Katherine J. Franz

Application of Metal Coordination Chemistry to Explore and Manipulate Cell Biology

Our desire to understand how the individual molecules that make up cells organize, interact, and communicate to form living systems has lead to the burgeoning field of chemical biology, an interfacial area of science that combines aspects of chemistry — the study of matter and its transformations, and biology — the study of living things and their interactions with the environment. The defining feature of chemical biology is the use of chemical approaches and small molecules to interrogate or manipulate biology.1,2 These small molecules are synthetic or naturally occurring ones that, for example, bind to DNA to affect protein expression levels, bind to proteins to inhibit their function, interact with lipids to alter membrane integrity, or become fluorescent in response to a metabolic event. Because small molecules can affect biochemical function, there is a clear link between chemical biology and pharmacology and medicine.3 While small molecules are usually implied as being organic compounds,4 inorganic small molecules also have a long history in both biology and medicine. Ancient civilizations used gold and copper for healing purposes, and the modern era of drug discovery was ushered in when arsenic-containing salvarsan was discovered as an anti-syphilis agent to become the world’s first blockbuster drug.5 Inorganic compounds should therefore not be overlooked in the realm of chemical biology, since their distinctive electronic, chemical, and photophysical properties render them particularly useful for a variety of applications.6-8 What are the properties of metal ions that impart utility to biology? Because inorganic elements comprise the bulk of the periodic table, the diversity of these properties is likewise broad and has been thoroughly covered by several books in the field of bioinorganic chemistry.9-11 A brief summary of the general chemical properties of metals is given below. Charge. Metal ions are positively charged in aqueous solution, but that charge can be manipulated depending on the coordination environment so that a metal complexed by ligands can be cationic, anionic, or neutral. Interactions with ligands. Metal ions bind to ligands (both organic and inorganic) via interactions that are often strong and selective. The ligands impart their own functionality and can tune properties of the overall complex that are unique from those of the individual ligand or metal. The thermodynamic and kinetic properties of metal—ligand interactions influence ligand exchange reactions. Structure and bonding. Metal—ligand complexes span a range of coordination geometries that give them unique shapes compared to organic molecules. The bond lengths, bond angles, and number of coordination sites can vary depending on the metal and its oxidation state. Lewis acid character. Metal ions with high electron affinity can significantly polarize groups that are coordinated to them, facilitating hydrolysis reactions. Partially filled d-shell. For the transition metals, the variable number of electrons in the d-shell orbitals (or f-shell for lanthanides) imparts interesting electronic and magnetic properties to transition metal complexes. Redox activity. Coupled with the variability of electrons in the d-shell is the ability for many transition metals to undergo 1-electron oxidation and reduction reactions. Biology has taken advantage of these chemical properties of metals to perform several functional roles, which are summarized in Table 1. This is by no means an exhaustive list, but rather a primer to highlight important themes. Some metal ions, particularly the alkali and alkaline earth metals, are stable in aqueous solution as cations, making Na+, K+ and Ca2+ ideal for maintaining charge balance and electrical conductivity.10 On the other hand, the distinct architectures accessible via metal—ligand bonding interactions impart important structural roles to metal ions that encompass both macroscopic structural stabilization, as in biomineralized tissues,12 as well as molecular structural stabilization, as in proteins and nucleic acids that are stabilized in a preferred fold by metal ions.13-16 Metal—ligand bonding is also significant in its reversibility. For example, Nature takes advantage of reversible binding of metal ions like Ca2+ and Zn2+ to proteins or other storage repositories in order to propagate various biochemical signals.13,17 Metal ions themselves can be their own signal to adjust DNA transcription, as in the case of metalloregulatory proteins.18,19 Reversible metal—ligand coordination is also exploited to bind and release molecules to and from a metal center, a prime example being O2 binding and release from hemoglobin. Table 1 Functional roles of inorganic elements found in biology, with selected representative examples. The reactivity of metallic centers in biology rests mostly in their Lewis acid or redox-active characters. Metal centers that are strong Lewis acids can activate coordinated ligands for reactivity, so for example a water molecule coordinated to a Zn(II) center becomes a potent nucleophile for amide bond hydrolysis of a protein substrate.20 In terms of redox activity, a wide variety of transition metals that can access variable oxidation states are found incorporated as enzyme cofactors to carry out oxidation/reduction chemistry. Electron transfer units like cytochromes, iron-sulfur clusters, and blue copper proteins shuttle electrons to other proteins that require redox chemistry for their function, while other redox proteins catalyze multielectron oxidation/reduction reactions directly on a substrate. Examples here involve oxygen metabolism, including the reduction of dioxygen to water by cytochrome c oxidase, and hydrocarbon oxidation catalyzed by cytochrome P-450 enzymes, to name just a few. When it comes to applying inorganic compounds to biology, chemists are not restricted to the naturally bioavailable set of metals and can take advantage of the properties of biologically exotic elements, including 2nd and 3rd row transition elements and the lanthanide (Ln) elements. This expansion leads to the list of functional roles of inorganic elements applied to biology shown in Table 2. Many of the functions listed in Table 2 mirror those of Table 1, but applied in novel ways. For example, the structures of kinetically inert metal complexes are found to interact with proteins and nucleic acids in unique ways, and the acid-base and redox activity of native and non-native metals can be harnessed for artificial reactivity. Metal complexes can also impart additional functionality not found naturally. The most striking addition to the list is in visualization, where the photophysical, magnetic, and radioactive properties of metals make possible studies based on luminescence, magnetic resonance, PET, and SPECT imaging modalities. Table 2 Functional roles of inorganic elements applied to biology, with selected representative examples and reference to the relevant section of this article. This review will explore how the properties of inorganic coordination complexes are applied in the context of inorganic chemical biology, with a particular focus on applications related to cellular trafficking and regulation. We will delve into the structure, bonding, spectroscopy, and reactivity of transition metal coordination compounds and explore how their unique properties can be used as probes and tools to understand or control biological processes. Our discussion will expand on the functions and examples listed in Table 2, which is really only a partial list, as the examples of inorganic and organometallic complexes applied to biology continue to grow. Our focus is on compounds used in cells to understand the trafficking or regulation of something, be it the metal itself or some other molecule or process that is enabled or visualized by a metal complex. Many of the compounds that are discussed have potential applications in medicine, but the reader is referred to other excellent sources for implicit coverage of medicinal and diagnostic uses of metal complexes.24-33 There have been significant advances in the development of fluorescent probes for monitoring cellular metals. Such molecules are clearly important tools in inorganic chemical biology but will not be covered here, as there are several excellent reviews available.34-39 We define a metal complex that is a “probe for biological systems” as one that can be used in ways to teach us about the chemical biology of living cells. It may be used in vivo or in vitro with the aim of understanding how cells operate. With this definition in mind, we will discuss metal chelators and metal complexes that are being used or have potential to be used to this end, with an emphasis on those that are applied in cellular studies.

