molecular docking
DESCRIPTION
drug design and molecular dockingTRANSCRIPT
Molecular Docking
• S. Shahriar Arab
Presented by
VIVEK K
RAHUL BS
Drug discovery
Take years to decade for discovering a new drug and
very costly
To cut down the research timeline and cost by
reducing wet-lab experiment use computer modeling
softwares
Drugs interact with their receptors in a highly specific
and complementary manner.
Core of the (target-based) structure-based drug design
(SBDD) is lead generation and optimization
Pharmacophore- the atoms and functional groups required
for a specific pharmacological activity, and their relative
position in space.
3D arrangement of functional groups that enable a
compound to exert a particular biological effect.
In-silico design
In silico
design
Receptor based
Ligand
based
Combinatorial
Denovo
based
In silico design
Active site
identification
No Ligand fragments grouping
Fit for receptor Complex growing yes
No yes Potential drug Change receptor
Receptor/structure based approach
Pharmacophore identification
Pharmacophore modification
No Fit to receptor
Yes Potential drug
Ligand based approach
• Automated or semiautomated process of synthesising large quantity of compounds in small scale
• Purely based on molecular modelling study of binding site.
• Searching large data bases to identify proper ligand.
Combinatorial based approach
Denovo based approach
Receptor/Host/Lock – receiving molecule (protein) – large.
Ligand/ Guest/ Key – molecule bind to receptor –small.
Docking – Computational simulation of a candidate – preffered orientation of ligand binding site to a receptor.
Binding mode – conformation of ligand-receptor bound to each other.
Pose – a candidate binding mode.
Scoring – evaluating a particular pose by counting the number of favourable intermolecular interactions.
Different terms used in in-silico design
Ranking – classify ligands most likely to interact favourably to a particular relation based on ∆G of binding.
Hit – Ligand with high rank.
Lead – hit with biological activity.
Pharmacophore – spacial arrangement of atoms or groups believed to be responsible for biological activity.
Rational drug design – Modulation of specific biological target may have therapeutic value.
QSAR – Study of physico chemical properties of a compound with its biological/pharmacological activity.
Drug design – design of ligands.
Docking attempts to find the “best” matching between two molecules
Docking
....a more serious definition….
Docking is a method which predicts the preffered orientation of one molecule to a second when bound to form a stable complex with overall minimum energy.
• Docking is used to predict both strength & type of signal produced.
• Aim of molecular docking is to achieve an optimized conformation & relative orientation between protein ligand such that ∆G is minimized.
It is to study. . . . .Whether the two molecules interact with each other
If so what is the orientation that maximizes the interaction which minimizing the total energy of the complex
Goal. . . Given a protein structure and predict its ligand
bindings.
It is of extreme relevance in cellular biology
It is the key to rational drug design
Why is docking important?
i. Uses a matching technique – describes the protein and ligand as complementary surfaces.
ii. Simulates the actual docking process in which ligand- protein pairwise interaction energies are calculated
Docking approaches
Receptor’s molecular surface – solvent accessible surface area.
Ligand’s molecular surface – matching surface description.
Advantage Fast & robust
Disadvantage Can't model the dynamic changes in the ligand /
protein conformations accurately.
a) Shape complementarity
Protein and ligands are separated by a physical distance
Binding takes place only after certain moves (translations, rotations,& internal changes like
torsional angle rotations) in its conformational space.
In every move total energy of the system is calculated.
Disadvantage It take longer time for evaluation (overcome by using
grid based technique & fast optimization methods)
b) Simulation
Intramolecular forces. . . . bond length bond angle dihedral angle
Intermolecular forces. . . . electrostatic dipolar H-bonding hydrophobicity Vander waals forces
Factors affecting docking
Interactions between particles can be defined as a consequence of forces between molecules connected by particles.
Kf
Drug + receptor Complex Kr
Kf – rate constant for association of the complex
Kr – rate constant of dissociation of the complex
Affinity, Kas = Kf / Kr
Biological activity of a drug is related to its affinity Kas for the receptor
Different type of interactions
Involves integration of overall electron clouds of the two molecule.
Longest range.
Electrostatic energy
Ion-ion(1/R)
Ion-dipole(1/R2)
Dipole- dipole(1/R3)
Attractive forces existing between all pairs of atoms,even between rare gas atoms.
Depends on polarizability & number of valence electrons of interacting molecule.
Polarization energy involves the interaction of a molecule that is already polar with another polar/non polar molecule.
Eg. London or Vander waals forces.
Electrodynamic forces
Each atom wthin the molecule occupies a certain amount of space.
If atoms are too closer there is an associated lost in
energy due to overlapping electron cloud – may affect molecules preferred shape, reactivity and activation energies of most chemical reaction.
Steric effect will determine how & at what rate a drug will interact with its target biomolecule.
Steric forces
these are forces generated due to chemical reaction between the solvent & protein or ligand.
