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Given the difficulties to identify chemical probes that can modulate protein-protein interactions (PPIs), actors in the field start to agree on the necessity to use PPI-tailored screening chemical collections. However, which type of scaffolds may promote the binding of compounds to PPI targets remains unclear. In this big data analysis, we have identified a list of privileged chemical substructures that are most often observed within inhibitors of PPIs. Using molecular frameworks as a way to perceive chemical substructures with the combination of an experimental and a machine-learning based predicted dataset of iPPI compounds, we propose a list of privileged substructures in the form of scaffolds and chemical moieties that can be substantially chemically functionalized and do not present any toxicophore nor Pan-assay interference (PAINS) alerts. We think that such chemical guidance will be valuable for medicinal chemists in their attempt to identify initial quality chemical probes on PPI targets.
This article was published in the following journal.
Name: Journal of chemical information and modeling
In bioinformatics, network alignment algorithms have been applied to protein-protein interaction (PPI) networks to discover evolutionary conserved substructures at the system level. However, most prev...
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Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
A protein that accounts for more than half of the peripheral nervous system myelin protein. The extracellular domain of this protein is believed to engage in adhesive interactions and thus hold the myelin membrane compact. It can behave as a homophilic adhesion molecule through interactions with its extracellular domains. (From J Cell Biol 1994;126(4):1089-97)
Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.
A serrate-jagged protein that functions to modulate signal transduction from NOTCH RECEPTORS in CELL DIFFERENTIATION. It may also regulate the expression of CYTOKINES.
Protein motif that contains a 33-amino acid long sequence that often occurs in tandem arrays. This repeating sequence of 33-amino acids was discovered in ANKYRIN where it is involved in interaction with the anion exchanger (ANION EXCHANGE PROTEIN 1, ERYTHROCYTE). Ankyrin repeats cooperatively fold into domains that mediate molecular recognition via protein-protein interactions.
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