Coordination chemistry of copper proteins: how nature handles a toxic cargo for essential function.

Biological copper is coordinated predominantly by just three ligand types: the side chains of histidine, cysteine, and methionine, with of course some exceptions. The arrangement of these components, however, is fascinating. The diversity provided by just these three ligands provides choices of nitrogen vs. sulfur, neutral vs. charged, hydrophilic vs. hydrophobic, susceptibility to oxidation, and degree of pH-sensitivity. In this review we examine how the total number of ligands, their spatial arrangement and solvent accessibility, the various combinations of imidazole, thiolate, and thioether donors, all work together to provide binding sites that either enable copper to carry out a function, or safely transport it in a way that prevents toxic reactivity. We separate copper proteins into two broad classes, those that utilize the metal as a cofactor, or those that traffic the metal. Enzymes and proteins that utilize copper as a cofactor use high affinity sites of high coordination numbers of 4-5 that prevent loss of the metal during redox cycling. Copper trafficking proteins, on the other hand, promote metal transfer either by having low affinity binding sites with moderate coordination number ~4, or by having lower coordinate binding sites of 2-3 ligands that bind with high affinity. Both strategies retain the metal but allow transfer under appropriate conditions. Analysis of studies from our own lab on model peptides, combined with those from other labs, raises an interesting hypothesis that various methionine/histidine/cysteine combinations provide organisms with dynamic, multifunctional domains on copper trafficking proteins that facilitate copper transfer under different extracellular, subcellular, and tissue-specific scenarios of pH, redox environment, and presence of other copper carriers or target proteins.

