Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization
© Ibrahim et al.; licensee Springer. 2015
Received: 12 January 2015
Accepted: 6 May 2015
Published: 20 May 2015
Structure-based virtual screening techniques can help to identify new lead structures and complement other screening approaches in drug discovery. Prior to docking, the data (protein crystal structures and ligands) should be prepared with great attention to molecular and chemical details.
Using a subset of 18 diverse targets from the recently introduced DEKOIS 2.0 benchmark set library, we found differences in the virtual screening performance of two popular docking tools (GOLD and Glide) when employing two different commercial packages (e.g. MOE and Maestro) for preparing input data. We systematically investigated the possible factors that can be responsible for the found differences in selected sets. For the Angiotensin-I-converting enzyme dataset, preparation of the bioactive molecules clearly exerted the highest influence on VS performance compared to preparation of the decoys or the target structure. The major contributing factors were different protonation states, molecular flexibility, and differences in the input conformation (particularly for cyclic moieties) of bioactives. In addition, score normalization strategies eliminated the biased docking scores shown by GOLD (ChemPLP) for the larger bioactives and produced a better performance. Generalizing these normalization strategies on the 18 DEKOIS 2.0 sets, improved the performances for the majority of GOLD (ChemPLP) docking, while it showed detrimental performances for the majority of Glide (SP) docking.
In conclusion, we exemplify herein possible issues particularly during the preparation stage of molecular data and demonstrate to which extent these issues can cause perturbations in the virtual screening performance. We provide insights into what problems can occur and should be avoided, when generating benchmarks to characterize the virtual screening performance. Particularly, careful selection of an appropriate molecular preparation setup for the bioactive set and the use of score normalization for docking with GOLD (ChemPLP) appear to have a great importance for the screening performance. For virtual screening campaigns, we recommend to invest time and effort into including alternative preparation workflows into the generation of the master library, even at the cost of including multiple representations of each molecule.
Virtual screening (VS) is a widely applied method in drug discovery that is used to predict novel bioactives from large chemical libraries [1–4]. In the last decade a multitude of successful VS applications have been reported [5–9]. In early-stage drug discovery especially structure-based virtual screening (SBVS) has been frequently used to identify new hits [10–14]. SBVS requires structures of target binding sites to predict potential interactions with ligand molecules. One of the most frequently used SBVS methods is molecular docking, which is used for docking molecules into the binding pocket to predict and score energetically favorable ligand binding modes [15–20].
Generally, it was found that VS performance depends strongly on the respective target properties [1, 21–24]. Different scoring and docking functions consequently favor different binding situations. To avoid wasting time and efforts on ineffective VS strategies, it is important to assess the performance of different VS setups in order to select the most effective workflow. Screening performance can be assessed using molecular benchmark sets, which consist of a set of bioactives and a set of inactive molecules, also known as decoys [23–25]. The higher the number of bioactives at the top of the score-ordered list of screened molecules, the better is the respective screening performance. Apart from the selection of a suitable docking tool, the success rate of VS tools depends strongly on various factors, such as the protonation/tautomerization state of the respective protein binding site residues  and of the input molecules [27–30], as well as the force field-minimized input conformation of the respective input molecules [31–35].
In this study, we investigate why and to which extent different protein/ligand preparation procedures affect VS performance by using our recently introduced DEKOIS 2.0 benchmark sets [21, 24, 36]. We test the widely applied docking tools GOLD and Glide with two comparable settings of input preparation using two different commercial packages (MOE and Maestro). In addition, we conduct a systematic in-depth analysis for one example (ACE, Angiotensin-I-converting enzyme) to evaluate the possible factors affecting the differences in screening performance between MOE and Maestro preparations. Interestingly, we found that the preparation of the bioactives caused a larger screening performance difference than the preparation of the decoys set or the target structure. Score normalization strategies eliminated the bias toward larger molecules in GOLD docking scores (ChemPLP) for ACE and also produced better performances in most of the other datasets.
