Transition Metal‐Promoted Reactions in Aqueous Media and Biological Settings

Expanding the Reach of Sustainable Solid-Phase Peptide Synthesis: One-Pot, Metal-Free Alloc Removal-Peptide Coupling

While the allyloxycarbonyl (Alloc) protecting group has played a key role in solid-phase peptide synthesis (SPPS), providing access to a wide range of peptides, its removal has suffered from relying on air-sensitive Pd(0) complexes in hazardous solvents. We report metal-free, on-resin Alloc removal using readily available iodine/water in environmentally sensible PolarClean (PC)/ethyl acetate (EtOAc) carried out in a one-pot manner with racemization-free peptide couplings employing both 9-fluorenylmethoxycarbonyl (Fmoc) and Alloc amino acids (AAs). Alloc SPPS has been demonstrated by performing consecutive one-pot Alloc removals-peptide couplings, whereas compatibility with long peptides has been proven by carrying out an Alloc removal-coupling on a 39 AA peptide resin. Upscaling to 10 g was combined with TFA-free peptide resin cleavage, opening up opportunities for employing Alloc-AAs as synthons for sustainable peptide manufacturing.

Exploring New Bioorthogonal Catalysts: Scaffold Diversity in Catalysis for Chemical Biology

Bioorthogonal catalysis has revolutionized the field of chemical biology by enabling selective and controlled chemical transformations within living systems. Research has converged on the development of innovative catalyst scaffolds, seeking to broaden the scope of bioorthogonal reactions, boost their efficiency, and surpass the limitations of conventional catalysts. This review provides a comprehensive overview of the latest advancements in bioorthogonal catalyst research based on different scaffold materials. Through an in-depth analysis of fabrication strategies and applications of bioorthogonal catalysts, this review discusses the design principles, mechanisms of action, and applications of these novel catalysts in chemical biology. Current challenges and future directions in exploring the scaffold diversity are also highlighted. The integration of diverse catalyst scaffolds offers exciting prospects for precise manipulation of biomolecules and the development of innovative therapeutic strategies in chemical biology. In addition, the review fills in the gaps in previous reviews, such as in fully summarizing the presented scaffold materials applied in bioorthogonal catalysts, emphasizing the potential impact on advancing bioorthogonal chemistry, and offering prospects for future development in this field.

Click-and-Release Formation of Urea Bonds in Living Cells Enabled by Micelle Nanoreactors

The development of innovative strategies enabling chemical reactions in living systems is of great interest for exploring and manipulating biological processes. Herein, we present a pioneering approach based on both bioorthogonal and confined chemistry for intracellular drug synthesis. Exploiting a click-to-release reaction, we engineered nanoparticles capable of synthesizing drugs within cellular environments through bioorthogonal reactions with cyclooctynes. Proof of concept experiments showed that this new approach could be successfully applied to the synthesis of the FDA-approved Sorafenib within cancer cells. The integration of bioorthogonal and confined chemistry not only offers exciting prospects for advancing therapeutic strategies but also opens up new avenues for exploring non-natural reactions within living systems. This innovative approach represents a fundamental extension of the biorthogonal chemistry concept and holds great promise for pioneering developments in therapeutic applications.

Metal-Catalyzed Abiotic Cleavage of C═C Bonds for Effective Fluorescence Imaging of Cu(II) and Fe(III) in Living Systems

Imaging abnormal copper/iron with effective fluorescent tools is essential to comprehensively put insight into many pathological events. However, conventional coordination-based detection is mired in the fluorescence quenching induced by paramagnetic Cu(II)/Fe(III). Moreover, the strong chelating property of the probe will consume dissociative metal ions and inevitably interfere with the physiological microenvironment. Here, a new strategy is developed by employing this aberrant Cu(II)/Fe(III) to catalyze bond cleavage for fluorescent imaging of them. A short series of near-infrared fluorescent molecules (NIRB1-NIRB6) is devised as substrates, wherein the specific C═C bonds can be effectively cleaved to activate red fluorophore by Cu(II)/Fe(III) catalyzing. Representatively, NIRB1 is applied for fluorescent imaging of Cu(II)/Fe(III) in living cells, zebrafish, and Alzheimer's disease (AD)-afflicted mouse brains which is of significance to monitor metal safety. The successful cleavage of C═C bonds catalyzed by Cu(II)/Fe(III) enriches the application of abiotic bond cleavage reactions in metal detection, and may also inspire the development of fluorescent tools for the future diagnosis and therapy of diseases.

