ArticleInternational journal of molecular sciences2020
Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 20 citations in OpenAlex.
- An Integrated Computational Workflow for Discovering Alkaloid-Derived Ligands of Cyclin-Dependent Kinase 2.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning.Molecules (Basel, Switzerland) · 2024Article
- Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin.Molecules (Basel, Switzerland) · 2022Article
- In Silico Drug Repurposing Approach: Investigation ofMolecules (Basel, Switzerland) · 2022Article
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].Living journal of computational molecular science · 2022Article
- Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy.Journal of chemical theory and computation · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4'-kinase (LpxK) ofRSC advances · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Reliable prediction of binding affinities for ligand-receptor complex has been the primary goal of a structure-based drug design process. In this respect, alchemical methods are evolving as a popular choice to predict the binding affinities for biomolecular complexes. However, the highly flexible protein-ligand systems pose a challenge to the accuracy of binding free energy calculations mostly due to insufficient sampling. Herein, integrated computational protocol combining free energy perturbation based absolute binding free energy calculation with free energy landscape method was proposed for improved prediction of binding free energy for flexible protein-ligand complexes. The proposed method is applied to the dataset of various classes of p53-MDM2 (murine double minute 2) inhibitors. The absolute binding free energy calculations for MDMX (murine double minute X) resulted in a mean absolute error value of 0.816 kcal/mol while it is 3.08 kcal/mol for MDM2, a highly flexible protein compared to MDMX. With the integration of the free energy landscape method, the mean absolute error for MDM2 is improved to 1.95 kcal/mol.
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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.