The Importance of Protein Science in Drug Discovery

Medicines today don’t work for everyone. 

Only between 1 in 25, and 1 in 4of the people who take the top 10 highest-grossing medications in the US say their medication helps them. 

Improving this statistic and moving away from ‘imprecision medicine’ will rely on developing our understanding of the building blocks behind cell function, and malfunction – proteins.

With the advent of AI and new novel therapeutic techniques, protein science is on the brink of transforming drug discovery and accelerating new, better outcomes for patients through the medtech, biotechnology and pharmaceutical sectors.

In this article, I’ll explore the impact of protein science in drug discovery in more detail, provide guidance on what employers are looking for in protein scientists today, and help you make the next step in your career.

Read on to find out:

• What is proteomics?
• How protein scientists influence drug discovery
• Key skills of protein scientists in drug discovery
•  What the future holds for protein scientists in drug discovery

What is proteomics?

Let’s start by defining a proteome. 

A proteome is a set of proteins that is expressed at a certain time, in certain conditions. 

Proteomics is the study of these proteomes in an organism. 

Proteomics involves analysing and measuring the expression of proteins at different levels to understand its effects on the cell, tissue, organ, and overall organism. 

Proteomics helps scientists identify new drug targets, and understand the networks that proteomes create to develop more effective medications for patients. 

The three types of proteomics are:

1. Expression proteomics – the study of protein expression to find disease-specific proteins, new proteins, and patterns of protein expression in different cells.
2. Structural proteomics – the study of the 3D structure of proteins across all protein interactions including membranes, cell organelles and ribosomes.
3. Functional proteomics – the study of the functions and mechanisms in the cell that affect interactions with other proteins to understand the biological role of a protein and clarify cellular signalling pathways.

How protein scientists influence drug discovery

The drug discovery process typically begins by identifying a druggable target – of which in most cases is a protein. This protein is then analysed in detail through a high-throughput screening to ensure that the target is worth investigating further. 

Proteomics creates the foundation behind the drug discovery process by exploring the capabilities of existing proteins and finding new proteins that could act as druggable targets. 

By creating an essential map of the vast network of protein interactions that occur throughout the human body, protein scientists can also reveal where drug targets are expressed to improve accuracy in drug development. The study of this protein-protein interaction network (PPI) provides drug developers with an understanding of the mechanisms behind a disease, alongside how medications affect treatment.

Structure-based Drug Discovery (SSD) is another area of focus for protein scientists in the early stages of drug development. SSD involves understanding the structure of protein with a tool compound to develop new chemical hypotheses and modifications to improve inhibitor affinity and consequently, drug efficacy.

Key skills of protein scientists in drug discovery

The skills required of protein scientists can in some cases, be transferable across different scientific disciplines. For example, if you’re experienced in genomics and DNA purification, you’re equipped to handle protein purification as the methods are mirrored. 

To be competitive in today’s job market, highlighting your technical skills and experience across proteomics and beyond can help you stand out as a candidate to employers. 

Some key skills of a protein scientist in drug discovery include:

• Cloning
• Expression in E.Coli
• Protein purification (using AKTA for example)
• High-performance liquid chromatography (HPLC)
• Liquid chromatography-mass spectrometry (LC-MS)
• Mass spectrometry
•  Western blotting

What does the future hold for protein scientists in drug discovery

I mentioned in the introduction that drug discovery is on the brink of transformation because of new advancements in protein science.

Here are three key innovative areas driving this new future today – 

1. AI and machine learning algorithms

Machine learning and AI algorithms are empowering protein scientists and researchers to harness the massive amounts of data produced in analysis, to drive biological understandings and more efficient outcomes.


AI tools including machine learning, are rapidly becoming central to finding new, and better protein biomarkers faster. 


What’s more, once those biomarkers have been found, machine learning can be used to analyse proteomic data into easy to interpret biomarker panels that diagnose and report on the efficacy of the drug targets in treatment.


Outside of biomarker discovery and research, machine learning is playing a key role in drug development today by predicting experimental peptide measurements from amino acid sequences to improve the quality and reliability of workflows. In one immunopeptidome’s dataset, using AI techniques resulted in a 50% increase in the number of identified peptides compared to traditional methods.

2. Precision medicine

Although precision medicine is rooted in tailoring medicine to suit genetics, the reality of creating personalised medicines needs to consider the full complexity of cellular physiology.

Proteomics enables this full analysis, as the study itself is dedicated to the continuous analysis of the ever-changing proteome as it reacts to different stimuli. 

The advancements in high throughput mass spectrometry in proteomics have created incredible databases of the human proteome. 

These databases are beginning to lay the foundations for precision medicine in practice. In the near future, doctors could be equipped with mass spectral analysis of patient proteomes to compare with the database average (or even eventually, the patient’s own healthy archives records) to improve diagnostic accuracy, reduce time and costs, and ensure that the best possible medications are prescribed on a personal basis. 

3. Targeted protein degradation

Targeted protein degradation, or TPD, is a new therapeutic modality that could overhaul disease-causing proteins that have historically been challenging or near impossible to target with traditional small-molecule medications. 

After over 20 years of research, TPD has moved from academia to industry, where organisations across the world have announced programmes in preclinical and early clinical development across a range of fields, including cancer treatment.

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