In-cell NMR: an emerging approach for monitoring metal-related events in living cells

NMR spectroscopy to study the fate of metallodrugs in cells

Metal-based drugs can modulate various biological processes and exhibit a rich variety of properties that foster their use in biomedicine and chemical biology. On the way to intracellular targets, ligand exchange and redox reactions can take place, thus making metallodrug speciation in vivo a challenging task. Advances in NMR spectroscopy have made it possible to move from solution to live-cell studies and elucidate the transport of metallodrugs and interactions with macromolecular targets in a physiological setting. In turn, the electronic properties and supramolecular chemistry of metal complexes can be exploited to characterize drug delivery nanosystems by NMR. The recent evolution of in-cell NMR methodology is presented with special emphasis on metal-related processes. Applications to paradigmatic cases of platinum and gold drugs are highlighted.

Recent advances in iron-complexes as drug candidates for cancer therapy: reactivity, mechanism of action and metabolites

In this perspective, we discuss iron-complexes as drug candidates that are promising alternatives to conventional platinum-based chemotherapies owing to their broad range of reactivities and to the targeting of different biological systems. Breakthroughs in the comprehension of iron complexes' structure-activity relationship contributed to the clarification of their metabolization pathways, sub-cellular localization and influence on iron homeostasis, while enlightening the primary molecular targets of theses likely multi-target metallodrugs. Both the antiproliferative activity and elevated safety index observed among the family of iron complexes showed encouraging results as per their therapeutic potential and selectivity also with the aim of reducing chemotherapy side-effects, and facilitated more pre-clinical investigations. The purpose of this perspective is to summarize the recent advances that contributed in unveiling the intricate relationships between the structural modifications on iron-complexes and their reactivity, cellular trafficking and global mechanisms of action to broaden their use as anticancer drugs and advance to clinical evaluation.

Alkyne Functionalization of a Photoactivated Ruthenium Polypyridyl Complex for Click-Enabled Serum Albumin Interaction Studies

Studying metal-protein interactions is key for understanding the fate of metallodrugs in biological systems. When a metal complex is not emissive and too weakly bound for mass spectrometry analysis, however, it may become challenging to study such interactions. In this work a synthetic procedure was developed for the alkyne functionalization of a photolabile ruthenium polypyridyl complex, [Ru(tpy)(bpy)(Hmte)](PF₆)₂, where tpy = 2,2′:6′,2′′-terpyridine, bpy = 2,2′-bipyridine, and Hmte = 2-(methylthio)ethanol. In the functionalized complex [Ru(HCC-tpy)(bpy)(Hmte)](PF₆)₂, where HCC-tpy = 4′-ethynyl-2,2′:6′,2′′-terpyridine, the alkyne group can be used for bioorthogonal ligation to an azide-labeled fluorophore using copper-catalyzed “click” chemistry. We developed a gel-based click chemistry method to study the interaction between this ruthenium complex and bovine serum albumin (BSA). Our results demonstrate that visualization of the interaction between the metal complex and the protein is possible, even when this interaction is too weak to be studied by conventional means such as UV–vis spectroscopy or ESI mass spectrometry. In addition, the weak metal complex-protein interaction is controlled by visible light irradiation, i.e., the complex and the protein do not interact in the dark, but they do interact via weak van der Waals interactions after light activation of the complex, which triggers photosubstitution of the Hmte ligand.

A “clickable” and photosubstitutionally active ruthenium complex has been prepared that bears a terminal alkyne group. In the dark, the saturated coordination sphere of the complex prevents it from interacting with serum albumin. Upon photosubstitution of one ligand, the complex interacts with the protein via weak interactions that were visualized using copper-catalyzed “click” chemistry postfunctionalization with an azide fluorophore on polyacrylamide gel electrophoresis. These studies demonstrate that the metal-protein interaction is triggered by light irradiation.

In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria

The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here, we apply the popular noncleavable cross-linker disuccinimidyl suberate (DSS) to human mitochondria and identify 5518 distance restraints between protein residues. Each distance restraint on proteins or their interactions provides structural information within mitochondria. Comparing these restraints to protein data bank (PDB)-deposited structures and comparative models reveals novel protein conformations. Our data suggest, among others, substrates and protein flexibility of mitochondrial heat shock proteins. Through this study, we bring forward two central points for the progression of CLMS towards large-scale in situ structural biology: First, clustered conflicts of cross-link data reveal in situ protein conformation states in contrast to error-rich individual conflicts. Second, noncleavable cross-linkers are compatible with proteome-wide studies.

Biophysical approaches for the study of metal-protein interactions

Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.

Probing the interaction of a quercetin bioconjugate with Bcl-2 in living human cancer cells with in-cell NMR spectroscopy

In-cell NMR spectroscopy has emerged as a powerful technique for monitoring biomolecular interactions at an atomic level inside intact cells. However, current methodologies are inadequate at charting intracellular interactions of nonlabeled proteins and require their prior isotopic labeling. Herein, we describe for the first time the monitoring of the quercetin-alanine bioconjugate interaction with the nonlabeled antiapoptotic protein Bcl-2 inside living human cancer cells. STD and Tr-NOESY in-cell NMR methodologies were successfully applied in the investigation of the binding, which was further validated in vitro. In-cell NMR proved a very promising strategy for the real-time probing of the interaction profile of potential drugs with their therapeutic targets in native cellular environments and could, thus, open a new avenue in drug discovery.

In-cell NMR: from metabolites to macromolecules

In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.

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

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

Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR

Paramagnetic resonance enhancement (PRE) is an NMR technique that allows studying three-dimensional structures of RNA-protein complexes in solution. RNA strands are typically spin labeled using nitroxide reagents, which provide minimal perturbation to the native structure. The current work describes an alternative approach, which is based on a Co2+-based probe that can be covalently attached to RNA in the vicinity of the protein's binding site using 'click' chemistry. Similar to nitroxide spin labels, the transition metal based probe is capable of attenuating NMR signal intensities from protein residues localized <40Å away. The extent of attenuation is related to the probe's distance, thus allowing for construction of the protein's contact surface map. This new paradigm has been applied to study binding of HIV-1 nucleocapsid protein 7, NCp7, to a model RNA pentanucleotide.

Metalloproteomics: focus on metabolic issues relating to metals

PURPOSE OF REVIEW

By determining metalloproteomes via high-throughput methodology, metalloproteomics provides a research strategy for investigating nutritional and metabolic issues relating to metals. In this review, we examine recent developments in metalloproteomics since its early days approximately 12 years ago, when we utilized metalloproteomics to investigate copper disposition in hepatocytes in relation to Wilson disease.

RECENT FINDINGS

A metalloproteome is the set of proteins that have metal-binding capacity by being metalloproteins or manifesting metal-binding sites. Like all proteomes, a metalloproteome is determined within the context of a well defined system. It can be ascertained for a single metal or multiple metals in that system. Apart from major technological advances in analytical techniques, recent work has examined metalloproteomes for metals other than copper, notably nickel, zinc and manganese. Given the importance of microbiomes to metabolism, microbial metalloproteomics is a rapidly expanding and promising new field.

SUMMARY

Metals play key roles in metabolic processes. Sufficient technological progress has taken place in the past decade to make metalloproteomics an exciting and innovative type of research in nutrition and metabolism. It elucidates how metals contribute to metabolic physiology across the phyla, including in microbes. For humans, it may clarify mechanisms as well as identify informative diagnostic or prognostic biomarkers.