Dinuclear Zn(2+) complexes of synthetic heptapeptides as artificial nucleases

Synthesis of metal-binding amino acids

The ability for amino acid residues to bind metals underpins the functions of metalloproteins to conduct a plethora of critical processes in living organisms as well as unnatural applications in the fields of catalysis, sensing and medicinal chemistry. The capability to access metal-binding peptides heavily relies on the ability to generate appropriate building blocks. This review outlines recently developed strategies for the synthesis of metal binding non-proteinogenic amino acids. The chemistries to access, as well as to incorporate these amino acids into peptides is presented herein.

Artificial phosphatase upon premicellar nanoarchitectonics of lanthanum complexes with long-chained imidazole derivatives

Four novel long chain-containing tridentate imidazole derivatives (Lⁿ, n = 1, 2, 3, 4) were synthesized for in situ formation of mononuclear lanthanum(III) complexes as artificial phosphodiesterases. These in-situ formed La(III) complexes (named LaLⁿ) were used to catalyze the transesterification of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP), a classic RNA model. Critical aggregation concentrations (CAC) were determined for the as-prepared tridentate imidazole derivatives as ligands and corresponding mixtures of equivalent ligand and La³⁺ ion with a mole rate of 1:1. It denotes that the introduction of La³⁺ ion increases the CAC values of imidazole derivatives by about 2 to 3 folds. Foaming test shows that the foam height is positively correlated with the length of hydrophobic chain. Transesterification of HPNP mediated by LaLⁿ nanoarchitectonics indicates that the introducing of hydrophobic chain benefits rate enhancement, showing excess three orders of magnitude acceleration under physiological conditions (pH 7.0, 25 °C). Moreover, catalytic reactivities of these La(III) complexes increased along with the increase in chain length: LaL¹ < LaL² < LaL³ < LaL⁴, suggesting a positive correlation to hydrophobic chain length.

α-Amino-iso-butyric acid foldamers terminated with rhodium(I) N-heterocyclic carbene catalysts

To investigate how remotely induced changes in ligand folding might affect catalysis by organometallic complexes, dynamic α‐amino‐iso‐butyric acid (Aib) peptide foldamers bearing rhodium(I) N‐heterocyclic carbene (NHC) complexes have been synthesized and studied. X‐ray crystallography of a foldamer with an N‐terminal azide and a C‐terminal Rh(NHC)(Cl)(diene) complex showed a racemate with a chiral axis in the Rh(NHC) complex and a distorted 3₁₀ helical body. Replacing the azide with either one or two chiral L‐α‐methylvaline (L‐αMeVal) residues gave diastereoisomeric foldamers that each possessed point, helical and axial chirality. NMR spectroscopy revealed an unequal ratio of diastereoisomers for some foldamers, indicating that the chiral conformational preference of the N‐terminal residue(s) was relayed down the 1 nm helical body to the axially chiral Rh(NHC) complex. Although the remote chiral residue(s) did not affect the stereoselectivity of hydrosilylation reactions catalysed by these foldamers, these studies suggest a potential pathway towards remote conformational control of organometallic catalysts.

A de novo binuclear zinc enzyme with DNA cleavage activity

Metallohydrolases are broadly used throughout biology, often to catalyze the degradation of macromolecules such as DNA and proteins. Many of these enzymes function with zinc in their active site, and an important subset of these enzymes utilize a binuclear zinc active site. Mimics of these enzymes have been developed, some of which catalyze the digestion of DNA. However, the majority of the mimics that utilize zinc are small molecules, and most are mononuclear. Herein, we report DNA cleavage activity by the de novo designed Due Ferri single-chain (DFsc) protein containing a binuclear zinc active site. This binuclear zinc-protein complex is able to digest plasmid DNA at rates up to 50 ng/h, and these cleavage rates are affected by changes to amino acid residues near the zinc-binding site. These results indicate that the DFsc scaffold is a good model system to carry out careful structure-function relationship studies to understand key structural features that influence reactivity in natural binuclear zinc hydrolases, as it is the first report of a binuclear model system in a protein scaffold.

