Conjugates between minor groove binders and Zn(II)-tach complexes: Synthesis,characterization, and interaction with plasmid DNA

A new family of conjugates between a Zn(II)-tach complex and (indole)₂ or benzofuran-indole amide minor groove binders connected through alkyl or oxyethyl linkers of different lengths has been prepared. The conjugates bind strongly to DNA. However, the complexation to DNA to promote the Zn(II) catalyzed hydrolytic cleavage of the DNA results instead in its inhibition. This inhibition effect has been confirmed also using Cu(II). Modeling studies suggest that in the most stable complex conformation, the minor groove binder and the linker lie in the minor groove hampering the interaction between the metal complex and the phosphate backbone of DNA. Therefore, the linear arrangement of minor groove binder-linker-metal complex appears to be effective to ensure tight binding but unproductive from a hydrolytic point of view.     

Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) tethering a Hoechst 33258 analogue: triplex and duplex stabilization by simultaneous minor groove binding

Deoxynucleic guanidine (DNG), a DNA analogue in which positively charged guanidine replaces the phosphodiester linkages, tethering to Hoechst 33258 fluorophore by varying lengths has been synthesized. A pentameric thymidine DNG was synthesized on solid phase in the 3' --> 5' direction that allowed stepwise incorporation of straight chain amino acid linkers and a bis-benzimidazole (Hoechst 33258) ligand at the 5'-terminus using PyBOP/HOBt chemistry. The stability of (DNA)(2).DNG-H triplexes and DNA.DNG-H duplexes formed by DNG and DNG-Hoechst 33258 (DNG-H) conjugates with 30-mer double-strand (ds) DNA, d(CGCCGCGCGCGCGAAAAACCCGGCGCGCGC)/d(GCGGCGCGCGCGCTTTTTGGGCCGCGCGCG), and single-strand (ss) DNA, 5'-CGCCGCGCGCGCGAAAAACCCGGCGCGCGC-3', respectively, has been evaluated by thermal melting and fluorescence emission experiments. The presence of tethered Hoechst ligand in the 5'-terminus of the DNG enhances the (DNA)(2).DNG-H triplex stability by a DeltaT(m) of 13 degrees C. The fluorescence emission studies of (DNA)(2).DNG-H triplex complexes show that the DNG moiety of the conjugates bind in the major groove while the Hoechst ligand resides in the A:T rich minor groove of dsDNA. A single G:C base pair mismatch in the target site decreases the (DNA)(2).DNG triplex stability by 11 degrees C, whereas (DNA)(2).DNG-H triplex stability was decreased by 23 degrees C. Inversion of A:T base pair into T:A base pair in the center of the binding site, which provides a mismatch selectively for DNG moiety, decreases the triplex stability by only 5-6 degrees C. Upon hybridization of DNG-Hoechst conjugates with the 30-mer ssDNA, the DNA.DNG-H duplex exhibited significant increase in the fluorescence emission due to the binding of the tethered Hoechst ligand in the generated DNA.DNG minor groove, and the duplex stability was enhanced by DeltaT(m) of 7 degrees C. The stability of (DNA)(2).DNG triplexes and DNA.DNG duplexes is independent of pH, whereas the stability of (DNA)(2).DNG-H triplexes decreases with increase in pH.     

Synthesis,crystal structure,DNA-binding properties,and antioxidant activity of a V-shaped ligand bis(N-methylbenzimidazol-2-ylmethyl)benzylamine and its zinc(II) complex

A V-shaped ligand bis(N-methylbenzimidazol-2-ylmethyl)benzylamine (L) and its zinc(II) complex, [ZnL ₂](pic)₂?·?2CH₃CN (pic?=?picrate), have been synthesized and characterized by physico-chemical and spectroscopic methods. Single-crystal X-ray crystallographic analysis revealed that the Zn(II) complex possesses a distorted trigonal bipyramidal geometry. Supramolecular interactions arising from various intra- or intermolecular π···π stacking interactions contributed to the form of the multidimensional configuration. Interactions of L and Zn(II) complex with DNA were monitored using spectrophotometric methods and viscosity measurements. The results suggest that L and Zn(II) complex both bind to DNA via intercalation and Zn(II) complex binds to DNA more strongly than L. Moreover, the Zn(II) complex also exhibited potential antioxidant properties in vitro.     

