Pharmacophore-based

Molecular Docking

Bert E. Thomas,
Diane Joseph-
McCarthy,
Juan C.Avarez
 Introduction
• Pharmacophore Concept
• Conformational Expansion Approach
• Docking Pre-Computed Conformers
– DOCK framework
– Conformational Ensembles Docking
– Pharmacophore-Based Docking
– Pros. & Cons.
• Implementation Details
• Latest Improvements
 Pharmacophore
• The term, traced to Emil Fischer (1894) and Paul
Ehrlich (1909).
• The term, introduced by Ehrlich, refers to the
molecular framework that carries (phoros) the
essential features responsible for a drug's biological
activity (pharmacon)
• Presently, the term has been expanded to refer to the
3D arrangement of functional groups that enable a
compound to exert a particular biological effect
• Many pharmacophores are defined simply in terms of
three atoms and three distances
 Pyridinyl imidazole P38 Inhibitors

H-bond to
Met109 NH
N

Hydrophobic
F
pocket
HN
N

O S
 Virtual Screening

Rapid computational
mining of 3D
molecular databases is
central to generating
new drug leads.

The algorithms must

be able to handle
hundreds of thousands
of molecules.
 Conformational Expansion Approach

• Conformational flexibility of the ligand

molecule must be considered.

• One of the approaches is to address

conformational flexibility at database generation
step, and not during the docking procedure.

• Allows rapid screening.

 Conformational Expansion
Disadvantages

• The total number of conformers must be kept

manageable.
• The torsional increment must give a good
coverage of conformational space.
• If the appropriate conformation for the ligand is
not explicitly represented in the database, the
“best” orientation will not be found, and the ligand
may be missed entirely!
 Conformational Expansion Methods

Two approaches for docking of pre-computed

conformers from a conformationaly extended
database will be compared:

1. Conformational ensembles docking

Lorber DM & Shoichet BK. Flexible ligand
docking using conformational ensembles.
2. Pharmacophore-based docking
Bert E. Thomas, Diane Joseph-McCarthy,
Juan C.Avarez
The DOCK Suite
 The DOCK Algorithm
Two steps in rigid ligand mode:
Orienting the putative ligand in the site
Guided by matching distances, between pre-
defined site points on the target to interatomic
distances of the ligand.The RT matrix is used for
the transform of the ligand.

Scoring the resulting orientation

Each orientation is scored for each quality fit. The
process is repeated a user-defined number of
orientations or maximum orientations
 1. Define the target
binding site points.

F
2. Match the distances.
H N
N

O S

N 3. Calculate the
transformation matrix
F

H N
N

O S

for the orientation.

N

H N
N

O S
4. Dock the molecule.
N

H N
N
F

5. Score the fit.

O S
 Site Points Generation
in DOCK

• Program SPHGEN identifies the active site, and

other sites of interest.
• Each invagination is characterized by a set of
overlapping spheres.
• For receptors, a negative image of the surface
invaginations is created;
• For a ligand, the program creates
a positive image of the entire molecule.
 The Matching
Can be directed by 2 additional features:
• Chemical matching - labeling the site points such
that only particular atom types are allowed to be
matched to them.
• Critical cluster - subsets of interest can be defined
as critical clusters, so that at least one member of
them will be part of any accepted ligand “match”.

Increase in efficiency and speed due to elimination

of potentially less promising orientations!
Conformational Ensembles
Docking
 Conformational Ensembles Docking

Observations:

1. Generating an orientation of a ligand in a binding site

may be separated from calculating a conformation of
the ligand in that particular orientation.

2. Multiple conformations of a given ligand usually

have some portion in common (internally rigid atoms
such as ring systems), and therefore, contain
redundancies.
 Conformational Ensemble Docking
• Conformational ensembles are generated by
overlaying all conformations of a given molecule
onto its largest rigid fragment.
• Only atoms within this largest rigid fragment are
used during the distance matching step. The RT
matrix is defined.
• Each of the conformers is oriented into the site
and scored. The score measures steric and
electrostatic complementarity.
• One matching steps - all the conformers are
docked and scored in the selected orientation.
Overview of the Ligand Ensemble Method
 Advantages of Conformational Ensemble
Docking

Speed increase due to:

• One matching step for all the conformers.

• The largest rigid fragment usually has

fewer atoms (less potential matches are
examined).
 Disadvantages of Conformational
Ensemble Docking

• Loss of information when the orientations are guided

only by a subset of the atoms in molecule.
Orientations may be missed because potential
distance matches from non-rigid portions of the
molecule are not considered.

• The ensemble method will fail for ligands that lack

internally rigid atoms.

• The use of chemical matching and critical clusters is

limited.
Pharmacophore-Based
Docking
 Pharmacophore-based Docking

Basic idea:

• Appropriate spatial disposition of a small number of

functional groups in a molecule is sufficient for
achieving a desired biological effect.

• The ensemble formation will be guided by these

functional groups.
3-D Representation of a Protein Binding Site

6.7
4.2-4.7
5.2 4.8

5.1-7.1
Distances
between
binding groups
in Angstroms and
the type of
interaction
 Pharmacophore Fingerprint
• Pharmacophore fingerprint - a set of
pharmacophore features and their relative position.
• Typical pharmacophore features:
– Hydrogen-bond donors and acceptors
– Positive and negative ionizable
– Hydrophobes and ring centroids
• Implemented in DOCK 4.0.1
– Hydrogen-bond donors
– Hydrogen-bond acceptors
– Dual hydrogen-bond donor and acceptor
– 5 or 6 membered ring centroids
 Notes on Pharmacophore Fingerprint

• Each conformer has pharmacophore

fingerprint.

