Drug Mechanism Analysis for the Anti-HIV Lead AVC Against the CCR5 Receptor firstname.lastname@example.org
Methods Docking Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex Schematic diagram illustrating the docking of a small moleculeligand (brown) to a proteinreceptor (green) to produce a complex.
Background Materials • QM Sun: Homology Modeling (Knowledge-Based Structure Modeling ) • Maeda K, Das D, Ogata-Aoki H, Nakata H, Miyakawa T, Tojo Y, Norman R, Takaoka Y, Ding J, Arnold GF et al: Structural and molecular interactions of CCR5 inhibitors with CCR5. The Journal of biological chemistry 2006, 281(18):12688-12698 • Tunaru S, Lattig J, Kero J, Krause G, Offermanns S: Characterization of determinants of ligand binding to the nicotinic acid receptor GPR109A (HM74A/PUMA-G). Molecular pharmacology 2005, 68(5):1271-1280.
Protocol • Get AVC 3D structure • Get CCR5 3D structure • Dock AVC into CCR5 • Analysis of atomic interaction • Scan up for literature support • Write up your report
1. AVC Structure • Check up Reference 2 to find out the name, systemic name, CAS No of the known CCR5 inhibitors AVC. (At your own interest, you can compare it with other known inhibitors SCH-C and AK-779) • Obtain the inhibitor structure from structure database, such as ChemIDPlus (http://chem.sis.nlm.nih.gov/chemidplus/) • Convert the structure into 3D (i.e. use Discovery Studio Visualizer http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html) • Optional: assess the quality of small molecule conformation (in terms of energy, flexibility)
2. CCR5 Structure • Get human CCR5 sequence from database. • Select structure template in PDB (sequence similarity, resolution, completeness, condition to crystallize). • Get other GPCRs from the database. • Construct a reliable multiple sequence alignment (active sites, boundaries of trans-membrane helices). • Predict the human CCR5 structure with homology modeling, e.g. use the Modeler Server (http://swissmodel.expasy.org/SWISS-MODEL.html) or the software (http://salilab.org/modeller/download_installation.html), or other options. • Check model quality, in terms of energy or dihedral angle compatibility or else. For example, use https://prosa.services.came.sbg.ac.at/prosa.php.
3. Molecular Docking • Get free docking software such as Dock and AutoDock. • Read its manual carefully. • Prepare your ligand and receptor structure. • Dock ligand into receptor, assess its quality (energy, contacts, flexibility, etc). • Tune parameters, repeat docking, until satisfactory structure was obtained.
4. Analysis of Atomic Interaction • Choose whatever structure visualization software you like, e.g. Rasmol. • Read its manual carefully. • Check for potential atomic interactions visually, such as below: • Hydrophobic contact • Electrostatic interaction • Hydrogen bond • Pi-Pi interaction • Optional: interaction hot-spots from an energy aspect, check http://robetta.bakerlab.org/ or other options.
5. Literature Evidence • Pubmed scan for CCR5 inhibitors. • Known key residues in CCR5 recognition of HIV gp120 / Human CD4. • Known key residues binding AVC and / or other inhibitors. • QSAR/QSPR studies on the key structure features of CCR5 inhibitors.
6. Report • Scientific article structure: Abstract, Introduction, Methods, Results, Discussions, Conclusions. • Comparison of your findings with existing reports of AVC inhibition mechanisms. • Advances and limitations of your study. • Ideas on potential modifications of AVC to achieve better inhibition. • Include snapshots to backup your claim of atomic interaction, with the referenced atoms clearly labeled. • Submit your complex structure together with your report.
References • QM Sun: Homology Modeling (Knowledge-Based Structure Modeling ) • Maeda K, Das D, Ogata-Aoki H, Nakata H, Miyakawa T, Tojo Y, Norman R, Takaoka Y, Ding J, Arnold GF et al: Structural and molecular interactions of CCR5 inhibitors with CCR5. The Journal of biological chemistry 2006, 281(18):12688-12698 • Tunaru S, Lattig J, Kero J, Krause G, Offermanns S: Characterization of determinants of ligand binding to the nicotinic acid receptor GPR109A (HM74A/PUMA-G). Molecular pharmacology 2005, 68(5):1271-1280. • http://www.ebi.ac.uk/Tools/clustalw2/ • http://salilab.org/modeller/download_installation.html • http://robetta.bakerlab.org/ • http://swissmodel.expasy.org/SWISS-MODEL.html • https://prosa.services.came.sbg.ac.at/prosa.php • http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html • http://dock.compbio.ucsf.edu/ • http://autodock.scripps.edu/ • Some other sources: • http://www.ebi.ac.uk/Tools/ • http://www.vls3d.com/links.html#section4 Write your experiment report according to the steps above, and hand it in three weeks.