UNIT-2
MOLECULAR DOCKING
✓ Docking is a structure-based technique which aim is to achieve an optimized
conformation for both receptor and ligand. And the relative orientation between the
protein and the ligand will be such that the free energy of the overall system us
minimized.
✓ Molecular docking is the prediction of conformation complementarity between
ligand and receptor molecule.
✓ Successful docking methods search high-dimensional spaces effectively and use a
scoring function that correctly ranks candidate dockings.
✓ It is a computational process to find out active ligand which can bind with target site
effectively. The molecular docking studies are useful to find out the lead compound
which can fit in to receptor effectively.
Two basic component of molecular docking are
1. Ligand → a ligand is a substance that forms a complex with a biomolecule to serve
a biological purpose. The etymology stems from ligare , which means ‘to bind ‘. In
docking the ligand is usually a molecule which produces a signal by binding to a site
on a target protein.
2. Receptor →It is a macromolecule in the membrane or inside the cell that
specifically bind to a ligand. These are smaller molecules that are capable of ligating
themselves to the receptor protein.
Why docking is important ?
▪ SIGNAL TRANSDUCTION:- The association between biological relevant molecules such as
proteins, nucleic acids, carbohydrates, and lipids play a important role n signal
transduction. Thus the relative orientation of the two interacting partners may affect the
type of signal produced that is either agonist or antagonist. Therefore, docking is useful
for predicting both the strength and type of signal produced.
▪ DRUG DESIGNING:- Docking is frequently used to predict the binding orientation of
small molecule drug candidates to their protein targets in order to predict the affinity
and activity of the small molecule. Hence docking plays important role in rational drug
designing.
TYPES OF DOCKING
1) RIGID DOCKING
✓ In this geometry of ligand and protein both are kept constant.
✓ It follows the lock and key model.
✓ However, since the conformations of both the ligand and protein are altered
upon the formation of the complex, most rigid body docking tools are unable to
accurately reproduce the experimental observed binding pose.
✓ The simulations based on rigid docking are generally preferred when time is
critical, i.e., if a large number of compounds are to be docked during an initial HTD.
✓ However, flexible docking methods are needed for further refinement and
optimization of poses obtained from an initial rigid docking procedure
2) FLEXIBLE DOCKING
✓ In flexible docking receptor and ligand kept flexible and the associated energy is
calculated this method is good to study about binding patterns of drug with
receptor.
Mechanism of docking
✓ To perform docking the first requirement is a structure of the protein of intrest.
Usually the structure has been determined using biophysical technique such at X-
RAY crystallography or NMR spectroscopy, or can also be derived from homology
modeling construction. The protein structure and a database of potential ligands
serve as inputs to a docking program
SEARCH ALGORITHMS
1)Systematic Methods:
✓ It consider Ligand’s flexibility
✓ This explores all degree of freedom both rotational and translational of the ligand
and generate all possible conformations of ligand within the active site of the
protein.
✓ The methods are largely applied to rigid protein and flexible ligand docking.
✓ The search is done by docking the ligands by dividing them into fragments as rigid
and flexible units.
✓ Then the fragments are incrementally grown by placing one fragment into the binding
site, or by placing all fragments appropriately in the binding site and covalently linking
all of them.
✓ Glide and FRED are two examples of this type of sampling methodology.
2)Stochastic Methods:( Heuristic method)
✓ Both the protein and ligand are flexible in this method
✓ Heuristic approaches provide promising alternatives for the exhaustive exploration
of the search space.
✓ In these stochastic-based (heuristic) methods, the orientation, and conformations of
a single or population of ligands are operated by random changes.
✓ Based on probabilistic criteria the newly obtained conformation of the ligand will be
accepted or rejected.
✓ These methods find a minimum solution, it is not necessarily the global minimum.
✓ Hence, there is a need for running these optimizations many times to improve the
probability of identifying the global minimum via statistic measurements.
✓ Hence, there is a need for running these optimizations many times to improve the
probability of identifying the global minimum via statistic measurements.
3)Genetic Algorithms
✓ Genetic algorithm have been used in molecular docking to search for optimal ligand
binding poses and to optimize ligand structures.