Cytotoxicity activity,in silico molecular docking,protein- and DNA-binding study of a new Ni(II) Schiff base complex

Abstract

One new nickel(II) complex, [Ni(L)] (1), was synthesized from the Schiff base ligand derived from pyrrole-2-carboxaldehyde and 1,3-diaminopropane. Complex 1 was characterized by elemental analysis, IR, UV-Vis and ESI mass spectroscopy, cyclic voltammetry, and single-crystal X-ray structure analysis. Crystallographic results show that two Ni(II) monomeric moieties are present with similar structural features but with slightly different bond lengths and bond angles. The geometry around the Ni(II) center is distorted square planar. DNA-binding properties of complex 1 were well explored by employing UV-Vis and fluorescence spectral methods, cyclic voltammetry, and by viscosity measurements. Similarly the protein-binding study was studied by multispectroscopic techniques using both BSA and HSA. The cytotoxicity study of the compound has also been evaluated. Notably, the in vitro cytotoxicity of complex 1 on two cancer cell lines (AGS and A549) demonstrates that complex 1 has very good anticancer activity. MTT assay, cell-cycle analysis, and annexin-V assay have been performed to know the extent of effect of complex 1 as anticancer agent. Further, in silico molecular docking study revealed that the nickel(II) complex fits into the minor groove of duplex DNA by hydrophobic interaction with functional groups of B-DNA.     

Synthesis and characterization of novel Cd(II), Zn(II) and Ni(II) complexes with 2-quinolinecarboxaldehyde selenosemicarbazone. Crystal structure of bis(2-quinolinecarboxaldehyde selenosemicarbazonato)nickel(II)

New complexes of Cd(II), Zn(II) and Ni(II) with 2-quinolinecarboxaldehyde selenosemicarbazone (Hqasesc) were synthesized and structurally characterized. The structure of the ligand, Cd(II) and Zn(II) complexes was determined by NMR and IR spectroscopy, elemental microanalysis and molar conductivity measurements. Both complexes occur in solution in two forms, the major tetrahedral and minor octahedral. In the major Cd(II) complex one qasesc⁻ ligand is coordinated as a tridentate, the fourth coordination site being occupied by acetate, while in the major Zn(II) complex two qasesc⁻ ligands are coordinated as bidentates. In both minor complexes two qasesc⁻ ligands are coordinated as tridentates forming the octahedral geometry around the central metal ion. The only paramagnetic complex in the series is Ni(II) complex for which X-ray structure analysis was performed. The complex has the angularly distorted octahedral geometry with two qasesc⁻ ligands coordinated as tridentates, in a similar way as in the minor complexes of Cd(II) and Zn(II).     

Oligodeoxynucleotide Duplexes Containing (5′S)‐5′‐C‐Alkyl‐Modified 2′‐Deoxynucleosides: Can an Alkyl Zipper across the DNA Minor‐Groove Enhance Duplex Stability?

A series of oligonucleotides containing (5′S)‐5′‐C‐butyl‐ and (5′S)‐5′‐C‐isopentyl‐substituted 2′‐deoxyribonucleosides were designed, prepared, and characterized with the intention to explore alkyl‐zipper formation between opposing alkyl chains across the minor groove of oligonucleotide duplexes as a means to modulate DNA‐duplex stability. From four possible arrangements of the alkyl groups that differ in the density of packing of the alkyl chains across the minor groove, three (duplex types I – III , Fig. 2) could experimentally be realized and their duplex‐forming properties analyzed by UV‐melting curves, CD spectroscopy, and isothermal titration calorimetry (ITC), as well as by molecular modeling. The results show that all arrangements of alkyl residues within the minor groove of DNA are thermally destabilizing by 1.5–3°/modification in T_m. We found that, within the proposed duplexes with more loosely packed alkyl groups (type‐ III duplexes), accommodation of alkyl residues without extended distorsion of the helical parameters of B‐DNA is possible but does not lead to higher thermodynamic stability. The more densely packed and more unevenly distributed arrangement (type‐ II duplexes) seems to suffer from ecliptic positioning of opposite alkyl groups, which might account for a systematic negative contribution to stability due to steric interactions. The decreased stability in the type‐ III duplexes described here may be due either to missing hydrophobic interactions of the alkyl groups (not bulky enough to make close contacts), or to an overcompensation of favorable alkyl‐zipper formation presumably by loss of structured H₂O in the minor groove.     

Structural characterization of a rigidified threading bisintercalator

NMR spectroscopy was used to explore the sequence-specific interaction of DNA with a new threading bisintercalator (C1) consisting of two intercalating 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) units connected by a rigid, tricyclic spiro linker. A structural model of C1 complexed to d(CGGTACCG)(2) was calculated using distance constraints obtained from solution NMR data. The model was also supported by the results from residual dipolar coupling (RDC) measurements obtained using Pf1-phage as a cosolvent. According to the model, the central cyclohexane ring of the linker connecting the two NDI units lies flat in the minor groove of DNA. Linker length, hydrogen bonding, steric, and hydrophobic factors all appear to contribute to the observed sequence specificity of binding. These results serve to illustrate the versatility of threading polyintercalation given that, in a previous study, a ligand consisiting of two NDI units joined by a flexible peptide linker was shown to bind sequence specifically within the major groove of this same sequence of DNA.     

