Biological Inorganic Chemistry

Guanidine- and purine-functionalized ligands of Fe III Zn II complexes: effects on the hydrolysis of DNA Abstract In this paper, the catalytic effects of aminoguanidine and aminopurine groups in the second sphere of a FeIIIZnII complex that mimics the active site of the metallohydrolase purple acid phosphatase (PAP) are investigated, with a particular view on DNA as substrate. The ligand 3-(((3-((bis(2-(pyridin-2-yl)ethyl)amino)methyl)-2-hydroxy-5-methylbenzyl)(pyridin-2-ylmethyl)amino)meth-yl)-2 hydroxy-5-methylbenzaldehyde—(H2L1bpea) was synthesized and its complex [(OH)FeIII(μ-OH)ZnII(H2O)(L1bpea)](ClO4) was used as a base for comparison with similar complexes previously published in the literature. Subsequent modifications were conducted in the aldehyde group, where aminoguanidine (amig) and aminopurine (apur) were used as side chain derivatives. The complexes [(OH)FeIII(μ-OH)ZnII(H2O)(L1bpea)](ClO4) (1), [(OH)FeIII(μ-OH)ZnII(H2O)(L1bpea–amig)](ClO4) (2) and [(OH)FeIII(μ-OH)ZnII(H2O)(L1bpea–apur)](ClO4) (3) were characterized by spectroscopic methods (infrared, UV–Vis) and ESI-MS spectrometry. Density functional theory (DFT) was also used to better understand the structure of the complexes. The hydrolytic activity of complexes 1, 2 and 3 was analyzed using both the model substrate 2,4-BDNPP (bis-(2,4-dinitrophenyl)phosphate) and DNA. Complexes 2 and 3, containing the derivatized ligands, have a significantly higher association constant (Kassoc≅ 1/KM) for the activated substrate 2,4-BDNPP compared to complex 1. The catalytic efficiency (kcat/KM) is also higher due to hydrogen bonds and/or π-stacking interactions between the substrate and the aminoguanidine or aminopurine groups present in 2 and 3, respectively. In the DNA cleavage assays, all complexes were able to cleave DNA, with 1 and 2having higher catalytic activity than 3. In addition, when compared to previously analyzed complexes, complex 2 is one of the most active, having a kcat of 0.21 h−1. Graphical abstract

Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine Abstract 1,3-Diaza-2-oxophenoxazine (X) has been introduced as a ligand in silver(I)-mediated base pairing in a parallel DNA duplex. This fluorescent cytosine analog is capable of forming stabilizing X–Ag(I)–X and X–Ag(I)–C base pairs in DNA duplexes, as confirmed by temperature-dependent UV spectroscopy and luminescence spectroscopy. DFT calculations of the silver(I)-mediated base pairs suggest the presence of a synergistic hydrogen bond. Molecular dynamics (MD) simulations of entire DNA duplexes nicely underline the geometrical flexibility of these base pairs, with the synergistic hydrogen bond facing either the major or the minor groove. Upon silver(I) binding to the X:X or X:C base pairs, the luminescence emission maximum experiences a red shift from 448 to 460 nm upon excitation at 370 nm. Importantly, the luminescence of the 1,3-diaza-2-oxophenoxazine ligand is not quenched significantly upon binding a silver(I) ion. In fact, the luminescence intensity even increases upon formation of a X–Ag(I)–C base pair, which is expected to be beneficial for the development of biosensors. As a consequence, the silver(I)-mediated phenoxazinone base pairs represent the first strongly fluorescent metal-mediated base pairs. Graphic abstract

Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme Abstract Glycyl radical enzymes (GREs) utilize a glycyl radical cofactor to carry out a diverse array of chemically challenging enzymatic reactions in anaerobic bacteria. Although the glycyl radical is a powerful catalyst, it is also oxygen sensitive such that oxygen exposure causes cleavage of the GRE at the site of the radical. This oxygen sensitivity presents a challenge to facultative anaerobes dwelling in areas prone to oxygen exposure. Once GREs are irreversibly oxygen damaged, cells either need to make new GREs or somehow repair the damaged one. One particular GRE, pyruvate formate lyase (PFL), can be repaired through the binding of a 14.3 kDa protein, termed YfiD, which is constitutively expressed in E. coli. Herein, we have solved a solution structure of this ‘spare part’ protein using nuclear magnetic resonance spectroscopy. These data, coupled with data from circular dichroism, indicate that YfiD has an inherently flexible N-terminal region (residues 1–60) that is followed by a C-terminal region (residues 72–127) that has high similarity to the glycyl radical domain of PFL. Reconstitution of PFL activity requires that YfiD binds within the core of the PFL barrel fold; however, modeling suggests that oxygen-damaged, i.e. cleaved, PFL cannot fully accommodate YfiD. We further report that a PFL variant that mimics the oxygen-damaged enzyme is highly susceptible to proteolysis, yielding additionally truncated forms of PFL. One such PFL variant of ~ 77 kDa makes an ideal scaffold for the accommodation of YfiD. A molecular model for the rescue of PFL activity by YfiD is presented. Graphic abstract

Activity and electrochemical properties: iron complexes of the anticancer drug triapine and its analogs Abstract Triapine (3-AP), is an iron-binding ligand and anticancer drug that is an inhibitor of human ribonucleotide reductase (RNR). Inhibition of RNR by 3-AP results in the depletion of dNTP precursors of DNA, thereby selectively starving fast-replicating cancer cells of nucleotides for survival. The redox-active form of 3-AP directly responsible for inhibition of RNR is the Fe(II)(3-AP)2 complex. In this work, we synthesize 12 analogs of 3-AP, test their inhibition of RNR in vitro, and study the electronic properties of their iron complexes. The reduction and oxidation events of 3-AP iron complexes that are crucial for the inhibition of RNR are modeled with solution studies. We monitor the pH necessary to induce reduction in iron complexes of 3-AP analogs in a reducing environment, as well as the kinetics of oxidation in an oxidizing environment. The oxidation state of the complex is monitored using UV–Vis spectroscopy. Isoquinoline analogs of 3-AP favor the maintenance of the biologically active reduced complex and possess oxidation kinetics that allow redox cycling, consistent with their effective inhibition of RNR seen in our in vitro experiments. In contrast, methylation on the thiosemicarbazone secondary amine moiety of 3-AP produces analogs that form iron complexes with much higher redox potentials, that do not redox cycle, and are inactive against RNR in vitro. Graphic abstract The catalytic subunit of human Ribonucleotide Reductase (RNR), contains a tyrosyl radical in the enzyme active site. Fe(II) complexes of 3-AP and its analogs can quench the radical and, subsequently, inactivate RNR. The potency of RNR inhibitors is highly dependent on the redox properties of the iron complexes, which can be tuned by ligand modifications. Complexes are found to be active within a narrow redox window imposed by the cellular environment.

Green synthesis of copper oxide nanoparticles using sinapic acid: an underpinning step towards antiangiogenic therapy for breast cancer Abstract Synthesis of copper oxide nanoparticles without any chemical reductant is always a challenging methodology for biological studies. In this study, sinapic acid, a phytochemical, is used for the synthesis of stable copper oxide nanoparticles. The as-synthesized nanoparticles were characterized thoroughly using UV–Visible, IR spectroscopy, Transmission Electron Microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). Nanoparticles collected during different time intervals of synthesis (60,120 and 180 min) were subjected for analysis, where the occurrence of copper oxide nanoparticles with substantial morphology was seen at 180 min. Further, nanoparticles synthesized at 120 and 180 min were studied for their potential biological applications. These copper oxide nanoparticles evinced potential cytotoxic effects on breast cancer cells, MCF7 and MDA-MB231. Supplementarily, it also exhibited anti-angiogenic effect on endothelial cells (EA.hy926), thus confirming its potential to inhibit angiogenesis in cancer. Graphic abstract

Compounds with capacity to quench the tyrosyl radical in Pseudomonas aeruginosa ribonucleotide reductase Abstract Ribonucleotide reductase (RNR) has been extensively probed as a target enzyme in the search for selective antibiotics. Here we report on the mechanism of inhibition of nine compounds, serving as representative examples of three different inhibitor classes previously identified by us to efficiently inhibit RNR. The interaction between the inhibitors and Pseudomonas aeruginosa RNR was elucidated using a combination of electron paramagnetic resonance spectroscopy and thermal shift analysis. All nine inhibitors were found to efficiently quench the tyrosyl radical present in RNR, required for catalysis. Three different mechanisms of radical quenching were identified, and shown to depend on reduction potential of the assay solution and quaternary structure of the protein complex. These results form a good foundation for further development of P. aeruginosaselective antibiotics. Moreover, this study underscores the complex nature of RNR inhibition and the need for detailed spectroscopic studies to unravel the mechanism of RNR inhibitors.

