Binding of Antitumor Ruthenium Complexes to DNA and Proteins: A Theoretical Approach

Pharmacological assessment of Ru(II) complex with GidA protein- A novel topoisomerase II inhibitor towards cancer therapeutics

The interactions of ruthenium(II) complex with Glucose inhibited division protein A (GidA protein) was studied through various spectroscopic techniques with the ultimate goal of preparing adducts with good selectivity for cancer cells. In all the cases, formation of a tight metal-protein conjugate was observed. The influence of pH, reducing agents and chelators on the formation of adduct was analysed by UV- visible spectroscopy. While there was no effect on the addition of sodium ascorbate, some alterations on some selected bands were seen on the UV-visible spectra on the addition of EDTA. The adduct was stable in the pH range of 5-8. Addition of ruthenium(II) complex effectively quenched the intrinsic fluorescence of GidA and it occurred through static quenching. The effect of ruthenium(II) complex on the conformation of GidA has been examined by analyzing CD spectrum. Though, there was some conformational changes observed in the presence of ruthenium(II) complex, α- helix in the secondary structure of GidA retained its identity. Molecular docking of ruthenium(II) complex with GidA also indicated that GidA docks through hydrophobic interaction. The stable semisynthetic complex (ruthenium(II) complex with GidA) was checked for topoisomerase II inhibition. Relaxation and decatenation assay proved topoisomerase II inhibition of semisynthetic complex.Communicated by Ramaswamy H. Sarma.

Ruthenium Complexes: An Alternative to Platinum Drugs in Colorectal Cancer Treatment

Colorectal cancer (CRC) is one of the intimidating causes of death around the world. CRC originated from mutations of tumor suppressor genes, proto-oncogenes and DNA repair genes. Though platinum (Pt)-based anticancer drugs have been widely used in the treatment of cancer, their toxicity and CRC cells' resistance to Pt drugs has piqued interest in the search for alternative metal-based drugs. Ruthenium (Ru)-based compounds displayed promising anticancer activity due to their unique chemical properties. Ru-complexes are reported to exert their anticancer activities in CRC cells by regulating different cell signaling pathways that are either directly or indirectly associated with cell growth, division, proliferation, and migration. Additionally, some Ru-based drug candidates showed higher potency compared to commercially available Pt-based anticancer drugs in CRC cell line models. Meanwhile Ru nanoparticles coupled with photosensitizers or anticancer agents have also shown theranostic potential towards CRC. Ru-nanoformulations improve drug efficacy, targeted drug delivery, immune activation, and biocompatibility, and therefore may be capable of overcoming some of the existing chemotherapeutic limitations. Among the potential Ru-based compounds, only Ru (III)-based drug NKP-1339 has undergone phase-Ib clinical trials in CRC treatment.

Anti-adhesive action of novel ruthenium(II) chlorophenyl terpyridine complexes with a high affinity for double-stranded DNA: in vitro and in silico

Interactions of three Ru(II) chlorophenyl terpyridine complexes: [Ru(Cl-Ph-tpy)(en)Cl]Cl (1), [Ru(Cl-Ph-tpy)(dach)Cl]Cl (2) and [Ru(Cl-Ph-tpy)(bpy)Cl]Cl (3) (Cl-Ph-tpy = 4'-(4-chlorophenyl)-2,2':6',2''-terpyridine, en = 1,2-diaminoethane, dach = 1,2-diaminocyclohexane, bpy = 2,2'-bipyridine) with human serum albumin (HSA), calf thymus DNA and a double-helical oligonucleotide d(CGCGAATTCGCG)₂ (1BNA) were examined. Fluorescence emission studies were used to assess the interactions of complexes with HSA, which were of moderate strength for 1 and 2. Molecular docking allowed us to predict mostly π-π stacking and van der Waals interactions between the complexes and the protein. We suggest that the complexes bind to a novel site on HSA, which is different from its druggable sites I, II or III. We suggest a partial intercalation of complexes through the minor groove as a possible mode of interaction with double-helical DNA. Finally, when applied to normal extravillous cell line HTR8/SVneo and JAr choriocarcinoma cell line, complexes 1 and 2 exerted anti-adhesive properties at very low doses, whereas complex 3 had a negligible effect. The obtained results are completion of our studies of Ru(II) terpyridyl complexes that carry N-N ancillary ligands. We suggest a new research direction towards studying the cellular effects of Ru(II) polypyridyl compounds.

Reactivity of Gold(I) Monocarbene Complexes with Protein Targets: A Theoretical Study

Neutral N–heterocyclic carbene gold(I) compounds such as IMeAuCl are widely used both in homogeneous catalysis and, more recently, in medicinal chemistry as promising antitumor agents. In order to shed light on their reactivity with protein side chains, we have carried out density functional theory (DFT) calculations on the thermodynamics and kinetics of their reactions with water and various nucleophiles as a model of plausible protein binding sites such as arginine, aspartic acid, asparagine, cysteine, glutamic acid, glutamine, histidine, lysine, methionine, selenocysteine, and the N-terminal group. In agreement with recent experimental data, our results suggest that IMeAuCl easily interacts with all considered biological targets before being hydrated—unless sterically prevented—and allows the establishment of an order of thermodynamic stability and of kinetic reactivity for its binding to protein residues.

