Core Strength
The experts in the LSI’s cores don’t just advance research projects — they pioneer new science
Even before many of the faculty lab spaces were occupied, the nascent Life Sciences Institute was investing in its scientific cores — research centers with specialized expertise and technologies that could advance faculty and industry projects. Its first two cores, the Center for Chemical Genomics (CCG) and the Center for Structural Biology (CSB), launched in 2004, less than a year after the institute opened.
In early 2019, with support from the University of Michigan’s Bioscience Initiative, the institute established the Cryo-Electron Microscopy Facility and the Natural Products Discovery Core (NPDC) to expand its strengths in structural biology and drug discovery technologies.
The cores provide research services in their respective domains to support projects from labs across and outside the university. They encapsulate the concept of normalized excellence, routinely completing complex experiments with enough frequency that they have become second nature.
“Researchers typically engage the cores for things that they aren’t capable of doing in-house, and the cores provide our technologies and experience to make those experiments successful,” explains Aaron Robida, a scientist in the CCG.
In the last decade alone, more than 400 scientists (both internal and external to U-M) have capitalized on the expertise and technologies within the cores — and that expertise has helped bring 16 drugs to pre-clinical and clinical development and supported 313 publications.
As instrumental as the cores have been in projects from other labs, the experts who manage the cores’ daily activities also originate their own novel projects. Center for Structural Biology Managing Director Jeanne Stuckey, for example, has contributed significantly to the development of three anti-cancer drugs that are now in clinical trials.
Now a new project initiated by NPDC Managing Director Ashu Tripathi has brought three of the cores together to reimagine how one common analytical tool, mass spectrometry, can aid drug discovery.
Weighty changes
Mass spectrometry works by breaking a compound into different pieces based on weight and charge, allowing scientists to understand what the original compound was made of.
“I began to wonder: Can we use high-throughput mass spectrometry as a screening tool to identify new drugs that work against specific disease targets?” Tripathi recalls. His idea was to use mass spectrometry to screen hundreds of molecules to see if they interfered with the function of a disease-causing protein.
To test the idea, Tripathi needed a protein that would yield an observable change in mass when working properly — specifically, one capable of modifying its target molecule by adding or removing a part of it. Ideally, the protein would also be relevant to a disease with high therapeutic demand and limited drug options. The SARS-CoV-2 Mpro protein, essential for viral replication in COVID-19,met both criteria.
“Mpro is a protease, which means it is a protein that cleaves peptides, or small chains of amino acids,” Tripathi explains. “When a peptide is cleaved into two pieces by Mpro, the molecular weight of the individual components provides an observable difference in a mass spectrometry experiment. So, we can use the cleaving of a peptide as our reporter of enzyme activity.”
When Tripathi began formulating this project in 2022, SARS-CoV-2 was a high-priority disease.
Additionally, the only on-market drug that targets the SARS-CoV-2 Mpro protein, Paxlovid, has a significant side-effect profile, making an alternative drug choice desirable.
Tripathi wanted to use his high-throughput mass spectrometry screening experiment to assess whether any of the natural product extracts in the NPDC could successfully combat the activity of the Mpro protein.
To validate this experimental system, Tripathi needed a lot of Mpro proteins. For that, he turned to another LSI core: the CSB.
“The CSB is a frequent entry point for working with the other LSI cores,” Stuckey says. “We are the first stop for people that want to do drug development and want to study a protein on the bench. People come here, get their protein, and can move very easily to the other cores.”
The production of Mpro was a critical step in allowing Tripathi to move forward to the screening phase of the project. Collaborating with the CCG, the team created a system of test plates to efficiently evaluate the activity of 7,500 natural product extracts.
“Each plate contains 320 wells,” Tripathi explains. “In each well, prepared by the CCG, we include Mpro protein source from the CSB, a reporter peptide designed to be cleaved by Mpro, and a natural product extract from the NPDC.”
Using high-throughput mass spectrometry, Tripathi identified wells where the peptide remained uncleaved, signaling that the natural product inhibited Mpro activity and potentially exhibited antiviral properties.
An exercise in optimization
After using mass spectrometry to identify compounds that showed potential, Tripathi partnered with Christiane Wobus, a virologist at Michigan Medicine, to test the compound against the real virus.
“Our lab is one of a few at Michigan that had access and clearance to work with the infectious virus. So, when someone wanted to test if their compounds impacted the infectivity of the virus, they reached out to us,” Wobus says.
Wobus and members of her lab assessed the toxicity of the compounds to determine what concentration would harm healthy cells. Then they compared that with the concentrations of compounds needed to show antiviral activity against the SARS-CoV-2 infection in cells.
The anti-viral molecule identified by the initial screening provided a crucial starting point for further development, and the team has been able to design a natural product mimic with enhanced antiviral activity, surpassing the efficacy of Paxlovid.
While the optimization process is ongoing, these advancements highlight the potential of natural product-inspired drug discovery in addressing critical therapeutic challenges. And the project itself offers a promising example of what can be accomplished through the LSI’s comprehensive suite of research services.
“Each of the cores has its own forte, and most researchers leverage only one or two of these specialties. Since I started the NPDC, I always thought we should have a flagship project involving all the cores,” Tripathi says. “When everyone’s interests align, there’s almost no science we cannot do here at Michigan.”