Due to their critical role in so many cellular functions, proteins that span the cell membrane are the target of more than half of all FDA-approved drugs. Some of these transmembrane proteins are single-pass, meaning they cross the membrane only once, while others are more complex, multipass proteins, meaning they cross the membrane in at least two places. Drugs targeting the latter are primarily small molecule inhibitors, named for their size relative to antibodies and other large proteins.

At the same time, antibodies—proteins in the blood that bind and neutralize pathogens—are the fastest-growing class of therapeutics, popular among cancer researchers for their highly specific binding affinity, which makes them less toxic than other drugs. As cancer therapies, antibodies bind to proteins found on the tumor cell surface, such as the epidermal growth factor receptor, either blocking the protein or “flagging” the cell for immune cell destruction.   

Currently, however, there is limited overlap between these two drug classes: multipass membrane proteins are mostly targeted by small molecules, while cancer antibodies mostly target single-pass proteins. The search for antibodies that can target a wider range of membrane proteins is therefore gaining momentum, as they hold the promise of safer and more effective targeted therapies.

Damon Runyon-Rachleff Innovator Jamie B. Spangler, PhD, and her colleagues at Johns Hopkins University are among those on the hunt. The conventional way of discovering new antibody drugs is by testing catalogs of antibodies against bioengineered versions of the target protein and seeing what binds. But complex transmembrane proteins are difficult to bioengineer. To overcome this challenge, Dr. Spangler’s team improved upon a whole-cell screening technique, testing antibodies against target proteins in their native environment.

Using this strategy, the team was able to discover antibodies against four multipass protein targets, including one with such a limited exposed surface area that the researchers were surprised the antibody could find a site to bind. For several of these proteins, small molecule inhibitors are available, but as discussed above, antibody therapies offer distinct advantages. The team’s findings also illustrate the potential of their method to advance the discovery of new antibodies for tumor proteins, both single- and multipass, beyond those highlighted by this study.

This research was published in Cell Reports Methods.