Tanmaya Joshi

Efficient Plasmid DNA Cleavage by Copper(II) Complexes of 1,4,7-Triazacyclononane Ligands Featuring Xylyl-Linked Guanidinium Groups

Three new metal-coordinating ligands, L(1), L(2), and L(3), have been prepared by appending o-, m-, and p-xylylguanidine pendants, respectively, to one of the nitrogen atoms of 1,4,7-triazacyclononane (tacn). The copper(II) complexes of these ligands are able to accelerate cleavage of the P-O bonds within the model phosphodiesters bis(p-nitrophenyl)phosphate (BNPP) and [2-(hydroxypropyl)-p-nitrophenyl]phosphate (HPNPP), as well as supercoiled pBR 322 plasmid DNA. Their reactivity toward BNPP and HPNPP is not significantly different from that of the nonguanidinylated analogues, [Cu(tacn)(OH(2))(2)](2+) and [Cu(1-benzyl-tacn)(OH(2))(2)](2+), but they cleave plasmid DNA at considerably faster rates than either of these two complexes. The complex of L(1), [Cu(L(1)H(+))(OH(2))(2)](3+), is the most active of the series, cleaving the supercoiled plasmid DNA (form I) to the relaxed circular form (form II) with a k(obs) value of (2.7 ± 0.3) × 10(-4) s(-1), which corresponds to a rate enhancement of 22- and 12-fold compared to those of [Cu(tacn)(OH(2))(2)](2+) and [Cu(1-benzyl-tacn)(OH(2))(2)](2+), respectively. Because of the relatively fast rate of plasmid DNA cleavage, an observed rate constant of (1.2 ± 0.5) × 10(-5) s(-1) for cleavage of form II DNA to form III was also able to be determined. The X-ray crystal structures of the copper(II) complexes of L(1) and L(3) show that the distorted square-pyramidal copper(II) coordination sphere is occupied by three nitrogen atoms from the tacn ring and two chloride ions. In both complexes, the protonated guanidinium pendants extend away from the metal and form hydrogen bonds with solvent molecules and counterions present in the crystal lattice. In the complex of L(1), the distance between the guanidinium group and the copper(II) center is similar to that separating the adjacent phosphodiester groups in DNA (ca. 6 Å). The overall geometry of the complex is also such that if the guanidinium group were to form charge-assisted hydrogen-bonding interactions with a phosphodiester group, a metal-bound hydroxide would be well-positioned to affect the nucleophilic attack on the neighboring phosphodiester linkage. The enhanced reactivity of the complex of L(1) at neutral pH appears to also be, in part, due to the relatively low pK(a) of 6.4 for one of the coordinated water molecules.

DMSO‐Mediated Ligand Dissociation: Renaissance for Biological Activity of N‐Heterocyclic‐[Ru(η6‐arene)Cl2] Drug Candidates

Slipped under the radar? (1) H NMR spectroscopic examination revealed that [Ru(η(6) -arene)Cl2 (L)] (L=N-heterocyclic ligands) complexes readily undergo ligand exchange reaction in DMSO, a popular medium for preparing stock solutions for biological screening. It is therefore highly important for researchers to study stability in DMSO before reporting on the biological activity of such type of complexes.

Synthesis, structure, and DNA cleavage properties of copper(II) complexes of 1,4,7-triazacyclononane ligands featuring pairs of guanidine pendants.

