Potent cyclometallated Pd(II) antitumor complexes bearing α-amino acids: synthesis, structural characterization, DNA/BSA binding, cytotoxicity and molecular dynamics simulation

A rational approach was adopted to design high-potential metal-based antitumor agents. A series of organometallic Pd(ii) complexes with a general formula of [Pd{κ2(C,C)-[(C6H4-2)PPh2]CH(CO)C6H4Ph-4}{κ2(N,O)}] (N,O = alanine (Pd-A), valine (Pd-V), leucine (Pd-L), l-isoleucine (Pd-I) and phenylalanine (Pd-F)) were prepared by cyclopalladation of the phosphorus ylide, bridge cleavage reaction and subsequent chelation of natural α-amino acids. The complexes were fully identified using IR and multinuclear 1H, 13C, 31P NMR spectroscopic methods. X-ray crystallography exhibited that the Pd(ii) atom is located in a slightly distorted square-planar environment surrounded by C,C-orthometallated phosphorus ylide as well as NO-pendant amino acid functionality. In vitro cytotoxicity evaluation of new cyclometallated Pd(ii) complexes toward a human leukemia (K562) cancer cell line indicated promising results. The highest cytotoxic activity was discovered in the case of phenylalanine (CH2C6H5). IC50 values of this complex on a panel of human tumor cell lines representative of liver (HepG2), breast (SKBR-3), and ovarian (A2780-Resistance/Sensitive) cancers also indicated promising antitumor effects in comparison with standard cisplatin. The binding interaction ability of the phenylalanine-containing orthopalladated complex, as the most efficient compound, with calf-thymus deoxyribonucleic acid (CT-DNA) and bovine serum albumin (BSA) was investigated. UV-Vis spectroscopy, competitive emission titration, and circular dichroism (CD) techniques demonstrated the intercalative binding of the Pd(ii) complex with DNA. Molecular docking studies also fully agreed with the experimental data. Examination of the reactivity towards the protein BSA revealed that the static quenching mechanism of BSA intrinsic fluorescence by the Pd(ii) complex with a binding constant (Kb) of ∼105 is indicative of the high affinity of the complex. The competitive binding experiment using site markers with definite binding sites demonstrated that the hydrophobic cavities of site I (subdomain IIA) are responsible for the bimolecular interaction between protein BSA and the complex. Molecular docking studies effectively confirmed the significance of hydrophobic interactions in Pd(ii)-BSA binding. The results of this study could greatly contribute to exploring new potent metal-based anticancer drugs.

Metallomics in Fish

Metallomics allows the integration of traditionally analytical studies with inorganic and biochemical studies. The study of metallomics in living organisms allows us to obtain information about how the metal ion is distributed and coordinated with proteins, the essentiality and/or toxicity, and the individual concentrations of metal species, thus contributing to elucidation of the physiological and functional aspects of these biomolecules. In this context, several lines of research have appeared in the literature with different terms and approaches. For example, metallomic, which deals with the characterization of the total metal/metalloid species present in an organism; metalloprotein, which deals with the characterization of the total elements present in a specific site of an organism (cellular behavior, protein, metalloprotein); and metallomic, which deals with a more in-depth study of metallome. In this area, information is sought on the interactions and functional connections of metal/metalloid species with genes, proteins, metabolites and other biomolecules of the organism and, therefore, the elucidation of the biological role exerted by the metal ions bound to the biomolecules. In this chapter, we will describe techniques used in animal studies.

