the active site, with the different drugs fitting into that active site model. Here, we present what we learned about the drug design process for a novel virus such as SARS‐CoV‐2. Our docking protocols and models are useful for teaching the fundamentals of drug design and about modern drug discovery and design processes.