Predicting Protein-Ligand Binding Affinities: A Low Scoring Game?
Dushyanthan Puvanendrampillai*, Philip M Marsden*, John BO Mitchell and Robert C Glen
Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
*Corresponding authors – dp274@cam.ac.uk , pmm36@cam.ac.uk
Introduction
Methods
Docking programs search for viable conformations of ligands to reside in target receptor sites and a
scoring function ranks these docked conformations in terms of the quality of the fit between the
ligand and receptor1,2.
Preparation of the Test Set.
•The test set used in this study consisted of 205 protein-ligand complexes with experimentally measured Kd values, which have been assembled from scoring function and/or docking evaluation studies.
•Dissociation constants of the complexes ranged from -1.49 to -13.97 in log Kd units, spanning over 12 orders of magnitude and measured by a variety of experimental methods.
•All ligand molecules bind non-covalently to their target proteins.
The scoring function should ideally also be able to make predictions of binding affinity, allowing
different candidate molecules to be ranked in terms of their predicted binding to a given target3.
Analysis
We have examined the square of the product moment correlation coefficient (r2) and Spearman’s rank correlation coefficient (Rs) between the binding free energies given by the five scoring functions with
experimentally measured log Kd values for the 205 protein-ligand complexes in the dataset.
This correlation between calculated binding energies and experimental values provides an indication of the performance of a scoring function, and of how well these values can predict the binding energies of proteinligand interactions.
-16
-10
-8
-6
-4
0
-2
0
Dataset
-2
-4
All
-6
A
-10
r2
0.59
0.32
GOLD
Rs
r2
0.31
0.11
Rs
r2
0.50
0.20
Serine proteinases
35
0.82
0.74
0.75
0.51
0.61
B
-14
Metalloproteinases
25
0.72
0.44
0.45
0.33
0.44
C
-18
Experimental log Kd
Figure 7. GOLD calculated log Kd vs. Experimental log Kd
-16
-14
r2
0.43
0.20
Rs
r2
0.45
0.18
0.47
0.83
0.69
0.13
0.00
0.14
0.42
0.20
0.43
0.17
-12
-10
-8
18
0.53
0.47
0.46
0.32
0.42
0.34
0.54
0.01
0.50
-14
-12
-10
-8
-6
-4
-2
-2
-6
-4
Sugar binding proteins
30
0.76
0.58
0.45
0.09
0.02
0.00
0.05
0.00
0.29
E
Aspartic proteinases
38
0.08
0.01
- 0.52
0.13
0.02
0.00
0.08
0.01
-0.08 0.00
Figure 8. DOCK calculated log Kd vs. experimental log Kd
0
-2
0
-4
-6
-8
-10
-12
-14
-16
-18
-16
-14
-12
-10
-8
-6
-4
-6
-8
-10
-12
-14
-16
-18
Experimental log Kd
Figure 9. ChemScore calculated log Kd vs. experimental log Kd
0
-2
-4
-6
-8
-10
-12
-14
-16
-18
2
r = 0.20
Experimental log Kd
0.09
0
-2
0
-4
0.28
D
-2
r = 0.20
Experimental log Kd
0
-16
-14
-12
-10
-8
-6
-4
-2
-2
0
-4
-6
-8
-10
-12
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r2 = 0.18
Experimental log Kd
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Results
Conclusions and Discussion
For all 205 protein-ligand complexes –
•The inescapable conclusion from these results is that the problem of accurately predicting the binding energies of a
large and diverse set of protein-ligand complexes is a difficult one.
•BLEEP gives the best agreement between its calculated binding free energy and experimental log Kd
values with Rs=0.59.
•None of the scoring functions tested here achieved r2 values above 0.32 when tested on the full 205 complex dataset.
•GOLD, ChemScore and DOCK have a similar level of binding free energy agreement with Rs values of
0.50, 0.45 and 0.43 respectively.
•This is a disappointing level of performance, although we should note in defence of the GOLD and DOCK functions
that they were designed to identify the correct geometries of bound complexes and not intended to be applied to the
problem of affinity prediction.
•PMF gives an Rs value of 0.31.
•The headline figures for the correlation coefficient given here seem less impressive than in previous work.
Figure 3. Representation of the BLEEP scoring
function for complex 1AAQ.
Pairwise potentials are calculated between the ligand and
protein atoms within a distance cut-off. Ligand atoms
(red) and protein atoms (green) within 8Å of the ligand
are shown in ball and stick representation.
Rs
-16
r2 = 0.32
2
function for complex 1AAQ.
Based on van der Waals interactions, hydrogen
bonds (yellow dashed lines), and ligand internal
torsional energy. External van der Waals shown by
the two complementary surfaces of the ligand
(green) and the protein (brown).
ChemScore
ChemScore calculated log Kd
r 2 = 0.11
Carbonic anhydrase ii
-18
Figure 2. Representation of the GOLD scoring
DOCK
-12
GOLD calculated log Kd
The development of such scoring functions to accurately predict experimental binding free energies
for protein-ligand complexes is currently a major challenge in structure-based drug design. We
expect that improvements in the scoring functions will be crucial in addressing this problem.
Rs
PMF
0
-16
5,6
We used the knowledge-based methods
and BLEEP
and empirical scoring functions of
GOLD7, DOCK8 and ChemScore9, as implemented by Sybyl® 6.910.
BLEEP
Figure 6. BLEEP calculated log Kd vs. Experimental log Kd
-8
We have compared the results of five different scoring functions to determine the binding energy of
a protein-ligand complex with known three-dimensional structure on a diverse dataset of 205
protein-ligand complexes, and also on various subsets of mutually similar complexes.
PMF4
No. of
complexes
205
DOCK calculated log Kd
isostere inhibitor (PDB ID 1AAQ). Protein secondary structure illustrated in cartoon
representation coloured by secondary structure type. A Connolly molecular surface
shown of the cavity coloured by electrostatic potential. Ligand shown in ball and stick
representation.
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PMF calculated log Kd
Figure 1. Crystal structure of HIV-1 protease complexed with an hydroxyethylene
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Table 1. Correlations Between Experimental and Calculated log Kd Values Given by Five Scoring Functions.
BLEEP calculated log Kd
Figure 5. PMF calculated log Kd vs. experimental log Kd
•All five scoring functions give modest
r2
•This is partly due to the choice of dataset. Six outliers were excluded from that previous analysis of BLEEP6, which
raised the r2 value from 0.40 to 0.55.
values, the highest being the 0.32 given by BLEEP.
References
Figure 4. Representation of the DOCK scoring
function for complex 1AAQ.
Based on shape complementarity. Molecular
surface of the ligand (yellow) and the
complementary surface of the protein (green).
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Acknowledgements
We thank Unilever, the EPSRC and the Newton Trust for their funding, and Tripos Inc. for the use of Sybyl®.