Protein - Ligand Docking

Flow:
Basics of Docking.
Classification.
Docking programs.
Importance and applications.
Introduction.
Protein modeling.
Modeling of protein flexibility using ligand properties.
Problems identified.
Conclusion.
 What is Docking?

Docking attempts to find the “best” matching

between two molecules.
…a more serious definition…
• Molecular docking is a widely-used computational
tool for the study of molecular recognition, which
aims to predict the binding mode and binding affinity
of a complex formed by two or more constituent
molecules with known structures.
• An important type of molecular docking is protein-
ligand docking because of its therapeutic applications
in modern structure-based drug design.
It is to study…..
• Whether the two molecules “interact with each
other”.

• If so, what is the orientation that maximizes the

“interaction” while minimizing the total “energy” of
the complex.

Goal:
Given a protein structure, predict its ligand bindings.
Factors Affecting docking:
Intramolecular Forces: (covalent)
• Bond lengths
• Bond angles
• Dihedral angles

Intermolecular Forces: (noncovalent)

• Electrostatics
• Dipolar interactions
• Hydrogen bonding
• Hydrophobicity
• van der Waals
Classification of Docking:

Docking

Protein- Protein-Protein
Ligand docking
docking
Both Protein and Ligand are considered as Rigid one

Protein is Rigid and Ligand is Flexible molecule

Flexible protein and Rigid Ligand Molecule

 Docking Programs:
 DOCK (I. D. Kuntz, UCSF)

 AutoDOCK (Arthur Olson, The Scripps Research

Institute)

 RosettaDOCK (Baker, Washington Univ., Gray,

Johns Hopkins Univ.)

More information in:

[Link]
1. Protein-Protein Docking

2. Protein-Ligand Docking

optimized
 Why is Docking important?
• It is of extreme relevance in cellular biology, where
function is accomplished by proteins interacting with
themselves and with other molecular components

• It is the key to rational drug design: The results of

docking can be used to find inhibitors for specific
target proteins and thus to design new drugs. It is
gaining importance as the number of proteins whose
structure is known increases.
 Applications:
• A binding interaction between a small molecule ligand
and an enzyme protein may result in activation or
inhibition of the enzyme. If the protein is a receptor,
ligand binding may result in agonism or antagonism.
Docking is most commonly used in the field of drug
design — most drugs are small organic molecules, and
docking may be applied.

• Hit identification – docking combined with a scoring

function can be used to quickly screen large databases
of potential drugs in silico to identify molecules that are
likely to bind to protein target of interest.
 Contd…
• Lead optimization – docking can be used to
predict, in where and in which relative
orientation a ligand binds to a protein . This
information may in turn be used to design
more potent and selective analogs.
• Bioremediation – Protein ligand docking can
also be used to predict pollutants that can be
degraded by enzymes.
Protein Flexibility:
Ligand binding commonly induces protein
conformational changes, which range from local
rearrangements of side-chains to large domain
motions. Due to the large size and many degrees of
freedom of proteins, their flexibility may be the most
challenging issue in molecular docking. Current
methods to account for protein flexibility can be
grouped into four categories:
soft docking, side-chain flexibility, molecular
relaxation, and protein ensemble
docking.
• Docking, virtual screening and structure-based drug design
are routinely used in modern drug discovery programs.
Although current docking methods deal with flexible
ligands, managing receptor flexibility has proved to be
challenging. The current state-of-the-art for
computationally handling receptor flexibility is important.
A combination of different methods is likely to provide the
most reliable solution to the problem of finding the right
protein conformation for a given ligand.
Virtual Screening
Virtual screening is the computational
analogue of biological screening.

It does a quick search of large libraries

of chemical structures in order to
identify those structures which are
most likely to bind to a drug target.

The aim of virtual screening is to score,

rank and/or filter a set of structures
using computational procedures.

Virtual Screening: Principles, Challenges, and

Practical Guidelines, Volume 48 Christoph Sotriffer
 Protein-ligand docking
• A Structure-Based Drug Design (SBDD) method
– “structure” means “using protein structure”
• Computational method that mimics the binding of a ligand to a
protein
• Given...

• Predicts...
• The pose of the molecule in
the binding site
• The binding affinity or a score
representing the strength of
binding
 Pose vs. binding site
• Binding site (or “active site”)
– the part of the protein where the ligand
binds
– generally a cavity on the protein surface
– can be identified by looking at the
crystal structure of the protein bound
with a known inhibitor
• Pose (or “binding mode”)
– The geometry of the ligand in the
binding site
– Geometry = location, orientation and
conformation
• Protein-ligand docking is not about
identifying the binding site
 Uses of docking
• The main uses of protein-ligand docking are for
– Virtual screening, to identify potential lead compounds
from a large dataset
– Pose prediction

• Pose prediction
• If we know exactly where and
how a known ligand binds...
– We can see which parts are
important for binding
– We can suggest changes to
improve affinity
– Avoid changes that will
‘clash’ with the protein
Prediction of the optimal physical configuration and
energy between two molecules

The docking problem optimizes:

 Binding between two molecules such that their

orientation maximizes the interaction

 Evaluates the total energy of interaction such that

for the best binding configuration the binding
energy is the minimum

 The resultant structural changes brought about by

the interaction
 SBDD
 Structure based drug design method-1980
 Computational modelling and simulation-integral part
 This tool was not only used for hit identification and
lead optimization, but also for analysis of drug
metabolism and toxicity.
 Earliest- lock and key theory- treated the ligand and
protein as rigid bodies.
 At the next stage, docking of flexible ligands to rigid
proteins was addressed and these remain the most
popular methods in use.
Contd..
 Considering the importance of protein flexibility on
ligand binding have given great interest.

