Eiichi Kimura

Intrinsic Properties of Zinc(II) Ion Pertinent To Zinc Enzymes

Publisher Summary This chapter discusses intrinsic properties of zinc(II) ion pertinent to zinc enzymes. Zinc(II) ion is a biologically essential element. The crystal structure of serine/threonine phosphatase-l revealed that it contains two metal ions M(1) and M(2) close to each other. Each of the metal ions is coordinated by five ligands. The distance between the two metal ions is 3.3 A, which is facilitated by Asp 92 and a water molecule (or OH - ion); each bridges the two ions. Both metal ions and two arginine residues together create the active site. Design of useful models is, therefore, a great help in elucidating the role of metals, functions of amino acid residues, and principles of multimetal functions. The metal ions, by stabilizing negative charges, can make a phosphomonoester more susceptible to nucleophilic attack, probably by the metal-bound H 2 O.

Macrocyclic polyamines with pendent phenol, catechol, hydroquinone, and pyridine group

Abatract Novel synthesis and properties of a new class of macromonocyclic polyamines having pendent phenol, catechol, hydroquinone, and pyridine are presented. The proximity of these potential donors to the center of the macrocyclic cavities renders otherwise (i.e. intermolecularly) unlikely coordination feasible. Those intramolecular axial donors affect the metal complex structure and stability, redox properties of the encapsulated metal ions, and possibly the reactivity of vacant coordination sites. The intramolecular, electroactive ligands such as phenol and catechol couple with electroactive metal ions, and both redox properties are greatly altered.

Macrocyclic zinc(II) complexes for selective recognition of nucleobases in single- and double-stranded polynucleotides

Abstract As an extension of our earlier discoveries that ZnII-cyclen complex (1) (cyclen=1,4,7,10-tetraazacyclododecane) and ZnII-acridine-pendant cyclen complex ZnII-N-(9-acridin)ylmethyl-cyclen (3) are the first compounds to selectively recognize thymidine and uridine nucleosides in aqueous solution at physiological pH, the interaction of these and a relevant complex, bis(ZnII-cyclen) (7), has been investigated with a series of polynucleotides, single-stranded poly(U) and poly(G), and double-stranded poly(A)·poly(U), poly(dA)·poly(dT) and poly(dG)·poly(dC). These ZnII-cyclen complexes interact with the imide-containing nucleobases in the single-stranded poly(U), unperturbed by the presence of the anionic phosphodiester backbone. The affinity constant of 1 for each N(3)-deprotonated uracil base in poly(U) is determined to be log K= 5.1 by a kinetic measurement, which is almost the same as log K=5.2 for the interaction of 1 with uridine. Thus, they disrupt the A-U (or A-T) hydrogen bonds to unzip the duplex of poly(A)·poly(U) or poly(dA)·poly(dT), as demonstrated by lowering of the melting temperatures (Tm) of poly(A)·poly(U) and poly(dA)·poly(dT) in 5 mM Tris-HCl buffer (pH 7.6, 10 mM NaCl) with increase in their concentrations. The order of the denaturing efficiency is well correlated with that of the 1 : 1 affinity constants for each complex with uracil or thymine;7>3>1. The comparison of circular dichroism (CD) spectra for poly(A)·poly(U), poly(A), and poly(U) in the presence of 3 has revealed a structural change from poly(A)·poly(U) to two single strands, poly(A) and poly(U), caused by 3 binding exclusively to uracils in poly(U). On the other hand, the acridine-pendant cyclen complex 3, which earlier was found to associate with guanine by the ZnII coordinating with guanine N(7), in addition to the π-π stacking, interacts with guanine in the double helix of poly(dG)·poly(dC) from outside and stabilized the double-stranded structure, as indicated by higher Tm.