Eg. Hydrogen bonds (hydrophyllic interactions)
Hydrophobic interactions
Solvent related forces
Methods to derive 3D structures
Mechanics of docking
X-ray crystallography
Proton detected heteronuclear
NMR
Homologous modelling
Protein + precipitating medium individual protein molecule
data collection using arrange to form a Computer controlled crystalline entity - detector (single crystalline x ray
diffraction) phase & amplitude of diffractedwaves calculated & combined with image of electronexperimentally observed structural diffracting cloudfunctions (electron density map) model building & refinementProtein structure (electron density fitting program FRODO, TNT)
X – ray crystallography
Protein + drug spectrum re run
Drug fail to combine drug bind to with protein protein
NMR still be nuclei will have shorter detected relaxation time
no NMR spectrum
Proton detected heteronuclear NMR
Align the amino acid sequence of protein with unknown structural agent, the sequence of a homologous protein whose 3D structure has already been determined.
By converting structurally conserved region & structural variable region, the core of the molecule can be identified.
Homologous modelling
Search algorithm
Scoring function
Success of docking program
Prepared protein
structure
Database of
potential ligands
Input to docking program
Determine all possible optimal conformation for a given complex (protein-ligand/ protein-protein)
Calculate the energy of resulting complex & of each individual interactions.
Conformational search strategies include
• Systematic/ stochastic torsional searches about rotatable bonds.
• Molecular dynamic simulations
• Genetic algorithms to evolve new low energy conformations
a) Search algorithm
Ligand flexibility Conformation of the ligand may be generated in the
absence of receptor or in the presence of receptor binding activity.
Receptor flexibility Large number of degrees of freedom
Force field energy
evaluation Knowledge based method
experime
ntally determin
ed multiple
steric structure
s
Rotamer libraries
of aminoaci
d side chain
surrounds the
binding cavity
b) Scoring function
Predict binding affinity between two molecules
Predict strength of intermolecular interactions btn
protein-protein, protein -DNA , protein-drug
Estimate the energy of pose
a) Lock and key/ rigid docking
b) b) Induced fitting/ flexible docking
Types of docking
MOLECULAR DOCKING
• Docking- the process by which molecular modeling
software fits a molecule into target binding sites.
• Used for finding binding modes of protein with
ligands/inhibitors
• In molecular docking, attempt to predict the structure of
the intermolecular complex formed between two or more
molecules
Dock or fit a molecule in the
binding site
Binding group on the ligand and binding site are known, defined by
the operator.
Binding group in the ligand is paired with its
complementary group in the binding site
Ideal bonding distance for
potential interaction is
defined.
Docking procedure is
started
The program try to get best fit, as defined by
the operator
MANUAL DOCKING
The paired groups are not directly overlaid, they are
fitted within preferred bonding distance.
Both ligand and protein remain same
conformation throughout the process
So this is a rigid fit, once a molecule successfully
docked fit optimization is carried out.
Same as in energy minimization.
Different conformation of molecule can be
docked to in same wayIdentify the best fit
FLEXIBLE DOCKING
Rigid docking- the protein and the ligand as rigid bodies.
The drawback of rigid docking is, since it neglects the
conformational degrees of freedom of ligands.
It fails to give satisfactory answer for flexible ligand, will
form different conformations.
To solve this, dock different conformations of ligand as
possible in order to get the best result.
FLOG (flexible ligand oriented on grid) is a program that
generates conformational libraries called flexibose, contain
10-20 conformations for each ligand studied.
DOCKING OF FLEXIBLE LIGANDS
Various programs are for generate different ligand conformations
The popular method is to fragment the
ligand , identify a rigid anchor
fragment which can be docked
Then reconstruct or grow the
molecule back onto the anchor.
Examples of programs
The algorithm identifies the
rotatable bonds present In the
ligand
Identification of flexible and rigid
region
Molecule is split into
fragments
Direct dock and dock 4.0
The most rigid fragment is termed
as anchor
Docked by shape complimentarity
Flexible parts then added sequentially
to the anchor.
Torison angle is varied for each
addition
This increases the partially build
structures(contructs)
Selection of limited number constructs
based on binding and difference in their
structures
The segments are added in layers working outwards
The segments in the layer 1 are added sequentially before
the segments in layer 2 .
FLEX
The software also uses the anchor and grow method
The anchor is docked according to chemical
complementarity.
Docking is determined by the intermolecular interactions
formed between the anchor and binding site.
Docking the anchor by chemical complementarity rather
than steric complementarity has the advantage to cut down
the number of possible binding orientation for the anchor.
An interaction surface consisting interaction points
Matching process occurs, it matches atoms on the anchor to interaction points in the binding sites
The distance between atoms on the anchor must match the distance between interaction points in the binding site
The anchor atom and corresponding interaction point must have binding compatibility
Docking requires identification of 3 matched pairs of anchor atoms, equal to identifying complimentary pharmacophore triangles for the anchor & binding site
Matching process -Comparison of pharmacophore triangles for the ligand and binding site
For a match a triangle for the ligand have same dimensions as a triangle for the binding site, but also the corners of the triangle must have binding compatibility
The docking is now carried out such that anchor atoms are overlaid with their matched interaction point in the binding site.
