Metalloproteomics for Biomedical Research: Methodology and Applications

Photosubstitution and photoreduction of a diazido platinum(IV) anticancer complex

The hyphenation of HPLC with its high separation ability and ICP-MS with its excellent sensitivity, allows the analysis of Pt drugs in biological samples at the low nanomolar concentration levels. On the other hand, LC-MS provides molecular structural confirmation for each species. Using a combination of these methods, we have investigated the speciation of the photoactive anticancer complex diazido Pt(IV) complex trans, trans, trans-[Pt(N3)2(OH)2(py)2] (FM-190) in aqueous solution and biofluids at single-digit nanomolar concentrations before and after irradiation. FM-190 displays high stability in human blood plasma in the dark at 37 °C. Interestingly, the polyhydroxido species [{PtIV(py)2(OH)4} + Na]+ and [{PtIV(py)2(N3)(OH)3} + Na]+ resulting from the replacement of azido ligands, as determined by LC-MS, were the major products after photoirradiation of FM-190 with blue light (463 nm). This finding suggests that such photosubstituted Pt(IV) tri- and tetra-hydroxido species could play important roles in the biological activity of this anticancer complex. Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) calculations show that these Pt(IV) species arising from FM-190 in aqueous media can be formed directly from a singlet excited state. The results highlight how speciation analysis (metallomics) can shed light on photoactivation pathways for FM-190 and formation of potential excited-state pharmacophores. The ability to detect and identify photoproducts at physiologically-relevant concentrations in cells and tissues will be important for preclinical development studies of this class of photoactivatable platinum drugs.

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.

Integration of metalloproteome and immunoproteome reveals a tight link of iron-related proteins with COVID-19 pathogenesis and immunity

Increasing clinical data show that the imbalance of host metallome is closely associated with different kinds of disease, however, the intrinsic mechanisms of action of metals in immunity and pathogenesis of disease remain largely undefined. There is lack of multiplexed profiling system to integrate the metalloproteome-immunoproteome information at systemic level for exploring the roles of metals in immunity and disease pathogenesis. In this study, we build up a metal-coding assisted multiplexed proteome assay platform for serum metalloproteomic and immunoproteomic profiling. By taking COVID-19 as a showcase, we unbiasedly uncovered the most evident modulation of iron-related proteins, i.e., Ft and Tf, in serum of severe COVID-19 patients, and the value of Ft/Tf could work as a robust biomarker for COVID-19 severity stratification, which overtakes the well-established clinical risk factors (cytokines). We further uncovered a tight association of transferrin with inflammation mediator IL-10 in COVID-19 patients, which was proved to be mainly governed by the monocyte/macrophage of liver, shedding light on new pathophysiological and immune regulatory mechanisms of COVID-19 disease. We finally validated the beneficial effects of iron chelators as anti-viral agents in SARS-CoV-2-infected K18-hACE2 mice through modulation of iron dyshomeostasis and alleviating inflammation response. Our findings highlight the critical role of liver-mediated iron dysregulation in COVID-19 disease severity, providing solid evidence on the involvement of iron-related proteins in COVID-19 pathophysiology and immunity.

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.

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.

Preliminary Insights of Brazilian Snake Venom Metalloproteomics

Snakebite envenoming is one of the most significantly neglected tropical diseases in the world. The lack of diagnosis/prognosis methods for snakebite is one of our motivations to develop innovative technological solutions for Brazilian health. The objective of this work was to evaluate the protein and metallic ion composition of Crotalus durissus terrificus, Bothrops jararaca, B. alternatus, B. jararacussu, B. moojeni, B. pauloensis, and Lachesis muta muta snake venoms. Brazilian snake venoms were subjected to the shotgun proteomic approach using mass spectrometry, and metal ion analysis was performed by atomic spectrometry. Shotgun proteomics has shown three abundant toxin classes (PLA2, serine proteases, and metalloproteinases) in all snake venoms, and metallic ions analysis has evidenced that the Cu2+ ion is present exclusively in the L. m. muta venom; Ca2+ and Mg2+ ions have shown a statistical difference between the species of Bothrops and Crotalus genus, whereas the Zn2+ ion presented a statistical difference among all species studied in this work. In addition, Mg2+ ions have shown 42 times more in the C. d. terrificus venom when compared to the average concentration in the other genera. Though metal ions are a minor fraction of snake venoms, several venom toxins depend on them. We believe that these non-protein fractions are capable of assisting in the development of unprecedented diagnostic devices for Brazilian snakebites.

