Research
Computational Physical Chemistry Research
- No name group
Research Lines
Computer Assisted Drug Design, protein engineering, enzyme catalysis
Participants
- Ing. en Bioinformática Jocelyn Solorza Márquez, Research Assistant
- M.Sc. Rodrigo Recabarren Hurtado, PhD Student
- Rubén Fritz Fritz, PhD Student
- Q.F. Jefferson Romero Marulanda, PhD Student
- Dra. Camila Muñoz Gutiérrez, PostDoctoral Researcher
Funding
- PI FONDECYT Regular No. 1181253, “Estimating residence time in protein-ligand complexes: New computational protocols for understanding binding kinetics of drugs.”
- Sponsoring Researcher, FONDECYT Postdoctoral No. 3180321, “EVALUATION OF THE MOLECULAR STABILITY OF CYLINDRIN-LIKE STRUCTURES VIA MICROSECOND MOLECULAR DYNAMICS SIMULATIONS”.
- Co-researcher, FONDECYT Regular No. 1150615 “DESIGNING CHEMICAL POLY-BULLETS FOR NICOTINIC ACETYLCHOLINE RECEPTORS AND MONOAMINE TRANSPORTERS (SERT, NET AND DAT). A POLY-PHARMACOLOGY APPROACH TO UNDERSTAND THE NICOTINE ADDICTION AND WITHDRAWAL SYNDROME MEDIATED BY MULTIPLE RECEPT”.
- Co-researcher, FONDECYT Regular No. 1170662 “Multisteric drugs: Design of polypharmacological agents that simultaneously interact with monoaminergic proteins and nicotinic receptors, based on similarities between their multiple binding sites”.
Computer Assisted Drug Design, protein engineering, enzyme catalysis
- Bio-nanomaterial Simulations group
Participants
Research Assistant
- Matias Valdes Peña
PhD Students
- Luis Gonzalo Espinoza Arcos
- Eduardo Cubillos Llanten
- Patricio Briones Rebolledo
- Matias Rojas Tapia
- Raul Sepulveda
- Francisca Salas Sepulveda
- Matias Valdes Peña
Research Lines
Theoretical and Computational Biophysics: Predicting the adsorption of proteins onto nano-surfaces, using molecular dynamics and Free-energy calculation for inorganic/biological systems. Design of new bio-nanomaterials for bio-medicine applications.
Research Interests
- Free-energy methods
- Biophysics
- Nanotechnology
- Metal surfaces
- Membrane dynamics
- Ion channels
- Transmembrane transporting.
Funding
- Fondecyt Regular 2017, PI “New Insights into conformational equilibria of proteins absorbed to nanometal surfaces using molecular dynamics simulations: structural effects and protein camouflage applicable to nanomedicine.” Universidad de Talca. 2017 – 2021
- Fondecyt Regular 2018, Co-Investigator: Horacio Poblete, PI: Jans Alzate-Morales “Estimating residence time in protein-ligand complexes: New computational tools for understanding the in-vivo pharmacological effects of drugs.” Universidad de Talca. 2018 – 2021
- Millennium Nucleus 2017, Young Investigator “Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD).” Universidad de Talca. 2017 – 2021
- Talca University Research support “Desarrollo Nucleo Cientifico Multidiciplinario” 2017-2020
Former Members
- Matias Zuñiga Bustos. Matías was a postdoctoral researcher in the group from 2017 to 2022. He played a key role in the execution of research projects and the supervision of students. In 2022, he was awarded a Fondecyt de Iniciación grant, which enabled him to secure a position as Assistant Professor at the Universidad Tecnológica Metropolitana, where he is currently establishing his own research group.
- Constanza Galaz Araya. Constanza was a Ph.D. student in the group (DoMoSQB program) from 2019 to 2025, successfully completing her doctoral studies with five scientific publications. Her Ph.D. thesis was titled “Nanoengineering of Short Peptide Sequences for the Stabilization of Metal Structures.”
Theoretical and Computational Biophysics: Predicting the adsorption of proteins onto nano-surfaces, using molecular dynamics and Free-energy calculation for inorganic/biological systems.
Design of new bio-nanomaterials for bio-medicine applications.
- The Julio Caballero Group
Participants
- Julio Caballero (Ph.D.)
- José Luis Velázquez-Libera (postdoc)
- Tomás Castro (PhD student)
- Jorge Luis Valdes (PhD student)
- Luis Castillo (PhD student)
- Fabian Gonzalez (PhD student)
- Sergio Alfaro (PhD student)
Research Lines
- Protein-ligand interactions using protocols including docking, molecular dynamics (MD), QSAR, hybrid calculation methods, pharmacophore modeling, de novo design, virtual screening.
- Ligand-based molecular modeling (QSAR, pharmacophore modeling, chemoinformatics). Applications to the study of the potency of synthetic bioactive compounds and natural products.
- Modeling of enzyme–inhibitor systems such as protein kinase inhibitors, angiotensin converting enzyme inhibitors, acetylcholinesterase inhibitors, etc.
- Structural features of target proteins, such as potassium channels, the sigma1 receptor, the TRPV-1 channel, etc.
- Methods of computational biochemistry, pharmaceutical modeling, protein structure and function, enzyme reactivity and selectivity, and contributions to medicinal chemistry topics.
Funding
- FONDECYT Regular # 1170718 ‘Design and synthesis of angiotensin-converting enzyme inhibitors using molecular modeling and multicomponent reactions’ 2017-2021.
- FONDECYT postdoctorade project Francisco Adasme Carreño. # 3180193 ” Derivation of amino acid structural propensities from theoretical potentials for protein structure prediction”, 2018-2021, (Sponsor)
- FONDECYT postdoctorade project Alexander Fernández de la Torre. # 3170003 ” Diseño, síntesis y evaluación biológica de una nueva librería de compuestos fosfono-peptidomiméticos como inhibidores de la enzima Pseudomona elastasa (LasB)”, 2017-2020, (Sponsor)
- FONDECYT postdoctorade project Erix Wiliam Hernández Rodríguez. # 3170107 ” Modelación computacional de capacidades para la producción fotosensibilizada de oxígeno singlete en rodopsinas mutantes asociadas a degeneración retiniana”, 2017-2020, (Sponsor)
- FONDECYT postdoctorade project Fabián Andrés Ávila Salas. # 3170909 “Diseño racional, síntesis y evaluación de nuevas nanoformulaciones basadas en polímeros para liberación controlada de feromonas sexuales de Lobesia botrana a través de una estrategia híbrida in-silico/experimental”, 2017-2020, (Sponsor)
Protein-ligand interactions using protocols including docking, molecular dynamics (MD), QSAR, hybrid calculation methods, pharmacophore modeling, de novo design, virtual screening.
Ligand-based molecular modeling (QSAR, pharmacophore modeling, chemoinformatics).
Applications to the study of the potency of synthetic bioactive compounds and natural products.
