DFT Protocol for EPR Prediction of Paramagnetic Cu(II) Complexes and Application to Protein Binding Sites

Exploiting the potential of rivastigmine-melatonin derivatives as multitarget metal-modulating drugs for neurodegenerative diseases

The multifaceted nature of the neurodegenerative diseases, as Alzheimer's disease (AD) and Parkinson's disease (PD) with several interconnected etiologies, and the absence of effective drugs, led herein to the development and study of a series of multi-target directed ligands (MTDLs). The developed RIV-IND hybrids, derived from the conjugation of an approved anti-AD drug, rivastigmine (RIV), with melatonin analogues, namely indole (IND) derivatives, revealed multifunctional properties, by associating the cholinesterase inhibition of the RIV drug with antioxidant activity, biometal (Cu(II), Zn(II), Fe(III)) chelation properties, inhibition of amyloid-β (Aβ) aggregation (self- and Cu-induced) and of monoamine oxidases (MAOs), as well as neuroprotection capacity in cell models of AD and PD. In particular, two hybrids with hydroxyl-substituted indoles (5a2 and 5a3) could be promising multifunctional compounds that inspire further development of novel anti-neurodegenerative drugs.

Interaction with CT-DNA and in vitro cytotoxicity of two new copper(II)-based potential drugs derived from octanoic hydrazide ligands

Two copper(II) complexes [Cu(Hpmoh)(NO3)(NCS)] (1) and [Cu(peoh)(N3)]2 (2) were designed and synthesized by reaction of Cu(NO3)2·3H2O with hydrazone Schiff base ligands,abbreviated with Hpmoh and Hpeoh. Hpmoh and Hpeoh were prepared by condensation reaction of octanoic hydrazide with pyridine-2-carboxyaldehyde and 2-acetylpyridine, respectively. Complexes 1 and 2 were characterized using different analytical techniques such as FT-IR, UV-Vis, IR, EPR and single X-ray diffraction (XRD) analyses as well as computational methods (DFT). The XRD of 1 and 2 shows a mononuclear or a dinuclear structure with the copper(II) centre adopting a slightly distorted square pyramidal geometry. In water-containing solution and in DMSO, 1 and 2 undergo a partial transformation with formation of [Cu(Hpmoh)(NO3)(NCS)] (1) and [Cu(Hpmoh)(NO3)(H2O/DMSO)] (1a) in one system and [Cu(peoh)(N3)] (2a) in the other one, as supported by DFT calculations. Docking simulations confirmed that the intercalation is the preferred binding mode with DNA for 1, 1a and 2a, but suggested that the minor groove binding is also possible. A significant fluorescence quenching of the DNA-ethidium bromide conjugate was observed upon the addition of complexes 1 and 2 with a quenching constant around 104 M-1 s-1. Finally, both 1 and 2 were examined for anti-cancer activity using MDA-MB-231 (human breast adenocarcinoma) and A375 (malignant melanoma) cell lines through in vitro MTT assay which suggest comparable cancer cell killing efficacy, with the higher effectiveness of 2 due to the dissociation into two [Cu(peoh)(N3)] units.

Experimental and Computational Studies on the Interaction of DNA with Hesperetin Schiff Base CuII Complexes

The interactions with calf thymus DNA (CT-DNA) of three Schiff bases formed by the condensation of hesperetin with benzohydrazide (HHSB or L1H3), isoniazid (HIN or L2H3), or thiosemicarbazide (HTSC or L3H3) and their CuII complexes (CuHHSB, CuHIN, and CuHTSC with the general formula [CuLnH2(AcO)]) were evaluated in aqueous solution both experimentally and theoretically. UV-Vis studies indicate that the ligands and complexes exhibit hypochromism, which suggests helical ordering in the DNA helix. The intrinsic binding constants (Kb) of the Cu compounds with CT-DNA, in the range (2.3-9.2) × 106, from CuHTSC to CuHHSB, were higher than other copper-based potential drugs, suggesting that π-π stacking interaction due to the presence of the aromatic rings favors the binding. Thiazole orange (TO) assays confirmed that ligands and Cu complexes displace TO from the DNA binding site, quenching the fluorescence emission. DFT calculations allow for an assessment of the equilibrium between [Cu(LnH2)(AcO)] and [Cu(LnH2)(H2O)]+, the tautomer that binds CuII, amido (am) and not imido (im), and the coordination mode of HTSC (O-, N, S), instead of (O-, N, NH2). The docking studies indicate that the intercalative is preferred over the minor groove binding to CT-DNA with the order [Cu(L1H2am)(AcO)] > [Cu(L2H2am)(AcO)] ≈ TO ≈ L1H3 > [Cu(L3H2am)(AcO)], in line with the experimental Kb constants, obtained from the UV-Vis spectroscopy. Moreover, dockings predict that the binding strength of [Cu(L1H2am)(AcO)] is larger than [Cu(L1H2am)(H2O)]+. Overall, the results suggest that when different enantiomers, tautomers, and donor sets are possible for a metal complex, a computational approach should be recommended to predict the type and strength of binding to DNA and, in general, to macromolecules.