Multi-omics and temporal dynamics profiling reveal disruption of central metabolism in Helicobacter pylori on bismuth treatment

Integration of multi-omics enables uncovering cellular responses to stimuli or the mechanism of action of a drug at a system level. Bismuth drugs have long been used for the treatment of Helicobacter pylori infection and their antimicrobial activity was attributed to dysfunction of multiple proteins based on previous proteome-wide studies. Herein, we investigated the response of H. pylori to a bismuth drug at transcriptome and metabolome levels. Our multi-omics data together with bioassays comprehensively reveal the impact of bismuth on a diverse array of intracellular pathways, in particular, disruption of central carbon metabolism is systematically evaluated as a primary bismuth-targeting system in H. pylori. Through temporal dynamics profiling, we demonstrate that bismuth initially perturbs the TCA cycle and then urease activity, followed by the induction of oxidative stress and inhibition of energy production, and in the meantime, induces extensive down-regulation in H. pylori metabolome. The present study thus expands our knowledge on the inhibitory actions of bismuth and provides a novel systematic perspective of H. pylori in response to a clinical drug that sheds light on enhanced therapeutic methodologies.

Metallomics: the history over the last decade and a future outlook

In 2004, the term "metallomics" was coined to describe integrated biometal science (H. Haraguchi, Metallomics as Integrated Biometal Science, J. Anal. At. Spectrom., 2004, 19, 5-14). Around 10 years have passed since then, and the history of metallomics over the last decade is reviewed here, discussing the development of metallomics before and after the proposal. Furthermore, the future outlook of metallomics research will be considered, in terms of topics such as the organization of platforms for metallomics research related to trace metal sciences, a simplified model of the biological system and omics-sciences, research subjects in metallomics, recent trends of metallomics research, and the challenge of single biological cell analysis.

Integration of fluorescence imaging with proteomics enables visualization and identification of metallo-proteomes in living cells

Metalloproteins account for nearly one-third of proteins in proteomes. To date, the identification of metalloproteins relies mainly on protein purification and the subsequent characterization of bound metals, which often leads to losses of metal ions bound weakly and transiently. Herein, we developed a strategy to visualize and subsequently identify endogenous metalloproteins and metal-binding proteins in living cells via integration of fluorescence imaging with proteomics. We synthesized a "metal-tunable" fluorescent probe (denoted as Mⁿ⁺-TRACER) that rapidly enters cells to target proteins with 4-40 fold fluorescence enhancements. By using Ni²⁺-TRACER as an example, we demonstrate the feasibility of tracking Ni²⁺-binding proteins in vitro, while cellular small molecules exhibit negligible interference on the labeling. We identified 44 Ni²⁺-binding proteins from microbes using Helicobacter pylori as a showcase. We further applied Cu²⁺-TRACER to mammalian cells and found 54 Cu²⁺-binding proteins. The strategy we report here provides a great opportunity to track various endogenous metallo-proteomes and to mine potential targets of metallodrugs.

Investigation of an optimal cell lysis method for the study of the zinc metalloproteome of Histoplasma capsulatum

This work sought to assess optimal extraction conditions in the study of the metalloproteome of the dimorphic fungus Histoplasma capsulatum. One of the body's responses to H. capsulatum infection is sequestration of zinc within host macrophage (MØ), as reported by Vignesh et al. (Immunity 39:697-710, 2013) and Vignesh et al. (PLOS Pathog 9:E1003815, 2013). Thus, metalloproteins containing zinc were of greatest interest as it plays a critical role in survival of the fungus. One challenge in metalloproteomics is the preservation of the native structure of proteins to retain non-covalently bound metals. Many of the conventional cell lysis, separation, and identification techniques in proteomics are carried out under conditions that could lead to protein denaturation. Various cell lysis techniques were investigated in an effort to both maintain the metalloproteins during lysis and subsequent analysis while, at the same time, serving to be strong enough to break the cell wall, allowing access to cytosolic metalloproteins. The addition of 1% Triton x-100, a non-ionic detergent, to the lysis buffer was also studied. Seven lysis methods were considered and these included: Glass Homogenizer (H), Bead Beater (BB), Sonication Probe (SP), Vortex with 1% Triton x-100 (V, T), Vortex with no Triton x-100 (V, NT), Sonication Bath, Vortex, and 1% Triton x-100 (SB, V, T) and Sonication Bath, Vortex, and no Triton x-100 (SB, V, NT). A Qubit® Assay was used to compare total protein concentration and inductively coupled plasma-mass spectrometry (ICP-MS) was utilized for total metal analysis of cell lysates. Size exclusion chromatography coupled to ICP-MS (SEC-HPLC-ICP-MS) was used for separation of the metalloproteins in the cell lysate and the concentration of Zn over a wide molecular weight range was examined. Additional factors such as potential contamination sources were also considered. A cell lysis method involving vortexing H. capsulatum yeast cells with 500 μm glass beads in a 1% Triton x-100 lysis buffer (V, T) was found to be most advantageous to extract intact zinc metalloproteins as demonstrated by the highest Zn to protein ratio, 1.030 ng Zn/μg protein, and Zn distribution among high, mid, and low molecular weights suggesting the least amount of protein denaturation. Graphical abstract In this work, several cell lysis techniques and two lysis buffers were investigated to evaluate the preservation of the zinc metalloproteome of H. capsulatum while maintaining compatibility with the analytical techniques employed.