Results and discussion
Selection of benchmark sets
To probe the impact of diverse docking setups on VS performance, suitable and diverse test datasets should be employed. Our recently introduced DEKOIS 2.0 library offers a wide variety of curated high-quality benchmark sets and is therefore well-suited for compiling a selection of evaluation kits [21, 24]. We selected 18 DEKOIS 2.0 datasets, each representing a different target class. Our compilation comprises proteases, kinases, transferases, oxido-reductases, nuclear receptors, and hydrolases, and describes various protein-ligand binding situations. This allows for a comprehensive analysis of performance differences for various VS setups. A complete list of selected datasets and the PDB codes of their target structures can be found in the Supporting Information (Additional file 1: Table S1).
Ligand and protein preparation protocols
We aim at comparing the impact of two comparable preparation setups on VS performance employing two different preparation packages. Two of the most widely used applications for input preparation are MOE (Chemical Computing Group) and Maestro (Schrodinger). The preparation of the data was done at comparable levels of complexity for both programs, which are described in more detail in the Methods section. We conducted the preparation of the dataset (bioactives and decoys sets) by the LigPrep module in Maestro and the Wash and Minimize functions of MOE. Similarly, target structures were prepared by the ProtAssign function in Maestro and the Prot3D function of MOE.
Impact of different preparation procedures on VS performance
We utilized the widely used pROC-AUC as a metric for the screening performance [21, 22, 24]. The pROC curve is a semi-logarithmic version of the standard linear curve of the receiver operating characteristics (ROC) . Therefore, pROC curves are emphasizing the recognition of the early recovered hits when calculating the “area under the curve” (AUC) .
Comparison of docking performances between MOE and Maestro data preparation schemes for diverse protein targets
ΔpROC-AUC prep a
Because of the heuristic and the stochastic nature of the docking process in GOLD , we defined a “safety margin” of ±0.05 resulted from the deviation of multiple runs representing a non-significant change of ΔpROC-AUC prep , , and to avoid over-interpreting small changes in docking performance.
We observed that VS performances of GOLD for four of the 18 targets did not significantly differ between the two preparation schemes (Table 1). The remaining 14 targets showed larger changes. Seven of these targets (50 %) showed higher pROC-AUC values for Maestro prepared data, while the other 7 targets (50 %) benefitted from MOE data preparation. This suggests that the GOLD screening performance does not generally depend on a particular preparation scheme. For some examples the docking performance was affected dramatically by the different preparation schemes. ACE, ERBB2 and TS docking results showed relatively large ΔpROC-AUC prep values, as shown in Table 1.
Despite the fact that the docking process in Glide is deterministic and multiple docking runs of the same input data yields exactly the same output every time , we still considered the “safety margin” of ±0.05 ΔpROC-AUC prep to avoid over-interpreting small changes in docking performance. Four of the 18 targets did not significantly differ between the two preparations. Five of 14 targets (~36 %) showed higher pROC-AUC values for Maestro prepared data. For the remaining nine targets (~64 %), Glide produced higher VS performance with MOE preparation. The screening performance differed substantially between the preparation schemes for DHFR, HDAC2 and PNP (Table 1), while the remaining targets showed only smaller performance differences.
Such screening performance differences can be caused by various factors, such as (a) the selected protonation/tautomerization state of the respective protein binding site residues , (b) the protonation/tautomerization states of the respective input molecules of the dataset [27–29], and (c) the force field-minimized input conformation of the respective input molecules of the dataset [31–35]. To elucidate the influence of (a) and (b), we compared protonation/tautomerization states of the binding sites and the molecules and quantified the differences. To get an idea to which extent (c) differs, we calculated the pairwise RMSD of the conformers of the bioactives produced by the two preparations. A comprehensive summary of these results can be found in the Supporting Information (Additional file 1: Table S2 and Table S3).
