Mixed quantum mechanical/molecular mechanical simulation of biological systems

During the last decade the field of computational chem. has experienced an enormous progress. Due to the exponential increase in computer power and the development of new computational methods it has now become possible to treat many complex chem. and biol. problems on an accurate and realistic level. Ab initio mol. dynamics simulations based on d. functional theory are among the most powerful of these new tools. Using parallel computers, systems of a few hundred of atoms can be studied routinely. By extending this approach to a mixed quantum-classical (QM/MM) hybrid scheme, the system size can be enlarged even further. This method paired with enhanced sampling techniques is esp. attractive for the in situ investigation of complex chem. and biochem. reactions that occur in a heterogeneous environment. The power of this approach will be demonstrated on different illustrative examples with a particular emphasis on applications to enzymic reactions and photoactive proteins. [on SciFinder (R)]

In silico DNA-binding and rational design of ruthenium-arene anticancer drugs

Christian Gossens

Organometallic ruthenium(II)-arene (RA) antitumour compounds of the general type [Ru(II)(η6-arene)(X)2(pta)], RA-pta, and [Ru(II)(η6-arene)X(en)], RA-en, (X=leaving group; pta=1,3,5-triaza-7-phosphaadamantane, en=ethylenediamine) have been investigated computationally. The main focus has been i.e. the hydrolysis properties, ligand exchange reactions, binding to DNA and the analysis of the resulting structural perturbations. The goal of this thesis was to elucidate key steps in the reactivity of the above drugs that are not readily accessible by experimental techniques. The methodologies employed cover tailor made force fields in classical molecular dynamics (MD), density functional theory (DFT) MD simulations in implicit and explicit solvent as well as combined classical/quantum (QM/MM) MD simulations. For RA-pta compounds, binding energies between the metal centres and the surrounding ligands were calculated. The calculated energies rationalize the experimentally observed tendencies for arene loss, and show that the pta ligands are relatively strongly bound. Exchange of metal centre, methylation or protonation of the pta-ligand, or change of the arene result in significant differences in the metal-arene binding energies while leaving the metalphosphine bond strength essentially unchanged. Significantly lower binding energies and reduced hapticity are predicted for the exchange of arene by nucleobases. The latter show higher binding energies for nitrogen π-bonding than for p-bonding. No influence on the ruthenium-arene interaction was observed for RA-pta complexes bearing arenes with functionalized side chains. A combined DFT/continuum electrostatics approach has been used to estimate the protonation states and absolute pKa values of a series of RA-pta compounds and their hydrolysis products. Our results suggest that the selective in vivo activity towards cancer cells and the observed pH dependent DNA damage is due to a pH dependent activation/deactivation mechanism. In the context of rational drug design, it is hypothesised that analogues with fluorinated arene rings should result in improved selectivity towards hypoxic cancer cells. For RA-en complexes, we rationalized the chemoselectivity towards guanine. The calculated DFT binding energies for the three investigated nucleobases (G, A, C) decreases in the order G(N7) >> C(O2) ∼ C(N3) > A(N7) > G(O6) > OH2. The G(N7) complex is the most stable product due to a C6=O-HNen hydrogen bond while the corresponding C6-NH2-HNen interaction in adenine is repulsive. A study of the reaction of [(η6-benzene)Ru(en)(OH2)]2+ (1) towards the nucleobases G, A and C reveals a strong preference for a formation of an H-bonded cis vs. trans reactant adduct. Only guanine can form a thermally stable trans reactant adduct. The potential reaction sites of adenine and cytosine might loose their nucleophilicity by protonation while simultaneously the aqua leaving group of 1 is converted into an unreactive hydroxo ligand. For the reaction of 1 with guanine three different reaction pathways were identified, however, a "direct trans" reaction pathway is probably the most biologically relevant. Using classical and QM/MM MD we showed that both investigated ruthenium compounds, RA-pta and RA-en, can bind to the major groove of duplex DNA and are stable in this position. The DNA is highly flexible, adapts very fast and widens the major groove to accommodate the ruthenium complex. The local and global structural changes of the DNA (e.g. bending towards the major groove) observed for the RA-pta series are similar to those reported for cisplatin. A severe perturbation of the Watson-Crick base pairing adjacent to the binding site of RA-en was observed that can be linked to recent experimental results. Finally, a tailor made force field for RA-en was derived from our QM/MM trajectories using a force matching approach.

EPFL2007

Exploring G-Protein Coupled Receptor Activation with Multiscale Molecular Simulations

Stefano Vanni

This thesis is devoted to the study of the activation mechanism of G-protein coupled receptors (GPCRs), one of the largest and most diverse protein families in mammalian genomes, by means of different computer-based simulation techniques. Using force field based classical molecular dynamics (MD), the time evolution of two prototypical GPCRs, rhodopsin and β adrenergic receptors, has been followed for microseconds under different external conditions. Within this approach, the non-native modifications induced by the different engineering techniques used to crystallize most of the known GPCR structures have been identified and some of the mechanisms through which these receptors have managed to optimize their function through evolution have been described and quantified. In detail, this has led to suggest a possible binding mode of agonists to β adrenergic receptors and to identify crucial micro-switches during receptor activation, as well as to describe an asymmetric pathway in the rhodopsin dimer that suggests oligomerization in GPCRs as a biological strategy to enhance activation efficiency. The increased knowledge of GPCR activation mechanism obtained from the classical molecular dynamics simulations hinted to a crucial role of chemical reactions inside the binding pocket of the receptors during the activation cycle. These events have been studied in this thesis using a hybrid quantum mechanics/molecular mechanics (QM/MM) protocol based on Density Functional Theory. Using this approach, it has been possible to characterize the optical properties of the different intermediates along the activation pathway of rhodopsin and to quantitatively estimate the barrier for the proton transfer reaction that induces active state formation. Finally, a novel activation mechanism in diffusible ligands class A GPCRs that indicates proton transfer from the bound ligand to the receptor as a crucial step to reach the active conformation is proposed.

EPFL2011

Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case

Fabio Trani

An integrated computational approach built on quantum mechanical (QM) methods, purposely tailored inter-and intra-molecular force fields and continuum solvent models combined with time-independent and timedependent schemes to account for nuclear motion effects is applied to the spectroscopic investigation of pyrimidine in the gas phase as well as in aqueous and CCl4 solutions. Accurate post-Hartree-Fock methodologies are employed to compute molecular structure, harmonic vibrational frequencies, energies and oscillator strengths for electronic transitions in order to validate the accuracy of approaches rooted into density functional theory with emphasis also on hybrid QM/QM' models. Within the time-independent approaches, IR spectra are computed including anharmonicities through perturbative corrections while UV-vis line-shapes are simulated accounting for the vibrational structure; in both cases, the environmental effects are described by continuum models. The effects of conformational flexibility, including solvent dynamics, are described through time-dependent models based on purposely DFT-tailored force fields applied to molecular dynamics simulations and on QM computations of spectroscopic properties. Such procedures are exploited to simulate IR and UV-vis spectra of pyrimidine in the gas phase and in solutions, leading in all cases to good agreement with experimental observations and allowing to dissect different effects underlying spectral phenomena.