Module 2_ Structure Based Ph4 Design - Pedeciba by hcj


									              Module 2: Structure Based Ph4 Design

MOE provides several applications to analyze protein information in
absence of ligands:

   • The Site Finder (using the binding site of a receptor to generate the
   • Contact preferences

   In part b) of the SBDD course:
   • The MCSS algorithm for de-novo design
   • Docking
                            Alpha Site Finder
   The Site Finder screens the surface of a protein for potential binding sites. In
   addition to locating cavities it also indicates preferred locations for
   hydrophilic or non-hydrophilic interaction points.

  Site Finder considers the relative positions and
  accessibility of the receptor atoms along with a
  rough classification of chemical type. The
  method applies alpha spheres. This is a special
  case of a contact sphere that circumscribes 4 atoms on its boundary and
  contain no internal atoms. Centers of alpha spheres are clustered into
  hydrophobic and hydrophilic areas.
                    Binding Site Identification

Geometric analysis of a molecule
   • Alpha spheres identify cavities
   • Sphere size is related to degree of exposure
   • Small spheres indicate "tight" cavities
   • The sphere size is not reflected in the graphical representation of
   • Centroids are clustered for display
   • Hydrophilic contact points are marked
     by red centroids
   • Hydrophobic (defined as
     non-hydrophilic) are colored white.

                                                P33 Protein Kinase
Exercise: Query generation and Search from Receptor
Site - Binding Site Identification I

Use alpha spheres to predict ligand

1. (MOE | File | Open) for the file

2. Open (MOE | Compute | Site

3. Click “Apply” on the Site Finder

17 sites are found …
                               Site Finder Panel

                                                   Site list:
Atoms included in the
calculation                                        Site: Site number
                                                   Size: Number of
                                                   contributing spheres
Display mode of alpha                              Hyd: Number of
spheres                                            hydrophobic atoms
                                                   contacted in receptor
Display mode of site(s);                           Side: Number of
Residue selection option                           sidechain contact
                                                   Residues: Residues at
                           Creates dummy atoms     local surface

Minimum sphere radii to
detect (non-) LP-active
atoms                                              Distance filter before
Settings for alpha
sphere clustering
Exercise: Query generation and Search from Receptor
Site - Binding Site Identification II
4. Examine the different sites. The 2nd site has
   more receptor contacts but fewer
   hydrophobic contacts.
5. Select the first site. To restrict the view to the
   immediate environment by selecting Isolate:
   “Atoms” and enable SE Residues.
   Ensure that (MOE | Selection | Synchronize)
   is ON. Invert the selection (MOE | Selection |
   Invert) and delete all hidden residues.
6. Keep the positions of the Alpha Centers by
   pressing “Dummies” and close the panel.
7. To increase the size of the dummy atoms
   <Ctrl>-click on one of the dummy atoms to
   select all of them. Select (Render | Space

                                                        Red: Potential hydrophilic contact
Exercise: Query generation and Search from Receptor
Site - Binding Site Identification III
8. Create a surface for the pocket using
    (MOE | Compute | Surfaces and
9. In the panel, keep default settings but
    Near: Dummy Atoms
    Click: Apply
The colours of the surface displays those
regions of the receptor surface suitable for
a hydrogen bond or metal-lone-pair
Try also different surface color schemes to
compare the results or modify the
transparency (TF, TB) settings.
10. Save the pocket as
                 Receptor Contact Preferences
  This approach complements the site finder information by identifying
  preferred areas for hydrophobic or hydrophilic interactions based on
  statistical preferences derived from non-bonding contacts in high
  resolution protein structures.
  Non-bonded protein-ligand interactions are
  analyzed with respect to distance, angle and
  out-of-plane preferences. The receptor and
  ligand atoms are classified into atom types
  and the experimental histograms of the
  contacts are fitted by analytical functions.
  Contour maps display likelihood ratios for
  hydrophobic over hydrophilic preferences
  (green) or vice versa (red).
                      Receptor Atom Classification
• For each receptor atom, A, define a coordinate system
    – Define vectors u and v derived from hybridization and heavy neighbors
    – Some atom types do not have a u or a v (taken to be zero)