A Powerful Combinatorial Screen to Identify High‐Affinity Terbium(III)‐Binding Peptides

Lanthanide‐binding tags (LBTs) are protein fusion partners consisting of encoded amino acids that bind lanthanide ions with high affinity. Herein, we present a new screening methodology for the identification of new LBT sequences with high affinity for Tb3+ ions and intense luminescence properties. This methodology utilizes solid‐phase split‐and‐pool combinatorial peptide synthesis. Orthogonally cleavable linkers allow an efficient two‐step screening procedure. The initial screen avoids the interference caused by on‐bead screening by photochemically releasing a portion of the peptides into an agarose matrix for evaluation. The secondary screen further characterizes each winning sequence in a defined aqueous solution. Employment of this methodology on a series of focused combinatorial libraries yielded a linear peptide sequence of 17 encoded amino acids that demonstrated a 140‐fold increase in affinity (57 nM dissociation constant, KD) over previously reported lanthanide‐binding peptides. This linear sequence was macrocyclized by introducing a disulfide bond between flanking cysteine residues to produce a peptide with a 2‐nM apparent dissociation constant for Tb3+ ions.

Minding metals: Tailoring multifunctional chelating agents for neurodegenerative disease

Neurodegenerative diseases like Alzheimers and Parkinsons disease are associated with elevated levels of iron, copper, and zinc and consequentially high levels of oxidative stress. Given the multifactorial nature of these diseases, it is becoming evident that the next generation of therapies must have multiple functions to combat multiple mechanisms of disease progression. Metal-chelating agents provide one such function as an intervention for ameliorating metal-associated damage in degenerative diseases. Targeting chelators to adjust localized metal imbalances in the brain, however, presents significant challenges. In this perspective, we focus on some noteworthy advances in the area of multifunctional metal chelators as potential therapeutic agents for neurodegenerative diseases. In addition to metal chelating ability, these agents also contain features designed to improve their uptake across the blood-brain barrier, increase their selectivity for metals in damage-prone environments, increase antioxidant capabilities, lower Abeta peptide aggregation, or inhibit disease-associated enzymes such as monoamine oxidase and acetylcholinesterase.

Lanthanide-Binding Tags as Versatile Protein Coexpression Probes

Comprehensive proteomic analyses require new methodologies to accelerate the correlation of gene sequence with protein function. Key tools for such efforts include biophysical probes that integrate into the covalent architecture of proteins. Lanthanide‐binding tags (LBTs) are expressible, multitasking fusion partners that are optimized to bind lanthanide ions and have several desirable attributes, which include long‐lived luminescence, excellent X‐ray scattering power for phase determination, and magnetic properties to facilitate NMR spectroscopic structure elucidation. Herein, we present peptide sequences with a 40‐fold higher affinity for Tb3+ ions and significantly brighter luminescence intensity compared with existing peptides. Incorporation of an LBT onto ubiquitin as a prototype fusion protein allows the use of powerful protein‐visualization techniques, which include rapid luminescence detection of LBT‐tagged proteins in SDS‐PAGE gels, as well as determination of protein concentrations in complex mixtures. The LBT strategy is a new alternative for expressing fluorescent fusion proteins by routine molecular biological techniques.

