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PPI Library
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Protein-Protein Interactions


ASINEX's Protein-Protein Interactions (PPI) Library
7000 compounds / 76 scaffolds

Exploring new areas of chemical space to find PPI inhibitors

For the Protein-Protein Interaction (PPI) group of targets, it has proved particularly challenging to find significantly active hit compounds [1,2]. To date screening efforts have so far been typified by very low hit rates. There has been very little data to allow for rational medchem design of PPI-disrupting compounds. The few hits and leads that have been found are relatively hydrophobic, rigid, often contain multiple aromatic residues and in general are not drug-like [3]. At Asinex we are committed to tackling the problem of designing compounds that are likely to produce higher valid hit rates when screened against pharmacologically relevant PPI targets, but at the same time lacking potential ADMET and solubility liabilities.

To address these issues, we have devised an algorithm based on combining highly hydrophilic more 3D-like scaffold cores, enriched in H-bond acceptors and donors, with PPI-specific lipophilic peripheries. The algorithm involves an extensive retro-synthetic analysis of known PPI hits from the literature and in-silico property filtering, including shape analysis. In total, 7000 unique final compounds have been produced, by a range of coupling reactions, utilizing 2-3 available synthetic handles of the 25 selected saturated scaffold cores. Despite having relatively high clogP values, all compounds have proved to be soluble at standard screening concentrations both in DMSO and PBS.

Protein-Protein Interactions (PPI) Library

By refining the design of the library, it has been possible to select the appropriate cores and periphery to create more focused compounds, with the increased likelihood of binding to a specific target. Thus, for example, we have identified several molecules that were predicted to bind well in the MDM2 pocket and were found active in the in-vitro screening assay afterwards.

Library specifics
Measured Solubility: 100% of compounds soluble in DMSO at 10 mM, and in PBS at 50 µM
Quality: min.purity of 90%, avg. of 95% (100% LC-MS, 15% NMR), stored as dry powder

ASINEX's PPI Compound Library is only available upon request, please contact us at:
Tel.: +7 (495) 780 34 15, +7 (495) 780 34 17
E-mail : or

1. Maria J. Vicent, Enrique Perez-Paya and Mar Orzaez, Discovery of inhibitors of protein-protein interactions from combinatorial libraries, Curr Top Med Chem. 2007;7(1):83-95.
2. Zinzalla G, Thurston D., Targeting protein-protein interactions for therapeutic intervention: a challenge for the future, Future Med Chem. 2009 Apr;1(1):65-93.
3. Olivier Sperandio et al., Rationalizing the chemical space of protein-protein interaction inhibitors, Drug Discovery Today Volume 15, Issues 5-6, March 2010, 220-229



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