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

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.

An all-in-one therapeutic platform for the treatment of resistant Helicobacter pylori infection

Helicobacter pylori (H. pylori) infection is a major cause of gastric diseases. Currently, bismuth-based quadruple therapy is widely adopted for eradicating H. pylori infection. However, this first-line strategy faces several challenges such as drug resistance, intestinal dysbacteriosis, and patients' poor compliance. To overcome these problems, an all-in-one therapeutic platform (CLA-Bi-ZnO2@Lipo) that composed of liposomes loading clarithromycin (CLA), Bi, and ZnO2 hybrid nanoparticles was developed for eradicating multidrug-resistant (MDR) H. pylori. The in vitro and in vivo results showed that CLA-Bi-ZnO2@Lipo could target the infection-induced inflammatory mucosa through liposome mediated nanoparticle-tissue surface charge interaction and quickly respond to the gastric acid environment to release CLA, Bi3+, Zn2+, and H2O2. By oral administration per day, the acid triggered decomposition of CLA-Bi-ZnO2@Lipo could significantly increase intragastric pH to 6 within 30 min; The released CLA, Zn2+, and H2O2 further exerted synergistical anti-bacterial effects in which a ∼2 order higher efficacy in reducing MDR H. pylori burden was achieved in comparison with standard quadruple therapy (p < 0.05); The released Zn2+ and Bi3+ could also alleviate mucosal inflammation. Most importantly, the CLA-Bi-ZnO2@Lipo exhibited superior biosafety and nearly no side effects on intestinal flora. Overall, this study developed a highly integrated and safe anti-MDR H. pylori agent which had great potential to be used as an alternative treatment for MDR H. pylori eradication.

Development of Pan-Anti-SARS-CoV-2 Agents through Allosteric Inhibition of nsp14/nsp10 Complex

SARS-CoV-2 nsp14 functions both as an exoribonuclease (ExoN) together with its critical cofactor nsp10 and as an S-adenosyl methionine-dependent (guanine-N7) methyltransferase (MTase), which makes it an attractive target for the development of pan-anti-SARS-CoV-2 drugs. Herein, we screened a panel of compounds (and drugs) and found that certain compounds, especially Bi(III)-based compounds, could allosterically inhibit both MTase and ExoN activities of nsp14 potently. We further demonstrated that Bi(III) binds to both nsp14 and nsp10, resulting in the release of Zn(II) ions from the enzymes as well as alternation of protein quaternary structures. The in vitro activities of the compounds were also validated in SARS-CoV-2-infected mammalian cells. Importantly, we showed that nsp14 serves as an authentic target of Bi(III)-based antivirals in SARS-CoV-2-infected mammalian cells by quantification of both the protein and inhibitor. This study highlights the importance of nsp14/nsp10 as a potential target for the development of pan-antivirals against SARS-CoV-2 infection.

Recent Advances in Metalloproteomics

Interactions between proteins and metal ions and their complexes are important in many areas of the life sciences, including physiology, medicine, and toxicology. Despite the involvement of essential elements in all major processes necessary for sustaining life, metalloproteomes remain ill-defined. This is not only owing to the complexity of metalloproteomes, but also to the non-covalent character of the complexes that most essential metals form, which complicates analysis. Similar issues may also be encountered for some toxic metals. The review discusses recently developed approaches and current challenges for the study of interactions involving entire (sub-)proteomes with such labile metal ions. In the second part, transition metals from the fourth and fifth periods are examined, most of which are xenobiotic and also tend to form more stable and/or inert complexes. A large research area in this respect concerns metallodrug-protein interactions. Particular attention is paid to separation approaches, as these need to be adapted to the reactivity of the metal under consideration.

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.

Metallo-sideromycin as a dual functional complex for combating antimicrobial resistance

The rapid emergence of antimicrobial resistance (AMR) pathogens highlights the urgent need to approach this global burden with alternative strategies. Cefiderocol (Fetroja®) is a clinically-used sideromycin, that is utilized for the treatment of severe drug-resistant infections, caused by Gram-negative bacteria; there is evidence of cefiderocol-resistance occurring in bacterial strains however. To increase the efficacy and extend the life-span of sideromycins, we demonstrate strong synergisms between cefiderocol and metallodrugs (e.g., colloidal bismuth citrate (CBS)), against Pseudomonas aeruginosa and Burkholderia cepacia. Moreover, CBS enhances cefiderocol efficacy against biofilm formation, suppresses the resistance development in P. aeruginosa and resensitizes clinically isolated resistant P. aeruginosa to cefiderocol. Notably, the co-therapy of CBS and cefiderocol significantly increases the survival rate of mice and decreases bacterial loads in the lung in a murine acute pneumonia model. The observed phenomena are partially attributable to the competitive binding of Bi3+ to cefiderocol with Fe3+, leading to enhanced uptake of Bi3+ and reduced levels of Fe3+ in cells. Our studies provide insight into the antimicrobial potential of metallo-sideromycins.