In general, we observed that the screening performance differences between the two preparations are variable in a target-dependent manner for both docking programs. We observed that the metal-containing targets (e.g. ACE and HDAC2) showed relatively high ΔpROC-AUC prep for both GOLD and Glide. This is not surprising, since the complexity of the metal-containing microenvironment of the binding sites is a well-known phenomenon [29, 38]. The targets that contained higher numbers of different protonation/tautomerization states (Additional file 1: Table S2 and Table S3) between the two preparations (particularly for the bioactives) frequently show higher ΔpROC-AUC prep for both docking programs (e.g. ERBB2 and TS). When ignoring the special cases ACE and HIVPR, there is a certain trend for the remaining 16 datasets, suggesting that difference in protonation/tautomerization states of the bioactives and ΔpROC-AUC prep are correlated (Additional file 1: Figure S1). This implies that the occurrence of different bioactive protomers and tautomers can be a major contribution to the obscured screening performance. Interestingly, in several cases (e.g. DHFR and HDAC2) where the ΔpROC-AUC prep values between Glide and GOLD differ significantly, a higher number of different protonation/tautomerization states was found for the bioactives. For a more in-depth analysis, we focus on examining ACE in more detail.
Impact of target, bioactive, and decoy preparation
We have chosen ACE, as a particular interesting example, because for this target we observed the highest ΔpROC-AUC prep value between MOE and Maestro prepared data for GOLD and a large ΔpROC-AUC prep for Glide. Therefore, we explored more thoroughly the various factors influencing the performance difference of GOLD. We also conducted a similar analysis on DHFR that showed the highest ΔpROC-AUC prep for Glide (see Additional file 1: Figure S2 and Figure S3 in SI).
Impact of bioactives preparation on the docking rank and score
From Fig. 1, it is clear that preparation of the bioactives of ACE had the highest impact on the screening performance, while different preparation of decoys and target structure was less crucial. In contrast to the decoy set, the bioactive set preparation with MOE was always beneficial. The target structure preparation caused only small performance differences, typically in favor of MOE.
Impact of dataset (bioactives vs. decoys) protonation
Basic statistics showing the distribution of Maestro and MOE protomers for the respective docking runs
Bioactives (n = 2)
Decoys (n = 435)
Upon totally deleting the two bioactives with different protomers and recalculating the pROC-AUC, we observed only non-significant differences (0.03 for Maestro and and 0.02 for MOE preparations). Still the difference between MOE and Maestro preparations in this case is significant (ΔpROC-AUC = 0.26). This observation suggests that the protonation state selection between the two preparations is only a minor factor and other factors (e.g. geometric features) should contribute much more to the observed performance differences.
Impact of bioactives geometric features?
To monitor differences in the input conformations between the two preparations of the bioactives, we calculated the pairwise RMSD for each bioactive molecule. We found a trend for bigger bioactives to show higher RMSD values between their input conformations (R2 = 0.52, see Additional file 1: Figure S6 in SI). This certainly makes sense, since it is challenging for the two force fields to find closely related energy minima, when molecular size and flexibility increases. However, we did not observe any reasonable trend (R2 always below 0.2) between the pairwise RMSD of the bioactive molecules and the Δfitness in any of the 18 datasets. It is evident from other studies in the literature [31, 32] that small changes in the input conformation of the molecule (e.g. torsional angles and bond lengths) can affect the docking performance to a vast extent. Thus, we cannot rule out that differences in the way the input conformations were generated in the two procedures will cause a significant influence on the different docking performances observed.
Impact of decoys preparation
Transforming the docking score information into the global docking rank (i.e. including the bioactives’ ranks) showed more scattering of some decoys around the fitted line (R2 = 0.81) for the rank correlation, as seen in Fig. 8b. For getting some answers about the possible factors that affected the difference in the docking rank between the two preparations for the decoys, we first looked at the most obvious outliers. Thus, we applied a cutoff value of the docking rank difference of 500 (i.e. Δdocking rank > 500) bearing in mind that the maximum Δdocking rank difference observed for the bioactives was 573. We ended up with 13 decoys that showed a Δdocking rank between the two preparations above the cutoff. In summary these 13 decoys exhibit the following properties: (a) four decoys showed differences in the protonation state, (b) one decoy had an altered tautomer state, (c) two decoys deviated in their ring conformations, and (d) six decoys did not show any of previous factors, but three of those had a rather high number of rotatable bonds (more than 8). It is noteworthy that the maximum Δdocking rank of the decoys is attributable to a difference in protonation state between the two preparations. Generally, we noticed that 49 % of the decoys (586 decoys) showed better ranks after the MOE preparation, while 51 % had better ranks after the Maestro preparation. Because this ratio is almost exactly 1:1, it does not provide any clues for understanding why the docking performance for ACE is superior in case of the MOE preparation. This indicates that the docking rank of the bioactives is certainly much more important for the overall result than the docking rank of the decoys. We conclude that similar aspects as discussed before for the bioactives cause differences between the two preparations, but the overall influence of such differences in the decoys is significantly inferior.
