BIOmodeling

Workshops

Workshop I

Homology modeling of GPCRs and optimization in the membrane

(Slawomir Filipek group, tutor: Krzysztof Młynarczyk,
University of Warsaw, Poland)

High structural conservation among the GPCR family members allows for homology modeling. Yet, crucial for drug binding deformations of transmembrane helices have to be considered while building a GPCR model. Recent advances in GPCR crystallography provided not only a variety of structural templates but also many hints for prediction of sequence-structure relationship.

You will be guided through sequence-based computational methods for GPCR structure prediction and molecular dynamics simulations for model refinement. For this workshop, you will use open source software including: web services such as GPCRM, ProQM and TOPCONS, standalone programs such as MODELLER and Rosetta and Pymol for data visualization. In the 2^nd part an efficient technique that shortens equilibration time due to efficient lipid packing around the protein will be employed. During molecular dynamics the restraints will be imposed onto the whole protein and gradually released.

Part 1: Homology modeling of GPCR structures (1.5 h)

Prediction of membrane proteins topology and other 1D structural data
Selection of template structures
Preparation of target-template alignments and model building
Running loop modeling
Final selection of the most probable homology model

Part 2: Embedding and optimization in model membrane (1.5 h)

Prediction of location of protein in a membrane (OPM database)
Stretchy insertion a protein into a pre-equilibrated membrane-water system avoiding lipid holes
Set up and running energy minimization and subsequent molecular dynamics with and without restraints

Workshop II

Ligand docking in structure-based drug design

(Peter Kolb group, tutors: Denis Schmidt and Florent Chevillard,
Philipps-University Marburg, Germany)

Workshop II will guide you through the basic application of structure-based drug design by docking. The basis of a docking study are a) the structure of a GPCR and b) a set of ligands for which the binding to the receptor should be evaluated.

Structural information can be taken from a database like the PDB or be obtained from modeling processes as described in workshop I. The choose of ligands to dock depends on the docking application which is used for. Typical applications of docking are either retrospective, where a-priori knowledge about the ligands is available, or prospective, where one aims to select ligands that potentially bind to the given receptor from a large set of molecules.

In the current workshop II, we provide GPCR structures together with sets of ligands specifically selected for these targets. These sets contain molecules known to bind to the specific receptor as well as decoy ligands that are inactive. Participants will be taken through the necessary structure and ligand preparation steps, and conduct a retrospective docking experiment. The results will be analyzed to assess to what extent the GPCR structures are able to discriminate between active and inactive molecules. Users can further investigate how changes within the binding site influence this discriminative power and will be guided towards a prospective docking analysis.

This workshop is closely integrated to workshops I & III:

Next to crystal structures, methods explained here are commonly applied to assess and further improve homology models as they are developed during workshop I. Workshop III, however, teaches subsequent techniques and introduces chemical databases that can be used to create target-specific ligand sets.

Workshop III

In silico chemogenomics and virtual screening

(Chris de Graaf group, tutors: Albert Kooistra and Chris de Graaf, Division Medicinal Chemistry,
VU University Amsterdam, Netherlands)

In the current workshop III we invite you to perform a chemogenomics analysis on one of the GPCRs that you are currently working on in your own research project. This analysis will allow you to define a customized virtual screening strategy for the intended GPCR target.

In the current tutorial you will learn how to:

Mine target annotated chemical databases and protein structure databases
Perform chemoinformatics analyses of focused chemical libraries
Analyze protein-ligand complexes and compare ligand binding sites
Derive important pharmacophore features from ligands and/or protein binding sites
Use the protein-ligand analysis in virtual screening studies.

In the current workshop you will apply several of the techniques that you have learned during workshops I (e.g. sequence analysis, protein modeling) and II (docking simulations). Furthermore the structural analysis in the current workshop will be useful input for workshop IV.

Workshop IV

Simulating the complex nature of membrane lipid-GPCR interaction

(Jana Selent group, tutors: Jana Selent and Juan Manuel Ramirez-Anguita,
Pompeu Fabra University, Barcelona, Spain)

Functionality of GPCRs is tightly linked to the membrane environment. Specific membrane lipid-receptor interactions as well as unspecific effects mediated by the bulk properties of the membrane (thickness, deformation, etc.) are key regulators of GPCR modulation which have to be considered when studying this important class of drug targets.

Workshop IV will teach you important skills needed to simulate and assess key features of membrane lipid-induced effects:

Part 1: Modeling the biophysical properties of membrane lipids (1.5 h)

Setting up and running multi-component membrane systems
Assessing parameters which determine general membrane properties using a membrane specific plugin tool for VMD

Part 2: Simulating membrane lipid-GPCR interaction (1.5 h)

Identification of specific lipid interaction sites (VOLMAP)
Detection of unspecific membrane effects
Limitations

For this workshop, you will use open source simulation (NAMD) and visualization (VMD) software. After successful participation, you will have reached a profound understanding of the dynamic interplay between the receptor and its membrane environment comprising direct and indirect effects.

Requirements: In workshop IV you will need a basic understanding of simulation techniques obtained during workshops I and II.

Technical help:

Paweł Pasznik, Marek Bajda, Aleksander Dębiński,
University of Warsaw, Poland.

Partners