Biological Activities of Bismuth Compounds: An Overview of the New Findings and the Old Challenges Not Yet Overcome

Bismuth-based drugs have been used primarily to treat ulcers caused by Helicobacter pylori and other gastrointestinal ailments. Combined with antibiotics, these drugs also possess synergistic activity, making them ideal for multiple therapy regimens and overcoming bacterial resistance. Compounds based on bismuth have a low cost, are safe for human use, and some of them are also effective against tumoral cells, leishmaniasis, fungi, and viruses. However, these compounds have limited bioavailability in physiological environments. As a result, there is a growing interest in developing new bismuth compounds and approaches to overcome this challenge. Considering the beneficial properties of bismuth and the importance of discovering new drugs, this review focused on the last decade's updates involving bismuth compounds, especially those with potent activity and low toxicity, desirable characteristics for developing new drugs. In addition, bismuth-based compounds with dual activity were also highlighted, as well as their modes of action and structure-activity relationship, among other relevant discoveries. In this way, we hope this review provides a fertile ground for rationalizing new bismuth-based drugs.

The effects of sodium sulfite on Helicobacter pylori by establishing a hypoxic environment

Helicobacter pylori (H. pylori) is an obligate microaerobion and does not survive in low oxygen. Sodium sulfite (SS) reacts and consume oxygen in solutions. The present study aimed to investigate the effects of SS on H. pylori. The effects of SS on oxygen concentrations in solutions and on H. pylori in vivo and in vitro were examined, and the mechanisms involved were explored. The results showed that SS decreased the oxygen concentration in water and artificial gastric juice. In Columbia blood agar and special peptone broth, SS concentration-dependently inhibited the proliferation of H. pylori ATCC43504 and Sydney strain-1 in Columbia blood agar or special peptone broth, and dose-dependently decreased the number of H. pylori in Mongolian gerbils and Kunming mouse infection models. The H. pylori was relapsed in 2 weeks withdrawal and the recurrence in the SS group was lower than that in the positive triple drug group. These effects were superior to positive triple drugs. After SS treatments, the cell membrane and cytoplasm structure of H. pylori were disrupted. SS-induced oxygen-free environment initially blocked aerobic respiration, triggered oxidative stress, disturbed energy production. In conclusion, SS consumes oxygen and creates an oxygen-free environment in which H. pylori does not survive. The present study provides a new strategy and perspective for the clinical treatment of H. pylori infectious disease.

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).

Transcriptomic and Functional Approaches Unveil the Role of tmRNA in Zinc Acetate Mediated Levofloxacin Sensitivity in Helicobacter pylori

Rapid increase in resistance of Helicobacter pylori (H. pylori) has hindered antibiotics-based eradication efforts worldwide and raises the need for additional approaches. Here, we investigate the role of zinc-based compounds in inhibiting H. pylori growth and modulating antibiotic sensitivities, interrogate their downstream transcriptomic changes, and highlight the potential mechanism driving the observed effects. We showed that zinc acetate inhibited H. pylori growth and increased H. pylori sensitivity to levofloxacin. Transcriptomic profiling showed distinct gene expression patterns between zinc acetate treated groups versus controls. In particular, we independently replicated the association between zinc acetate treatment and increased ssrA expression. Knockdown of ssrA restored levofloxacin resistance to levels of the control group. In this study, we first demonstrated the role of zinc acetate in H. pylori growth and antibiotic sensitivities. Additionally, we explored the transcriptomic perturbations of zinc acetate followed by functional knockdown follow-up of differentially expressed ssrA, highlighting the role of tmRNA and trans-translation in H. pylori levofloxacin resistance. Our results provide alternative and complementary strategies for H. pylori treatment and shed light on the underlying mechanisms driving these effects. IMPORTANCE Helicobacter pylori (H. pylori) eradication plays an important role in gastric cancer prevention, but the antimicrobial resistance of H. pylori is fast becoming a growing concern. In this study, we investigated the role of zinc acetate in inhibiting H. pylori growth and modulating antibiotic sensitivities in vitro. Additionally, we explored the transcriptomic perturbations of zinc acetate followed by functional knockdown follow-up of differentially expressed ssrA, highlighting the role of tmRNA and trans-translation in H. pylori levofloxacin resistance. Our results open up a new horizon for the treatment of antibiotic-resistant H. pylori.

Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori

Bacterial antibiotic resistance is a major threat to human health. A combination of antibiotics with metals is among the proposed alternative treatments. Only one such combination is successfully used in clinics; it associates antibiotics with the metal bismuth to treat infections by Helicobacter pylori. This bacterial pathogen colonizes the human stomach and is associated with gastric cancer, killing 800,000 individuals yearly. The effect of bismuth in H. pylori treatment is not well understood in particular for sublethal doses such as those measured in the plasma of treated patients. We addressed this question and observed that bismuth induces the formation of homogeneously sized membrane vesicles (MVs) with unique protein cargo content enriched in bismuth-binding proteins, as shown by quantitative proteomics. Purified MVs of bismuth-exposed bacteria were strongly enriched in bismuth as measured by inductively coupled plasma optical emission spectrometry (ICP-OES), unlike bacterial cells from which they originate. Thus, our results revealed a novel function of MVs in bismuth detoxification, where secreted MVs act as tool to discard bismuth from the bacteria. Bismuth also induces the formation of intracellular polyphosphate granules that are associated with changes in nucleoid structure. Nucleoid compaction in response to bismuth was established by immunogold electron microscopy and refined by the first chromosome conformation capture (Hi-C) analysis of H. pylori. Our results reveal that even low doses of bismuth induce profound changes in H. pylori physiology and highlight a novel defense mechanism that involves MV-mediated bismuth extrusion from the bacteria and a probable local DNA protective response where polyphosphate granules are associated with nucleoid compaction.