Exploring the Limits of Ligand Rigidification in Transition Metal Complexes with Mono-N-Functionalized Pyclen Derivatives

We report the synthesis of a new family of side-bridged pyclen ligands. The incorporation of an ethylene bridge between two adjacent nitrogen atoms was reached from the pyclen-oxalate precursor described previously. Three new side-bridged pyclen macrocycles, Hsb-3-pc1a, sb-3-pc1py, and Hsb-3-pc1pa, were obtained with the aim to assess their coordination properties toward Cu2+ and Zn2+ ions. We also prepared their nonreinforced analogues H3-pc1a, 3-pc1py, and H3-pc1pa as comparative benchmarks. The two series of ligands were characterized and their coordination properties were investigated in detail. The Zn2+ and Cu2+ complexes with the nonside-bridged series H3-pc1a, 3-pc1py, and H3-pc1pa were successfully isolated and their structures were assessed by X-ray diffraction studies. In the case of the side-bridged family, the synthesis of the complexes was far more difficult and, in some cases, unsuccessful. The results of our studies demonstrate that this difficulty is related to the extreme stiffening and basicity of such side-bridged pyclens.

Structure and Flexibility of Copper-Modified DNA G-Quadruplexes Investigated by 19 F ENDOR Experiments at 34 GHz

DNA G-quadruplexes (GQs) are of great interest due to their involvement in crucial biological processes such as telomerase maintenance and gene expression. Furthermore, they are reported as catalytically active DNAzymes and building blocks in bio-nanotechnology. GQs exhibit remarkable structural diversity and conformational heterogeneity, necessitating precise and reliable tools to unravel their structure-function relationships. Here, we present insights into the structure and conformational flexibility of a unimolecular GQ with high spatial resolution via electron-nuclear double resonance (ENDOR) experiments combined with Cu(II) and fluorine labeling. These findings showcase the successful application of the 19 F-ENDOR methodology at 34 GHz, overcoming the limitations posed by the complexity and scarcity of higher-frequency spectrometers. Importantly, our approach retains both sensitivity and orientational resolution. This integrated study not only enhances our understanding of GQs but also expands the methodological toolbox for studying other macromolecules.

Copper(II) Affects the Biochemical Behavior of Proinsulin C-peptide by Forming Ternary Complexes with Serum Albumin

Peptide hormones are essential signaling molecules with therapeutic importance. Identifying regulatory factors that drive their activity gives important insight into their mode of action and clinical development. In this work, we demonstrate the combined impact of Cu(II) and the serum protein albumin on the activity of C-peptide, a 31-mer peptide derived from the same prohormone as insulin. C-peptide exhibits beneficial effects, particularly in diabetic patients, but its clinical use has been hampered by a lack of mechanistic understanding. We show that Cu(II) mediates the formation of ternary complexes between albumin and C-peptide and that the resulting species depend on the order of addition. These ternary complexes notably alter peptide activity, showing differences from the peptide or Cu(II)/peptide complexes alone in redox protection as well as in cellular internalization of the peptide. In standard clinical immunoassays for measuring C-peptide levels, the complexes inflate the quantitation of the peptide, suggesting that such adducts may affect biomarker quantitation. Altogether, our work points to the potential relevance of Cu(II)-linked C-peptide/albumin complexes in the peptide's mechanism of action and application as a biomarker.

Fluorescent Mechanism of a Highly Selective Probe for Copper(II) Detection: A Theoretical Study

A highly selective probe for copper(II) detection based on the dansyl group was theoretically studied by means of (time-dependent) density functional theory. The calculated results indicated that the oscillator strength of the fluorescent process for the probe molecule is considerably large, but the counterpart of its copper(II) complex is nearly zero; therefore, the predicted radiative rate k_r of the probe is several orders of magnitude larger than that of its complex; however, the predicted internal conversion rate k_ic of both the probe and its complex is of the same order of magnitude. In addition, the simulated intersystem crossing rate k_isc of the complex is much greater than that of the probe due to the effect of heavy atom from the copper atom in the complex. Based on the above information, the calculated fluorescence quantum yield of the probe is 0.16% and that of the complex becomes 10^-6%, which implies that the first excited state of the probe is bright state and that of the complex is dark state. For the complex, the hole-electron pair analysis indicates that the process of S₀ → S₁ belongs to metal-to-ligand charge transfer; its density-of-state diagram visually illustrates that the highest occupied molecular orbital (HOMO) contains the ingredient of the s orbital from the copper atom, which decreases the frontier orbital energy level and the overlap integral of HOMO and LUMO.

A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme

A novel hybrid protein composed of a superoxide dismutase-active Cu(II) complex (CuST) and lysozyme (CuST@lysozyme) was prepared. The results of the spectroscopic and electrochemical analyses confirmed that CuST binds to lysozyme. We determined the crystal structure of CuST@lysozyme at 0.92 Å resolution, which revealed that the His15 imidazole group of lysozyme binds to the Cu(II) center of CuST in the equatorial position. In addition, CuST was fixed in position by the weak axial coordination of the Thr89 hydroxyl group and the hydrogen bond between the guanidinium group of the Arg14 residue and the hydroxyl group of CuST. Furthermore, the combination of CuST with lysozyme did not decrease the superoxide dismutase activity of CuST. Based on the spectral, electrochemical, structural studies, and quantum chemical calculations, an O₂^- disproportionation mechanism catalyzed by CuST@lysozyme is proposed.

