Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM

Since the design of metal complexes with better biological activities is important, herein a new palladium(II) complex bearing en and acac (en and acac stand for ethylenediamine and acetylacetonato, respectively) as its ligands, [Pd(en)(acac)]NO3 complex, was synthesized and fully characterized. Quantum chemical computations of the palladium(II) complex were done via DFT/B3LYP method. Cytotoxicity activity of the new compound on leukemia cell line (K562) was assessed via MTT method. The findings indicated that the metal complex has remarkable cytotoxic effect than cisplatin. OSIRIS DataWarrior software was employed to calculate in-silico physicochemical and toxicity parameters of the synthesized complex which rendered significant results. To comprehend the interaction type of new metal compound with macromolecules, the in depth investigation of interaction of mentioned complex with CT-DNA and BSA was accomplished by fluorescence, UV-Visible absorption spectroscopy, viscosity measurement, gel electrophoresis, FRET analysis and circular dichroism (CD) spectroscopy. On the other hand, computational molecular docking was carried out and the obtained data demonstrated that H-bond and van der Waals forces are the dominant forces for the binding of the compound to the mentioned biomolecules. Molecular dynamics simulation was also done and confirmed the stability of best docked pose of palladium(II) complex inside DNA or BSA over the time and in presence of water solvent. Also, Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) methodology based on the hybridization of quantum mechanics and molecular mechanics (QM/MM) methodology was accomplished to inquire about binding of Pd(II) complex with DNA or BSA.HIGHLIGHTSNew biologically active Pd(II) complex was synthesized and characterized.The in silico studies of the designed complex and its ligands were accomplished by OSIRIS DataWarrior softwareInteraction with CT-DNA and BSA was assessed by various spectroscopic methods.Molecular docking simulation supported the interaction with both macromolecules.Based on ONIOM analysis, the structures of the complex and biomolecules are altered after binding. Communicated by Ramaswamy H. Sarma.

Novel Benzimidazole Derived Imine Ligand and Its Co(III) and Cu(II) Complexes as Anticancer Agents: Chemical Synthesis, DFT Studies, In Vitro and In Vivo Biological Investigations

The emerging interest in the field of coordination chemistry and their biological applications has created a novel impact in the field of chemical biology. With this motivation, in this work we have synthesized a novel benzimidazole derived imine ligand, 2-((E)-((1H-benzo[d]-2-yl)methylimino)methyl)-4-fluorophenol (HBMF) and its Co(III) and Cu(II) complexes. The metal complexes (C1-C4) were synthesized in 2:1 (HBMF: metal ion) and 1:1:1 (HBMF: metal ion: 1,10-phen) ratios. Structural elucidations of all the synthesized compounds were performed using FT-IR, UV-Visible, NMR, Mass spectroscopy and elemental analysis techniques. A combination of first principles calculations and molecular dynamics simulations was applied to computationally investigate the structural, reactive, and spectroscopic properties of the newly synthesized HBMF ligand and its complexes with copper and cobalt metal ions. Quantum-mechanical calculations in this study were based on the density functional theory (DFT), while molecular dynamics (MD) simulations were based on the OPLS4 force field. The DFT calculations were used to obtain the reactive and spectroscopic properties of the ligand and its complexes, while molecular dynamics (MD) simulations were used to address the ligand's reactivity with water. Further, the in vitro anti-proliferative activity of the compounds was tested against the A549, Ehrlich-Lettre ascites carcinoma (EAC), SIHA and NIH3T3 cell lines. The biological results depicted that the compound C4, with molecular formula C₂₇H₂₃Cl₂CoFN₅O₃ exhibited profound anti-proliferative activity against the EAC cell line with a significant IC₅₀ value of 10 µm when compared to its parent ligand and other remaining metal complexes under study. Various assays of hematological parameters (alkaline phosphate, creatinine, urea, RBC and WBC) were performed, and significant results were obtained from the experiments. Furthermore, the effect of C4 on neovascularization was evaluated by stimulating the angiogenesis with rVEGF₁₆₅, which was compared with non-tumor models. The EAC cells were cultured in vivo and administrated with 50 and 75 mg/kg of two doses and tumor parameters were evaluated.

Half-Sandwich Cyclometalated RhIII Complexes Bearing Thiolate Ligands: Biomolecular Interactions and In Vitro and In Vivo Evaluations

A class of cyclometalated RhIII complexes [Cp*Rh(ppy)(SR)] bearing thiolate ligands, Cp* = pentamethylcyclopentadienyl, ppy = 2-phenylpyridinate, and R = pyridyl (Spy, 2), pyrimidyl (SpyN, 3), benzimidazolyl (Sbi, 4), and benzothiazolyl (Sbt, 5), were produced and identified by means of spectroscopic methods. The in vitro cytotoxicity of the RhIII compounds in three different human mortal cancerous cell lines (ovarian, SKOV3; breast, MCF-7; lung, A549) and a normal lung (MRC-5) cell line were evaluated, indicating the selectivity of these cyclometalated RhIII complexes to cancer cells. Complex 5, selected for in vivo experiment, has shown an effective inhibition of tumor growth in SKOV3 xenograft mouse model relative to control (p-values < 0.05 and < 0.01). Importantly, the outcomes of H&E (hematoxylin and eosin) staining and hematological analysis revealed negligible toxicity of 5 compared to cisplatin on a functioning of the main organs of mouse. Molecular docking, UV-vis, and emission spectroscopies (fluorescence, 3D fluorescence, synchronous) techniques were carried out on 1-5 to peruse the mechanism of the anticancer activities of these complexes. The obtained data help to manifest the binding affinity between the rhodium compounds and calf thymus DNA (CT-DNA) through the interaction by DNA minor groove and moderate binding affinity with bovine serum albumin (BSA), particularly with the cavity in the subdomain IIA. It can be concluded that the Rh-thiolate complexes are highly promising leads for the development of novel effective DNA-targeted anticancer drugs.

