title: Entwicklung von Modellen zur Beschreibung der Dynamik und Interaktion mit Wasser Molekülen bei der Protein-Ligand Bindung
title: Development of models to describe the dynamics and interaction with water molecules in protein-ligand binding
Creators: name: Betz, Michael
Publisher: name: Philipps-Universität Marburg
Year: 2015
Subjects: Wasser
Water
Protein, Simulation
Proteinbindung , Simulation
Medical sciences, Medicine
Medizin, Gesundheit

description: Wassermoleküle formen Netzwerke,
      die einen erheblichen Einfluss auf die Protein-Ligand Bingung
      nehmen. Sowohl strukturelle als auch thermodynamische Daten
      werden miteinander korreliert. Durch Molekulardynamische
      Simulationen werden Netzwerke erfolgreich reproduziert und
      vorhergesagt.
description: In modern drug design, lead
      optimization is usually performed in a step- wise fashion by
      adding and replacing functional groups at a given lead
      scaffold. Promising lead scaffolds with systematically varied
      substituents are synthesized and the structural variations
      are correlated with observed trends in binding affinity.
      Assigning contributions to particular functional groups, to
      estimate by how much an added group will enhance the binding
      affinity, is on first sight a very pragmatic but often
      misleading approach and does not follow simple additivity
      rules. The resulting structure–activity relationships
      frequently do not reflect the expected gradual changes in a
      congeneric ligand series. Often enough, the thermodynamic
      binding profiles of such ligands are modulated or can switch
      unpredictably and unexpected candidates surprisingly turn out
      to be the highest affinity binders of a series. The binding
      affinity to be optimized is a Gibbs free energy, which is the
      sum of an enthalpic and an entropic contribution, which
      usually cannot be factorized into simple additive functional
      group contributions. Regarding the complexity of the
      protein-ligand complex formation, one must consider that
      changes in ∆G, ∆H and T∆S reflect how the system is modified
      as a whole. Often such effects on binding affinity are not
      obvious, as they are frequently masked by a mutual
      compensation of binding enthalpy and entropy resulting in
      only a minor change in the Gibbs free energy. Nevertheless, a
      thoroughly combined analysis of both, thermodynamic terms
      along with structural information, as presented in many
      studies described in this thesis, provides profound insights
      into the underlying structure–activity relationships. In the
      present thesis two aspects have been studied that are
      recognized as increasingly import for rational computer-aided
      drug design. The first aspect relates to the influence of
      water on the non-additivity of functional group contributions
      to the binding affinity and it is important to elucidate the
      driving forces behind the so-called hydrophobic effect. Using
      high resolution crystal structures allowed us to explain and
      correlate observed changes in the thermodynamic binding
      profiles with changes in the local solvation structure on the
      molecular level. As a model system to investigate the
      influence of water on thermodynamic binding profiles we used
      the zinc metalloprotease thermolysin (TLN). Because the TLN
      has itself a rather rigid geometry and because the studied
      congeneric ligands differ only slightly, many important
      aspects of the binding process, e.g. ligand desolvation and
      differences in ligand conforma- tional properties can be
      assumed as virtually identical in the comparison of the
      protein-ligand binding event. The most important observation
      is the fact that water molecules do not interact with the
      solutes as separate and independent particles, but rather as
      “supramolecular assemblies” reflecting repeatedly occurring
      geometric arrangements. These local assemblies are parts of a
      large hydrogen-bonded network. Undoubtedly, the completeness
      and quality of the formed local network influences binding
      entropy and enthalpy in a systematic manner. This suggests
      that, rational approaches will have to incorporate concepts
      how to regard and optimize solvent exposure of molecular
      surfaces. For this purpose, we developed a molecular dynamics
      (MD) simulation protocol, with which we successfully
      predicted the detailed solvation structure around different
      TLN-inhibitor complexes. In reality, however, most proteins
      are more flexible than TLN, for which the factorization of
      the thermodynamic profile correlates remarkably well with
      high resolution crystal structures. Thus, in the second part
      of this thesis, it was investigated whether such correlations
      can also be observed for more flexible proteins. Therefore,
      the properties of several lin-benzopurine derivatives binding
      to the tRNA-modifying enzyme tRNA-guanine transg- lycosylase
      (TGT) were investigated. In a straight-forward computer-aided
      drug design procedure, e.g. docking, the protein part is
      regarded as virtually rigid while the ligands are flexible.
      More sophisticated docking methods take protein side chain
      flexibility into account, to reflect, e.g. an induced-fitting
      upon ligand binding. But such methods are not capable to
      describe the highly dynamic changes as observed for TGT. To
      inhibit TGT, which is only active as a homodimer, we followed
      different concepts by either blocking the active site
      (Chapter 7), but also by destabilizing the protein-protein
      interface of the homodimer. We demonstrated that ligands
      differing merely by an exocyclic amino group trigger
      large-scale rearrangements in the protein structure.
      Therefore, changes in the thermodynamic profile, which relate
      to the entire protein-ligand binding process and the involved
      protein flexibility, prevent that individual contributions
      can be assigned to single interactions or individual binding
      steps. Despite of the available high-resolution crystal
      structure of TGT and its complexes, some uncertainties in the
      models remain. For example, active-site ligands that insert a
      needle-like rigid substructure into the protein-protein
      interface, to perturb certain hot spot regions in order to
      destabilize the homodimer, are not fully visible in the
      crystal structures due to an ill-defined electron density. By
      use of different modeling techniques such as MD simula- tions
      we provide a model in agreement with experimental data. The
      simulations reveal how a loop region in TGT, despite its high
      flexibility, prevents solvent access of the residues forming
      the protein-protein interface. The research in the present
      thesis about the two aspects — the influence of water and
      protein flexibility — allow for a better understanding of
      funda- mental aspects of protein-ligand binding. Taking such
      aspects into account will make computational simulations more
      complex, but hopefully better in predicting ligand-binding
      affinity, as well as the molecular recognition
      process.