Thermodynamics as a Tool for the Optimization of Drug by Matesanz, R.; Pera, B.; Díaz, J.F

By Matesanz, R.; Pera, B.; Díaz, J.F

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Extra info for Thermodynamics as a Tool for the Optimization of Drug Binding, Thermodynamics - Interaction Studies - Solids, Liquids and Gases

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Bottom panel: Entropy differences for series 2 ligands (per N-H bond vector), obtained by NMR. 39 Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design Comparing these results with ITC data by Krishnamurthy et al. (2006), it is clear that a poor correlation exists between the change in ligand conformational entropy determined from NMR relaxation studies and the entropies of binding derived from ITC (Figure 14, middle panel). It indicates that a model based on increased dynamics of the ligand in the bound state is not a plausible explanation for the observed thermodynamic binding data.

This colouring scheme is consistent with colouring in Figure 10. , 2004), in terms of the different contributions. It is clear that formation of a ligand-protein complex will involve the loss of entropy associated with constraining the translational and rotational degrees of freedom of one binding partner with respect to the other. The magnitude of these unfavourable contributions to the ligand-protein interaction can be approximated. In the case of galactoseABP interactions, we took an estimate of the loss of ligand translational and rotational entropy from the work by Turnbull et al (2004) and Lundquist and his coworkers (Lundquist and Toone, 2002), which gave at approximately 25 kJ/mol for the free energy penalty.

This contribution is favourable. However, the overall entropic contribution to binding is unfavourable, which indicates that the entropic contribution from desolvation of the protein binding pocket is strongly unfavourable. In MUP, a favourable contribution to binding entropy is also derived from ligand desolvation, but is unable to overcome the unfavourable contribution from “freezing” 32 Thermodynamics – Interaction Studies – Solids, Liquids and Gases ligand degrees of freedom upon binding. The favourable entropic contribution from desolvation of the protein binding pocket that one would predict in a “classical” hydrophobic interaction is absent in MUP, since the occluded binding pocket is substantially desolvated prior to binding.

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