Post on 12-May-2018
Docking and Drug Design
Dr. Andrew C.R. Martin, UCL
With thanks toDr. Marketa Zvelebil, LICR, Breakthrough Breast Cancer
Aims and Objectives
• 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
• 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
What is a drug?
• 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
Steps in drug design
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...
Defining the pocket
ProMate: http://bioportal.weizmann.ac.il/promate/promate.html
P53 analyzed by ProMate.
Predicted region shown in RED.
Corresponds to known binding site for ASPP2 (YELLOW)
Predicting protein binding sites
PPIPRED: http://www.bioinformatics.leeds.ac.uk/ppi_pred/
Predicting protein binding sites
P53 analyzed by PPI_PRED.
Predicted regions shown in RED.
ASPP2 shown in YELLOW
Peptide interface
Peptide binding sites
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
Small ligand binding sites are usually clefts or pockets
Finding pockets and cleftsPocketfinderPotential binding sites based only on geometry
QsiteFinder and GridFind 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
Van der Waals forcesElectrostatic (Salt bridge) InteractionHydrogen bondsHydrophobic bonding
+ + + +
Surface complementarity
+ + + ++
Docking can be between...
• Protein / small ligand• Protein / peptide• Protein / protein• Protein / nucleotide
Both molecules are flexible:• Hundreds of degrees of freedom
• Astronomical number of possible conformations
Difficulties in docking
Protein / ligand• Often treat protein as rigid
Six degrees of freedom protein and ligand both treated as rigid 3 rotations / 3 translations
Docking methods rigid body
Just like docking the space shuttle with a satellite
Image from NASA
Treat receptor as static / ligand as flexibleDock ligand into binding pocket
generate large number of possible orientationsEvaluate and select by energy function
Docking methods flexible ligand
Many programs available
• Make use of:• cavities• surface complementarity• electrostatics• full energy function
DOCK: http://www.cmpharm.ucsf.edu/kuntz/dock.htmlAUTODOCK: http://www.scripps.edu/pub/olsonweb/doc/autodock/FTDOCK: http://www.bmm.icnet.uk/ftdock/HOTDOCK: http://www.unipaderborn.de/~lst/HotDock/features.html
Automated docking
HIV1 protease as the target receptor
Active site aspartyl groups shown in red.
Generate molecular surface for the receptor
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 locationsfor 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
DOCK
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
Scoring docked models
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.
Potential Site Real Site Potential Site
10 kcal/mol15 kcal/mol
8 kcal/mol
Energy
Lowest Energy
Energy scoring
Topscoring orientation for thioketal docked to HIV1protease (forcefield scoring).
Comparison with crystal structure…
Performance of DOCK
7 of 10 final orientations fit well with crystal structure3 fit in NADPH binding site
Inhibitor docked into Dihydrofolate reductase (DHFR) using pocket identified by PocketFinder
GOLD flexible genetic algorithm docking
Virtual Screening
• Docking can be used for virtual screening
• Scan a library of potential drug molecules• Identify leads
LUDI (InsightII) find fragments that can bindGRID uses molecular mechanics potential to find interaction sites for probe groupsXsite uses an empirical potential to find interaction sites for probe groups
De Novo Drug Design
Designing specific ligands
First designed drug was Relenza (influenza).Identified molecules to bind to conserved regions of neuraminidase
Relenza
Drugs to treat HIVDesigned to inhibit viral proteases
Retinovir and Indinavir
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