1

Copyright 2006 Chemical Computing Group Inc.

All Rights Reserved.
Chemical
Computing
Group Inc.
Docking and
Multi Fragment Search
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Copyright 2006 Chemical Computing Group Inc.
All Rights Reserved.
Outline
Part A: Docking
Docking is based on a more complete and quantitative description and
analysis of ligand-protein interactions compared to Ph4 queries.
Examines the ensemble of all actual and potential interactions
between ligands and their binding sites while optimizing the
geometry of the complex.
Typically involves forcefield minimization and eventually further
terms to predict binding poses.

Part B: Multi-Fragment Search
Attempts to predict poses of smaller functional groups rather than
whole molecules.
The accuracy of those predictions increases while the search space
is less constrained to a given set of molecules.
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Copyright 2006 Chemical Computing Group Inc.
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Docking
Objective
MOE-Dock identifies favorable poses of flexible ligands in rigid
binding sites of macromolecules, typically proteins. MOE-Dock consists
of a toolbox which offers different routines for conformational
sampling, placement and scoring. This enables the user to optimize
his workflow for a given target.




Note: The MOE-Dock algorithm
was completely rewritten in
MOE 2005.06.
Torsion Rules
Receptor
3D ligand
Scoring
PH4 Filter
Annotation
Placement
3D conformations
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Copyright 2006 Chemical Computing Group Inc.
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Placement Methods
The Alpha PMI method generates poses by
aligning ligand conformations' principal moments of
inertia to a randomly chosen subset of alpha sphere
dummies in the receptor site. This method is
preferred for tight pockets.

The Alpha Triangle placement method (default)
derives poses by random superposition of ligand
atom triplets and alpha sphere dummies in the
receptor site.

The Triangle Matcher method generates poses by
aligning ligand triplets of atoms on triplets of alpha
spheres in a more systematic way than the Alpha
Triangle method. (most complete screen of poses)
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Scoring Methods
The Affinity dG scoring function estimates
the enthalpic contribution to the free energy
of binding using a linear function of
hydrophobic, ionic, hydrogen bond and
metal ligation terms.

The DephtHB scoring function is a linear
combination of two terms:
*)

- the burying of the ligand and
- the hydrogen bond effects.

The London scoring function (default) estimates the free energy of
ligand binding from a given pose. The functional form is a sum of
energy term (ligand flexibility, H-bonds, desolvation) and geometric
imperfections.
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Affinity dG Scoring Function
G is the sum of terms (fit from ~100 pK
i
complexes)


H-bonds are between donor
and acceptor heavy atoms
Metal ligations are between
transition metal and O, N and S
Ionic contacts are between
functional groups (not just ions)
Contacts are between heavy atoms of receptor and ligand

Functions f decrease with distance
f
I
and f
B
functions have
7.5 cutoff
Close contacts not penalized


+ + + = A
j i contacts
ij B B
j i ionic
ij I j i I
j i lig metal
ij M M
j i hbonds
ij H H
r f C r f q q C r f C r f C G
: : : :
) ( ) ( ) ( ) (
C(+1)
O(-1)
O(-1)
N(+1)
O(-1/2)
O(-1/2)
(+1)P
O(-1)
O(-1)
(+2)S
O(-1)
O(-1)
N(+1/2)
N(+1/2)
N(+1/2)
N(+1/2)
N(+1/2)
N(+1)
Na+1
Zn+2
0
0,2
0,4
0,6
0,8
1
1,2
1 1,25 1,5 1,75 2 2,25 2,5 2,75 3 3,25 3,5 3,75 4 4,25 4,5 4,75 5
fH fM fI fB
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http://webpages.ull.es/users/bioquibi/temascompletos/InteraccionesNC/i
nicial/radio_de_van_der_waals.htm
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Copyright 2006 Chemical Computing Group Inc.
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London dG Scoring Function
Sum of terms intended to estimate G of binding


