Development and validation of the force field parameters for drug-like molecules and their applications in structure-based drug design

Abstract

Computational approaches are widely used to help discover and develop new drugs, in particular, to understand how these molecules interact with their biomolecular targets. There are well-optimised and validated force field parameters available to describe interactions of common biomolecules, such as proteins, lipids and nucleotides. However, these force fields are not designed to represent heteromolecular ligands such as substrates, inhibitors, co-factors and potential drug molecules. Errors in parameters may result in incorrect predictions of ligand structure, orientation and conformation, which in turn can lead to the failure of computational drug design efforts. With over 25% of all the structures in the Protein Data Bank (PDB) containing ligands and over a million ligand molecules of potential interest in drug design in other databases, ligand validation and parameterisation represents a significant scientific challenge. While several automated parameterisation protocols have been proposed to generate the parameters, none of the current procedures are properly validated. As a response to the high demand for interaction parameters for ligands compatible with the GROMOS force field, a web accessible Automated force field Topology Builder (ATB; http://atb.uq.edu.au/) and Repository was developed. The ATB and Repository is intended to facilitate the development of molecular force fields and generates parameters that can be used in X-ray refinement, structure-based drug design and study of biomolecule-ligand complexes. In this thesis, molecular dynamics (MD) simulations were used to calculate the thermodynamic properties for the validation and refinement of ATB force fields parameters. A fully automated validation protocol of the ATB force field parameters for small organic molecules based on thermodynamic and structural information was developed and incorporated into the ATB. A novel integration and convergence protocol which increases the efficiency of the TI method for free energy calculations was also proposed. The validation has shown good overall agreement between the experimental and computed values and indicated problematic functional groups with parameters to be refined. The generation of parameters for novel molecules that are compatible with a given biomolecular force field can be tedious, time-consuming and error-prone. Here, a novel method to refine parameters in classical force fields in an automated manner that can be extended to the parameterisation of all other atom types is also presented. Single-step perturbation protocols were developed for small halogenated molecules to establish alternative van der Waals parameters which describe the interactions of these molecules with high precision. Parameters were successfully refined against experimental hydration free energies, densities and heats of vaporisation. As a result, alternative van der Waals interactions parameters for chlorine and bromine were proposed. Properties calculated with these proposed parameters closely matched the experiment data. The quality of the ATB force field parameters in validating the X-ray structures and investigating binding of ligands to the protein endothiapepsin was also investigated. Analysis of the MD trajectories showed that the protein structure remained relatively stable after 10 ns of simulations. The results for the validation of the ligands were mixed. While in some cases the simulations reproduced the binding mode and the interactions between the protein and the ligand with high accuracy suggesting the ATB parameters performed well, in other cases the complexes were unstable. This was despite the fact that the electron density for all ligands was well defined and the parameters for the ligand were generated using the same procedure. Endothiapepsin contains a catalytic dyad consisting of two aspartates that are generally assumed to share a proton. We demonstrated that the protonation of both the ligand and the residues with the binding site were critical to the ability to reproduce the crystal complex. To conclude, the work presented in this thesis provided insight into the development and validation of the force field parameters for drug-like molecules and their applications in structure-based drug design.