A new 4-(pyridinyl)-4 H -benzo[ g ]chromene-5,10-dione ruthenium(II) complex inducing senescence in 518A2 melanoma cells Abstract 2-Amino-5,10-dihydro-5,10-dioxo-4(pyridine-3-yl)-4H-benzo[g]chromene-3-carbonitrile 5, a cytotoxic lawsone derivative, was reacted with [Ru(p-cymene)Cl2]2 to afford a new Ru(II) ‘piano-stool’ complex 6 which differed from its ligand 5 by a greater selectivity for highly invasive 518A2 melanoma cells over human dermal fibroblasts in MTT cytotoxicity assays, and by inducing senescence rather than apoptosis in the former. DNA is a likely cellular target of complex 6 as it bound, presumably non-covalently, to linear and circular double-stranded DNA in vitro and as ruthenium was found in the lysate of nuclei of treated 518A2 melanoma cells. It also caused a fivefold increase of reactive oxygen species in these cells, originating from a more persistent redox cycling as visualised by cyclic voltammetry.

Ironing out pyoverdine’s chromophore structure: serendipity or design? Abstract Pyoverdines are Pseudomonas aeruginosa’s primary siderophores. These molecules, composed of a fluorescent chromophore attached to a peptide chain of 6–14 amino acids, are synthesized by the bacterium to scavenge iron (essential to its survival and growth) from its environment. Hijacking the siderophore pathway to use pyoverdine–antibiotic compounds in a Trojan horse approach has shown promise but remains very challenging because of the synthetic efforts involved. Indeed, both possible approaches (grafting an antibiotic on pyoverdine harvested from Pseudomonas or designing a total synthesis route) are costly, time-consuming and low-yield tasks. Designing comparatively simple analogs featuring the salient properties of the original siderophore is thus crucial for the conception of novel antibiotics to fight bacterial resistance. In this work, we focus on the replacement of the pyoverdine chromophore, a major roadblock on the synthetic pathway. We propose three simpler analogs and evaluate their ability to complex iron and interact with the FpvA transporter using molecular modeling techniques. Based on these results, we discuss the role of the native chromophore’s main features (polycyclicity, positive charge, flexibility) on pyoverdine’s ability to bind iron and be recognized by membrane transporter FpvA and propose guidelines for the design of effective synthetic siderophores. Graphic abstract

Proton affinity studies of nickel N 2 S 2 complexes and control of aggregation Abstract The thiolate ligands of [NiFe]-H2ase enzymes have been implicated as proton-binding sites for the reduction/oxidation of H+/H2. This study examines the ligand effect on reactivity of NiN2S2 complexes with an array of acids in methanol solution. UV–Vis absorption spectroscopy is utilized to observe the transformation from the monomeric species to a trimetallic complex that is formed after proton-induced ligand dissociation. Nickel complexes with a flexible (propyl and ethyl) N to N linker were found to readily form the trimetallic complex with acids as weak as ammonium (pKa = 10.9 in methanol). A more constrained nickel complex with a diazacycloheptane N to N linker required stronger acids such as 2,2-dichloroacetic acid (pKa = 6.38 in methanol) to form the trimetallic complex and featured the formation of an NiN2S2H+ complex with acetic acid (pKa = 9.63 in methanol). The most strained ligand, which featured a diazacyclohexane backbone, readily dissociated from the nickel center upon mixture with acids with pKa ≤ 9.63 and showed no evidence of a trimetallic species with any acid. This research highlights the dramatic differences in reactivity with proton sources that can be imparted by minor alterations to ligand geometry and strain. Graphical abstract

Note from the President