Laboratorium Symulacji Systemów Chemicznych i Biologicznych

Celem grupy jest rozwijanie metod obliczeniowych i ich zastosowanie w symulowaniu układów chemicznych i biologicznych. Interesuje nas przewidywanie struktur, właściwości i funkcji białek, układów makromolekularnych i nanoukładów, katalizatorów reakcji chemicznych oraz zastosowanie metod teoretycznych do projektowania nowych materiałów/ligandów/związków chemicznych mających zastosowanie w farmacji, naukach materiałowych, nanotechnologii i katalizie.

W naszym głównym projekcie zajmujemy się przewidywaniem struktur białek membranowych z rodziny receptorów sprzężonych z białkami G (GPCR) oraz sodowych kanałów jonowych (Nav) oraz projektowaniem nowych antagonistów/agonistów dla tych białek.

Po więcej informacji, zapraszamy na stronę zespołu. 

dr hab. Bartosz Trzaskowski
e-mail: b.trzaskowski@cent.uw.edu.pl
telefon: +48 22 55 43671
pokój: 04.59

Degrees: MSc (Chemistry), PhD (Chemistry), DSc (Habilitation, Chemistry)
Tel: (+48) 554 36 71 Fax: (+4822) 554 08 01
Email: b.trzaskowski@cent.uw.edu.pl

Affiliation: Center of New Technologies, University of Warsaw, Poland

Research Interests:

Bartosz Trzaskowski interests are focused on the development and use of computational methods for the description of chemical, physical and biological phenomena. Currently he is involved mainly in projects related to homogenous catalysis with the aim to better understand the mechanisms of actions of catalysts and use this knowledge to design new, better catalysts for important chemical reactions. Earlier his main research area was the development and coding of new protocols for the prediction of the 3-dimensional, all-atom structure of G protein-coupled receptors (GPCRs). Most of his work in this topic was related to the CCR5 receptor which is used by HIV to enter target cells. He is an expert in modeling the structures of other chemokine receptors, their activation mechanisms and rational drug design and development. He is also interested in material science and combining biological systems with inorganic/organic ones to design and produce novel materials.

Research Summary (Past & Current):

Head of the Chemical and Biological Systems Simulation Laboratory.
His main expertise covers computational chemistry, biochemistry, biology, materials science and drug design. He is actively performing atomic scale simulations, applying computational models to solve problems in various fields of science and developing computational algorithms. His recent achievements cover the thorough mechanistic description of catalytic processes related to olefin metathesis.
He received an MS degree in Computational Chemistry (Faculty of Chemistry, University of Warsaw) under the supervision of Andrzej Leś in 2001. In 2005 he defended his PhD degree in Computational Chemistry (Faculty of Chemistry, University of Warsaw) under the same supervisor. From 2005 to 2008 he was a postdoctoral researcher at the Department of Chemistry, University of Arizona (Tucson, USA) in Ludwik Adamowicz group. In 2008 he moved for his second postdoctoral researcher position to California Institute of Technology where he worked in William A. Goddard III group at the Department of Chemistry. In 2010 he came back to Poland working for a short time at the International Institute of Molecular and Cell Biology in Warsaw before moving to the Faculty of Chemistry (Sławomir Filipek lab).
From 2013 he is the head of the Chemical and Biological Systems Simulation Laboratory at the Centre of New Technologies. He was also a visiting professor at the University of Arizona in 2013-2014 within the Mobility program.

