Modeling the Interactions of Anticancer Compounds with DNA and Lipid Membranes

Resumen

This thesis presents a systematic theoretical study on some anticancer molecules to gain unprecedented insights on some of the key steps in their mechanism of action. The anticarcinogenic molecules under study consist of cis-diaminedichloroplatinum(II) (cisplatin), anthraquinone and some of its derivatives, which present different mechanisms of action. Specifically, although both molecules permeate the cell membrane of a cancer cell prior to triggering their anticancer activity, the main difference resides in the fact that cisplatin is active at the electronic ground state, whereas the anthraquinone molecules need to be photoexcited by irradiating them with a suitable wavelength of electromagnetic radiation to trigger their anticancer activity. The mechanism of action also depends on the target tissue of the drug, which could involve the cellular lipid membrane or the DNA present in some organelles such as the cell nucleus or the mitochondria. Cisplatin is perhaps the most representative -- as well as the most widely used -- compound of a family of Pt(II) and Pt(IV) chemotherapeutic drugs, which present a common mechanism of action consisting of the permeation of the drug inside the carcinogenic cell followed by binding to a DNA strand, in a process that ultimately leads to the cell death. As such, cisplatin is used as scaffold that can be tailored by modifying its functional groups to tune its cytotoxic activity, selectivity, specificity, and other chemical and biological properties. Likewise, anthraquinone can be considered as the "progenitor" of a family of anticancer chromophores which bears its name, that are active following photoexitation towards a certain electronic excited state. The mechanism of action of anthraquinones differs from that of the platinum drugs, in that they react with the neighbouring tissues (usually the lipid membrane or DNA) by means of either electron transfer or energy transfer reactions that generate reactive radical species, ultimately disrupting the structure of these tissues and inducing cell death. As such, anthraquinone also represents a scaffold prone to chemical modification to obtain more efficient drugs. Thus, it is the fact of cisplatin and anthraquinone of being the ``progenitors" of the corresponding families, that poses the need for studying to a great detail the key features of the mechanisms of action of these drugs, so that future tailoring of anticancer derivatives can be performed in an efficient manner. For this reason, the present thesis focuses on modeling at an atomistic scale the permeation of these drugs into a lipid membrane, as well as the interactions of the drugs with a model of a double strand of DNA. These studies involve state-of-the art computational techniques that include classical molecular dynamics (MD) to study the conformational motion of the systems of inderest and quantum mechanics to describe at a high level of accuracy the electronic structure of the drugs under study, which ultimately is the main feature that determines the chemistry of these drugs, and therefore their cytotoxic activity. In this work, a large amount of effort is dedicated to obtaining an accurate description of the interactions between the above mentioned tissues and the drugs, in particular the influence the complex biological environment that surrounds the drug has upon the electronic structure of the latter. Therefore, sophisticated quantum mechanics/molecular mechanics (QM/MM) techniques are employed to accurately compute physical observables, such as interaction energies and electronic absorption spectra, which give an account on the nature of the interactions established between the drug and the target tissue. In this thesis, the approach adopted is to interface the generation of an ensemble of geometries \textit{via} classical MD to account for conformational motion, with the calculation of a given observable on top of each sampled geometry by means of QM/MM so that the observable of interest is obtained as an ensemble average. Although nowadays there are a manifold of software available to either perform the classical MD simulations or the QM/MM calculations, the resources at hand to readily interface both methodologies in the manner described above are limited, and in most cases lack of the generality (in the observables to be computed, the systems to be treated, the difficulty in their application, etc.) required by the present thesis. Therefore, part of this thesis has been dedicated to the development of a set of computational tools that interfaces the MD and the QM/MM methodologies in a straightforward manner, and with the degree of generality required by the systems under study. The present thesis consists of 8 Chapters, plus the conclusions and perspectives, which are organized as follows: Chapter 1 provides a general introduction on the mechanism of action of cisplatin and anthraquinone derivatives, and the state-of-the-art of the computational techniques employed in the study of analogous anticancer drugs. Chapter 2 gives an overview of the theoretical methods used in the present thesis, spanning from the equations of motion in classical MD to the electronic structure theory to describe ground and excited states of molecular systems at different levels of approximation. The main results of this thesis are presented from Chapter 3 to Chapter 8. In particular, Chapters 3 and 4 introduce the computational tools developed to facilitate and automatize the procedure to perform QM/MM computations. A particular emphasis is done in the application of wavefunction methods, such as the \gls{casscf}, on ensembles of geometries, for which an algorithm has been proposed to preserve the active space along the ensemble of geometries. Chapter 5 focuses on the study of the permeation mechanism of cisplatin through a lipid membrane model, in which classical MD simulations using a force field were performed in conjunction with an enhanced sampling technique called umbrella sampling, to compute the energetics of the permeation process. The interaction energies (and their decomposition in energy components) between cisplatin and the lipid membrane were also computed using a force field. Chapter 6 represents a follow-up of the work in Chapter 5, where the interaction energy and the energy decomposition were computed using a QM/MM version of an energy decomposition analysis based on electron densities. Chapter 7 presents a conformational study of the anthraquinone molecule when intercalated in a double strand of DNA, in which two predominant orientations of the anthraquinone molecule relative to the surrounding nucleobases were identified. The conformational analysis was followed by the computation of the excited states of the anthraquinone molecule on different orientations, whereby the excited states were characterized in terms of their charge transfer and delocalization nature. Chapter 8 provides some results of a work currently in progress, in which the permeation mechanism of some derivatives of the anthraquinone molecule into a lipid membrane model, and the excited states of these molecules in the presence of the lipid environment, have been studied. Finally, Chapter 9 provides some general conclusions and perspectives of the present thesis work.