ArticleACS central science2023
What Makes a Good Protein-Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism.
Article in ACS central science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 36 citations in OpenAlex.
- ERα/SIRT1 signaling mediates the metabolic regulatory benefits of pterostilbene.The Journal of biological chemistry · 2026Article
- Protein-Protein Interaction Stabilizers from MD Simulation-Derived Pharmacophores.Journal of chemical information and modeling · 2026Article
- Natural Products Beyond Inhibition: A Mechanistic Framework Spanning Pockets, Interfaces, and Kinetic Barriers.Molecules (Basel, Switzerland) · 2026Review
- Structure-Guided Design of an Interface-Derived Inhibitor Peptide Against Spodoptera frugiperda Digestive Trypsins.Archives of insect biochemistry and physiology · 2026Article
- In Silico Analysis of Potential Stabilizer Binding Sites at Protein-RNA Interfaces.Computational and structural biotechnology journal · 2026Article
- Regulation of receptor tyrosine kinase hetero-interactions.Current opinion in structural biology · 2025Review
- Cooperative Free Energy: Induced Protein-Protein Interactions and Cooperative Solvation in Ternary Complexes.Journal of chemical theory and computation · 2025Article
- Experimental Conditions to Retrieve Intrinsic Cooperativity α Directly from Single Binding Assay Data Exemplified by the Ternary Complex Formation of FKBP12, MAPRE1 and Macrocyclic Molecular Glues.International journal of molecular sciences · 2025Article
- SF3B1: from core splicing factor to oncogenic driver.RNA (New York, N.Y.) · 2025Review
- Multilayered Computational Framework for Designing Peptide Inhibitors of HVEM-LIGHT Interaction.The journal of physical chemistry. B · 2024Article
- Unity Is Strength: The Mutual Alliance between CFTR and SLC26A6 as Therapeutic Opportunity in Cystic Fibrosis.Pharmaceuticals (Basel, Switzerland) · 2024Article
- A Comprehensive Computational Insight into the PD-L1 Binding to PD-1 and Small Molecules.Pharmaceuticals (Basel, Switzerland) · 2024Review
- Virtual screening and molecular dynamics studies of novel small molecules targetingIn silico pharmacology · 2024Article
- MGPPI: multiscale graph neural networks for explainable protein-protein interaction prediction.Frontiers in genetics · 2024Article
- Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3σ/ERα Protein-Protein Interaction from Nonselective Fragments.Journal of the American Chemical Society · 2023Article
- TowardACS central science · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-protein interactions (PPIs) are essential for biological processes including immune reactions and diseases. Inhibition of PPIs by drug-like compounds is a common basis for therapeutic approaches. In many cases the flat interface of PP complexes prevents discovery of specific compound binding to cavities on one partner and PPI inhibition. However, frequently new pockets are formed at the PP interface that allow accommodation of stabilizers which is often as desirable as inhibition but a much less explored alternative strategy. Herein, we employ molecular dynamics simulations and pocket detection to investigate 18 known stabilizers and associated PP complexes. For most cases, we find that a dual-binding mechanism, a similar stabilizer interaction strength with each protein partner, is an important prerequisite for effective stabilization. A few stabilizers follow an allosteric mechanism by stabilizing the protein bound structure and/or increase the PPI indirectly. On 226 protein-protein complexes, we find in >75% of the cases interface cavities suitable for binding of drug-like compounds. We propose a computational compound identification workflow that exploits new PP interface cavities and optimizes the dual-binding mechanism and apply it to 5 PP complexes. Our study demonstrates a great potential for
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.