Five new complexes with deferiprone and N,N-donor ligands: evaluation of cytotoxicity against breast cancer MCF-7 cell line and HSA-binding determination

In this study, five new complexes containing deferiprone (dfp) and N,N-donor ligands [bipyridine (bpy), 1,10-phenanthroline (phen) and ethylenediamine (en)] were synthesized: [Fe(dfp)₂(bpy)](PF₆) (1), [Fe(dfp)₂(phen)](PF₆) (2), [Cu₂(dfp)₂(bpy)₂](PF₆)₂ (3), [Ga(dfp)₂(bpy)](PF₆) (4), and [Fe(dfp)₂(en)](PF₆) (5). Characterization of these complexes was carried out through elemental analysis and FT-IR, and single-crystal X-ray crystallography was used to determine their structures. Whilst the polyhedron has a distorted octahedral geometry in 1, 2, 4, and 5, it adopts a distorted square-pyramidal geometry in 3. Interaction of these compounds with human serum albumin (HSA) has been investigated through electronic absorption and fluorescence titration techniques. Emission quenching was performed separately for each complex at three different temperatures and thermodynamic parameters were calculated using binding constants to better understand the power of different binding forces with the HSA. Results demonstrated that compounds interact strongly with the HSA with a static quenching mechanism. Our evaluation of the cytotoxicity of complexes against the breast cancer MCF-7 cell line showed that complex 2 presents a better cytotoxicity than the standard cis-Pt. Finally, using the AutoDock 4.2 program, simulations to analyze the mechanism of complex-HSA interactions and their binding mode were carried out. Results showed that the best binding mode is located in subdomain IB for 1, 2, and 4, in I/II for 3, and in IA/IIA for 5. Communicated by Ramaswamy H. Sarma.

K, Bodke YD, Malojirao VH, T. R. RN, Kandagalla S, B. T. P. Synthesis, characterization and tumor inhibitory activity of a novel Pd(ii) complex derived from methanethiol-bridged (2-((1H-benzo[d]imidazol-2-yl)methylthio)-1H-benzo[d]imidazol-6-yl)(phenyl)methanone

This manuscript demonstrates the synthesis and tumor inhibitory activity of (2-((1H-benzo[d]imidazol-2-yl)methylthio)-1H-benzo[d]imidazol-6-yl)(phenyl)methanone and its Pd(ii) complex.

A saccharinate-bridged palladacyclic dimer with a Pd–Pd bond: experimental and molecular docking studies of the interaction with DNA and BSA and in vitro cytotoxicity against human cancer cell lines

The synthesis, characterization and biological activities of a saccharinate-bridged palladacyclic dimer are reported in this work.

Do the fragments from decomposed ZIF-8 greatly affect some of the intramolecular proton-transfer of thymine? A quantum chemical study

The intramolecular proton-transfer processes of thymine were investigated by the density functional theory method. It is shown that the mutation from keto (T) to enol (T′) form is affected by zeolitic imidazolate framework-8 (ZIF-8) fragments such as single 2-methylimidazole neutral crystals (M), and negatively charged 2-methylimidazole ligands (M⁻). Results show that with the number (n) of water (w) molecules that assist proton-transfer increasing from 1 to 4, the order of the tautomeric energy barriers (in kcal mol⁻¹) is T-2w (16.3) < T-1w (17.6) < T-3w (17.8) < T-4w (20.5). In the presence of M, the order of energy barrier is MT-2w (16.6) < MT-1w (17.7) < MT-3w (18.9) < MT-4w (20.8). M⁻ has a catalysis effect on the energy barrier and the order is M⁻T-2w (14.4) < M⁻T-3w (15.2) < M⁻T-1w (16.3) < M⁻T-4w (16.8). The attachment of the M⁻ fragment slightly promotes the proton-transfer processes in some instances. The characterization of the proton-transfer processes is helpful to understand the genotoxicity of ZIF-8 during drug delivery applications.

Investigations on whether fragments from decomposed ZIF-8 would affect the intramolecular proton-transfer of thymine by DFT modeling.

The influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine: a quantum chemical study

The influence of isolated and penta-hydrated Zn²⁺ on some of the intramolecular proton-transfer processes of thymine is investigated by DFT modeling.

A water-soluble Pd(ii) complex with a terpyridine ligand: experimental and molecular modeling studies of the interaction with DNA and BSA; and in vitro cytotoxicity investigations against five human cancer cell lines

[Pd(4-OHPh-tpy)Cl]Cl was prepared. The complex interacts with DNA via a combination of covalent, intercalation, and hydrogen bonding interactions.