New tool makes quick health, environmental monitoring possible

University of Wisconsin–Madison biochemists have developed a new, efficient method that may give first responders, environmental monitoring groups, or even you, the ability to quickly detect harmful and health-relevant substances in our bodies and environments.

Small molecules that interact with proteins can initiate, enhance, and inhibit vital biological processes. Some small molecules, like vitamins or hormones, are linked to our health. Others, like opioids, are toxic, and knowing whether they’re in a patient’s system can be essential for emergency medical treatment. The presence of certain small molecules can even indicate the presence of pollutants and environmental toxins, such as metals in our drinking water.

Detecting small molecules in a sample often involves expensive and time-consuming lab tests. In emergencies like a drug overdose, any delay can defer life-saving treatment. An on-site test kit that quickly and inexpensively identifies the presence of specific small molecules could improve first-response and emergency medicine, at-home health monitoring, and detection of environmental toxins.

“Small molecules are pervasive in all of biology,” says Vatsan Raman, a UW–Madison biochemistry professor. “Nature is really good at creating proteins that bind to small molecules with exquisite specificity. The question for us was, can we redesign nature’s proteins to bind to whatever small molecule we are interested in detecting.”

Since small molecules can interact with certain proteins, a well-designed protein could initiate a biochemical alert system in the presence of a specific molecule, such as a narcotic or metabolite (small molecules produced when our bodies break down bigger substances like food).

Raman was interested in designing such a system. But, while some proteins naturally evolved to interact with one or more small molecules, engineering a protein to interact with a specific small molecule involves testing tens of thousands of possibilities to find the best fit. This process can be cost- and time-prohibitive.

To expedite this process, researchers in Raman’s lab developed Sensor-seq, a method (known as an assay) that screens tens of thousands of protein mutations simultaneously to identify which ones bind to a molecule of interest. The proteins can be further modified to act as a switch, flipping on a visual signal (for example, a green glow) that a small molecule is present in a sample and activating a kind of biochemical alert system.

The researchers tested Sensor-seq with several small molecules of interest, including naltrexone, a drug that mimics opioids. Out of tens of thousands of possible protein mutations they designed, they identified which ones sensed naltrexone. Then, they created a biosensor that made the protein glow green when it interacts with naltrexone.

Their method worked: Naltrexone induced a green glow visible to the naked eye. The researchers’ findings were published in Nature Communications.

Now, the researchers are building computer models that will narrow down possible protein matches for other small molecules relevant to human and environmental health.

“What we learn from these large datasets will make our process more effective and efficient. As we gather more data, and refine the models, we will get better and better at building biosensors.” Raman says. “My goal is that if you tell me what molecule you want to sense, we should be able to give you a protein biosensor for that molecule in just a couple of weeks.”

The research’s potential includes applications for the military. The Raman Lab’s work was done in collaboration with the Air Force Research Laboratory, with support from the U.S. Army.

“We’re excited about these results from Professor Raman and his research team, supported under an initial basic research grant from the U.S Army Combat Capabilities Development Command Army Research Laboratory and a subsequent Army Small Business Technology Transfer program contract focused on development of a commercial platform for rapid biosensor discovery,” said Stephanie McElhinny, program manager in the Army Research Office, DEVCOM ARL. “The DEVCOM Chemical Biological Center is exploring the potential of the Sensor-seq biosensor discovery approach to rapidly develop biosensors to protect warfighters from chemical and biological threats, drinking water contaminants, and emerging toxins.”

Raman, who has received a provisional patent for this work, sees broad applications for the technology his lab developed, including field tests that identify pollutants in local water sources in minutes and at-home tests that track health indicators.

“We started with naltrexone because there’s a strong need for low-cost ways to detect opioid use in rural communities with limited access to health care,” explains Raman. “But, in principle, we can create a biosensor for any small molecule. That is exciting because there are so many commercial applications for this with the potential to transform at-home and field-based health care and environmental health.”

This research was supported by United States Army Research Office Grants W911NF20C0005 and W911NF1710043.