using waterswap to predict and understand binding affinities
DESCRIPTION
TRANSCRIPT
Using waterswap to predict and understand binding affinities
Christopher Woods
Introduction
• Developer of software and algorithms to predict protein-ligand binding free energies
• Binding free energy measures binding affinity, can be directly related to Ki
• Developed “waterswap”. First-principles, calculation of absolute binding free energies
Protein
Ligand
+
Protein
Ligand
Complex
Protein
Ligand
Complex
ΔGbind
Protein
Ligand
Complex
ΔGbind
Biochemistry occurs in the aqueous phase
Prot
ein (
aq)
Liga
nd(a
q)
Prot
ein (
aq)
Liga
nd(a
q)
Wat
erC
ompl
ex(a
q)
Prot
ein (
aq)
Liga
nd(a
q)
Wat
erC
ompl
ex(a
q)
ΔGbind
Prot
ein (
aq)
Liga
nd(a
q)
Wat
erC
ompl
ex(a
q)
ΔGbind
Prot
ein (
aq)
Liga
nd(a
q)
Wat
erC
ompl
ex(a
q)
ΔGbind
Prot
ein (
aq)
Liga
nd(a
q)
Wat
erC
ompl
ex(a
q)
ΔGbind
• Woods,&J&Chem&Phys,&Vol&134,&p054114,&2011&• &h7p://dx.doi.org/10.1063/1.3519057&
Waterswap&Method&&Uses&the&fact&that&proteinJligand&binding&is&really&a&compeLLon&between&the&ligand&and&water&for&binding&to&the&protein&
Prot
ein:
Wat
er(a
q)Li
gand
(aq)
Prot
ein:
Wat
er(a
q)Li
gand
(aq)
Prot
ein:
Wat
er(a
q)Li
gand
(aq)
Wat
er(a
q)Pr
otei
n:Li
gand
(aq)
Prot
ein:
Wat
er(a
q)Li
gand
(aq)
Wat
er(a
q)Pr
otei
n:Li
gand
(aq)
ΔGbind
Prot
ein:
Wat
er(a
q)Li
gand
(aq)
Wat
er(a
q)Pr
otei
n:Li
gand
(aq)
ΔGbind
(*)
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
λ=0.0
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
λ=0.0
100%
0%
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
λ=0.2
80%
20%
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
λ=0.5
50%
50%
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
λ=0.8
20%
80%
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
λ=1.0
0%
100%
Perform Thermodynamic Integration (TI) along the Waterswap λ coordinate. This results, directly,
in the absolute binding free energy
!20$
!18$
!16$
!14$
!12$
!10$
!8$
!6$
!4$
!2$
0$0.0$ 0.2$ 0.4$ 0.6$ 0.8$ 1.0$
Free$Ene
rgy$/$kcal$m
ol01$
λ$
Perform Thermodynamic Integration (TI) along the Waterswap λ coordinate. This results, directly,
in the absolute binding free energy
!20$
!18$
!16$
!14$
!12$
!10$
!8$
!6$
!4$
!2$
0$0.0$ 0.2$ 0.4$ 0.6$ 0.8$ 1.0$
Free$Ene
rgy$/$kcal$m
ol01$
λ$
Perform Thermodynamic Integration (TI) along the Waterswap λ coordinate. This results, directly,
in the absolute binding free energy
!20$
!18$
!16$
!14$
!12$
!10$
!8$
!6$
!4$
!2$
0$0.0$ 0.2$ 0.4$ 0.6$ 0.8$ 1.0$
Free$Ene
rgy$/$kcal$m
ol01$
λ$
ΔGbind
How to use Waterswap?
Sire can be downloaded using
the links on this site...