Triazole based Schiff bases and their Oxovanadium(IV) complexes: Synthesis, characterization, antibacterial assay, and computational assessments

The synthesis and characterization of two new Schiff base ligands containing 1,2,4-triazole moieties and their oxovanadium(IV) complexes have been reported. The ligands and their complexes were studied by ultraviolet-visible (UV-Vis), Fourier transform infrared (FTIR), proton nuclear magnetic resonance (¹H NMR), electron paramagnetic resonance (EPR), X-ray diffraction (XRD), conductivity measurement, cyclic voltammetry (CV), and elemental analyses. The molar conductance of oxovanadium(IV) complexes were found to be relatively low, depicting their non-electrolytic nature. The XRD patterns reveal the size of particles to be 47.53 nm and 26.28 nm for the two complexes in the monoclinic crystal system. The molecular structures, geometrical parameters, chemical reactivity, stability, and frontier molecular orbital pictures were determined by density functional theory (DFT) calculations. The theoretical vibrational frequencies and EPR g-factors (1.98) were found to correlate well with the experimental values. A distorted square pyramidal geometry with C₂ symmetry of the complexes has been proposed from experimental and theoretical results in a synergistic manner. The antimicrobial sensitivity of the ligands and their metal complexes assayed in vitro against four bacterial pathogens viz. Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Salmonella Typhi showed that the oxovanadium(IV) complexes are slightly stronger antibacterial agents than their corresponding Schiff base precursors. The binding affinities obtained from the molecular docking calculations with the receptor proteins of bacterial strains (2EUG, 3UWZ, 4GVF, and 4JVD) showed that the Schiff bases and their oxovanadium(IV) complexes have considerable capacity inferring activeness for effective inhibition. The molecular dynamics simulation of a protein-ligand (4JVD-HL₂) complex with the best binding affinity of -12.8 kcal/mol for 100 ns showed acceptable stability of the docked pose and binding free energy of -15.17 ± 2.29 kcal/mol from molecular mechanics-generalized Born surface area (MM-GBSA) calculations indicated spontaneity of the reaction. The outcome of the research shows the complementary role of computational methods in material characterization and provides an interesting avenue to pursue for exploring new triazole based Schiff's bases and its vanadium compounds for better properties.

Investigations on the local structure and the spin Hamiltonian parameters for Cu2+ in xCuO-(68-x)V2 O5 -32TeO2 glasses

The defect structure, spin Hamiltonian parameters (SHPs: anisotropic g factors g ‖ and g ⊥ and the hyperfine structure constants A ‖ and A ⊥ ), and their compositional dependence of Cu 2 + in x CuO - ( 68 - x ) V 2 O 5 - 32 TeO 2 ( x = 5, 10, 20, 30 mol%) glasses are quantitatively analyzed by using the higher-order perturbation formula of octahedral complex with tetrahedral elongation distortion. Due to the Jahn-Teller effect, the [ CuO 6 ] 10 - group is subjected to tetragonal elongation distortion of varying degrees. D q , N , ρ , κ , and H show nonlinear changes with the concentrations of Cu 2 + . When x = 10 mol% CuO, the degree of distortion ( ρ ≈ 0 . 1 % ) is the smallest; when x = 30 mol% CuO, the degree of distortion ( ρ ≈ 15 % ) is the largest, which indicates that excessive distortion leads to the appearance of Z -axis oxygen vacancies and the coordination number of copper ions from six to four. The increasing tendency of the evaluated N and H reveals decreasing covalency of the whole glass system. Present theoretical studies would be useful to the explore the structural properties and optical applications of glass with different CuO concentrations.

Refining details of the structural and electronic properties of the CuB site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations

This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the Cu_B catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His³³, His¹³⁷, and His¹³⁹ on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the Cu_B site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the Cu_B center is an essential factor that makes it less efficient than the Cu_C site in the methane oxidation. Therefore, according to the Cu_B site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O₂ molecule prior to its activation must be necessary. This scenario is less likely to occur in the Cu_C center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.

Decoding the Ambiguous Electron Paramagnetic Resonance Signals in the Lytic Polysaccharide Monooxygenase from Photorhabdus luminescens