Metal-based strategies for the fight against COVID-19

The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed over six million lives globally to date. Despite the availability of vaccines, the pandemic still cannot be fully controlled owing to rapid mutation of the virus that renders enhanced transmissibility and antibody evasion. This is thus an unmet need to develop safe and effective therapeutic options for COVID-19, in particular, remedies that can be used at home. Considering the great success of multi-targeted cocktail therapy for the treatment of viral infections, metal-based drugs might represent a unique and new source of antivirals that resemble a cocktail therapy in terms of their mode of actions. In this review, we first summarize the role that metal ions played in SARS-CoV-2 viral replication and pathogenesis, then highlight the chemistry of metal-based strategies in the fight against SARS-CoV-2 infection, including both metal displacement and chelation based approaches. Finally, we outline a perspective and direction on how to design and develop metal-based antivirals for the fight against the current or future coronavirus pandemic.

Target Profiling of an Iridium(III)-Based Immunogenic Cell Death Inducer Unveils the Engagement of Unfolded Protein Response Regulator BiP

Clinical chemotherapeutic drugs have occasionally been observed to induce antitumor immune responses beyond the direct cytotoxicity. Such effects are coined as immunogenic cell death (ICD), representing a "second hit" from the host immune system to tumor cells. Although chemo-immunotherapy is highly promising, ICD inducers remain sparse with vague drug-target mechanisms. Here, we report an endoplasmic reticulum stress-inducing cyclometalated Ir(III)-bisNHC complex (1a) as a new ICD inducer, and based on this compound, a clickable photoaffinity probe was designed for target identification, which unveiled the engagement of the master regulator protein BiP (binding immunoglobulin protein)/GRP78 of the unfolded protein response pathway. This has been confirmed by a series of cellular and biochemical studies including fluorescence microscopy, cellular thermal shift assay, enzymatic assays, and so forth, showing the capability of 1a for BiP destabilization. Notably, besides 1a, the previously reported ICD inducers including KP1339, mitoxantrone, and oxaliplatin were also found to engage BiP interaction, suggesting the important role of BiP in eliciting anticancer immunity. We believe that the ICD-related target information in this work will help to understand the mode of action of ICD that is beneficial to designing new ICD agents with high specificity and improved efficacy.

Re-sensitization of mcr carrying multidrug resistant bacteria to colistin by silver

Superbugs carrying a mobile colistin resistance gene (mcr) are jeopardizing the clinical efficacy of the last-line antibiotic colistin. The development of MCR inhibitors is urgently required to cope with antibiotic-resistance emergencies. Here, we show that silver (Ag⁺) fully restores the susceptibility of mcr-1–carrying superbugs against colistin both in vitro and in vivo. We found an unprecedented tetra-silver center in the active-site pocket of MCR-1 through the substitution of the essential Zn²⁺ ions in the intact enzyme, leading to the prevention of substrate binding (i.e. the dysfunction of MCR-1 in transferring phosphorylethanolamine to lipid A). Importantly, the ability of Ag⁺ to suppress resistance evolution extends the lifespan of currently used antibiotics, providing a strategy to treat infections by mcr-positive bacteria.

Colistin is considered the last-line antimicrobial for the treatment of multidrug-resistant gram-negative bacterial infections. The emergence and spread of superbugs carrying the mobile colistin resistance gene (mcr) have become the most serious and urgent threat to healthcare. Here, we discover that silver (Ag⁺), including silver nanoparticles, could restore colistin efficacy against mcr-positive bacteria. We show that Ag⁺ inhibits the activity of the MCR-1 enzyme via substitution of Zn²⁺ in the active site. Unexpectedly, a tetra-silver center was found in the active-site pocket of MCR-1 as revealed by the X-ray structure of the Ag-bound MCR-1, resulting in the prevention of substrate binding. Moreover, Ag⁺ effectively slows down the development of higher-level resistance and reduces mutation frequency. Importantly, the combined use of Ag⁺ at a low concentration with colistin could relieve dermonecrotic lesions and reduce the bacterial load of mice infected with mcr-1–carrying pathogens. This study depicts a mechanism of Ag⁺ inhibition of MCR enzymes and demonstrates the potentials of Ag⁺ as broad-spectrum inhibitors for the treatment of mcr-positive bacterial infection in combination with colistin.

