One of the biggest obstacles to obtaining a special and prized kind of antibody is that you need to know someone with a camel.
Fine. An alpaca would do as well.
But given that these animals aren’t exactly hanging around many research centers — and that they’re not so easy to work with — scientists have been developing synthetic ways of producing these antibodies.
“How many camels are there around?” said Tom Moran, the director of the Center for Therapeutic Antibody Development at Mount Sinai’s Icahn School of Medicine. “Yeah, I think that’s a real pain.”
On Monday, a team reported in the journal Nature Structural and Molecular Biology a new way of creating a synthetic antibody library, one that uses yeast cells in a vial, as opposed to llamas at a farm, and that is being made available for free to other researchers. Already, the platform’s creators have sent the vials — each of which can generate 500 million different versions of these antibodies — to about 40 other labs.
While antibodies are often studied as potential new medicines, the scientists behind the new platform said these particular antibodies are more immediately valuable as a basic research tool. They can lock onto shape-shifting proteins and trap them in a certain position like a molecular freeze ray, allowing researchers to study the structure of those proteins. By understanding a protein’s structure, drug designers can then figure out how to target them.
Camelids include llamas and alpacas, among other animals. The reason their antibodies are so important to science is the result of an evolutionary quirk. The animals produce conventional antibodies like humans and other mammals, but they also have a secondary set of antibodies that can bind to key proteins that standard antibodies cannot reach, likely because they are smaller. That means that the binding portions of these antibodies — which are called nanobodies — can sneak into the nooks and crannies of these key proteins and stabilize them.
Nanobodies are particularly helpful when it comes to studying membrane proteins — like those that sit on a cell’s surface — a major target for researchers seeking to develop new medications.
“We are using this library to basically probe how membrane proteins that are important in various diseases work,” said study author Dr. Aashish Manglik of the University of California, San Francisco.
Here’s why Manglik and other researchers have been searching for alternative ways of collecting nanobodies:
To get them from a llama, first you need to make enough of the protein you want to target. Then — and this is once you find that person with a llama — you need to immunize the animal with the protein. (This is normally done at certain farms or by contract research organizations.) Then you draw blood from the animal and hope that the protein generates an immune response and triggers the production of the desired antibodies. The whole process takes months even when it works, and can be costly.
For the new platform, a team steered by Manglik and Harvard Medical School’s Andrew Kruse created their collection of nanobodies with genes similar to the DNA that encodes the camelid nanobodies in nature. Each nanobody is displayed on the surface of a yeast cell, so that when a target protein, which can be linked to a fluorescent marker, is dropped into the pool of yeast cells, those with the matching nanobodies start to glow. Scientists can then isolate those yeast cells, sequence the DNA encoding those nanobodies, and grow a collection of them using bacterial cells.
The process using the synthetic immune system takes a couple of weeks.
“If you have a target protein, there’s at least one nanobody in that pool that will bind to it with reasonably affinity,” Kruse said. “It’s just a matter of finding it.”
Other scientists have developed their own libraries of synthetic nanobodies, but this is the first one to be made available for free to nonprofit researchers.
Companies have been pursuing camelid nanobodies as potential treatments — just last month, Sanofi bought nanobody-focused Ablynx for almost $5 billion — but these synthetic nanobodies are for now more beneficial for research purposes, experts said.
Mount Sinai’s Moran, who was not involved with developing the platform, said he was skeptical that the nanobodies would have strong enough affinity for their targets to be viable treatments. But he, too, said it could likely be a useful research tool. As part of their study, Kruse and Manglik validated their platform on two difficult-to-bind proteins called G-protein-coupled receptors.
“That’s not easy,” Moran said. “That’s saying something.”
About the Author Reprints
As an “expert” in nanobody, I am appalled by the claims in such article and even more appalled it was published on a Nature journal. It is really true, ignorance is a bliss.
Nanobody libraries are routinely built using phage display technology as nanobodies can be easily expressed in bacteria. This approach is cheaper, faster and allows to build libraries with far greater diversity.
One “true” fact is that laboratories using nanobodies usually generate “immune” libraries, i.e. after having immunized a camelid. That is mainly due to the fact that these kind of libraries allow for an easier selection of candidates with the best affinities, as compared to “naive” libraries like the one in the article. In addition, so far, nanobody technology is not widely in use, and the labs working with it have indeed access to the animals. Bottom line, to build naive nanobody libraries in bacteria/phages, which is the best and most efficient way, is a rather dull accomplishment if you are in the business of making combinatorial libraries. Making them in yeast is a pointless and inefficient complication.
And mark my words: Sanofi has just wasted almost 5 billions on a company that uses nanobody technology (the use of nanobody as therapeutics patent has just recently expired BTW), that in its fundamental form is not suitable for making human therapeutics.