✓ In docking the goal is to find the best pose of a ligand molecule that maximizes its
binding affinity with a target protein.
✓ The fitness function in this case typically a scoring function that evaluates the quality
of the ligand-protein complex based on factors such as electrostatics , vanderwaals
forces and hydrogen bonding interactions.
✓ Genetic algorithm can be used to search the space of possible ligand conformations
and orientations as well as to optimize the structure of the ligand itself.
Scoring Functions
✓ Scoring function is used to predict the strength of the binding affinity between
protein-protein, protein-ligand etc. the configuration of the binding affinity is decided
by scoring function.
✓ Score is determined by four index
▪ Scoring power→this power index has the ability to produce score based on
experimentally finding of affinity data.
▪ Ranking power→the ability to ranked a set of ligand based on their binding
affinity where their binding pose are known.
▪ Docking score→identify the best ligand based on docking score
▪ Screening power→identify the best ligand based on screening power.
✓ Scoring functions can be grouped into four types:
1. forcefield or molecular mechanics-based scoring functions
2. empirical scoring functions
3. knowledge-based scoring functions
4. consensus scoring functions
STEPS FOR DOCKING
1) It starts with crystal co-ordinates of the target receptor
2) Generate molecular surface for receptor.
3) Generate spears to fill the active site of the receptor the sphears become potential
locations for ligand atoms.
4) Spheres centres are then matched with the ligand atoms to determine possible
orientations for the ligand.
5) Find the top scoring or the best ranking.
Three scoring schemes are
a) shape scoring
b) electrostatic scoring
c) force-field scoring.
Applications of Molecular Docking
Molecular docking can demonstrate the feasibility of any biochemical reaction as it is
carried out before experimental part of any investigation. There are some areas, where
molecular docking has revolutionized the findings. In particular, interaction between small
molecules (ligand) and protein target (may be an enzyme) may predict the activation or
inhibition of enzyme. Such type of information may provide a raw material for the rational
drug designing. Some of the major applications of molecular docking are described below:
Lead optimization
Molecular docking can predict an optimized orientation of ligand on its target. It can predict
different binding modes of ligand in the groove of target molecule. This can be used to
develop more potent, selective and efficient drug candidates .
Hit identifications
Docking in combination with scoring function can be used to evaluate large databases for
finding out potent drug candidate in silico, which can target the molecule of interest .
Drug-DNA interaction
Molecular docking plays a prominent role in the initial prediction of drug’s binding
properties to nucleic acid. This information establishes the correlation between drug’s
molecular structure and its cytotoxicity.
Remediation
Additionally, protein-ligand docking may be utilized to forecast which contaminants are
degradable by enzymes. It can be utilized for the determination of the desired location,
collection of the most effective medication. Molecular docking can be used to identify
enzymes and their mode of action. It can also be utilized to determine relationships
between proteins. Molecules are screened virtually by using the remediation method.
Some others applications are
▪ Determination of lowest free energy structures for the receptor-ligand complex.
▪ Study the geometry of a particular complex.
▪ De novo design for lead generation.
▪ Library design.
▪ To check the specificity of the potential drug against homologous proteins through
docking.
DOCKING SOFTWARES
Components of docking Softwares :
Docking software can be categorised in the following criteria :
1. Molecular representation → a way to represent structures and properties (atomic
,surface ,grid representation)
2. Scoring method → a method to access the quality of docked complexes(force field,
knowledge-base approach etc…)
3. Searching algorithm → an efficient search algorithm that decides which poses to
generate (exhaustive search , monte carlo , genetic algorithms , simulated annealing
, tabu search )
GOLD( Genetic Optimization for Ligand Docking)
✓ GOLD is the validated, configurable protein–ligand docking software for expert drug
discovery.
✓ GOLD is a program for calculating the docking mode of small molecules into protein
binding sites.
✓ In GOLD Jones et al. use a genetic algorithm (GA) to dock a flexible ligand to a
semiflexible protein.
✓ GA is an optimization method that derives its behaviour from a metaphor of the
process of evolution.
✓ This program takes into account not only the position and conformation of the ligand
but also hydrogen bonding network in the binding site.