Synthesis and Characterization of Ni(II), Cu(II), Zn(II) and Cd(II) Complexes of a New Vic-Dioxime Ligand

In this study, 1,2-dihydroxyimino-3,7-di-aza-9,10-O-α-methyl benzal decane (LH₂) was synthesized starting from 1,2-O-α-methyl benzal-4-aza-7-amino heptane (RNH₂) and antichloroglyoxime. With this ligand, complexes were synthesized using Ni(II) and Cu(II) salts with a metal:ligand ratio of 1:2. However, the reaction of the ligand with salts of Zn(II) and Cd(II) gave products with metal:ligand ratio of 1:1. Structures of the ligand and its complexes are proposed based on elemental analyses, IR, ¹³C- and ¹H-NMR spectra, magnetic susceptibility measurements and thermogravimetric analyses (TGA).     

ApA Cleavage Promoted by Oxa-aza Macrocycles and Their Zn(II) Complexes. The Role of pH and Metal Coordination in the Hydrolytic Mechanism

Abstract

The thermodynamic parameters for protonation and Zn(II) complex formation with ligand 1,4,7,16,19,22-hexaza-10,13,25,28-tetraoxacyclotriacontane (L1) have been determined. L1 forms stable dizinc complexes from neutral to alkaline pH. The hydrolytic ability toward adenylyl(3′-5′)adenosine (ApA) of L1 and its dizinc(II) complexes have been analyzed by means of HPLC chromatography. Only partially protonated species of L promote ApA hydrolysis suggesting that the cleavage process is cooperatively promoted by a general base catalysis by neutral amine groups and a general acid catalysis by protonated ammonium functions. Concerning the Zn(II) complexes, the hydrolysis rates increase in the presence of the hydroxo complexes [Zn₂L1(OH)]³⁺ and [Zn₂L1(OH)²]²⁺. This indicates that Zn-OH functions play a crucial role in the hydrolytic process, assisting the deprotonation of the 2′-OH group of ApA, which may act as nucleophile in the cleavage process. Both binuclear L1 complexes are better catalysts than the mononuclear [ZnL₂(OH)]⁺ complex (L₂ = 1,4-Dioxa-7,10,13-triazacyclopentadecane), indicating a cooperative role of the two Zn(II) ions in ApA cleavage by [Zn₂L1(OH)]³⁺ and [Zn₂L1(OH)₂]²⁺, probably due to a bridging coordination of the phosphate moiety of ApA to the two metal centers.     

Benzo[h]quinoline based Macrocyclic Copper(II), Cobalt(II) Complexes: Synthesis,Characterization and Light induced DNA Cleavage Studies

A new ligand dibenzo[h]quinolineno[1,3,7,9] tetraazacyclododecine-7,15 (14H, 16H)-dibenzene (L) and its Co(II)/Cu(II) metal complexes of type [MLX₂] (Where (M = Co(II) (5), Cu(II) (6) and X = Cl) were synthesized and are well characterized by FT-IR, ¹H-NMR, FAB mass elemental analysis, and electronic spectral data. The role of the cobalt/copper metals in photo-induced DNA cleavage reactions was explored by designing complex molecules having macrocyclic structure. Finally, we have shown that photocleavage of plasmid DNA is more efficiently enhanced when this macrocyclic ligand is irradiated in the presence of copper(II) than that of cobalt metal.     

A new amino alcohol NpyNimineNamineOalcohol-donor ligand: coordination toward zinc(II) and cadmium(II) halides and enantioselective products

In the present work a new ligand, 2-(2-(phenyl(pyridin-2-yl)methyleneamino)ethylamino)ethanol (L), and its Zn(II) and Cd(II) complexes, [Zn(L)Br₂] (1), [Cd(L)Br₂] (2) and [Cd(L)I₂] (3), have been synthesized and characterized by elemental analysis, FT-IR, Raman and ¹H NMR spectroscopies as well as X-ray crystallography. All complexes are isostructural and their metal ions have distorted square pyramidal geometry with an MN₃X₂ (X: Br, I) environment. During the complexation process, the amine group of the ligand becomes a chiral center. In the solid-state, an R-configuration was observed in all three complexes. Furthermore, the molecules form intermolecular C–H?O, C–H?X and O–H?X (X: Br, I) hydrogen bonds in the solid-state.     