Bioorthogonal Synthetic Chemistry Enabled by Visible-Light Photocatalysis

The field of bioorthogonal chemistry has revolutionized our ability to interrogate and manipulate biological systems at the molecular level. However, the range of chemical reactions that can operate efficiently in biological environments without interfering with the native cellular machinery, remains limited. In this context, the rapidly growing area of photocatalysis offers a promising avenue for developing new type of bioorthogonal tools. The inherent mildness, tunability, chemoselectivity, and external controllability of photocatalytic transformations make them particularly well-suited for applications in biological and living systems. This minireview summarizes recent advances in bioorthogonal photocatalytic technologies, with a particular focus on their potential to enable the selective generation of designed products within biologically relevant or living settings.

Synthesis of phenanthridine derivatives by a water-compatible gold-catalyzed hydroamination

Since transition-metal-catalyzed reactions are one of the most powerful and direct approaches for the synthesis of organic molecules, translating them to biological systems for biomedical applications is an emerging field. The manipulation of transition metal reactions in biological settings for uncaging prodrugs and synthesizing bioactive drugs has been widely studied. To expand the toolbox of transition-metal-mediated prodrug strategy, this work introduces the 2'-alkynl-biphenylamine precursors for the synthesis of phenanthridine derivatives using a water-compatible gold-catalyzed hydroamination under mild conditions. Moreover, the structure-reactivity relationship revealed that the nucleophilicity of the amine group in the precursor was critical for facilitating the gold-catalyzed synthesis of phenanthridine derivatives. The research shows the potential to be used for phenanthridine-based prodrug designs in an aqueous solution.

Fluorescent probes for investigating the internalisation and action of bioorthogonal ruthenium catalysts within Gram-positive bacteria

Bioorthogonal reactions are extremely useful for the chemical modification of biomolecules, and are already well studied in mammalian cells. In contrast, very little attention has been given to the feasibility of such reactions in bacteria. Herein we report modified coumarin dyes for monitoring the internalisation and activity of bioorthogonal catalysts in the Gram-positive bacterial species Bacillus subtilis. Two fluorophores based on 7-aminocoumarin were synthesised and characterised to establish their luminescence properties. The introduction of an allyl carbamate (R2N-COOR') group onto the nitrogen atom of two 7-aminocoumarin derivatives with different solubility led to decreased fluorescence emission intensities and remarkable blue-shifts of the emission maxima. Importantly, this allyl carbamate group could be uncaged by the bioorthogonal, organometallic ruthenium catalyst investigated in this work, to yield the fluorescent product under biologically-relevant conditions. The internalisation of this catalyst was confirmed and quantified by ICP-OES analysis. Investigation of the bacterial cytoplasm and extracellular fractions separately, following incubation of the bacteria with the two caged dyes, facilitated their localisation, as well as that of their uncaged form by catalyst addition. In fact, significant differences were observed, as only the more lipophilic dye was located inside the cells and importantly remained there, seemingly avoiding efflux mechanisms. However, the uncaged form of this dye is not retained, and was found predominantly in the extracellular space. Finally, a range of siderophore-conjugated derivatives of the catalyst were investigated for the same transformations. Even though uptake was observed, albeit less significant than for the non-conjugated version, the fact that similar intracellular reaction rates were observed regardless of the iron content of the medium supports the notion that their uptake is independent of the iron transporters utilised by Gram-positive Bacillus subtilis cells.

De Novo Engineering of Pd-Metalloproteins and Their Use as Intracellular Catalysts

The development of transition metal-based catalytic platforms that promote bioorthogonal reactions inside living cells remains a major challenge in chemical biology. This is particularly true for palladium-based catalysts, which are very powerful in organic synthesis but perform poorly in the cellular environment, mainly due to their rapid deactivation. We now demonstrate that grafting Pd(II) complexes into engineered β-sheets of a model WW domain results in cell-compatible palladominiproteins that effectively catalyze depropargylation reactions inside HeLa cells. The concave shape of the WW domain β-sheet proved particularly suitable for accommodating the metal center and protecting it from rapid deactivation in the cellular environment. A thorough NMR and computational study confirmed the formation of the metal-stapled peptides and allowed us to propose a three-dimensional structure for this novel metalloprotein motif.

