Powerful drug discovery technique leads to potential compound for obesity and diabetes
Scientists demonstrate a versatile approach for finding enzyme-activating drugs; the technique could have applications across dozens of disease areas.
June 08, 2020
LA JOLLA, CA—Scientists at Scripps Research have devised a technique for discovering new enzyme-activating compounds that could be developed into drugs or used as laboratory tools for studying enzymes.
The scientists, whose study appears in Nature Chemical Biology, demonstrated their technique by identifying an enzyme activator that reverses diabetes-like signs in obese mice. Enzymes are vital molecules in the body that bring about chemical reactions in cells; they’re known to play an important role in functions such as digestion and metabolism.
“We can now apply this technique to a variety of enzyme classes to find activators that have therapeutic effects or are useful scientifically for exploring the functions of enzymes,” says study co-senior author Enrique Saez, PhD, an associate professor in the Department of Molecular Medicine at Scripps Research.
The study featured a close collaboration among several laboratories at Scripps Research, including Saez’s and those of co-senior author Dale Boger, PhD, the Richard and Alice Cramer Professor of Chemistry, and Benjamin Cravatt, PhD, the Gilula Chair of Chemical Biology.
A useful extension of protein profiling method
The new technique builds on a versatile method called activity-based protein profiling (ABPP), developed by Cravatt’s lab starting in the late 1990s.
Since that time, ABPP has become a standard tool among enzyme biologists and pharmaceutical researchers and is applicable to several major enzyme classes. It involves using small molecular probes that can attach—for example, in a cell culture or even in a live animal—to all of the active enzymes in a given family of enzymes. When equipped with fluorescent beacons or other molecular tags, these probes can be used to map the sites in cells where enzymes of interest are active, isolate unknown enzymes for further study and discover potential drug compounds that work by inhibiting the enzymes’ activity.
A large share of existing drugs, from aspirin to cancer drugs, work by inhibiting enzyme activity.
“Cancers and other common human diseases are often driven by the abnormal overexpression of certain enzymes, which has led the pharmaceutical industry to focus to a great extent on drugs that can inhibit these enzymes,” says study co-first author Bernard Kok, PhD, a research associate in the Saez lab. “It also has been conceptually easier to inhibit overactive enzymes than to understand and reverse a loss of enzyme activity.”
For this project, however, the researchers developed an ABPP-based method that can be used to find not only compounds that inhibit enzyme activity but also those that enhance enzyme activity—enzyme activators. The method involves tagging enzymes of interest with fluorescent beacons that show one type of change when enzyme activity is reduced, and another type of change when it is increased.
Investigating a mysterious enzyme implicated in metabolism
Their initial enzyme of interest, called LYPLAL1, has—like thousands of other human enzymes—a largely unknown role in biology. However, genetic association studies have linked multiple mutations and DNA variants in the vicinity of LYPLAL1’s gene to metabolic disorders and traits such as type 2 diabetes, blood cholesterol levels, and fatty liver disease. In essence, scientists have not known whether these DNA variations alter the risks of metabolic disorders by enhancing the enzyme’s activity, or by inhibiting it.
Using their ABPP-based test, the scientists screened a “library” of 16,000 chemical compounds to see if any could activate LYPLAL1, and to their surprise found many. Of these, they optimized a screening lead from the library, whose structure was found to be wrong and was corrected, and ultimately developed a particularly potent and selective activator they call PAL-12. They then tested PAL-12 against a selective inhibitor of LYPLAL1, which had been developed by researchers at Pfizer in their own effort to explore LYPLAL1 as a potential drug target. Saez and colleagues found that while their new activator markedly improved insulin sensitivity and other signs in a mouse model of obesity-driven diabetes, adding Pfizer’s inhibitor compound reversed these beneficial effects.
The Scripps Research investigators now are continuing to evaluate PAL-12 as a potential drug for obesity and/or diabetes, and are using it as a probe for studying the still-mysterious role of LYPLAL1 in metabolism. They are also expanding their activator-finding technique to use with other types of enzymes.
“One possibility we’re considering is that PAL-12, and perhaps many of the enzyme activators we’ll discover in the future, mimic the actions of natural, endogenous enzyme-regulating compounds,” says Boger. “In that sense, conceivably, the action of such activators could be relatively safe.”
“Discovery of small-molecule enzyme activators by activity-based protein profiling” was authored by Bernard Kok , co-first author Srijana Ghimire, Woojoo Kim, Shreyosree Chatterjee, Tyler Johns, Seiya Kitamura, Jerome Eberhardt, Daisuke Ogasawara, Janice Xu, Ara Sukiasyan, Sean Kim, Cristina Godio, Julia Bittencourt, Michael Cameron, Andrea Galmozzi, Stefano Forli, Dennis Wolan, Benjamin Cravatt, Dale Boger, and Enrique Saez, all of Scripps Research.
Funding was provided by the National Institutes of Health (DA015648, GM069832, DK099810, and DK114785).
For more information, contact press@scripps.edu