Ramírez Lab

Pharmacoinformatics & Drug Design

Welcome to the Ramírez Lab

We are a multidisciplinary group focused on the study of biomolecular systems by using theoretical and experimental approaches. We aim to use computational polypharmacology with wet lab analyses to strengthen the drug design and development processes. Our work involves collaboration with medicinal chemists, biochemists, and biologists, and we are part of the Pharmacology Department - Faculty of Biological Sciences at University of Concepción.

Active research areas

  • Systems and network pharmacology: We integrate biological data across various levels of organization, such as genomics, proteomics, and metabolomics. By doing so, we gain a better understanding of the intricate interactions between drugs and biological pathways in the body. This knowledge strengthens our ability to design drugs that target multiple targets/pathways simultaneously, achieving better and more comprehensive therapeutic outcomes. Our approach offers a promising direction toward developing more effective treatments for a range of complex diseases.
  • Structural bioinformatics: We use of computational methods such as molecular dynamics simulations, to predict and analyze the structure of protein-ligand complexes, which can be used to identify potential therapeutic targets and design new drugs. Furthermore, we validate our findings through experimental testing to ensure their accuracy and reliability. Our approach in structural bioinformatics offers a promising avenue for discovering novel treatments for a range of diseases.

  • Multitarget drug design aimed at complex diseases: We employed machine learning and artificial intelligence to analyze large datasets and identify novel targets. We then designed new molecules using this information to create multitarget-directed ligands. The designed molecules are tested and optimized through medicinal chemistry campaigns.

  • Latest publication

    Trends and challenges in chemoinformatics research in Latin America

    Miranda-Salasa, J.; Peña-Varasb, C.; Valenzuela, I.; Olmedod, D.; Zamorae, W.; Chávez-Fumagallig, M.; Azevedoh, D.; Oliveira R.; Maltarolloh, V.; Ramírez, D.; and Medina-Franco, L.

    Artificial Intelligence in the Life Sciences. 3 (2023) 100077. DOI: 10.1016/j.ailsci.2023.100077

    Chemoinformatics is an independent inter-discipline with a broad impact in drug design and discovery, medicinal chemistry, biochemistry, analytical and organic chemistry, natural products, and several other areas in chemistry. Through collaborations, scientific exchanges, and participation in international research networks, Latin American scientists have contributed to the development of this subject. The aim of this perspective is to discuss the status and progress of the chemoinformatic discipline in Latin America. We team up to provide an author ́s perspective on the topics that have been investigated and published over the past twelve years, collaborations between Latin America researchers and others worldwide, contributions to open-access chemoinformatic tools such as web servers, and educational-related resources and events, such as scientific conferences. We conclude that linking and fostering collaboration within each nation as well as among other Latin American nations and globally is made possible by open science and the democratization of science. We also outline strategic actions that can boost the development and practice of chemoinformatics in the region and enhance the interaction between Latin American countries and the rest of the world.


    Grant Funded by Role Date
    Open Chemoinformatics. Chile - Universidad de Concepción No. 2023014 Principal Investigator 2023 – 2024
    Uso de un Escape Room como recurso docente en las asignaturas de Faramcología. Chile - Universidad de Concepción No. 2023015 Co-investigator 2023 – 2024
    Ori-tanpakushitsu: creación de modelos tridimensionales para la comprensión de las fuerzas intermoleculares involucradas en la acción farmacológica. Chile - Universidad de Concepción No. 2023023 Co-investigator 2023 – 2024
    Ligand and structure-based polypharmacology of K+ channels from the nociceptive primary sensory neurons: an alternative in pain treatment. Chile - Fondecyt Regular No. 1230446 Co-investigator 2023 – 2027
    Development of an infectious process-activated protide with therapeutic potential for control of fish farming diseases. Chile - Fondecyt Regular No. 1231088 Co-investigator 2023 – 2027
    Interdisciplinary generation of highly specific peptidic blockers of TASK-3 channel with antitumoral effect and targeting moiety for nanotherapeutics. Chile - Fondecyt Regular No. 1230996 Co-investigator 2023 – 2027
    Multidisplinary Center for Biotechnology and Molecular Biology for Climate Change Adaptation in Forest Resources (CeBioCliF). Chile - ANID No. ATE220043 Principal Investigator 2022 – 2025
    Towards systems pharmacology to design multi-target directed ligands as therapeutic alternatives for Alzheimer’s disease. Chile - Fondecyt Regular No. 1220656 Principal Investigator 2022 – 2025
    Let's talk pharmacology!!! Chile - Universidad de Concepción No. UCO1966 Principal Investigator 2022
    Identificación de moduladores del canal iónico TMC1 como alternativa terapéutica para el tratamiento de la sordera. Chile - ANID No. FOVI210027 Principal Investigator 2022 - 2023
    Development of novel therapeutic alternatives for alcohol-use disorders: a multidisciplinary approach. Chile - ANID No. ACT210012 Deputy Director 2022 - 2025
    Coupling artificial intelligence and neurosciences to potentiate pharmacological actions of tibolone over neuroglobin signaling in traumatic brain injury. Ireland - Science Foundation Ireland Associate Investigator 2021 - 2024
    Reposicionamiento de medicamentos para tratamiento de la pandemia por coronavirus (COVID-19). Chile - ANID No. COVID0199 Principal Investigator 2021 - 2022
    Actualización de los servicios de ANSEP (Astrocyte-neuron simulation environment platform) bajo el estudio integrativo de enfermedades neurodegenerativas. Colombia - Pontificia Universidad Javeriana Associate Investigator 2021 - 2022
    Target- and ligand-based drugs to control SARS-CoV-2 pandemic (CoV2Drugs). Spain - CSIC-COV19-015 Associate Investigator 2020 - 2021
    Multi-Target Drug Design Against Neurodegenerative Diseases. Chile - Conicyt No. REDES190074 Principal Investigator 2020 - 2021
    INSECTR – International Network to Study Secondary Metabolite Transport In Plants. Chile - Conicyt No. REDES1900254 Associate Investigator 2020 - 2021
    Identificación de reacciones controladoras de lipotoxicidad inducida por ácido palmítico en un modelo computacional multiómico astrocitario. Colombia - Colciencias No. 67270 Associate Investigator 2020 - 2022
    Scholarship Programme for Young Professors and Researchers from Latin American Universities. Spain - Coimbra group Principal Investigator 2019
    Structural insights into the substrate specificity and transport mechanisms in the Nitrate/Peptide Transporter (NPF) Family. Chile - Fondecyt Iniciación No. 11180604 Principal Investigator 2018 – 2021
    Análisis metabolómico de los efectos neuroprotectores de la tibolona en un modelo astrocitico humano de lipotoxicidad con ácido palmítico. Colombia - Colciencias International Advisor 2017 - 2020