Immuto Technology and Platform

What is Protein Footprinting, and How Can it Be Used in Drug Discovery?

Hetal Marble, PhD

Head of Commercial, Immuto Scientific

In the rapidly evolving field of drug discovery, researchers face the challenge of understanding the intricate interplay between proteins and their associated ligands. This knowledge is essential for developing effective, safe, and specific drug candidates.

But traditional methods can be slow, labor-intensive, and not always accurate. The stakes are high, as getting this crucial aspect of drug development wrong can lead to costly delays, failed clinical trials, or even harmful side effects in patients. 

This challenge begs for a more efficient, accurate, and cost-effective solution.

Protein footprinting 101

Enter protein footprinting, a technique that provides a pragmatic means of scrutinizing the interplay between proteins and their associated ligands, encompassing peptides, other proteins, or small molecule ligands.

The technique involves tagging the protein with a reactive group, and then subjecting it to a range of chemical or physical treatments. This, in turn, allows for the identification of protein regions that remain protected or altered by the ligand.

Here at Immuto Scientific, we've developed a novel method called PLIMB (Plasma-Induced Modification of Biomolecules) that utilizes hydroxyl radicals and mass spectrometry to provide structural data of a protein in its native solution and conformation. 

The advantages for drug discovery are huge, as PLIMB can analyze proteins in their native solution and conformation without the need for crystallization or mutations. The advantages for drug discovery are huge, as PLIMB can analyze proteins in their native solution and conformation without the need for crystallization or mutations. 

This translates into a range of benefits, including:

  • Low sample consumption
  • Precise temperature control
  • High throughput analysis
  • Compatibility with challenging protein targets. 

In short, PLIMB accelerates lead development, reduces costs, improves the chances of success in clinical trials, and strengthens IP claims, making it a valuable tool in drug discovery. Talk to us if you’re like to learn more.

In the rest of this guide, we briefly explore how, specifically, protein footprinting is being used in drug discovery.

Protein footprinting for drug discovery—a primer

Protein footprinting is a powerful tool in drug discovery, providing essential structural and interaction data that help researchers develop and optimize effective, safe, and specific drug candidates. The technique provides insights into protein structure, conformation, and interactions with other molecules, including drug candidates.

Below, we've taken each of its applications in drug discovery and briefly unpacked them.

1. Identifying a drug's binding site on a protein

Protein footprinting offers a practical approach to identifying a drug's binding site on a protein, the critical region responsible for mediating the drug's activity. Researchers can precisely pinpoint the binding site on the protein by determining which protein segments are protected or modified by the drug. This knowledge is indispensable in developing drugs with enhanced potency and specificity and in avoiding undesirable drug-protein interactions that could give rise to adverse effects.

2. Understanding the mechanism of drug action

Protein footprinting also plays a crucial role in understanding the mechanism of drug action. (The term 'mechanism of drug action' in this context refers to the intricate molecular interplay between a drug and its target protein that ultimately results in the desired therapeutic effect.) A careful examination of the changes in the protein upon drug binding gives researchers valuable insights into this mechanism. Such insights are vital for fine-tuning drug design and producing more potent and efficacious therapeutic agents.

3. Detecting drug side effects

Protein footprinting also serves as a helpful tool in detecting potential side effects of drugs. Some drugs may produce off-target effects, resulting in unintended changes in the activity or stability of proteins not meant to be targeted, compromising the drug's efficacy and making it less valuable. Researchers are now using protein footprinting to examine drug-protein interactions and identify any alterations in the target protein's activity or stability that may indicate the likelihood of side effects. This information can refine drug design or identify other proteins that may be affected by the drug.

4. Characterizing protein-ligand interactions

Protein footprinting also offers a valuable means of characterizing protein-ligand interactions, which can inform drug design and optimize the efficacy of existing drugs. The strength and specificity of protein-ligand interactions can be ascertained, enabling researchers to modify drugs to enhance their potency and selectivity, particularly when studying complex protein targets or designing drugs for specific populations. Using protein footprinting, researchers can fine-tune drug design to augment the overall therapeutic potential and effectiveness of the drug.

5. In vitro studies

In addition, protein footprinting allows for in vitro studies to be conducted, providing researchers with a high degree of experimental control and reduced complexity compared to in vivo studies. Moreover, the ability to study protein-ligand interactions in isolation and without interference from other proteins or factors in the body is an added benefit of in vitro studies.

The speed and simplicity of protein footprinting

Protein footprinting is a straightforward and relatively simple technique that requires commonly available equipment and reagents. This simplicity makes the technique accessible — positioning it as a promising method for drug discovery. 

The technique is also quite fast, producing actionable structural data within just a few weeks. This speed is of utmost importance in drug discovery programs, where time-to-market is crucial. The technique is not only fast but also user-friendly and reliable, generating usable structural data within a few weeks, which can save drug research programs both time and money. The method's flexibility makes it valuable in optimizing drug design and developing efficacious therapeutic agents.

The key takeaway

Protein footprinting is a powerful technique in drug discovery, providing crucial insights into protein structure, conformation, and interactions with drug candidates.

Immuto Scientific's novel method, PLIMB, uses hydroxyl radicals and mass spectrometry to analyze proteins in their native state, offering a range of benefits such as low sample consumption, precise temperature control, and high throughput analysis. 

By accelerating lead development, reducing costs, improving the chances of success in clinical trials, and strengthening IP claims, PLIMB is poised to become an invaluable tool in many areas of drug discovery.

Resources and next steps

Download our free white paperHydroxyl Radical Protein Footprinting: A Breakthrough Technique for Epitope Mapping—to see exactly how your development lifecycle stands to gain from the latest techniques.

Explore our technology to learn more about how we’re revolutionizing the drug discovery process and helping our partners tackle previously incurable diseases, and promoting a healthier world. Contact us to learn more and schedule a discovery session.


Hetal Marble, PhD

Head of Commercial, Immuto Scientific

Dr. Hetal Marble is a seasoned leader in the life science industry with experience in product management, companion diagnostics, biomarker development, business development, and strategic marketing. She holds a Ph.D. from Brown University and is the holder of two U.S. patents. Currently, she is the Chair of Diversity, Equity, and Inclusion for the Association for Molecular Pathology and a member of the 2022 Women in Bio cohort of Emerging Executives. She is also a contributing author for a book on precision medicine being published by the Mayo Clinic Press in October 2022.

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