As one of its first efforts, IPI launched a campaign to generate antibodies to a group of related proteins that play an essential role in the body’s immune system. Ironically, that effort promises to first pay off for the neuroscience community.
There is a saying: “nature is a tinkerer and not an inventor.” Indeed, cells borrow existing modules of protein sequences, called domains, to create new structures, rather than reinventing them from scratch. For this reason, similar domains can be found in proteins with different functions.
Understanding this dynamic, the IPI team came up with a strategy: it would first create antigens based on the structures of cell surface receptors that share at least one domain. The team chose a superfamily of proteins that contained at least one immunoglobulin (Ig) domain. Immunoglobulins, also known as antibodies, latch onto foreign substances, such as viruses, and help destroy them. The Ig domains are very sturdy and can function well, even as their DNA sequences vary. In fact, changing their sequences, even slightly, allows Igs to latch onto many different proteins. By choosing targets with Ig domains as a first run of the IPI pipeline, the IPI team could test the high throughput processes for protein production and also yield important information about the immunoglobulin receptors themselves.
Before the COVID outbreak, the IPI Protein Group set to work selecting and producing specific targets in the IgSF family to scale. The team then handed the targets, called antigens, to the Molecular Interaction Group, which pushed them through the IPI antibody discovery platform. The goal was to screen for antibodies that specifically and tightly bound to each antigen and to unveil the identity of the best “binders” through the sequencing of antibody DNA.
In the end, IPI scientists produced 2,304 unique synthetic recombinant antibodies. Returning from a pandemic-induced shut-down, the Protein Group then fully characterized them for their binding ability, specificity and behavior.
The results are astonishing: more than 96% of the IGSF antigens had at least one successful binder. An array of tests — including immunoblotting, ELISA and cell-display — confirmed that the antibodies did interact with their respective antigen targets and validated their high quality.
The next step is to get these antibodies into the hands of researchers for validation in assays outside IPI walls. This is the basis for IPI’s Neurobiology Validation Campaign, which aims to generate a robust collection of high quality, well-characterized synthetic antibodies that target neuronal cell surface receptors. Many of these receptors are highly conserved in animals — the same mice and rabbits that traditionally are used to create antibodies for research and therapeutics. Thus, the animal route to antibody production does not work well, if at all, for these targets.
By generating high-quality antibodies using yeast, IPI can address a huge unmet need in the fields of neurobiology and development. The team has produced antibodies to targets such as DCC, L1CAM and the ROBO and UNC5 families, and is enlisting members of the neurobiology community to join the effort, to great success.
“The IgSF campaign is filling an important niche,” says Rob Meijers, head of biological discovery at IPI. “We discovered antibodies for many targets that to date have no good antibodies available. IPI has created a gold mine of tools that we anticipate researchers can use to accelerate their discoveries.”