Metalloproteomics for Biomedical Research: Methodology and Applications

Metals are essential components in life processes and participate in many important biological processes. Dysregulation of metal homeostasis is correlated with many diseases. Metals are also frequently incorporated into diagnosis and therapeutics. Understanding of metal homeostasis under (patho)physiological conditions and the molecular mechanisms of action of metallodrugs in biological systems has positive impacts on human health. As an emerging interdisciplinary area of research, metalloproteomics involves investigating metal-protein interactions in biological systems at a proteome-wide scale, has received growing attention, and has been implemented into metal-related research. In this review, we summarize the recent advances in metalloproteomics methodologies and applications. We also highlight emerging single-cell metalloproteomics, including time-resolved inductively coupled plasma mass spectrometry, mass cytometry, and secondary ion mass spectrometry. Finally, we discuss future perspectives in metalloproteomics, aiming to attract more original research to develop more advanced methodologies, which could be utilized rapidly by biochemists or biologists to expand our knowledge of how metal functions in biology and medicine. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Nickel, an essential virulence determinant of Helicobacter pylori: Transport and trafficking pathways and their targeting by bismuth

Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. Nickel is required for the pathogenicity of H. pylori. This bacterial pathogen colonizes the stomach of about half of the human population worldwide and is associated with gastric cancer that is responsible for 800,000 deaths per year. H. pylori possesses two nickel-enzymes that are essential for in vivo colonization, a [NiFe] hydrogenase and an abundant urease responsible for resistance to gastric acidity. Because of these two enzymes, survival of H. pylori relies on an important supply of nickel, implying tight control strategies to avoid its toxic accumulation or deprivation. H. pylori possesses original mechanisms for nickel uptake, distribution, storage and trafficking that will be discussed in this review. During evolution, acquisition of nickel transporters and specific nickel-binding proteins has been a decisive event to allow Helicobacter species to become able to colonize the stomach. Accordingly, many of the factors involved in these mechanisms are required for mouse colonization by H. pylori. These mechanisms are controlled at different levels including protein interaction networks, transcriptional, post-transcriptional and post-translational regulation. Bismuth is another metal used in combination with antibiotics to efficiently treat H. pylori infections. Although the precise mode of action of bismuth is unknown, many targets have been identified in H. pylori and there is growing evidence that bismuth interferes with the essential nickel pathways. Understanding the metal pathways will help improve treatments against H. pylori and other pathogens.

Bismuth Drugs Reverse Tet(X)-Conferred Tigecycline Resistance in Gram-Negative Bacteria

Antibiotic resistance has caused a serious threat to public health and human safety. Recently, the emergence of novel resistance gene tet(X4) and its variants threatens the clinical utility of tigecycline, one of the last-line antibiotics for multidrug-resistant (MDR) bacterial infections. It is highly promising to develop effective antibiotic adjuvants to restore the clinical efficacy of existing drugs and extend their life spans. Metal compounds, such as silver, have been widely used as potential antimicrobial agents for decades. However, the potentiating effect of metallo-agents on the existing antibiotics is not fully understood. Here, we found that five bismuth drugs, especially bismuth nitrate [Bi(NO₃)₃], commonly used in clinical treatment of stomach-associated diseases, effectively boost the antibacterial activity of tigecycline against tet(X)-positive bacteria by inhibiting the enzymatic activity of Tet(X) protein. Furthermore, the combination of Bi(NO₃)₃ and tigecycline prevents the development of higher-level resistance in Tet(X)-expressing Gram-negative bacteria. Using molecular docking and dynamics simulation assays, we revealed that Bi(NO₃)₃ can competitively bind to the active center of Tet(X4) protein, while the bismuth atom targets the Tet(X4) protein in a noncompetitive manner and changes the structure of the primary binding pocket. These two mechanisms of action both antagonize the enzymatic activity of Tet(X4) resistance protein on tigecycline. Collectively, these findings indicate the high potential of bismuth drugs as novel Tet(X) inhibitors to treat tet(X4)-positive bacteria-associated infections in combination with tigecycline.

IMPORTANCE Recently, high-level tigecycline resistance mediated by tet(X4) and its variants represents a serious challenge for global public health. Antibiotic adjuvant strategy that enhances the activity of the existing antibiotics by using nonantibiotic drugs offers a distinct approach to combat the antibiotic resistance crisis. In this study, we found that bismuth drugs involve bismuth nitrate, a compound previously approved for treatment of stomach-associated diseases, remarkably potentiates tigecycline activity against tet(X)-positive bacteria. Mechanistic studies showed that bismuth drugs effectively suppress the enzymatic activity of Tet(X) resistance protein. Specifically, bismuth nitrate targets the active center of Tet(X4) protein, while bismuth binds to the resistance protein in a noncompetitive manner. Our data open up a new horizon for the treatment of infections caused by tet(X)-bearing superbugs.

