Identification of metal-associated proteins in cells by using continuous-flow gel electrophoresis and inductively coupled plasma mass spectrometry

Bismuth drug eradicates multi-drug resistant Burkholderia cepacia complex via aerobic respiration

Burkholderia cepacia complex (Bcc) is a group of Gram-negative opportunistic pathogens highly responsible for chronic pulmonary infection in cystic fibrosis (CF). Current therapies involving double or triple antibiotic combinations can rarely eradicate the pathogen in chronically infected patients owing to its intrinsic resistance to a variety of antibiotics. Herein, we show that a bismuth drug (and related compounds) could inhibit the growth of clinically antibiotic-resistant Bcc strains, with MIC (ca. 25 μg mL-1) comparable to that for Helicobacter pylori, and the combination of a bismuth drug and antibiotics also demonstrated excellent activity against biofilm and persisters of Bcc. Importantly, the in vitro antimicrobial activity of a bismuth drug could be well translated into in vivo evidenced by about 50% survival rates in the Galleria mellonella infection model. Transcriptomics analysis shows the dynamic responses of Bcc to bismuth treatment. Using a homemade metalloproteomic approach, we could identify 26 BiIII-binding proteins (15 cytosolic proteins and 11 membrane proteins). Further mechanistic studies reveal that bismuth drugs initially target the TCA cycle through the binding and inactivation of a series of enzymes including malate dehydrogenase (MDH), malate synthase (AceB), and succinyl coenzyme A synthetase (SCS), then interfere oxidative phosphorylation through binding to terminal oxidases, i.e., CyoC and CydA, to disrupt electron transport chain, eventually, disrupt protein translation and ribosome via binding and down-regulation of key proteins. Our studies highlight the great potential of bismuth drugs and/or compounds to treat multidrug-resistant Bcc infections.

Metal-Based Approaches for the Fight against Antimicrobial Resistance: Mechanisms, Opportunities, and Challenges

The rapid emergency and spread of antimicrobial-resistant (AMR) bacteria and the lack of new antibiotics being developed pose serious threats to the global healthcare system. Therefore, the development of more effective therapies to overcome AMR is highly desirable. Metal ions have a long history of serving as antimicrobial agents, and metal-based compounds are now attracting more interest from scientific communities in the fight against AMR owing to their unique mechanism. Moreover, they may also serve as antibiotic adjuvants to enhance the efficacy of clinically used antibiotics. In this perspective, we highlight important showcase studies in the last 10 years on the development of metal-based strategies to overcome the AMR crisis. Specifically, we categorize these metallo-antimicrobials into five classes based on their modes of action (i.e., metallo-enzymes and metal-binding enzyme inhibitors, membrane perturbants, uptake/efflux system inhibitors/regulators, persisters inhibitors, and oxidative stress inducers). The significant advantages of metallo-antimicrobials over traditional antibiotics lie in their multitargeted mechanisms, which render less likelihood to generate resistance. However, we notice that such modes of action of metallo-antimicrobials may also raise concern over their potential side effects owing to the low selectivity toward pathogens and host, which appears to be the biggest obstacle for downstream translational research. We anticipate that combination therapy through repurposing (metallo)drugs with antibiotics and the optimization of their absorption route through formulation to achieve a target-oriented delivery will be a powerful way to combat AMR. Despite significant challenges, metallo-antimicrobials hold great opportunities for the therapeutic intervention of infection by resistant bacteria.

Lighting Up and Identifying Metal-Binding Proteins in Cells

Metal ions, either essential or therapeutic, play critical roles in life processes or in the treatment of diseases. Proteins and enzymes are involved in metal homeostasis and the action of metallodrugs. Imaging and identifying these metal-binding proteins will facilitate the elucidation of metal-mediated life processes. The emerging research field of metallomics and metalloproteomics has significantly advanced our understanding of metal homeostasis and the roles that metals play in biology and medicine. Fluorescence-based metalloproteomics offers the possibility of not only visualization but also identification of metal-binding proteins in living cells and tissues. Herein, we summarize different strategies of labeling and tracking of metal-binding proteins with the aid of fluorescent probes. We highlight several examples as showcases of how this fluorescence-based metalloproteomics approach could be utilized in metallobiology and chemical biology. In conclusion, we also discuss the advantages and limitations of fluorescence-based metalloproteomics approaches and point out future directions of metalloproteomics including development of more sensitive and selective fluorescence probes, integration with other omics approaches, as well as application of emerging advanced super-resolution imaging techniques that utilize fluorescent molecules or proteins. We aim to attract more scientists to engage in this exciting field.

Metal-detection based techniques and their applications in metallobiology

Metals are essential for human health and play a crucial role in numerous biological processes and pathways. Gaining a deeper insight into these biological events will facilitate novel strategies for disease prevention, early detection, and personalized treatment. In recent years, there has been significant progress in the development of metal-detection based techniques from single cell metallome and proteome profiling to multiplex imaging, which greatly enhance our comprehension of the intricate roles played by metals in complex biological systems. This perspective summarizes the recent progress in advanced metal-detection based techniques and highlights successful applications in elucidating the roles of metals in biology and medicine. Technologies including machine learning that couple with single-cell analysis such as mass cytometry and their application in metallobiology, cancer biology and immunology are also emphasized. Finally, we provide insights into future prospects and challenges involved in metal-detection based techniques, with the aim of inspiring further methodological advancements and applications that are accessible to chemists, biologists, and clinicians.