Design of catalytic polypeptides and proteins

The first part of this review article lists examples of complete, empirical de novo design that made important contributions to the development of the field and initiated challenging projects. The second part of this article deals with computational design of novel enzymes in native protein scaffolds; active designs were refined through random and site-directed mutagenesis producing artificial enzymes with nearly native enzyme- like activities against a number of non-natural substrates. Combining aspects of de novo design and biological evolution of nature's enzymes has started and will accelerate the development of novel enzyme activities.

Medicinal chemistry of acridine and its analogues

'Acridine' along with its functional analogue 'Acridone' is the most privileged pharmacophore in medicinal chemistry with diverse applications ranging from DNA intercalators, endonuclease mimics, ratiometric selective ion sensors, and P-glycoprotein inhibitors in countering the multi-drug resistance, enzyme inhibitors, and reversals of neurodegenerative disorders. Their interaction with DNA and ability of selectively identifying numerous biologically useful ions has cemented exploitability of the acridone nucleus in modern day therapeutics. Additionally, most derivatives and salts of acridine are planar, crystalline, and stable displaying a strong fluorescence which, when coupled with their marked bio selectivity and low cytotoxicity, enables the studying and monitoring of several biochemical, metabolic, and pharmacological processes. In this review, a detailed picture covering the important therapeutic aspects of the acridone nucleus and its functional analogues is discussed.

Dinuclear Lanthanide(III)-m-ODO2A-dimer Macrocyclic Complexes: Solution Speciation, DFT Calculations, Luminescence Properties, and Promoted Nitrophenyl-Phosphate Hydrolysis Rates

Potentiometric speciation studies, mass spectrometry, and DFT calculations helped to predict the various structural possibilities of the dinuclear trivalent lanthanide ion (Ln^III , Ln=La, Eu, Tb, Yb, Y) complexes of a novel macrocyclic ligand, m-ODO2A-dimer (H₄ L), to correlate with their luminescence properties and the promoted BNPP and HPNP phosphodiester bond hydrolysis reaction rates. The stability constants of the dinuclear Ln₂ (m-ODO2A-dimer) complexes and various hydrolytic species confirmed by mass spectrometry were determined. DFT calculations revealed that the Y₂ LH_-1 and the Y₂ LH_-2 species tended to form structures with the respective closed- and open-form conformations. Luminescence lifetime data for the heterodimetallic TbEuL system confirmed the fluorescence resonance energy transfer from the Tb^III to Eu^III ion. The internuclear distance R_TbEu values were estimated to be in the range of 9.4-11.3 Å (pH 6.7-10.6), which were comparable to those of the DFT calculated open-form conformations. Multiple linear regression analysis of the k_obs data was performed using the equation: k_obs,corr. =k_obs -k_obs,OH =kLn2LHM->1 [Ln₂ LH_-1 ]+kLn2LH-2 [Ln₂ LH_-2 ] for the observed Ln₂ L-promoted BNPP/HPNP hydrolysis reactions in solution pH from 7 to 10.5 (Ln=Eu, Yb). The results showed that the second-order rate constants for the Eu₂ LH_-2 and Yb₂ LH_-2 species were about 50-400 times more reactive than the structural analogous Zn₂ (m-12 N₃ O-dimer) system.

Amino acid or peptide conjugates of acridine/acridone and quinoline/quinolone-containing drugs. A critical examination of their clinical effectiveness within a twenty-year timeframe in antitumor chemotherapy and treatment of infectious diseases

Acridines/acridones, quinolines/quinolones (chromophores) and their derivatives constitute extremely important family of compounds in current medicine. Great significance of the compounds is connected with antimicrobial and antitumor activities. Combining these features together in one drug seems to be long-term benefit, especially in oncology therapy. The attractiveness of the chromophore drugs is still enhanced by elimination their toxicity and improvement not only selectivity, specificity but also bioavailability. The best results are reached by conjugation to natural peptides. This paper highlights significant advance in the study of amino acid or peptide chromophore conjugates that provide highly encouraging data for novel drug development. The structures and clinical significance of amino acid or peptide chromophore conjugates are widely discussed.

