Peptide Antigen: the Successful Strategy of "Less is More"

The Unique Value and Challenges of Peptide Antigens in Antibody Discovery

Choosing the right antigen is crucial in antibody discovery. The method of using peptides as antigens has been around for over 60 years. With technological advancements, we now have more novel avenues to choose from, such as recombinant proteins, engineered cells, and DNA encoding proteins, all of which can display a variety of epitopes or potential antibody recognition sites. Compared to these newer forms of antigens, peptides may be slightly lacking in epitope coverage, as they cannot display longer or full parts of the target protein as comprehensively as other antigens. Though peptides are a basic route for antibody discovery, their diversity seems to still have limitations.

 

1. The Benefits of Using Peptides as Antigens

(1) Compared to other forms of antigens, peptides usually lack some immunodominant sites. (Immunodominant sites might mask the sites we are interested in)

(2) Peptides allow for precise targeting to specific positions or areas.

(3) Peptides can highlight a particular epitope. This epitope might show high similarity or significant differences in sequence across different species.

 

From a purely practical perspective, compared to other forms of antigens, the synthesis of peptides also has the advantages of being simple, fast, and inexpensive.

 

The Key to Designing the Right Peptides

Peptides have long been the preferred antigen for antibody development in immunohistochemistry and Western Blot applications. These types of assays are performed under denaturing conditions, so short linear peptides can generate high-quality antibodies suitable for these applications.

 

However, not all peptides are applicable in scenarios that require the recognition of natural folding structures. Especially for those with complex secondary structures or conformational epitopes composed of discontinuous (or remote) sequences, peptides face huge challenges. These sequences are tightly connected in the naturally folded target antigen, making the design and application of peptides particularly complex. To find antibodies that can be used as therapeutic antibodies or effectively applied in ELISA, flow cytometry, and blocking assays, we urgently need to design a peptide that can accurately mimic the structure of natural proteins.

 

In the design process, considerations need to be made for the known structure, predicted structure of the target antigen, and practical applications. To determine which peptide is most suitable, you can first use online databases (like UniProt) to compare with the target antigen, analyze cross-reactions between different species, and predict its secondary structure.

 

Additionally, 3D modeling software can be used to predict the secondary and tertiary structures of various peptide candidates and compare them with the structure of the natural protein. Such in-depth analysis is conducted because the length and amino acid sequence of the peptide have a significant impact on its secondary structure. In some cases, disulfide bonds can be constructed to mimic target structural features.

 

Peptides must have good water solubility and carry groups that can bind with carrier proteins. To ensure the solubility of the peptide, the designed peptide needs to contain a sufficient number of hydrophilic residues. Usually, we will bind the peptide with the carrier protein, avoiding the most immunogenic end of the peptide.