Macrocyclic metal complexes for selective recognition of nucleic acid bases and manipulation of gene expression

Interaction of Znn-cyclen complexes 1, 3, 6, and 7 with uracil and thymine bases in double-,stranded poly(A).poly(U) and poly(dA).poly(dT) has been investigated. These zinc@) complexes lowered the melting temperatures (T,S of poly(A).poly(U) and poly(dA).poly(dT) in 5 mM Tris-HC1 buffer (pH 7.6) containing 10 mM NaCl as their concentrations increased, indicating that they destabilized the duplex structure of polynucleotides. The comparison of circular dichroism (CD) spectra of poly(A).poly(U), poly(A), and poly(U) in the presence of zinc(II) complex 3 led us to conclude that the spectral changes of poly(A).poly(U) were due to a structural change from double to single-strand, caused by zinc(II) complex 3 binding exclusively to uracils in poly(U). The destabilization effect of zinc(II) complexes was not observed with poly(dG).poly(dC) in thermal denaturation experiments (50 % formamide aqueous solution, 2.5 mM Tris-HC1 buffer (pH 7.6) and 5 mM NaCl). However, the acridine-pendant cyclen complex 3, which associates with guanine at N, and 0,, and through 7c-7c stacking, interacted with poly(dG) in the double helix and greatly stabilized the poly(dG).poly(dC) double-strand, as was indicated by the higher T, than those with reference intercalating agents. Poly(A).poly(U) double-strand was most effectively disrupted with a bis(Znn-cyclen) bridged by para-xylyl group 6 that was designed as a host molecule to bind to two neighboring uracils in a 1:2 complex. Znn-cyclen complexes thus may become a prototype of small molecules that can affect the biological properties of nucleic acids at the molecular level.

Dynamic anion recognition by macrocyclic polyamines in neutral pH aqueous solution: development from static anion complexes to an enolate complex

Multiprotonated macrocyclic polyamines are useful host molecules for anion guests at neutral pH in aqueous solution. An intramolecular uracil anion complex with a diprotonated macrocyclic tetraamine recently provided a unique example of electrostatic stabilization of the uracil N1 anion at neutral pH, which may be relevant to the facile glycosylation and deglycosylation of uracil at N1 in DNA. Macrocyclic polyamine complexes with Zn2+ possess strong anion affinities and hence can deprotonate weak acids at neutral pH to bind with the resulting conjugate bases: e.g. H2O → HO–, ROH → RO–, ArSO2NH2 → ArSO2NH–, RCONHR′ → RCON–R′, RCONHCOR′ → RCON–COR′. The Zn2+–conjugate base complexes act as catalytic nucleophiles (i.e. HO––Zn2+, RO––Zn2+), fluorescence sensors (ArSO2NH––Zn2+), and thymine or barbital recognition hosts, which are often found in zinc–enzyme functions. Enolate anion complex formation has recently been observed in intramolecular interaction of carbonyl oxygen with Zn2+.

A new cyclam with a triphenylphosphine-pendant and its metal complexes

Abstract A new triphenylphosphine-pendant cyclam (triphenylphosphine = TPP; cyclam = 1,4,8,11-tetraazacyclotetradecane) was synthesized by reaction of an ethyl cinnamate derivative bearing a diphenylphosphine group at the ortho position of the phenyl group with 2,3,2-tetraamine (= 1,9-diamino-3,7-diazanonane) in refluxing McOH, followed by BH 3 reduction. Triphenylphosphine oxide-pendant cyclam (triphenylphosphine oxide = TPPO) was derived by treatment of TPP-pendant cyclam with benzyl alcohol in CCl 4 . The TPP-pendant cyclam formed stable 1:1 metal inclusion complexes with Ni II and Mn III . The TPPO-pendant cyclam yielded a 1:1 Ni II complex which was the best catalyst among the cyclam-Ni II and -Mn III complexes for epoxidation of trans -stilbene with NaClO in CH 2 Cl 2 . Gold(I) reacted with TPP-pendant cyclam to yield a stable 1:1 complex, in which Au I binds only to the pendant phosphine. On the other hand, gold(III) reacted with TPP-pendant cyclam to give an Au III -inclusion complex with the pendant TPP coordination. The Au I complex reacted with [Au III (dien)Cl] 2+ in CH 3 CN to yield an Au I (out)-Au III (in-cyclam) mixed complex. The Ni II complex with TPP-pendant cyclam reacted with Au I (PEt 3 )Cl in CH 2 Cl 2 , yielding a novel Aul(out)-Ni II (in-cyclam) binuclear complex.

