Making use of a combination of advanced chemical, biological and artificial intelligence advances, scientists at the University of Pittsburgh School of Medicine have developed an unusually fast and efficient way to detect tiny particles with potential great for development to therapeutic treatment against deadly diseases.
The approach, published today in the journal Cellular systems, this is the same process the Pitt team would use to extract tiny particles of SARS-CoV-2 from llamas, which may be the inhaled COVID-19 treatment for humans. This approach has the potential to identify a number of robust nanobodies that target different components of a pathogen – inhibiting changes.
Most vaccines and anti-SARS-CoV-2 treatments target the spike protein, but if that part of the virus mutates, which we know it does, it may not. these vaccines and treatments are so effective. Our approach is an effective way to develop therapeutic cocktails that contain multiple nanobodies that can launch a multifaceted attack to neutralize the pathogen. “
Yi Shi, Ph.D., Lead Author, Associate Professor of Cell Biology, University of Pittsburgh
Shi and his team are particularly on the lookout for nanobodies – which are small, unique particles of antibodies made by llamas and other camelids. Nanobodies are particularly attractive for development to therapeutic medicine because they are easy to manufacture and bioengineer. In addition, they exhibit high stability and flexibility, and can be aerosolized and ingested, rather than administered through intravenous infiltration, like traditional antibodies.
By vaccinating a llama with a piece of a pathogen, the animal’s immune system releases an abundance of mature nanobodies in about two months. Then it’s a matter of figuring out which nanobodies are best at neutralizing the pathogen – and most promising for development into cures for humans.
That’s where Shi’s “high-throughput proteomics strategy” comes in handy.
“Using this new method, in a few days we usually identify tens of thousands of unique, potent nanobodies from the vaccine llama serum and study them for specific features, such as where they bind to the patch, “Shi said.” Prior to this approach, it has been very challenging to identify high-affinity nanobodies. “
After drawing a llama blood sample that is rich in mature nanobodies, the researchers separate those nanobodies that specifically bind to the target of interest on the pathogen. The nanobodies are then broken down to release tiny “fingerprint” peptides that are unique to each nanobody. These fingerprint peptides are placed in a mass spectrometer, which is a device that measures their mass. By knowing their mass, the scientists can discover their amino acid order – the building blocks of proteins that determine the structure of the nanobody. Then, from the amino acids, the researchers can work back to DNA – the guide to building more nanobodies.
At the same time, the amino acid series is uploaded to a computer by artificial intelligence software. By quickly filtering through data mountains, the program “learns” which nanobodies bind the tightest to the pathogen and where on the pathogen they bind. As for most of the currently available COVID-19 treatments, this is the spike protein, but recently it has become apparent that some sites on the spike are prone to mutations which changes its shape and allows an antibody to “escape.” Shi’s approach can be to opt for binding sites on the spike that are evolving sustainably, and therefore less likely to allow new changes to slip by.
Finally, the guidelines for building the most powerful and diverse nanobodies can be applied to batches of bacterial cells, which will act as small factories, churning out orders of magnitude larger nanobodies compared to human cells. ‘needed to produce traditional antibodies. Bacterial cells double in 10 minutes, effectively doubling the nanobodies with them, but human cells take 24 hours to do the same.
“This greatly reduces the cost of performing these treatments,” Shi said.
Shi and his team believe their technology could be beneficial for more than just the development of anti-COVID-19 therapy – or even the next pandemic.
“The potential uses of nanobodies are particularly strong and unique that can be identified quickly and cheaply,” Shi said. “We are studying their use in the treatment of cancer and neurodegenerative diseases. Our method could be used even in personalized medicine, developing specific remedies for mutated superbugs that are not all another antibiotic has failed. “