personal photo of Álex Pérez Sánchez

Álex Pérez Sánchez

Tagline:PhD Student & Teaching Assistant @ Universitat Autònoma de Barcelona

Barcelona, España

About me

Hello! I'm a computational chemist who is deeply interested in understanding how inflammation works. My research focuses on cyclooxygenase pathways, which are crucial for creating new drugs that could be important in treating cancer.

🧪 Research Focus: During my PhD, I explore how inflammation happens using computational methods. My goal is to learn more about cyclooxygenase processes, which could help in developing new drugs for cancer treatment.

🎓 Teaching Experience: I have more than ten years of teaching experience. I currently help with lab and problem sessions for basic and computational chemistry, working with undergraduate students to support their scientific growth.

Education

  • Doctor of Philosophy

    from: 2022, until: present

    Field of study:Computational Chemistry applied to BiosystemsSchool:Universitat Autònoma de BarcelonaLocation:Cerdanyola del Vallès, Barcelona

    Description

    This programme aims to train researchers both for the business and academic sectors covering a wide range of areas from molecular structures to industrial applications.

  • Master's Degree Erasmus Mundus in Theoretical Chemistry and Computational Modelling

    from: 2021, until: 2023

    Field of study:Computational ChemistrySchool:Universitat de BarcelonaLocation:Barcelona

    Description

    The TCCM master will teach you the fundamental of Quantum Chemistry, which is at the core of most accurate techniques in Theoretical Chemistry, but will also provide you with the necessary skills to use and modify the most advanced software codes used to perform simulations of real systems. You will also learn to simulate complex systems by combining techniques based on Quantum Mechanics with classical Molecular Dynamics techniques.

  • Bachelor's Degree in Chemistry

    from: 2017, until: 2021

    Field of study:ScienceSchool:Universitat Autònoma de BarcelonaLocation:Cerdanyola del Vallès, Barcelona

    Description

    A bachelor’s degree offering theoretical and experimental training in what matter is and how it can be analysed and transformed, both from the scientific perspective as well as possible industrial applications

Academic Positions

  • PhD Student Representative on the Academic Personnel Committee

    from: 2024, until: present

    Organization:Universitat Autónoma de BarcelonaLocation:Cerdanyola de Vallès, Barcelona

  • Visiting PhD Student

    from: 2024, until: 2024

    Organization:Stockholms universitetLocation: Stockholm, Sweden

    Description:

    3-months stay at Kaila Lab working on EP4 receptor under the supervision of Ville Kaila and mentored by Patricia Saura.

  • PhD Student

    from: 2022, until: present

    Organization:Universitat Autònoma de BarcelonaLocation:Cerdanyola del Vallès, Barcelona

    Description:

    Supervised by Prof. Àngels González-Lafont & José M. Lluch

  • Teaching Assistant

    from: 2022, until: present

    Organization:Universitat Autònoma de BarelonaLocation:Cerdanyola del Vallès, Barcelona

  • Master Student Researcher

    from: 2022, until: 2023

    Organization:Universitat de Barcelona

  • Research Collaborator

    from: 2021, until: 2022

    Organization:Universitat Autònoma de BarcelonaLocation:Cerdanyola del Vallès, Barcelona

  • Undergraduate Student Researcher

    from: 2020, until: 2021

    Organization:Universitat Autònoma de BarcelonaLocation:Cerdanyola del Vallès, Barcelona

Publications

  • First-principles simulations of the fluorescence modulation of a COX-2 specific fluorogenic probe upon protein dimerization for cancer discrimination

    ManuscriptDate:unpublished
    Authors:
    Álex Pérez-SánchezCarles CurutchetÀngels González-LafontJosé M. Lluch
  • Computational Calculation of the Fluorescence Spectrum of a COX-2-specific Fluorogenic Probe Inside the Human COX-2

    ThesisPublisher:Universitat de BarcelonaDate:2023
    Authors:
    Supervised by Carles Curutchet, Àngels González-Lafont & José M. Lluch
  • Estudi Teòric de Fotointerruptors Moleculars com Possibles Inhibidors de l'Activitat Enzimàtica

    ThesisPublisher:Universitat Autònoma de BarcelonaDate:2021
    Authors:
    Supervised by Àngels González-Lafont

Research Projects

  • Using Biomolecular Engineering and Theoretical Photopharmacology to Design and Obtain New Drugs for Human Diseases, Including COVID-19

    date: 2021

    Organization:Universitat Autònoma de Barcelona

    Description:

    In this project in the field of theoretical molecular biology we aim to apply the most powerful tools of theoretical chemistry (quantum chemistry, statistical mechanics and biomolecular simulations) to the central problems of the biotechnological and pharmaceutical industry.

Communications

  • Oral Communication | Insights Into PGE2-mediated EP4 Receptor Activation Explored by Molecular Simulations

    Date: Jun 2024

    Event name: 9th European Workshop on Lipid Mediators (9EWLM) .Location: University of Edinburgh, Edinburgh, Scotland, United Kingdom .

