© UDE

Project Area B - Chemical Biology

Prof. Dr. Elsa Sánchez-García

Fakultät Bio- und Chemieingenieurwesen

Technische Universität Dortmund


Email

Hybrid computational strategies for the study of cell states

Computational approaches play an essential role in the study of biological processes and well as in the design and optimization of compounds that can be used for monitoring and regulating such processes. In project B04, we employ novel in-house as well as state-of-the-art computational methodologies including machine learning tools, docking techniques, molecular dynamics simulations and free energy calculations to deliver molecular insights into protein-protein interactions relevant for cell transitions. In addition, our computational strategy allows the in-silico design of chemical tools and inhibitors targeting these processes. This way, in close collaboration with our chemistry and biology experimental partners, we contribute a deeper mechanistic understanding of key cellular processes.

Project Members

Julio Cesar Vieyto Nuñez

julio.vieyto-nunez@tu-dortmund.de

Dr. Yasser Almeida-Hernandez

yasser.almeida@tu-dortmund.de

Dr. Joel Mieres Pérez

joel.mieresperez@tu-dortmund.de

Publications

    Journal articles

  • Brenner, Joel Cyrille; Zirden, Linda; Almeida-Hernandez, Yasser; Kaschani, Farnusch; Kaiser, Markus; Sanchez-Garcia, Elsa; Poepsel, Simon; Hellerschmied-Jelinek, Doris
    Conformational plasticity of a BiP-GRP94 chaperone complex
    In: Nature Structural & Molecular Biology, Vol. 32, 2025, Nr. 10, pp. 1947 – 1958
  • Lawrenz, Jan; Wettstein, Lukas; Rodríguez Alfonso, Armando; Nchioua, Rayhane; von Maltitz, Pascal; Albers, Dan Pascal Jean; Zech, Fabian; Vandeput, Julie; Naesens, Lieve; Fois, Giorgio; Neubauer, Veronika; Preising, Nico; Schmierer, Emilia; Almeida-Hernandez, Yasser; Petersen, Moritz; Ständker, Ludger; Wiese, Sebastian; Braubach, Peter; Frick, Manfred; Barth, Eberhard; Sauter, Daniel; Kirchhoff, Frank; Sanchez-Garcia, Elsa; Stevaert, Annelies; Münch, Jan
    Trypstatin as a Novel TMPRSS2 Inhibitor with Broad-Spectrum Efficacy against Corona and Influenza Viruses
    In: Advanced Science, Vol. 12, 2025, Nr. 25, 2506430
  • Beaufort, Nathalie; Ingendahl, Linda; Merdanovic, Melisa; Schmidt, Andree; Podlesainski, David; Richter, Tim; Neumann, Thorben; Kuszner, Michael; Vetter, Ingrid R.; Stege, Patricia; Burston, Steven G.; Filipovic, Anto; Ruiz-Blanco, Yasser B.; Bravo Rodriguez, Kenny; Mieres-Perez, Joel; Beuck, Christine; Uebel, Stephan; Zobawa, Monika; Schillinger, Jasmin; Malik, Rainer; Todorov-Völgyi, Katalin; Rey, Juliana; Roberti, Annabell; Hagemeier, Birte; Wefers, Benedikt; Müller, Stephan A.; Wurst, Wolfgang; Sanchez-Garcia, Elsa; Zimmermann, Alexander; Hu, Xiao-Yu; Clausen, Tim; Huber, Robert; Lichtenthaler, Stefan F.; Schmuck, Carsten; Giese, Michael; Kaiser, Markus; Ehrmann, Michael; Dichgans, Martin
    Rational correction of pathogenic conformational defects in HTRA1
    In: Nature Communications, Vol. 15, 2024, Nr. 1, 5944
  • Day, Matthew; Tetik, Bilal; Parlak, Milena; Almeida-Hernández, Yasser; Räschle, Markus; Kaschani, Farnusch; Siegert, Heike; Marko, Anika; Sanchez-Garcia, Elsa; Kaiser, Markus; Barker, Isabel A.; Pearl, Laurence H.; Oliver, Antony W.; Boos, Dominik
    TopBP1 utilises a bipartite GINS binding mode to support genome replication
    In: Nature Communications, Vol. 15, 2024, Nr. 1, 1797
  • Ruiz-Blanco, Yasser B.; Agüero-Chapin, Guillermin; Romero-Molina, Sandra; Antunes, Agostinho; Olari, Lia-Raluca; Spellerberg, Barbara; Münch, Jan; Sanchez-Garcia, Elsa
    ABP-Finder : A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria
    In: Antibiotics, Vol. 11, 2022, Nr. 12, 1708
  • Rey, Juliana; Breiden, Maike; Lux, Vanda; Bluemke, Anika; Steindel, Maike; Ripkens, Kamilla; Möllers, Bastian; Bravo Rodriguez, Kenny; Boisguerin, Prisca; Volkmer, Rudolf; Mieres-Perez, Joel; Clausen, Tim; Sánchez-García, Elsa; Ehrmann, Michael
    An allosteric HTRA1-calpain 2 complex with restricted activation profile
    In: Proceedings of the National Academy of Sciences of the United States of America (PNAS), Vol. 119, 2022, Nr. 14, e2113520119
  • Harms, Mirja; Hansson, Rikke Fabech; Carmali, Sheiliza; Almeida-Hernández, Yasser; Sanchez-Garcia, Elsa; Münch, Jan; Zelikin, Alexander N.
    Dimerization of the Peptide CXCR4-Antagonist on Macromolecular and Supramolecular Protraction Arms Affords Increased Potency and Enhanced Plasma Stability
    In: Bioconjugate Chemistry, Vol. 33, 2022, Nr. 4, pp. 594 – 607
  • Romero-Molina, Sandra; Ruiz-Blanco, Yasser B.; Mieres-Perez, Joel; Harms, Mirja; Münch, Jan; Ehrmann, Michael; Sanchez-Garcia, Elsa
    PPI-Affinity : A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity
    In: Journal of Proteome Research, Vol. 21, 2022, Nr. 8, pp. 1829 – 1841
  • Böhm, Miriam; Killinger, Kerstin; Dudziak, Alexander; Pant, Pradeep; Jänen, Karolin; Hohoff, Simone; Mechtler, Karl; Örd, Mihkel; Loog, Mart; Sánchez-García, Elsa; Westermann, Stefan
    Cdc4 phospho-degrons allow differential regulation of ame1ceⁿp⁻u protein stability across the cell cycle
    In: eLife, Vol. 10, 2021, e67390
  • Preprints

  • Zaffar, Eman; Vieyto-Nuñez, Julio; Pravi, Katerina; Aslam, Mohammed Faidh; Almeida-Hernández, Yasser; Mieres-Pérez, Joel; Kaschani, Farnusch; Kaiser, Markus; Kroesen, Anika; Boos, Dominik; Sánchez-García, Elsa
    MTBP allosterically activates Cdk8-CycC kinase activity
    2025