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Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: implications for drug development.

Martinez M, Ahmed AH, Loh AP, Oswald RE - Biochemistry (2014)

Bottom Line: The binding of the charged form is largely driven by enthalpy, while that of the uncharged form is largely driven by entropy.This is due at least in part to changes in the hydrogen bonding network within the binding site involving one water molecule.This work illustrates the importance of charge to the thermodynamics of binding of agonists and antagonists to AMPA receptors and provides clues for further drug discovery.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States.

ABSTRACT
Understanding the thermodynamics of binding of a lead compound to a receptor can provide valuable information for drug design. The binding of compounds, particularly partial agonists, to subtypes of the α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor is, in some cases, driven by increases in entropy. Using a series of partial agonists based on the structure of the natural product, willardiine, we show that the charged state of the ligand determines the enthalpic contribution to binding. Willardiines have uracil rings with pKa values ranging from 5.5 to 10. The binding of the charged form is largely driven by enthalpy, while that of the uncharged form is largely driven by entropy. This is due at least in part to changes in the hydrogen bonding network within the binding site involving one water molecule. This work illustrates the importance of charge to the thermodynamics of binding of agonists and antagonists to AMPA receptors and provides clues for further drug discovery.

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Thermograms showing raw (top) and integrated(bottom) data forNW (A) and IW (B) displacement of glutamate from the GluA2 LBD at20 °C. The molar ratio is the ratio of ligand to protein. Fitswere performed as described by Sigurskjold et al.21 (C) Calculated ΔΔH, −TΔΔS°, and ΔΔG values for displacement of glutamate by the five willardiinederivatives. (D) Structures of the willardiine derivatives.
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fig1: Thermograms showing raw (top) and integrated(bottom) data forNW (A) and IW (B) displacement of glutamate from the GluA2 LBD at20 °C. The molar ratio is the ratio of ligand to protein. Fitswere performed as described by Sigurskjold et al.21 (C) Calculated ΔΔH, −TΔΔS°, and ΔΔG values for displacement of glutamate by the five willardiinederivatives. (D) Structures of the willardiine derivatives.

Mentions: Because of the low stability of the apo state in combination withthe difficulty of completely removing glutamate from the GluA2 LBDsample, more consistent results were obtained using competition experiments,that is, the competition of a given ligand with glutamate. The groundstate is, in this case, defined as the glutamate-bound state ratherthan the apo state. For a related AMPA receptor LBD (GluA4), Maddenand collaborators22 were able to obtainthermodynamic parameters for the binding of glutamate to the apo state(ΔH values of −2.49 ± 0.03 and−4.21 ± 0.03 kcal/mol at 15 and 20 °C, respectively;−TΔS° values of−5.39 and −3.96 kcal/mol at 15 and 20 °C, respectively;ΔCp of −171cal mol–1 K–1). Despite the factthat the binding sites of all AMPA receptors are very similar,23−25 the thermodynamic parameters for GluA4 LBD cannot necessarily becompared directly to the quantities determined for the GluA2 LBD.However, referencing the glutamate-bound state of GluA2 at physiologicalpH does reveal the quantitative and qualitative differences betweenthe thermodynamic parameters of the binding of willardiine ligands,as shown in Figure 1C. Likewise, in the calculationof ΔΔCp (slopeof ΔΔH vs temperature), the referencestate is constant for each temperature (Figure 3). ΔCp (heat capacityrelative to the apo state) would be determined by the difference betweenΔΔCp andthe ΔCp for glutamaterelative to the apo state.


Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: implications for drug development.

Martinez M, Ahmed AH, Loh AP, Oswald RE - Biochemistry (2014)

Thermograms showing raw (top) and integrated(bottom) data forNW (A) and IW (B) displacement of glutamate from the GluA2 LBD at20 °C. The molar ratio is the ratio of ligand to protein. Fitswere performed as described by Sigurskjold et al.21 (C) Calculated ΔΔH, −TΔΔS°, and ΔΔG values for displacement of glutamate by the five willardiinederivatives. (D) Structures of the willardiine derivatives.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215890&req=5

fig1: Thermograms showing raw (top) and integrated(bottom) data forNW (A) and IW (B) displacement of glutamate from the GluA2 LBD at20 °C. The molar ratio is the ratio of ligand to protein. Fitswere performed as described by Sigurskjold et al.21 (C) Calculated ΔΔH, −TΔΔS°, and ΔΔG values for displacement of glutamate by the five willardiinederivatives. (D) Structures of the willardiine derivatives.
Mentions: Because of the low stability of the apo state in combination withthe difficulty of completely removing glutamate from the GluA2 LBDsample, more consistent results were obtained using competition experiments,that is, the competition of a given ligand with glutamate. The groundstate is, in this case, defined as the glutamate-bound state ratherthan the apo state. For a related AMPA receptor LBD (GluA4), Maddenand collaborators22 were able to obtainthermodynamic parameters for the binding of glutamate to the apo state(ΔH values of −2.49 ± 0.03 and−4.21 ± 0.03 kcal/mol at 15 and 20 °C, respectively;−TΔS° values of−5.39 and −3.96 kcal/mol at 15 and 20 °C, respectively;ΔCp of −171cal mol–1 K–1). Despite the factthat the binding sites of all AMPA receptors are very similar,23−25 the thermodynamic parameters for GluA4 LBD cannot necessarily becompared directly to the quantities determined for the GluA2 LBD.However, referencing the glutamate-bound state of GluA2 at physiologicalpH does reveal the quantitative and qualitative differences betweenthe thermodynamic parameters of the binding of willardiine ligands,as shown in Figure 1C. Likewise, in the calculationof ΔΔCp (slopeof ΔΔH vs temperature), the referencestate is constant for each temperature (Figure 3). ΔCp (heat capacityrelative to the apo state) would be determined by the difference betweenΔΔCp andthe ΔCp for glutamaterelative to the apo state.

Bottom Line: The binding of the charged form is largely driven by enthalpy, while that of the uncharged form is largely driven by entropy.This is due at least in part to changes in the hydrogen bonding network within the binding site involving one water molecule.This work illustrates the importance of charge to the thermodynamics of binding of agonists and antagonists to AMPA receptors and provides clues for further drug discovery.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States.

ABSTRACT
Understanding the thermodynamics of binding of a lead compound to a receptor can provide valuable information for drug design. The binding of compounds, particularly partial agonists, to subtypes of the α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor is, in some cases, driven by increases in entropy. Using a series of partial agonists based on the structure of the natural product, willardiine, we show that the charged state of the ligand determines the enthalpic contribution to binding. Willardiines have uracil rings with pKa values ranging from 5.5 to 10. The binding of the charged form is largely driven by enthalpy, while that of the uncharged form is largely driven by entropy. This is due at least in part to changes in the hydrogen bonding network within the binding site involving one water molecule. This work illustrates the importance of charge to the thermodynamics of binding of agonists and antagonists to AMPA receptors and provides clues for further drug discovery.

Show MeSH