DOCKING Modeling Protein Complexes

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DOCKINGModeling Protein Complexes

• Dr. Victor Lesk
• 29th October 2008

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• Protein / small molecules
• Enzyme / substrates
• Enzyme / drug
• Protein / protein
• Enzyme / inhibitor
• Inhibitor / modulator
• Macromolecular assemblies
• Protein / nucleic acid
• RNA/DNA / polymerase
• Ribosome / peptide

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• Docking two molecules means constructing the
  coordinates of the bound state.
• Bound state is called the complex.
• We require coordinates for the independent
  molecules as input
• Molecules move towards each other and bind/dock
  
• But aim is to predict their docked configuration
  (not describe their motion).

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Hydrophobicity

• Hydrophobic molecules stick to other molecules
• Specificity of interactions tend to be conferred
  by polar areas through e.g. salt bridges and
  hydrogen bonds
• Hydrophobic drugs are less quickly metabolized,
  go to places where they are not meant to
• Some hydrophobicity is required for good activity

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Drug design

• Drugs typically affect a protein targets ability
  to bind substrate (compet. or non-).
• Require clinical trials expensive, risky,
  require animals
• Use screening steps to eliminate unlikely
  candidates, end up with leads
• Start from library experimental screening using
  physical library
• Or virtual screening using an electronic database

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Virtual screening

• Start from electronic library with millions of
  compounds ZINC (free) has 16 million
• Take fastest steps first structural docking
  (slow) can be final step when protein target is
  known
• First library decimated according to ADME
  criteria
• Absorption- Distribution- Metabolism- Excretion
• Lipinskis rule of 5 implements ADME well

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Virtual screening II

• QSAR when structure of protein target is unknown
• When protein structure is known, docking the
  drugs onto the protein can be tried
  (small-molecule docking).
• If partner is also protein and binding site is
  cannot be identified by expt. or bioinformatics,
  protein-protein docking may be used to help find
  it.

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Small-Molecule Dockingnot just for drug design

• For
• Drug design
• Lead optimization
• Toxicology
• Metabolism study
• Development of tags for imaging

• Software e.g.
• Commercial
• DOCK
• GOLD
• FlexX
• Free for non-commercial use
• Autodock

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Structural Drug Library

• Cambridge Structural Database has 450,000 organic
  compounds (and growing)
• Files are in CIF format
• (note mmCIF, macromolecular CIF, as
• proposed replacement for PDB)
• Also exist databases for inorganic, oligo-
  peptide and oligonucleotide structures

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Small molecule docking for drug design

• Try to dock putative drug molecule on to protein
• Each molecule has few atoms, so docking of each
  is computationally efficient.. but many
  molecules.
• Search from library of millions of compounds
• Pre-filtered using heuristics (Lipinski)?
• Score with pairwise energy function
• Protein remains rigid
• Torsion angles of drug are allowed to rotate.
  Bonds are not generally allowed to stretch or
  flex.

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MACROMOLECULE DOCKING(proteins and
polynucleotides)?

• Background
• Basic concepts
• Methods
• Assessment
• Summary

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Background why do protein-protein docking?

• Aside from helping with virtual screening,
• Protein-protein interaction networks are of
  widespread interest in systems biology
• Exist proteins with no information, arising from
  genome projects
• And known proteins having as yet unknown
  interactions
• Structure prediction technology advances

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What information do we want?

• Structures of complexes
• (within reach, particularly if not much
• conformational change)
• Do A and B bind?
• Affinity information
• (distant future)

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Protein-Protein Docking

• Configuration space large, computationally
  intensive problem
• Even larger when one of interactors is not rigid
  enough
• Throw away as many atoms as possible
• Search remaining space efficiently
• And/or use high performance computing

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Protein-protein dockingMethods

• Set of configurations must contain good enough
  one
• Good enough configuration must have nearly the
  best score
• Use non-structural help where possible
• Use a series of methods, or protocol

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Scores for selecting the best configuration

• Free energy
• Electostatics
• Stereochemistry
• Solvation score
• Statistical scores
• Geometric scores
• Phylogenetic scores
• Weighted sums of the above.

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Free energy

• Contribution from all pairs of atoms
• Same/opposite electric charge repel/attract
• Electron clouds exclude each other
• Atoms try to make glancing contact
• Hydrogen bonds are favourable (difficult to model
  and calculate, direction-dependent)?

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Solvation score

• Water attracts polar groups
• Non-polar groups buried by interface
• Atomic contact energy (Zhang)?