Understanding the structure and function of lytic polysaccharide monooxygenases (LPMOs), copper enzymes that degrade recalcitrant polysaccharides, requires the reliable atomistic interpretation of electron paramagnetic resonance (EPR) data on the Cu(II) active site. Among various LPMO families, the chitin-active PlAA10 shows an intriguing phenomenology with distinct EPR signals, a major rhombic and a minor axial signal. Here, we combine experimental and computational investigations to uncover the structural identity of these signals. X-band EPR spectra recorded at different pH values demonstrate pH-dependent population inversion: the major rhombic signal at pH 6.5 becomes minor at pH 8.5, where the axial signal dominates. This suggests that a protonation change is involved in the interconversion. Precise structural interpretations are pursued with quantum chemical calculations. Given that accurate calculations of Cu g-tensors remain challenging for quantum chemistry, we first address this problem via a thorough calibration study. This enables us to define a density functional that achieves accurate and reliable prediction of g-tensors, giving confidence in our evaluation of PlAA10 LPMO models. Large models were considered that include all parts of the protein matrix surrounding the Cu site, along with the characteristic second-sphere features of PlAA10. The results uniquely identify the rhombic signal with a five-coordinate Cu ion bearing two water molecules in addition to three N-donor ligands. The axial signal is attributed to a four-coordinate Cu ion where only one of the waters remains bound, as hydroxy. Alternatives that involve decoordination of the histidine brace amino group are unlikely based on energetics and spectroscopy. These results provide a reliable spectroscopy-consistent view on the plasticity of the resting state in PlAA10 LPMO as a foundation for further elucidating structure-property relationships and the formation of catalytically competent species. Our strategy is generally applicable to the study of EPR parameters of mononuclear copper-containing metalloenzymes.

Quantification and Improvement of the Dynamics of Human Serum Albumin and Glycated Human Serum Albumin with Astaxanthin/Astaxanthin-Metal Ion Complexes: Physico-Chemical and Computational Approaches

Glycated human serum albumin (gHSA) undergoes conformational changes and unfolding events caused by free radicals. The glycation process results in a reduced ability of albumin to act as an endogenous scavenger and transporter protein in diabetes mellitus type 2 (T2DM) patients. Astaxanthin (ASX) in native form and complexed with metal ions (Cu²⁺ and Zn²⁺) has been shown to prevent gHSA from experiencing unfolding events. Furthermore, it improves protein stability of gHSA and human serum albumin (HSA) as it is shown through molecular dynamics studies. In this study, the ASX/ASX-metal ion complexes were reacted with both HSA/gHSA and analyzed with electronic paramagnetic resonance (EPR) spectroscopy, rheology and zeta sizer (particle size and zeta potential) analysis, circular dichroism (CD) spectroscopy and UV-Vis spectrophotometer measurements, as well as molecular electrostatic potential (MEP) and molecular docking calculations. The addition of metal ions to ASX improves its ability to act as an antioxidant and both ASX or ASX-metal ion complexes maintain HSA and gHSA stability while performing their functions.

Oxygen Activation by a Copper Complex with Sulfur-Only Coordination Relevant to the Formylglycine Generating Enzyme

Synthesizing hydrosulfido Cu thiolate complexes is quite challenging. In this report, two new and rare hydrosulfido Cu thiolate complexes, [Et₄N]₂[(mnt)Cu-SH] (2, mnt = maleonitrile dithiolene = S₂C₂(CN)₂) and [Et₄N]₃[(mnt)Cu-(μ-SH)-Cu(mnt)] (3), have been synthesized. Coordination sites and O₂ activation by complex 2 resemble the formylglycine generating enzyme (FGE), an enzyme recently crystallographically characterized with sulfur-only coordination around Cu (three thiolate ligands). The function of this enzyme (and complex 2) is surprising because vulnerable thiolates should not be well suited for O₂ activation rationally. Indeed, activation of oxygen by such an all-sulfur-coordinated Cu complex 2 is lacking in the literature. Aerial O₂ (ambient O₂ from the air) activation by complex 2 could proceed through a superoxide radical intermediate and a sulfur radical intermediate detected by resonance Raman (rR) spectroscopy and electron paramagnetic resonance (EPR) spectroscopy, respectively. The chemistry of 2 has been examined by its reactivity, crystal structure, and spectroscopic and cyclic voltammetric analyses. In addition, the results have been complemented with density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations.

EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory

Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the present work, we approach the problem of Cu(II) g-tensor calculations using double-hybrid density functional theory (DHDFT). Using a reference set of 18 structurally and spectroscopically characterized Cu(II) complexes, we evaluate a wide range of modern double-hybrid density functionals (DHDFs) that have not been applied previously to this problem. Our results suggest that the current generation of DHDFs consistently and systematically outperform other computational approaches. The B2GP-PLYP and PBE0-DH functionals are singled out as the best DHDFs on average for the prediction of Cu(II) g-tensors. The performance of the different functionals is discussed and suggestions are made for practical applications and future methodological developments.

Copper(II) Complexes of Pyridine-2,6-dicarboxamide Ligands with High SOD Activity

Copper(II) complexes of pyridine-based ligands functionalized with alanine (PydiAla) and tyrosine (PydiTyr) moieties have been synthesized as novel superoxide dismutase mimics. The complexes were characterized by pH-potentiometric, spectroscopic (UV-vis, circular dichroism, mass spectrometry, electron paramagnetic resonance spectroscopy), computational (DFT), and X-ray diffraction methods. Both ligands form high stability copper(II) complexes via the (Npy,N-,N-) donor set supported by the binding of the carboxylate pendant arms. Although the coordination mode is the same for the two systems, the tyrosine containing counterpart exhibits increased copper(II) binding affinity, which is most likely due to the presence of the aromatic moiety of the side chains. Both copper(II) complexes are capable of binding N-methylimidazole, and the formation of the corresponding ternary species was observed at physiological pH. The binary and ternary copper(II) complexes exhibit high SOD activity. The PydiTyr complex exhibits about 1 order of magnitude higher activity than the PydiAla complex. This is probably due to the presence of the phenolic OH group in the former species, which promotes the binding of the superoxide anion radical to the metal center. The results serve as a basis for designing highly efficient copper(II) mimics for medical and practical applications.

