Thymines in Single-Stranded Oligonucleotides and G-Quadruplex DNA Are Competitive with Guanines for Binding to an Organoruthenium Anticancer Complex

Abstract

Organometallic ruthenium(II) complexes [(η(6)-arene)Ru(en)Cl](+) (arene = e.g., biphenyl (1), dihydrophenanthrene, tetrahydroanthracene) show promising anticancer activity both in vitro and in vivo and are cytotoxic to cisplatin-resistant cancer cells, implying that these monofunctional complexes have a different mechanism of action from that of bifunctional cisplatin. We demonstrate here that complex 1 binds selectively to the guanine base in the 15-mer single-stranded oligodeoxynucleotides (ODNs) 5'-CTCTCTX7G8Y9CTTCTC-3' [X = Y = T; X = C, Y = A; X = A, Y = T; X = T, Y = A] to form thermodynamically stable adducts, but thymine bases (T7/T11 or T6/T11) compete kinetically with guanine for binding to 1. The T-bound monoruthenated species eventually convert to diruthenated products via a second step of binding at G or/and to G-bound monoruthenated species through dissociation of the diruthenated adducts. Complex 1 was further shown to bind preferentially to the middle T in a sequence rather than to a T near the terminus and favor coordination to a 5'-T compared to a 3'-T. Interestingly, the T bases in the human telomeric G-quadruplex sequence (5'-AGGGTTAGGGTTAGGGTTAGGG-3') were found to be more competitive both kinetically and thermodynamically with G bases for binding to 1. These results suggest that thymine bases play a unique role in the pathways of ruthenation of DNA by organoruthenium anticancer complexes and illustrate that kinetic studies can provide new insight into the mechanism of action of metallodrugs in addition to study of the structures and functions of the thermodynamically stable end products.

Selective binding of an organoruthenium complex to G‐rich human telomeric sequence by tandem mass spectrometry

“…N7 of guanine (G) is the most affinitive site for ruthenium(II) complexes in nucleosides, nucleotides, single‐ and double‐stranded DNA . Recently, N3 of thymine (T) has also been identified as the kinetically competitive binding site on single‐stranded oligonucleotides (ODNs) . Interestingly, despite the fact that the T‐bound ruthenated single‐stranded DNA was not thermodynamically stable, the T bases in the human telomeric G‐quadruplex DNA were found to be both kinetically and thermodynamically competitive with G bases for binding to ruthenium complexes .…”

“…The interactions between cisplatin and the human telomere G‐quadruplex oligonucleotides (AG 3 (T 2 AG 3 ) 3 and (T 2 AG 3 ) 4 ) have also been explored, demonstrating that all four adenines in the loop of each sequence and four out of the 12 guanines participated in the formation of cisplatinated crosslinks. We have intended to map the binding sites of an organometallic ruthenium complex on a 22‐mer human telomeric sequence by liquid chromatography/mass spectrometry (LC/MS) combined with exonuclease digestion, termed the ladder‐sequencing MS method . However, the ruthenation sites were not ambiguously identified due to the steric hinderance of the large arene ligand to exonuclease‐substrate recognition.…”

Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound

“…1A, right panel) is higher than that of paddlewheel diruthenium species (Barral et al 2007(Barral et al , 2008, we decided to test the reactivity of the compound [Ru 2 Cl 2 (µ-DPhF) 3 (DMSO)] (designated OPW-Ru) (DPhF = N,N ′ -diphenylformamidinate) toward RNA. Numerous ruthenium compounds have been designed to interact with nucleic acid such as mononuclear ruthenium complexes with labile ligands (Busto et al 2013;Wu et al 2013;Adhireksan et al 2014) or tris(chelate)ruthenium(II) compounds (Song et al 2012;Li et al 2015). The existence of labile ligands in the first type of compounds allows establishing direct ruthenium-nucleic acid bonds; the coordination mode implies bond angles of 90°.…”

From Traditional Drug Design to Catalytic Metallodrugs: A Brief History of the Use of Metals in Medicine

“…The focus of this review, following a historical perspective, is on actual, or potential, metal-based drugs that promote therapeutic activity through direct metal-centered binding or reactivity. Other approaches that employ outer sphere contacts of coordination complexes or reactivity toward ill-defined cellular targets are not included for reasons of space limitations, although interested readers are directed to other informative reviews and articles [13][14][15][16][17][18][19][20].…”

“…Their effectiveness and contributions to human health are undeniable but there is room for improvement in specificity in order to achieve lower toxicity. Resistance to cisplatin is also a major hurdle to overcome and novel approaches to treating cisplatin-resistance are needed, such as the use of gold(III) porphyrin complexes [17], as well as iridium and ruthenium compounds [16,20]. Multiple side reactions for platinum complexes, and the fact that the drug is irreversibly consumed by its mode of action, lead to a requirement for high doses, and targeted approaches are also being explored [14,19].…”