MACROCYCLIC ZINC(II) COMPLEXES FOR SELECTIVE RECOGNITION OF NUCLEOBASES IN SINGLE- AND DOUBLE-STRANDED POLYNUCLEOTIDES

The model study of zinc enzyme by Zn2+–cyclen complexes (cyclen = 1, 4, 7, 10-tetraazacyclododecane) disclosed the intrinsic properties of zinc(II) as having strong anion affinities and yet the resulting Zn2+–anion bonds have a labile nature. The basic understanding has evolved into novel selective nucleobase recognition by the Zn2+–cyclen complexes. The Zn2+–aromatic pendant cyclen complexes selectively and effectively bind to thymine T (or uracil U) in single- and double-stranded DNA (or RNA). The Zn2+ complexes work like molecular zippers to break A–T pairs in double-stranded DNA, as proven by various physicochemical and DNA footprinting measurements. Moreover, these Zn2+–complexes affect relevant biochemical and ultimately biological properties such as inhibition of a transcriptional factor and antimicrobial activities.

Synthesis, spectroscopic, redox properties, and DNA cleavage activity of low-spin iron(III) complexes of bleomycin analogues

Abstract The reaction of the bleomycin (BLM) analogues, 2-[((2-(4-imidazoyl)ethyl)amino)carbonyl]-6-[((2-aminoethyl)amino)methyl]pyridine= L 1 or 2-[((2-(4-imidazoyl)ethyl)amino)carbonyl]-6-[((2-amino-2-carbamoylethyl)amino)methyl]pyridine= L 2 with an equimolar amount of FeCl 3 ·6H 2 O in ethanol in the presence of N -methylimidazole afforded deep-red microcrystals, [Fe III (H −1 L 1 )(H 2 O)]Cl 2 ( 1 ) or [Fe III (H −1 L 2 )(H 2 O)]Cl 2 ·0.5H 2 O ( 2 ), respectively. These Fe III complexes have been characterized by electronic and EPR spectroscopies and cyclic voltammetry. The electronic spectra of 1 and 2 in methanol are similar to that of authentic Fe III -pepleomycin, which is a member of the family of BLMs. The EPR spectra of 1 and 2 in frozen methanol at 77 K exhibited rhombic low-spin Fe III signals ( g 1 =2.40, g 2 =2.32, and g 3 =1.86 for 1 and g 1 =2.38, g 2 =2.31, and g 3 =1.86 for 2 ). The cyclic voltammograms of 1 and 2 in DMF at I =0.1 M tetraethylammonium chloride, TEACl, displayed one-electron Fe III/II redox process at E 1/2 =−0.04 V and +0.05 V versus Ag/AgCl for 1 and 2 , respectively. Both Fe III complexes, 1 and 2 , cleaved pUC19 DNA at 0.1 mM in the presence of H 2 O 2 . Complex 1 was found to cleave 293 base-pair DNA with a little selectivity as compared with the Fe III –BLM complex, indicating that the metal-chelating moiety may be necessary for the sequence selectivity of DNA strand scission by BLM.

Stabilization of nickel(III) ion by new macrocyclic dioxotetraamines bearing functional pendant donors

Abstract Two new macrocyclic dioxotetraamine ligands bearing 2-methyl pyridine and 8-methylquinoline as additional pendant donors have been found to stabilize the trivalent oxidation state of nickel, but destabilize the trivalent oxidation state of copper