Rajendra Kumar

Protein Docking

The functional units of the cell

Polymers of amino acids

Maintain a key role in intra and intercellular processes

Maintain the control functions as Enzymes

Characteristic elements are :

carbon,hydrogen,oxygen,nitrogen

Proteins Are…

To place a ligand into the binding site of a protein in the appropriate manner for optimal interactions with a receptor protein

Goal: To be able to search a database of molecular structures and

retrieve all molecules that can interact with the query structure

Definition

Aim: predict the structure of a protein complex from its partners

+

Monomers

Complex

Protein-protein Docking

(James meiler,2007)

Protein-Protein Docking Both molecules usually considered rigid 6 degrees of freedom Search space and the energetics of possible binding

conformations Protein-Ligand Docking

Flexible ligand, rigid-receptor Reduce flexible ligand to rigid fragments connected

by one or several hinges, or search the conformational space using molecular dynamics

Types of Docking studies

Rigid Body Docking: No modification in bond angles, lengths & torsion

angles of the components

Flexible Docking : Takes in to the conformational changes

Rigid Vs Flexible docking

Protein docking is the computational determination of protein complex structure from individual protein structures.

(Smith and Sternberg, 2002)

Ligand binds to the active site of protein

Binding leads to conformational changes in protein

Conformational changes thermodynamically most stable

Lowest Gibb’s energy

Interactions lead to …

Protein –Protein interaction Thermodynamics

(Smith and Sternberg, 2002)

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.

Why docking is important?

Structure of protein of interest should be known

X-ray Crystallography NMR Spectroscopy

Basic Requirements For Docking

The spacing of atoms in a crystal lattice can be determined by measuring the locations and intensities of spots produced on photographic film.

x-ray analysis of sodium chloride crystals shows that Na and Cl ions are arranged in a simple cubic lattice.

X – rays, wavelengths in the range of 0.7 to 1.5 Å (0.07 to 0.15 nm).

X-Ray Diffraction

( Hubbard, 2006)

cont..

( Hubbard, 2006)

( Hubbard, 2006)

Modern NMR techniques are being used to determine the structures of larger macromolecules.

NMR is based on nuclear spin angular momentum.

Only certain atoms, including 1H, 13C, 15N, 19F,and 31P, possess the kind of nuclear spin that gives rise to an NMR signal.

(James,1998)

Nuclear Magnetic Resonance

(James, 1998)

Both molecules are flexible and may alter each other’s structure as they interact:

Hundreds to thousands of degrees of freedom (DOF)

Why this is difficult?

Surface representation, that efficiently represents the docking surface and identifies the regions of interest (cavities and protrusions)

Connolly surface Clustered-Spheres Alpha shapes

Surface matching- that matches surfaces to optimize a binding score:

Some techniques

(Fernandez et al.,2005)

Each atomic sphere is given the van der Waals radius of the atom

Rolling a Probe Sphere over the Van der Waals Surface leads to the Connolly surface

Surface Representation

(Fernandez et al.,2005)

Uses clustered-spheres to identify cavities on the receptor and protrusions on the ligand

Regions where cavities (on the receptor) or protrusions (on the ligand)

i

j

Clustered-Spheres

(Fernandez et al.,2005)

In 2D an “edge” between two points is “alpha-exposed” if there exists a circle of radius alpha such that the two points lie on the surface of the circle and the circle contains no other points from the point set

Alpha Shapes

(Fernandez et al.,2005)

Alpha Shapes: Example

(Fernandez et al.,2005)

5.24.2-4.7

6.7

4.8

5.1-7.1

3-D Representation of a Protein Binding Site

(Fernandez et al.,2005)

Find the transformation (rotation + translation) that will maximize the number of matching surface points from the receptor and the ligand

First Condition Find the best fit of the receptor and ligand

Use energy calculations to refine the docking Select the fit that has the minimum energy

Surface Matching

(Fernandez et al.,2005)

Critical Assessment of Prediction of Interactions

launched to:

To assess & compare current docking algorithms

To stimulate further developments in the field

(Gray et al.,2003)

CAPRI

The 7 CAPRI Docking Targets

CAPRI Challenge (2002)

(Gray et al.,2003)

DOCK works in 5 steps:

Step 1 Start with crystal coordinates of target receptor

Step 2 Generate molecular surface for receptor

Step 3Step 3 Generate spheres to fill the active site of the receptor: Generate spheres to fill the active site of the receptor: The spheres become potential locations for ligand atomsThe spheres become potential locations for ligand atoms

Step 4 Matching: Sphere centers are then matched to the ligand atoms, to determine possible orientations for the ligand

Step 5 Scoring: Find the top scoring orientation

DOCK

(Gray et al.,2003)

Docking protocol

(Gray et al.,2003)

RANDOM START POSITIONRANDOM START POSITION

Creation of a decoy begins with a random orientation of each partner and a translation of one partner along the line of protein centers to create a glancing contact between the proteins

