A Generic Approach for Targeting Protein-Protein Interactions Using Multi-functional Piperazines

Protein-protein interactions (PPIs) play a pivotal role in most biological
processes and misfunction in disease. PPIs have been considered challenging
targets for modulation using small molecule ligands, due to their large,
comparatively flat interfaces. Indeed, small molecule PPI inhibitors represent only
a tiny fraction of current molecular therapeutics. α-Helix mediated PPIs are of
particular interest given they have been observed in around 60% of PPIs and are
potentially amenable to a common inhibitor strategy. This possible characteristic
of PPIs could be advantageous when developing new tools or compounds for
targeting these interactions. Example targets include p53/hDM2 and NOXAB/
MCL-1, which are important targets in oncology.
A computational workflow (carried out by collaborators) was used to identify
a number of generic small molecule scaffolds with the potential to be functionalised
to target different α-helix mediated PPIs. Guided by the computational results, two
libraries of bi-decorated piperazines were designed and subsequently synthesised
by the author. Synthesis of decorated diazepanes was also explored but was not
found to be suitable for efficient library synthesis. The synthesised piperazines
were evaluated against p53/hDM2 and NOXA-B/MCL-1 using a combination of
biophysical techniques including 15N-1H HSQC NMR spectroscopy and
fluorescence anisotropy. The results from this screening, alongside further
computational analysis, were used in the design of a more focussed library of tridecorated
piperazines. These were synthesised and evaluated against the same
targets in a similar way. Through this work, four compounds were identified with
the potential for further development to low μM inhibitors, or at least a starting point
for potential drug compound design.
Overall, this integrated approach offers access towards discovery of novel,
effective, low molecular weight PPI inhibitors, through combining several
interdisciplinary work packages: computationally informed rational design;
chemical synthesis of libraries of decorated small molecules; and biophysical
screening using orthogonal assays.