Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Bioinspired nonheme iron complex that triggers mitochondrial apoptotic signalling pathway specifically for colorectal cancer cells

The activation of dioxygen is the keystone of all forms of aerobic life. Many biological functions rely on the redox versatility of metal ions to perform reductive activation-mediated processes entailing dioxygen and its partially reduced species including superoxide, hydrogen peroxide, and hydroxyl radicals, also known as reactive oxygen species (ROS). In biomimetic chemistry, a number of synthetic approaches have sought to design, synthesize and characterize reactive intermediates such as the metal-superoxo, -peroxo, and -oxo species, which are commonly found as key intermediates in the enzymatic catalytic cycle. However, the use of these designed complexes and their corresponding intermediates as potential candidates for cancer therapeutics has scarcely been endeavored. In this context, a series of biomimetic first-row transition metal complexes bearing a picolylamine-based water-soluble ligand, [M(HN₃O₂)]²⁺ (M = Mn²⁺, Fe²⁺, Co²⁺, Cu²⁺; HN₃O₂ = 2-(2-(bis(pyridin-2-ylmethyl)amino)ethoxy)ethanol) were synthesized and characterized by various spectroscopic methods including X-ray crystallography and their dioxygen and ROS activation reactivity were evaluated in situ and in vitro. It turned out that among these metal complexes, the iron complex, [Fe(HN₃O₂)(H₂O)]²⁺, was capable of activating dioxygen and hydrogen peroxide and produced the ROS species (e.g., hydroxyl radical). Upon the incubation of these complexes with different cancer cells, such as cervical, breast, and colorectal cancer cells (MDA-MB-231, AU565, SK-BR-3, HeLa S3, HT-29, and HCT116 cells), only the iron complex triggered cellular apoptosis specifically for colorectal cancer cells; the other metal complexes show negligible anti-proliferative activity. More importantly, the biomimetic complexes were harmless to normal cells and produced less ROS therein. The use of immunocytochemistry combined with western blot analysis strongly supported that apoptosis occurred via the intrinsic mitochondrial pathway; in the intracellular network, [Fe(HN₃O₂)(H₂O)]²⁺ resulted in (i) the activation and/or production of ROS species, (ii) the induction of intracellular impaired redox balance, and (iii) the promotion of the mitochondrial apoptotic signaling pathway in colorectal cancer cells. The results have implications for developing novel biomimetic complexes in cancer treatments and for designing potent candidates with cancer-specific antitumor activity.

A water-soluble iron complex that produces hydroxyl radical species triggers colorectal cancer cell death via the mitochondrial apoptotic pathway.

C-H Bond Cleavage by Bioinspired Nonheme Metal Complexes

The functionalization of C-H bonds is one of the most challenging transformations in synthetic chemistry. In biology, these processes are well-known and are achieved with a variety of metalloenzymes, many of which contain a single metal center within their active sites. The most well studied are those with Fe centers, and the emerging experimental data show that high-valent iron oxido species are the intermediates responsible for cleaving the C-H bond. This Forum Article describes the state of this field with an emphasis on nonheme Fe enzymes and current experimental results that provide insights into the properties that make these species capable of C-H bond cleavage. These parameters are also briefly considered in regard to manganese oxido complexes and Cu-containing metalloenzymes. Synthetic iron oxido complexes are discussed to highlight their utility as spectroscopic and mechanistic probes and reagents for C-H bond functionalization. Avenues for future research are also examined.

pH Changes That Induce an Axial Ligand Effect on Nonheme Iron(IV) Oxo Complexes with an Appended Aminopropyl Functionality

Nonheme iron enzymes often utilize a high-valent iron(IV) oxo species for the biosynthesis of natural products, but their high reactivity often precludes structural and functional studies of these complexes. In this work, a combined experimental and computational study is presented on a biomimetic nonheme iron(IV) oxo complex bearing an aminopyridine macrocyclic ligand and its reactivity toward olefin epoxidation upon changes in the identity and coordination ability of the axial ligand. Herein, we show a dramatic effect of the pH on the oxygen-atom-transfer (OAT) reaction with substrates. In particular, these changes have occurred because of protonation of the axial-bound pendant amine group, where its coordination to iron is replaced by a solvent molecule or anionic ligand. This axial ligand effect influences the catalysis, and we observe enhanced cyclooctene epoxidation yields and turnover numbers in the presence of the unbound protonated pendant amine group. Density functional theory studies were performed to support the experiments and highlight that replacement of the pendant amine with a neutral or anionic ligand dramatically lowers the rate-determining barriers of cyclooctene epoxidation. The computational work further establishes that the change in OAT is due to electrostatic interactions of the pendant amine cation that favorably affect the barrier heights.

Repurposing metalloproteins as mimics of natural metalloenzymes for small-molecule activation

Artificial metalloenzymes (ArMs) consist of an unnatural metal or cofactor embedded in a protein scaffold, and are an excellent platform for applying the concepts of protein engineering to catalysis. In this Focused Review, we describe the application of ArMs as simple, tunable artificial models of the active sites of complex natural metalloenzymes for small-molecule activation. In this sense, ArMs expand the strategies of synthetic model chemistry to protein-based supporting ligands with potential for participation from the second coordination sphere. We focus specifically on ArMs that are structural, spectroscopic, and functional models of enzymes for activation of small molecules like CO, CO₂, O₂, N₂, and NO, as well as production/consumption of H₂. These ArMs give insight into the identities and roles of metalloenzyme structural features within and near the cofactor. We give examples of ArM work relevant to hydrogenases, acetyl-coenzyme A synthase, superoxide dismutase, heme oxygenases, nitric oxide reductase, methyl-coenzyme M reductase, copper-O₂ enzymes, and nitrogenases.

Chemical modifications of proteins and their applications in metalloenzyme studies

Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Herein, we summarize some of the recent efforts in these areas with an emphasis on a few metalloenzyme case studies.

Macromolecular crystallography for f-element complex characterization

Single crystal X-ray diffraction is a technique that measures interatomic distances with atomic resolution. Utilizing this technique for metal complexes featuring lanthanide and actinide elements is complicated by the scarcity and radioactivity of many of the metals of the f-block, as sub-milligram samples are difficult to crystallize for small molecule X-ray diffraction experiments. In this chapter, we present a protocol developed in our group that circumvents these challenges by exploiting macromolecular crystallography, wherein a protein with a large and well-characterized binding calyx is used as a scaffold to crystallize small-molecule metal complexes. Highlighting several examples, we identify the structural and chemical information that can be acquired by this method, and delineate the benefits of directing crystal growth with proteins, such as decreasing the amount of metal used to the sub-microgram scale. Moreover, since protein recognition depends on the nature of the metal-chelator bonds, subtle effects in the lanthanide and actinide coordination chemistry, such as metal-ligand covalency, can be qualitatively assessed.

Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers

Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin-streptavidin (Sav) technology in which Fe complexes from adjacent subunits can assemble to form [Fe^III-(μ-OH)-Fe^III] cores. The assembly process is promoted by the site-specific localization of the Fe complexes within a subunit through the designed mutation of a tyrosinate side chain to coordinate the Fe centers. An important outcome is that the Sav host can regulate the Fe···Fe separation, which is known to be important for function in natural metalloproteins. Spectroscopic and structural studies from X-ray diffraction methods revealed uncommonly long Fe···Fe separations that change by less than 0.3 Å upon the binding of additional bridging ligands. The structural constraints imposed by the protein host on the di-Fe cores are unique and create examples of active sites having entatic states within engineered artificial metalloproteins.

Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources

Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.