Docking protocol

(Gray et al.,2003)

LOW-RESOLUTION MONTE CARLO SEARCHLOW-RESOLUTION MONTE CARLO SEARCH

One partner is translated and rotated around the surface of the other

The score is based in the correctness of each decoy and residue-residue interactions terms

Docking protocol

(Gray et al.,2003)

HIGH-RESOLUTION REFINEMENTHIGH-RESOLUTION REFINEMENT

Side-chains are added to the protein backbones to changing the energy surface

• A filter is employed to detect inferior decoys and reject them without further refinement

Docking protocol

(Gray et al.,2003)

CLUSTERING & PREDICTIONS

The search procedure is repeated to create approximately 105 decoys per target

The 200 best-scoring decoys are then clustered

The clusters with the most members are selected as the final predictions and ranked according to cluster sizes

Docking protocol

(Gray et al.,2003)

To evaluate the interactions to discriminate the observed mode from others

Binding affinity of the complex to be worked out

Energetically favorable complexes to be predicted

Large no: of degrees of freedom to be considered

Scoring Function

(Gray et al.,2003)

# A molecular modeling technique

# Goal is to predict the position and orientation of a ligand when it is bound to a protein receptor or enzyme

# Pertinent to field of drug design

PROTEIN-LIGAND DOCKING

Drugs are small molecules of therapeutic importance

Drug discovery costs are too high [~$800 millions]

Time consuming [8~14 years]

Drugs interact with their receptors in a highly specific and complementary manner.

Effort to cut down the research timeline and cost by reducing lab experiment use computer modelling.

In drug designing…

(Wei et al ., 2004)

By computational means, screen large databases of potential drugs against protein targets

HIV protease inhibitors - Invirase ,Norvir , Crixivan

Influenza neuraminidase inhibitor - zanamivir

contd…

(Wei et al ., 2004)

Active Site(Aspartyl groups)

DOCK: Example HIV-1 Protease

(Wei et al ., 2004)

TRADITIONAL DRUG DESIGN

Natural ligand / Screening

Biological Testing

Synthesis of New Compounds

Drug Design CycleDrug Design Cycle

If promising

Pre-Clinical Studies

(Wei et al ., 2004)

drug targets (usually proteins) binding of ligands to the target (docking)

↓

“rational” drug design

(benefits = saved time and $$$)

SBDD

(Wei et al ., 2004)

Molecular Biology & Protein Chemistry

3D Structure Determination of Target and Target-Ligand Complex

Modelling

Structure Analysisand Compound Design

Biological Testing

Synthesis of New Compounds

If promising

Pre-Clinical Studies

Drug Design CycleDrug Design Cycle

Natural ligand / Screening

Structure-based Drug Design (SBDD)

(Wei et al ., 2004)

Ligand database

Target Protein

Molecular docking

Ligand docked into protein’s active site

contd…

(Wei et al ., 2004)

Molecular Docking Introduction Page

Introduction Page

Molecular Docking Page

Input Page

Input Page (cont..)

Submitting Job

Results

Results (in visualization form)

The voltage-gated sodium channel underlies the propagation of action potentials in neuronal cells of both vertebrates and invertebrates.

During an action potential of the sodium channel undergoes transitions between activated and inactivated functional states, and toxins binding to specific sites on the channel and the channel pore.

Introduction

(Andrias et al .,2006)

Transmembrane topology of the voltage- gated sodium channel

(Andrias et al .,2006)

Model of voltage- gated sodium channel

(Andrias et al .,2006)

Chemical structure

(Andrias et al .,2006)

Fenvalerate

(Andrias et al .,2006)

Acrinathrin

(Andrias et al .,2006)

More information in: http://www.bmm.icnet.uk/~smithgr/soft.html

The programmes are:

DOCK (I. D. Kuntz, UCSF)

AutoDOCK (Arthur Olson, The Scripps Research Institute)

RosettaDOCK (Baker, Washington Univ., Gray, Johns Hopkins Univ.)

Docking Programs

(Smith and Michael , 2002)

Affinity- (Accelrys Inc.) AutoDock- (The Scripps Research institute) FlexX -(BioSolve IT) GLIDE- (Schrödinger ) GOLD - (CCDC) LIGPLOT -(University College of London) FlexiDOCK -(Tripos)

PROTEIN-LIGAND DOCKING

(Smith and Michael , 2002)

DOCK -(UCSF Molecular Design Institute )

GRAMM- (SUNY)

ICM-Dock- (MolSoft LIC)

Protein-Legand & Protein-Protein Docking

(Smith and Michael ,2002)

Protein docking is important in :

Understanding / predicting interactions

Developing drugs and cures

The field continuous to progress & is developed by CAPRI

CONCLUSION

Discussion

Have a Nice Day !