Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry

Abstract

Human type II topoisomerase (Top2) isoforms, hTop2α and hTop2β, are targeted by some of the most successful anticancer drugs. These drugs induce Top2-mediated DNA cleavage to trigger cell-death pathways. The potency of these drugs correlates positively with their efficacy in stabilizing the enzyme-mediated DNA breaks. Structural analysis of hTop2α and hTop2β revealed the presence of methionine residues in the drug-binding pocket, we therefore tested whether a tighter Top2-drug association may be accomplished by introducing a methionine-reactive Pt2+ into a drug to further stabilize the DNA break. Herein, we synthesized an organoplatinum compound, etoplatin-N2β, by replacing the methionine-juxtaposing group of the drug etoposide with a cis-dichlorodiammineplatinum(II) moiety. Compared to etoposide, etoplatin-N2β more potently inhibits both human Top2s. While the DNA breaks arrested by etoposide can be rejoined, those captured by etoplatin-N2β are practically irreversible. Crystallographic analyses of hTop2β complexed with DNA and etoplatin-N2β demonstrate coordinate bond formation between Pt2+ and a flanking methionine. Notably, this stable coordinate tether can be loosened by disrupting the structural integrity of drug-binding pocket, suggesting that Pt2+ coordination chemistry may allow for the development of potent inhibitors with protein conformation-dependent reversibility. This approach may be exploited to achieve isoform-specific targeting of human Top2s.

A Novel Cytotoxic Conjugate Derived from the Natural Product Podophyllotoxin as a Direct-Target Protein Dual Inhibitor

“…This pocket is embedded in the β-subunit, close to the interface with α−tubulin and GTP binding site. It is thought that ligands that occupy the colchicine binding site inhibit tubulin dimerization via dimer destabilization, thus preventing the required contacts of the protomers from forming the microtubule [ 37 , 38 ].…”

“…Our models for tubulin dimer and Topo-II were based on the PDB 1SA1 and 5GWK [ 37 , 38 ], respectively. In 1SA1, the podophyllotoxin was resolved at the colchicine site, close to the dimerization interface.…”

Coupling the core of the anticancer drug etoposide to an oligonucleotide induces topoisomerase II-mediated cleavage at specific DNA sequences

“…OTIs were designed to generate single-stranded, topoisomerase II-mediated cleavage on the strand opposite the etoposide core attachment site (Figure 1 ) ( 8 ). To this end, crystal structures of human topoisomerase IIβ ( 18 ) and IIα ( 33 ) with two etoposide molecules and the bacterial Staphylococcus aureus DNA gyrase with one or two etoposide molecules ( 34 ) served as the basis for modeling studies ( Supplementary Figure S1 ). As a result of these studies, a linker consisting of a terminal alkyne moiety was attached to the C5 position of a cytosine or thymine residue and was coupled to a 4-azide-modified DEPT via copper-catalyzed click chemistry (Figure 2 ).…”

“…To guide the placement and length of the chemical linker that joined the active demethylepipodophyllotoxin (DEPT) core of etoposide to the modified base in the oligonucleotides, structures of OTI complexes were modeled using Coot ( 31 ), MOE ( 32 ), and Maestro (Schrödinger Release February 2017: Maestro, Schrödinger, LLC, New York, NY, 2017). Models were based on the crystal structures of the human topoisomerase IIβ and topoisomerase IIα cleavage complexes with DNA and two etoposide molecules (one at each scissile bond) (PDB code: 3QX3 ( 18 ) and PDB code: 5GWK ( 33 ), respectively), and the Staphylococcus aureus gyrase–DNA complex with one etoposide molecule (PDB code: 5CDP) ( 34 ) ( Supplementary Figure S1 ). The positions of the etoposide molecules in the DNA complexes with human and bacterial enzymes are essentially the same ( Supplementary Figure S1 ).…”

Newly Synthesized Imino-Derivatives Analogues of Resveratrol Exert Inhibitory Effects in Breast Tumor Cells

“…We adopted a consolidated protocol we already used is several other cases for our docking simulations and that has been described in different of our previous publications [ 75 , 76 ]. As a target for all our simulations, we used the molecular structure of the human topoisomerase IIalpha in complex with DNA and etoposide [ 77 ] [PDB code 5GWK]. Figure 4 and Figure 5 were drawn with the program Chimera [ 78 ].…”