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