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Key Points Microbial pathogens require nutrient metals in order to grow and cause disease. However, excess metals are toxic, so metal levels must be tightly regulated during infection. Vertebrates have evolved to exploit this metal dependence and metal toxicity through strategies that either prevent access to nutrient metal or direct excess metals towards invading pathogens. Collectively, these processes are known as nutritional immunity. The struggle between host and pathogen for nutrient metals is best studied in the area of Fe. Fe is sequestered from invading pathogens either intracellularly or in high-affinity Fe-binding proteins. To combat host-mediated Fe sequestration, microbial pathogens elaborate several high-affinity Fe acquisition systems. Recently, vertebrate proteins of the innate immune system have been identified that prevent microbial infection through the chelation of nutrient Mn and Zn. These proteins are members of the S100 family of Ca-binding proteins and are abundant at sites of inflammation. In addition to Mn and Zn sequestration, vertebrates can use strategies to direct toxic levels of Mn and Zn towards microbial pathogens. Bacterial measures to combat Mn and Zn sequestration, as well as the toxicity that is associated with excess levels of these metals, are beginning to be uncovered. It is becoming increasingly evident that host-mediated direction of excess Cu towards microbial pathogens is a crucial aspect of vertebrate defence against infection. This observation has provided an explanation for the broad conservation of Cu detoxification systems across disease-causing microorganisms. The importance of nutritional immunity for defence against infection is highlighted by the observation that inherited defects in transition metal homeostasis dramatically affect host susceptibility to certain infectious diseases. This fact underscores the tremendous therapeutic potential of targeting bacterial metal acquisition systems. Vertebrates protect against infection through the sequestration of nutrient metals, and bacterial pathogens have evolved sophisticated acquisition strategies to circumvent this host defence. In this Review, Hood and Skaar describe this molecular arms race for nutrients. Transition metals occupy an essential niche in biological systems. Their electrostatic properties stabilize substrates or reaction intermediates in the active sites of enzymes, and their heightened reactivity is harnessed for catalysis. However, this heightened activity also renders transition metals toxic at high concentrations. Bacteria, like all living organisms, must regulate their intracellular levels of these elements to satisfy their physiological needs while avoiding harm. It is therefore not surprising that the host capitalizes on both the essentiality and toxicity of transition metals to defend against bacterial invaders. This Review discusses established and emerging paradigms in nutrient metal homeostasis at the pathogen–host interface.

The recent emergence of signaling roles for transition metals presages a broader contribution of these elements beyond their traditional functions as metabolic cofactors. New chemical approaches to identify the sources, targets and physiologies of transition-metal signaling can help expand understanding of the periodic table in a biological context.

The development of transition metal catalysts capable of promoting non-natural transformations within living cells can open significant new avenues in chemical and cell biology. Unfortunately, the complexity of the cell makes it extremely difficult to translate standard organometallic chemistry to living environments. Therefore, progress in this field has been very slow, and many challenges, including the possibility of localizing active metal catalysts into specific subcellular sites or organelles, remain to be addressed. Herein, we report a designed ruthenium complex that accumulates preferentially inside the mitochondria of mammalian cells, while keeping its ability to react with exogenous substrates in a bioorthogonal way. Importantly, we show that the subcellular catalytic activity can be used for the confined release of fluorophores, and even allows selective functional alterations in the mitochondria by the localized transformation of inert precursors into uncouplers of the membrane potential. Due to the complexity of the cell, getting transition metal catalysts localized while retaining their activity is highly challenging. Here, the authors report a ruthenium complex that accumulates in mitochondria and is capable of promoting the confined release of fluorophores or mitochondrial uncouplers.

Changes in the transition metal homeostasis in the brain are closely linked with Alzheimer’s disease (AD), including intraneuronal iron accumulation and extracellular copper and zinc pooling in the amyloid plague. The brain copper, zinc, and iron surplus are commonly acknowledged characteristics of AD, despite disagreements among some. This has led to the theory that oxidative stress resulting from abnormal homeostasis of these transition metals may be a causative explanation behind AD. In the nervous system, the interaction of metals with proteins appears to be an essential variable in the development or suppression of neurodegeneration. Chelation treatment may be an option for treating neurodegeneration induced by transition metal ion dyshomeostasis. Some clinicians even recommend using chelating agents as an adjunct therapy for AD. The current review also looks at the therapeutic strategies that have been attempted, primarily with metal-chelating drugs. Metal buildup in the nervous system, as reported in the AD, could be the result of compensatory mechanisms designed to improve metal availability for physiological functions.

Transition-metal-based compounds are promising therapeutic agents, particularly in cancer treatment. However, predicting the binding sites of such compounds remains a major challenge. In this work, we investigate the applicability of two tools, Metal3D and Metal1D, for this purpose. Although originally trained to predict zinc ion binding sites only, both predictors correctly identify at least one of the experimentally observed binding sites for transition metal complexes in each of the apo protein structures tested. At the same time, we highlight current limitations, such as the sensitivity to side-chain conformations, and discuss possible strategies for improvement. This work provides a first step toward establishing a robust computational pipeline in which rapid and low-cost predictors are able to identify putative hotspots for transition metal binding, which can then be refined using more accurate but computationally demanding methods.

Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural, catalytic, or regulatory roles. Modeling transition metal ions, especially in transient, reversible, and concentration-dependent regulatory sites, remains challenging. We present PinMyMetal (PMM), a hybrid machine learning system designed to accurately predict transition metal localization and environment in macromolecules, tailored to tetrahedral and octahedral geometries. PMM outperforms other predictors, achieving high accuracy in ligand and coordinate predictions. It excels in predicting regulatory sites (median deviation 0.36 Å), demonstrating superior accuracy in locating catalytic sites (0.33 Å) and structural sites (0.19 Å). Each predicted site is assigned a certainty score based on local structural and physicochemical features, independent of homologs. Interactive validation through our server, CheckMyMetal, expands PMM’s scope, enabling it to pinpoint and validate diverse functional metal sites from different structure sources (predicted structures, cryo-EM, and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top . The PMM workflow can interrogate with protein sequence to characterize the localization of the most probable transition metals, which is often interchangeable and hard to differentiate by nature. PinMyMetal (PMM) is an accurate tool for predicting transition metal binding sites in proteins. It integrates geometric and chemical features, outperforms existing methods, and supports large-scale genome analysis and drug design.

The widespread occurrence of cadmium in the environment continues to pose a threat to human health despite attempts at limiting its technological uses. The biologically significant ionic form of cadmium, Cd²⁺, binds to many bio-molecules and these interactions underlie the toxicity mechanisms of cadmium. Some of the molecules specialized in the handling of alkaline earth (Mg²⁺, Ca²⁺) and transition metal ions (e.g. Zn²⁺, Cu²⁺/⁺, Fe³⁺/²⁺) should be particularly sensitive to the presence of Cd²⁺, because they enclose cationic sites to which the toxic metal can bind. The possible molecular targets of this kind for cadmium are considered herein. Whereas in vitro evidence for native cation replacement by Cd²⁺ in bio-molecules has been largely provided, the demonstration of such occurrences in vivo is scarce, with the notable exception of metallothionein. One reason might be that realistic low-level Cd²⁺ contaminations involve cellular concentrations far smaller than those of endogenous cations that usually saturate their binding sites. It is very likely that cadmium toxicity is most often mediated by biological systems amplifying the signals triggered by the presence of Cd²⁺. The interference of Cd²⁺ with redox sensitive systems acting at the transcriptional and post-transcriptional levels is instrumental in such processes. A better understanding of cadmium toxicity to tackle the environmental challenges lying ahead thus requires properly designed studies implementing biologically relevant cadmium concentrations on different cell types, improved knowledge of the homeostasis of essential metals, and use of these data in a theoretical framework integrating all cellular aspects of cadmium effects.

Essential transition metals have key roles in oxygen transport, neurotransmitter synthesis, nucleic acid repair, cellular structure maintenance and stability, oxidative phosphorylation, and metabolism. The balance between metal deficiency and excess is typically ensured by several extracellular and intracellular mechanisms involved in uptake, distribution, and excretion. However, provoked by either intrinsic or extrinsic factors, excess iron, zinc, copper, or manganese can lead to cellular damage upon chronic or acute exposure, frequently attributed to oxidative stress. Intracellularly, mitochondria are the organelles that require the tightest control concerning reactive oxygen species production, which inevitably leaves them to be one of the most vulnerable targets of metal toxicity. Current therapies to counteract metal overload are focused on chelators, which often cause secondary effects decreasing patients’ quality of life. New therapeutic options based on synthetic or natural antioxidants have proven positive effects against metal intoxication. In this review, we briefly address the cellular metabolism of transition metals, consequences of their overload, and current therapies, followed by their potential role in inducing oxidative stress and remedies thereof.

The essential transition metal ions are avidly accumulated by cells, yet they have two faces: They are put to use as required cofactors, but they also can catalyze cytotoxic reactions. Several families of proteins are emerging that control the activity of intracellular metal ions and help confine them to vital roles. These include integral transmembrane transporters, metalloregulatory sensors, and diffusible cytoplasmic metallochaperone proteins that protect and guide metal ions to targets. It is becoming clear that many of these proteins use atypical coordination chemistry to accomplish their unique goals. The different coordination numbers, types of coordinating residues, and solvent accessibilities of these sites are providing insight into the inorganic chemistry of the cytoplasm.

Neurodegenerative diseases pose a significant health challenge for the elderly. The escalating presence of toxic metals and chemicals in the environment is a potential contributor to central nervous system dysfunction and the onset of neurodegenerative conditions. Transition metals play a crucial role in various pathophysiological mechanisms associated with prevalent neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Given the ubiquitous exposure to metals from diverse sources in everyday life, the workplace, and the environment, most of the population faces regular contact with different forms of these metals. Disturbances in the levels and homeostasis of certain transition metals are closely linked to the manifestation of neurodegenerative disorders. Oxidative damage further exacerbates the progression of neurological consequences. Presently, there exists no curative therapy for individuals afflicted by neurodegenerative diseases, with treatment approaches primarily focusing on alleviating pathological symptoms. Within the realm of biologically active compounds derived from plants, flavonoids and curcuminoids stand out for their extensively documented antioxidant, antiplatelet, and neuroprotective properties. The utilization of these compounds holds the potential to formulate highly effective therapeutic strategies for managing neurodegenerative diseases. This review provides a comprehensive overview of the impact of abnormal metal levels, particularly copper, iron, and zinc, on the initiation and progression of neurodegenerative diseases. Additionally, it aims to elucidate the potential of fisetin and curcumin to inhibit or decelerate the neurodegenerative process.