Toxicological effects of hypoxanthine on Heterosigmaakashiwo: Mechanism of growth inhibition and change in hemolytic toxin content

Heterosigmaakashiwo is an algal species that causes harmful algal blooms (HABs) with strong hemolytic toxicity on coastal aquatic organisms. This study investigated the mechanism of growth inhibition and changes in hemolytic toxin contents in algal culture after exposure to hypoxanthine, a compound secreted by algicidal bacterium Bacillus sp.strain B1. An algal inhibition rate of 86% was observed with 1.0 mM hypoxanthine treatment on day 15. The levels of superoxide dismutase and catalase in algal cell culture increased while that of glutathione decreased during the treatment. In addition,the level of hemolytic toxin contents increased on day 3 under hypoxanthine treatment, and significantly decreased on days 6, 9, 12, and 15. Twelve fatty acids in H.akashiwo were detected by GC-MS, and the changes in the contents of C16, C18, C18:4ω3, and C20:5ω3 in the treatment group were consistent with the change in hemolytic toxin content. The four fatty acids were tested for hemolysis and it was observed that the hemolysis rate of 25 μg/mL C18:4ω3 and 5 μg/mL C20:5ω3 reached more than 80%, but C16 and C18 exhibited no hemolytic capability.Therefore, our results showed that hypoxanthine inhibited the growth of H. akashiwo through the changes of levels of antioxidants and hemolytic toxin content in the cultures, and fatty acids C18:4ω3 and C20:5ω3 were contributors to hemolytic toxins. The results confirmed that hypoxanthine is a potential algal inhibitor to prevent HABs.

Integrative proteomic and metabolomic analyses reveal the mechanism by which bismuth enables Helicobacter pylori eradication

BACKGROUND

Bismuth-based drugs are used to treat Helicobacter pylori infection; however, the antibacterial activity of bismuth, especially against H. pylori, has not been fully elucidated. In this study, the mechanisms by which bismuth exerts its detrimental effects on H. pylori were evaluated. Methods Six H. pylori strains isolated from different patients were cultured with or without bismuth; proteins and metabolites differentially expressed in these two sets of bacteria were detected via data independent acquisition proteomic and gas chromatography-mass spectrometry metabolic approaches, respectively. Gene ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes database were used to identity pathway enrichment.

RESULTS

Bismuth inhibited H. pylori growth in vitro via the following mechanisms: downregulation of virulence proteins CagA and VacA; disruption of flagella assembly responsible for bacterial colonization; and inhibition of antioxidant enzymes, including catalase, catalase-related peroxidase, and superoxide dismutase. Diverse metabolic pathways related to growth and RNA translation in H. pylori were disrupted by bismuth. Bismuth treatment impaired many biological processes in H. pylori, including antioxidant response and purine, pyrimidine, amino acid, and carbon metabolism. Conclusions The findings of this study suggest that motility, virulence factors CagA and VacA, antioxidant defense system, and many important metabolic pathways associated with bacterial growth, including nucleotide and amino acid metabolism and translation in H. pylori, are inhibited by bismuth. This study provides novel insights into the mechanism by which bismuth eradicates H. pylori upon being incorporated into quadruple therapy.

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.

Pnictogens in medicinal chemistry: evolution from erstwhile drugs to emerging layered photonic nanomedicine

Pnictogens (the non-metal phosphorus, metalloids arsenic and antimony, and metal bismuth) possess diverse chemical characteristics that support the formation of extended molecular structures. As witnessed by the centuries-old (and ongoing) clinical utilities, pnictogen-based compounds have secured their places in history as "magic bullet" therapeutic drugs in medicinal contexts. Moreover, with the development of recent metalloproteomics and bio-coordination chemistry, the pnictogen-based drugs functionally binding to proteins/enzymes in biological systems have been underlaid for "drug repurposing" with promising opportunities. Furthermore, advances in the modern materials science and nonotechnology have stimulated a revolution in other newly discovered forms of pnictogens-phosphorene, arsenene, antimonene, and bismuthine (layered pnictogens). Based on their favorable optoelectronic properties, layered pnictogens have shown dramatic superiority as emerging photonic nanomedicines for the treatment of various diseases. This tutorial review outlines the history and mechanism of action of ancient pnictogen-based drugs (e.g., arsenical compounds in traditional Chinese medicine) and their repurposing into modern therapeutics. Then, the revolutionary use of emerging layered pnictogens as photonic nanomedicines, alongside assessments of their in vivo biosafety, is discussed. Finally, the challenges to further development of pnictogens are set forth and insights for further exploration of their appealing properties are offered. This tutorial review may also provide some deep insights into the fields of integrated traditional Chinese and Western medicines from the perspective of materials science and nanotechnology.