 Will not discuss about rigid ligand-protein docking.

 some of the methods currently being investigated to

model protein flexibility and discuss their strengths
and limitations.
 Modeling protein flexibility:
 Although the existence of ligand-induced flexibility has
been known for almost half a century, it was generally
considered to be rare.
 A recent statistical analysis of the PDB revealed that 85%
of the proteins contain one to three flexible residues in
the active site.
 It is also reported that single rigid receptor dockings
predict incorrect binding pose for 50–70% of all ligands.
 Flexible residues are subject to conformational changes
ranging from simple side-chain movements to backbone-
loop movements to major domain rearrangements.
 Condt..
 Conformational changes observed in X-ray crystal structures.

 Many factors have hindered the development of methods for

dealing with ligand-induced protein conformational changes.
 Lack of a clear understanding of what kinds of changes may
be induced by a ligand in a given protein.
 Any form of the protein was thought to take care of the
conformational changes that may be induced by any other
ligand adequately.
 Ligands with diverse chemical scaffolds and of different sizes
are- induce different types, or different extents, of changes in
protein conformation.
 [Link] Docking
Soft docking is the simplest method which considers
protein flexibility implicitly. It works by allowing for a
small degree of overlap between the ligand and the
protein through softening the interatomic van der Waals
interactions in docking calculations.
Only subtle side-chain changes detected
And
Completely novel conformation
cannot be found

Low computional
Cost and easy to intrerpret.
 [Link] methods – rotamer exploration
and multiple proteins Structures (MPS):
 Survey methods offers an alternative method to model
receptor flexibility.

 One of these methods is the exploration of rotamer

libraries to simulate side-chain movements. Other types
of conformational changes cannot be handled by this
approach and, hence, this method fails to simulate
ligand-induced flexibility fully.

 Another simple implementation of the survey method is

the docking of the ligand to multiple receptor structures.
 Condt…
o While virtually simulating protein conformation
selection by ligand, this becomes computationally very
expensive as the number of conformations increases.

o As the number of structures used increases, the

computational effort increases, chances of false positive
results also increase.

o The number and choice of protein structures is,

however, an issue that remains to be resolved.
 Modeling protein flexibility
using ligand properties
• None of the methods discussed above, except perhaps
rotamer exploration, considers ligand-induced flexibility
in a quantitative manner.
• A recently proposed knowledge-based approach for
handling receptor flexibility, which interfaces chemistry
(small molecule properties) with biology (protein
structure) using data analysis and modeling techniques.
• It is referred as quantitative structure-induced
conformation relationship (QSiCR) analysis.
• It is similar in spirit to the quantitative structure–activity
relationship (QSAR) approach.
 Condt..
• In the QSiCR approach, the conformational differences
that can be observed in the active site of mainly ligand-
bound forms of crystal structures of proteins are first
identified, typically at the level of residues.
• Suitable position-invariant residues in the active site are
then identified from the same set of structures, to
define a frame of reference.
• Conformational changes are defined in terms of
distances of variable residues from invariant residues.
These geometric quantities are modeled as functions of
ligand properties using statistical–computational
methods.
 Hybrid methods:
• A popular commercial software program, uses a
combination of soft potentials, rotamer exploration
and/or active-site mutation to simulate induced-fit
effects.
• The ligand is first docked to the active site of the protein
by using Glide with soft potentials, and multiple poses of
the ligand are selected.
• For each pose, side-chains of the residues to which the
ligand has very close contacts are removed and rebuilt
by rotamer exploration, keeping the ligand rigid in its
position in the active site; this simulates induced-fit
effects of ligand on protein.
 Condt..
• Then, the complex is energy minimized to allow for
backbone rearrangements.
• At the next step, the ligand is re-docked to the optimized
protein conformation.
• This procedure is repeated for all the selected poses, the
results are compared and the best-docked pose is
selected.
 Molecular Dynamics Simulations
• Some researchers have used MDS after docking to
examine the stability of the docked conformation and
the strength of binding, which also allows for receptor
and ligand rearrangements to obtain lower energy
conformations of the docked complex.
• High computational cost.
• The conformations explored by MDS are dependent on
the starting solution provided to the simulator.
• Another approach could be to obtain a good starting
solution by QSiCR or a hybrid approach and then carry
out MDS.
 Problems
• A recent progress in molecular docking and scoring by
the description of several applications and case studies.
• Successful usage of these techniques has still severe
limitations.
• The identification of an overall reliable and robust
scoring function seems to be one of the main challenges
to be addressed in the near future.
• Using flexible proteins, computational biologists are able
to quite accurately simulate protein-ligand binding, but
the computation is very heavy. A single simulation can
take days of high-throughput computation.
 Condt..

• A problem related to docking is the recognition of

motifs in proteins, which are substructures of the
proteins with similar geometry. Matching motifs may
indicate genetic links or active sites with similar
properties.
Conclusion:
 All methods have their own merits and shortcomings.

 A combination of methods may help in improving the

reliability of docking to flexible proteins, and hence for

SBDD.

 Some such attempts have been made but there is still scope

for investigating many other combinations.

 It would be interesting to find out whether a single ideal

combination exists that would work well for all proteins.