    Description:

    Lipid mediators, such as prostaglandin E2 (PGE2), play fundamental roles in cellular communication and in the development of diseases like cancer. The lipid mediators interact with specialized proteins called G protein-coupled receptors (GPCRs), with Prostaglandin E2 Receptor Type 4 (EP4) being particularly significant in cancer and inflammation, driving tumor growth, metastasis, and immune evasion. By employing advanced Free Energy Perturbation (FEP) and atomistic Molecular Dynamics (MD) simulations of the receptor-G proteins complex in its native membrane, we study here how PGE2 activates EP4, offering novel molecular insight into the treatment of diseases. In this regard, we unravel the complex interactions between PGE2 and EP4, revealing mechanisms behind receptor and G protein activation process. Our combined findings provide insights into the functional dynamics of for GPCRs for the future development of innovative therapeutic strategies for cancer by targeting key cellular signalling pathways

    • oral9ewlm
  • Poster Communication | Insights Into PGE2-mediated EP4 Receptor Activation Explored by Molecular Simulations

    Date: Jun 2024

    Event name: 9th European Workshop on Lipid Mediators (9EWLM) .Location: University of Edinburgh, Edinburgh, Scotland, United Kingdom .

    Description:

    Lipid mediators, such as prostaglandin E2 (PGE2), play fundamental roles in cellular communication and in the development of diseases like cancer. The lipid mediators interact with specialized proteins called G protein-coupled receptors (GPCRs), with Prostaglandin E2 Receptor Type 4 (EP4) being particularly significant in cancer and inflammation, driving tumor growth, metastasis, and immune evasion. By employing advanced Free Energy Perturbation (FEP) and atomistic Molecular Dynamics (MD) simulations of the receptor-G proteins complex in its native membrane, we study here how PGE2 activates EP4, offering novel molecular insight into the treatment of diseases. In this regard, we unravel the complex interactions between PGE2 and EP4, revealing mechanisms behind receptor and G protein activation process. Our combined findings provide insights into the functional dynamics of for GPCRs for the future development of innovative therapeutic strategies for cancer by targeting key cellular signalling pathways

    • 9ewlm
  • Oral Communication | Unraveling the Activation of EP4 Receptor by Prostaglandin E2

    Date: Jun 2024

    Event name: Electronic Structure Principles and Applications (ESPA2024) .Location: Tarragona, Catalunya, Espanya .

    Description:

    G protein-coupled receptors (GPCRs) are central players in cellular signaling pathways and represent
    prominent targets for drug development in various diseases, including cancer. The EP4 receptor belongs to the
    prostaglandin E2 (PGE2) receptor family of GPCRs that has received significant attention due to its
    involvement in cancer progression and inflammation. Overexpression of EP4 promotes tumor growth,
    metastasis, and evasion of immune surveillance in numerous cancer types. Understanding the molecular
    mechanisms underlying the EP4 receptor activation by its endogenous ligand, PGE2, and subsequent
    engagement with G proteins is crucial for unraveling its role in cancer pathogenesis and devising targeted
    therapeutic strategies. Using atomistic molecular dynamics (MD) simulations in combination with enhanced
    sampling methods and free energy calculations, we study here the mechanisms of EP4 receptor activation by
    PGE2 and its interaction with G proteins, offering insights into cancer-associated signaling pathways regulated
    by this receptor.

    • espa2024_poster
  • Oral Communication | Understanding COX-2 for the Design of New Cancer Drugs: Computational Study with Specific Photochromic Compounds

    Date: Feb 2024

    Event name: 15th Young Researchers in Atomic and Molecular Physics Conference (J2IFAM) .Location: Insitut de Ciència Molecular (ICMol), Parc Científic de la Universitat de València, València, España .

    Description:

    Cyclooxygenases are a family of enzymes essential in the regulation of inflammation and other processes in the human body. There are two main isoforms, COX-1 and COX-2, with different roles and patterns of expression in tissues. COX-1 is widely expressed and maintains homeostasis, while COX-2 is restricted to specific regions and it is inducible, especially in at inflamed tissues and cancer cells. COX-2 overexpression is associated with the development of cancer in several types of tumors. To investigate this phenomenon, fluorescent compounds derived from anti-inflammatory drugs are usually experimentally used for the detection of COX-2 in cancer cells.
    Using different computational techniques (Molecular Docking, Molecular Dynamics Simulations, QM/MM and TD-DFT Calculations) we have calculated and analyzed the fluorescence spectra of a photochromic compound bound to the monomer and dimer of human COX-2. The differences between the monomeric and dimeric spectra reveals molecular insights of the protein’s behavior in cells with COX-2 overexpressed. This research provides valuable information for the possible future design of specific drugs for cancer treatments.

    • alex_j2ifam
    • j2ifam_todos
  • Oral Communication | Entendre la COX-2 pel Dissney de Fàrmacs Contra el Càncer: Estudi Computacional Mitjançant un Compost Fluorogènic Específic

    Date: Jan 2024

    Event name: 13a Trobada de Joves Investigadors dels Països Catalans .Location: Tarragona, Catalunya, Espanya .

