Download Docking and Drug Design

Docking and Drug Design
Dr. Andrew C.R. Martin, UCL
With thanks to
Dr. Marketa Zvelebil, LICR, Breakthrough Breast Cancer
Aims and Objectives
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Understand the nature of drugs
Know the steps in rational drug design
Understand forms of docking
Using docking for virtual screening
Describe principles of de novo drug design
What is a drug?
• Ligands that bind to a specific protein
• Either increase its activity (an agonist)
­­or­­ decrease/block its activity (an antagonist)
• Many problems…
solubility, stability, selectivity
• Most drugs are not very selective…
side effects
• Rational drug design…
exploit structure of the protein and its natural ligands
Steps in drug design
• Having a protein structure to dock into
(X­ray, model)
• Defining the pocket
• Having a database of ligands ­or­ designing a specific ligand(s)
• Docking
• Sorting the docked structures
• Minimization and Dynamics
• Analysis
Defining the pocket
Two types of interactions:
• (1) Protein ­ protein/peptide/DNA ­ usually relatively flat on the surface
• (2) Protein ­ small­ligand ­ usually clefts/pockets
Defining the pocket
Type 1 ­ usually defined manually
• Known interactions sites
• Explore the protein surface
• Multiple alignment
­ conserved hydrophobics on the surface ­ patches of conserved residues
Also automated methods...
Predicting protein binding sites
P53 analyzed by ProMate.
Predicted region shown in RED.
Corresponds to known binding site for ASPP2 (YELLOW)
ProMate: http://bioportal.weizmann.ac.il/promate/promate.html
Predicting protein binding sites
P53 analyzed by PPI_PRED.
Predicted regions shown in RED.
ASPP2 shown in YELLOW
PPI­PRED: http://www.bioinformatics.leeds.ac.uk/ppi_pred/
Peptide binding sites
Peptide interface
Finding pockets and clefts
Small ligand binding sites are usually clefts or pockets
Search the surface for pockets. • Define the solvent­accessible surface
• Identify clefts and cavities
• Usually the largest pocket is the binding site
Finding pockets and clefts
Pocket­finder
Potential binding sites based only on geometry
Q­siteFinder ­and­ Grid
Find regions with favourable interaction energy with a probe group
Pocket­finder: http://www.bioinformatics.leeds.ac.uk/pocketfinder/
Q­siteFinder: http://www.bioinformatics.leeds.ac.uk/qsitefinder/
Grid: http://www.moldiscovery.com/soft_grid.php Virtual Docking
Surface complementarity
 Van der Waals forces
 Electrostatic (Salt bridge) Interaction
 Hydrogen bonds
 Hydrophobic bonding
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Docking can be between...
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Protein / small ligand
Protein / peptide
Protein / protein
Protein / nucleotide
Difficulties in docking
Both molecules are flexible:
• Hundreds of degrees of freedom • Astronomical number of possible conformations
Protein / ligand
• Often treat protein as rigid
Docking methods ­ rigid body
Six degrees of freedom
­ protein and ligand both treated as rigid
­ 3 rotations / 3 translations
Just like docking the space shuttle with a satellite
Image from NASA
Docking methods ­ flexible ligand
Treat receptor as static / ligand as flexible
Dock ligand into binding pocket
­ generate large number of possible orientations
Evaluate and select by energy function
Automated docking
Many programs available
• Make use of:
• cavities
• surface complementarity
• electrostatics
• full energy function
DOCK:
AUTODOCK: FTDOCK: HOTDOCK: http://www.cmpharm.ucsf.edu/kuntz/dock.html
http://www.scripps.edu/pub/olson­web/doc/autodock/
http://www.bmm.icnet.uk/ftdock/
http://www.uni­paderborn.de/~lst/HotDock/features.html
DOCK
Generate molecular surface for the receptor
HIV­1 protease as the target receptor
Active site aspartyl groups shown in red.
Connolly's molecular surface (MS)
Shown in yellow
DOCK
Generate spheres to fill the active site Cavities in the receptor used to define spheres
Sphere centres become potential locations
for ligand atoms
DOCK
Ligand Matching • Match sphere centres against ligand atoms
• Find possible ligand orientations
• Often >10,000 orientations possible Find the transformation (rotation + translation) to maximize sphere matching
Scoring docked models
Each orientation is scored
Dock provides 3 scoring schemes: • Shape scoring
• Electrostatic scoring ­ uses DELPHI to calculate electrostatic potential • Force­field scoring ­ uses the AMBER potential
Scoring docked models
Shape complementarity is key! Protein/ligand surfaces are complementary ­ a simple geometric descriptor
Evaluation differs between methods
­ two basic approaches:
• use surface curvature or surface areas (based on Connolly surface)
• grid­based evaluation of surface packing
Energy scoring
1.Best binding site is not always lowest energy
2.True binding site often has an energy barrier around the site
1.Need more energy to leave the true site than other potential sites. Energy
15 kcal/mol
8 kcal/mol
10 kcal/mol
Potential Site
Real Site
Lowest Energy
Potential Site
Performance of DOCK
Top­scoring orientation for thioketal docked to HIV1­protease (force­field scoring). Comparison with crystal structure…
GOLD ­ flexible genetic algorithm docking
Inhibitor docked into Dihydrofolate reductase (DHFR) using pocket identified by Pocket­Finder
7 of 10 final orientations fit well with crystal structure
3 fit in NADPH binding site
Virtual Screening
• Docking can be used for virtual screening
• Scan a library of potential drug molecules
• Identify leads
De Novo Drug Design
LUDI (InsightII) ­ find fragments that can bind
GRID ­ uses molecular mechanics potential to find interaction sites for probe groups
X­site ­ uses an empirical potential to find interaction sites for probe groups
Designing specific ligands
Relenza
First designed drug was Relenza (influenza).
Identified molecules to bind to conserved regions of neuraminidase
Retinovir and Indinavir
Drugs to treat HIV
Designed to inhibit viral proteases
Side effects
Side effects can be interesting...
• A drug designed for heart problems had unexpected side­effects…
• Viagra!
Summary
• Find pockets
• Principles for docking ­ complementarity
• Docking
– rigid body / ligand flexibility
• Virtual screening
• Identifying probe interaction sites
– build ligands de novo