Two new ligands, L(1) and L(2), have been prepared via N-functionalization of 1,4,7-triazacyclononane (tacn) with pairs of ethyl- or propyl-guanidine pendants, respectively. The X-ray crystal structure of [CuL(1)](ClO4)2 (C1) isolated from basic solution (pH 9) indicates that a secondary amine nitrogen from each guanidine pendants coordinates to the copper(II) center in addition to the nitrogen atoms in the tacn macrocycle, resulting in a five-coordinate complex with intermediate square-pyramidal/trigonal bipyramidal geometry. The guanidines adopt an unusual coordination mode in that their amine nitrogen nearest to the tacn macrocycle binds to the copper(II) center, forming very stable five-membered chelate rings. A spectrophotometric pH titration established the pK(app) for the deprotonation and coordination of each guanidine group to be 3.98 and 5.72, and revealed that [CuL(1)](2+) is the only detectable species present in solution above pH ∼ 8. The solution speciation of the CuL(2) complex (C2) is more complex, with at least 5 deprotonation steps over the pH range 4-12.5, and mononuclear and binuclear complexes coexisting. Analysis of the spectrophotometric data provided apparent deprotonation constants, and suggests that solutions at pH ∼ 7.5 contain the maximum proportion of polynuclear complexes. Complex C1 exhibits virtually no cleavage activity toward the model phosphate diesters, bis(p-nitrophenyl)phosphate (BNPP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP), while C2 exhibits moderate activity. For C2, the respective kobs values measured at pH 7.0 (7.24 (± 0.08) × 10(-5) s(-1) (BNPP at 50 °C) and 3.2 (± 0.3) × 10(-5) s(-1) (HPNPP at 25 °C)) are 40- and 10-times faster than [Cu(tacn)(OH2)2](2+) complex. Both complexes cleave supercoiled pBR 322 plasmid DNA, indicating that the guanidine pendants of [CuL(1)](2+) may have been displaced from the copper coordination sphere to allow for DNA binding and subsequent cleavage. The rate of DNA cleavage by C2 is twice that measured for [Cu(tacn)(OH2)2](2+), suggesting some degree of cooperativity between the copper center and guanidinium pendants in the hydrolysis of the phosphate ester linkages of DNA. A predominantly hydrolytic cleavage mechanism was confirmed through experiments performed either in the presence of various radical scavengers or under anaerobic conditions.

Phosphodiester cleavage properties of copper(II) complexes of 1,4,7-triazacyclononane ligands bearing single alkyl guanidine pendants.

Three new metal-coordinating ligands, L(1)·4HCl [1-(2-guanidinoethyl)-1,4,7-triazacyclononane tetrahydrochloride], L(2)·4HCl [1-(3-guanidinopropyl)-1,4,7-triazacyclononane tetrahydrochloride], and L(3)·4HCl [1-(4-guanidinobutyl)-1,4,7-triazacyclononane tetrahydrochloride], have been prepared via the selective N-functionalization of 1,4,7-triazacyclononane (tacn) with ethylguanidine, propylguanidine, and butylguanidine pendants, respectively. Reaction of L(1)·4HCl with Cu(ClO(4))(2)·6H(2)O in basic aqueous solution led to the crystallization of a monohydroxo-bridged binuclear copper(II) complex, [Cu(2)L(1)(2)(μ-OH)](ClO(4))(3)·H(2)O (C1), while for L(2) and L(3), mononuclear complexes of composition [Cu(L(2)H)Cl(2)]Cl·(MeOH)(0.5)·(H(2)O)(0.5) (C2) and [Cu(L(3)H)Cl(2)]Cl·(DMF)(0.5)·(H(2)O)(0.5) (C3) were crystallized from methanol and DMF solutions, respectively. X-ray crystallography revealed that in addition to a tacn ring from L(1) ligand, each copper(II) center in C1 is coordinated to a neutral guanidine pendant. In contrast, the guanidinium pendants in C2 and C3 are protonated and extend away from the Cu(II)-tacn units. Complex C1 features a single μ-hydroxo bridge between the two copper(II) centers, which mediates strong antiferromagnetic coupling between the metal centers. Complexes C2 and C3 cleave two model phosphodiesters, bis(p-nitrophenyl)phosphate (BNPP) and 2-hydroxypropyl-p-nitrophenylphosphate (HPNPP), more rapidly than C1, which displays similar reactivity to [Cu(tacn)(OH(2))(2)](2+). All three complexes cleave supercoiled plasmid DNA (pBR 322) at significantly faster rates than the corresponding bis(alkylguanidine) complexes and [Cu(tacn)(OH(2))(2)](2+). The high DNA cleavage rate for C1 {k(obs) = 1.30 (±0.01) × 10(-4) s(-1) vs 1.23 (±0.37) × 10(-5) s(-1) for [Cu(tacn)(OH(2))(2)](2+) and 1.58 (±0.05) × 10(-5) s(-1) for the corresponding bis(ethylguanidine) analogue} indicates that the coordinated guanidine group in C1 may be displaced to allow for substrate binding/activation. Comparison of the phosphate ester cleavage properties of complexes C1-C3 with those of related complexes suggests some degree of cooperativity between the Cu(II) centers and the guanidinium groups.

