Epitope mapping services

High-resolution conformational epitope mapping with >95% success even for complex proteins and conformational epitopes.

How will epitope data help me?

A reliable method for epitope mapping gives you the ability to progress lead candidates based on mechanism of action and protect MAbs using stronger patents.
Epitopes Differentiate Mechanism of Action
Epitope Maps Strengthen Intellectual Property

How is your epitope mapping technology different?

Integral Molecular's proprietary Shotgun Mutagenesis technology is the only high-throughput technique that can reliably map conformational epitopes at single amino acid resolution.
 Conformational Epitopes High ResolutionComplex ProteinsEnergetic Hot-SpotsSpeed
Peptide Scanning
Epitope Binning
H/D Exchange
Shotgun Mutagenesis Epitope Mapping

"The epitope mapping that Integral Molecular has done has greatly supported both our mechanistic understanding and the intellectual property claims of our proprietary antibodies."

Why is this approach so successful?

Integral Molecular assesses antibody binding on target proteins directly within intact cells. Each individual residue is mutated using proprietary Shotgun Mutagenesis technology for high-throughput creation of mutants, allowing precise resolution of binding specificity.

Epitope mapping using Shotgun Mutagenesis technology:

  • Automated creation of hundreds to thousands of point mutations covering every residue in a target protein so epitopes can be mapped with single amino acid resolution.
  • Mutagenesis to alanine or any other desired residue(s).
  • Native expression of individual mutants in human cells, enabling mapping of conformational epitopes.
  • High-throughput testing of each mutant for expression, antibody reactivity, and function.
  • Epitope visualization on three-dimensional structures.
Contact us today to start your project >

What epitope mapping services do you offer?

Epitope mapping services are provided on a fee-for-service basis, and Integral Molecular provides access to all data in order to enable regulatory and intellectual property filings.

Epitope Mapping Services include:

  • Assay setup report with optimized conditions for screening customer’s MAbs.
  • Alanine-scan mutagenesis of the target protein.
  • MAb screening on the Ala-scan mutation array.
  • Final report showing:
    • 1. Graphical representation of the data.
    • 2. Identification of critical interacting residues.
    • 3. Epitope mapped onto the target protein structure (if available).

Custom Epitope Mapping Services

An Ala-scan mutation library is created for the protein target of interest and used to test binding of customer's MAbs/ligands by flow cytometry to identify epitope residues.

Contact us to discuss your project.

Epitope Mapping Services on Pre-Validated Targets

Integral Molecular offers a selection of pre-validated targets for epitope mapping services, including:

CXCR4 Infectious disease/Oncology
HER2 Oncology
RSVF Virology
Zika prM/E Virology

Please contact us for a full list of pre-validated targets.

Mapping Small Molecule Binding Sites

An Ala-scan mutation library is created for the protein target of interest. Small molecules are screened on the library using functional assays to identify amino acid residues that are critical for binding or function.

Epitope Mapping Publications

"Integral Molecular was able to identify critical binding residues for an antibody for which no mapping had been successfully done after years in development."

"Excellent team, excellent communication, results when promised, results with impact to drive decision making."


Frequently Asked Questions

1How does Integral Molecular perform their Epitope Mapping Services?
Our epitope mapping approach utilizes Shotgun Mutagenesis, a proprietary platform for high-throughput mutagenesis. Essentially, we take the sequence of your protein and synthesize variants that have each amino acid individually mutated to alanine (or serine if it is already alanine). Each of these variants, which encode the full-length protein with only a single alanine mutation, is then arrayed into individual wells of a 384-well plate and expressed in human cells. Using high-throughput flow cytometry we can then determine the binding of your antibody to each individual protein variant and control for defects in expression, trafficking and folding. Accordingly, this method identifies the amino acids critical for the binding of your antibody to the target protein. The ability to map antibody epitopes in the context of full-length protein using an alanine-scanning approach allows us to rapidly identify linear and conformational epitopes at an amino acid resolution with a 95% success rate.
2What are the benefits of Shotgun Mutagenesis Epitope Mapping compared to other methods such as peptide mapping or H/D exchange?
Shotgun Mutagenesis Epitope Mapping works by individually mutating each amino acid of the target protein in the context of the full-length protein, expressing these variants in human cells and measuring binding of your antibody to each variant. Using this method, both linear and conformational epitopes can be identified at amino acid resolution. This is in contrast to peptide mapping, which determines binding of an antibody to short peptides, independent of protein tertiary structure, precluding its use for mapping conformational epitopes. Compared to H/D exchange, Shotgun Mutagenesis Epitope Mapping does not require a soluble form of the target protein and relies on easily interpretable flow cytometry data, simplifying analysis and interpretation. Ultimately, Shotgun Mutagenesis Epitope Mapping is ideally suited to mapping antibody epitopes on any protein target including multipass membrane proteins such as GPCRs and ion channels, and proteins with complex folds such as immuno-oncology targets.
3How do you control for mutations that cause protein misfolds or expression and/or trafficking defects?
Control antibodies are used to validate that the mutated protein exhibits proper trafficking, expression, and folding. Typically, a commercially available reagent antibody, or a non-competing antibody generated by the customer against the same target will be used as a control. If no control antibodies exist for a given protein, an epitope-tag (FLAG, V5, HIS6, etc) can be added to the target protein and used to as a control for expression and trafficking.
4What are the deliverables of an Epitope Mapping project?
The first deliverable is an Assay Setup report, showing optimal high-throughput screening conditions for each antibody using a wild-type protein construct prior to initiation of mutagenesis. Upon completion of the project, a Final Report is compiled that includes a graphical representation of the data, identification of critical interacting residues, and the epitope mapped onto the target protein structure (if available). If required, Integral Molecular is happy to assist customers in preparing epitope mapping data for publication, presentation or patent/regulatory filings.
5What kinds of proteins can be tested?
Epitope mapping can be done on any protein that can be expressed in mammalian cells, including soluble proteins and conformationally complex proteins such as GPCRs, ion channels, transporters and viral envelope proteins.
6What is the typical turnaround time for an Epitope Mapping project?
Custom epitope mapping projects typically take 3-4 months. Please contact us if you have tight filing/regulatory deadlines.
7What is needed to start?
We require the protein sequence and 500 µg of each antibody that is being mapped.
8What kinds of assays can be used in Shotgun Mutagenesis?
Any cell-based assay that is adapted to microplate format can be used for Shotgun Mutagenesis. Prior projects have commonly included calcium-flux, viral infection, and flow-cytometry- based immunofluorescence assays.

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