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Hướng dẫn sử dụng phần mềm MOE nhằm xây dựng mô hình đánh giá hoạt tính cuả enzyme và các tương tác ligand với các hợp chất tiềm năng, ứng dụng trong lĩnh vực Hoá Dược. Đây là một gói công cụ gồm rất nhiều phần mềm khác nhau. MOE không phải là phần mềm duy nhất nhưng đây là phần mềm miễn phí hỗ trợ gần như đầy đủ nhất các tính năng về sự tương tác, đánh giá laị các số liệu thực nghiệm.
The Main MOE Windows The MOE Window (MOE) or ( ) Small molecule bioinformaticsMole cular mechanics, Small molecu MOE Database Viewer (DBV) Cheminformatics, Conformational search, fingerprints, clustering, combinatorial library design SVL Commands Window (CLI) Custom SVL, interactive scripting, session logging Sequence Editor (SE) Protein bioinformatics, homology modeling, sequence analysis The MOE Window Main Menu Commands Task Cancel Button RHS Button Bar SVL Command Line 3D Rendering Area Footer Pager Bar MOE Menu Command Conventions • Commands from the MOE Window are preceded by MOE or () (Render | Backbone | Color | Chain Color) or (MOE | Render | Backbone | Color | Chain Color) Mouse Conventions in MOE General Mouse Actions LEFT 3-Button Mouse – 2-Button Mouse Mapping - Selecting objects, menu commands MIDDLE - Rotating, translating moving objects RIGHT Press and release key - SE and DBV Popup menus Input / Output File Formats in MOE MOE MOE MDLMol SD PDB Tripos MOL2 PDB Mol2 Macromodel SMILES MSI XTL Paste from ChemDraw Capture / Print: PNG, GIF, JPEG, Postscript, printer Exercise: Opening a file Open the File Open panel (File | Open) Use the pull-down menu to switch to the $MOE/sample/mol directory Exercise: Opening a File (cont.) Find the file $MOE/sample/mol/trypsin72.moe Open MOE file into the MOE Window by either: a: Selecting the file and clicking OK or Open MOE File b: Double left-clicking on the filename Exercise: Opening a File (cont.) Center the View (Render | View or RHS | View) Render the molecule as ball and stick (Render | Ball and Stick) Exercise: Create course directory • Create a directory where all course files will be stored • MOE | File | Save … Create a directory called ‘course’ Select as new working directory Selecting Atoms with the Left Mouse Button Left Click: Select atoms one at a time -Left Click: Auto-extend selection to residue -Left Click: Add to / toggle atom selection Left Drag: Selection Box 10 Contact Statistics This is a method of mapping areas of hydrophilic and hydrophobic preference within a binding site or around a single molecule Produced from statistics extracted from protein-ligand contacts in the PDB; - atoms on receptor and ligand are typed - contacts are binned into histograms in polar co-ordinate space - histograms are fitted by functional forms for computational efficiency c.f GRID, SuperStar 40 Contact Statistics Atom Typing: Receptor atoms are classified according to element and chemical context Receptor atom types depend on local coordinate system parameters Avoid dependence on protonation state and tautomer state Just enough types are used to distinguish statistics Ligand atoms are classified into one of two types LPA (“lone pair active”) for H-bond donors, acceptors and metals HYD for all other atoms (hydrophobic or non-LPA) Types allow for distinguishing hydrophobic vs hydrophilic environments 41 Contact Statistics Receptor Atom Types: Type T_CH1 T_CH2 T_CH3 T_cQ3 T_cQ2 T_NQ1 T_nQ1 T_nQ2 T_nQ3 T_oQ1 T_OQ1 T_OQ1i T_OQ2 T_OW T_SQ1 T_SQ2 T_F1 T_Cl1 T_Br1 T_I1 T_TM u yes yes yes no yes yes yes yes no yes yes yes yes yes yes yes yes yes yes yes no v no yes no yes yes no yes yes yes yes yes yes yes yes no yes no no no no no El C C C C C N N N N O O O O O S S F Cl Br I ? Description sp3 carbon with Hs sp3 carbon with Hs sp3 carbon with Hs sp2 carbon with heavy bonds sp2 carbon with heavy bonds sp3 nitrogen with heavy bond sp2 nitrogen with heavy bond sp2 nitrogen with heavy bonds sp2 nitrogen with heavy bonds sp2 oxygen with heavy bond sp3 oxygen not bonded to pi, heavy bond sp3 oxygen bonded to pi with heavy bond any oxygen with heavy bonds any oxygen with heavy bonds (water) sulfur with heavy bonds sulfur with heavy bonds fluorine with heavy bonds chlorine with heavy bonds bromine with heavy bonds iodine with heavy bonds transition metal (treated as ion) 