Alex Chavez and Rodney Rothstein: Multiplexed antiviral drug discovery (covid-19 symposium)

Summary by: Arooba Ahmed (CC '23)

     Dr. Chavez’s work is on multiplexed antiviral drug discovery. Multidrug discovery is done on a single cell line, which saves lots of resources but returns only one answer specific to that cell line. This is a problem for coronaviruses since there are hundreds of them circulating within animals. Therefore, this group wants to develop a drug that targets many coronaviruses. They are studying the protein 3CL protease, which is common to all coronaviruses. Protease inhibitors have been successful in the past, such as those for HIV and HepC that have changed the way those patients are treated. 
     To achieve their goal, they need to change the way drug screens are done to be able to look at multiple viral proteases at a time. If you take yeast and put a viral protease in it, they will not grow. However, near protease inhibitors, they will grow. This allows them to use yeast as a biosensor for protease activity. If the yeast grows, it means that the protease is inactive. They can then generate dozens of different protease-expressing yeast to test their inhibitors.
     They screened against the dozens of proteases at once by using DNA barcoding technology. They take each yeast strain and give each one a known DNA strand inserted into a specific location. If they do not express any of the proteases, the cells grow fine and maintain a 1:1:1:1 distribution which can be observed by simply sequencing the DNA barcodes within the population. But when they do express the proteases, the ratio changes as the cells expressing the proteases do not grow as well as the control. Finally, if they take the starting pool and express the proteases in the presence of a known SARS protease inhibitor, the cells containing the SARS 3CL protease grow very well. 
     In their pilot study, they used a pool of over 50 different DNA barcoded strains and tested them against 96 compounds to obtain 4800 tests. In the future, they hope to finalize a viral protease library with over 70 proteases, of which 20 are coronavirus proteases. They are also working towards testing 10,000 compounds. Finally, they are working through a method to test the second coronavirus protease (PLP).