...and there are full instructions on how to use
waterswap
…but,
• waterswap is easy to use…
• …but setting up a protein-ligand complex for simulation requires expert knowledge and is not trivial
• waterswap results depend on the quality of the input model
Test Application to Thrombin
Cl
NHO
N
R
O
CH3
H2
C
CH3
H2
C
CH2
CH3
H2
CHC
CH3
CH3
H2
C
CH2
CH
CH3
CH3
H2
C
H2
C
H2
C
CH2
H2
C
CH2
H2
C
CH2
1
2
3
4
5
6
7
8
9
10
R
20 30 40 50 60 70Dynamics
Dynamics + Waterswap
20 30 40 50 60 70Dynamics
20.crd 20.top
Dynamics + Waterswap
20 30 40 50 60 70Dynamics
Wat
ersw
ap
20.crd 20.top
Dynamics + Waterswap
20 30 40 50 60 70Dynamics
Wat
ersw
ap
�G20ns
20.crd 20.top
Dynamics + Waterswap
20 30 40 50 60 70Dynamics
Wat
ersw
ap
�G20ns
20.crd 20.top
30.crd 30.top
�G30ns
Wat
ersw
ap
Dynamics + Waterswap
20 30 40 50 60 70Dynamics
Wat
ersw
ap
�G20ns
20.crd 20.top
30.crd 30.top
�G30ns
Wat
ersw
ap40.crd 40.top
50.crd 50.top
60.crd 60.top
70.crd 70.top
�G40ns �G50ns �G60ns �G70ns
Wat
ersw
ap
Wat
ersw
ap
Wat
ersw
ap
Wat
ersw
ap
Dynamics + Waterswap
20 30 40 50 60 70Dynamics
Wat
ersw
ap
�G20ns
20.crd 20.top
30.crd 30.top
�G30ns
Wat
ersw
ap40.crd 40.top
50.crd 50.top
60.crd 60.top
70.crd 70.top
�G40ns �G50ns �G60ns �G70ns
Wat
ersw
ap
Wat
ersw
ap
Wat
ersw
ap
Wat
ersw
ap
Dynamics + Waterswap
< >
20 30 40 50 60 70Dynamics
Wat
ersw
ap
�G20ns
20.crd 20.top
30.crd 30.top
�G30ns
Wat
ersw
ap40.crd 40.top
50.crd 50.top
60.crd 60.top
70.crd 70.top
�G40ns �G50ns �G60ns �G70ns
Wat
ersw
ap
Wat
ersw
ap
Wat
ersw
ap
Wat
ersw
ap
Dynamics + Waterswap
< >
�Gbind
Cl
NHO
N
R
O
CH3
H2
C
CH3
H2
C
CH2
CH3
H2
CHC
CH3
CH3
H2
C
CH2
CH
CH3
CH3
H2
C
H2
C
H2
C
CH2
H2
C
CH2
H2
C
CH2
1
2
3
4
5
6
7
8
9
10
R
-6.5
-6.0
-5.5
-5.0
-4.5
-4.0
-3.5 -32 -30 -28 -26 -24 -22 -20
Exp
erim
ent /
kca
l mol
-1
Simulation / kcal mol-1
R2=0.82
1
2 3
4 10 8
5 6
7 9
!
Simulation should not try to compete with experiment.
!
The job of simulation is to provide inspiration and insight
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
Free Energy Decomposition
• As we integrate the total waterswap binding free energy...
• ...we also integrate free energy changes in the “protein” box and the “water” box
• Result are free energies that tell you if a ligand’s binding strength comes from a natural affinity for the protein, or an aversion to water
-6.5
-6.0
-5.5
-5.0
-4.5
-4.0
-3.5 -10 -8 -6 -4 -2
Exp
erim
ent /
kca
l mol
-1
Simulation / kcal mol-1
R2=0.14
1
2 3 4 8 10
6 7
5
9 -6.5
-6.0
-5.5
-5.0
-4.5
-4.0
-3.5 -26 -24 -22 -20 -18 -16 -14 -12
Exp
erim
ent /
kca
l mol
-1
Simulation / kcal mol-1
R2=0.84
1
2 3
4 5
6
10 8
7 9
Specificity driven by “water” box, i.e. the more hydrophobic the ligand, the less it
wants to be in the water box, and the more it wants to be in the protein box.
!
This shows that a “better” ligand is only better because it is more hydrophobic
Protein Box Water Box
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
Waterswap uses a λ-coordinate to swap a ligand and a water cluster between a protein box and a water box
Protein Box Water Box
E� = (1� �)[Eprotein:cluster
+ Ewater:ligand
]+
(�)[Eprotein:ligand
+ Ewater:cluster
]
Eresidue:cluster
Eresidue:ligand
Free Energy Decomposition
• As we integrate the total waterswap binding free energy...