Bis(dipyridophenazine)(2-(2′-pyridyl)pyrimidine-4-carboxylic acid)ruthenium(II) Hexafluorophosphate: A Lesson in Stubbornness

Ruthenium complexes are currently considered to be among the most promising alternatives to platinum anticancer drugs. In this work, thirteen structural analogues and organelle/receptor‐targeting peptide bioconjugates of a cytotoxic bis(dppz)‐RuII complex [Ru(dppz)2(CppH)](PF6)2 (1) were prepared, characterized, and assessed for their cytotoxicity and cellular localization (CppH=2‐(2′‐pyridyl)pyrimidine‐4‐carboxylic acid; dppz=dipyrido[3,2‐a:2′,3′‐c]phenazine). It was observed that structural modifications (lipophilicity, charge, and size‐based) result in the cytotoxic potency of 1 being compromised. Confocal microscopy studies revealed that unlike 1, the screened complexes/bioconjugates do not have a preferential accumulation in mitochondria. The results of this important structure–activity relationship strongly support our initial hypothesis that accumulation in mitochondria is crucial for 1 to exert its cytotoxic action.

Di-heterometalation of thiol-functionalized peptide nucleic acids

As a proof-of-principle, two hetero-bimetallic PNA oligomers containing a ruthenium(II) polypyridyl and a cyclopentadienyl manganese tricarbonyl complex have been prepared by serial combination of solid-phase peptide coupling and in-solution thiol chemistry. Solid-phase N-terminus attachment of Ru(II)-polypyridyl carboxylic acid derivative, C1, onto the thiol-functionalized PNA backbone (H-a-a-g-t-c-t-g-c-linker-cys-NH2) has been performed by standard peptide coupling method. As two parallel approaches, the strong affinity of thiols for maleimide and haloacetyl group has been exploited for subsequent post-SPPS addition of cymantrene-based organometallic cores, C2 and C3. Michael-like addition and thioether ligation of thiol functionalized PNA1 (H-gly-a-a-g-t-c-t-g-c-linker-cys-NH2) and PNA2 (C1-a-a-g-t-c-t-g-c-linker-cys-NH2) to cymantrene maleimide and chloroacetyl derivatives, C2 and C3, respectively, has been performed. The synthesized ruthenium(II)-cymantrenyl PNA oligomers have been characterized by mass spectrometry (ESI-MS) and IR spectroscopy. The distinct Mn-CO vibrational IR stretches, between 1,924–2,074 cm−1, have been used as markers to confirm the presence of cymantrenyl units in the PNA sequences and the purity of the HPLC-purified PNA thioethers assessed using LC-MS.

Specific uptake and interactions of peptide nucleic acid derivatives with biomimetic membranes

There is a growing interest in understanding the uptake mechanism of metal-containing peptide nucleic acid (PNA) bioconjugates into living cells. In this study, quartz crystal microbalance with dissipation monitoring (QCM-D) has been used to explore the membrane specific uptake and interactions of PNA/peptide/Ru(II) conjugates. For all lipid compositions, the unmodified PNA oligomer and its Ru(II) conjugate were found to traverse freely across the membrane in a trans-membrane manner, causing no significant changes in the membrane structure. The nuclear localised signal peptide (NLS) conjugated sequences showed membrane specific activities. In model mammalian and bacterial-mimetic membranes, rapid trans-membrane insertion was observed followed by a concentration dependent disruption and irreversible structural changes to the membrane system. The variations in the magnitude of the structural changes and in their tendency to facilitate disruption are ascribed to hydrophobicity, the cationic charge introduced on modification of the original PNA backbone as well as the physical state of the model membrane used.

