ArticleFrontiers in molecular biosciences2018
Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes.
Article in Frontiers in molecular biosciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 23 citations in OpenAlex.
- Discovery of Novel Pyridin-2-yl Urea Inhibitors Targeting ASK1 Kinase and Its Binding Mode by Absolute Protein-Ligand Binding Free Energy Calculations.International journal of molecular sciences · 2025Article
- Leveraging machine learning models for peptide-protein interaction prediction.RSC chemical biology · 2024Review
- Article
- Alchemical Free Energy Calculations to Investigate Protein-Protein Interactions: the Case of the CDC42/PAK1 Complex.Journal of chemical information and modeling · 2022Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations.Journal of computer-aided molecular design · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.Journal of computational chemistry · 2020Article
- Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?Frontiers in molecular biosciences · 2020Review
- Specific Residue Interactions Regulate the Binding of Dengue Antigens to Broadly Neutralizing EDE Antibodies.ChemistryOpen · 2018Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The computational modeling of peptide inhibitors to target protein-protein binding interfaces is growing in interest as these are often too large, too shallow, and too feature-less for conventional small molecule compounds. Here, we present a rare successful application of an alchemical binding free energy method for the calculation of converged absolute binding free energies of a series of protein-peptide complexes. Specifically, we report the binding free energies of a series of cyclic peptides derived from the LEDGF/p75 protein to the integrase receptor of the HIV1 virus. The simulations recapitulate the effect of mutations relative to the wild-type binding motif of LEDGF/p75, providing structural, energetic and dynamical interpretations of the observed trends. The equilibration and convergence of the calculations are carefully analyzed. Convergence is aided by the adoption of a single-decoupling alchemical approach with implicit solvation, which circumvents the convergence difficulties of conventional double-decoupling protocols. We hereby present the single-decoupling methodology and critically evaluate its advantages and limitations. We also discuss some of the challenges and potential pitfalls of binding free energy calculations for complex molecular systems which have generally limited their applicability to the quantitative study of protein-peptide binding equilibria.
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