Identification of lead-binding proteins as carriers and potential molecular targets associated with systolic blood pressure

Lead (Pb) exposure is well recognized as a significant environmental factor associated with the high incidence of cardiovascular diseases. However, the carriers and molecular targets of Pb in human blood remain to be understood, especially for a real Pb exposure scenario. In this study, a total of 350 blood samples were collected from the smelting workers and systematically analyzed using metallomics and metalloproteomics approaches. The results showed that the majority of Pb (∼99.4%) could be presented in the blood cells. Pb in the cytoplasm of blood cells accounted for approximately 83.1% of the total blood Pb, with nearly half of Pb being bound to proteins. Pb-binding proteins in the blood of workers were identified as hemoglobin, catalase, haptoglobin, δ-aminolevulinic acid dehydratase, and peroxiredoxin-2. Multiple linear regression analysis demonstrated that higher levels of Pb bound to proteins (Mix-bound Pb and Protein-bound Pb) were positively associated with higher systolic blood pressure (p < 0.05). However, the association between blood lead level, Pb levels in the blood cells and systolic blood pressure was not observed (p > 0.05). This study suggested that Pb bound to proteins could be a suitable biomarker for indicating the potential risk of occupational hypertension.

Nickel(II) Phototheranostics: A Case Study in Photoactivated H2O2-Enhanced Immunotherapy

Phototheranostics have emerged as a promising subset of cancer theranostics owing to their potential to provide precise photoinduced diagnoses and therapeutic outcomes. However, the design of phototheranostics remains challenging due to the nature of tumors and their microenvironment, including limitations to the oxygen supply, high rates of recurrence and metastasis, and the immunosuppressive state of cancer cells. Here we report a dual-functional oxygen-independent phototheranostic agent, Ni-2, rationally designed to provide a near-infrared (NIR) photoactivated thermal- and hydroxyl radical (•OH)-enhanced photoimmunotherapeutic anticancer response. Under 880 nm laser irradiation, Ni-2 exhibited high photostability and excellent photoacoustic and photothermal effects with a photothermal conversion efficacy of 58.0%, as well as novel photoredox features that allowed the catalytic conversion of H2O2 to •OH upon photooxidation of Ni(II) to Ni(III). As a multifunctional photoagent, Ni-2 was found not only to inhibit tumor growth in a CT26 tumor-bearing mouse model but also to activate an immune response via a combination of photothermal- and H2O2-induced effects. When combined with an antiprogrammed death-ligand 1 (aPD-L1), Ni-2 treatment allowed for the suppression of distant tumor growth and cancer metastasis. Collectively, the present results provide support for the proposition that Ni-2 or its analogues could emerge as useful tools for photoimmunotherapy. They also highlight the potential of appropriately designed 3d transition metal complexes as "all- in-one" phototheranostics.

Proteogenomics in Cancer: Then and Now

For years, the paths of sequencing technologies and mass spectrometry have occurred in isolation, with each developing its own unique culture and expertise. These two technologies are crucial for inspecting complementary aspects of the molecular phenotype across the central dogma. Integrative multiomics strives to bridge the analysis gap among different fields to complete more comprehensive mechanisms of life events and diseases. Proteogenomics is one integrated multiomics field. Here in this review, we mainly summarize and discuss three aspects: workflow of proteogenomics, proteogenomics applications in cancer research, and the SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis of proteogenomics in cancer research. In conclusion, proteogenomics has a promising future as it clarifies the functional consequences of many unannotated genomic abnormalities or noncanonical variants and identifies driver genes and novel therapeutic targets across cancers, which would substantially accelerate the development of precision oncology.

Metal-coding assisted serological multi-omics profiling deciphers the role of selenium in COVID-19 immunity

Uncovering how host metal(loid)s mediate the immune response against invading pathogens is critical for better understanding the pathogenesis mechanism of infectious disease. Clinical data show that imbalance of host metal(loid)s is closely associated with the severity and mortality of COVID-19. However, it remains elusive how metal(loid)s, which are essential elements for all forms of life and closely associated with multiple diseases if dysregulated, are involved in COVID-19 pathophysiology and immunopathology. Herein, we built up a metal-coding assisted multiplexed serological metallome and immunoproteome profiling system to characterize the links of metallome with COVID-19 pathogenesis and immunity. We found distinct metallome features in COVID-19 patients compared with non-infected control subjects, which may serve as a biomarker for disease diagnosis. Moreover, we generated the first correlation network between the host metallome and immunity mediators, and unbiasedly uncovered a strong association of selenium with interleukin-10 (IL-10). Supplementation of selenium to immune cells resulted in enhanced IL-10 expression in B cells and reduced induction of proinflammatory cytokines in B and CD4+ T cells. The selenium-enhanced IL-10 production in B cells was confirmed to be attributable to the activation of ERK and Akt pathways. We further validated our cellular data in SARS-CoV-2-infected K18-hACE2 mice, and found that selenium supplementation alleviated SARS-CoV-2-induced lung damage characterized by decreased alveolar inflammatory infiltrates through restoration of virus-repressed selenoproteins to alleviate oxidative stress. Our approach can be readily extended to other diseases to understand how the host defends against invading pathogens through regulation of metallome.

