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Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Protein-Protein Interfaces

Protein-Protein Interfaces

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding Sites

Ligand Binding Sites

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Related Experiment Video

Updated: Mar 26, 2026

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

SPLINTS: small-molecule protein ligand interface stabilizers.

Eric S Fischer¹, Eunyoung Park², Michael J Eck²

¹Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

Current Opinion in Structural Biology

|February 2, 2016

Summary

This summary is machine-generated.

Small molecules can stabilize protein-protein interactions, a strategy underutilized in drug discovery. This approach, using small-molecule protein-ligand interface stabilizers (SPLINTS), offers new avenues for therapeutic development.

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Area of Science:

Biochemistry
Medicinal Chemistry
Structural Biology

Background:

Protein-protein interactions (PPIs) are crucial in biological regulation.
Small molecule PPI inhibitors are a major drug discovery focus.
Stabilizing PPIs is an under-explored therapeutic strategy.

Purpose of the Study:

To review small molecules that stabilize protein-protein interactions.
To analyze the structural mechanisms of these compounds.
To explore their potential in drug discovery.

Main Methods:

Structural analysis of small molecules.
Review of existing literature on PPI stabilizers.
Categorization of compounds based on targeted pathways.

Main Results:

Identified small molecules (SPLINTS) that stabilize PPIs across various signaling pathways (nuclear hormone, GTPase, kinase, phosphatase, ubiquitin ligase).
Observed diverse structural mechanisms employed by SPLINTS.
Demonstrated that SPLINTS can stabilize both physiologically relevant and adventitious interactions.

Conclusions:

Small-molecule stabilization of PPIs is a viable therapeutic strategy.
Diverse structural approaches exist for designing PPI stabilizers.
Systematic identification of SPLINTS can expand drug discovery efforts.