Impact of target structure preparation
Overview of the screening performance based on the normalized scores obtained by GOLD docking after MOE preparation. Further data on the normalization of the docking performances for Glide and GOLD after MOE and Maestro preparation are available in Additional file 1: Table S4 in the Supporting Information
ΔpROC-AUC N a
MW c mean per dataset
NHA d mean per dataset
In general, we found that the GOLD screening performance for many datasets (see Table 3) was improved when applying the docking score normalization. In contrast, the Glide docking performance was reduced for almost all benchmark sets when applying the score normalizations (data in Additional file 1: Table S4 in SI). We found that the N2/3 normalization, which emphasizes the number of heavy atoms more strongly than N1/2 in the final score, yielded worse performance results than the N1/2 normalization. Interestingly, GOLD docking into HSP90 with the MOE preparation displayed a pROC-AUC < 0.434 – worse than random performance – with the original setup, but gave a significantly improved enrichment for both N2/3 and N1/2 normalizations and the screening performance was shifted to be better than random (>0.434). It is obvious that for several targets with a larger average size (e.g. average number of heavy atoms or molecular weight) of their datasets (e.g. HIV1PR and ERBB2), their performance after normalization was penalized quite significantly, and vice versa for targets that show a relatively small average size (e.g. PNP), their performance after normalizations has been improved (Table 3).
Based on our results, we would recommend that the medicinal/computational chemists may test the performance of the N1/2 normalization for GOLD (ChemPLP), whereas for Glide, no normalization appears to be required. This may not be surprising, since the ChemPLP scoring function of GOLD has been originally developed for pose prediction purposes [43, 44], while Glide SP had been optimized for screening enrichment and docking accuracy [45, 46].
Preparation of targets
Maestro preparation scheme: For each crystal structure the coordinates were retrieved from the Protein Data Bank (PDB) in our dataset. A comprehensive list of PDB codes is given in Additional file 1: Table S1. The preparation of the original PDB files was conducted by assigning bond orders, adding explicit hydrogens, creating zero-order bonds to metals, and converting selenomethionines to methionines using the Protein Preparation Wizard in Maestro (version 9.1) . Redundant and identical macromolecule chains with non-essential co-factors, ions, water molecules and ligands were discarded. Exceptions were made for (PDB code: 1i00) with a co-substrate in the ligand binding site, and for structures that contained metal ions (e.g. Zn2+, and Mg2+) in their ligand binding pocket (PDB code: 1uze and 3max). The metal binding states were generated at pH 7.0 by Epik [48, 49]. H-bond network optimization, protonation and tautomeric states of Asp, Glu, Arg, Lys and His were sampled by “ProtAssign” in the standard mode. Possible alternative orientations of Asn and Gln residues were also generated. The native geometry of the binding sites was preserved without in-place ligand-protein minimization. Prepared structures were saved as MAE and PDB files. The MAE files were used for Glide [45, 46] (version 5.6) docking, the PDB files were used for GOLD (version 5.1) docking [50–53].
Overview of Maestro and MOE preparation schemes for targets and datasets. This table shows comparable settings for preparing the input
1) Targets preparation
Adding hydrogens and H-bond optimization
Asn and Gln flipping
Protonation/tautomerization states of Asp, Glu, Arg, Lys and His
Number of protomer/tautomer retrieved for Asp, Glu, Arg, Lys and His
2) Dataset (bioactives and decoys) preparation
wash and minimize
Number of protomer/tautomer retrieved
Input chirality retained
Preparation of DEKOIS 2.0 datasets
Maestro preparation scheme: All molecules of the datasets were prepared by LigPrep (version 2.4) . The molecules were minimized using the OPLS-2005 force field. The protonation state was generated at pH 7.0 for each molecule. The specified stereoconfiguration of all bioactives and decoys of the datasets was retained. All prepared molecules were saved as SD files for Glide and GOLD docking. MOE preparation scheme: “molecule wash” function was used to generate meaningful protonation states by deprotonating strong acids and protonating strong bases. Energy minimization of all molecules was then performed using the MMFF94x force field at a gradient of 0.01 RMSD (i.e. if the gradient falls below RMSD, the minimization stops). Existing chirality was preserved and partial charges were calculated according to the standard parameters of the force field.
