Dataset Information

Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.

ABSTRACT: Alchemical relative binding free energy (ΔΔG) calculations have shown high accuracy in predicting ligand binding affinity and have been used as important tools in computer-aided drug discovery and design. However, there has been limited research on the application of ΔΔG methods to membrane proteins despite the fact that these proteins represent a significant proportion of drug targets, play crucial roles in biological processes, and are implicated in numerous diseases. In this study, to predict the binding affinity of ligands to G protein-coupled receptors (GPCRs), we employed two ΔΔG calculation methods: thermodynamic integration (TI) with AMBER and the alchemical transfer method (AToM) with OpenMM. We calculated ΔΔG values for 53 transformations involving four class A GPCRs and evaluated the performance of AMBER-TI and AToM-OpenMM. In addition, we conducted tests using different numbers of windows and varying simulation times to achieve reliable ΔΔG results and to optimize resource utilization. Overall, both AMBER-TI and AToM-OpenMM show good agreement with the experimental data. Our results validate the applicability of AMBER-TI and AToM-OpenMM for optimization of lead compounds targeting membrane proteins.

SUBMITTER: Zhang H

PROVIDER: S-EPMC11267607 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.

Zhang Han H Im Wonpil W

Journal of chemical information and modeling 20240703 14

Alchemical relative binding free energy (ΔΔ<i>G</i>) calculations have shown high accuracy in predicting ligand binding affinity and have been used as important tools in computer-aided drug discovery and design. However, there has been limited research on the application of ΔΔ<i>G</i> methods to membrane proteins despite the fact that these proteins represent a significant proportion of drug targets, play crucial roles in biological processes, and are implicated in numerous diseases. In this stu ...[more]

PMID: 38959405

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Dataset Information

Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.

Publications

Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.

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