Evaluation of metal-based antimicrobial compounds for the treatment of bacterial pathogens

Antimicrobial resistance (AMR) is one of the greatest global health challenges of modern times and its prevalence is rising worldwide. AMR within bacteria reduces the efficacy of antibiotics and increases both the morbidity and the mortality associated with bacterial infections. Despite this growing risk, few antibiotics with a novel mode of action are being produced, leading to a lack of antibiotics that can effectively treat bacterial infections with AMR. Metals have a history of antibacterial use but upon the discovery of antibiotics, often became overlooked as antibacterial agents. Meanwhile, metal-based complexes have been used as treatments for other diseases, such as the gold-containing drug auranofin, used to treat rheumatoid arthritis. Metal-based antibacterial compounds have novel modes of action that provide an advantage for the treatment of bacterial infections with resistance to conventional antibiotics. In this review, the antibacterial activity, mode of action, and potential for systemic use of a number of metal-based antibacterial complexes are discussed. The current limitations of these compounds are highlighted to determine if metal-based agents are a potential solution for the treatment of bacterial infections, especially those resistant to conventional antibiotics.

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.

Potential of Bacterial Cellulose Chemisorbed with Anti-Metabolites, 3-Bromopyruvate or Sertraline, to Fight against Helicobacter pylori Lawn Biofilm

Helicobacter pylori is a bacterium known mainly of its ability to cause persistent inflammations of the human stomach, resulting in peptic ulcer diseases and gastric cancers. Continuous exposure of this bacterium to antibiotics has resulted in high detection of multidrug-resistant strains and difficulties in obtaining a therapeutic effect. The purpose of the present study was to determine the usability of bacterial cellulose (BC) chemisorbed with 3-bromopyruvate (3-BP) or sertraline (SER) to act against lawn H. pylori biofilms. The characterization of BC carriers was made using a N2 adsorption/desorption analysis, tensile strength test, and scanning electron microscopy (SEM) observations. Determination of an antimicrobial activity was performed using a modified disk-diffusion method and a self-designed method of testing antibacterial activity against biofilm microbial forms. In addition, bacterial morphology was checked by SEM. It was found that BC disks were characterized by a high cross-linking and shear/stretch resistance. Growth inhibition zones for BC disks chemisorbed with 2 mg of SER or 3-BP were equal to 26.5-27.5 mm and 27-30 mm, respectively. The viability of lawn biofilm H. pylori cells after a 4-h incubation with 2 mg SER or 3-BP chemisorbed on BC disks was ≥4 log lower, suggesting their antibacterial effect. SEM observations showed a number of morphostructural changes in H. pylori cells exposed to these substances. Concluding, SER and 3-BP chemisorbed on BC carriers presented a promising antibacterial activity against biofilm H. pylori cells in in vitro conditions.

A Visible and Near-Infrared Light Activatable Diazocoumarin Probe for Fluorogenic Protein Labeling in Living Cells

Chemical modification of proteins in living cells permits valuable glimpses into the molecular interactions that underpin dynamic cellular events. While genetic engineering methods are often preferred, selective labeling of endogenous proteins in a complex intracellular milieu with chemical approaches represents a significant challenge. In this study, we report novel diazocoumarin compounds that can be photoactivated by visible (430-490 nm) and near-infrared light (800 nm) irradiation to photo-uncage reactive carbene intermediates, which could subsequently undergo an insertion reaction with concomitant fluorescence "turned on". With these new molecules in hand, we have developed a new approach for rapid, selective, and fluorogenic labeling of endogenous protein in living cells. By using CA-II and eDHFR as model proteins, we demonstrated that subcellular localization of proteins can be precisely visualized by live-cell imaging and protein levels can be reliably quantified in multiple cell types using flow cytometry. Dynamic protein regulations such as hypoxia-induced CA-IX accumulation can also be detected. In addition, by two-photon excitation with an 800 nm laser, cell-selective labeling can also be achieved with spatially controlled irradiation. Our method circumvents the cytotoxicity of UV light and obviates the need for introducing external reporters with "click chemistries". We believe that this approach of fluorescence labeling of endogenous protein by bioorthogonal photoirradiation opens up exciting opportunities for discoveries and mechanistic interrogation in chemical biology.

Bismuth drugs tackle Porphyromonas gingivalis and attune cytokine response in human cells

Periodontitis is the leading cause of severe tooth loss and edentulism in adults worldwide and is closely linked to systemic conditions such as diabetes and cardiovascular disease. Porphyromonas gingivalis is the key pathogen in periodontitis. Herein, we provided the first evidence that bismuth drugs suppress P. gingivalis in its planktonic, biofilm, and intracellular states. In total, 42 bismuth-associated proteins were identified including its major virulent factors (e.g., gingipains, hemagglutinin HagA, and fimbriae). Bismuth perturbed its iron acquisition, disturbed the energy metabolism and virulence, and deactivated multiple key enzymes (e.g., superoxide dismutase and thioredoxins). Moreover, bismuth inhibited its biofilm formation and disrupted the 3-day matured biofilms. Notably, the internalized P. gingivalis in various human cells (e.g., human gingival epithelium progenitors, HGEPs) was oppressed by bismuth but not the commonly used antibiotic metronidazole. Importantly, bismuth drugs enabled the counteraction of immuno-inflammatory responses in different host cells perturbed by P. gingivalis. The production of IL-6 and IL-8 attenuated by P. gingivalis in both of native and IL-1β-stimulated HGEPs was restored, while the bacterium-enhanced expression of IL-6, IL-1β, and TNFα in THP-1 macrophages was alleviated. This proof-of-concept study brings prospects for the potential reposition of the routinely used anti-Helicobacter pylori bismuth drugs to better manage inflammatory diseases such as periodontitis and P. gingivalis-related complex systemic disorders.