• ...we also integrate the individual contributions from all of the binding site residues
• Result is a “free energy” that indicates whether the residue:ligand or residue:water complex is more stable
Ligand Water Cluster
Tota
l E
lect
rost
atic
va
n de
r Waa
ls
Phe227
Phe227
Phe227
Phe227
Phe227
Phe227
Ligand Water Cluster
Tota
l E
lect
rost
atic
va
n de
r Waa
ls
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Ligand Water Cluster
Tota
l E
lect
rost
atic
va
n de
r Waa
ls
Phe227
Phe227
Phe227
Phe227
Phe227
Phe227
Ligand Water Cluster
Tota
l E
lect
rost
atic
va
n de
r Waa
ls
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
Asp189
Glu192
SUPPORTING INFORMATION
Rapid Decomposition and Visualisation of Protein-Ligand Binding Free Energies by Residue and by Water
Christopher J. Woods, Maturos Malaisree, Julien Michel, Ben Long, Simon McIntosh-Smith and Adrian J. Mulholland
Figure S1. Experimentally measured binding affinities for the 10 ligands studied in this work (m-chlorobenzyl) and for the ten benzamidine analogs. Binding affinities are taken from Muley et al., doi: 10.1021/jm9016416 (reference 32 in our paper).
Figure S2. Components of the waterswap free energy for selected residues as calculated using averages calculated over individual Monte Carlo iterations for the 20 ns snapshot of ligand 9 bound to thrombin.
-10
-8
-6
-4
-2
0
2
4
6
8
10
0 100 200 300 400 500 600 700 800 900 1000
Free
Ene
rgy
/ kca
l mol
-1
Monte Carlo Iteration
His57
Lys60
Arg173
Ile174
Asp189
Ser195
Ser214
Trp215
Gly216
-9
-8
-7
-6
-5
-4
-3 0 1 2 3 4 5 6 7 8 9 10
Bin
ding
Aff
inity
/ kc
al m
ol-1
Ligand
m-chlorobenzyl
benzamidine
Replacing m-chlorobenzyl group with benzamidine group systematically improves binding of the ligands
Conclusion
• Waterswap enables direct, first-principles calculation of absolute binding free energies
• (but results depend on quality of model!)
• Free energies can be decomposed to per-residue and per-water components
• Aim is to provide inspiration and insight
Appendix
• waterswap is just one of our tools…
• Also have ligandswap, which calculates relative binding free energies by swapping one ligand with another
• Also have waterview, that lets you quickly visualise water dynamics in a binding site, e.g.
Acknowledgements• Organisers for inviting me and allowing me to talk
• You for your attention
• Dr. Maturos Malaisree (doing most of the work!)
• Dr. Julien Michel (discussions and providing thrombin test system)
• Prof. Adrian Mulholland, Simon McIntosh-Smith, Ben Long
• EPSRC and now BBSRC for funding
• eInfraStructureSouth for GPU compute
• ACRC (Bristol) for CPU compute
• Get the software at http://siremol.org
• Get in touch via [email protected]
Identity Constraint
• How do we “identify” the cluster of water to be swapped with the drug?
• We developed the identity constraint. This is a new way of labelling water molecules in a simulation that is based on where the molecule is in space, rather than where it is located in the input coordinate file.
• Allows definition of water clusters without using restraints or external perturbations
Connect boxes to the same thermostat
Connect boxes to the same thermostatPlace identity points on the atoms of the ligand
Connect boxes to the same thermostatPlace identity points on the atoms of the ligand
Copy those points into the water box to identify a cluster
λ"="0.0" λ"="0.3" λ"="0.6" λ"="1.0"
• Binding"free"energy"is"calculated"by"running"simula:ons"across"λ."Using"one"8>core"node,"one"free"energy"takes"24>48"hours"to"compute"
• Implemented"in"Sire:"hHp://siremol.org""
• Woods,"J"Chem"Phys,"Vol"134,"p054114,"2011"• "hHp://dx.doi.org/10.1063/1.3519057"
Reflection Sphere• Only waters
whose centers are inside the sphere can move
• Any move that takes the center of a water outside the sphere is reflected back into the sphere
• This prevents waters from leaving
Grid Electrostatics• Interactions inside
reflection sphere calculated normally
• Interactions between reflection sphere atoms and atoms within buffer (dotted sphere) calculated normally
• Coulomb interactions between reflection sphere and fixed atoms outside the buffer are calculated using a pre-computed cubic grid
Grid Electrostatics• Use of pre-computed
grid means that there is no penalty to using a long-range electrostatic cutoff
• Compatible with advanced boundary conditions, such as reaction field or force-shifted cutoff
• Fine grid (0.5 Å) and tri-linear interpolation give high accuracy compared to direct calculation