Article ; Online: Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.
The journal of physical chemistry. B
2024 Volume 128, Issue 7, Page(s) 1595–1605
Abstract: Alchemical transformations can be used to quantitatively estimate absolute binding free energies at a reasonable computational cost. However, most of the approaches currently in use require knowledge of the correct (crystallographic) pose. In this paper, ...
| Abstract | Alchemical transformations can be used to quantitatively estimate absolute binding free energies at a reasonable computational cost. However, most of the approaches currently in use require knowledge of the correct (crystallographic) pose. In this paper, we present a combined Hamiltonian replica exchange nonequilibrium alchemical method that allows us to reliably calculate absolute binding free energies, even when starting from suboptimal initial binding poses. Performing a preliminary Hamiltonian replica exchange enhances the sampling of slow degrees of freedom of the ligand and the target, allowing the system to populate the correct binding pose when starting from an approximate docking pose. We apply the method on 6 ligands of the first bromodomain of the BRD4 bromodomain-containing protein. For each ligand, we start nonequilibrium alchemical transformations from both the crystallographic pose and the top-scoring docked pose that are often significantly different. We show that the method produces statistically equivalent binding free energies, making it a useful tool for computational drug discovery pipelines. |
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| MeSH term(s) | Protein Binding ; Thermodynamics ; Molecular Dynamics Simulation ; Ligands ; Nuclear Proteins ; Transcription Factors |
| Chemical Substances | Ligands ; Nuclear Proteins ; Transcription Factors |
| Language | English |
| Publishing date | 2024-02-07 |
| Publishing country | United States |
| Document type | Journal Article |
| ISSN | 1520-5207 |
| ISSN (online) | 1520-5207 |
| DOI | 10.1021/acs.jpcb.3c06516 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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