Download Molecular Interactions Lecture 2 Dock

Molecular Interactions
Lecture 2
Dock-umentary
Overview
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Molecular Recognition
Historical background
What’s docking?
Illustrative example: actin-toxin
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Physics of Molecular Recognition
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Van der Waals
Electrostatics – provide specificity
Hydrogen bonds – provide specificity
Hydrophobic effect – provides stability
– Increase in solvent entropy upon burial of nonpolar surfaces
• Solute entropy
• Internal energies (“strain”)
Thermodynamics
Equilibrium binding constant, Keq; on-rate kon;
off-rate koff of the reaction
Relative binding
energies
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Historical background
Lock, dock and barrel
“. . . the intimate contact between the
molecules . . . is possible only with
similar geometrical configurations.
To use a picture, I would say that the
enzyme and the substrate must fit
together like a lock and key.”
Receptor
Emil Fischer, Ber. Dtsch.
Chem. Ges. 1894, 27, 2985.
versus “induced fit” (Koshland)
Proc. Natl. Acad. Sci. USA 44:98–104 (1958)
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Dock around the clock
• 1960’s
• Protein structures
– Myoglobin: Nature 1958, Kendrew, Phillips, …
– Haemoglobin: Nature 1963, Perutz
– Lysozyme: Nature 1965, Blake, Phillips, …
• Levinthal. “Molecular model building by
computer” Sci Am 1966.
• Hansch: QSAR – Nature 1962.
Dock around the clock
• 1970’s
• Protein Data Bank - 1977
• Captopril
– early example of structure-based drug design.
• FRODO (later “O”) – Alwyn Jones
• Langridge et al. “Real time color graphics
in studies of molecular interaction”. Science
1981.
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Dock around the clock
• 1980’s
• X-plor – X-ray structure refinement; NMR
• Molecular mechanics – CHARMM
• GRID – Goodford. J Med Chem 1985.
• SGI
• Connolly surface
http://www.biohedron.com/msg.pdf
Dock around the clock
• 1990’s
• DOCK. Kuntz et al. 1992.
• Empirical scoring functions – Bohm
– GOLD, FlexX.
• Relenza
– Nature 1993.
• HIV protease inhibitors
– Vacca & Condra. Drug Discovery Today 1997.
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Dock around the clock
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2000’s
Genomics
Better homology models
Virtual high throughput screening
Better scoring functions / potential energies
Is there a dock-tor in the house?
Drug
Compound
Target
PDB
Vioxx
Rofecoxib
COX-2
1CX2
Viagra
Sildenafil
PDE5
1TBF
Gleevec
Imatinib
Abl kinase
1XBB
Viracept
Nelfinavir
HIV protease
1LKM
Relenza
Zanamivir
Influenza
1A4G
neuraminidase
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Structure-based drug design
• Requires (crystal) structure for complexes
of some analogues with the biomolecular
target.
• has contributed to the introduction of 50
compounds into clinical trials and to
numerous drug approvals
What’s docking?
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Dock, dock. Who’s there?
Docking: the prediction of the structure of
receptor-ligand complexes, where the
receptor is usually a protein or a protein
oligomer and the ligand is either a small
molecule or another protein.
Hickory, dickory, dock
1) Add protons, vdW
parameters, and
partial charges for
both target and
small molecule.
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The mouse ran up the clock
2) Calculate solvent
accessible surface
area of target (shown
here coloured by
element).
The clock struck one
3) Create negative
image of surface
features surrounding
active site using
spheres.
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The mouse ran down
4) Calculate energy
grid for target.
Each grid point
stores vdW score
and charge for that
area of space.
Hickory, dickory
5) Match ligand atoms
to sphere centres
and score against
grid.
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DOCK
6) Rank best scoring
poses (top ten poses
from DOCK run
shown here).
