Laboratory of Biomodeling

Description of the Group

The group studies proteins, especially in the cell membrane environment. This research includes ligand docking and revealing the activation mechanism of GPCRs. This family of receptors includes, among others, adrenergic, dopa-mine, adenosine, histamine, serotonin, opioid, cannabinoid receptors, and many others. Modelling allows predicting the action of ligands (activate or block the receptor) in order to design selective drugs with desired function

Research Activities

To model GPCRs more effectively, the Biomodeling Labo-ratory has developed a web service GPCRM (http://gpcrm.biomodellab.eu/) for the homology modelling of these receptors. This service is available for all research groups and allows for obtaining models of GPCR structures in auto-matic mode for casual user as well as in the manual mode for experienced users. The service is regularly updated upon the availability of new structures of GPCRs in the Protein Data Bank database.The Biomodeling Laboratory also designs drugs against various molecular targets, including APP cutting proteas-es producing beta-amyloid, as well as drugs preventing beta-amyloid aggregation and formation of deposits, which are found in the brains of patients with Alzheimer’s disease. We also study the interactions of proteins with graphene, carbon nanotubes and other electrode materials for use in bio-sensors.

Offer

• Advanced modeling of GPCRs (modeling by homology, optimization in cell membrane model).
• Docking of small ligands to orthosteric and allosteric sites of GPCRs.
• Virtual screening of databases of small molecules as potential ligands of
• Molecular dynamics simulations of GPCRs with ligands – study of stability of these systems, optimization of ligand-protein interactions, study of activation processes, influence of allosteric factors.
• Predicting the function of GPCR ligands (agonist/non-agonist)

Team Leader

Professor Sławomir Filipek conducts scientific activity in the field of molecular modeling and molecular dynamics simulations of biological systems, mainly the membrane proteins and their complexes with small ligands, drugs, as well as with other proteins. His scientific interests also include research on the activation processes of these proteins, in particular G-protein coupled receptors (GPCRs) under the influence of agonist binding, and how the allosteric factors (lipids, ions, etc.) affect the functions of these proteins. Prof. Filipek completed his scientific internship in 2001-2002 in the group of Prof. Palczewski in Seattle USA, just after crystallization of the structure of the first GPCR receptor – rhodopsin – in this laboratory and publishing it in 2000.