Figure 1.
Docking pose of etoposide in Top2α and development of complex-based pharmacophore.
A) Docking pose of etoposide relative to Top2α. Protein backbone and surface shown in cyan. Two residues interacting with etoposide are shown as sticks. B) Docking pose of etoposide relative to DNA. DNA residues shown as green sticks. Hydrogen bonds indicated as green, hydrophobic interactions as blue and stacking interactions as orange lines. C) and D) 2D- and 3D-representation of complex-based pharmacophore developed from the etoposide docking pose. Colour code of pharmacophore features: hydrogen bond acceptor (HBA), green; hydrogen bond donor (HBD), pink; hydrophobic group, blue; cyclic π-interaction (CYPI), orange; excluded volume, grey.
Figure 2.
Sequence alignment of Top2α and Top2β ligand binding pocket residues. Non-conserved residues are highlighted.
Figure 3.
Possible residues to be targeted by Top2α versus Top2β-selective molecules.
Superimposition of Top2α homology model (dark cyan) and Top2β crystal structure (light blue) [34], shown in cartoon representation. Residues in the etoposide binding pocket which differ between the Top2α and Top2β isoform are indicated as sticks (residue names: Top2α/Top2β). Etoposide pose from the Top2β crystal structure (stick representation, carbons white) shown for clarity.
Table 1.
Compounds suggested from Top2α docking studies.
Figure 4.
Topoisomerase 2α-mediated DNA cleavage by mitonafide, etoposide and in silico selected compounds.
Structures of tested compounds and controls are shown on the right. A) Compounds were tested on a portion of SV40 sequence at three different concentrations (100, 10 and 1 µM). The first lane represents the DNA without enzyme and the second lane the DNA with enzyme in presence of DMSO (drug solvent). B) Same as in (A) but compounds were tested on pBR322 plasmid DNA at 100 µM concentration. C) The four active inhibitors of Top2α identified in (B) were additionally tested at 100, 10 and 1 µM concentration on pBR322 substrate.
Table 2.
Compounds selected from screening with etoposide pharmacophores – biological results.
Figure 5.
Top2α and β cleavage assays with selected compounds.
A) The 4 active inhibitors of Top2α identified in Fig. 4B) were additionally tested at 100 µM concentration on both isoforms. The arrows show bands used for densitometric analysis. B) Preferential selectivity of selected compounds for the Top2α isoform. Semiquantitative analysis of cleavage product band densities was performed with Image Quant software (Molecular Dynamics). Data are reported from representative experiments as frequency of cleavage.