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Statistical scores

• Interacting residue or atom type profile
• Profile from known complex interfaces

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Geometric scores

• Convex hull of surfaces
• Buried surface area
• Volume of intersection

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Phylogenetic scores

• Needs homologues for all interactors
• Conservation score
• Correlation of mutations across interface

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Protein-protein dockingMethods

• Fourier series methods
• Monte Carlo methods
• Surface methods
• Bioinformatics methods
• Normal modes

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Fast correlation methods for protein-protein
docking

• Correlation scores only dot product
• Non-structural help cannot be used efficiently
• Conformational change not allowed

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Monte-Carlo methods for protein-protein docking

• Make small random change
• Prefer to accept change with better score
• Random change may include non-rigidity

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Surface method for protein-protein docking

• Superpose a point on each proteins molecular
  surface
• Rotate to make normals antiparallel
• Surfaces created with marching cubes

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Movie of surface method protein-protein docking

• 2 x Plasmodium vivax 25kD protein
• Homodimer complex
• Symmetry not imposed
• 1000 active triangles on each protein
• 60,000,000 configurations total
• Score rate 30 configurations per second

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Marching cubes (Lorensen and Cline,1987)?

• Originally for medical imaging

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Marching cubes animated demonstration

• Molecular surface of P25 being constructed
• Low resolution

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Marching cubes properties

• Surface is constructed out of triangles
  (simplicial complex)?
• All mathematical topologies ok
• Restrictable to specified patches
• Internal pockets must be eliminated
• Major flexibility requires refinement stage
  (although better than Fourier method)

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Marching cubes variables
Molecular surface
Solvent-accessible surface
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Marching cubes patches
800 sq. A patch around GLU152.Oe2
Sample from patch


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Bioinformatics methods for protein-protein docking

• Mutagenesis effects on affinity
• Surface residue conservation
• Correlated mutation between interactors
• Homologous complexes
• Bioinformatics auxiliary, not stand-alone

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Normal Modes

• About 10000 n.m.s, distinct oscillatory motion
  patterns with distinct frequencies, for average
  protein
• Lowest frequency n.m.s may suggest
  conformational changes on complexation
• Can be used to restrict otherwise impossible
  conformer search of backbone

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Normal Modes II

• Proteins that do not undergo large conformational
  change on binding, but remain rigid, can be
  identified by the absence of very low frequency
  normal modes.

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Free energy

• Contribution from all pairs of atoms
• Same/opposite electric charge repel/attract
• Electron clouds exclude each other
• Atoms try to make glancing contact
• Hydrogen bonds are favourable (difficult to model
  and calculate, direction-dependent)?

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Solvation score

• Water attracts polar groups
• Non-polar groups buried by interface
• Atomic contact energy (Zhang)?

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Statistical scores

• Interacting residue or atom type profile
• Profile from known complex interfaces

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Geometric scores

• Convex hull of surfaces
• Buried surface area
• Volume of intersection

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Phylogenetic scores

• Needs homologues for all interactors
• Conservation score
• Correlation of mutations across interface

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Combined scores

• best/worst rank(s1,s2,s3 )?
• reverse -s1
• s1 with configurations filtered out if s2gt5.7
• weighted sum a x s1 b x s2
• weighted product s1a x s2b x s3c
• Automated combined score trials

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Assessment of docking methods

• Benchmark
• Assessment event
• CAPRI double-blind trial

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Protein-protein docking benchmark

• 124 protein-protein complexes
• Unique structural family combinations
• Diverse biological roles
• Maintained by Prof. Z. Weng at Boston U.

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Protein-DNA docking benchmark

• 40 protein-DNA complexes
• Maintained by Prof. A Bonvin at Utrecht

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CAPRI Critical Assessment of PRotein Interactions

• Every 6 months or so, irregular
• Set of 1 to 6 target complexes
• Centralized double-blind assessment
• International meetings
• Proteins journal special CAPRI edition

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Interpretation of docking

• Not simulation (maybe Monte Carlo is)?
• Energy functions are no more than inspired by
  physics
• With greater understanding affinity prediction
  could become possible

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Imperial structural bioinformatics group

• Virtual screening
• Prof. Mike Sternberg
• Dr. Ata Amini
• Dr. Paul Shrimpton

• Protein-protein docking
• Prof. Mike Sternberg
• Dr. Suhail Islam
• Dr. Victor Lesk
• Philip Carter
• Sara Dobbins

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Glossary

• Complex
• Interactor
• Ligand/Receptor
• Bond torsion
• Torsion angle
• Bond angle
• Configuration
• Decoy
• Blind Trial
• PDB file
• Coordinate file