Education

  • MSc: 2001, Faculty of Chemistry, University of Warsaw, Poland. Major: computational chemistry.
    Thesis title:
    “Octahedral manganese complexes – an introduction to the modeling of inhibitors of the small cell lung cancer”;
  • PhD: 2005, Faculty of Chemistry, University of Warsaw, Poland.
    Major: computational chemistry.
    Dissertation title:
    „Diffusion of curved surfaces”;
  • PostDoc: 2005 – 2008, Department of Chemistry, University of Arizona, USA.
    Research project: “Electroless Plating of Protein Templates for the Fabrication of Straight Nanowires on Silicon“;
  • PostDoc: 2008 – 2010, Department of Chemistry, California Institute of Technology, USA
    Research project:
    “Prediction of Structures and Ligands for GPCRs“;
  • Habilitation: 2017, Faculty of Chemistry, University of Warsaw, Poland
    Major: Chemistry
    Dissertation title: “Modelling of structures and reactions paths of ruthenium complexes, potential olefin metathesis catalysts”

Positions held

  • 2013 – present – Head of Chemical and Biological Systems Simulation Laboratory, Centre of New Technologies, Warsaw University, Poland.
  • 2012 – 2013 – Assistant Professor, Faculty of Chemistry, Warsaw University, Poland.

Visiting Researcher

  • 2013 – 2014, Department of Chemistry, University of Arizona, USA
  • 2009 – Department of Chemistry, University of Sidney, Australia
  • 2003 – 2014, Department of Chemistry, Stockholm University, Sweden

Other professional activities and memberships

  • Member of the Polish Chemical Society

Recent major publications

  1. S. Osella, M. Kiliszek, E. Harputlu, C.G. Unlu, K. Ocakoglu, J. Kargul, B. Trzaskowski, „Controlling the Charge Transfer Flow at the Graphene/Pyrene-Nitrilotriacetic Acid Interface”, J. Mater. Chem. C, 6, 5046-5054 (2018).
  2. R. Gawin, A. Tracz, M Chwalba, A. Kozakiewicz, B. Trzaskowski, K. Skowerski, „Cyclic Alkyl Amino Carbene Ruthenium Complexes – Unprecedented Efficiency in Macrocyclization and Acrylonitrile Cross Metathesis”, ACS Catal., 7, 5443-5449 (2017).
  3. K. Grudzień, B. Trzaskowski, M. Smoleń, R. Gajda, K. Woźniak, K. Grela, „Hoveyda-Grubbs catalyst analogues bearing derivatives of N-phenylpyrrol in carbene ligand – structure, stability, activity and unique ruthenium-phenyl interactions”, Dalton Trans., 46, 11790-11799 (2017).
  4. B. Żyżyńska-Granica, B. Trzaskowski, S. Niewieczerzal, S. Filipek, O. Zegrocka-Stendel, M. Dutkiewicz, P. Krzeczyński, M. Kowalewska, K. Koziak, „Pharmacophore guided discovery of small-molecule interleukin 15 inhibitors”, Eur. J. Med. Chem., 136, 543-547 (2017)
  5. R. Abrol, B. Trzaskowski, W.A. Goddard, A. Nesterov, I. Olave, C. Irons, „Ligand and mutation induced conformational selection in the CCR5 Chemokine G protein-coupled receptor”, Proc. Natl. Acad. Sci. USA, 111, 13040-13045 (2014).
  6. J. Bray, R. Abrol, W.A. Goddard, B. Trzaskowski, C. Scott, „The SuperBiHelix Method for Predicting the Pleiotropic Ensemble of G-Protein Coupled Receptor Conformations”, Proc. Natl. Acad. Sci. USA, 111, E72-E78 (2014).

