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 proteins-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 aim 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

    Network pharmacology reveals multitarget mechanism of action of drugs to be repurposed for COVID-19

    Alegría-Arcos, M.; Barbosa, T.; Sepúlveda, F.; Combariza, G.; González, J.; Gil, C.; Martínez, A.; and Ramírez, D.

    Frontiers in Pharmacology. 13:952192. DOI: 10.3389/fphar.2022.952192

    The coronavirus disease 2019 pandemic accelerated drug/vaccine development processes, integrating scientists all over the globe to create therapeutic alternatives against this virus. In this work, we have collected information regarding proteins from SARS-CoV-2 and humans and how these proteins interact. We have also collected information from public databases on protein–drug interactions. We represent this data as networks that allow us to gain insights into protein–protein interactions between both organisms. With the collected data, we have obtained statistical metrics of the networks. This data analysis has allowed us to find relevant information on which proteins and drugs are the most relevant from the network pharmacology perspective. This method not only allows us to focus on viral proteins as the main targets for COVID-19 but also reveals that some human proteins could be also important in drug repurposing campaigns. As a result of the analysis of the SARS-CoV-2–human interactome, we have identified some old drugs, such as disulfiram, auranofin, gefitinib, suloctidil, and bromhexine as potential therapies for the treatment of COVID-19 deciphering their potential complex mechanism of action.


    Grant Funded by Role Date
    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