Final Report Summary - PHOTOBLUE (Towards rational design of cancer therapeutic drugs: a first principles study of the photosensitization mechanism of methylene blue (Photoblue))
Photosensitizers are molecules that induce a chemical change in another molecule upon absorption of light. This class of compounds is employed in photodynamic therapy, a well-recognized process for the treatment of cancer and other diseases. The photodynamic therapy mechanism involves several steps shown in Scheme 1: (i) penetration of the drug into the cancer cell by diffusion throughout the cell membrane, (ii) binding of the drug to a biomolecule, (iii) absorption of light energy and subsequent reorganization of the electrons of the drug, (iv) energy transfer from the drug to the oxygen present in the cell forming reactive oxygen and, (v) oxidation of the biomolecule by the reactive oxygen resulting in the cell death. The goal of Photoblue was to investigate by means of computational chemistry methods the steps (ii) and (iii) employing a photosensitizer called methylene blue as model. According to these two steps, the main work achieved in Photoblue can be divided into two different parts, which led to two publications.
1. Simulation of the binding process of methylene to DNA. Small and planar molecules like methylene blue can bind to DNA in four different ways as can be seen in Scheme 2. The goal of this work was to elucidate which binding mode is more energetically favorable by means of classical molecular dynamics. In this type of simulations, Newton classical equations of motion are solved for every atom to obtain a time-resolved picture of the evolution of the system. The analysis of the simulations allowed us to clarify that intercalation (Scheme 2) is the most favorable binding mode. In addition, the nature of the interactions that dominated the binding process and the influence of different DNA sequences and physicochemical conditions were investigated. This work was published in the journal Biochemistry 53 (2014) 2391-2412.
2. Once the binding mode of methylene blue into DNA was known, the reorganization of the electrons of the drug after absorption of light was studied. A proper electronic distribution of the photosensitizer is necessary in order to efficiently transfer the excitation energy to oxygen and initiate the DNA damage of the cancer cell. This appropriate electronic distribution is achieved by means of a process called intersystem crossing. The goal of this part of the project was to investigate the effect of aqueous solution and DNA environment on the intersystem crossing of methylene blue. To carry out this calculations, methylene blue was described by very accurate quantum mechanically methods, which are necessary to properly account for the electrons of the photosensitizer, and the DNA sequence and solvent were treated by the less computationally expensive methodology called molecular mechanics. Our simulations predicted that intersystem crossing of the drug intercalated into DNA is more favorable than that when the drug is in aqueous solution. In addition, we also discussed the possibility of modifying the structure of methylene blue in order to increase the efficiency of intersystem crossing. This work has been published in the high-impact journal (impact factor 13.45): Angewandte Chemie International Edition 54 (2015) 4375-4378. This publication triggered several press releases to explain our results to the general public (see Dissemination Measures section).
Besides of the work described above, additional calculations related to Photoblue are still in progress. In particular, the simulations performed in Photoblue showed that the DNA and aqueous solution environments can play a crucial role in the mode of action of photosensitizers. Therefore, the description of the environment with low-accuracy methods (like molecular mechanics) can be unsuitable and can provide wrong conclusions. In collaboration with Prof. Christian Ochsenfeld (University of Munich), we are developing a new procedure to describe the environment quantum mechanically with the so-called linear scaling methods, which allow decreasing the computational cost without compromising accuracy. Two publications are expected to come in the near future.
Since Dr. Nogueira will start his habilitation in the host group under the supervision of Prof. González, different studies arising from Photoblue will continue in the future. Nowadays, two aspects are being considered presently:
1. One of the conclusions of our publication in Angewandte Chemie was that methylene blue can be functionalized in order to enhance its anticancer effect. Currently, we are designing new derivatives of methylene blue based on a rational analysis of our theoretical simulations. Some of the designed candidates show a very promising behavior and one of them clearly presents a more appropriate electronic distribution than methylene blue.
2. One important step in the photodynamic therapy mechanism is the penetration of the drug into the cancer cell (step (i) of Scheme 1). The diffusion of methylene blue and one of the theoretically designed derivatives through the cell membrane was investigated by a bachelor student (Marius Bittermann) under the supervision of Dr. Nogueira. This study is planned to be extended by Mr. Bittermann during his Master Thesis, where the interaction between light and the drug in the presence of the cell membrane will be studied.