Computational Approach to Unravel the Role of Hydrogen Bonding in the Interaction of NAMI-A with DNA Nucleobases and Nucleotides

Density functional theory method in combination with a continuum solvation model is used to understand the role of hydrogen bonding in the interactions of tertiary nitrogen centers of guanine and adenine with monoaqua and diaqua NAMI-A. In the case of adenine, the interaction of N3 with monoaqua NAMI-A is preferred over that of N7 and N1 whereas, N7 site is the most preferred site over N3 and N1 in the diaqua ruthenium-adenine interaction. In the monoaqua and diaqua NAMI-A-guanine interactions, the N7 site is the most preferred site over the N3 site. Here, the strength and number of H-bonds play important roles in stabilizing intermediates and transition states involved in the interaction of NAMI-A and purine bases. Atoms in molecules and Becke surface analysis confirm that the interactions between monoaqua and diaqua NAMI-A with the base pairs of GC and AT dinucleotides leads to the structural deformation in the geometry of the base pairs of dinucleotides. The diaqua NAMI-A adducts induce more disruption in the base pairs as compared to monoaqua NAMI-A adducts. which suggests that diaqua NAMI-A could be a better anticancer agent than monoaqua NAMI-A. This study can be extended to envisage the potential applications of computational studies in the development of new drugs and targeted drug delivery systems.

Ru(II) Compounds: Next-Generation Anticancer Metallotherapeutics?

Metal based therapeutics are a precious class of drugs in oncology research that include examples of theranostic drugs, which are active in both diagnostic, specifically imaging, and therapeutics applications. Ruthenium compounds have shown selective bioactivity and the ability to overcome the resistance that platinum-based therapeutics face, making them effective oncotherapeutic competitors in rational drug invention approaches. The development of antineoplastic ruthenium therapeutics is of particular interest because ruthenium containing complexes NAMI-A, KP1019, and KP1339 entered clinical trials and DW1/2 is in preclinical levels. The very robust, conformationally rigid organometallic Ru(II) compound DW1/2 is a protein kinase inhibitor and presents new Ru(II) compound designs as anticancer agents. Over the recent years, numerous strategies have been used to encapsulate Ru(II) derived compounds in a nanomaterial system, improving their targeting and delivery into neoplastic cells. A new photodynamic therapy based Ru(II) therapeutic, TLD-1433, has also entered clinical trials. Ru(II)-based compounds can also be photosensitizers for photodynamic therapy, which has proven to be an effective new, alternative, and noninvasive oncotherapy modality.

Mechanisms of reactions of Ru(iii)-based drug NAMI-A and its aquated products with DNA purine bases: a DFT study

The mechanism of reaction of NAMI-A with guanine has been investigated theoretically using density functional theory.

Interactions of the aquated forms of ruthenium(iii) anticancer drugs with protein: a detailed molecular docking and QM/MM investigation

The interaction of monoaqua and diaqua ruthenium complexes which are formed after intracellular aquation of their respective complexes with human serum albumin (HSA) has been computationally investigated by molecular docking and two layer QM/MM hybrid methods.

In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines

Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.

Photodissociation of a ruthenium(II) arene complex and its subsequent interactions with biomolecules: a density functional theory study

The piano-stool Ru(II) arene complex [(η⁶-benz)Ru(bpm)(py)]²⁺ (benz = benzene, bpm = 2,2'-bipyrimidine, and py = pyridine), which is conventionally nonlabile (on a timescale and under conditions relevant for biological reactivity), can be activated by visible light to selectively photodissociate the monodentate ligand (py). In the present study, the aquation and binding of the photocontrolled ruthenium(II) arene complex [(η⁶-benz)Ru(bpm)(py)]²⁺ to various biomolecules are studied by density functional theory (DFT) and time-dependent DFT (TDDFT). Potential energy curves (PECs) calculated for the Ru-N (py) bonds in [(η⁶-benz)Ru(bpm)(py)]²⁺ in the singlet and triplet state give useful insights into the photodissociation mechanism of py. The binding energies of the various biomolecules are calculated, which allows the order of binding affinities among the considered nuleic-acid- or protein-binding sites to be discerned. The kinetics for the replacement of water in the aqua complex with biomolecules is also considered, and the results demonstrate that guanine is superior to other biomolecules in terms of coordinating with the Ru(II) aqua adduct, which is in reasonable agreement with experimental observations.

Rhenium(IV) compounds inducing apoptosis in cancer cells

The anticancer properties of a series of mononuclear Re(IV) compounds of formula ReCl(4)L (where L is bpy = 2,2'-bipyridine; bpym = 2,2'-bipyrimidine; dmbpy = 4,4'-dimethyl-2,2'-bipyridine; phen = 1,10-phenanthroline) were investigated for the first time. All compounds displayed potent in vitro antiproliferative activity against selected cancer cells.

Lipid based nanovectors containing ruthenium complexes: a potential route in cancer therapy

Ruthenium complexes offer new perspectives in cancer therapy; towards this aim we have synthesized a new amphiphilic unimer able to coordinate ruthenium complexes and to form liposomes.