✓ This program performs very well for hydrophilic ligands but encounters some
difficulties when trying to dock hydrophobic ligands due to the reduced contribution
of hydrogen bonding to the binding process.
Features of GOLD:
1. A genetic algorithm for protein ligand docking .
2. Full ligand and partial protein flexibility .
3. Highly configurable constraints – uses existing knowledge of the system to bias
results and focus on known features and behaviours.
4. Multiple scoring functions – Score and rescore to build a full picture of the system
and consensus scoring
5. Water handling – Access how structural waters affect binding and see if the ligand
displaces waters or mediates the interaction during docking.
6. Virtual screening – Unlimited potential with virtual screening by cloud or cluster.
7. Covalent docking – understands irreversible binding with covalent docking to explore
cancer , immunology and infectious disease targets.
8. Energy functions partly based on conformational and non-bonded contact
information from the CSD.
9. A number of constraints , or restraints to allow greater control over the output
solutions.
AUTODOCK
✓ AutoDock is a suite of automated docking tools.
✓ AutoDock is the first docking package to model ligand with full conformational
flexibility(Morris et al. 1966).
✓ The package consists of two sequentially applied programs , AutoGrid and
AutoDock.
✓ It is designed to predict how small molecules, such as substrates or drug candidates,
bind to a receptor of known 3D structure.
✓ Over the years, it has been modified and improved to add new functionalities, and
multiple engines have been developed.
✓ AutoDock is used to perform computational molecular docking of small molecules
to proteins, DNA, RNA and other important macromolecules, by treating the ligand
and selected parts of the target as conformationally flexible
✓ Current distributions of AutoDock consist of two generations of software: AutoDock
4 and AutoDock Vina.
✓ More recently Autodock-GPU is developed, an accelerated version of AutoDock4
that is hundreds of times faster than the original single-CPU docking code.
✓ AutoDock 4 actually consists of two main programs:
✓ Autodock performs the docking of the ligand to a set of grids describing the target
protein;
✓ Autogrid pre-calculates these grids.
✓ In addition to using them for docking, the atomic affinity grids can be visualised. This
can help, for example, to guide organic synthetic chemists design better binders.
✓ AutoDock Vina does not require choosing atom types and pre-calculating grid maps
for them. Instead, it calculates the grids internally, for the atom types that are
needed, and it does this virtually instantly.
✓ It has also developed a graphical user interface called AutoDock tools or ADT for
short, which amongst other things helps to set up which bonds will treated as
rotatable in the ligand and to analyze dockings.
✓ AutoDock’s main strengths are
1) Receptor flexibility
2) Blind-docking
3) Precalculated grid maps on a binding site
4) Free energy scoring functions based on linear regression analysis, the
AMBER force field and a large set of protein ligand-complexes with known
inhibition constants.
5) Good correlation between predicted inhibition constants and experimental
data.
• AUTODOCK-4
✓ AutoDock4 is a computational docking program based on an empirical free
energy force field and rapid Lamarckian genetic algorithm search method.
✓ Docking is performed in two steps: first, a grid-based lookup table of interaction
energies is calculated for the receptor using AutoGrid , then ligands are docked
with AutoDock using this information.
✓ AutoDock4 is a core element of the AutoDock suite of free open source software
for the computational docking and virtual screening of small molecules to
macromolecular receptors.
✓ AutoDock is being developed and maintained in the Forli laboratory, with
support from the US National Institutes of Health.
• AUTODOCK VINA
✓ AutoDock Vina is an open-source program for doing molecular docking.
✓ It was originally designed and implemented by Dr. Oleg Trott in the Molecular
Graphics Lab (now CCSB) at The Scripps Research Institute.
✓ The latest version of AutoDock Vina is v.1.2.0.
✓ AutoDock Vina is one of the docking engines of the AutoDock Suite.
✓ AutoDock has applications in :
1) X-ray crystallography
2) structure-based drug design
3) lead optimization
4) virtual screening (HTS)
5) combinatorial library design
6) protein-protein docking
7) chemical mechanism studies
DOCK
✓ DOCK is a docking software program generally used to address small molecules.
✓ Docking is the identification of low-energy binding modes of small molecules or
ligand with the active site of a macromolecule or receptor with a known structured
molecule.
