Lead Finder has been able to achieve significant enrichments for almost all protein targets. The most outstanding enrichments were obtained for oligopeptide-binding
protein (OppA), orotidine-5´-phosphate decarboxylase (OPD), protein tyrosine phosphatase 1B (PTP1B),
beta-secretase, HIV-1 protease, factor Xa, peroxisome proliferator activated receptor gamma (PPAR-γ).
Analysis of docked ligand poses revealed that for OppA and OPD Lead Finder correctly found multiple hydrogen bonds and
complementary electrostatic interactions of charged groups, which yielded high enrichments for those targets.
For PPAR-γ, HIV-1 protease and beta-secretase the basis for impressive results was in correct
detection of crucial hydrogen bonds and hydrophobic contacts between active ligands and corresponding proteins.
Interestingly, that PPAR-γ was traditionally recognized as a difficult
and even two protein
models were used for virtual screening studies of PPAR-γ5
, however Lead Finder was able to achieve excellent
results using a single protein structure model. Successful docking of positively charged fragment of factor
Xa inhibitors gave rise to high enrichment for the corresponding target.
Nuclear receptors demonstrated from moderate (for glucocorticoid receptor (GR) and progesterone
receptor (PR)) to high (for estrogen receptor and mineralocorticoid receptor) enrichments.
Close analysis of GR and PR reveals that their ligand binding cavities are too spacious and
can easily accommodate ligands of diverse shape and size, giving rise to false positives.
Thymidylate synthase also revealed quite modest enrichment. In this case we attribute results
to insufficiently specific binding of its native ligands (predicted average binding energy over
active ligands comprised -8.7 kcal/mol only), which is probably stipulated by relatively
shallow and surface exposed binding site of the enzyme. Probably, similar situation takes place
for neuraminidase, which binding site represents extended funnel; ligands have too much freedom
to slide along protein surface, which dilutes the specificity of binding. As in the case
with TS, native ligands of neuraminidase reveal quite modest binding energy
(-7.3 on average).
Finally, protein kinases deserve special attention as they are intensively studied
as drug targets nowadays8
. Currently, 7 protein kinases were assessed by Lead Finder
in virtual screening experiments. Overall, kinases revealed good enrichment from ROC = 0.86 for
fibroblast growth factor receptor kinase (FGFR) and vascular endothelial growth factor receptor kinase
2 (VEGFR) to ROC = 0.95 for epidermal growth factor receptor kinase (EGFR) and
ROC = 0.96 for tyrosine kinase C-SRC (SRC). Close examination of predicted poses for active
kinase ligands revealed common feature determining the degree of virtual screening success: targets,
for which active ligands succeeded forming crucial correlated hydrogen bonds with hinge fragment
of a kinase, demonstrated higher enrichment than targets for which these hydrogen bonds were
observed less frequently. We also found that relative mobility of N- and C-terminal lobes
of a catalytic kinase domain influences accessibility of correct ligand-binding pose.
For this reason evaluation of multiple protein conformers is suggested to achieve high
enrichment results in case of kinases.