- c is average entropy loss/gain due to rotational/translational motion
- E
flex
is entropy loss due to conformational flexibility (ligand topology only)
H-bond f
HB
measures geometric imperfections
- c
HB
is H-bond maximum energy
- Distance, in-plane and out-of-plane angles into account
- Functional forms and distributions taken from MOE contact statistics
Metal ligation f
M
measures geometric imperfections
- c
M
is metal ligation maximum energy
- Landiss VALBOND sd
3
hybridization potential for angles
D
i
estimates desolvation energy of each atom i
- HB and M terms recover desolvation energy for hydrophilic atoms
- Desolvation energy is the main component of the model
- No ionic effects are part of the model (difficult to incorporate consistently)

A + + + + = A
i atoms
i
lig m
M M
bonds h
HB HB flex
D f c f c E c G
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London dG Desolvation Model
For atom i with radius R
i
estimate desolvation energy by integrating London
dispersion forces over solvent space


Implementation:
Radii are OPLS-AA van der Waals radii plus 0.5
Coefficients c
i
are assigned for each of ~12 atom types (e.g., Csp
3
/Csp
2
)
Integration approximated with GB/VI type integrals over solutes A and B
)
`

= A
}}} }}}
e

B u B A u
i i i
du u du u R c D
6 6 3
| | | |
+
i i
A
B B
A
D
i
solvent

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Copyright 2006 Chemical Computing Group Inc.
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Molecular Docking Updates
Placement
AlphaTriangle and TriangleMatcher
placement methods updated for speed
Scoring
New London dG scoring function
for binding affinity estimation
New DepthHB scoring function
for ranking poses (no affinity estimate)
Ligand strain energy no longer used in pose selection
Strain energy rarely helps and often hurts pose selection
Structural binding affinity database
A new database of 500+ complexes and experimental pK
i
data
($MOE/sample/mol/complex.mdb)
Ligands verified for correctness, receptors verified for close contacts
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: MOE-Dock Binding Site Preparation
Perform a docking study with a kinase receptor and a ligand using alpha sphere
dummy atoms defining the binding site.

1. Open 1ke6_rec.moe
(MOE | File | Open)
2. Add hydrogens before docking
(MOE | Edit | Hydrogens | Add Hydrogens)
and calculate the partial charges
(MOE | Compute | Partial Charges)
with Amber99 forcefield
*)
.
In addition, MOE-Dock requires definition of a
docking site in the receptor. This can be done in various ways:
Select the ligand (it will be ignored during docking),
Select the residues of the pocket,
Select dummy atoms generated by MOEs Site Finder
3. Open the Alpha Site Finder (MOE | Compute | Site Finder) to isolate the
active site. Identify and select the relevant site and create Dummies.
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MOE-Dock Panel
MOE-Dock can be launched with (MOE | Compute | Simulations | Dock).
Choose between various options for receptor, binding site and ligand
atoms definitions
Ph4 query can be
loaded.
Specifies which
atoms in MOE are
used as receptor.
Specifies the
placement and
scoring method
Specifies which
atoms in MOE (or
mdb-file) are used
as ligand(s).
Specifies which
atoms in MOE are
used as docking
site.
Verification of the
selected atoms.
Visualize backbone,
binding site residues
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: MOE-Dock I
4. Launch MOE-Dock (MOE | Compute | Simulations | Dock).
5. Specify an output database file name (e.g. dock_tm_lon.mdb).
6. Ensure that Receptor is set to "Receptor
Atoms".
7. Ensure that Site is set to Dummy Atoms".
8. Use the Render button to isolate the
docking site.
9. Switch Ligand to MDB File and select
the conformation database of the ligand
(conf_out_1ke6.mdb); disable
Conformational Search.
10. Select Placement and Scoring Methods:
Triangle Matcher and London dG
11. Click OK.
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: MOE-Dock II
12. Examine the results in the output database (dock_tm_lon.mdb) :

The poses of each ligand (mseq) are already
ranked according to the best score, i.e.
lowest S value at the top.

Compare the position of the original,
co-crystallized ligand with the docked
conformations of the database.