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.

Metal Complexes, an Untapped Source of Antibiotic Potential?

With the widespread rise of antimicrobial resistance, most traditional sources for new drug compounds have been explored intensively for new classes of antibiotics. Meanwhile, metal complexes have long had only a niche presence in the medicinal chemistry landscape, despite some compounds, such as the anticancer drug cisplatin, having had a profound impact and still being used extensively in cancer treatments today. Indeed, metal complexes have been largely ignored for antibiotic development. This is surprising as metal compounds have access to unique modes of action and exist in a wider range of three-dimensional geometries than purely organic compounds. These properties make them interesting starting points for the development of new drugs. In this perspective article, , the encouraging work that has been done on antimicrobial metal complexes, mainly over the last decade, is highlighted. Promising metal complexes, their activity profiles, and possible modes of action are discussed and issues that remain to be addressed are emphasized.

Zn-HA/Bi-HA biphasic coatings on Titanium: Fabrication, characterization, antibacterial and biological activity

Hydroxyapatite (HA) coatings have been of important as biocompatible coatings for dental and bone tissue engineering application. However, the poor antibacterial performance and weak biological activity of HA coatings limited their clinical applications. As a strategy to improve the antibacterial performance and biological activity of HA, Zinc and bismuth ions were incorporated into HA lattice by substituting Ca²⁺ ions, respectively, and thus zinc substituted hydroxyapatite/bismuth substituted hydroxyapatite (Zn-HA/Bi-HA) biphasic coatings on titanium plates with various ratios were fabricated via sol-gel and dip-coating processes. The purity of the Zn-HA and Bi-HA phase was confirmed by X-ray diffraction (XRD) test. The biphasic coatings showed slower dissolution rate than pure HA coating. Furthermore, the Zn-HA/Bi-HA coatings reveal good biomineralization activity in simulated body fluid (SBF) by forming regular spherical apatite agglomerates. Moreover, the biphasic Zn-HA/Bi-HA coatings exhibited that improved antimicrobial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) as compared to pure HA coatings. The CCK-8 assays demonstrate Zn-HA/Bi-HA coatings showed no toxicity to MG63 cells, and the Zn-HA/Bi-HA2 (Zn-HA:Bi-HA=64:1) coating is more effective to enhance the proliferation of MG63 cells compared to other coatings. This finding suggests Zn-HA/Bi-HA biphasic coatings are promising candidates for biomedical applications.

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.

Recognition of Proteins by Metal Chelation-Based Fluorescent Probes in Cells

Fluorescent probes such as thiol-reactive and Ni2+-nitrilotriacetate (NTA) based probes provide a powerful toolbox for real-time visualization of a protein and a proteome in living cells. Herein, we first went through basic principles and applications of thiol-reactive based probes in protein imaging and recognition. We then summarize a family of metal-NTA based fluorescence probes in the visualization of His6-tagged protein and identification of metalloproteins at proteome-wide scale. The pros and cons of the probes, as well as ways to optimize them, are discussed.

Gel electrophoresis in combination with laser ablation-inductively coupled plasma mass spectrometry to quantify the interaction of cisplatin with human serum albumin

Cisplatin and its second and third generation analogues are widely used in the treatment of cancer. To study their reactions with proteins, we present a method based on SDS-PAGE separation and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) for platinum detection in the reaction between human serum albumin (HSA) and cisplatin. We developed matrix-matched standards of HSA/cisplatin mixtures and used them to quantify the amount of adducts formed at different HSA:cisplatin ratios. We noted that cisplatin incubation with HSA resulted in the formation of higher order HSA n-mers, depending on the amount of cisplatin added. This caused a depletion of the HSA dimer bands, while the majority of HSA was present as the monomer. Inducing the formation of such higher molecular weight species may have an impact on the mode of action of metallodrugs.

Combination of gallium(iii) with acetate for combating antibiotic resistant Pseudomonas aeruginosa

Combination of Ga(iii) with acetate greatly enhances the antimicrobial activity of Ga(iii) against P. aeruginosa, and shows promise to combat the crisis of antimicrobial resistance.