Characterizing metal-biomolecule interactions by mass spectrometry

Metal micronutrients are essential for life and exist in a delicate balance to maintain an organism's health. The labile nature of metal-biomolecule interactions clouds the understanding of metal binders and metal-mediated conformational changes that are influential to health and disease. Mass spectrometry (MS)-based methods and technologies have been developed to better understand metal micronutrient dynamics in the intra- and extracellular environment. In this review, we describe the challenges associated with studying labile metals in human biology and highlight MS-based methods for the discovery and study of metal-biomolecule interactions.

Exploring the Potential of Metal-Based Candidate Drugs as Modulators of the Cytoskeleton

During recent years, accumulating evidence suggested that metal-based candidate drugs are promising modulators of cytoskeletal and cytoskeleton-associated proteins. This was substantiated by the identification and validation of actin, vimentin and plectin as targets of distinct ruthenium(II)- and platinum(II)-based modulators. Despite this, structural information about molecular interaction is scarcely available. Here, we compile the scattered reports about metal-based candidate molecules that influence the cytoskeleton, its associated proteins and explore their potential to interfere in cancer-related processes, including proliferation, invasion and the epithelial-to-mesenchymal transition. Advances in this field depend crucially on determining binding sites and on gaining comprehensive insight into molecular drug-target interactions. These are key steps towards establishing yet elusive structure-activity relationships.

From the Discovery of Targets to Delivery Systems: How to Decipher and Improve the Metallodrugs' Actions at a Molecular Level

Metals are indispensable for the life of all organisms, and their dysregulation leads to various disorders due to the disruption of their homeostasis. Nowadays, various transition metals are used in pharmaceutical products as diagnostic and therapeutic agents because their electronic structure allows them to adjust the properties of molecules differently from organic molecules. Therefore, interest in the study of metal-drug complexes from different aspects has been aroused, and numerous approaches have been developed to characterize, activate, deliver, and clarify molecular mechanisms. The integration of these different approaches, ranging from chemoproteomics to nanoparticle systems and various activation strategies, enables the understanding of the cellular responses to metal drugs, which may form the basis for the development of new drugs and/or the modification of currently used drugs. The purpose of this review is to briefly summarize the recent advances in this field by describing the technological platforms and their potential applications for identifying protein targets for discovering the mechanisms of action of metallodrugs and improving their efficiency during delivery.

Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives

The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.

Methods to identify protein targets of metal-based drugs

Metal-based anticancer agents occupy a distinct chemical space due to their particular coordination geometry and reactivity. Despite the initial DNA-targeting paradigm for this class of compounds, it is now clear that they can also be tuned to target proteins in cells, depending on the metal and ligand scaffold. Since metallodrug discovery is dominated by phenotypic screenings, tailored proteomics strategies were crucial to identify and validate protein targets of several investigative and clinically advanced metal-based drugs. Here, such experimental approaches are discussed, which showed that metallodrugs based on ruthenium, gold, rhenium and even platinum, can selectively and specifically target proteins with clear-cut down-stream effects. Target identification strategies are expected to support significantly the mechanism-driven clinical translation of metal-based drugs.

Integrative Metallomics Studies of Toxic Metal(loid) Substances at the Blood Plasma–Red Blood Cell–Organ/Tumor Nexus

Globally, an estimated 9 million deaths per year are caused by human exposure to environmental pollutants, including toxic metal(loid) species. Since pollution is underestimated in calculations of the global burden of disease, the actual number of pollution-related deaths per year is likely to be substantially greater. Conversely, anticancer metallodrugs are deliberately administered to cancer patients, but their often dose-limiting severe adverse side-effects necessitate the urgent development of more effective metallodrugs that offer fewer off-target effects. What these seemingly unrelated events have in common is our limited understanding of what happens when each of these toxic metal(loid) substances enter the human bloodstream. However, the bioinorganic chemistry that unfolds at the plasma/red blood cell interface is directly implicated in mediating organ/tumor damage and, therefore, is of immediate toxicological and pharmacological relevance. This perspective will provide a brief synopsis of the bioinorganic chemistry of AsIII, Cd2+, Hg2+, CH3Hg+ and the anticancer metallodrug cisplatin in the bloodstream. Probing these processes at near-physiological conditions and integrating the results with biochemical events within organs and/or tumors has the potential to causally link chronic human exposure to toxic metal(loid) species with disease etiology and to translate more novel anticancer metal complexes to clinical studies, which will significantly improve human health in the 21st century.

Lanmodulin Remains Unfold and Fails to Interact with Lanthanide Ions in Escherichia coli Cells

We report the conformation of a newly discovered specific lanthanide ions (Ln3+) binding protein, Lanmodulin (LanM), and its inteaction with Ln3+ in Escherichia coli cells using In-cell NMR. We found...