Pertuzumab IgM (blue; shown as a monomer) can simultaneously bind to multiple extracellular domains of HER2 (represented in green and orange).

© Bioinformatics Institute (BII)

Finding the perfect fit

7 Jul 2020

A*STAR scientists aim to design better immunotherapies by simulating the binding of antibodies to their targets.

When a spacecraft docks at the International Space Station, it must ensure a perfect fit to prevent malfunction. Although on a much smaller scale, antibodies produced by our bodies against a foreign invader must also 'dock' perfectly on their target to elicit an effective immune response.

In recent years, scientists have co-opted the body’s natural defenses to fight cancer. Called immunotherapy, one example of it uses therapeutic monoclonal antibodies to find and destroy cancer cells.

“Monoclonal antibodies like pertuzumab and trastuzumab are widely used in targeted therapies against HER2-overexpressing breast cancer,” said co-corresponding author Peter Bond, a Senior Principal Investigator at A*STAR’s Bioinformatics Institute (BII).

Both pertuzumab and trastuzumab inhibit cellular signaling by targeting HER2, a cell-surface receptor upregulated in about 20 percent of breast cancers. Co-corresponding author Samuel Gan, a Principal Investigator at BII, also of the Experimental Drug Development Centre (EDDC) and p53 Lab, previously showed that although the trastuzumab IgG subtype bound to HER2 with higher affinity as compared to pertuzumab IgG, pertuzumab IgM conversely showed stronger binding as compared to trastuzumab IgM.

To explain their antibody binding data, the collaborative team used a combination of structural data and modeling to derive complete models of trastuzumab IgM and pertuzumab IgM. They also conducted multiscale modeling and simulations to predict molecular interactions with HER2.

Based on this work, they discovered a protruding surface of the HER2 protein that causes ‘steric clashes,’ or poor binding, with trastuzumab IgM. In contrast, pertuzumab IgM utilized all of its antigen-binding sites with HER2, which resulted in stronger binding.

In laboratory studies, the researchers validated their simulation data by showing that pertuzumab IgM inhibited the proliferation of HER2-positive breast cancer cells more effectively than trastuzumab IgM and pertuzumab IgG.

“There is a need for guidance to ensure maximum success in the rational design of IgM therapeutics,” explained Bond. “Our findings highlight the importance of studying complete antibody-antigen interactions at the molecular level for the evaluation of ‘designer antibody therapies’ that would deliver the most effective and cost-effective outcomes for patients.”

Moving forward, the team envisions that modeling and simulation will be incorporated into the design and selection of immunotherapies against metastatic cancer.

The A*STAR-affiliated researchers contributing to this research are from the Bioinformatics Institute (BII), p53 Laboratory (p53Lab) and the Experimental Drug Development Centre (EDDC).

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Samsudin, F., Yeo, J. Y., Gan, S. K. and Bond, P. J. Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab. Chemical Science 11(10), 2843-2854. (2020) | article

About the Researchers

Peter J. Bond

Senior Principal Investigator

Bioinformatics Institute
Peter J. Bond is a Senior Principal Investigator of the Multiscale Simulation, Modeling and Design (MSMD) group at the Bioinformatics Institute A*STAR. His group develops computational models to resolve the dynamics of biomolecules over multiple time and length scales, focusing particularly on mechanisms of infectious disease, the host immune response to bacterial and viral pathogens, and ultimately, therapeutic intervention strategies.

Samuel Gan

Principal Investigator

Bioinformatics Institute
Samuel Gan is a Principal Investigator at the Antibody and Product Development Lab of A*STAR’s Bioinformatics Institute (BII) & Experimental Drug Development Centre (EDDC) and adjunct Associate Professor at James Cook University Singapore (JCUS). Gan’s cross-disciplinary research interests include antibody engineering and virus drug resistance for sagacious drug design. He has been recognized as one of the “world’s most promising researchers” in the Interstellar Initiative by the New York Academy of Sciences and the Japan Agency for Medical Research and Development, as well as one of the 30 world class fusion innovators in the book “Innovation Through Fusion” by SP Jain School of Global Management.

This article was made for A*STAR Research by Wildtype Media Group