13. Load the original ligand (copy the
structure from the crystal field in
1ke6_crystal.mdb into the MOE
window), select it, and color the
ligand orange to better distinguish the
crystal ligand from the docking poses.
Scoring function
[kcal/mol]
Distance based
scoring function
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: MOE-Dock III
14. Use the Browser in the Database Viewer (DBV | File | Browser) to step
through the output database, one by one.
15. Select the first pose in the MOE window,
and render it by (MOE | Render | Stick).
1)
16. Evaluate the position of the best scored
pose (lowest S) and the pose with the
lowest RMSD
2)
with the co-crystallized
ligand (orange).

Best scored pose:
S = -10.26 kcal/mol
RMSD = 1.6
Lowest RMSD (rank 88):
S = -8.1 kcal/mol
RMSD = 0.69
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Copyright 2006 Chemical Computing Group Inc.
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Validation of the Docking Scores I
Placement methodologies in MOE may be compared by calculating the
RMSDs of the docked poses and the X-ray structure of the ligand.
Ideally, the correlation plot of the ASE score vs. the RMSD should show
a clear trend from lower left to upper right.

The figure shows three
independent docking runs with
the Alpha PMI placement
methodology. Smallest RMSDs
(most similar to the crystal pose)
correlate with the highest
scores.
As search space is not covered
systematically results may differ
slightly from one simulation to
another.
Red diamonds: 1st run; green dots: 2nd run;
blue squares: 3rd run
3 Docking Simulations with the Alpha Triangle Placement
Methodology
-9
-8
-7
-6
-5
-4
-3
-2
0 1 2 3 4 5 6 7 8 9 10
RMSD [A]
A
S
E

s
c
o
r
e
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Copyright 2006 Chemical Computing Group Inc.
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Validation of the Docking Scores II
Successful scoring functions will rank lowest RMSD placements at the
top with about 80 % accuracy. The plot compares lowest E versus lowest
RMSD placements for three runs using different placement strategies. In
this case lowest RMSD solutions are ranked quite low (11-30). Since the
implementation of docking routines in MOE is in the form of a toolbox
derive an optimal combination of tools for each project.



Docking Methods
Alpha PMI
Triangle Matcher
Alpha PMI
Triangle Matcher
Alpha Triangle
Alpha
Triangle
-5
-4
-3
-2
-1
1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5
RMSD [A]
E
n
e
r
g
y

[
k
c
a
l
/
m
o
l
]
sorted by lowest E sorted by lowset RMSD (Rank indicated in brackets)
(25) (30)
(11)
(1)
(1)
(1)
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Copyright 2006 Chemical Computing Group Inc.
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Validation of the Docking Scores III
To compare the performance of different
placement strategies 5 different CDK2 ligands
are cross-docked into the 5 different pockets to
give an idea about the variability of results
obtained with different methods. This also
shows that some pockets tend to perform better
than others thus also validate the pockets
before starting a large scale screening.
As a rule of thumb alpha PMI tends to provide
best results for small pockets.
Alpha Triangle
0
1
2
3
4
5
6
7
8
1ke6 pocket 1ke7 pocket 1ke8 pocket 1oiy pocket 1oit pocket
protein pockets
R
M
S
D
1ke6
1ke7
1ke8
1oiy
1oit
Triangle Matcher
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
5
1ke6 pocket 1ke7 pocket 1ke8 pocket 1oiy pocket 1oit pocket
protein pockets
R
M
S
D
1ke6
1ke7
1ke8
1oiy
1oit
Alpha PMI
0
2
4
6
8
10
1ke6 pocket 1ke7 pocket 1ke8 pocket 1oiy pocket 1oit pocket
protein pockets
R
M
S
D
1ke6
1ke7
1ke8
1oiy
1oit
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Copyright 2006 Chemical Computing Group Inc.
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Multi-Fragment Search I
Objective
Multi-fragment search (MFS) attempts to determine preferred positions
and interactions for certain functional groups in a given receptor.
Docking small fragments of limited flexibility can be achieved at higher
accuracies than docking entire molecules. Results may be used as
input to a de novo design procedure or to derive a pharmacophore.
Miranker, A., Karplus, M. Functionality Maps of Binding Sites:
A Multiple Copy Simultaneous Search Method. Proteins:
Structure, Function, and Genetics, 1991, 11, 29-34
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Copyright 2006 Chemical Computing Group Inc.
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Multi-Fragment Search II
Methodology
The active site of a receptor is randomly populated with many copies of
a fragment and then energy minimized (fragments do not interact).