Research projects

  • 2018-2020 NCN Beethoven 2 grant “Anionic Carbenes and Borylanions: Tuning the properties of ruthenium metal complexes in olefin metathesis” to B. Trzaskowski, PI;
  • 2017-2021 NCN SONATA BIS 6 grant “ Anionic, cationic and mesoionic analogues of N-heterocyclic carbenes in homogenous catalysis” to B. Trzaskowski, PI;
  • 2012-2015 NCBiR 3rd Polish-Singaporean competition grant “Green and sustainable catalysts for chemical, agrochemical and pharmaceutical industry” to B. Trzaskowski and K. Grela, coPIs;
  • 2013-2015 NCN OPUS 3 grant “New analogues of N-heterocyclic carbenes in Ruthenium-based metathesis catalysts – design, modeling, synthesis, analysis” to B. Trzaskowski, PI;
  • 2013-2014 MNiSW Mobility Plus grant “New hybrid materials and biomaterials – design, structure and properties modelling and synthesis” to B. Trzaskowski, PI;
  • 2012-2013 Polpharma Scientific Foundation grant “Identification of a new chemical compounds inhibiting biological effects of interleukin 15 (IL-15) via selective blocking of IL-15R  receptor”, key personnel
  • 2011-2012 National Science Foundation (US) grant “EAGER: Mattressene – A 3D Carbon Nanostructure Superlattice: Experimental and Theoretical Synthesis and Characterization”, key personnel
  • 2009-2011 Foundation for Polish Science Homing/Powroty grant “First Principles Predictions of the Structure and Function of Chemokine Receptors” to B. Trzaskowski, PI;
  • 2009-2010 Chevron grant “Low-temperature methane-to-methanol oxidation”, key personnel
  • 2008-2019 PharmSelex grant “Prediction of Structures and Ligands for GPCRs”, key personnel
  • 2005-2008, National Science Foundation (US) NIRT grant “Electroless Plating of Protein Templates for the Fabrication of Straight Nanowires on Silicon”, key personnel
  • 2004-2005, Ministry of Science and Higher Education (Poland) grant “Quantum mechanical study of the solvolysis of CMP-NeuAc and its application in modelling of sialyltransferase inhibitors” to B. Trzaskowski, PI;

Teaching experience

  • University of Warsaw: Basic Informatics, Advanced Informatics, Quantum Chemistry A, Inorganic Chemistry, General Chemistry, Calculations in Analytical Chemistry
  • Warsaw Medical University: Medicinal Chemistry, Biochemistry with elements of chemistry

Awards

  • 2012-2015, Stipend for outstanding young scientists, Ministry of Science and Higher Education (Poland)

Languages:
Polish (native), English (fluent)

 