Synthesis,Crystal Structure,Antioxidation and DNA‐Binding Studies of a Zinc(II) Complex with the Bis(N‐allylbenzimidazol‐2‐ylmethyl)aniline

A complex of zinc(II) picrate (pic) with bis(N‐allylbenzimidazol‐2‐ylmethyl)aniline (abba), with composition [Zn(abba)₂](pic)₂, was synthesized and characterized by elemental analysis, electrical conductivity, IR and UV/Vis spectral measurements. The crystal structure of the zinc(II) complex has been determined by single‐crystal X‐ray diffraction. The Zn(II) is bonded to two abba ligands through four benzimidazole nitrogen, resulting in a distorted tetrahedron geometry. The DNA‐binding properties of the ligand and the zinc(II) complex were investigated by electronic absorption, fluorescence spectra and viscosity measurements. The experimental results suggest that the zinc(II) complex binds to DNA in an intercalation mode. In addition, the ligand abba and Zn(II) complex have scavenging effects for hydroxyl radicals and the complex shows stronger scavenging effects for hydroxyl radicals than the ligand.     

The Synthesis,Characterization and Conductance Studies of New Cu(II), Ni(Ii) And Zn(II) Complexes with the Schiff Base Derived from 1,2-Bis-(o-Aminophenoxy)Ethane and Salicylaldehyde

Cu(II), Ni(II) and Zn(II) complexes with the Schiff base derived from 1,2-bis-(o-aminophenoxy)ethane with salicylaldehyde have been prepared. The complexes have been characterized by elemental analysis, magnetic measurements, ¹H NMR, ¹³C NMR, UV, visible and IR spectra as well as conductance measurements. The ligand is coordinated to the central metal as a tetradentate ONNO ligand. The four bonding sites are the central azomethine nitrogen and aldehydic OH groups. The ligand was used for complexation studies. Stability constants were measured by a conductometric method. Furthermore, the stability constants for complexation between ZnCl₂ and Cu(NO₃)₂ salts and N,N′-bis(salicylidene)-1,2-bis-(o-aminophenoxy)ethane (H₂L) in 80% dioxane/water and pure methanol were determined from conductance measurements. The magnitudes of these ion association constants are related to the nature of the solvation of the cation and the complexed cation. The mobilities of the complexes are also dependent, in part, upon solvation effects.     

Zinc coordination polymers with rigid dicarboxylates and semirigid 3,5-bis(imidazole-1-yl) pyridine: syntheses,structural topologies,and luminescent properties

Two metal coordination polymers, {[Zn(bpdc)(bip)]·2H₂O}_n (1) and [Zn(tdc)(bip)] (2) [H₂bpdc?=?biphenyl-4,4’-dicarboxylate, H₂tdc?=?thiophene-2,5-dicarboxylate, bip?=?3,5-bis(imidazole-1-yl)pyridine], have been synthesized and characterized by IR, elemental analysis, XRD, and X-ray single-crystal diffraction. In 1, bpdc and bip link Zn(II) ions into a corrugated 2D layer. The corrugated 2D layers polycatenate each other, yielding a 2D→3D polycatenation net. In 2, dinuclear Zn(II) units are formed by bip and further connected by tdc to construct a 2D 3-connected framework. The luminescent properties of 1 and 2 are investigated in the solid state at room temperature.     

Toward efficient Zn(II)-based artificial nucleases

A series of cis-cis-triaminocyclohexane Zn(II) complex-anthraquinone intercalator conjugates, designed in such a way to allow their easy synthesis and modification, have been investigated as hydrolytic cleaving agents for plasmid DNA. The ligand structure comprises a triaminocyclohexane platform linked by means of alkyl spacers of different length (from C(4) to C(8)) to the anthraquinone group which may intercalate the DNA. At a concentration of 5 microM, the complex of the derivative with a C(8) alkyl spacer induces the hydrolytic stand scission of supercoiled DNA with a rate of 4.6 x 10(-6) s(-1) at pH 7 and 37 degrees C. The conjugation of the metal complex with the anthraquinone group leads to a 15-fold increase of the cleavage efficiency when compared with the anthraquinone lacking Zn-triaminocyclohexane complex. The straightforward synthetic procedure employed, allowing a systematic change of the spacer length, made possible to gain more insight on the role of the intercalating group in determining the reactivity of the systems. Comparison of the reactivity of the different complexes shows a remarkable increase of the DNA cleaving efficiency with the length of the spacer. In the case of too-short spacers, the advantages due to the increased DNA affinity are canceled due to the incorrect positioning of the reactive group, thus leading to cleavage inhibition.     