Transition Metal Complexes of a Diaza-Crown Ether with two Carbamoylmethyl Substituents: Synthesis and Assessment as a Functional Nuclease

We report the synthesis, catalytic function and catalytic mechanism of two transition metal complexes (CuL, ZnL) of a diaza-crown ether with two acetylamino side arms [L = 2,2′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl)diacetamide] in the hydrolysis of DNA. Their nuclease functions on pUC19 DNA cleavage were investigated. The results indicated that the active species might be formed by the deprotonation of the water-coordinated molecules in the complex and the optimum pH is 8.0 for both CuL and ZnL. The catalytic activity of CuL is higher than that of ZnL in DNA hydrolytic cleavage due to the difference in the Lewis acidity of the central metal ions, which is contrary to the result with the Cu and Zn complexes of the parent ligand L0 (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane) as artificial nuclease. Comparison studies of DNA cleavage in the presence and absence of several oxygen scavengers showed that these complexes can promote DNA cleavage by a hydrolytic pathway. Our proposed mechanism suggests that the negative charge on the phosphorus oxygen atom of the substrate molecule is dispersed and the intermediate is formed and stabilised by hydrogen bonding between the DNA molecule and the acetylamino group of the complex.

DNA cleavage by oxymyoglobin and cysteine-introduced metmyoglobin

DNA was cleaved oxidatively by oxygenated myoglobin, whereas Lys96Cys metmyoglobin functioned as an artificial nuclease under air by formation of an oxygenated species.

Progress in artificial metallonucleases

The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.

Anomalous behavior of pentacoordinate copper complexes of dimethylphenanthroline and derivatives of terpyridine ligands: Studies on DNA binding, cleavage and apoptotic activity

Copper(II) complexes with substituted terpyridine ligands, namely [Cu(itpy)(dmp)](NO3)2 (1) and [Cu(ptpy)(dmp)](NO3)2 (2) have been synthesized and characterized. The interaction of the complexes with CT-DNA has been explored using spectroscopic techniques and viscosity. Complexes 1 and 2 bind in the grooves of DNA, interestingly 1 in the minor and 2 in the major groove. Both the complexes have been found to promote DNA cleavage; complex 1 through hydrolytic and 2 oxidative. Complexes 1 and 2 have been found to be cytotoxic and bring about apoptosis of human lung cancer cell line A549.

A New Synthesis of TE2A-a Potential Bifunctional Chelator for (64)Cu

PURPOSE

The development of a new bifunctional chelator, which holds radiometals strongly in living systems, is a prerequisite for the successful application of disease-specific biomolecules to medical diagnosis and therapy. Recently, TE2A was reported to make kinetically more stable Cu(II) complexes than TETA. Herein, we report a new synthetic route to TE2A and explore its potential as a bifunctional chelator.

METHODS

TE2A was synthesized using the regioselective alkylation of benzyl bromoacetate and successive deprotection of the methylene bridge and benzyl group. Salt-free TE2A was radiolabeled with (64)Cu and microPET imaging was performed to follow the clearance pattern of the (64)Cu-TE2A complex. TE2A was conjugated with cyclic RGD peptide and the TE2A-c(RGDyK) conjugate was radiolabeled with (64)Cu.

RESULTS

TE2A was prepared in salt-free form from cyclam in an overall yield of 74%. The microPET images showed that (64)Cu-TE2A is excreted rapidly from the body by the kidney and liver. TE2A was successfully conjugated with c(RGDyK) peptide through one carboxylate group and the TE2A-c(RGDyK) conjugate was radiolabeled with (64)Cu in 94% yield within 30 min.