Azoliniums, Adducts, NHCs and Azomethine Ylides: Divergence in Wanzlick Equilibrium and Olefin Metathesis Catalyst Formation
Jolly, P. I., Marczyk, A., Małecki, P., Ablialimov, O., Trzybiński, D., Woźniak, K., ... & Grela, K. (2018).
Chemistry–A European Journal, 24(19), 4785-4789.
Efficient glycosylation of natural Danshensu and its enantiomer by sugar and 2-deoxy sugar donors
Sidoryk, K., Cmoch, P., Świtalska, M., Trzaskowski, B., Wietrzyk, J., & Cybulski, M. (2018).
Carbohydrate research, 460, 19-28.
5-HT1A and 5-HT2A receptors affinity, docking studies and pharmacological evaluation of a series of 8-acetyl-7-hydroxy-4-methylcoumarin derivatives
Ostrowska, K., Grzeszczuk, D., Głuch-Lutwin, M., Gryboś, A., Siwek, A., Leśniak, A., ... & Trzaskowski, B. (2018).
Bioorganic & medicinal chemistry, 26(2), 527-535.
Controlling the charge transfer flow at the graphene/pyrene-nitrilotriacetic acid interface
Osella S*, Kiliszek M, Harputlu E, Unlu CG, Ocakoglu K, Kargul J*, Trzaskowski B (2018).
J. Mater. Chem. C. 6, 5046-5054
Ruthenium Olefin Metathesis Catalysts Systematically Modified in Chelating Benzylidene Ether Fragment: Experiment and Computations
Grela, K., Zieliński, A., Szczepaniak, G., Gajda, R., Woźniak, K., Trzaskowski, B., ... & Kajetanowicz, A. (2018).
European Journal of Inorganic Chemistry, 2018(32), 3675-3685.
Identification of prion protein-derived peptides of potential use in Alzheimer’s disease therapy
Nieznanska, H., Bandyszewska, M., Surewicz, K., Zajkowski, T., Surewicz, W. K., & Nieznanski, K. (2018).
Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 1864(6), 2143-2153
Energy Level Alignment at Interfaces Between Au (111) and Thiolated Oligophenylenes of Increasing Chain Size: Theoretical Evidence of Pinning Effects
Diez‐Cabanes, V., Gonzalez, S. R., Osella, S., Cornil, D., Van Dyck, C., & Cornil, J. (2018).
Advanced Theory and Simulations, 1(3), 1700020
Hoveyda–Grubbs catalyst analogues bearing the derivatives of N-phenylpyrrol in the carbene ligand–structure, stability, activity and unique ruthenium–phenyl interactions.
Grudzień, K., Trzaskowski, B., Smoleń, M., Gajda, R., Woźniak, K., & Grela, K. (2017).
Dalton Transactions, 46(35), 11790-11799.
Pharmacophore guided discovery of small-molecule interleukin 15 inhibitors.
Żyżyńska-Granica, B., Trzaskowski, B., Niewieczerzał, S., Filipek, S., Zegrocka-Stendel, O., Dutkiewicz, M., Krzeczyński, P., Kowalewska, M. and Koziak, K., (2017).
European journal of medicinal chemistry, 136, 543-547.
Development of selective agents targeting serotonin 5HT 1A receptors with subnanomolar activities based on a coumarin core.
Ostrowska, K., Grzeszczuk, D., Głuch-Lutwin, M., Gryboś, A., Siwek, A., & Trzaskowski, B. (2017).
MedChemComm, 8(8), 1690-1696.
Hoveyda-Grubbs complexes with boryl anions are predicted to be fast metathesis catalysts
Trzaskowski, B., & Grela, K. (2016).
Catalysis Communications, 86, 133-138.
Geodesic arenes
Trzaskowski, B., Ostrowska, K., & Adamowicz, L. (2016).
Carbon Nanomaterials Sourcebook: Nanoparticles, Nanocapsules, Nanofibers, Nanoporous Structures, and Nanocomposites (pp. 115-139). CRC Press.
Nitrenium ions and trivalent boron ligands as analogues of N-heterocyclic carbenes in olefin metathesis; a computational study
Pazio, A., Woźniak, K., Grela, K., & Trzaskowski, B. (2015)
Dalton Transactions, 44(46), 20021-20026
Conformational flexibility of Hoveyda-type and Grubbs-type complexes bearing acyclic carbenes and its impact on their catalytic properties.
Pazio, A., Woźniak, K., Grela, K., & Trzaskowski, B. (2015).
Organometallics, 34(3), 563-570.
Ligand-and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor
Abrol, R., Trzaskowski, B., Goddard, W. A., Nesterov, A., Olave, I., & Irons, C. (2014).
Proceedings of the National Academy of Sciences, 111(36), 13040-13045
SuperBiHelix method for predicting the pleiotropic ensemble of G-protein–coupled receptor conformations.
Bray, J. K., Abrol, R., Goddard, W. A., Trzaskowski, B., & Scott, C. E. (2014).
Proceedings of the National Academy of Sciences, 111(1), E72-E78.
Exploring structures and properties of new geodesic polyarenes.
Trzaskowski, B., Adamowicz, L., Beck, W., Muralidharan, K., & Deymier, P. A. (2014).
Chemical Physics Letters, 595, 6-12.
Selective NaNO 2 recognition by a simple heteroditopic salt receptor based on l-ornithine molecular scaffold.
Romański, J., Trzaskowski, B., & Piątek, P. (2013).
Dalton Transactions, 42(43), 15271-15274.
Impact of Local Curvature and Structural Defects on Graphene–C60 Fullerene Fusion Reaction Barriers.
Trzaskowski, B., Adamowicz, L., Beck, W., Muralidharan, K., & Deymier, P. A. (2013).
The Journal of Physical Chemistry C, 117(38), 19664-19671.
Selective NaNO2 recognition by a simple heteroditopic salt receptor based on L-ornithine molecular scaffold
Romański, J., Trzaskowski, B., & Piątek, P. (2013).
Dalton Transactions, 42(43), 15271-15274