Fasten the analysis of metal-binding proteins with GE-ICP-MS via increasing the electrolyte concentration of the running buffer

The coupled system of column gel electrophoresis and inductively coupled plasma mass spectrometry (GE-ICP-MS) is a highly effective technique for detecting metal-binding proteins. However, it takes a long time for this method to test a single sample, which greatly limits its application. In this study, GE-ICP-MS system was optimized by adjusting the analytical conditions, including the concentration and pH of running buffer and the proportion of polyacrylamide gel. The results of the experiment showed that the migration speed of proteins in GE was enhanced by increasing the electrolyte concentration in the running buffer solution. Additionally, the ICP-MS response, which was dramatically decreased because of the change in running buffer solution, can be stabilized by adjusting pH of running buffer. Meanwhile, the optimization of polyacrylamide gel ratio allows GE-ICP-MS to maintain high resolution for proteins of similar molecular weight with increased detection speed. After increasing the concentration of running buffer by 10 times, four iodine labeled proteins were successfully separated at baseline by the GE-ICP-MS system at pH 8.0 in 40 min using a resolving gel (8%, 7 cm) and a stacking gel (4%, 1 cm), which was three times faster than the original one. Finally, the optimized method was proved by detecting a silver-binding protein in rat plasma samples. The above method provided an effective and rapid detection for metal-binding proteins in organism.

Comparative proteomics unveils the bacteriostatic mechanisms of Ga(III) on the regulation of metabolic pathways in Pseudomonas aeruginosa

Gallium has a long history as a chemotherapeutic agent. The mechanisms of action of Ga(III)-based anti-infectives are different from conventional antibiotics, which primarily result from the chemical similarities of Ga(III) with Fe(III) and substitution of gallium into iron-dependent biological pathways. However, more aspects of the molecular mechanisms of Ga(III) against human pathogens, especially the effects on bacterial metabolic processes, remain to be understood. Herein, by using conventional quantitative proteomics, we identified the protein changes of Pseudomonas aeruginosa (P. aeruginosa) in response to Ga(NO3)3 treatment. We show that Ga(III) exhibits bacteriostatic mode of action against P. aeruginosa through affecting the expressions of a number of key enzymes in the main metabolic pathways, including glycolysis, TCA cycle, amino acid metabolism, and protein and nucleic acid biosynthesis. In addition, decreased expressions of proteins associated with pathogenesis and virulence of P. aeruginosa were also identified. Moreover, the correlations between protein expressions and metabolome changes in P. aeruginosa upon Ga(III) treatment were identified and discussed. Our findings thus expand the understanding on the antimicrobial mechanisms of Ga(III) that shed light on enhanced therapeutic strategies. BIOLOGICAL SIGNIFICANCE: Mounting evidence suggest that the efficacy and resistance of clinical antibiotics are closely related to the metabolic homeostasis in bacterial pathogens. Ga(III)-based compounds have been repurposed as antibacterial therapeutic candidates against antibiotics resistant pathogens, and represent a safe and promising treatment for clinical human infections, while more thorough understandings of how bacteria respond to Ga(III) treatment are needed. In the present study, we provide evidences at the proteome level that indicate Ga(III)-induced metabolic perturbations in P. aeruginosa. We identified and discussed the interference of Ga(III) on the expressions and activities of enzymes in the main metabolic pathways in P. aeruginosa. In view of our previous report that the antimicrobial efficacy of Ga(III) could be modulated according to Ga(III)-induced metabolome changes in P. aeruginosa, our current analyses may provide theoretical basis at the proteome level for the development of efficient gallium-based therapies by exploiting bacterial metabolic mechanisms.

Mitochondrial ATP synthase as a direct molecular target of chromium(III) to ameliorate hyperglycaemia stress

Chromium(III) is extensively used as a supplement for muscle development and the treatment of diabetes mellitus. However, its mode of action, essentiality, and physiological/pharmacological effects have been a subject of scientific debate for over half a century owing to the failure in identifying the molecular targets of Cr(III). Herein, by integrating fluorescence imaging with a proteomic approach, we visualized the Cr(III) proteome being mainly localized in the mitochondria, and subsequently identified and validated eight Cr(III)-binding proteins, which are predominately associated with ATP synthesis. We show that Cr(III) binds to ATP synthase at its beta subunit via the catalytic residues of Thr213/Glu242 and the nucleotide in the active site. Such a binding suppresses ATP synthase activity, leading to the activation of AMPK, improving glucose metabolism, and rescuing mitochondria from hyperglycaemia-induced fragmentation. The mode of action of Cr(III) in cells also holds true in type II diabetic male mice. Through this study, we resolve the long-standing question of how Cr(III) ameliorates hyperglycaemia stress at the molecular level, opening a new horizon for further exploration of the pharmacological effects of Cr(III).

Metal-Organic Frameworks Encapsulating Carbon Dots Enable Fast Speciation of Mono- and Divalent Copper

Copper is an essential element to play significant roles in human health associated to the strong redox properties of Cu(I) and Cu(II). The concurrent monitoring of copper species in biological matrixes is highly desired. Herein, a dual-channel fluorescence nanoprobe was designed for the speciation of mono- and divalent copper by conjugating carbon dots (CDs) with Eu-based metal-organic frameworks (Eu-MOFs). The obtained Eu-MOFs@CD nanoprobe exhibits fluorescence at λ_ex/λ_em = 380/454 nm from CDs and λ_ex/λ_em = 275/615 nm from Eu-MOFs. Bathocuproine disulfonate (BCS) specifically chelates Cu⁺ to produce a BCS-Cu⁺ adduct with absorption at 480 nm, which quenches the fluorescence of CDs at 454 nm due to the inner filter effect. On the other hand, Cu²⁺ quenches the fluorescence of Eu-MOFs due to the replacement of Eu³⁺ by Cu²⁺. Thus, Eu-MOFs@CDs enable extremely fast detection of Cu⁺ and Cu²⁺ within 1 min. Furthermore, the nanoprobe is demonstrated by monitoring the variation of Cu⁺ and Cu²⁺ in the degradation process of copper nanoparticles and Cu-based MOFs.

