Principal investigator

Research Overview

The BioComp group  is devoted to the computational description of catalysis phenomena in biological systems, mostly enzyme catalyzed processes. For this purpose, theories, methods and techniques of theoretical and computational chemistry are developed, implemented and used. Computational algorithms and protocols, based on hybrid QM/MM potentials, are created and this new knowledge is exploited in designing new materials with properties to be used in biomedicine and biotechnology. In particular, these applications are focused on elucidating enzyme reaction mechanisms including fundamental new quantum and dynamical perspectives, to design new pharmacological agents to inhibit enzyme activity, or new catalysts mimicking the catalytic efficiency and features of natural enzymes.

Group's research interests

  • Development of QM/MM methods, combined with ML techniques, for the study of biochemical processes.

  • Deciphering the mode of action of enzymes.

  • Predicting enzymatic properties by computational simulations.(rate constants, Michaelis constants, inhibition constants, kinetic isotope effects, etc).

  • Design of new enzymes.

  • Design of new enzyme-inhibitors.

  • Development of new biological materials with specific properties.

Members

Katarzyna Świderek's picture
Katarzyna Świderek

Senior Researcher
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Raquel Castillo's picture
Raquel Castillo

Senior Researcher
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Sergio Martí's picture
Sergio Martí

Senior Researcher
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María Teresa Roca Moliner's picture
María Teresa Roca Moliner

Senior Researcher
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Kemel Arafet Cruz's picture
Kemel Arafet Cruz

Research Scientist
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Victor Batista's picture
Victor Batista

Research Scientist
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Álvaro Serrano López de la Vieja's picture
Álvaro Serrano López de la Vieja

Doctoral Candidate
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Adrián Fernández de la Pradilla Ibáñez's picture
Adrián Fernández de la Pradilla Ibáñez

Doctoral Candidate
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CARMEN RAMOS VELLÓN's picture
CARMEN RAMOS VELLÓN

Doctoral Candidate
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Santiago Movilla Núñez's picture
Santiago Movilla Núñez

Doctoral Candidate
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Publications

2024

  1. ACS Catalysis, 2024, 14, 15237.

    Ferrer, S.; Moliner, V.; Świderek, K.

    Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits.

    Article page: https://pubs.acs.org/doi/10.1021/acscatal.4c04964

  2. ChemMedChem, 2024, e202400545.

    Zhang, L.; Calvo-Barreiro, L.; Batista, deSousa; Świderek, K.; Gabr, M.

    Discovery of ICOS-targeted small molecules using affinity selection mass spectrometry screening.

    Article page: https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmdc.202400545

  3. Angewandte Chemie International Edition, 2024, 136, e202403098.

    Williams, L.; Taily, I.M.; Hatton, L.; Berezin, A.A.; Wu, Y.L.; Moliner, V.; Świderek, K.; Tsai, Y.; Luk, L.Y.P.

    Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion.

    Article page: https://onlinelibrary.wiley.com/doi/full/10.1002/ange.202403098

  4. Faraday Discussions, 2024, 252, 323.

    Świderek, K.; Martí, S.; Arafet, K.; Moliner, V.

    Computational study of the Mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis.

    Article page: https://pubs.rsc.org/en/content/articlehtml/2024/fd/d4fd00022f

  5. Advance Science, 2024, 11, 2308956.

    Gabirondo, E.; Świderek, K.; Marin, E.; Maiz-Iginitz, A.; Larranaga, A.; Moliner, V.; Etxeberria, A.; Sardon, H.

    A Single Amino Acid Able to Promote High-Temperature Ring-Opening Polymerization by Dual Activation.

    Article page: https://onlinelibrary.wiley.com/doi/10.1002/advs.202308956

  6. Communications chemistry, 2024, 7, 15.

    Medrano, F.J.; de la Hoz-Rodríguez, S.; Martí, S.; Arafet, K.; Schirmeister, T.; Hammerschmidt, S.J.; Müller, C.; González-Martínez, Á.; Santillana, E.; Ziebuhr, J.; Romero, A.; Zimmer, C.; Weldert, A.; Zimmermann, R.; Lodola, A.; Świderek, K.; Moliner, V.; González, F.V.

    Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2..

    Article page: https://www.nature.com/articles/s42004-024-01104-7

2023

  1. RSC Medicinal Chemistry, 2023, 14, 1767-1777.

    Abdel-Rahman, S.A.; Świderek, K.; Gabr, M.T.

    First-in-class small molecule inhibitors of ICOS/ICOSL interaction as a novel class of immunomodulators.

    Article page: https://pubs.rsc.org/en/content/articlelanding/2023/md/d3md00150d

  2. Journal of Chemical Informatics and Modeling, 2023, 63, 1301-1312.

    Arafet, K.; Scalvini, L.; Galvani, F.; Martí, S.; Moliner, V.; Mor, M.; Lodola, A.

    Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents.

  3. Journal of American Chemical Society, 2023, 145,

    Movilla, S.; Roca, M.; Moliner, V.; Magistrato, A.

    Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases.

  4. ACS Catalysis, 2023, 13, 6289-6300.

    Arafet, K.; Royo, S.; Schirmeister, T.; Barthels, F.; González, F.V.; Moliner, V.

    Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L.

  5. Nature Communications, 2023, 14, 3556.

    Świderek, K.; Velasco-Lozano, S.; Galmés, M.À.; Olazabal, I.; Sardon, H.; López-Gallego, F.; Moliner, V.

    Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules.

  6. ACS Catalysis, 2023, 13, 13354-13368.

    Fernández-de-la-Pradilla, A.; Royo, S.; Schirmeister, T.; Barthels, F.; Świderek, K.; González, F.V.; Moliner, V.

    Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L.

  7. mathematics, 2023, 11, 279.

    Pérez, G.Alfonso; Castillo, R.

    Categorical Variable Mapping Considerations in Classification Problems: Protein Application.

  8. Medicine, 2023, 59, 1218.

    Pérez, G.Alfonso; Castillo, R.

    Gene Identification in Inflammatory Bowel Disease via a Machine Learning Approach.

  9. mathematics, 2023, 11, 1795.

    Pérez, G.Alfonso; Castillo, R.

    Nonlinear Techniques and Ridge Regression as a Combined Approach: Carcinoma Identification Case Study.

  10. Angewandte Chemie International Edition, 2023, 62, e202301914.

    Ibáñez, S.; Świderek, K.; Peris, E.

    Unlocking a (Pseudo)-Mechanically Interlocked Molecule with a Coronene "Shoehorn".

    Article page: https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202301914

  11. Angewandte Chemie International Edition, 2023,

    de Santos, G.; González-Benjumea, A.; Fernandez-Garcia, A.; Aranda, C.; Wu, Y.; But, A.; Molina-Espeja, P.; Maté, M.; Gonzalez-Perez, D.; Zhang, W.; Kiebist, J.; Scheibner, K.; Hofrichter, M.; Świderek, K.; Moliner, V.; Sanz-Aparicio, J.; Hollmann, F.; Gutiérrez, A.; Alcalde, M.

    Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids.

  12. Journal of Chemical Informatics and Modeling, 2023,

    Movilla, S.; Martí, S.; Roca, M.; Moliner, V.

    Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer’s Disease.

2022

  1. mathematics, 2022, 10, 4632.

    Alfonso, G.; Castillo, R.

    Identification of Systemic Sclerosis through Machine Learning Algorithms and Gene Expression.

  2. Pharmaceuticals, 2022, 15, 531.

    Serrano-Aparicio, N.; Ferrer, S.; Świderek, K.

    Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies.
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