From the Physicochemical Characteristic of Novel Hesperetin Hydrazone to Its In Vitro Antimicrobial Aspects

Microorganisms are able to give rise to biofilm formation on food matrixes and along food industry infrastructures or medical equipment. This growth may be reduced by the application of molecules preventing bacterial adhesion on these surfaces. A new Schiff base ligand, derivative of hesperetin, HABH (2-amino-N'-(2,3-dihydro-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chromen-4-ylidene)benzohydrazide), and its copper complex, CuHABH [CuLH₂(OAc)], were designed, synthesized and analyzed in terms of their structure and physicochemical properties, and tested as antibacterial agents. Their structures both in a solid state and in solution were established using several methods: FT-IR, ¹H NMR, ¹³C NMR, UV-Vis, FAB MS, EPR, ESI-MS and potentiometry. Coordination binding of the copper(II) complex dominating at the physiological pH region in the solution was found to be the same as that detected in the solid state. Furthermore, the interaction between the HABH and CuHABH with calf-thymus DNA (CT-DNA) were investigated. These interactions were tracked by UV-Vis, CD (circular dichroism) and spectrofluorimetry. The results indicate a stronger interaction of the CuHABH with the CT-DNA than the HABH. It can be assumed that the nature of the interactions is of the intercalating type, but in the high concentration range, the complex can bind to the DNA externally to phosphate residues or to a minor/major groove. The prepared compounds possess antibacterial and antibiofilm activities against Gram-positive and Gram-negative bacteria. Their antagonistic activity depends on the factor-strain test system. The glass was selected as a model surface for the experiments on antibiofilm activity. The adhesion of bacterial cells to the glass surface in the presence of the compounds was traced by luminometry and the best antiadhesive action against both bacterial strains was detected for the CuHABH complex. This molecule may play a crucial role in disrupting exopolymers (DNA/proteins) in biofilm formation and can be used to prevent bacterial adhesion especially on glass equipment.

Effects of the halogenido ligands on the Kumada-coupling catalytic activity of [Ni{ t BuN(PPh2)2-κ2P}X2], X = Cl, Br, I, complexes

Novel nickel(ii) complexes bearing ( t butyl)bis(diphenylphosphanyl)amine and different halogenido ligands, [Ni(P,P)X2] = [Ni{ t BuN(PPh2)2-κ2P}X2], (X = Cl, Br, I) are prepared, characterized by IR and NMR spectroscopy, mass spectrometry and X-ray crystallography, and tested as catalysts in the Kumada cross-coupling reaction of model substituted iodobenzenes and p-tolylmagnesium bromide. The data obtained together with DFT calculations indicate that these new catalysts operate in the Ni(i)-Ni(iii) mode. The highest catalytic activity and selectivity are exhibited by [Ni(P,P)Cl2], which is most easily reduced by the used Grignard reagent to the Ni(i) state. This process is much more energy demanding in the case of the bromido and iodido complexes, causing the appearance of the induction period. [Ni(P,P)Cl2] is also very active in the cross-couplings of substrates with iodine atoms sterically shielded by ortho substituents. The data obtained are in good accordance with the described positive effect of the increased electron-releasing power of N-substituents R' on the overall catalytic performance of [Ni{R'N(PPh2)2-κ2P}X2] complexes.

Copper(II) and Zinc(II) Complexation with N Ethylene hydroxycyclams and Consequences on the Macrocyclic Backbone Configuration

We report a series of four cyclams and cross-bridged cyclams, N-functionalized by one hydroxyethyl arm, which may incorporate additional methyl(s) group(s). The Cu(II) and Zn(II) complexes of these ligands were...

Exceptionally fast formation of stable rigidified cross-bridged complexes formed with Cu(II) isotopes for Molecular Imaging

64Cu is considered to be one of the most promising radioisotope in radiotheragnostics (combining therapeutics with diagnostics) because its positron emission is suitable for PET imaging while the combination of...

Incorporation of β-Alanine in Cu(II) ATCUN Peptide Complexes Increases ROS Levels, DNA Cleavage and Antiproliferative Activity

Redox-active Cu(II) complexes are able to form reactive oxygen species (ROS) in the presence of oxygen and reducing agents. Recently, Faller et al. reported that ROS generation by Cu(II) ATCUN complexes is not as high as assumed for decades. High complex stability results in silencing of the Cu(II)/Cu(I) redox cycle and therefore leads to low ROS generation. In this work, we demonstrate that an exchange of the α-amino acid Gly with the β-amino acid β-Ala at position 2 (Gly2→β-Ala2) of the ATCUN motif reinstates ROS production (• OH and H2 O2 ). Potentiometry, cyclic voltammetry, EPR spectroscopy and DFT simulations were utilized to explain the increased ROS generation of these β-Ala2-containing ATCUN complexes. We also observed enhanced oxidative cleavage activity towards plasmid DNA for β-Ala2 compared to the Gly2 complexes. Modifications with positively charged Lys residues increased the DNA affinity through electrostatic interactions as determined by UV/VIS, fluorescence, and CD spectroscopy, and consequently led to a further increase in nuclease activity. A similar trend was observed regarding the cytotoxic activity of the complexes against several human cancer cell lines where β-Ala2 peptide complexes had lower IC50 values compared to Gly2. The higher cytotoxicity could be attributed to an increased cellular uptake as determined by ICP-MS measurements.