Medicinal chemistry and biomedical applications of bismuth-based compounds and nanoparticles

Bismuth as a relatively non-toxic and inexpensive metal with exceptional properties has numerous biomedical applications. Bismuth-based compounds are used extensively as medicines for the treatment of gastrointestinal disorders including dyspepsia, gastric ulcers and H. pylori infections. Recently, its medicinal application was further extended to potential treatments of viral infection, multidrug resistant microbial infections, cancer and also imaging, drug delivery and biosensing. In this review we have highlighted the unique chemistry and biological chemistry of bismuth-209 as a prelude to sections covering the unique antibacterial activity of bismuth including a description of research undertaken to date to elucidate key molecular mechanisms of action against H. pylori, the development of novel compounds to treat infection from microbes beyond H. pylori and the significant role bismuth compounds can play as resistance breakers. Furthermore we have provided an account of the potential therapeutic application of bismuth-213 in targeted alpha therapy as well as a summary of the biomedical applications of bismuth-based nanoparticles and composites. Ultimately this review aims to provide the state of the art, highlight the untapped biomedical potential of bismuth and encourage original contributions to this exciting and important field.

Arsenic trioxide targets Hsp60, triggering degradation of p53 and survivin

The mechanisms of action of arsenic trioxide (ATO), a clinically used drug for the treatment of acute promyelocytic leukemia (APL), have been actively studied mainly through characterization of individual putative protein targets. There appear to be no studies at a system level. Herein, we integrate metalloproteomics through a newly developed organoarsenic probe, As-AC (C₂₀H₁₇AsN₄O₃S₂) with quantitative proteomics, allowing 37 arsenic binding and 250 arsenic regulated proteins to be identified in NB4, a human APL cell line. Bioinformatics analysis reveals that ATO disrupts multiple physiological processes, in particular, chaperone-related protein folding and cellular response to stress. Furthermore, we discover heat shock protein 60 (Hsp60) as a vital target of ATO. Through biophysical and cell-based assays, we demonstrate that ATO binds to Hsp60, leading to abolishment of Hsp60 refolding capability. Significantly, the binding of ATO to Hsp60 disrupts the formation of Hsp60-p53 and Hsp60-survivin complexes, resulting in degradation of p53 and survivin. This study provides significant insights into the mechanism of action of ATO at a systemic perspective, and serves as guidance for the rational design of metal-based anticancer drugs.

A highly selective organoarsenic fluorescent probe As-AC and quantitative proteomics were employed to track arsenic-binding and regulating proteins in live leukemia cells. Hsp60 was validated as a new target of ATO.

Native Separation and Metallation Analysis of SOD1 Protein from the Human Central Nervous System: a Methodological Workflow

Studies of the metal content of metalloproteins in tissues from the human central nervous system (CNS) can be compromised by preparative techniques which alter levels of, or interactions between, metals and the protein of interest within a complex mixture. We developed a methodological workflow combining size exclusion chromatography, native isoelectric focusing, and either proton or synchrotron X-ray fluorescence within electrophoresis gels to analyze the endogenous metal content of copper-zinc superoxide dismutase (SOD1) purified from minimal amounts (<20 mg) of post-mortem human brain and spinal cord tissue. Abnormal metallation and aggregation of SOD1 are suspected to play a role in amyotrophic lateral sclerosis and Parkinson's disease, but data describing SOD1 metal occupancy in human tissues have not previously been reported. Validating our novel approach, we demonstrated step-by-step metal preservation, preserved SOD1 activity, and substantial enrichment of SOD1 protein versus confounding metalloproteins. We analyzed tissues from nine healthy individuals and five CNS regions (occipital cortex, substantia nigra, locus coeruleus, dorsal spinal cord, and ventral spinal cord). We found that Cu and Zn were bound to SOD1 in a ratio of 1.12 ± 0.28, a ratio very close to the expected value of 1. Our methodological workflow can be applied to the study of endogenous native SOD1 in a pathological context and adapted to a range of metalloproteins from human tissues and other sources.

Multi-target mode of action of silver against Staphylococcus aureus endows it with capability to combat antibiotic resistance

The rapid emergence of drug resistant Staphylococcus aureus (S. aureus) poses a serious threat to public health globally. Silver (Ag)-based antimicrobials are promising to combat antibiotic resistant S. aureus, yet their molecular targets are largely elusive. Herein, we separate and identify 38 authentic Ag⁺-binding proteins in S. aureus at the whole-cell scale. We then capture the molecular snapshot on the dynamic action of Ag⁺ against S. aureus and further validate that Ag⁺ could inhibit a key target 6-phosphogluconate dehydrogenase through binding to catalytic His185 by X-ray crystallography. Significantly, the multi-target mode of action of Ag⁺ (and nanosilver) endows its sustainable antimicrobial efficacy, leading to enhanced efficacy of conventional antibiotics and resensitization of MRSA to antibiotics. Our study resolves the long-standing question of the molecular targets of silver in S. aureus and offers insights into the sustainable bacterial susceptibility of silver, providing a potential approach for combating antimicrobial resistance.

Silver (Ag) has been used as an antimicrobial agent since a long time, but its molecular mechanism of action was not elucidated due to technical challenges. Here, the authors develop a mass spectrometric approach to identify the Ag-proteome in Staphylococcus aureus, and capture a molecular snapshot of the dynamic bactericidal mode of action of Ag through targeting multiple biological pathways.

