MoBioTools is a toolkit to automatically setup quantum mechanics/molecular mechanics (QM/MM) calculations for ensembles of geometries generated from molecular dynamics trajectories. We are also implemeting the automatization of some analysis tasks, such a the computation of absorption and emission spectra, redox potentials or energy-decomposition analysis.
Chemotherapy Pt-based agents
The use of Pt drugs (e.g., cisplatin, oxaliplatin) in chemotherapy is well established to treat different cancer types. The mode of action of these compounds involves different processes whose mechanistic details are in many cases poorly understood. We theoretically investigate two of the the main steps of the biological route of Pt complexes: the permeation of the drug through the lipid membrane and the binding to DNA strands.
Photosensitizers for DNA and Lipid-Membrane Damage
Photosensitizers are employed in photodynamic therapy to treat cancer and other diseases. Since these drugs only exert their cytotoxicity after light-induced activation, they can be spatio-temporally controlled with high precision. Our goal is to understand the mechanism by which the photosensitizer induces damage to lipid bilayers and DNA strands after absorption of UV-vis light.
Ion Conduction and Selectivity through Ion Channels
The movement of ions across cell membranes through ion channels underlies a wide range of biological processes such as the transmission of nerve impulses and stimulation of muscle contraction. We simulate the transport of ions through several channels to get insight into the factors that are relevant for ion permeation and selectivity, including the nature of intermolecular interactions involved in the process.
Photoswitches as Ion-Channel Blockers in Pain Treatments
Ion channels located in pain-sensing neurons are responsible for the signal propagation to the brain which causes the pain sensation. For this reason, many anaesthetics were developed to block the ion channels which initiate the pain signal. In this project we aim to theoretically design photoswitches able to block ion permeation after undergoing a conformational change induced by UV-vis light absorption.
DNA/Metal Surface-Based Biosensors
DNA-based biosensors are powerful tools when trying to detect specific sequences of nucleic acids, organic analytes, and heavy metals, among others. Charge-transfer processes often play an important role in the detection task and, thus, their theoretical modeling is of fundamental importance. We theoretically investigate the redox properties of DNA-based biosensors to get knowledge on the factors that lead to an enhancement of their electronic properties.