The procedure ensures that the angle requirements for hydrogen bonding are fine with respect to the interaction points in the binding site .
Problems
The anchor has to be chosen manually, becomes difficult when large number of structures
Vast number of different pharmacophore triangles constructed to represent the binding site.
HAMMERHEAD PROGRAM
Anchor and grow program
Probes are placed into the binding site in order to identify locations of binding interactions
The probes used are hydrogen atoms as well as c=o and NH fragments
Each probes can be scored as high scoring or low scoring based on No. of hydrogen bonds it can form.
Once the probe has positioned, they act as the targets for docking procedure.
Matching of atoms of a molecular fragment with probes, docking must involve at least one of the high scoring probes.
Both steric and chemical complementarity is used in the matching process.
Once the match has been identified the docking operation is carried out.
Since the ligand is split into fragments, have limited number of rotatable bonds
All fragments that are formed contain an atom or bond that is shared with another fragment.
For each fragment, a number of conformations are generated.
The fragments are docked and scored
Fragments that are particularly high scoring are defined as head and act as an anchors
The remaining fragments are defined as tails
The reconstruction phase is carried out for each fragment that has been identified as potential anchor.
The tails are then docked
The first fragments share an atom or bond with the anchor and is docked like that it is aligned both to the relevant atom
or bond on the anchor.
Two fragments are then merged by overlaying the shared bonds or atoms.
The tail fragments moves to the anchor
Advantages
Anchors are chosen automatically
Different anchors possible and investigated
Docking Of Flexible Ligands, By Simulated Annealing And Genetic Algorithm
This method is viable for docking of the flexible ligands.
It involves use of metropolis method by using montecarlo
algorithms for conformational analysis.
The ligand is placed randomly in the space close to the
binding site.
Montecarlo algorithms are used to generate different
conformations
The molecules are translated and rotated such that it
tumbles within the binding site.
Different conformations are generated at different
position and orientation with in the binding site.
Binding energy of each structure is measured as it is
formed and compared with the previous structure.
Docking Programs Using Monte Carlo Algorithms For Docking
Auto dock
Mcdock
Prodock and pro-lead.
Disadvantage
The quality of result is often depends on how the initial
structure s placed in the binding site.
This can be over come by using combination of programs
Eg; DOCK and Montecarlo based programs
Docking programs
DOCK (I. D. Kuntz, UCSF)
AutoDock (Arthur Olson, The Scripps Research Institute)
AutoDock was designed to dock flexible ligands into receptor binding sites
The strongest feature of AutoDock is the range of powerful optimization algorithms available
RosettaDOCK (Baker, Washington Univ., Gray, Johns Hopkins Univ.)
Docking programs
1) Get the complex from P.D.B2) Clean the complex3) Add the missing hydrogens/side chain atoms &
minimized the complex4) Clean the minimized complex5) Separate the minimized complex in macromolecule
(lock) & ligand (key)6) Prepare the docking suitable files for lock & key7) Prepare all the needing files for docking8) Run the docking9) Analyze the docking results
Overall steps in docking
i. Protein preparation (protein preparation wizard) Prepare co crystallized ligands – correctly define
multiple bonds & adding hydrogen Neutralize residues that do not participate in the salt
bridge Preprocess the receptor before grid generation Optimization of the protein
ii. Ligand preparation (ligprep) Generate energy minimized 3D structures –
tautomeric, stereochemical and ionization variations as well as energy
minimizations
Working methodology of Schrodinger
iii. Docking Generate receptor grid around the site using glide Docking conducted using XP GLIDE (Extra
precision)
iv. Visual inspection Images were obtained using Glide XP Vsualiser
panel
Hit identification
Lead optimization
Bio remediation
virtual screening of large databases
Applications
i. Introduction to molecular docking; Edelmiromomen;
Pharmaceutical & Medicinal chemistry; Saarland
university.
ii. Protein-ligand docking methods; Thomas Funkhouser;Princeton
university
iii.Introduction to molecular docking; Carlos. P.Sosa; university of Minnesofa
iv. Molecular docking tutorial; Khuled.H.Brakat; Pharma matrix work
shopin, Computational biophysics.
v. Principles of Docking: An overview of search Algorithm & a guide to scoring functions;
Inbal Halperin,Buyon Ma.
vi. An introduction to medicinal chemistry; 4th edition; Graham.L.Patrick; Pg no. 352-361
vii. The organic chemistry of drug design & drug action. 2nd edition; Richard.B.Silverman
References
THANK YOU ALL
All informations in this presentation is collected from various sources available on internet and text
books….This presentation is only for educational purpose….
we sincerely saying thanks to all