Die Wechselwirkung mit ribosomalen Proteinen begleitet die Stressinduktion des Wirkstoffkandidaten BOLD-100/KP1339 im endoplasmatischen Retikulum

Der metallhaltige Wirkstoff BOLD‐100/KP1339 zeigte bereits vielversprechende Resultate in verschiedenen In vitro‐ und In vivo‐Tumormodellen sowie in klinischen Studien. Der detaillierte Wirkmechanismus wurde jedoch noch nicht komplett aufgeklärt. Als entscheidende Wirkstoffeffekte kristallisierten sich kürzlich die Stressinduktion im endoplasmatischen Retikulum (ER) und die damit einhergehende Modulierung von HSPA5 (GRP78) heraus. Das spontane und stabile Addukt zwischen BOLD‐100 und menschlichem Serumalbumin wurde als Immobilisierungsstrategie ausgewählt, um einen chemoproteomischen Ansatz auszuführen, der die ribosomalen Proteine RPL10, RPL24 und den Transkriptionsfaktor GTF2I als potentielle Interaktoren dieser Ru(III)‐Verbindung identifizierten. Dieses Ergebnis wurde mit proteomischen und transkriptomischen Profiling‐Experimenten kombiniert, was die Interpretation einer ribosomalen Beeinträchtigung sowie der Induktion von ER‐Stress unterstützte. Die Bildung von Polyribosomen und begleitende ER‐Schwellungen in behandelten Krebszellen wurden zudem durch TEM‐Messungen bestätigt. Somit scheint eine direkte Wechselwirkung von BOLD‐100 mit ribosomalen Proteinen die ER‐Stressinduktion und die Modulierung von GRP78 in Krebszellen zu begleiten.

Interaction with Ribosomal Proteins Accompanies Stress Induction of the Anticancer Metallodrug BOLD-100/KP1339 in the Endoplasmic Reticulum

The ruthenium-based anticancer agent BOLD-100/KP1339 has shown promising results in several in vitro and in vivo tumour models as well as in early clinical trials. However, its mode of action remains to be fully elucidated. Recent evidence identified stress induction in the endoplasmic reticulum (ER) and concomitant down-modulation of HSPA5 (GRP78) as key drug effects. By exploiting the naturally formed adduct between BOLD-100 and human serum albumin as an immobilization strategy, we were able to perform target-profiling experiments that revealed the ribosomal proteins RPL10, RPL24, and the transcription factor GTF2I as potential interactors of this ruthenium(III) anticancer agent. Integrating these findings with proteomic profiling and transcriptomic experiments supported ribosomal disturbance and concomitant induction of ER stress. The formation of polyribosomes and ER swelling of treated cancer cells revealed by TEM validated this finding. Thus, the direct interaction of BOLD-100 with ribosomal proteins seems to accompany ER stress-induction and modulation of GRP78 in cancer cells.

A novel mode of control of nickel uptake by a multifunctional metallochaperone

Cellular metal homeostasis is a critical process for all organisms, requiring tight regulation. In the major pathogen Helicobacter pylori, the acquisition of nickel is an essential virulence determinant as this metal is a cofactor for the acid-resistance enzyme, urease. Nickel uptake relies on the NixA permease and the NiuBDE ABC transporter. Till now, bacterial metal transporters were reported to be controlled at their transcriptional level. Here we uncovered post-translational regulation of the essential Niu transporter in H. pylori. Indeed, we demonstrate that SlyD, a protein combining peptidyl-prolyl isomerase (PPIase), chaperone, and metal-binding properties, is required for the activity of the Niu transporter. Using two-hybrid assays, we found that SlyD directly interacts with the NiuD permease subunit and identified a motif critical for this contact. Mutants of the different SlyD functional domains were constructed and used to perform in vitro PPIase activity assays and four different in vivo tests measuring nickel intracellular accumulation or transport in H. pylori. In vitro, SlyD PPIase activity is down-regulated by nickel, independently of its C-terminal region reported to bind metals. In vivo, a role of SlyD PPIase function was only revealed upon exposure to high nickel concentrations. Most importantly, the IF chaperone domain of SlyD was shown to be mandatory for Niu activation under all in vivo conditions. These data suggest that SlyD is required for the active functional conformation of the Niu permease and regulates its activity through a novel mechanism implying direct protein interaction, thereby acting as a gatekeeper of nickel uptake. Finally, in agreement with a central role of SlyD, this protein is essential for the colonization of the mouse model by H. pylori.

Metal ions are essential for the viability of all living organisms. Indeed, more than one-third of all proteins need metal cofactors for their function. Intracellular metal concentrations require tight control as non-physiological amounts are very toxic. In particular, nickel plays a unique role in Helicobacter pylori, a bacterial pathogen that colonizes the stomach of about half of the human population worldwide and is associated with the development of gastric cancer. Nickel is essential for H. pylori as it is the cofactor of urease, an enzyme indispensable for resistance to the gastric acidity of the stomach and thus for in vivo colonization. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms. Till now, control of nickel uptake was only reported to rely on transcriptional regulators. In the present study, we uncovered a novel mechanism of regulation of nickel acquisition. SlyD, a multifunctional enzyme was found to control, by direct protein interaction, the activity of an essential nickel uptake system in H. pylori. We revealed that the SlyD chaperone activity is mandatory for the active conformation and thus functionality of the nickel permease.

Metalloproteomics for molecular target identification of protein-binding anticancer metallodrugs

Proteomics has played an important role in elucidating the fundamental processes occuring in living cells. Translating these methods to metallodrug research ('metalloproteomics') has provided a means for molecular target identification of metal-based anticancer agents which should signifcantly advance the research field. In combination with biological assays, these techniques have enabled the mechanisms of action of metallodrugs to be linked to their interactions with molecular targets and aid understanding of their biological properties. Such investigations have profoundly increased our knowledge of the complex and dynamic nature of metallodrug-biomolecule interactions and have provided, at least for some compound types, a more detailed picture on their specific protein-binding patterns. This perspective highlights the progression of metallodrug proteomics research for the identification of non-DNA targets from standard analytical techniques to powerful metallodrug pull-down methods.