Structural and electronic analysis of the octarepeat region of prion protein with four Cu2+ by polarizable MD and QM/MM simulations

Prions have been linked to neurodegenerative diseases that affect various species of mammals including humans. The prion protein, located mainly in neurons, is believed to play the role of metal ion transporter. High levels of copper ions have been related to structural changes. A 32-residue region of the N-terminal domain, known as octarepeat, can bind up to four copper ions. Different coordination modes have been observed and are strongly dependent on Cu2+ concentration. Many theoretical studies carried out so far have focused on studying the coordination modes of a single copper ion. In this work we investigate the octarepeat region coordinated with four copper ions. Molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations using the polarizable AMOEBA force field have been carried out. The polarizable MD simulations starting from a fully extended conformation indicate that the tetra-Cu2+/octarepeat complex forms a globular structure. The globular form is stabilized by interactions between Cu2+ and tryptophan residues resulting in some coordination sites observed to be in close proximity, in agreement with experimental results. Subsequent QM/MM simulations on several snapshots suggests the system is in a high-spin quintet state, with all Cu2+ bearing one single electron, and all unpaired electrons are ferromagnetically coupled. NMR simulations on selected structures provides insights on the chemical shifts of the first shell ligands around the metals with respect to inter-metal distances.

Interaction of the potent antitumoral compounds Casiopeinas® with blood serum and cellular bioligands

Casiopeinas® are among the few Cu^II compounds patented for their antitumor activity, but their mode of action has not been fully elucidated yet. One of them, Cas II-gly, is formed by 4,7-dimethyl-1,10-phenanthroline (Me₂phen) and glycinato (Gly). In blood and cells, Cas II-gly can keep its identity or form mixed species with serum or cytosol bioligands (bL or cL) with composition Cu^II-Me₂phen-bL/cL, Cu^II-Gly-bL/cL, or Cu^II-bL/cL. In this study, the binding of Cas II-gly with low molecular mass bioligands of blood serum (citric, L-lactic acid, and L-histidine) and cytosol (reduced glutathione (GSH), reduced nicotinamide adenine dinucleotide (NADH), adenosine triphosphate (ATP), and l-ascorbic acid) was examined through the application of instrumental (ElectroSpray Ionization-Mass Spectrometry and Electron Paramagnetic Resonance) and computational (Density Functional Theory) methods. The results indicated that mixed species Cu^II-Me₂phen-bL/cL are formed, with the bioligands replacing glycinato. The formation of these adducts may participate in the copper transport toward the target organs and facilitate the cellular uptake or, in constrast, preclude it. In the systems with GSH, NADH and L-ascorbate, a redox reaction occurs with the partial oxidation of cL to the corresponding oxidized form (GSSG, NAD⁺ and dehydroascorbate) which interact with Cu^II. Formed Cu^I ion does not give complexation reactions with reduced or oxidized form of bioligands for its 'soft' character and low affinity for oxygen and nitrogen donors compared to Cu^II. However, Cu^I could promote Fenton-like reactions with production of reactive oxygen species (ROS) related to the antitumor activity of Casiopeinas®.

Complexation of C-Functionalized Cyclams with Copper(II) and Zinc(II): Similarities and Changes When Compared to Parent Cyclam Analogues

Herein, we report a comprehensive coordination study of the previously reported ligands cyclam, CB-cyclam, TMC, DMC, and CB-DMC and of their C-functional analogues, cyclam-E, CB-cyclam-E, TMC-E, DMC-E, and CB-DMC-E. This group of ligands includes cyclam, cross-bridged cyclams, their di- or tetramethylated derivatives, and the analogues bearing an additional hydroxyethyl group on one β-N position of the ring. The Cu(II) and Zn(II) complexes of these macrocycles have been highlighted previously for the biological interest, but the details of their structures in the solid state and in solution remained largely unexplored. In particular, we analyzed the impact that adding noncoordinating N-methyl and C-hydroxyethyl functionalities has in the structures of the complexes. All the Cu(II) and Zn(II) complexes were synthesized and investigated using single crystal X-ray diffraction and NMR, electronic absorption, and EPR spectroscopies, along with DFT studies. Dissociation kinetics experiments in acidic conditions and electrochemical studies were also performed. Special attention was paid to analyze the different configurations present in solution and in the solid state, as well as the impact of the C-appended hydroxyethyl group on the coordination behavior. Various ratios of the trans-I, trans-III, and cis-V configurations have been observed depending on the degree of N-methylation and the presence of the ethylene cross-bridge.