Coordination chemistry of a mono-dibenzofuran derivative of 1,4,7,10-tetraazacyclododecane

Copper(II) and cadmium(II) complex of a mono-dibenzofuran derivative of 1,4,7,10-tetraazacyclododecane (cyclen), L1, have been prepared by reaction of the mono-dibenzofuran-substituted cyclen with either copper(II) or cadmium(II) perchlorate in acetonitrile. This yielded the corresponding divalent metal complexes, [Cu(L1)](ClO4)2·H2O (C1) and [Cd(L1)](ClO4)2·H2O (C2), which were isolated as single crystals suitable for X-ray crystallography by diffusing diethyl ether into an acetonitrile solution of each complex. For the copper(II) complex, C1, the X-ray crystal structure revealed a distorted square pyramidal Cu(II) coordination sphere occupied by four amine nitrogens from the cyclen ring and one oxygen from the amide linkage present in L1. On the other hand, the metal center in the cadmium complex is seven coordinate, with two weakly bound acetonitrile molecules occupying two additional coordination sites about the Cd(II) center; these bind cis to the amide oxygen. The coordination geometry is best described as monocapped trigonal prismatic. In both complexes, the secondary amine nitrogens on the cyclen macrocycle form hydrogen bonds with perchlorate counterions present in the crystal lattice. Titration of L1 with various metal ions (Mn2+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+) in acetonitrile revealed a gradual quenching of the benzofuran emission with increasing [M2+] consistent with formation of metal complexes with a 1 : 1 M2+ : L1 stoichiometry. From the emission data, the conditional stability constant was determined to be 10–20 times higher for the Cu(II) complex than the other divalent metal complexes investigated.

Neomycin B-cyclen conjugates and their Zn(II) complexes as RNA-binding agents.

Three new conjugates featuring the aminoglycoside antibiotic neomycin B linked to the 1,4,7,10-tetraazacyclododecane (cyclen) macrocycle via alkyl chains of varying lengths were synthesized from suitably protected derivatives of these precursors via conventional peptide coupling protocols. The final products were characterized by 1H NMR spectroscopy, mass spectrometry, and elemental analysis. FRET-based measurements examining the ability of the compounds to displace coumarin-labelled kanamycin A or neomycin B from Dy547-labelled prokaryotic ribosomal A-site RNA revealed that they bind to the A-site with slightly higher affinities than the parent aminoglycoside (e.g., IC50 at pH7=1.42-2.30μM vs. 2.35μM for neomycin B). This is attributed to the higher overall positive charge of the conjugates, resulting from protonation of the macrocylic amines. Consistent with a predominantly electrostatic mode of interaction, the binding affinities of the conjugates were found to increase with decreasing pH, reflecting a greater degree of protonation at lower pH. The zinc(II) complexes of the neomycin B-cyclen conjugates were found to bind to A-site RNA with even higher affinities (IC50=0.85-1.32μM), due to the Zn(II)-cyclen motif forming coordinative (and/or electrostatic) interactions with the uracil bases and/or phosphate groups within the A-site. These results highlight the potential for the nucleic acid-binding properties of aminoglycosides to be tuned via the covalent attachment of metal complexes, which could ultimately prove useful to the development of new anti-bacterial and anti-viral agents.

Comprehensive Vibrational Spectroscopic Investigation of trans,trans,trans-[Pt(N3)2(OH)2(py)2], a Pt(IV) Diazido Anticancer Prodrug Candidate.

We report a detailed study of a promising photoactivatable metal-based anticancer prodrug candidate, trans,trans,trans-[Pt(N3)2(OH)2(py)2] (C1; py = pyridine), using vibrational spectroscopic techniques. Attenuated total reflection Fourier transform infrared (ATR-FTIR), Raman, and synchrotron radiation far-IR (SR-FIR) spectroscopies were applied to obtain highly resolved ligand and Pt-ligand vibrations for C1 and its precursors (trans-[Pt(N3)2(py)2] (C2) and trans-[PtCl2(py)2] (C3)). Distinct IR- and Raman-active vibrational modes were assigned with the aid of density functional theory calculations, and trends in the frequency shifts as a function of changing Pt coordination environment were determined and detailed for the first time. The data provide the ligand and Pt-ligand (azide, hydroxide, pyridine) vibrational signatures for C1 in the mid- and far-IR region, which will provide a basis for the better understanding of the interaction of C1 with biomolecules.