• Different conformers of the same molecule

can have identical pharmacophore
fingerprints.
Pharmacophore DOCK
 Advantages of Pharmacophore-based
Docking

• Rapid elimination of ligands containing functional

groups which would interfere with binding.

• Speed increase over docking of individual molecules.

• More information pertaining to the entire molecule is

retained (no rigid portions).

• Chemical matching and critical clusters are encouraged.

 Speed Comparison Between Ensemble
and Pharmacophore-based Docking.

Pharmacophore-based advantage:
• Reduced number of ligand points considered
during distance matching.
Ensemble docking advantage:
• The average number of conformers per molecule is
higher than the average number of conformers per
fingerprint. The one step matching speed reduction
is slightly higher.
 Speed Reduction Cont.

• Ensemble docking:
the average number of conformers per molecule is
297.
Rigid Fragment Conformer 1 Conformer 2 Confomer 297

• Pharmacophore-based:
50-100 conformers per pharmacophore
Pharmacophore
Conformer 1 Conformer 2 Conformer 100
Fingerprint
 Database Preparation
• Generating molecular conformations
– Systematic search method with SYBYL.
• Overlaying molecular conformers onto
pharmacophores
1. Extract 3D pharmacophore from the first molecule of a
cluster
2. Use it to perform a rigid 3D UNITY search of the rest of
that cluster to find matches
3. Save the pharmacophore query
with the associated molecules
4. Process until all molecules are
associated with a pharmacophore
 Site Points Generation
• Chemically labeled site point are generated in an automated
fashion using the script MCSS2SPTS .

• The script runs a series of MCSS (Multiple Copy

Simultaneous Searches) calculations.

• MCSS – methodology for finding energetically favorable

positions and orientations of small functional group in a
binding site.

• Uses CHARMM potential energy function to determine the

preferred locations or potential energy minima
simultaneously for thousands of copies of a given chemical
group.
Improvements Underway ...
 MCSS Extension to Include the Target
Flexibility

• Standard MCSS methodology was lately extended to

include the flexibility of the target.

• Reference:
Collin M Stultz, Martin Karplus
“MCSS functionality maps for flexible protein”.
 Expansion of Conformational Ensembles
Docking
Su AI, Lorber DM, Weston GS, Baase WA, Matthew BW,
Shoichet BK. Docking molecules by families to increase the
diversity of hits in database screens: computational strategy and
experimental evaluation. Proteins 42, 279-93 (2001).

The problem: When one compound fits the site well, close
analogs typically do the same.

The Solution: The database is grouped into families based on the

common rigid fragment. Only the best scoring molecule of a
high-ranking family was allowed to hit the list.
 Improvements to
Pharmacophore-based Docking

• Optimization of database processing.

• Additional scoring functions (currently only contact

scoring).

• Addition of solvation correction (electristatic and

non-polar solvation free energy).
Proteins 34:4-16 (1999), Shoichet et al.

• Pharmacophore fingerprint enrichment.

 Closing Remarks...
• The Pharmacophore is a useful concept,
which has assisted in the discovery of many
biologically active compounds.

• There is still much to develop

– Pharmacophore identification
– Pharmacophore-based docking methods
Happy New Year!
 Limitations of Pharmacophore-based
Searching

• A limited subset of key interactions (typically 4-6)

which must be extracted from the target site with
dozens of potential interactions.
• Complex queries are extremely slow.
• The majority of the information contained in the
target structure is not considered during the search.
There is no scoring function beyond the binary
(match/no match). Any steric or electronic
constraints imposed by the target, but not defined by
the target are ignored.
 Validation
Implemented in DOCK 4.0.1.
• The test case
– methotrexate (MTX) bound to dihydrofolate reductase
(DHFR)

• Database preparation
– MTX translated away and conformationally expanded (500
pharmacophore 1 conformer each).
– DOCK's chemical matching and contact scoring set to manual.
– Max orientations = 5000.
 Validation Results
• Site points = all pharmacophore points.
• Score range: -111 to –3.
• RMSD between X-ray and docked conformations was 0.38A.
• The best scoring conformer = X-ray complex
• Site points = MCSS2SPTS script generated.
• Score range: -121 to –60.
• RMSD between X-ray and docked conformations was 0.78A.
• The best scoring conformer = X-ray complex.
 Search Methods
• Database searches fall in to two major classes:
– ligand-based (pharmacophore)
– Target-based (molecular docking)
• Pharmacophore searches consist of finding
molecules that match a set of distances between
specific types of atoms or functional groups which
interact favorably with the target
• Docking methods search for electronic and steric
complementary between putative ligands and
macromolecule target
 Molecular-docking Challenges
• Aim to predict the conformations and the
orientations of a ligand bound to a macromolecule
target. A 3D structure is required.

• Ligand and target conformational flexibility must

be taken into account.

• For being used for virtual screening of large

compound databases the algorithms must be really
fast
 MCSS Methodology

• Determines energetically favorable positions for

various functional group types in the binding site
of a target macromolecule structure.

• Uses CHARMM potential energy function to

determine the preferred locations or potential
energy minima simultaneously for thousands of
copies of a given chemical group.
 Improvements to
Pharmacophore-based Docking

• Optimization of database processing

• Additional scoring functions (currently only
contact scoring).
• Addition of solvation correction and energy
minimization.
– Shoichet et al. Have calculated electrostatic and non-
polar solvation free energies for molecules in ACD
database. Correcting for ligand solvation improved the
ranking of known ligands and discriminated against
molecules with inappropriate charge states and sizes.