The evolution of environmental metalloproteomics over the last 15 years through bibliometric techniques

Metalloproteomic studies in environmental scenarios are of significant value in elucidating metal uptake, trafficking, accumulation and metabolism linked to biomolecules in biological systems. The advent of this field occurred in the early 2000s, and it has since become an interesting and growing area of interdisciplinary research, although the number of publications in Environmental Metalloprotemics is still very low compared to other metallomic areas. In this context, the evolution of Environmental Metalloprotemics in the last decades was evaluated herein through the use of bibliometric techniques, identifying variables that may aid researchers in this area to form collaborative networks with established scientists in this regard, such as main authors, published articles, institutions, countries and established collaborations involved in academic research on this subject. Results indicate a growing trend of publications over time, reflecting the interest of the scientific community in Environmental Metalloprotemics, but also demonstrated that the research interactions in this field are still country- and organization-specific. Higher amounts of publications are observed from the late 2000's onwards, related to the increasing technological advances in the area, such as the development of techniques combining atomic spectroscopy and biochemical or proteomic techniques. The retrieved publications also indicate that the recent advances in genomic, proteomic and metallomic areas have allowed for extended applications of Environmental Metalloprotemics in non-model organisms. The results reported herein indicate that Environmental Metalloprotemics seems to now be reaching a more mature stage, in which analytical techniques are now well established and can be routinely applied in environmental scenarios, benefitting researchers and allowing for further insights into this fascinating field.

Investigation of thermostable metalloproteins in Perna perna mussels from differentially contaminated areas in Southeastern Brazil by bioanalytical techniques

Metallomic studies regarding environmental contamination by metals are of value in elucidating metal uptake, trafficking, accumulation and metabolism in biological systems. Many proven bioindicator species, such as bivalves, have not yet, however, been well-characterized regarding their metalloprotein expression in response to environmental contaminants. In this context, the aim of the present study was to investigate metalloprotein expressions in the thermostable protein fraction of muscle tissue and digestive glands from mussels (Perna perna) from three differentially metal-contaminated sites in Southeastern Brazil in comparison with a reference site. The thermostable protein fractions were analyzed by SDS-PAGE and SEC-HPLC-ICP-MS. Metal content was also determined in both the crude and the purified extracts. Several inter-organ differences were observed, which is to be expected, while inter-site differences regarding thermostable protein content were also verified, indicating accumulation of these elements in muscle tissue and digestive glands and disruption of homeostasis of essential elements, with detoxification attempts by metal-bound proteins, since all metalloproteins present in both matrices eluted bound to at least one non-essential metal. These results are also noteworthy with regard to the adopted reference site, that also seems to be contaminated by toxic metals.

Recent advances in affinity capillary electrophoresis for binding studies

The present review covers recent advances and important applications of affinity capillary electrophoresis (ACE). It provides an overview about various ACE types, including ACE-MS, the multiple injection mode, the use of microchips and field-amplified sample injection-ACE. The most common scenarios of the studied affinity interactions are protein-drug, protein-metal ion, protein-protein, protein-DNA, protein-carbohydrate, carbohydrate-drug, peptide-peptide, DNA-drug and antigen-antibody. Approaches for the improvements of ACE in term of precision, rinsing protocols and sensitivity are discussed. The combined use of computer simulation programs to support data evaluation is presented. In conclusion, the performance of ACE is compared with other techniques such as equilibrium dialysis, parallel artificial membrane permeability assay, high-performance affinity chromatography as well as surface plasmon resonance, ultraviolet, circular dichroism, nuclear magnetic resonance, Fourier transform infrared, fluorescence, MS and isothermal titration calorimetry.

