Natur- und Biowissenschaften, Medizin
Ordering of Water on Biomolecules
Universität Innsbruck
01.03.2013 - 29.02.2016
Entropy, Biomolecular Hydration, MD Simulation,

Biomolecular chemical reactions invariably involve association of molecules at hydrated surfaces. Furthermore, drugs bind to hydrated biomolecular surfaces and pockets. Hence, the study of these interactions needs robust and accurate computational tools capable of elucidating the effects of solvation at atomistic resolution.

The aim of this project is to investigate the role of water ordering in biomolecular interfaces. Gibbs Free Energy determines progression and direction of chemical reactions. Entropy is a key
contribution to Gibbs Free Energy. Whereas enthalpy arises from specific interactions, such as hydrogen bonds and Van der Waals contacts, entropy is determined by the number of adiabatically accessible states at a certain temperature. Entropy is difficult to calculate, as all states including rare events contribute to the result. It is therefore necessary to rely on converged ensembles generated by simulation techniques.

The number of states is not a countable property, as water around biomolecules exhibit a quasi-conituous state spectrum. Therefore, the state spectrum will be quantified by state probability density functions. Explicit solvent molecular dynamics simulations will be performed to sample hydration states of different biomolecules. Subsequently, analyses of local solvent density within binding pockets will be used to identify hydration sites. These sites will be analyzed in terms of entropy to identify Gibbs Free Energy hotspots. Residence times and angular orientations of the individual molecules associated with a site will be used to determine the degree of ordering. The observed degree of ordering will be quantified by calculating probability density functions for the respective translational and rotational degrees of freedom. A quantitative measure of hydration entropy is calculated from these probability density functions. Following this approach, a rigorous procedure will be established which will allow us to quantify local hydration entropy.

The first test system will be water ordering within the minor groove of DNA. Our group has established sequence-dependent differences in water ordering from X-ray structure analyses within the minor groove. A more rigorous investigation of this phenomenon will be carried out by molecular dynamics simulations. The methodological goal for the first test system is to demonstrate the ability of the presented approach to quantify the known sequence-specific differences in hydration entropy.

As a second test system surface hydration on the large and exposed binding pocket of Factor Xa will be investigated. In-depth free energy calculations were already performed by our group on this highly prominent drug target. Factor Xa is a well-suited target for this project, as some inhibitors incorporate water in their binding mode whereas others do not. Moreover, Factor Xa has a large hydrophobic region at its S4 site. This hydrophobic surface offers no immediate anchor points for directed interactions. This properties are in sharp contrast to the highly polar and charged interface of the DNA minor groove. Therefore, Factor Xa will allow us to assess the reliability of our approach in different surroundings by comparing our results with experimental affinity data and free energy calculations. This target will serve as a benchmark to refine our approach on a challenging and well-studied protein.

The third benchmark system will be Influenza Neuraminidase. Starting from known inhibitors, we intend to rationalize differences in their affinity resulting from differences in hydration. In contrast to Factor Xa, Influenza Neuraminidase has an unusually polar binding pocket. Therefore, it offers various anchor points for water in apo as well as in ligand-bound state. Several new inhibitors of Influenza Neuraminidase have been identified recently. Furthermore, series of structurally related compounds with associated experimental affinity data are available for this target. These compounds will be investigated in respect to chemical and structural features that displace and/or employ water at binding pocket free energy hotspots. Hence, the sensitivity of our approach can be assessed. The central aim for the third test system is to demonstrate the ability to provide relevant information for rational drug design from molecular dynamics simulations and the subsequent analysis of localized biomolecular hydration entropy.

The overall goal of the project is to develop entropy calculation by the outlined methodology as a useful tool in rational drug design. It shall enable researchers to efficiently identify consequences to affinity if certain water molecules are displaced or incorporated into the binding pose.