A Prochelator Activated by Hydrogen Peroxide Prevents Metal-Induced Amyloid β Aggregation

Alzheimer’s is a progressive and fatal brain disease that is the most common form of dementia. Its characteristic pathology includes extracellular amyloid plaques that form as a result of abnormal clearance and/or increased production of amyloid-β peptides (Aβ) that are released from the amyloid precursor protein (APP).[1, 2] Metal ions, particularly Cu+/2+ and Zn2+ but also Fe2+/3+, have been implicated in two processes related to Aβ pathology: peptide aggregation and formation of reactive oxygen species (ROS).[3]

A comparison of methionine, histidine and cysteine in copper(I)-binding peptides reveals differences relevant to copper uptake by organisms in diverse environments

The N-terminal, extracellular regions of eukaryotic high affinity copper transport (Ctr) proteins vary in composition of the Cu(i) binding amino acids: methionine, histidine, and cysteine. To examine why certain amino acids are exploited over others in Ctrs from different organisms, the relative Cu(i) binding affinity and the dependence of binding on pH were examined for 3 peptides of the sequence MG(2)XG(2)MK, where X is either Met, His, or Cys. Cu(i) affinity was examined using an ascorbic acid oxidation assay, an electrospray ionization mass spectrometry technique, and spectrophotometric titration with a competitive Cu(i) chelator. The relative affinities of the peptides with Cu(i) reveal a trend whereby Cys > His > Met at pH 7.4 and Cys > Met > His at pH 4.5. Ligand geometry and metric parameters were determined with X-ray absorption spectroscopy. Susceptibility of the peptides to oxidation by hydrogen peroxide and copper-catalyzed oxidative conditions was evaluated by mass spectrometry. These results support hypotheses as to why certain Cu(i) binding amino acids are preferred over others in proteins expressed at different pH and exposed to oxidative environments. The results also have implications for interpreting site-directed mutagenesis studies aimed at identifying copper binding amino acids in copper trafficking proteins.

A prochelator activated by beta-secretase inhibits Abeta aggregation and suppresses copper-induced reactive oxygen species formation.

The intersection of the amyloid cascade hypothesis and the implication of metal ions in Alzheimers disease progression has sparked an interest in using metal-binding compounds as potential therapeutic agents. In the present work, we describe a prochelator SWH that is enzymatically activated by beta-secretase to produce a high affinity copper chelator CP. Because beta-secretase is responsible for the amyloidogenic processing of the amyloid precursor protein, this prochelator strategy imparts disease specificity toward copper chelation not possible with general metal chelators. Furthermore, once activated, CP efficiently sequesters copper from amyloid-beta, prevents and disassembles copper-induced amyloid-beta aggregation, and diminishes copper-promoted reactive oxygen species formation.

A Photolabile Ligand for Light-Activated Release of Caged Copper

A photosensitive caged copper complex has been prepared from a tetradentate ligand (H2cage) composed of two pyridyl-amide arms connected by a photoreactive nitrophenyl group. H2cage binds Cu2+ in aqueous solution with a stability constant (log beta) of 10.8, which corresponds to a KD of 16 pM at pH 7.4. The neutral Cu2+ complex, [Cu(OH2)(cage)], crystallizes as a distorted trigonal bipyramid coordinated by two amide and two pyridyl N atoms, with a water molecule bound in the trigonal plane. Photolysis with 350 nm UV light cleaves the ligand backbone to release photoproducts with significantly diminished affinity for Cu2+, thereby uncaging the metal ion. When coordinated as the caged complex, copper has diminished reactivity to produce hydroxyl radicals from Fenton-like reaction mixtures containing hydrogen peroxide and ascorbic acid. Postphotolysis, uncaged copper promotes hydroxyl radical formation under the same conditions. The strategy of caging copper is promising for applications where light could be used to trigger release of copper as a pro-oxidant to increase oxidative stress or as a tool to release copper intracellularly to study mechanisms of copper trafficking.

Keys for Unlocking Photolabile Metal‐Containing Cages

Photolabile metal-containing cages are metal complexes that undergo a change in coordination environment upon exposure to light of an appropriate wavelength. The light-responsive functionality can either be a component of the encapsulating ligand or a property of the metal complex itself. The altered coordination properties of light-responsive complexes can result in release of the coordinated metal ion into its surroundings, a differential reactivity of the metal center, or the liberation of a reactive molecule that had been passivated by binding to the metal center. These triggerable agents can be useful tools for manipulating the bioavailability of metals or their coordinating ligands in order to study biological pathways or for potential therapeutic purposes.