Atomic differentiation of silver binding preference in protein targets: Escherichia coli malate dehydrogenase as a paradigm

Understanding how metallodrugs interact with their protein targets is of vital importance for uncovering their molecular mode of actions as well as overall pharmacological/toxicological profiles, which in turn facilitates the development of novel metallodrugs. Silver has been used as an antimicrobial agent since antiquity, yet there is limited knowledge about silver-binding proteins. Given the multiple dispersed cysteine residues and histidine-methionine pairs, Escherichia coli malate dehydrogenase (EcMDH) represents an excellent model to investigate silver coordination chemistry as well as its targeting sites in enzymes. We show by systematic biochemical characterizations that silver ions (Ag+) bind EcMDH at multiple sites including three cysteine-containing sites. By X-ray crystallography, we unravel the binding preference of Ag+ to multiple binding sites in EcMDH, i.e., Cys113 > Cys251 > Cys109 > Met227. Silver exhibits preferences to the donor atoms and residues in the order of S > N > O and Cys > Met > His > Lys > Val, respectively, in EcMDH. For the first time, we report the coordination of silver to a lysine in proteins. Besides, we also observed argentophilic interactions (Ag⋯Ag, 2.7 to 3.3 Å) between two silver ions coordinating to one thiolate. Combined with site-directed mutagenesis and an enzymatic activity test, we unveil that the binding of Ag+ to the site IV (His177-Ag-Met227 site) plays a vital role in Ag+-mediated MDH inactivation. This work stands as the first unusual and explicit study of silver binding preference to multiple binding sites in its authentic protein target at the atomic resolution. These findings enrich our knowledge on the biocoordination chemistry of silver(i), which in turn facilitates the prediction of the unknown silver-binding proteins and extends the pharmaceutical potentials of metal-based drugs.

Time-dependent shotgun proteomics revealed distinct effects of an organoruthenium prodrug and its activation product on colon carcinoma cells

Activation kinetics of metallo-prodrugs control the types of possible interactions with biomolecules. The intact metallo-prodrug is able to engage with potential targets by purely non-covalent bonding, while the activated metallodrug can form additional coordination bonds. It is hypothesized that the additional coordinative bonding might be favourable with respect to the target selectivity of activated metallodrugs. Thus, a time-dependent shotgun proteomics study was conducted in HCT116 colon carcinoma cells with plecstatins, which are organoruthenium anticancer drug candidates. First, the target selectivity was evaluated in a time-dependent fashion, which accounted for their hydrolysis kinetics. The binding selectivity increased from 50- to 160-fold and the average specificity from 0.72 to 0.86, respectively, from the 2 h to the 4 h target profiling experiment. Target profiling after 19 h did not reveal significant enrichments, possibly due to deactivation of the probe via arene cleavage. Up to 450 interactors were identified in the target profiling experiments. A plecstatin analogue that substituted a hydrogen bond acceptor with a hydrogen bond donor abrogated the target selectivity for plectin in HCT116 whole cell lysates, underlining the necessity of this hydrogen bond acceptor for a strong interaction between plecstatin and plectin. Second, time-dependent response profiling experiments provided evidence that plecstatin-2 induced an integrated stress response (ISR) in HCT116 cell culture. The phosphorylation of eIF2α, a key mediator of the ISR, after 3 h treatment indicated that this perturbation was initiated by the intact plecstatin-2 prodrug, while the effects of plectin-targeting are mediated by activated plecstatin-2.

Metalloproteomics in conjunction with other omics for uncovering the mechanism of action of metallodrugs: Mechanism-driven new therapy development

Medicinal inorganic chemistry has been largely stimulated by the clinic success of platinum anticancer drugs. An array of metal-based drugs (e.g. platinum, gold, bismuth, and silver) are currently used clinically for the treatment of various diseases. Integrating multiomics approaches, particularly metalloproteomics, with other biochemical characterizations enables comprehensive understanding of cellular responses of metallodrugs, which in turn will guide the rational design of a new drug and modification of the presently used drugs. This review aims to summarize the recent progress in this area. We will describe the technology platforms and their applications for uncovering the mechanisms of action of metallodrugs, for which remarkable advances have been achieved recently. Moreover, we will also highlight the application of newly generated knowledge for the development of novel therapeutic strategies.

Antibacterial mechanism of silver nanoparticles in Pseudomonas aeruginosa: proteomics approach

Silver nanoparticles (AgNPs) are the nanomaterials most widely used as antimicrobial agents in a range of consumer products, due to the environmental release of either the AgNPs themselves or silver ions. Although AgNPs appear to be more potent than silver ions, the mechanism behind the activity is not fully elucidated yet. The most common mechanism of toxicity of AgNPs proposed to date is the release of silver ions and/or the particle-specific functions. In this study, Pseudomonas aeruginosa (a model for Gram-negative bacteria) was treated with AgNPs, and its proteomic response was comprehensively characterized to elucidate the antimicrobial mechanism of AgNPs in the microorganism. In total, 59 silver-regulated proteins (27 up-regulated and 32 down-regulated proteins) and 5 silver-binding proteins were identified. Bioinformatic analysis revealed that interference with the cell-membrane function and generation of intracellular reactive oxygen species (ROS) were the main pathways for the antibacterial effect. The pattern of membrane proteins regulated by AgNPs was similar to that found for silver ions. In addition, the same silver-binding proteins were obtained with both AgNPs and silver ions, which indicated that AgNPs probably affect the cell membrane and react with proteins by releasing silver ions. The elevation of intracellular ROS relative to that with silver ions confirmed oxidative damage caused by AgNPs, which may be ascribed to the nano-characteristics and higher uptake efficiency of the particles. These results demonstrate that the antimicrobial activity of AgNPs is due to the synergistic action of release of dissolved silver ions and particle-specific effects. The proteomic analysis of silver-binding and silver-regulated proteins in the present study provides insight into the mechanism of antimicrobial activity of such nanomaterials.

Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis of E. coli

Silver has long been used as an antibacterial agent, yet its molecular targets remain largely unknown. Using a custom-designed coupling of gel electrophoresis with inductively coupled plasma mass spectrometry (GE-ICP-MS), we identified six silver-binding proteins in E. coli. The majority of the identified proteins are associated with the central carbon metabolism of E. coli. Among them, we unveil that GAPDH, an essential enzyme in glycolysis, serves as a vital target of Ag+ in E. coli for the first time. We demonstrate that silver inhibits the enzymatic function of GAPDH through targeting Cys149 in its catalytic site. The X-ray structure reveals that Ag+ coordinates to Cys149 and His176 with a quasi-linear geometry (S-Ag-N angle of 157°). And unexpectedly, two Ag+ ions coordinate to Cys288 in the non-catalytic site with weak argentophilic interaction (Ag···Ag distance of 2.9 Å). This is the first report on antimicrobial Ag+ targeting a key enzyme in the glycolytic pathway of E. coli. The findings expand our knowledge on the mode of action and bio-coordination chemistry of silver, particularly silver-targeting residues in proteins at the atomic level.

Deciphering molecular mechanism of silver by integrated omic approaches enables enhancing its antimicrobial efficacy in E. coli

Despite the broad-spectrum antimicrobial activities of silver, its internal usage is restricted, owing to the toxicity. Strategies to enhance its efficacy are highly desirable but rely heavily on the understanding of its molecular mechanism of action. However, up to now, no direct silver-targeting proteins have been mined at a proteome-wide scale, which hinders systemic studies on the biological pathways interrupted by silver. Herein, we build up a unique system, namely liquid chromatography gel electrophoresis inductively coupled plasma mass spectrometry (LC-GE-ICP-MS), allowing 34 proteins directly bound by silver ions to be identified in Escherichia coli. By using integrated omic approaches, including metalloproteomics, metabolomics, bioinformatics, and systemic biology, we delineated the first dynamic antimicrobial actions of silver (Ag+) in E. coli, i.e., it primarily damages multiple enzymes in glycolysis and tricarboxylic acid (TCA) cycle, leading to the stalling of the oxidative branch of the TCA cycle and an adaptive metabolic divergence to the reductive glyoxylate pathway. It then further damages the adaptive glyoxylate pathway and suppresses the cellular oxidative stress responses, causing systemic damages and death of the bacterium. To harness these novel findings, we coadministrated metabolites involved in the Krebs cycles with Ag+ and found that they can significantly potentiate the efficacy of silver both in vitro and in an animal model. Our study reveals the comprehensive and dynamic mechanisms of Ag+ toxicity in E. coli cells and offers a novel and general approach for deciphering molecular mechanisms of metallodrugs in various pathogens and cells to facilitate the development of new therapeutics.

Enabling Methods to Elucidate the Effects of Metal-based Anticancer Agents

Next-generation metal-based pharmaceuticals are considered promising therapeutic agents, which may follow novel modes of action and engage with different targets compared to classical platinum(ii) anticancer agents. However, appropriate methods and assays are required to provide evidence of such unprecedented drug effects. Mass spectrometry (MS) has proved useful in probing the reactivity and selectivity of metal-based anticancer agents on a molecular level and recently also in the cellular context, especially with regard to the proteome. This chapter will discuss the design and use of competitive experiments to investigate activation pathways and binding preferences of metal-based anticancer agents by identifying reaction products via different MS setups. Moreover, cell-based approaches are described to obtain insights into novel potential targets and modes of action. Thus, mass spectrometry emerges as an enabling technology that connects molecules to mechanisms, highlighting the broad applicability of this analytical technique to the discovery and understanding of metal-based anticancer agents.

A unique Pb-binding flagellin as an effective remediation tool for Pb contamination in aquatic environment

Metal contaminants present persistent and deleterious threats to environmental ecosystems and human health. Microorganisms can rapidly develop protective mechanisms against metal toxicity, such as metallothionein production. The identification of biological factors related to these protective mechanisms is essential for effective metal remediation. This study presents a robust pathway to rapidly locate and characterize a Pb-binding flagellin in Serratia Se1998, which can bind Pb at a 16:1 Pb: protein ratio. A column gel electrophoresis system hyphenated with inductively coupled plasma mass spectrometry (ICP MS) was constructed to efficiently separate and identify Pb-binding proteins from the whole bacterial proteome. PCR and transgenic assays were used to elucidate the exact sequences and biological function of Pb-binding proteins and heterogeneous expression of Pb-binding flagellin in E. coli could significantly enhance Pb removal from aqueous solution by approximately 45%. This method provides a benchmark procedure to rapidly identify biological factors responsible for metal biosorption. Identification of this unique Pb-binding flagellin highlights that microorganisms can survive high metal stresses due to various complex biological pathways for metal detoxification and remediation.

