Our interest here is to examine the chemical properties of molecules to understand their propensity to participate in reactive processes and to form noncovalent interactions. In this context, we are interested in the chemical reactivity of small compounds that can be used as reduced models of biomolecular systems, as well as to the influence exerted by the environment on the modulation of chemical reactivity. We are also interested in the mechanistic events that dictate the outcome of complex reactions.
CBDD group is mainly focused on three different fields, all of them, related to the computational field.
Computational Chemistry
Computational Biology
Recent studies have demonstrated that compositional and functional alterations in the gut microbiome have an impact on metabolic and cardiovascular diseases.
Our aim is to translate the knowledge about the properties of molecules to the interaction with macromolecular targets and the regulation of the biological response. This interest has been focused on the development of multitarget compounds targeting neurodegenerative diseases, where our studies have led to the development of compounds interacting with cholinesterases, beta-secretase, monoamino oxidase, and beta-amyloid aggregation.
Another area of interest has been the role of the truncated hemoglobin N from M. tuberculosis, which plays a key role in eliminating nitric oxide, thus contributing to the survival of the bacillus.
Current interests comprise the development of bioactive compounds able to interfere with two key targets in the influenza A virus, the M2 channel proton, and hemagluttinin, and the development of inhibitors againts P. falciparum glucose-6-phosphate dehydrogense as antimalarial strategy.
Food science
The role of leptin resistance in obesity is well-known
Computational gastronomy is an emerging discipline placed at the data analytics–gastronomy interface. Two projects are currently being developed within this field: CC-Cuina (Culinary Corpora Comparison) and Appetit. CC-Cuina analyzes ingredients, techniques and the relationship between them in culinary recipes applying information extraction, natural language processing and network analysis techniques. Classification of ingredients and techniques as well as terminology are in the core of this project. Appetit is a tool developed by Telefónica I+D designed to suggest ingredient combinations based on the food-bridging hypothesis. This hypothesis assumes that two ingredients may become affine through a chain of pairwise affinities even if they have never appeared together in recipies or don’t share flavor compounds. Telefónica I+D and the University of Barcelona signed an agreement and now the Computational Gastronomy research group is in charge of its further development.
Biophysical Studies
The role of leptin resistance in obesity is well-known
Computational gastronomy is an emerging discipline placed at the data analytics–gastronomy interface. Two projects are currently being developed within this field: CC-Cuina (Culinary Corpora Comparison) and Appetit. CC-Cuina analyzes ingredients, techniques and the relationship between them in culinary recipes applying information extraction, natural language processing and network analysis techniques. Classification of ingredients and techniques as well as terminology are in the core of this project. Appetit is a tool developed by Telefónica I+D designed to suggest ingredient combinations based on the food-bridging hypothesis. This hypothesis assumes that two ingredients may become affine through a chain of pairwise affinities even if they have never appeared together in recipies or don’t share flavor compounds. Telefónica I+D and the University of Barcelona signed an agreement and now the Computational Gastronomy research group is in charge of its further development.
Chemical syntesis
The role of leptin resistance in obesity is well-known
Computational gastronomy is an emerging discipline placed at the data analytics–gastronomy interface. Two projects are currently being developed within this field: CC-Cuina (Culinary Corpora Comparison) and Appetit. CC-Cuina analyzes ingredients, techniques and the relationship between them in culinary recipes applying information extraction, natural language processing and network analysis techniques. Classification of ingredients and techniques as well as terminology are in the core of this project. Appetit is a tool developed by Telefónica I+D designed to suggest ingredient combinations based on the food-bridging hypothesis. This hypothesis assumes that two ingredients may become affine through a chain of pairwise affinities even if they have never appeared together in recipies or don’t share flavor compounds. Telefónica I+D and the University of Barcelona signed an agreement and now the Computational Gastronomy research group is in charge of its further development.
QM Skills…
We use Quantum Mechanics (QM) computations for the full characterization of small organic molecules, like minima optimization, determination of transition states or the calculation of different physicochemical properties in gas and implicit solvents.
Likewise, we have used quantum semiempirical calculations, DFT and post-HF methods for the understanding of the interplay between different noncovalent interactions or the determination of the reaction mechanisms.
Additionally, due to the study of different metalloproteins and IDPs, we have developed a key understanding of re-parameterization of complex systems, helping us to modify specifically some force field features.
MM Skills…
We use Molecular Mechanics (MM) simulations, mainly Molecular dynamics simulations to characterize the protein dynamics in absence and in presence of small organic molecules or peptides. Our main effort is on the understanding of the structural dynamics of complex hetero- mers systems to understand the effect over its activity. With this information, our aim is to design a new bioactive compound determining the hotspots of the active site or design a new therapeutic strategies based on allosteric pockets determining the network communication.
Additionally, we have focused our attention on the folding and aggregation process of small peptides, and the binding of small ligands to PPIs where the use of enhanced sampling techniques, like FEPs, Metadynamics or aMD have been widely used by the group.
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