Katarzyna Świderek's picture
Senior researcher
Research Group: RG9. Computational Biochemistry
Office: TC1203DD
Workphone: +34964728070
E-mail: swiderek@uji.es
Address:
Institute of Advanced Materials (INAM)
Universitat Jaume I
12006 Castelló
Spain
Researcher information:
Personal website: http://www.biocomp.uji.es/swiderek/home.html
ORCID: http://orcid.org/0000-0002-7528-1551
Researcher ID: http://www.researcherid.com/rid/B-2851-2012
Google scholar: https://scholar.google.es/citations?user=https://scholar.google.es/citations?hl=pl&user=kntRtkUAAAAJ&view_op=list_works
Bio and research interests
Katarzyna Świderek, studied Chemistry and obtained her Master (2007) and Ph.D. (2011) degrees in Physical Chemistry at the Lodz University of Technology (Poland), under the supervision of Prof. P. Paneth. During 2007 she was working in a crystallographic laboratory in the Institute of Technical Biochemistry at the same University and in 2008 she stayed 3 months in the Helmholtz Centre for Environmental Research-UFZ in Leipzig (Germany) funded by an AXIOM - Marie Curie Host Fellowship. In 2011, she moved to the University of Valencia (Spain) for her first postdoctoral stay under the supervision of Professor I. Tuñón, until the end of 2014. In 2015 she obtained a 3-year contract in an NIH project (National Institute of Health, USA) as a postdoctoral researcher at University Jaume I (UJI, Spain) under the supervision of Professors V. Moliner (UJI) and A. Kohen (University of Iowa, USA). At the same time, she became principal investigator (PI) of an “Iuventus Plus” project funded by the Polish Ministry of Science and Higher Education dedicated to talented young researchers (under 35). In 2017 she spent 6 months in the laboratory of Professor I. H. Williams at the University of Bath (UK). In 2018 she obtained a two years Juan de la Cierva-Incorporation contract from the Spanish Ministry of Economy and Competitiveness that allowed her to be involved in the projects conducted in the BioComp group at Universitat Jaume I. Recently, (1/10/2020), she obtained a 3-years contract as a PI in a JIN project funded by the Spanish Ministry of Science, Innovation, and Universities at the same University, and her research is funded by SEJI 2020 (Scientific Excellence Junior Researchers Grants) program of Valencian Regional Government and a project founded by UJI, in which she is also PI. The professional activity and the main research line of Dr. Świderek are focused on theoretical studies of reactivity present in cellular processes, from inhibition to design. In general, three closely connected areas to the mainline of interest can be distinguished in her recent career path i.e. the origin of biocatalysis, inhibition and drug design, and design of biocatalysts. In particular, most of Dr. Świderek’s studies are based on molecular dynamic (MD) simulations with hybrid QM/MM potentials. Obtained results of computational studies of biological catalysts can provide information to be widely exploited in pharmacological, medical, and industrial areas. The investigation projects conducted by Dr. Świderek involve national and international collaborators including researchers from Spain, Poland, the USA, UK, Canada, and Italy.

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. 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.

  3. 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.

  4. 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

  5. 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.

2022

  1. 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.

  2. ACS Catalysis, 2022, 12, 698-708.

    Martí, S.; Arafet, K.; Lodola, A.; Mulholland, A.J.; Świderek, K.; Moliner, V.

    Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations.

  3. Chemical Science, 2022, 13, 4779.

    Galmés, M.À.; Nödling, A.R.; He, K.; Luk, L.Y.P.; Świderek, K.; Moliner, V.

    Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases.

  4. ACS Catalysis, 2022, 12, 14667–14678.

    Akintola, O.; Farren-Dai, M.; Ren, W.; Bhosale, S.; Britton, R.; Świderek, K.; Moliner, V.; Bennet, A.J.

    Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States?.

2021

  1. Top Catalysis, 2021, 1-12.

    Serrano-Aparicio, N.; Świderek, K.; Tuñón, I.; Moliner, V.; Bertran, J.

    Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism.

  2. ACS Catalysis, 2021, 11, 10383-10393.

    Farren-Dai, M.; Sannikova, N.; Świderek, K.; Moliner, V.; Bennet, A.J.

    Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates–Glycopyranosyl Fluorides.

  3. Chemical Science, 2021, 12, 13686-13703.

    Chan, H.T.H.; Moesser, M.A.; Walters, R.K.; Malla, T.R.; Twidale, R.M.; John, T.; Deeks, H.M.; Johnston-Wood, T.; Mikhailov, V.; Sessions, R.B.; Dawsonl, W.; Saleh, E.; Lukacik, P.; Strain-Damerell, C.; Owen, C.D.; Nakajima, T.; Świderek, K.; Lodola, A.; Moliner, V.; Glowacki, D.R.; Spencer, J.; Walsh, M.A.A.; Schofield, .J.; Genovese, L.; Shoemark, D.K.; Mulholland, A.J.; Duarte, F.; Morris, G.M.

    Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding.

  4. ACS Catalysis, 2021, 11, 11806–11819.

    Serrano-Aparicio, N.; Moliner, V.; Świderek, K.

    On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome.

  5. Org. Biomol. Chem., 2021, 19, 10424-10431.

    Nödling, A.R.; Santi, N.; Castillo, R.; Lipka-Lloyd, M.; Jin, Y.; Morrill, L.C.; Świderek, K.; Moliner, V.; Luk, L.Y.P.

    The role of streptavidin and its variants in catalysis by biotinylated secondary amines..
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