On-line coupling of continuous-flow gel electrophoresis with inductively coupled plasma-mass spectrometry to quantitatively evaluate intracellular metal binding properties of metallochaperones HpHypA and HpHspA in E. coli cells

On-line coupling of gel electrophoresis with inductively coupled plasma-mass spectrometry (GE-ICP-MS) offers a strategy to monitor intracellular metals and their associated proteins simultaneously. Herein, we examine the feasibility of the GE-ICP-MS system in the quantitative analysis of intracellular metal binding properties using two Helicobacter pylori metallochaperones HypA and HspA overexpressed in E. coli cells as showcases. We show that parallel detection of metal and sulfur signals allows accurate quantification of intracellular metal-protein stoichiometries, even for metalloproteins that bind metal ions with micromolar affinities. Using this approach, we demonstrate that only a trace amount of Ni(2+) is associated with HpHypA in cells, distinct from the in vitro observation of stoichiometric binding, while HpHypA exhibits high fidelity towards its structural metal Zn(2+) with stoichiometric Zn(2+) binding. In contrast, HpHspA associates with Zn(2+), Ni(2+), Cu(2+) and Co(2+) from an essential metal pool with ca. 0.5 molar equivalents of total metals bound per HpHspA monomer. The metal binding properties of both HpHypA and HpHspA were altered by Bi(3+). The binding of both Zn(2+) and Ni(2+) to HpHypA was suppressed under the stress of Bi(3+) in cells, different from in vitro studies that showed that Bi(3+) interfered with Zn(2+) but not Ni(2+) binding. This study provides an analytical approach to investigate the intracellular metal selectivity of overexpressed metalloproteins.

Metallomic and metalloproteomic strategies in elucidating the molecular mechanisms of metallodrugs

Advances in the mechanistic studies of metallodrugs by metallomic and metalloproteomic approaches will improve our understanding of the mechanism of action and allow more metallodrugs to be developed.

Recent advances in bioinorganic chemistry of bismuth

Bismuth has been used in medicine for over two centuries for the treatment of various diseases, in particular for gastrointestinal disorders, owing to its antimicrobial activity. Recent structural characterization of bismuth drugs provides an insight into assembly and pharmacokinetic pathway of the drugs. Mining potential protein targets inside the pathogen via metallomic/metalloproteomic approach and further characterization on the interactions of bismuth drugs with these targets laid foundation in understanding the mechanism of action of bismuth drugs. Such studies would be beneficial in rational design of new potential drugs.

Metallothionein-inspired prototype of molecular pincer

Study of Zn and Pb release from complexes with natural and synthetic amidothiol motifs inspired the design of a "molecular pincer" that scavenges quantitatively metals from liquid environment and releases them, on-demand, under very mild oxidative conditions.

Tracking bismuth antiulcer drug uptake in single Helicobacter pylori cells

Bismuth-based drugs have long been used for the treatment of Helicobacter pylori infection. In this work, the metal content in H. pylori was monitored at the single-cell level by time-resolved inductively coupled plasma mass spectrometry, and ∼2.9 × 10(7) Mg atoms/cell was determined for the wild-type. Bacteria treated with a Bi antiulcer drug deposited nearly 1.0 × 10(6) Bi atoms/cell, whereas the uptake process took ∼3 h to reach the half-maximum. Interference of ferric ions on bismuth uptake was demonstrated, suggesting that the metallodrug can utilize certain iron-transport pathways in the pathogen. The approach provides a general strategy for monitoring metals in single cells, facilitating exploration of metal-relevant bioprocesses.