Screening-based approaches to identify small molecules that inhibit protein–protein interactions

Abstract

Protein-protein interactions (PPIs) are very attractive targets for drug development as they play important roles in regulating many aspects of pathophysiologies. It has recently been revealed that the functionally important region of most PPIs is small enough to be modulated by small molecules. Thus, many studies in this field have achieved amazing progress, together with diverse and advanced screening technologies. Areas covered: This article presents screening technologies to identify small molecule inhibitors of PPIs in addition to discussing the suitability of PPIs as molecular targets. The phases in the processes of selecting compounds are discussed and appropriate steps are proposed, including methodologies to test binding affinity, kinetics, structural analysis, and cellular function. Expert opinion: Targeting PPIs is still a challenging approach in drug development and relatively few small molecules have reached clinical development. Potential candidates should be assessed and optimized by properly using the multiple assay systems to develop ideal small molecule drugs. Although there remain some barriers to be overcome, small molecule inhibitors of PPIs are fascinating and first-in-class as therapeutic agents to treat various diseases.

Creating and screening natural product libraries

“…In addition to enzymatic biochemical screens, new cell-free technologies have recently emerged that allow for the direct interrogation of the interaction between biomolecules and small molecules in the context of a high throughput NPD screen. [153][154][155] For many disease-associated molecular targets that are not enzymes but do have structural features that can be probed for small molecule binding biophysical screening techniques are useful. Since these newly developed HTS technologies do not rely on biochemically catalyzed reactions but rather on a physical interaction between the small molecule and the target protein/nucleic acid, they are considered biophysical high throughput assays.…”

“…153,155,159 Among the earliest high throughput biophysical drug discovery assays was the scintillation proximity assay (SPA). 142,154 An early iteration of this microbead based assay used target protein coated scintillant microbeads and radiolabeled ligands to detect substances that interfered with the target-ligand interaction, detectible as a decrease in bead (target) dependent scintillation. As the eld moved away from radiolabeled ligands the SPA was replaced with Förster Resonance Energy Transfer (FRET) based bead dependent assays, such as the LANCE format, whereby a lanthanide containing microbead coated with one member of an interacting pair was incubated with a complimentary FRET acceptor labeled interactor and then probed with a chemical library to nd substances that competed with this interaction.…”

“…BLI is a technology for quantitating the interaction between a target and a ligand by measuring the degree of photometric interference as light transverses an optically clear probe that has a target of interest attached to the end. 154,165,166 In a MWP format, the degree of interaction between the target coated probe and anything in the well (like a natural product) can be assessed by the effect on light reected to the detector (relative to control wells). While there are currently both 96 and 384 well compatible systems, the visualization optics is limited to 8 and 16 wells, respectively; requiring column by column progression across a plate and increasing the read time per plate.…”

Extraction of molecular features for the drug discovery targeting protein‐protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2

“…Many protein‐protein interactions (PPIs) regulate the disease state; therefore targeting the PPIs is crucial for drug discovery . Usually, the PPI‐interacting surfaces are large, flat, and lack the deep and well‐defined binding cavities.…”

“…9,17,19,20 Many protein-protein interactions (PPIs) regulate the disease state; therefore targeting the PPIs is crucial for drug discovery. 12,14,[21][22][23][24] Usually, the PPI-interacting surfaces are large, flat, and lack the deep and well-defined binding cavities. However, mutational analyses of PPI interfaces revealed that the binding affinity is not evenly distributed across the binding interfaces, but instead contributed by the small patch of amino acid residues know as hot spot.…”