Strategies to search and design stabilizers of protein–protein interactions: A feasibility study

Abstract

Since protein-protein interactions play a pivotal role in the communication on the molecular level in virtually every biological system and process, the search and design for modulators of such interactions is of utmost importance. In recent years many inhibitors for specific protein-protein interactions have been developed, however, in only a few cases, small and druglike molecules are able to interfere in the complex formation of proteins. On the other hand, there are several small molecules known to modulate protein-protein interactions by means of stabilizing an already assembled complex. To achieve this goal, a ligand is binding to a pocket, which is located rim-exposed at the interface of the interacting proteins, for example as the phytotoxin Fusicoccin, which stabilizes the interaction of plant H+-ATPase and 14-3-3 protein by nearly a factor of 100. To suggest alternative leads, we performed a virtual screening campaign to discover new molecules putatively stabilizing this complex. Furthermore, we screen a dataset of 198 transient recognition protein-protein complexes for cavities, which are located rim-exposed at their interfaces. We provide evidence for high similarity between such rim-exposed cavities and usual ligands accommodating active sites of enzymes. This analysis suggests that rim-exposed cavities at protein-protein interfaces are druggable binding sites. Therefore, the principle of stabilizing protein-protein interactions seems to be a promising alternative to the approach of the competitive inhibition of such interactions by small molecules.

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

“…Furthermore, we investigated several complexes from the bound collection [86] and noticed that next to the interface, druggable pockets are often present, suggesting that allosteric sites are likely to be present at many interfaces, definitively opening possibilities for the design of tomorrow's new drugs (i.e., antagonists and stabilizers). Our identification of potential allosteric sites is in agreement with the investigation of interfaces recently reported by Block et al [160] (see below).…”

“…+ ATPase-14-3-3 protein complex Recently Block et al [160] have been trying to design protein-protein stabilizers, arguing that it could be easier from a thermodynamic standpoint than finding antagonists. They also suggested that to find PPI antagonists via in silico approaches, it is necessary to identify a druggable pocket at the interface, a situation that is unlikely to occur.…”

“…From our initial investigation of experimental complexes, we, to the opposite, find that a druggable pocket is very often present at the interface although we also noticed cavities near the interface. In order to carry out a proof of concept study, Block et al [160] decided to search stabilizers of the interaction between plant H + -ATPase and 14-3-3 protein. This interaction is boosted by a fungal phytotoxin named Fusicoccin.…”

“…For instance, some authors suggest that inhibiting protein association is not really possible from a thermodynamic standpoint assuming that protein-protein interfaces should be mostly flat [160]. This is understandable but among the many proteinprotein interactions taking place in living organisms, certainly a sizable number will present a druggable pocket at the interface.…”

Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design

“…Protein-protein interactions between an enzyme and its substrate, between a catalytic domain and its regulatory domains, and between protein motifs and scaffolding domains are involved in most signal-transduction processes in the cell. Stabilization of protein-protein interactions, 4,5 disruption of protein-protein interactions 6 and disruption of intra-protein contacts during folding 7 are all being pursued. However, despite some success stories, discovering small-molecule drugs that modulate protein-protein interactions remains an enormous challenge.…”