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Targeted protein degradation represents a groundbreaking approach to addressing previously “undruggable” targets in drug discovery. Among the most promising advancements in this field are proteolysis-targeting chimeras (PROTACs), which leverage the body’s natural protein degradation pathways to eliminate disease-causing proteins. However, optimizing PROTAC design requires a deep understanding of their mechanism of action, particularly the formation of the ternary complex.
To explore how PROTACs are transforming drug discovery, Technology Networks spoke with Robyn Stoller, business development manager at Cytiva. Robyn discussed the advantages of PROTACS over conventional therapeutics, the importance of studying ternary complex formation and how surface plasmon resonance (SPR) technology is enabling more precise characterization of these molecules.
Anna MacDonald (AM):
Senior Science Editor
Technology Networks
Anna is a senior science editor at Technology Networks. She holds a first-class honors degree in biological sciences from the University of East Anglia. Before joining Technology Networks she helped organize scientific conferences.
What advantages do PROTACs offer over traditional small-molecule drugs, and how could they help to revolutionize drug discovery for previously “undruggable” targets?
Business Development Manager
Cytiva
Robyn Stoller is a business development manager supporting Biacore and Imaging at Cytiva, serving both the United States and Canada. She was trained at the University of Minnesota and has been working with biophysical techniques for 15 years.
Traditional small-molecule drugs generally modulate function by directly binding an active pocket on the target. Not every target has an amenable active pocket, and this limits the number of potential targets for therapeutic development.
PROTACs and other targeted protein degradation molecules modulate function of the target by bringing the target into close proximity with another molecule, commonly an E3 ligase, which will activate natural degradation pathways. This strategy does not require an active pocket, therefore many more targets are eligible for potential therapeutic development.
Senior Science Editor
Technology Networks
Anna is a senior science editor at Technology Networks. She holds a first-class honors degree in biological sciences from the University of East Anglia. Before joining Technology Networks she helped organize scientific conferences.
How does the ternary complex contribute to the mechanism of action in PROTACs, and why is it important to study?
RS:
Business Development Manager
Cytiva
Robyn Stoller is a business development manager supporting Biacore and Imaging at Cytiva, serving both the United States and Canada. She was trained at the University of Minnesota and has been working with biophysical techniques for 15 years.
Formation of a ternary complex is required in order to degrade the target of interest. Binding of the PROTAC to the target alone does not produce this result, rather, it is the proximity of the target and a specific E3 ligase that activates the cellular degradation machinery. Defining the cooperativity of the system requires accurate binary and ternary affinity measurements, and this, in turn, can provide valuable information on the efficiency of degradation.
AM:
Senior Science Editor
Technology Networks
Anna is a senior science editor at Technology Networks. She holds a first-class honors degree in biological sciences from the University of East Anglia. Before joining Technology Networks she helped organize scientific conferences.
What are the main limitations in the traditional biophysical characterization of PROTACs, and how can SPR technology address them?
RS:
Business Development Manager
Cytiva
Robyn Stoller is a business development manager supporting Biacore and Imaging at Cytiva, serving both the United States and Canada. She was trained at the University of Minnesota and has been working with biophysical techniques for 15 years.
Today a variety of competition-based assays are used, including fluorescence polarization (FP), time-resolved fluorescence energy transfer (TR-FRET) and AlphaScreen/AlphaLISA technologies. However, these techniques can’t measure certain important biophysical parameters, such as the kinetic rate constants of complex formation.
SPR technology measures a real-time binding signal, which enables measurement of accurate kinetic rate constants without the need for fluorescent or enzymatic labels on the molecules being studied. These kinetic rate constants can be compared among candidate PROTAC molecules to select and optimize for precisely the behavior that will improve ternary complex formation and lead to more efficient degradation.
Another key benefit of modern Biacore™ instruments specifically, is the ability to study many combinations of molecules within the same assay using advanced injection modes like ABA. These injection modes allow precise control over all molecules of the complex via sequential injections, dramatically reducing both sample consumption and other signal artifacts that would otherwise complicate ternary complex measurements.
Senior Science Editor
Technology Networks
Anna is a senior science editor at Technology Networks. She holds a first-class honors degree in biological sciences from the University of East Anglia. Before joining Technology Networks she helped organize scientific conferences.
Can you share examples of SPR being effectively used to characterize PROTACs? What insights were gained from these studies?
RS:
Business Development Manager
Cytiva
Robyn Stoller is a business development manager supporting Biacore and Imaging at Cytiva, serving both the United States and Canada. She was trained at the University of Minnesota and has been working with biophysical techniques for 15 years.
There has been excellent work published by Alessio Ciulli’s team at the Centre for Targeted Protein Degradation, Dundee, UK. In one study, the team used SPR assays extensively to investigate ternary complex formation and stability, showing that improved kinetic rate constants measured via SPR correlate to rapid initial degradation of the target in a cellular environment.
The team at Arvinas has also published outstanding work detailing their use of SPR to optimize PROTAC design, evaluating both binary and ternary affinity of candidate molecules when characterizing a relatively recently classified E3 ligase called KLHDC2.
Senior Science Editor
Technology Networks
Anna is a senior science editor at Technology Networks. She holds a first-class honors degree in biological sciences from the University of East Anglia. Before joining Technology Networks she helped organize scientific conferences.
What advancements do you anticipate in SPR technology that could further enhance its application in PROTAC research and development?
RS:
Business Development Manager
Cytiva
Robyn Stoller is a business development manager supporting Biacore and Imaging at Cytiva, serving both the United States and Canada. She was trained at the University of Minnesota and has been working with biophysical techniques for 15 years.
Our newest instrument, Biacore 1 Series, introduced an advanced injection feature called Poly, which allows sequential injection of up to five separate molecules. Using this feature, researchers can design binding assays containing many components. This enables studies using challenging targets, as well as studying the precise complex formation mechanism like never before.