• Energy function
• Scoring function
• Fitness function
• Pairwise energy
• Electrostatics
• Solvation
• Dielectric
• Affinity
• Fourier Transform
• Mutagenesis

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Summary

• Surface method fast, versatile, flexibility ok
• 600 processor hours for full rigid search

• To be done
• Score improvement
• Fast sidechain flexibility
• Backbone flexibility

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Bibliography

• Virtual screening
• Virtual Screening in Drug Discovery, Alvarez
  Shoichet, CRC Press (2005)?
• Structure-based virtual screening an overview,
  Lyne, DDT 7 20 1047 (2002)?
• Lipinskis rule of 5
• Experimental and computational approaches to
  estimate solubility and permeability in drug
  discovery and development settings, Lipinski et
  al., Adv. Drug Del. Rev.. 26 1-3 3(2001)?
• Protein-protein docking Fourier method
• Molecular surface recognition determination of
  geometric fit between proteins and their ligands
  by correlation methods, Katzir et al., PNAS 89
  2195(1992)?

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• Protein-protein docking Monte Carlo
• Protein-protein docking with simultaneous
  optimization of rigid-body displacement and
  side-chain conformations, Gray et al., JMB 331 1
  281 (2003)?
• Benchmark for protein-protein docking
• Protein-Protein Docking Benchmark 2.0, Mintseris
  et al., Proteins 60 2 216(2005)
• Solvation modeling for proteins
• Determination of atomic desolvation energies from
  the structures of crystallized proteins, Zhang et
  al., JMB 267 3 707(1997)?
• Automated protein-protein docking server
• CLUSPRO, Comeau et al., Bioinf. 20 1 45 (2004)
  http//nrc.bu.edu/cluster/

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• CAPRI docking assessment
• Welcome to CAPRI, Janin, Proteins SFG 47 3
  257(2002)?
• CAPRI methods articles, Proteins SFG 52 1(2003)?
• The CAPRI experiment, its evaluation and
  implications, Wodak Mendex, Curr Opin Struct
  Biol 14 2 242
• Marching Cubes
• Marching cubes A high resolution 3d surface
  construction algorithm, Lorensen Cline, Proc.
  ACM Siggraph Aug 1987 163

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Critical
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• Scores and hybrid scores
• How to describe the success rate of a docking
  method
• Benchmark
• Changes in protein structure upon complexation

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Basic Scores

• electrostatic energy
• hard core repulsion penalty score (e.g.
  Lennard-Jones)?
• solvation score

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Quality of method

• In x of different protein-protein complexes the
  best n guesses of method M contain at least one
  guess closer than r Angstroms.

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Benchmark

• Benchmark of 39 complexes, filtered for
  redundancy
• Ranked in 3 difficulty classes based on degree of
  conformational change
• Enzyme-inhibitor complexes11
• Antibody-antigen complexes11
• 27 others of unclassified functional role

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Conformational change

• Proteins change shape a little (example) or a lot
  (example) upon complexation
• When conformational change is small, docking
  methods can ignore it.

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Strategy

• Any docking method must work unfailingly in cases
  of zero conformational change.
• Methods are first tested with zero conformational
  change imposed.

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Surface-based docking

• Automatically excludes a large subset of known
  undesirable conformations
• Can impose contact between specified surface
  patches
• N-fold rotational symmetry
• Provides alternative visualization

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Construction of Surface from pdb file

• Step 1 read pdb file and identify atom types
• Step 2 replace points with overlapping clouds of
  density
• Step 3 apply marching cubes to generate a set of
  interlocking triangles representing the atomic
  surface

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Generation of guesses for complexed structure

• A possible structure for the complex can be
  generated by specifying
• A triangle from the surface representing
  interactor 1
• A triangle from interactor 2
• An angle
• Put triangle 1 against triangle 2 and rotate by
  angle around the centre of the triangle.
• Score the configuration and record the structure.
  Repeat 1M times.

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Ultimate aims of Protein-Protein Docking, in
order of difficulty

• What is the complexed structure of proteins x, y
  of known structure which are known to form a
  complex? (Hard)?
• Could proteins a, b of known structure form a
  stable complex in vivo? (Very Hard)?
• What, approximately, is the chemical affinity for
  given interacting proteins? (Very Hard)?

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Hybrid scores

• Hybrid scores are scores produced by operations
  on basic scores s1,s2,s3
• reverse(s1)?
• s1 with configurations filtered out if s2gt5.7
• weighted sum as1 bs2 cs3
• weighted product s1a x s2b. x s3c