Systems Approaches for Unveiling the Mechanism of Action of Bismuth Drugs: New Medicinal Applications beyond Helicobacter Pylori Infection

Metallodrugs have been widely used as diagnostic and therapeutic agents. Understanding their mechanisms of action may lead to advances in rational drug design. However, to achieve this, diversified approaches are required because of the complexity of metal-biomolecule interactions. Bismuth drugs in combination with antibiotics as a quadruple therapy show excellent success rates in the eradication of Helicobacter pylori, even for antibiotic-resistant strains, and in fact, they have been used in the clinic for decades for the treatment of infection. Understanding the mechanism of action of bismuth drugs may extend their medicinal application beyond the treatment of H. pylori infection. This Account describes several general strategies for mechanistic studies of metallodrugs, including system pharmacology and metalloproteomics approaches. The application of these approaches is exemplified using bismuth drugs. Through a system pharmacology approach, we showed that glutathione- and multidrug-resistance-associated protein 1-mediated self-propelled disposal of bismuth in human cells might explain the selective toxicity of bismuth drugs to H. pylori but not the human host. The development of metalloproteomics has enabled extensive studies of the putative protein targets of metallodrugs with a dynamic range of affinity. Continuous-flow GE-ICP-MS allows simultaneous monitoring of metals and their associated proteins with relatively high affinity on a proteome-wide scale. The fluorescence approach relies on unique M ⁿ⁺-NTA-based fluorescence probes and is particularly applicable for mining those proteins that bind to metals/metallodrugs weakly or transiently. Integration of these methods with quantitative proteomics makes it possible to maximum coverage of bismuth-associated proteins, and the sustained efficacy of bismuth drugs lies in their ability to disrupt multiple biological pathways through binding and functional perturbation of key enzymes. The knowledge acquired by mechanistic studies of bismuth drugs led to the discovery of UreG as a new target for the development of urease inhibitors. The ability of Bi(III) to inhibit metallo-β-lactamase (MBL) activity through displacement of the Zn(II) cofactor renders bismuth drugs new potential as broad-spectrum inhibitors of MBLs. Therefore, bismuth drugs could be repurposed together with clinically used antibiotics as a cotherapy to cope with the current antimicrobial resistance crisis. We anticipate that the methodologies described in this Account are generally applicable for understanding the (patho)physiological roles of metals/metallodrugs. Our mechanism-guided discovery of new druggable targets as well as new medicinal applications of bismuth drugs will inspire researchers in relevant fields to engage in the rational design of drugs and reuse of existing drugs, eventually leading to the development of new effective therapeutics.

3D printed gel electrophoresis device coupling with ICP-MS for online separation and detection of metalloproteins

We successfully developed a strategy to combine a customized gel electrophoresis device with ICP-MS for online separation and detection of metalloproteins. The self-designed horizontal column gel electrophoresis device was rapidly and easily fabricated in the laboratory via 3D printing with a low cost. The feasibility of 3D printing to fabricate this device was investigated by offline separation of commercial protein standards. And a better separation efficiency was found when using gel tubes printed with higher printing precision. As a proof-of-concept, the performance of the whole system is demonstrated by online separation and detection of both iodinated protein standards and proteins in rat blood plasma samples. Benefits from 3D printing, customized modification or further optimization can be readily achieved for a better protein separation and detection efficiency.

Structure-activity relationships for ruthenium and osmium anticancer agents - towards clinical development

Anticancer metallodrugs based on ruthenium and osmium are among the most investigated and advanced non-platinum metallodrugs. Inorganic drug discovery with these agents has undergone considerable advances over the past two decades and has currently two representatives in active clinical trials. As many ruthenium and osmium metallodrugs are prodrugs, a key question to be addressed is how the molecular reactivity of such metal-based therapeutics dictates the selectivity and the type of interaction with molecular targets. Within this frame, this review introduces the field by the examples of the most advanced ruthenium lead structures. Then, global structure-activity relationships are discussed for ruthenium and osmium metallodrugs with respect to in vitro antiproliferative/cytotoxic activity and in vivo tumor-inhibiting properties, as well as pharmacokinetics. Determining and validating global mechanisms of action and molecular targets are still major current challenges. Moreover, significant efforts must be invested in screening in vivo tumor models that mimic human pathophysiology to increase the predictability for successful preclinical and clinical development of ruthenium and osmium metallodrugs.

Metallochaperone UreG serves as a new target for design of urease inhibitor: A novel strategy for development of antimicrobials

Urease as a potential target of antimicrobial drugs has received considerable attention given its versatile roles in microbial infection. Development of effective urease inhibitors, however, is a significant challenge due to the deeply buried active site and highly specific substrate of a bacterial urease. Conventionally, urease inhibitors are designed by either targeting the active site or mimicking substrate of urease, which is not efficient. Up to now, only one effective inhibitor—acetohydroxamic acid (AHA)—is clinically available, but it has adverse side effects. Herein, we demonstrate that a clinically used drug, colloidal bismuth subcitrate, utilizes an unusual way to inhibit urease activity, i.e., disruption of urease maturation process via functional perturbation of a metallochaperone, UreG. Similar phenomena were also observed in various pathogenic bacteria, suggesting that UreG may serve as a general target for design of new types of urease inhibitors. Using Helicobacter pylori UreG as a showcase, by virtual screening combined with experimental validation, we show that two compounds targeting UreG also efficiently inhibited urease activity with inhibitory concentration (IC)₅₀ values of micromolar level, resulting in attenuated virulence of the pathogen. We further demonstrate the efficacy of the compounds in a mammalian cell infection model. This study opens up a new opportunity for the design of more effective urease inhibitors and clearly indicates that metallochaperones involved in the maturation of important microbial metalloenzymes serve as new targets for devising a new type of antimicrobial drugs.

Urease, a metalloenzyme that catalyzes the hydrolysis of urea, plays important roles in the survival and virulence of many microbial pathogens, and has long been considered an important drug target for the development of novel antimicrobials. However, its deeply buried active site and highly specific substrate of bacterial urease make it very challenging to design effective urease inhibitors by conventional approaches. In this study, we reveal that a bismuth-based drug (colloidal bismuth subcitrate) inhibits urease activity in an unusual way. This drug binds the urease accessary protein UreG and inhibits its GTPase activity, thus perturbing nickel insertion into the apo-urease, a process called urease maturation. UreG is therefore proposed as an alternative target for the development of urease inhibitors. Using H. pylori UreG as an example, combined with virtual screening and experimental validation, we further show that several small molecules that bind and functionally disrupt UreG could indeed inhibit urease activity in bacteria and in a cell infection model and possess potent antimicrobial activity. In summary, we discovered metallochaperone UreG as a new target for the design of urease inhibitors. Such a strategy should have a broad application in the development of metalloenzyme inhibitors.

