Institute for Protein Design

Computational Design of a pH Sensitive Antibody Binder

January 1, 2014

According to bio-industry reportsmonoclonal antibodies (mABs) have become the fastest growing segment of the pharmaceutical industry.   As of 2012, more than 30 FDA approved monoclonal antibody therapies generated annual sales of more than US$ 40 Billion.  Our immune systems have evolved to produce antibodies (e.g. Immunoglobulin G, aka IgG), globular proteins that circulate in the blood and serve as the first line of defense against pathogens ranging from viruses to parasites.

Designed pH-dependent Fc binder (blue) exploits protonation of Histidine-433 (orange) in the Fc portion Immunoglobulin G (IgG, light cyan surface)

Designed pH-dependent Fc binder (blue) exploits protonation of Histidine-433 (orange) in the Fc portion Immunoglobulin G (IgG, light cyan surface)

Now, researchers at the Institute for Protein Design (IPD) have used computational methods to generate a new protein to replace Protein A.  Published on-line at PNAS (Dec. 31, 2013), the paper entitled Computational design of a pH-sensitive IgG binding protein by Strauch, E. – M., Fleishman S. J., & Baker D., describes the design a new protein (called “Fc-Binder”) that is programed to bind to the constant portion of IgG (aka “Fc” region) at basic pH (8.0) but to release the IgG at slightly acidic pH (5.5).  Hence, by engineering protein-protein interfaces, IPD researchers have generated a new pH-dependent Fc binding protein which also happens to be very heat stable.

Significance

AvastinHerceptinLucentisRituxan and Xolair are all mABs which work by binding tightly to a known protein target which either interferes with the function of that target, or serves as tag to promote the eventual destruction of the target by the immune system.   Globally, mAb therapies such as these have estimated annual sales approaching US$ 60 Billion.

Protein A was originally discovered in the cell wall of the bacterium Staphylococcus aureus.   Protein A binds tightly to the constant (“Fc”) domain of IgG antibodies.   The captured antibodies are washed and then eluted from Protein A using a very acidic pH (3.0) buffer.  Unfortunately, not all antibodies can survive this low pH elution step.   Also Protein A affinity matrices are relatively expensive.

Protein–protein interactions are part of almost every biological process; hence, the ability to manipulate and design protein binding has widespread applications.  The Strauch et al. paper describes a new method to design pH-dependent protein-protein interfaces.   The new computationally designed Fc-Binder protein binds IgG at high pH but poorly at low pH.  This enables antibody purification without the harsh acidic low pH (3.0) conditions required by Protein A affinity purification methods.

What’s Next ?

The applications for this designed Fc-IgG binding protein start with its use as a novel reagent to cost effectively purify and detect IgG antibodies.  In the future it may be used to help improve the blood half-life and body distribution of other proteins by piggybacking on IgG antibodies.

More Information

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This article was authored by Dr. Lance Stewart, Sr. Director of Strategy (ljs5@uw.edu) at the Institute for Protein Design, with kind input and guidance from UW colleagues, and with the aid of web resources linked throughout this posting.  The Figure was prepared by Dr. Eva-Maria Struach.