The work was funded by a $1.7 million R35 grant from the National Institutes of Health (NIH) and drew on researchers from the Delaware Biotechnology Institute’s Bio-Imaging Center, supported in part by Delaware INBRE. 

A molecular switch

The protein at the center of the research is a bacterial enzyme called GdpP; it shows up in some pathogens that medicine worries about most, including MRSA. Parashar’s team caught GdpP in three different shapes, including the moment the enzyme flips from “on” to “off.” 

That flip matters because of a single small molecule – c-di-AMP, which acts as a chemical messenger that tells stressed cells to batten down the hatches to survive an antibiotic attack. 

“If you could shut GdpP down, the message would pile up,” explained Parashar. “The bacterium would lock itself into a kind of permanent panic and start to choke its own signal, making it far easier for an existing antibiotic to finish the job.” 

GdpP has been difficult to study because of its shape-shifting tendencies, which put it out of reach for traditional X-ray crystallography. Cryo-EM works differently by flash-freezing millions of copies of a protein in motion, providing snapshots of the molecule at work. 

“Without seeing the structure, it’s hard to predict how an enzyme functions, and without that understanding, we can’t design drugs that target only the parts we want to target,” said Parashar. “With three different snapshots of GdpP structural states, we can now see exactly where the switch sits. Once we can see the switch, we can start designing molecules that flip it.” 

Smarter antibiotics

Antibiotics have served us for nearly a century, with the first, penicillin, discovered in 1928. Twelve years later, MRSA first surfaced, before penicillin was even widely available. 

Parashar’s work points to a different strategy for staying ahead of superbugs – not a new antibiotic, but a companion drug that shuts down bacterial defenses, so the antibiotics we already have can do their job more effectively. 

"The next generation of antibiotics has to be more precise,” Parashar said.

Their structural biology work could also have applications beyond infectious disease. Batish points to cancer immunotherapy.

“We can use what we learned about GdpP to design small molecules that drive c-di-AMP levels up in a controlled way,” said Batish. “Paired with existing immunotherapies, this could help make ‘cold’ tumors visible to the immune system, so they go after them.” 

Training the next generation

Working in Parashar’s lab gave Leif Boddie, the undergraduate co-author on this research, his first look at how basic science feeds back into medicine. He aims to pursue a career as a physician in primary care or emergency medicine, where antibiotic-resistant infections are common. 

“Research is critical for physicians because you have to be able to read new studies and adapt patient care as medicine evolves,” Boddie said. “With antibiotic resistance on the rise, exploring new pathways to fight superbugs is how physicians will be better equipped to treat patients.” 

For Parashar, the paper is one step in building out structural biology at UD, with UD students at the bench. 

“We’re still bags of bacteria,” he said. “But we’re getting much better at understanding what’s inside the bag and where the next generation of drugs is going to come from.”