Metallomic study on the metabolism of RAPTA-C and cisplatin in cell culture medium and its impact on cell accumulation

The different extracellular speciation of cisplatin and the organoruthenium developmental anticancer agent RAPTA-C impacts the accumulation in cancer cells.

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.

Identification of catabolite control protein A from Staphylococcus aureus as a target of silver ions

Staphylococcus aureus is one of the most common pathogenic bacteria that causes human infectious diseases. The emergence of antibiotic-resistant strains of S. aureus promotes the development of new anti-bacterial strategies. Silver ions (Ag⁺) have attracted profound attention due to their broad-spectrum antimicrobial activities. Although the antibacterial properties of silver have been well known for many centuries, its mechanism of action remains unclear and its protein targets are rarely reported. Herein, we identify the catabolite control protein A (CcpA) of S. aureus as a putative target for Ag⁺. CcpA binds 2 molar equivalents of Ag⁺via its two cysteine residues (Cys216 and Cys242). Importantly, Ag⁺ binding induces CcpA oligomerization and abolishes its DNA binding capability, which further attenuates S. aureus growth and suppresses α-hemolysin toxicity. This study extends our understanding of the bactericidal effects of silver.

Integrative approach for the analysis of the proteome-wide response to bismuth drugs in Helicobacter pylori

An integrative metalloproteomic approach to unveil the role of antimicrobial metals in general using bismuth as an example.

Bismuth drugs, despite being clinically used for decades, surprisingly remain in use and effective for the treatment of Helicobacter pylori infection, even for resistant strains when co-administrated with antibiotics. However, the molecular mechanisms underlying the clinically sustained susceptibility of H. pylori to bismuth drugs remain elusive. Herein, we report that integration of in-house metalloproteomics and quantitative proteomics allows comprehensive uncovering of the bismuth-associated proteomes, including 63 bismuth-binding and 119 bismuth-regulated proteins from Helicobacter pylori, with over 60% being annotated with catalytic functions. Through bioinformatics analysis in combination with bioassays, we demonstrated that bismuth drugs disrupted multiple essential pathways in the pathogen, including ROS defence and pH buffering, by binding and functional perturbation of a number of key enzymes. Moreover, we discovered that HpDnaK may serve as a new target of bismuth drugs to inhibit bacterium-host cell adhesion. The integrative approach we report, herein, provides a novel strategy to unveil the molecular mechanisms of antimicrobial metals against pathogens in general. This study sheds light on the design of new types of antimicrobial agents with multiple targets to tackle the current crisis of antimicrobial resistance.

Functional disruption of peroxiredoxin by bismuth antiulcer drugs attenuates Helicobacter pylori survival

Bismuth drugs have been used clinically to treat infections from Helicobacter pylori, a pathogen that is strongly related to gastrointestinal diseases even stomach cancer. Despite extensive studies, the mechanisms of action of bismuth drugs are not fully understood. Alkyl hydroperoxide reductase subunit C (AhpC) is the most abundant 2-cysteine peroxiredoxin, crucial for H. pylori survival in the host by defense of oxidative stress. Herein we show that a Bi(III) antiulcer drug (CBS) binds to the highly conserved cysteine residues (Cys49 and Cys169) with a dissociation constant (K _d) of Bi(III) to AhpC of 3.0 (±1.0) × 10^-24 M. Significantly the interaction of CBS with AhpC disrupts the peroxiredoxin and chaperone activities of the enzyme both in vitro and in bacterial cells, leading to attenuated bacterial survival. Moreover, using a home-made fluorescent probe, we demonstrate that Bi(III) also perturbs AhpC relocation between the cytoplasm and membrane region in decomposing the exogenous ROS. Our study suggests that disruption of redox homeostasis by bismuth drugs via interaction with key enzymes such as AhpC contributes to their antimicrobial activity.

Analytical approaches for the characterization of nickel proteome

Analytical strategies to study the nickel proteome and their advantages and limitations.

Binding States of Protein-Metal Complexes in Cells

The identification of endogenous proteins as well as their binding to metal ions in living cells is determined by combining pulsed electrophoretic separations with nanoelectrospray ionization followed by mass spectrometric detection. This approach avoids problems resulting from the complicated cellular environment. In this manner, we demonstrate the rapid identification (300 ms or less) of intact proteins from living E. coli cells including the complexation of calmodulin with calcium ion. The latter showed different binding states from those observed in in vitro studies. These observations also reveal in vitro measurements do not necessarily represent the actual situation in living cells. We conclude that the attempted in situ measurement of intracellular proteins with minimal sampling processes should be preferred.

Novel class of Bi(iii) hydroxamato complexes: synthesis, urease inhibitory activity and activity against H. pylori

Reaction of Bi(NO3)3 with benzohydroxamic acid (Bha) and salicylhydroxamic acid (Sha) gives the novel Bi(iii) complexes [Bi2(Bha-1H)2(μ-Bha-1H)2(η(2)-NO3)2] () and [Bi6(CH3OH)2(η(1)-NO3)2(η(2)-NO3)(OH2)2(Sha-1H)12](NO3)2 (). X-ray crystal structure of reveals two hydroxamato coordination modes; bidentate bridging (O, O') and bidentate non-bridging (O, O') and of reveals one coordination mode; bidentate bridging (O, O'). , specifically designed to and demonstrated to inhibit the activity of urease, exhibits excellent antibacterial activity against three strains of Helicobacter pylori with MIC ≥ 16 μg mL(-1).