The Dock Ness Monster
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Actin
• Important part of cytoskeleton
• Muscle cells comprise 10%
actin
• 2 forms:
– polar, double helical polymer
form, filamentous actin (F-actin),
– Monomeric, globular form (Gactin)
• appears in many aspects of
molecular oncology
www.sci.sdsu.edu/movies/actin_myosin.html
Structure of the Glob
• Several crystal structures of
toxins bound to actin:
• kabiramide C (1QZ5)
jaspisamide A (1QZ6)
ulapualide A (1S22)
swinholide A (1YXQ)
reidispongiolide A (2ASM)
sphinxolide B (2ASO)
reidispongiolide C (2ASP)
aplyronine A (1WUA)
bistramide A (2FXU)
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Bio-inspired
• Natural products: a rich
source of potential drugs.
• Find important interactions in
the hydrophobic binding site of
G-actin across all the structural
classes for which X-ray data
exist
• Aid future development of
small molecule binders to actin
Yueng & Paterson. Angew Chem Int Ed 2002, 41, 4632.
Motivation
• Pattenden (Chemistry, Nottingham)
– Synthetic ulapualide A derivatives
• Shaw (Biomedical Sciences, Nottingham)
– Fluorescence actin-binding cell-based assay
• Can we characterize actin-toxin
interactions? Can we explain differences in
binding affinity? Can we design new
ligands?
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The
Chemistry
Docking
• widely used & successful in
virtual screening for drug
design
• computationally cheaper than
MD simulations
• large flexible molecules still
challenging
• ‘scan’ the actin binding site
using flexible docking of
smaller substructures (or
fragments) of the macrolides
• AutoDock
Atomic affinity isosurface for a portion
of G-actin, showing potential for carbon
(white), nitrogen (blue) and oxygen (red)
as derived from atomic affinity grids.
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Substructure docking
• Interactions relevant
• Smaller size
– Cheaper; better convergence
– Can access regions not accessible to full
macrolide
• Binding affinities too difficult to calculate
anyway (e.g. via FEP)
• Semi-quantitative picture
Sanity check
• For each of the ligands, 10
docking runs converged to
the same structure: RMSD
< 0.5Å
• x-ray coordinates of
kabiramide C after
superposition of the C-α
atoms of actin in 1QZ5 and
1YXQ (RMSD = 0.71 Å)
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Binding pocket
1. the hydrophobic pocket, where most macrolides
have a large hydrophobic ‘anchor’ (except for
bistramide A)
2. the hydrophobic ‘cleft’, where a hydrophobic tail
is intercalated and which is responsible for the
depolymerization effects of the molecules
3. a region at the other end of the cleft, where only
bistramide A has been found to bind.
Visualization
• retain atoms from any structure that
contribute > 0.6 kcal/mol to docking score
via van der Waals interactions and > 0.3
kcal/mol through electrostatic interactions.
• Hydrophobic interactions - cyan spheres
• H-bond acceptor interactions - red spheres
• H-bond donor sites - blue spheres
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Hydrophobic pocket
• Kabiramide A (blue) and
reidispongiolide A (yellow) are
shown for reference.
• A—hydrophobic interaction at
Gly23
• B — hydrophobic interaction at
Ser141, Ala144, Pro332, Ser338
• C— hydrogen-bond acceptor
interaction with Arg147
• D hydrogen-bond donor
interaction with Glu334
• E — hydrogen-bond donor
interaction with Asp25.
Better
• Illustrate the potential use of these interaction maps
• Modify structure of kabiramide C in silico a ligand that
bound more ‘‘efficiently’’ (i.e., docking score / heavy atom
was larger) than the original structure.
• Do not consider synthetic feasibility, nor entropic penalties
Parts in red deleted; parts in green added
increased the best
docking score by
3.2 kcal/mol over
kabiramide C - increase
of 20% and a decrease
in Ki by 100-fold; MW
reduced from 943 Da
748 Da, i.e., by 20%.
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Conclusion
• flexible docking of ligand fragments is a valuable
tool to rationalize and unify structural data across
several ligands
• simple visual confirmation of several observations
• extend analysis to potential interaction sites yet to
be exploited.
• For actin, focus on a small number of residues:
– hydrophobic interaction between the trisoxazole ring of
the kabiramide C and related compounds at Gly-23,
– hydrophobic interaction between the macrolactone ring
of reidispongiolide A at Pro-332
Dock-ing in the free world
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