42 Contact Statistics • For each receptor atom, A, define a coordinate system – Define vectors u and v derived from hybridization and heavy neighbors – Some atom types not have a u or a v (taken to be zero) u A • • v v A u A v taken from pi system v Define polar coordinate system from u and v – Distance from atom A r “distance” – Angle with u vector a “lone pair angle” – Angle with u in u-v plane p “out-of-plane angle” A contact atom, B, is mapped to (r,a,p) local coordinates u u p a A B r 43 Contact Statistics T_nQ1 0.12 r 0.1 0.08 0.06 0.04 0.02 1.5 1.74 1.98 2.22 2.46 2.7 2.94 3.18 3.42 3.66 3.9 4.14 4.38 0.2 a 0.16 0.12 0.08 0.04 2.5 22.5 42.5 62.5 82.5 102.5 122.5 142.5 162.5 0.32 r a p HYD lognorm beta gamma LPA 12-6 beta cauchy O NH p 0.24 0.16 NH 0.08 2.5 17.5 32.5 47.5 62.5 77.5 44 Contact Statistics T_nQ2 0.16 r 0.12 0.08 0.04 1.5 1.74 1.98 2.22 2.46 2.7 2.94 3.18 3.42 3.66 3.9 4.14 4.38 0.32 a 0.24 0.16 0.08 r a p HYD lognorm gamma gamma LPA 12-6 cauchy cauchy 2.5 22.5 42.5 62.5 82.5 102.5 122.5 142.5 162.5 N NH 0.32 p 0.24 O 0.16 HN N 0.08 NH 2.5 17.5 32.5 47.5 62.5 77.5 45 Exercise: Contact Statistics in a Binding Site Open the moe file you created of the biotin receptor site with the pocket surface MOE | Compute | Contact Statistics Select the dummy atoms (Ctrl-left click) and calculate contact statistics for unselected atoms, near selected Take the threshold up to about 95% for each surface type Rotate round and see if you can relate the visible preferences to groups on the protein surface Toggle off the pocket surface in the Graphic Objects window to help 46 Exercise: Contact Statistics in a Binding Site File | Open | $MOE/sample/mol/biotin.moe Rotate round and see how the biotin molecule fits the hydrophilic and hydrophobic preferences in the binding site environment 47 Preparation for Docking • • • Hide all Graphic Objects MOE | Render | Show | All MOE | Edit | Hydrogens | Add Hydrogens Select the ligand (Ctrl-left click on any of its atoms) and pull it out of the pocket using Middle mouse button drag Leave the ligand selected 48 Forcefields in MOE MOE | Window | Potential Setup The default molecular mechanics forcefield in MOE is MMFF94x This is suitable for small molecules but not optimal for protein structures However, here we will be working with an interaction of both, with the protein rigid, and so we will stay with this forcefield Others in MOE include AMBER, CHARMM, etc … Fix Charges 49 Exercise: Docking MOE | Compute | Simulations | Dock … Set the definitions of receptor, site and ligand as shown MOE’s docker will flex the ligand and attempt to match it to the shape of the pocket Each attempt will have an “Affinity dG” calculated, based on the current forcefield The best poses will be output to a MOE database Press OK 50 Exercise: Docking Left-click and drag in the “mol” field to see the output poses From the DBV toolbar, select File | Browser As you browse through the entries, they are displayed in the MOE Window in the right frame of reference to the receptor Show the pocket surface again (in the Graphic Objects window) Select the “browsed” ligand and change its rendering to “Stick” and its colour to (e.g.) red 51 Exercise: Docking 52 Exercise: Docking Close the Browser Copy the first entry molecule into MOE by right-clicking on it in the database and selecting “Copy to MOE” DO NOT “Clear molecular data” when asked! MOE | Selection | Receptor (selects the whole protein) MOE | Edit | Potential | Fix (makes the protein rigid and immovable, but still “felt”) MOE | RHS | Minimize When minimization is complete, MOE | File | Open | $MOE/sample/mol/biotin.moe – compare the relaxed docking solution with experiment 53 Exercise: Docking 54 ... Prepare for next exercise … MOE | Render | Backbone | None MOE | Render | Show | All MOE | Selection | Solvent, Delete MOE | Selection | Ligand MOE | Render | Ball and Stick MOE | Render | Color |... save picture MOE | Edit | Automatic | Depict as 2D 17 Save Molecule Save the current MOE 3D window as a MOE file MOE | File | Save Enter filename to save Save ‘Molecule’ Choose Format MOE 18 Close... – Deletes contents of MOE system but does not close program 19 Exercise: Opening Biotin and Receptor Open the files $MOE/ sample/mol/biotin .moe $MOE/ sample/mol/biotin_rec .moe 20 The Sequence