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**28** 

*Spain* 

**Thermodynamics as a Tool for** 

**the Optimization of Drug Binding** 

A non-covalent interaction is a kind of chemical bond, typically between macromolecules, that involves dispersed variations of electromagnetic interactions (Alberts *et al.* 1994; Connors & Mecozzi 2010). Non-covalent interactions are individually weak as compared with covalent bonds, but their net strength is higher than the sum of that of the individual interactions. There are few drugs that bind irreversibly to their targets, in pharmacology, most drugs establish non-covalent interactions with their target molecules (usually

From a chemical point of view, the affinity constant (Ka) is a very useful measurement for the study of binding reactions as it provides much information about the mechanism. In many cases some chemical or physical properties of ligand or target change with the interaction between them, these changes might help to measure binding constants. It is important to establish the stoichiometry of the complex to be sure that the constants are accurately calculated. From the affinity constants measured it is possible to calculate the standard thermodynamic quantities for the binding reaction: free-energy (ΔG), enthalpy

Our group has already demonstrated that, in some cases, binding affinity measurements are very helpful for the optimization of ligand binding as it can be determined the contribution of every single chemical modification of the ligand to the binding affinity (Buey *et al.* 2004;

One of the objectives of drug development is the search of new or modified compounds with improved properties such as better potency, higher selectivity, better pharmacokinetics or superior drug resistance profiles. An important goal in this objective is the optimization of drugs binding affinity towards their targets, as binding affinity is directly related to potency (Ruben *et al.* 2006). Moreover, it has been shown that extremely high affinity drugs reflect as well changes in other properties like selectivity (Ohtaka *et al.* 2004; Ohtaka & Freire

Examples of the importance of ligand affinity in drug optimization can be observed in the development of HIV-1 protease inhibitors and statins (cholesterol lowering drugs) over the

In this chapter we will study the nature of non-covalent interations and the concept of binding constant for these interactions. Examples of methodologies to measure binding constants of small ligands to macromolecules will be introduced and we will emphasize the

2005) or resistance overcoming ability (Matesanz *et al.* 2008).

**1. Introduction**

proteins).

(ΔH) and entropy (ΔS).

Matesanz *et al.* 2008)

years as remarked in (Freire 2008).

Ruth Matesanz, Benet Pera and J. Fernando Díaz

*Centro de Investigaciones Biológicas (C.S.I.C.)* 

