JOOMI AHN^1,2, JOHN R. ENGEN¹*
*Corresponding author
1. Northeastern University, Department of Chemistry & Chemical Biology, Boston, MA 02115, USA
2. Waters Corporation, Milford, MA 01757, USA

Abstract

Discovery and development of effective biologic drugs such as antibodies are challenging tasks. Understanding the antibody/antigen interaction and determining the epitope are important components of therapeutic antibody design and eventual commercialization. In recent years, various techniques have been described for epitope mapping, each with its own strengths and weaknesses. Here we highlight the mass spectrometry (MS) based approach of hydrogen/deuterium exchange (HDX) and describe its utility in epitope mapping. While there are many advantages to HDX MS for epitope mapping, there are also challenges. After a description of how a typical HDX MS epitope mapping experiment can be performed, some cautionary notes about the technique are presented.

INTRODUCTION

Monoclonal antibodies can be used to treat a variety of diseases including, for example, cancer, multiple sclerosis, and arthritis (reviewed in (1-3)). Recent breakthroughs in broadly neutralizing antibodies against the highly antigenically diverse viruses such as HIV, influenza, and hepatitis C (4, 5) aid the design of new vaccines and can drive drug development and targeting forward. However, discovery and development of effective biologic drugs such as monoclonal antibodies can be challenging tasks. Monoclonal antibodies specifically interact with antigens and can provide therapeutic benefit either by rendering the antigen incapable of binding to other substrates or by inactivating it (2, 3). Understanding the antibody:antigen binding interaction through a process of epitope mapping – locating and characterizing the site(s) of interaction on the antigen – is an important component in development of effective antibody therapeutics (6-8). Different kinds of antibodies might be developed against the same target, for example antibodies recognizing different epitopes on HIV-1 envelope proteins (9, 10) or influenza hemaglutinin (11). Each a ...