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Jun-Prof. Dr. Mercedes Alfonso Prieto

Junior Professor

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Group leader at Forschungszentrum Jülich (INM-9/IAS-5 Computational Biomedicine).
Position partly funded by the Ernesto Illy Foundation through the grant "Computational science of chemical senses".

Professional career

12.2016 - 11.2021

Assistant Professor (W1 Junior-Professor)

Cécile and Oskar Vogt Institute for Brain Research

Heinrich Heine University Düsseldorf

10.2014 - 09.2016Marie Curie postdoctoral fellow (Univ. of Barcelona, Spain)
Advisor: Prof. Carme Rovira
04.2010 - 09.2014Postdoctoral researcher (Temple University, USA)
Advisor: Prof. Michael L. Klein
10.2004 - 12.2009Master and PhD student (Barcelona Science Park, Spain)
Supervisor: Prof. Carme Rovira



12.2009PhD degree (Autonomous University of Barcelona, Spain)
05.2006Master degree (Autonomous University of Barcelona, Spain)
02.2005Degree in Biochemistry (University of Barcelona, Spain)
Prize for excellence as undergraduate student
09.2004Degree in Chemistry (University of Barcelona, Spain)


Scientific honours

10.2014 - 09.2016        Marie Curie postdoctoral fellow at Univ. of Barcelona (Spain)

Ongoing funded project as PI

Name of the GrantCo-PIsCallTime PeriodAmount
DFG Research Unit DynIon – Project P6: Proton transfer and substrate recognition in SLC17 transportersProf. Paolo Carloni (FZJ, INM-9/IAS-5) and Prof. Christoph Fahlke (FZJ, IBI-1)DFG Research Unit05.2020 – 05.2023173,100
Multidisciplinary approach for mapping protein-protein interactions surfaces: From mass spectrometry to computational and cell biologyProf. Patricia Hidalgo (FZJ, IBI-1) and Dr. Beatrix Santiago-Schuebel (FZJ, ZEA-3)Networking Doctoral Position funded by the FZJ Board of Directors10.2019 – 09.20223 year PhD position
Prediction of ligand protein interactions and brain signaling cascades using machine learning approaches: olfaction as a test scenarioProf. Marc Spehr (RWTH Aachen University) and Prof. Alejandro Giorgetti (FZJ)Doctoral position in Simulation and Data Sciences06.2019 – 06.20223 year PhD position

Ongoing funded projects contributing as participant personnel

Name of the GrantPICallTime PeriodAmount
Molecular simulation-based rational design of painkillers targeting the opioid receptor (PaTOR)Prof. Paolo CarloniBMBF call for funding for bilateral cooperation with Vietnam02.2019 – 01.2022240,000


  • Mr. Giuliano Santarpia, PhD student co-supervised with Prof. Marc Spehr and Prof. Alejandro Giorgetti.
  • Mr. Francisco Castilla Porras, PhD student co-supervised with Prof. Patricia Hidalgo and Dr. Beatrix Santiago-Schuebel.
  • Mr. Nicolas P. Müller (02.2020 – present), PhD student.
  • Dr. Samira Gholami Semsury (11.2021 – present), postdoc working with Prof. Paolo Carloni, Prof. Christoph Fahlke, Prof. Ana-Nicoleta Bondar and Dr. Emiliano Ippoliti.
  • Mr. Sabahuddin Ahmad (09.2021 – present), postdoc working with Prof. Paolo Carloni and Prof. Alejandro Giorgetti.

Research interest and activity

Our research aims at understanding the function of chemosensory receptors [1-6] and ion channels [7-10] at the molecular level, combining structural bioinformatics and multiscale molecular dynamics simulations (both atomistic and hybrid atomistic/coarse-grained).

Selected publications (2019 - 2021)
* denotes corresponding or co-corresponding author and # equal first authorship.

  1. Dual binding mode of “bitter sugars” to their human bitter taste receptor target.
    F. Fierro, A. Giorgetti, P. Carloni, W. Meyerhof, M. Alfonso-Prieto*, Sci. Rep. 9, 8437 (2019). (Link)
  2. Understanding ligand binding to G-protein coupled receptors using multiscale simulations.

