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Tytuł pozycji:

Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation.

Tytuł:
Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation.
Autorzy:
Rifai EA; AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands.
Ferrario V; Institute of Biochemistry and Technical Biochemistry , Universität Stuttgart , Allmandring 31 , 70569 Stuttgart , Germany.
Pleiss J; Institute of Biochemistry and Technical Biochemistry , Universität Stuttgart , Allmandring 31 , 70569 Stuttgart , Germany.
Geerke DP; AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands.
Źródło:
Journal of chemical theory and computation [J Chem Theory Comput] 2020 Feb 11; Vol. 16 (2), pp. 1300-1310. Date of Electronic Publication: 2020 Jan 21.
Typ publikacji:
Journal Article
Język:
English
Imprint Name(s):
Original Publication: Washington, D.C. : American Chemical Society, c2005-
MeSH Terms:
Ligands*
Molecular Dynamics Simulation*
Cytochrome P-450 CYP2A6/*chemistry
Cytochrome P-450 CYP2A6/metabolism ; Cytochrome P-450 Enzyme Inhibitors/chemistry ; Cytochrome P-450 Enzyme Inhibitors/metabolism ; Humans ; Protein Binding ; Thermodynamics
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Substance Nomenclature:
0 (Cytochrome P-450 Enzyme Inhibitors)
0 (Ligands)
EC 1.14.14.1 (CYP2A6 protein, human)
EC 1.14.14.1 (Cytochrome P-450 CYP2A6)
Entry Date(s):
Date Created: 20200103 Date Completed: 20200312 Latest Revision: 20200312
Update Code:
20240104
PubMed Central ID:
PMC7017367
DOI:
10.1021/acs.jctc.9b00890
PMID:
31894691
Czasopismo naukowe
Calculating free energies of binding (Δ G bind ) between ligands and their target protein is of major interest to drug discovery and safety, yet it is still associated with several challenges and difficulties. Linear interaction energy (LIE) is an efficient in silico method for Δ G bind computation. LIE models can be trained and used to directly calculate binding affinities from interaction energies involving ligands in the bound and unbound states only, and LIE can be combined with statistical weighting to calculate Δ G bind for flexible proteins that may bind their ligands in multiple orientations. Here, we investigate if LIE predictions can be effectively improved by explicitly including the entropy of (de)solvation into our free-energy calculations. For that purpose, we combine LIE calculations for the protein-ligand-bound state with explicit free-energy perturbation to rigorously compute the unbound ligand's solvation free energy. We show that for 28 Cytochrome P450 2A6 (CYP2A6) ligands, coupling LIE with alchemical solvation free-energy calculation helps to improve obtained correlation between computed and reference (experimental) binding data.

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