Is my PROTAC cell-permeable?
Your PROTAC has to cross the cell membrane
to interact with the E3 ligase and the target
protein. But because of their high molecular
weight and polarity, PROTACs have relatively
low cellular permeability.
The good news is that you can design your
PROTAC to be more membrane permeable
by understanding and improving their
physicochemical properties. Specific assays
have been designed to help with this — like
Caco-2 cell permeability assays, competitive
E3 engagement assays, and chloroalkane
penetrating assays.
Does my PROTAC form a ternary complex?
Ternary complex formation is essential
for target ubiquitination and subsequent
degradation, making it perhaps the most
critical step of the protein degradation
pathway. So it's no surprise that its
optimization is a major focus of yours.
Several studies show that the PROTACs'
ability to degrade its target protein can be
predicted by the ternary binding affinity and
cooperativity. You can use a technology like
Spectral Shi to characterize ternary complex
formation, and get valuable feedback about
PROTAC development and rational lead
optimization.
If you are characterizing the ternary
complex formation, your assay conditions
must preserve the binary complex while
you're measuring the binding of the third
component. As a result, you have to choose a
bioanalytical method that allows for precise
control of the assay conditions and for
accurate quantification of both low binary
binding affinities and high ternary binding
affinities.
Overcome roadblocks
in your ternary complex
characterization
Having a method in place that
effectively evaluates ternary
interactions and cooperativity is
essential for understanding the
structure–activity relationship of
PROTACs.
Learn how Dianthus helps you
characterize ternary interactions.