We conducted the pairwise RMSD calculation for the respective molecules of the datasets between Maestro and MOE schemes by employing in-house python script applying the “smart_rms” function of GOLD.
The docking runs were performed with Glide and GOLD at the default settings. Only the best pose per molecule was retrieved for the molecules of the datasets from the docking and pROC-AUC values were calculated thereof. For Glide (version 5.6) docking, we generated the receptor grid-box by default settings, with an approximate size (on average) 20 x 20 x 20 angstroms for most of the targets. We conducted the standard precision docking mode (SP) and also considered Epik state penalties for metal-containing binding sites. By default, the cutoff for keeping initial docking poses was 100.0 kcal/mol (relative to the best scored initial pose). The best five final docking poses per molecule were selected for post-docking minimization within Glide. For GOLD (version 5.1) docking, residues of the binding site were defined by specifying the crystal structure ligand coordinates and using a cutoff radius of 10 Å, with the ‘detect cavity’ option enabled. The scoring function used for GOLD docking experiments was ChemPLP. The search efficiency of the genetic algorithm was kept at the standard 100 % setting. The docking was early terminated when the top three solutions were within 1.5 Å RMSD.
Conclusion and outlook
We have shown in this study that application of comparable setups for the preparation of targets, bioactives and decoys by different modeling packages (Maestro or MOE) affected the screening performance of Glide and GOLD in the majority of the investigated targets. These differences in the screening performance are attributable to multiple factors, such as the different selection of: (a) the protonation/tautomerization state of the target’s binding site residues and molecules of the datasets, and (b) the input geometry of the prepared molecules due to the intrinsic differences between the force field parameters of both preparation schemes. Match versus mismatch docking runs of the ACE dataset as a case example demonstrated that the preparation of the bioactive molecules has the highest impact on the screening performance. The impact of the protonation state differences in the decoys or bioactives was assessed by a shuffling experiment. In both cases the importance of the protonation state differences seemed small, yet slightly more relevant for the bioactive molecules. Having a look at the docking rank and score of the respective bioactive between the two preparations, we found that the maximum difference of the rank is attributable to a bioactive ligand that showed a difference in its protonation state between the two preparations. The maximum fitness difference (Δfitness) was caused by a bioactive ligand that showed a highly flexible structure. Analyzing the geometric features as possible impact factors on the screening performance difference, we found that the flexibility features (e.g. number of rotatable bonds and number of heavy atoms) showed a reasonable correlation (R2 = 0.49 and 0.51, respectively), with the Δfitness for a subset of ten bioactives, which exhibited the highest deviations in the fitness values. For the remaining 30 bioactives, fitness values between the two preparations were highly similar (R2 = 0.93). Among the geometric features identified is also the impact of selecting different conformations of flexible rings in bioactives as well as the input conformation of the dataset for docking. Analysis of the decoys behavior between the two preparation schemes agreed widely with the general findings observed for the bioactives.
Elucidating the effect of two different preparations on the screening performance and deconstructing the possible factors behind these performance differences is certainly useful for making reasonable decisions in virtual screening campaigns. In addition, another important factor for understanding benchmarking results can be the composition of the set of bioactives with respect to the frequent occurrence of similar scaffolds or common substructures. For achieving this, we aim at studying the impact of the two preparation schemes on the chemotype recognition during the docking process in a subsequent publication.
T.M.I. is grateful to the GERLS (German-Egyptian Long-Term Scholarship) program of the German Academic Exchange Service (DAAD) for funding his Ph.D. fellowship. We thank Thomas Exner for his valuable comments regarding the manuscript and Johannes Heidrich for proof-reading the manuscript.
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