Unraveling the implications of multiple histidine residues in the potent antimicrobial peptide Gaduscidin-1

The development of antimicrobial peptides (AMPs) as potential therapeutics requires resolving the foundational principles behind their structure-activity relationships. The role of histidine residues within AMPs remains a mystery despite the fact that several potent peptides containing this amino acid are being considered for further clinical development. Gaduscidin-1 (Gad-1) is a potent AMP from Atlantic cod fish that has a total of five His residues. Herein, the role of His residues and metal-potentiated activity of Gad-1 was studied. The five His residues contribute to the broad-spectrum activity of Gad-1. We demonstrated that Gad-1 can coordinate two Cu²⁺ ions, one at the N-terminus and one at the C-terminus, where the C-terminal binding site is a novel Cu²⁺ binding motif. High affinity Cu²⁺ binding at both sites was observed using mass spectrometry and isothermal titration calorimetry. Electron paramagnetic resonance was used to determine the coordination environment of the Cu²⁺ ions. Cu²⁺ binding was shown to be responsible for an increase in antimicrobial activity and a new mode of action. Along with the traditional AMP mode of action of pore formation, Gad-1 in the presence of Cu²⁺ (per)oxidizes lipids. Importantly, His3, His11, His17, and His21 were found to be important to lipid (per)oxidation. This insight will help further understand the inclusion and role of His residues in AMPs, the role of the novel C-terminal binding site, and can contribute to the field of designing potent AMPs that bind metal ions to potentiate activity.

Copper(II) N,N,O-Chelating Complexes as Potential Anticancer Agents

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (−H, −Cl, and −Br) have been synthesized and characterized. The experimental and computational data obtained suggest that all three complexes exist in the dimeric form in the solid state and adopt the same conformation. The mass spectrometry and electron paramagnetic resonance results indicate that the dimeric structure coexists with the monomeric form in solution upon solvent (dimethyl sulfoxide and water) coordination. The three synthesized Cu(II) complexes exhibit high potentiality as ROS generators, with the Cu(II)/Cu(I) redox potential inside the biological redox window, and thus being able to biologically undergo Cu(II)/Cu(I) redox cycling. The formation of ROS is one of the most promising reported cell death mechanisms for metal complexes to offer an inherent selectivity to cancer cells. In vitro cytotoxic studies in two different cancer cell lines (HeLa and MCF7) and in a normal fibroblast cell line show promising selective cytotoxicity for cancer cells (IC₅₀ about 25 μM in HeLa cells, which is in the range of cisplatin and improved with respect to carboplatin), hence placing this N,N,O-chelating salphen-like metallic core as a promising scaffold to be explored in the design of future tailor-made Cu(II) cytotoxic compounds.

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (−H, −Cl, and −Br) have been synthesized and characterized. They three exhibit high potentiality as reactive oxygen species (ROS) generators, with the Cu(II)/Cu(I) redox potential inside the biological redox window. In vitro studies in two different cancer cell lines (HeLa and MCF7) and in a normal fibroblast cell line show promising selective cytotoxicity for cancer cells.

Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes

An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.

Comparison of Density Functional and Correlated Wave Function Methods for the Prediction of Cu(II) Hyperfine Coupling Constants

The reliable prediction of Cu(II) hyperfine coupling constants remains a challenge for quantum chemistry. Until recently only density functional theory (DFT) could target this property for systems of realistic size. However, wave function based methods become increasingly applicable. In the present work, we define a large set of Cu(II) complexes with experimentally known hyperfine coupling constants and use it to investigate the performance of modern quantum chemical methods for the prediction of this challenging spectroscopic parameter. DFT methods are evaluated against orbital‐optimized second‐order Møller‐Plesset (OO‐MP2) theory and coupled cluster calculations including singles and doubles excitations, driven by the domain‐based local pair natural orbital approach (DLPNO‐CCSD). Special attention is paid to the definition of a basis set that converges adequately toward the basis set limit for the given property for all methods considered in this study, and a specifically optimized basis set is proposed for this purpose. The results suggest that wave function based methods can supplant but do not outcompete DFT for the calculation of Cu(II) hyperfine coupling constants. Mainstream hybrid functionals such as B3PW91 remain on average the best choice.

Unusual 31P Hyperfine Strain Effects in a Conformationally Flexible Cu(II) Complex Revealed by Two-Dimensional Pulse EPR Spectroscopy

Strain effects on g and metal hyperfine coupling tensors, A, are often manifested in Electron Paramagnetic Resonance (EPR) spectra of transition metal complexes, as a result of their intrinsic and/or solvent-mediated structural variations. Although distributions of these tensors are quite common and well understood in continuous-wave (cw) EPR spectroscopy, reported strain effects on ligand hyperfine coupling constants are rather scarce. Here we explore the case of a conformationally flexible Cu(II) complex, [Cu{Ph₂P(O)NP(O)Ph₂-κ²O,O'}₂], bearing P atoms in its second coordination sphere and exhibiting two structurally distinct CuO₄ coordination spheres, namely a square planar and a tetrahedrally distorted one, as revealed by X-ray crystallography. The Hyperfine Sublevel Correlation (HYSCORE) spectra of this complex exhibit ³¹P correlation ridges that have unusual inverse or so-called "boomerang" shapes and features that cannot be reproduced by standard simulation procedures assuming only one set of magnetic parameters. Our work shows that a distribution of isotropic hyperfine coupling constants (hfc) spanning a range between negative and positive values is necessary in order to describe in detail the unusual shapes of HYSCORE spectra. By employing DFT calculations we show that these hfc correspond to molecules showing variable distortions from square planar to tetrahedral geometry, and we demonstrate that line shape analysis of such HYSCORE spectra provides new insight into the conformation-dependent spectroscopic response of the spin system under investigation.