    M. Alfonso-Prieto, L. Navarini, P. Carloni, Front. Mol. Biosci. 6, 29 (2019). (Link)

  3. Multiscale simulations on human Frizzled and Taste2 GPCRs.

    M. Alfonso-Prieto#, A. Giorgetti#, P. Carloni, Curr. Opin. Struct. Biol. 55, 8-16 (2019). (Link)

  4. Hybrid MM/CG Webserver: Automatic set up of molecular mechanics/coarse-grained simulations for human G protein-coupled receptor/ligand complexes.

    J. Schneider, R. Ribeiro, M. Alfonso-Prieto, P. Carloni, Alejandro Giorgetti, Front. Mol. Biosci., 7, 576689 (2020). (Link)

  5. Ligand pose predictions for human G protein-coupled receptors: insights from the Amber-based hybrid Molecular Mechanics/Coarse-Grained approach.

    J. Schneider, K. Korshunova, Z. Si Chaib, A. Giorgetti, M. Alfonso-Prieto, P. Carloni, J. Chem. Inf. Model., 60, 5103-5116 (2020). (Link)

  6. Bitter taste and olfactory receptors: Beyond chemical sensing in the tongue and the nose.

    M. Alfonso-Prieto, J. Membr. Biol., 254, 343–352 (2021). (Link)

  7. A photoswitchable GABA receptor channel blocker.

    G. Maleeva,  D. Wutz,  K. Rustler,  A. Nin‐Hill,  C. Rovira, E. Petukhova,  A. Bautista‐Barrufet,  A. Gomila‐Juaneda, P. Scholze, F. Peiretti, M. Alfonso-Prieto*, B. König, P. Gorostiza*, P. Bregestovski*, Br. J. Pharmacol. 176, 2661-2677 (2019). (Link)

  8. Photocontrol of endogenous glycine receptors in vivo.

    A. Gomila-Juaneda, K. Rustler, G. Maleeva, A. Nin-Hill, D. Wutz, A. Bautista-Barrufet, X. Rovira, M. Bosch, E. Mukhametova, F. Mukhamedyarov, F. Peiretti, M. Alfonso-Prieto, C. Rovira, B. König, P. Bregestovski, P. Gorostiza, Cell Chem. Biol., 27, 1425-1433 (2020). (Link)

  9. Subunit-specific photocontrol of glycine receptors by azobenzene-nitrazepam photoswitcher.

    G. Maleeva*, A. Nin-Hill, K. Rustler, E. Petukhova, D. Ponomareva, E. Mukhametova, A. Gomila-Juaneda, D. Wutz, M. Alfonso-Prieto*, B. König, P. Gorostiza, P. Bregestovski*, eNeuro, 8, ENEURO.0294-20.2020 (2021). (Link)

  10. Mechanisms underlying proton release in CLC-type F–/H+ antiporters.

    M. G. Chiariello*, M. Alfonso-Prieto, E. Ippoliti, Ch. Fahlke*, P. Carloni, J. Phys. Chem. Lett., 12, 4415–4420 (2021). (Link)


  • Prof. Paolo Carloni, Forschungszentrum Jülich and RWTH Aachen University (Germany).
  • Prof. Alejandro Giorgetti, University of Verona (Italy).
  • Ernesto Illy Foundation, Trieste (Italy).
  • Prof. Patricia Hidalgo, Forschungszentrum Jülich and Heinrich Heine University Düsseldorf (Germany).
  • Dr. Beatrix Santiago-Schuebel, Forschungszentrum Jülich (Germany).
  • Prof. Christoph Fahlke, Forschungszentrum Jülich and Heinrich Heine University Düsseldorf (Germany).
  • Prof. Ana-Nicoleta Bondar, University of Bucharest (Romania).
  • Prof. Olga Sergeeva, Heinrich Heine University Düsseldorf (Germany).
  • Prof. Carme Rovira, University of Barcelona (Spain).


IAS-5 / INM-9
Computational Biomedicine
Forschungszentrum Jülich
52428 Jülich


Phone: +49 2461 61 8934
Fax: +49 2461 61 4823