PPI Fragment Library
Fragments able to mimic protein structural motifs and hot-spot residues
3 600 compounds
Protein-protein interactions regulate most aspects of life cycle thereof being the most attractive and perspective target for contemporary drug development. This field is still not well explored and there are no common rules for proteins involved in this type of interaction. Such intricate biological systems cannot be cost-efficiently tackled using conventional high-throughput screening methods and algorithms. However, fragment-based approach showed fruitful results in search of new PPI inhibitors. We created new library of PPI fragments with dedicated design that consists of systematical knowledge of common PPI inhibitors and selection by privileged structural motifs.
Recent researches in the field of PPI fragments revealed the requirement of higher molecular weight molecules compared to common fragments due to a larger contact surface area. Therefore “Rule of four” restriction were used to extract initial PPI fragments subset, as they are typically larger and more lipophilic . Additionally, machine-learning method (decision tree) with number of validated descriptors was used to refine the library.
The “hot-spots” concept has been applied, implying the use of “key” amino acid residues involved in PPIs. A significant number of the selected fragments contains groups/moieties which correspond to these hot-spots. Additionally, library was enriched with the molecules having alpha helix-like structure, able to mimic protein motifs. Also since hydrogen bonds often play a crucial role in PPIs the preference was set for the molecules bearing at least one H-bond donor (> 70 %) and one H-bond acceptor (100%).