Gallium(iii) has been widely used as a diagnostic and therapeutic agent in clinics for the treatment of various diseases, in particular, Ga-based drugs have been exploited as antimicrobials to combat the crisis of antimicrobial resistance. The therapeutic properties of Ga(iii) are believed to be attributable to its chemical similarity to Fe(iii). However, the molecular mechanisms of action of gallium remain unclear. Herein, by integrating metalloproteomics with metabolomics and transcriptomics, we for the first time identified RpoB and RpoC, two subunits of RNA polymerase, as Ga-binding proteins in Pseudomonas aeruginosa. We show that Ga(iii) targets the essential transcription enzyme RNA polymerase to suppress RNA synthesis, resulting in reduced metabolic rates and energy utilization. Significantly, we show that exogenous supplementation of acetate could enhance the antimicrobial activity of Ga(iii), evidenced by the inhibited growth of persister cells and attenuated bacterial virulence. The effectiveness of co-therapy of Ga(iii) and acetate was further validated in mammalian cell and murine skin infection models, which is attributable to enhanced uptake of Ga(iii), and reduced TCA cycle flow and bacterial respiration. Our study provides novel insights into the mechanistic understanding of the antimicrobial activity of Ga(iii) and offers a safe and practical strategy of using metabolites to enhance the efficacy of Ga(iii)-based antimicrobials to fight drug resistance.

Inactivation of NikR from Helicobacter pylori by a bismuth drug

The NikR protein is an essential DNA regulator of Helicobacter pylori, a human pathogen, which infects almost half of the world's population. Herein, we comprehensively characterized the interaction of a bismuth drug with Helicobacter pylori NikR. We show that Bi(III) can occupy the high-affinity Ni(II) site of NikR. The highly-conserved residue Cys107 at this site is critical for Bi(III) binding. Importantly, such a binding disassembles physiologically functional NikR tetramer into inactive dimer, leading to abrogation of the DNA-binding capability of NikR. Bi(III)-binding also significantly disturbs regulatory function of Helicobacter pylori NikR in vivo. Therefore, NikR might serve as a potential intracellular target of a bismuth drug.

A Novel Synthetic Compound, Bismuth Zinc Citrate, Could Potentially Reduce Cisplatin-Induced Toxicity Without Compromising the Anticancer Effect Through Enhanced Expression of Antioxidant Protein

Cisplatin is a common anticancer drug, but it comes with significant nephrotoxicity. Further cisplatin-induced oxidative stress contributes to the pathogenesis of the nephrotoxicity. A new compound, BiZn, can potentially prevent this complication. We verified our postulation by in vitro and in vivo models. From our findings, BiZn did not affect cisplatin-induced cytotoxicity on neuroblastoma cells under both in vitro and in vivo settings. However, BiZn significantly reduced the blood urea nitrogen and creatinine levels in cisplatin-treated mice. Under the lethal dosage of cisplatin, co-treatment of BiZn significantly increased the survival rate. BiZn stimulated antioxidant proteins metallothionein (MT) and glutathione (GSH) generation from kidney cells and minimized cisplatin-induced apoptosis. Knocking down MT-IIA and inhibiting GSH abolished such protection. In conclusion, pretreatment of BiZn decreased cisplatin-induced renal toxicity without affecting its antitumor activity. BiZn-induced antioxidant proteins MT and GSH may contribute to the renal protection effect.

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.

Bismuth: Environmental Pollution and Health Effects☆

Although it has been used for centuries, bismuth remains one of the least understood elements in the periodic table. Metallic bismuth and bismuth compounds have been widely used in the manufacture of alloys, pigments, cosmetics, and pharmaceuticals. As a “green” heavy metal, the substitution of lead with bismuth in some industries may partially resolve the environmental problems related to heavy metal pollution. In health care, as bismuth has low toxicity to humans, bismuth-based drugs such as colloidal bismuth subcitrate (CBS), ranitidine bismuth citrate (RBC), bismuth subsalicylate (BSS), bismuth iodoform and radioactive bismuth (²¹²Bi/²¹³Bi) complexes have been developed and used in clinics to treat various diseases. In most cases, bismuth therapies exhibit high therapeutic efficacies and little side effects; nevertheless, there are still reported cases of bismuth toxicity caused by bismuth over-dosage.

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.

Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis

The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.

An Efficient Approach for Selective Enrichment of Histone Modification Readers Using Self-Assembled Multivalent Photoaffinity Peptide Probes

Histone post-translational modifications (HPTMs) provide signaling platforms to recruit proteins or protein complexes (e.g., transcription factors, the so-called "readers" of the histone code), changing DNA accessibility in the regulation of gene expression. Thus, it is an essential task to identify HPTM readers for understanding of epigenetic regulation. Herein we designed and prepared a novel HPTM probe based on self-assembled multivalent photo-cross-linking technique for selective enrichment and identification of HPTM readers. By use of trimethylation of histone H3 lysine 4, we showcased that the functionalized HPTM probe was able to capture its reader with high enrichment efficiency and remarkable specificity even in a complex environment. Notably, this approach was readily applicable for exploring crosstalk among multiple HPTMs. Combining the probes with a mass spectrometry-based proteomic approach, our approach reached a fairly high coverage of known H3K4me3 readers. We further demonstrated that the HPTM probes can enrich a new type of HPTM readers and uncovered several novel putative binders of crotonylation of histone H3 lysine 9, expanding the repertoire of readers for this epigenetic mark. More broadly, our work provides a general strategy for rapid and robust interrogating HPTM readers and will be of great importance to elucidate epigenetic mechanism in regulating gene activity.

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.