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Structure Prediction of GPCRs

Our goal is to to develop and use computational strategies and techniques for predicting the three-dimensional structure of G protein-coupled receptors (GPCRs). GPCRs form a remarkable modular system that allows transmission of a wide variety of signals over the cell membrane, between cells and over long distances in the body. Recent developments in structural studies and crystallography of human GPCRs (acknowledged in 2012 by the Nobel prize committee) improved our understanding of these systems and made the rational molecular-based drug discovery a viable option. We are particularly interested in chemokine receptors family and in the CCR5 system, which is used by the HIV virus to enter human cells.


Prediction of ligand/receptor binding affinities

We are also interested in using computational methods predict the ligand/receptor binding affinities for a number of interesting biological systems. The main focus of our research is on GPCRs ligands with potential antidepressant activities and investigation of structure-activity relationships in large and diverse sets of chemical compounds; however, we also work with other proteins, both memebrane-bound and soluble in water. In this project we're looking for ways to harness the computational chemistry/biology methods to describe in atomistic-scale details of ligand-receptors interactions. We also extensively use ADMET simulations to obtain even more detailed information about the new compounds with possible use in various therapies.


Selected publications:

K. Ostrowska, D. Grzeszczuk, M. Głuch-Lutwin, A. Gryboś, A. Siwek, A. Leśniak, M. Sacharczuk, B. Trzaskowski, "5-HT1A and 5-HT2A receptors affinity, docking studies and pharmacological evaluation of a series of 8-acetyl-7-hydroxy-4-methylcoumarin", Bioorg. Med. Chem., 26, 527-535 (2018).

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).

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).


membrane

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).

A. Grunbeck, T. Huber, R. Abrol, B. Trzaskowski, W.A. Goddard, T.P. Sakmar, "Genetically Encoded Photo-cross-linkers Map the Binding Site of an Allosteric Drug on a G Protein-Coupled Receptor", ACS Chem. Biol., 7, 967-972 (2012).
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