NMR structural analysis of a modular threading tetraintercalator bound to DNA

The synthesis and NMR structural studies are reported for a modular threading tetraintercalator bound to DNA. The tetraintercalator design is based on 1,4,5,8-tetracarboxylic naphthalene diimide units connected through flexible peptide linkers. Aided by an overall C(2) symmetry, NMR analysis verified a threading polyintercalation mode of binding, with linkers alternating in the order minor groove, major groove, minor groove, analogous to how a snake might climb a ladder. This study represents the first NMR analysis of a threading tetraintercalator and, as such, structurally characterizes a new topology for molecules that bind to relatively long DNA sequences with extensive access to both DNA grooves.     

Structural diversity controlled by alkali/alkaline earth metals for heterometallic AeI/AeII-ZnII coordination polymers based on 4-nitrobenzene-1,2-dicarboxylate

Six heterometallic Zn(II) coordination polymers, Zn(H₂O)₃(FNA) (1), [NH₄]₂[Zn(H₂O)₂(FNA)₂] (2), [ZnNa₂(FNA)₂]·3H₂O (3), [ZnK₂(FNA)₂]·H₂O (4), [ZnRb₂(FNA)₂]·2H₂O (5) and [ZnMg(FNA)₂]·4H₂O (6) (H₂FNA = 4-nitrobenzene-1,2-dicarboxylic acid), were synthesised by introducing different alkali/alkaline earth (Ae^I/Ae^II) metals. These complexes exhibit diverse structures with the different Ae^I/Ae^II metals used and distinct ligand coordination modes the ions provide. For 1 and 2, the Zn(II) centres with distorted octahedra are connected by FNA to form 1-D chain structures. The Zn(II) centres in 3–6 with distorted tetrahedra are linked by FNA to form 2-D anionic grid layers. For 3–5, these 2-D anionic grid layers are connected by alkali metal (Na, K and Rb) with the O–Ae^I–O connectivity to exhibit 3-D framework structures, while 6 features a 2-D Zn–Mg network. Luminescence properties of 1–6 have been investigated.     

新型双核配合物的形成、与DNA的作用机制及荧光性质研究

利用紫外、荧光和粘度等方法研究了含不同配体的钌(II)配合物[Ru(phen)₂CImP]^2＋(CImP＝3,4-二羟基-咪唑并[4,5-i][1,10]邻菲咯啉)和[Ru(phen)₂TPPZ]^2＋(TPPZ＝四吡啶[3,2-a:2',3'-c:3',2'-h:2'',3''-j]吩嗪)与DNA的作用机制, 并研究了配合物与Zn^2＋配合后荧光性质变化. 结果表明[Ru(phen)₂TPPZ]^2＋与DNA以插入模式作用, 而[Ru(phen)₂CImP]^2＋与DNA则以沟面结合模式作用. 向配合物溶液中滴加Zn^2＋后, 配合物[Ru(phen)₂TPPZ]^2＋和[Ru(phen)₂CImP]^2＋均可以与Zn^2＋形成双核配合物[Ru(phen)₂(TPPZ)Zn]^4＋和[Ru(phen)₂(CImP)Zn]^4＋, 配合物的荧光减弱. 与DNA作用后, 配合物仍可以与Zn^2＋配位形成双核配合物, 但[Ru(phen)₂(TPPZ)Zn]^4＋保持插入模式与DNA作用, 配合物的荧光减弱. 而[Ru(phen)₂(CImP)Zn]^4＋与DNA则由沟面结合改为插入结合, 配合物的荧光增强.     

p-Nitrophenyl acetate hydrolysis promoted by Zn(II) and Co(II) complexes with the tripodal ligand of N,N′-bis(2-quinolinylmethyl)amantadine

To mimic the function of metallohydrolase, [M(bqad)Cl₂] (M = Zn(II) (1), Co(II) (2), where bqad = N,N′-bis(2-quinolinylmethyl)amantadine), have been synthesized and characterized by elemental analysis, electronic absorption, IR, and single crystal X-ray diffraction. The structural analysis indicated that metal ions in 1 and 2 were coordinated by three nitrogens from bqad and two chlorides, resulting in a distorted trigonal bipyramidal geometry. Kinetic experiments for hydrolytic cleavage of p-nitrophenyl acetate (pNA) catalyzed by 1 and 2 were performed at pH 7.50–10.00 and 298 K. The second-order rate constants (k_obs) increased exponentially with variation of pH values. The Co(II) complex exhibited potent catalytic activity.