PPI Hotspot Targeting: Recent Approaches
Commentary on Protein-Protein and Protein-Peptide Interactions, peptidomimetics and related topics in drug discovery.

PPI Hotspot Targeting: Recent Approaches

Intensive investigation has been conducted in order to rationally identify the “hotspot” of PPI for a decade or even more. In spite of the presence of a myriad of PPI in human, estimated to be 130,0001) to 650,0002), targeting PPIs is has long been an “undruggable” field.

This issue originates from the difficulty in controlling and modulating the PPI of interest by a small molecule. Generally speaking, the contact area of a small molecule inhibitor is thought to be 300 to 1,000 Å2.3) However, most of the PPIs covers larger contact surface, which causes energetical difficulty in the development of small-molecule PPI inhibitors.4),5) That is the reason why hotspot is focused for long in order to drive a conformational change or block the crucial contact site by covering the relatively small surface region of the target protein.

The flexibility of protein-protein interfaces is the key of hotspot theory for PPI targeting strategy. PPIs are dynamic and Kd of the interaction is not always high as well.6) Small molecule-based targeting is probable by the discovery of the hotspot of the PPI of interest.

PPI hotspot identification is, as you can easily imagine, of no ease even with the X-ray or cryo-EM structure of the protein. The hot region of the protein surfaces has been explored by alanine-scanning7) and computational methodologies in structural biology8) and physical chemistry9) fields.

Owing to extensive interdisciplinary research, there has been so many key findings like the importance of the assembly of tryptophan, tyrosine or arginine residues to form a hotspot in, at least, selected PPIs.7) Recent research are generally focused on computational approaches in order for comprehensive interpretation of hotspot theory.

Computational methodologies are budding and visualization of the hotspot of PD-1 and PD-L1 was demonstrated in 2019 by the use of 3-dimensional scattered pair interactions energies (3D-SPIEs) in combination with FMO (Fragment-based Molecular Orbital).10)

It is worth noting that PPI hotspot database, PPI-HotSpotDB was released.11) This database is based on the protein mutation to disrupt PPI and limited information is available right now. But like PPI databases, hotspot databases are probably under development in different approaches and they provide you and us more easiness to target PPI by small molecules.
We are extensively constructing approaches for targeting the hotspot as well. If interested, please contact us and have a discussion to find a hit of your interest.


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