To help prevent and defend against antibiotic-resistant infections, two scientists—microbiologist Dr. Anna Konovalova and synthetic chemist Dr. Tian Qin—are developing new strategies to accelerate the development of bacterial vaccines. Their project aims to solve a critical bottleneck in infectious disease research: identifying surface-exposed proteins in gram-negative bacteria, which can cause deadly infections such as pneumonia and food poisoning.
“This project is a long-term dream of mine,” said Dr. Konovalova. “It addresses a really important need in infectious disease: how to identify good vaccine targets for bacteria. It’s a lot trickier than for viruses.”
Unlike viruses, which have relatively simple structures with clear vaccine targets, gram-negative bacteria have a complex outer membrane that makes them highly resistant to both antibiotics and the human immune system. This unique barrier has contributed to the CDC and WHO listing gram-negative bacteria as urgent public health threats. However, vaccines that protect against bacterial disease remain scarce because it is very difficult to pinpoint which proteins the vaccines should target.
Existing methods for identifying these proteins are costly, time-consuming and technically challenging. Many key surface-exposed proteins, particularly lipoproteins, cannot be predicted using bioinformatics alone, making experimental validation essential.
“A major goal of the project is to develop a cost-effective approach. It’s not impossible to find these proteins, but the amount of human labor and cost are so high that you cannot do it on a systematic basis. One famous example is the vaccine for the bacteria that causes meningitis. A pharmaceutical company developed a vaccine for it. But since they didn’t know what proteins were on the cell surface, it took many years of work and almost a billion dollars. That is inaccessible for routine applications,” said Dr. Konovalova.
To overcome these challenges, Dr. Konovalova and Dr. Qin are developing highly selective chemical probes designed to target proteins on the bacterial surface without penetrating deeper into the cell. Their approach leverages mass spectrometry workflows to map the topology of the outer membrane, distinguishing surface-exposed proteins from those embedded within the membrane. By enhancing sensitivity to low-abundance proteins, reducing false positives and enabling cost-effective multiplexing, their method could revolutionize bacterial vaccine development.
“This type of project requires an interdisciplinary approach. I’m a biologist. Tian with his organic chemistry expertise, who has developed so many different chemical probes for translational applications, was a perfect match,” said Dr. Konovalova. Dr. Qin agreed, “We create different versions of the compounds and generations of the probe to synthesize. We give that probe to Anna, and then, based on her results, we further modify the structure.”
The team is currently testing their probes in E. coli and Pseudomonas aeruginosa, two well-characterized bacteria that serve as proof-of-concept models. They aim to refine a list of surface-accessible proteins that can be used as a foundation for vaccine development and research for other gram-negative pathogens, including those flagged by global health organizations. Beyond vaccine development, their work could also inform predictive computational models for identifying bacterial surface proteins directly from genomic data.
Their work represents a vital step toward a replicable method for developing vaccines to protect against deadly bacterial infections. If successful, the method could facilitate the identification of vaccine targets and make bacterial vaccine development far more accessible by reducing the high cost and labor associated with current methods.
The WelchX pilot grant played a crucial role in supporting this high-risk, high-reward research, allowing the team to test their first-generation probe, develop an improved version, and bring on additional researchers. Dr. Konovalova and Dr. Qin also credited the WelchX retreat for fostering the kind of interdisciplinary collaboration needed to tackle such a complex challenge. Dr. Qin said, “This has been a wonderful experience. At WelchX, we had all these scientists sitting together, thinking about ideas that were totally new and creative, but also definitely a bit risky. It was my first time at WelchX; I had never been there before. After I came back, I recommended it to all my colleagues.”