Thermodynamics of ligand binding to histone deacetylase like amidohydrolase from Bordetella/Alcaligenes.
Thermodynamic studies on ligand-protein binding have become increasingly important in the process of drug design. In combination with structural data and molecular dynamics simulations, thermodynamic studies provide relevant information about the mode of interaction between compounds and their target proteins and therefore build a sound basis for further drug optimization. Using the example of histone deacetylases (HDACs), particularly the histone deacetylase like amidohydrolase (HDAH) from Bordetella/Alcaligenes, a novel sensitive competitive fluorescence resonance energy transfer-based binding assay was developed and the thermodynamics of interaction of both fluorescent ligands and inhibitors to histone deacetylase like amidohydrolase were investigated. The assay consumes only small amounts of valuable target proteins and is suitable for fast kinetic and mechanistic studies as well as high throughput screening applications. Binding affinity increased with increasing length of aliphatic spacers (n = 4-7) between the hydroxamate moiety and the dansyl head group of ligand probes. Van't Hoff plots revealed an optimum in enthalpy contribution to the free energy of binding for the dansyl-ligand with hexyl spacer. The selectivity in the series of dansyl-ligands against human class I HDAC1 but not class II HDACs 4 and 6 increased with the ratio of ΔH(0)/ΔG(0). The data clearly emphasize the importance of thermodynamic signatures as useful general guidance for the optimization of ligands or rational drug design.
Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, 64287, Germany.
Christian
C
Meyners
Matthias G J
MG
Baud
Matthew J
MJ
Fuchter
Franz-Josef
FJ
Meyer-Almes
D000421:Alcaligenes / Q000737:chemistry* / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D001667:Binding, Competitive; D001681:Biological Assay; D001884:Bordetella / Q000737:chemistry* / Q000201:enzymology; D003619:Dansyl Compounds / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer; D056284:Histone Deacetylase 1 / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D015335:Molecular Probes / Q000737:chemistry; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics
D001426:Bacterial Proteins; D003619:Dansyl Compounds; D004791:Enzyme Inhibitors; D008024:Ligands; D015335:Molecular Probes; D011994:Recombinant Proteins; C110550:HDAC1 protein, human; D056284:Histone Deacetylase 1
HDAC; histone deacetylase; inhibitors; ligand binding; thermodynamic signatures