CONCLUSION

TE2A can be used by itself as a bifunctional chelator without any further structural modification.

Conformational effects of the non-natural alpha-methylserine on small peptides and glycopeptides

The synthesis and the conformational analysis in aqueous solution of a peptide and a glycopeptide containing the sequence threonine-alanine-alanine (Thr-Ala-Ala) are reported. Furthermore, the threonine residue has been replaced by the quaternary amino acid alpha-methylserine (MeSer) and their corresponding non-natural peptide and glycopeptide are also studied. The conformational analysis in aqueous solution combines NOEs and coupling constants data with Molecular Dynamics (MD) simulations with time-averaged restraints. The study reveals that the beta-O-glycosylation produces a remarkable and completely different effect on the backbone of the peptide derived from Thr and MeSer. In the former, the beta-O-glycosylation is responsible for the experimentally observed shift from extended conformations (peptide) to folded ones (glycopeptide). In contrast, the beta-O-glycosylation of the MeSer-containing peptide, which clearly shows two main conformations in aqueous solution [extended ones (70%) and beta-turn (30%)], causes a high degree of flexibility for the backbone.

Synthesis and biophysical studies of bis-macrocyclic cobalt/copper(II) complexes having a pyridine spacer with CT DNA and 5'-GMP

New bis-macrocyclic complexes of Co(III), 1, Ni(II), 2, and Cu(II), 3, containing pyridyl bridges between 13-membered macrocyclic subunits, have been synthesized via an in situ one-pot template condensation reaction (IOPTCR). The proposed structures of these new dinuclear complexes are consistent with the data obtained from elemental analysis, molar conductance, IR, EPR, UV/VIS, (1)H- and 13C-NMR, and ESI-MS. The complexes 2 and 3 possess square-planar geometry with four secondary N-atoms coordinated to the metal ion, while complex 1 reveals octahedral geometry in solution due to coordinated H(2)O molecules. DNA-Binding properties of the complexes 1 and 3 were investigated by absorption and emission titrations, cyclic voltammetry, and viscosity measurements. Complexes 1 and 3 are strong DNA binders with binding constants, K(b), of 1.64 x 10(5) and 2.05 x 10(5) M(-1), respectively. Hyperchromism, decrease in emission intensity of DNA-bound ethidium bromide (EB), and changes observed in the viscosity and cyclic voltammograms in the presence of added metal complexes reveals that the complexes bind to DNA predominantly by electrostatic attraction, substantiated by absorption titration with 5'-GMP.

Synthesis, spectroscopic, magnetic and thermal properties of bimetallic salts, [Ni(L)][MCl4] [where M=Co(II), Zn(II), Hg(II) and L=3,7-bis(2-aminoethyl)-1,3,5,7-tetraazabicyclo(3.3.1)nonane]. X-ray structure of [Ni(L)][CoCl4]

New bimetallic complex salts corresponding to the formulation [Ni(L)][MCl(4)] have been synthesized by the facile reaction between [Ni(L)](ClO(4))(2) and [MCl(2)(PPh(3))(2)] in high yields [where M=Co(II), Zn(II), Hg(II) and L=3,7-bis(2-aminoethyl)-1,3,5,7-tetraazabicyclo(3.3.1)nonane]. The complexes were characterized by IR, electronic spectra, TGA/DSC, magnetic moment and conductivity measurements. The X-ray crystal structure for [Ni(L)][CoCl(4)] clearly establishes the cationic-anionic interaction. It crystallizes in the space group P1 with unit cell dimensions a=7.1740(15)A, b=8.1583(16)A and c=8.3102(16)A. A square-planar geometry is evident for the [Ni(L)](2+) cation while the anion is found to be tetrahedral. A two-step thermolytic pattern is observed in the pyrolysis of the bimetallic complex salts.