All the work that was and is being performed in Photoblue will provide an invaluable help to understand at molecular level the photodynamic therapy mechanism when the drug is interacting with DNA and lipid membranes. Our conclusions will drive experimentalists in the design of new and efficient photosensitizers. It is planned that Dr. Nogueira extends the research carried out in Photoblue to new photosensitizers, biological environments and theoretical methods within the framework of his habilitation.
1. Simulation of the binding process of methylene to DNA. Small and planar molecules like methylene blue can bind to DNA in four different ways as can be seen in Scheme 2. The goal of this work was to elucidate which binding mode is more energetically favorable by means of classical molecular dynamics. In this type of simulations, Newton classical equations of motion are solved for every atom to obtain a time-resolved picture of the evolution of the system. The analysis of the simulations allowed us to clarify that intercalation (Scheme 2) is the most favorable binding mode. In addition, the nature of the interactions that dominated the binding process and the influence of different DNA sequences and physicochemical conditions were investigated. This work was published in the journal Biochemistry 53 (2014) 2391-2412.
2. Once the binding mode of methylene blue into DNA was known, the reorganization of the electrons of the drug after absorption of light was studied. A proper electronic distribution of the photosensitizer is necessary in order to efficiently transfer the excitation energy to oxygen and initiate the DNA damage of the cancer cell. This appropriate electronic distribution is achieved by means of a process called intersystem crossing. The goal of this part of the project was to investigate the effect of aqueous solution and DNA environment on the intersystem crossing of methylene blue. To carry out this calculations, methylene blue was described by very accurate quantum mechanically methods, which are necessary to properly account for the electrons of the photosensitizer, and the DNA sequence and solvent were treated by the less computationally expensive methodology called molecular mechanics. Our simulations predicted that intersystem crossing of the drug intercalated into DNA is more favorable than that when the drug is in aqueous solution. In addition, we also discussed the possibility of modifying the structure of methylene blue in order to increase the efficiency of intersystem crossing. This work has been published in the high-impact journal (impact factor 13.45): Angewandte Chemie International Edition 54 (2015) 4375-4378. This publication triggered several press releases to explain our results to the general public (see Dissemination Measures section).
Besides of the work described above, additional calculations related to Photoblue are still in progress. In particular, the simulations performed in Photoblue showed that the DNA and aqueous solution environments can play a crucial role in the mode of action of photosensitizers. Therefore, the description of the environment with low-accuracy methods (like molecular mechanics) can be unsuitable and can provide wrong conclusions. In collaboration with Prof. Christian Ochsenfeld (University of Munich), we are developing a new procedure to describe the environment quantum mechanically with the so-called linear scaling methods, which allow decreasing the computational cost without compromising accuracy. Two publications are expected to come in the near future.
Since Dr. Nogueira will start his habilitation in the host group under the supervision of Prof. González, different studies arising from Photoblue will continue in the future. Nowadays, two aspects are being considered presently:
1. One of the conclusions of our publication in Angewandte Chemie was that methylene blue can be functionalized in order to enhance its anticancer effect. Currently, we are designing new derivatives of methylene blue based on a rational analysis of our theoretical simulations. Some of the designed candidates show a very promising behavior and one of them clearly presents a more appropriate electronic distribution than methylene blue.
2. One important step in the photodynamic therapy mechanism is the penetration of the drug into the cancer cell (step (i) of Scheme 1). The diffusion of methylene blue and one of the theoretically designed derivatives through the cell membrane was investigated by a bachelor student (Marius Bittermann) under the supervision of Dr. Nogueira. This study is planned to be extended by Mr. Bittermann during his Master Thesis, where the interaction between light and the drug in the presence of the cell membrane will be studied.
All the work that was and is being performed in Photoblue will provide an invaluable help to understand at molecular level the photodynamic therapy mechanism when the drug is interacting with DNA and lipid membranes. Our conclusions will drive experimentalists in the design of new and efficient photosensitizers. It is planned that Dr. Nogueira extends the research carried out in Photoblue to new photosensitizers, biological environments and theoretical methods within the framework of his habilitation.