                                       v                                      v

                  A                                                                       u
                                       A                                 A
                                                              v taken from pi system

• Define polar coordinate system from u and v
    – Distance from atom A         r       “distance”                     v
    – Angle with u vector          a       “lone pair angle”
    – Angle with u in u-v plane p          “out-of-plane angle”                   p
• A contact atom, B, is mapped to (r,a,p) local coordinates                                   B
       Receptor Atom Classification - Atom Typing
T_nQ2: HYD (50%) LPA (50%)


                                     a         HYD       LPA
                                           r   lognorm   12-6
                                           a   gamma     cauchy
                                           p   gamma     cauchy

Exercise: Query generation and Search from Receptor Site
- Contact Preferences
Contact preferences can be used to generate or refine a Ph4 query.

1. Hide the molecular surface from the
   previous exercise in (MOE | Window |
   Graphic Objects) to concentrate on contact

2. Select Surface: “Contact Preference” in the
   Surface and Maps panel and press Apply.

3. Play with different contour levels and display
Exercise: Query generation and Search from Receptor Site
- Pharmacophore Query Editor I
The suggestions for preferred interactions in the binding site may be used to
derive a Ph4 query in absence of any known ligands.

1.   Open (MOE | File | New | Pharmacophore Query),
     select an Ph4 scheme, e.g. PPCH_all.
     Features are created in clusters of hydrophilic or
     hydrophobic groups.
2.   Select individual dummy atoms to place the new
     feature. In the Query Editor, press Feature. A
     generic ‘Any’ feature will be created.
3.   Adjust the feature positions by using
     <Shift><Alt><middle mouse button>.
4.   Furthermore modify and reassign the feature types
     adjusting the radii, expressions, etc. according to
     chemical intuition.
Exercise: Query generation and Search from Receptor
Site - Pharmacophore Query Editor II
5. Once finished creating features, an excluded volume
   may be added.*)
   Use a surface representation to guide the adjustment
   of tolerances for the excluded volume.
Exercise: Query generation and Search from Receptor
Site - Pharmacophore Search
 Save and use this query in the same way as the ones
      generated in the previous exercises.
 6.   Save the query as PPCH_ALL_sitefindV.ph4
 7.   Press Search and define the databases to be
      searched, consecutively double clicking on them,
      or select and then press Add.*)
 8.   Once the list is complete, press OK
 9.   The Search panel will reflect multiple databases.
      Continue with search process as previous
 10. Note that the databases should be pre-annotated
     with the ph4 scheme
            Case Studies in Pharmacophore Search
Module 3: Structure-based design with known actives and structural
          binding site details

       Case studies                         Small molecules
                                      Yes                     no


      Protein                      Module 1


                                   Module 3               Module 2
            Module 3: Structure Based Ph4 Design

If structural information about both proteins and their ligands is available, the
essential (conserved) protein ligand interactions (e.g. H-bonds) can be
identified and used to focus on the key Ph4 features. Since those interactions
include “projected” protein interaction sites, the results should be more
meaningful than a small molecule alignment in itself.*)
MOE provides several applications to analyze protein-ligand information:

   • Alignment and superposition of proteins
   • Ph4 consensus analysis
   • Surface properties and contact preferences

   In the Protein course:
   • Homology modeling (if only the amino acid
     sequence of a protein is available)
          Workflow of Structure Based Ph4 Design
1. Align a set of proteins with their co-crystallized ligands.
      • Ligands should already be docked in the binding site
2. Generate the relevant pharmacophore features based on SAR
      • Identify conserved Ph4 features with a Ph4 consensus analysis
      • Define the features based on biological/chemical knowledge of
      • Identify key features based on interactions using Contact Statistics,
        Molecular Surfaces or Hydrogen Bonding interactions
3. Save pharmacophore model
      • Refine using Excluded volumes, or
        Interior Volumes for SMILES strings
4. Search conformational database(s) for
   ligands that contain the relevant pharmacophores
5. Re-design the pharmacophore model, if
   necessary and search again

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