Removes duplicates and
calculates interaction energies
with or without solvation effects
Fragment output is sent to a
molecular database for analysis
All or part of a receptor can be
held fixed during minimization
Save System
Place Fragments
Save Fragments
Fix Atoms
Minimize Classes
Minimize Receptor
Delete Duplicates
Save System
Save Fragments
Save Receptor
Input system mfss_orgsys.moe
mfss_orgcop.moe
mfss_output.mdb
mfss_mincop.moe
mfss_minrec.moe
convergence
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: Multi-Fragment Search I
First, prepare the receptor for Multi-Fragment Search:

1. Open the receptor file 1ke6_rec.pdb
(MOE | File | Open)
2. Add hydrogens
(MOE | Edit | Hydrogens | Add Hydrogens)
and calculate the partial charges
(MOE | Compute | Partial Charges)
with the Amber99 forcefield. After calculation
use the Potential Setup panel (MOE | Window | Potential Setup) to choose
an appropriate forcefield for receptor-ligand interactions (e.g. MMFF94x).
*)
3. Select the atoms of the active site to guide placement of fragments. Be careful
to pick only the solvent exposed atoms of the active site (to improve the speed
of fragment placement). Use Site Finder dummies in absence of any other
ligand information.
Select the ligand atoms/ Site Finder dummies and extend the selection to 4.5
(MOE | Selection | Extend | Nearby (4.5A))
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: Multi-Fragment Search II
4. Delete the chain of the ligand/alpha spheres in the SE (without deselecting the
pocket
*)
.
5. Choose (Compute | Simulations | MultiFragment Search) in the MOE
window to open the MultiFragment Search panel.
6. Select the fragments that should be included:
E.g. acetate ion and phenol.




7. Click Next.
Fragment list contained in
the fragment database.
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: Multi-Fragment Search III
8. The next window contains parameters
for minimization (stay with defaults).
Click Next.

9. Before starting the MF-search choose
several output file names (stay with
defaults).

10. Click Start.

The selected fragments will be flooded
into the pocket and minimized. This
may take some time.
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: Multi-Fragment Search IV
11. Examine the results:

Open the *_orgcop.moe into the MOE window.
This is the molecular system after initial
placement of the fragments together with the
receptor but prior to energy minimization (the
original copies).


Open the *_mincop.moe into the MOE window.
These are all the resulting unique fragments and
the receptor after energy minimization (the
minimized copies).
The same picture will result if all entries from the
*_output.mdb are copied into the MOE
window.
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: Multi-Fragment Search V
12. Open the *_output.mdb
This fragment database contains 58 entries of
the acetate and 74 entries of the phenol
fragment after minimization including
interaction energy information.
Sort the entries according to different criteria:
best binding, lowest potential, best binding in
fragment class, or lowest potential in fragment
class.
*)
(All values are in kcal/mol.)
13. Open the receptor again (please use the
prepared pocket.moe file for examination;
otherwise the surface etc. has the be
generated).
Copy all entries of one fragment into the
receptor pocket to get a first impression if there
are some preferred regions (clusters) of the
fragment. In this phenol example there are two
main clusters one inside and one more
exterior to the pocket.
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Copyright 2006 Chemical Computing Group Inc.
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Exercise: Multi-Fragment Search VI
14. Examine each placement individually using
the Browser in the Database Viewer (BDV |
File | Browser) and step through the output
fragments. Each fragment will be placed in
the receptor context. (delete the fragments
of point 13 before.)
15. If a placement may be a suitable starting
point for de novo design, keep the entry in
the MOE window by clicking Keep in the
Browser panel.
16. Compare also the positions of the
fragments with the original ligand position.

With knowledge of preferred fragment
positions it may now be possible to join the
fragments to new ligands, build
combinatorial libraries, or derive
pharmacophores.