First-Principles Calculation of Transition Metal Hyperfine Coupling Constants with the Strongly Constrained and Appropriately Normed (SCAN) Density Functional and its Hybrid Variants

Density functional theory (DFT) is used extensively for the first-principles calculation of hyperfine coupling constants in both main-group and transition metal systems. As with many other properties, the performance of DFT for hyperfine coupling constants is of variable quality, particularly for transition metal complexes, because it strongly depends on the nature of the chemical system and the type of approximation to the exchange-correlation functional. Recently, a meta-generalized-gradient approximation (mGGA) functional was proposed that obeys all known exact constraints for such a method, known as the Strongly Constrained and Appropriately Normed (SCAN) functional. In view of its theoretically superior formulation a benchmark set of complexes is used to assess the performance of SCAN for the challenging case of transition metal hyperfine coupling constants. In addition, two global hybrid versions of the functional, SCANh and SCAN0, are described and tested. The values computed with the new functionals are compared with experiment and with those of other DFT approximations. Although the original SCAN and the SCAN-based hybrids may offer improved hyperfine coupling constants for specific systems, no uniform improvement is observed. On the contrary, there are specific cases where the new functionals fail badly due to a flawed description of the underlying electronic structure. Therefore, despite these methodological advances, systematically accurate and system-independent prediction of transition metal hyperfine coupling constants with DFT remains an unmet challenge.

Quantitative prediction of electronic absorption spectra of copper(II)-bioligand systems: Validation and applications

The visible region of the electronic absorption spectra of Cu(II) complexes was studied by time-dependent density functional theory (TD-DFT). The performance of twelve functionals in the prediction of absorption maxima (λ_max) was tested on eleven compounds with different geometry, donors and charge. The ranking of the functionals for λ_max was determined in terms of mean absolute percent deviation (MAPD) and standard deviation (SD) and it is as follows: BHandHLYP > M06 ≫ CAM-B3LYP ≫ MPW1PW91 ~ B1LYP ~ BLYP > HSE06 ~ B3LYP > B3P86 ~ ω-B97x-D ≫ TPSSh ≫ M06-2X (MAPD) and BHandHLYP > M06 ~ HSE06 > ω-B97x-D ~ CAM-B3LYP ~ MPW1PW91 > B1LYP ~ B3LYP > B3P86 > BLYP ≫ TPSSh ≫ M06-2X (SD). With BHandHLYP functional the MAPD is 3.1% and SD is 2.3%, while with M06 the MAPD is 3.7% and SD is 3.7%. The protocol validated in the first step of the study was applied to: i) calculate the number of transitions in the spectra and relate them to the geometry of Cu(II) species; ii) determine the coordination of axial water(s); iii) predict the electronic spectra of the systems where Cu(II) is bound to human serum albumin (HSA) and to the regions 94-97 and 108-112 of prion protein (PrP). The results indicate that the proposed computational protocol allows a successful prediction of the electronic spectra of Cu(II) species and to relate an experimental spectrum to a specific structure.

Conformational Analyses of Physiological Binary and Ternary Copper(II) Complexes with l-Asparagine and l-Histidine; Study of Tridentate Binding of Copper(II) in Aqueous Solution

This study explores the structural properties and energy landscapes of the physiologically important bis(l-asparaginato)copper(II) [Cu(l-Asn)2] and (l-histidinato)(l-asparaginato)copper(II) [Cu(l-His)(l-Asn)]. The conformational analyses in the gas phase and implicitly modeled water medium, and magnetic parameters of electron paramagnetic resonance spectra were attained using density functional theory calculations. The apical CuII coordination and hydrogen bonding were analyzed. Predicted lower-energy structures enabled the confirmation and, for apical bonding, also the refinement of structural proposals from literature. Available experimental results were indecisive regarding the amido-group binding in the CuII equatorial plane in solutions, but the examination of the relative stability of Cu(l-Asn)2 conformers in 30 binding modes confirms the glycine-like mode as the most stable one. Previously reported experimental results for Cu(l-His)(l-Asn) were interpreted for l-His to have a tridentate histamine-like mode. However, the aqueous conformers with l-His in the glycinato mode are also predicted to have low energies, which does not contradict the tridentate l-His binding. The predicted magnetic parameters of conformers with an apical oxygen atom (intramolecular or from a water molecule) can reproduce the experimental data. An extent of conformational flexibility and abundance of l-His-containing ternary copper(II) amino acid complexes under physiological conditions may be related.