✓ DOCK is applicable for predicting the binding mode of small molecule-protein
complexes or searching for a database of ligands for compounds that inhibit
enzyme activity, for a compound that binds to a particular protein, a compound
that binds to nucleic acid targets, or to see the possibility of protein-protein
interactions.
✓ It uses a geometric matching algorithm to superimpose the ligand onto a negative
image of the binding pocket.
Flex-X
✓ Flexibly Dock ligands into a binding site Flex-X rapidly docks a conformationally
flexible ligand into a binding site, using an incremental construction algorithm that
builds the ligand in the site.
✓ The resulting docked conformations are scored based on the strength of ligand-
receptor interactions.
✓ The speed and robustness of Flex-X make it possible to dock and score libraries of
compounds in order to prioritarize synthetic and screening efforts.
✓ Flex-X includes conformational flexibility of the ligand of critical importance since
the low energy conformation is rarely the bioactive one.
✓ Flex-X is composed of four basic components:
1) conformational flexibility
2) the set of possible protein-ligand interactions
3) the scoring functions for the interactions
4) and the algorithm for placement and incremental growth of the ligand from a
defined core.
FTDock
✓ FTDock is an algorithm for docking rigid molecules.
✓ It represents the two molecules onto orthogonal grids and performs a global scan of
rotational and transitional space.
✓ The scoring method is primarily a surface complementary score between two grids.
✓ FTDock performs docking on two biomolecules in order to predict their correct
binding geometry.
ENERGY MINIMIZATION
✓ It is essential to determine the proper molecular arrangement in space since the
drawn chemical structures are not energetically favourable. The P.E of a molecule
contains different energy components like stretching , bending and torsion , hence
when an energy minimization program is run , it will immediately reach a minimum
local energy value and it might stop if the employed program is not exhaustive .
✓ Energy minimization is used to reduce the overall potential energy of a protein and
the ligand .
FREE ENERGY PERTURBATIONS
✓ It is used to calculate the pre-energy between the two state of molecules or system.
✓ It involves gradually transforming and calculate the changes in potential energy and
entropy . These difference between P.E and entropy gives an estimate of energy
between two states.
✓ Free energy perturbation (FEP) is a method based on statistical mechanics that is used
in computational chemistry for computing free energy differences from molecular
dynamics or Metropolis Monte Carlo simulations.
✓ The FEP method was introduced by Robert W. Zwanzig in 1954.
✓ According to the free-energy perturbation method, the free energy difference for
going from state A to state B is obtained from the following equation, known as the
Zwanzig equation:
where T is the temperature, kB is Boltzmann's constant, and the angular brackets
denote an average over a simulation run for state A.
✓ In practice, one runs a normal simulation for state A, but each time a new
configuration is accepted, the energy for state B is also computed.
✓ The difference between states A and B may be in the atom types involved, in which
case the ΔF obtained is for "mutating" one molecule onto another, or it may be a
difference of geometry, in which case one obtains a free energy map along one or
more reaction coordinates. This free energy map is also known as a potential of mean
force or PMF.
✓ Free energy perturbation calculations only converge properly when the difference
between the two states is small enough; therefore, it is usually necessary to divide a
perturbation into a series of smaller "windows", which are computed independently.
✓ Since there is no need for constant communication between the simulation for one
window and the next, the process can be trivially parallelized by running each window
on a different CPU, in what is known as an "embarrassingly parallel" setup.
Application
✓ FEP calculations have been used for studying host–guest binding energetics, pKa
predictions, solvent effects on reactions, and enzymatic reactions. Other applications
are the virtual screening of ligands in drug discovery, as well as for in silico
mutagenesis studies.
✓ For the study of reactions, it is often necessary to involve a quantum-mechanical (QM)
representation of the reaction center because the molecular mechanics (MM) force
fields used for FEP simulations can't handle breaking bonds. A hybrid method that has
the advantages of both QM and MM calculations is called QM/MM.
✓ Umbrella sampling (US), a widely used free energy calculation method, has long been
used to explore the dissociation process of ligand–receptor systems and compute
binding free energy.
✓ Also Umbrella sampling can also be used for a chemical transformation when the
"chemical" coordinate is treated as a dynamic variable.