  • Poster Communication | lluminating the Dark Side of COX-2: Insights from Computational Simulations and Fluorescent Probes in Cancer Research

    Date: Aug 2023

    Event name: European Conference on Computational & Theoretical Chemistry .Location: Thessaloniki, Greece .

    Description:

    Exploring Molecular Space. Presented by the Division of Computational and Theoretical Chemistry

    • 1693483678256

Teaching

  • Interactive Chemistry Sessions

    From: 2024, Until: 2024

    Organization:Chemistry DepartmentField:ARGO Program

  • Co-Supervision of Research Activities

    From: 2023, Until: 2024

    Organization:Chemistry DepartmentField:Final Bachelor's Degree Project

    Description:

    Co-supervision of two final bachelor’s degree projects.

  • Chemistry Fundamentals

    From: 2023, Until: 2024

    Organization:Department of ChemistryField:Bachelor's Degree in Chemical Engineering

    Description:

    Professor for problems sessions of Chemistry Foundations (51.9 hours)

  • Quantum Chemistry

    From: 2023, Until: 2024

    Organization:Chemistry DepartmentField:Bachelor's Degree in Chemistry

    Description:

    Professor for the computational laboratories of Quantum Chemistry (20 hours)

  • Correction and Supervision of University Entrance Tests

    From: 2023, Until: 2023

    Organization:Generalitat de CatalunyaField:University Entrance Tests

    Description:

    Chemistry Corrector and Supervisor of Court 329

  • Quantum Chemistry

    From: 2022, Until: 2023

    Organization:Chemistry DepartmentField:Bachelor's Degree in Chemistry

    Description:

    Professor for the computational laboratories of Quantum Chemistry (20 hours)

  • Co-Supervision of Research Activities

    From: 2022, Until: 2023

    Organization:Chemistry DepartmentField:Final Bachelor's Degree Project

    Description:

    Co-supervision of one final bachelor’s degree projects.

  • Chemical Bonding and Structure of Matter

    From: 2022, Until: 2023

    Organization:Chemistry DepartmentField:Bachelor's Degree in Nanoscience and Nanotechonology

    Description:

    Professor for the experimental laboratories of Chemical Bonding and Structure of Matter (12 hours)

  • Thermodynamics, Kinetics and Phase Transformations

    From: 2022, Until: 2023

    Organization:Chemistry DepartmentField:Bachelor's Degree in Nanoscience and Nanotechnology

    Description:

    Professor for the experimental laboratories of Thermodynamics, Kinetics and Phase Transformations (12 hours)

  • Interactive Chemistry Sessions

    From: 2022, Until: 2023

    Organization:Chemistry DepartmentField:ARGO Program

Courses

  • Practical Tools for the Inclusion of Students with Functional Diversity in Teaching Types

    from: Dec 2023, until: Dec 2023

    Organization: Suport a estudiants amb Necessitats Educatives Específiques (PIUNE) .

  • Workshop for Implementation Challenge-Based Learning by Dorothea Ellinger (Technische Universität Hamburg)

    from: Dec 2023, until: Dec 2023

    Organization: Projecte “Desenvolupament de metodologies actives, ApS i ABR, aplicades a les assignatures de Pràctiques Externes i TFE. Una acció tutorial transversal i interdisciplinària envers els ODS”. En col·laboració amb l’Oficina de Reptes UAB .

  • Research data: publish open research data and create a Data Management Plan (DMP)

    from: Nov 2023, until: Nov 2023

    Organization: Servei de Bibloteques. Universitat Autònoma de Barcelona .

  • What can do Charmm-GUI for you?

    from: Jun 2023, until: Jun 2023

    Organization: Centro de Investigaciones Biológicas Margarita Salas | CSIC .

  • Chemical Risks in the Laboratory

    from: Nov 2022, until: Nov 2022

    Organization: Universitat Autònoma de Barcelona .

  • Molecular Modelling: Biomolecules and Drug Design 2022. An Advanced Course in Computational Chemistry

    from: Jun 2022, until: Jul 2022

    Organization: Institut de Química Teòrica i Computacional (IQTC-UB) .

    Description:

    The advanced course intended to broaden the vision of the potentials of computing in the research and development of new drugs, new materials or new compounds.
    The course takes place for a whole week and is mainly addressed to Chemistry, Biology, Pharmacy and Chemical Engineering students.

  • School on Quantum and Mixed Quantum Classical Dynamics in Photochemistry

    from: May 2022, until: May 2022

    Course Number: CECAM-ES .Organization: Universidad de Zaragoza .

    Description:

    Photoinitiated processes are important for the understanding of natural phenomena and they also play an essential role in emerging fields as renewable energy, material design and nano-medicine.

  • School on Kinetics and Dynamics of Chemical Reactions

    from: May 2022, until: May 2022

    Course Number: CECAM-ES .Organization: Universidad de Zaragoza .

    Description:

    Molecular reaction dynamics is the study of elementary processes and the means of probing them, understanding them, and controlling them. It can be applied to reactions in gas phase, in solution and onto surfaces, exploring the elementary steps in catalysis. Nowadays, chemistry requires a molecular level understanding of the reactivity.