Gas Evolution as a Tool to Study Reaction Kinetics Under Biomimetic Conditions

The field of bioorthogonal chemistry is rapidly growing, presenting successful applications of organic and transition metal-catalysed reactions in cells and living systems (in vivo). The development of such reactions typically proceeds through many iterative steps focused on biocompatibility and fast reaction kinetics to ensure product formation. However, obtaining kinetic data, even under simulated biological (biomimetic) conditions, remains a challenge due to substantial concentrations of salts and biomolecules hampering the use of typically employed solution-phase analytical techniques. In this study, we explored the suitability of gas evolution as a probe to study kinetics under biomimetic conditions. As proof of concept, we show that the progress of two transition metal-catalysed bioorthogonal chemical reactions can be accurately monitored, regardless of the complexity of the medium. As such, we introduce a protocol to gain more insight into the performance of a catalytic system under biomimetic conditions to further progress iterative catalyst development for in vivo applications.

Copper-Catalyzed Sulfimidation in Aqueous Media: a Fast, Chemoselective and Biomolecule-Compatible Reaction

Performing transition metal-catalyzed reactions in cells and living systems has equipped scientists with a toolbox to study biological processes and release drugs on demand. Thus far, an impressive scope of reactions has been performed in these settings, but many are yet to be introduced. Nitrene transfer presents a rather unexplored new-to-nature reaction. The reaction products are frequently encountered motifs in pharmaceuticals, presenting opportunities for the controlled, intracellular synthesis of drugs. Hence, we explored the transition metal-catalyzed sulfimidation reaction in water for future in vivo application. Two Cu(I) complexes containing trispyrazolylborate ligands (Tpx ) were selected, and the catalytic system was evaluated with the aid of three fitness factors. The excellent nitrene transfer reactivity and high chemoselectivity of the catalysts, coupled with good biomolecule compatibility, successfully enabled the sulfimidation of thioethers in aqueous media. We envision that this copper-catalyzed sulfimidation reaction could be an interesting starting point to unlock the potential of nitrene transfer catalysis in vivo.

Intracellular Synthesis of Indoles Enabled by Visible-Light Photocatalysis

Performing abiotic synthetic transformations in live cell environments represents a new, promising approach to interrogate and manipulate biology and to uncover new types of biomedical tools. We now found that photocatalytic bond-forming reactions can be added to the toolbox of bioorthogonal synthetic chemistry. Specifically, we demonstrate that exogenous styryl aryl azides can be converted into indoles inside living mammalian cells under photocatalytic conditions.

Controlled Supramolecular Assemblies of Chiral Cyclometalated Gold (III) Amphiphiles in Aqueous Media

Gold (III) cyclometalated based amphiphiles in aqueous media have been revealed with excellent supramolecular transformations to external stimuli to open new pathways for soft functional material fabrications. Herein, we report a new chiral cyclometalated gold (III) amphiphile (GA) assembling into lamellar nanostructures in aqueous media confirmed with transmission electron microscopy (TEM). Counterion exchange with D-, L-, or racemic-camphorsulfonates features the significant supramolecular helicity enhancements, enabling transformations of GA from lamellar structure to vesicles and to nanotubes with multi-equivalents of counterion. The limited cytotoxicity of GA in aqueous media exhibits good biocompatibility.

Bioorthogonal chemistry for prodrug activation in vivo

Prodrugs have emerged as a major strategy for addressing clinical challenges by improving drug pharmacokinetics, reducing toxicity, and enhancing treatment efficacy. The emergence of new bioorthogonal chemistry has greatly facilitated the development of prodrug strategies, enabling their activation through chemical and physical stimuli. This "on-demand" activation using bioorthogonal chemistry has revolutionized the research and development of prodrugs. Consequently, prodrug activation has garnered significant attention and emerged as an exciting field of translational research. This review summarizes the latest advancements in prodrug activation by utilizing bioorthogonal chemistry and mainly focuses on the activation of small-molecule prodrugs and antibody-drug conjugates. In addition, this review also discusses the opportunities and challenges of translating these advancements into clinical practice.

Combining lipid-mimicking-enabled transition metal and enzyme-mediated catalysis at the cell surface of E. coli

Being an essential multifunctional platform and interface to the extracellular environment, the cell membrane constitutes a valuable target for the modification and manipulation of cells and cellular behavior, as well as for the implementation of artificial, new-to-nature functionality. While bacterial cell surface functionalization via expression and presentation of recombinant proteins has extensively been applied, the corresponding application of functionalizable lipid mimetics has only rarely been reported. Herein, we describe an approach to equip E. coli cells with a lipid-mimicking, readily membrane-integrating imidazolium salt and a corresponding NHC-palladium complex that allows for flexible bacterial membrane surface functionalization and enables E. coli cells to perform cleavage of propargyl ethers present in the surrounding cell medium. We show that this approach can be combined with already established on-surface functionalization, such as bacterial surface display of enzymes, i.e. laccases, leading to a new type of cascade reaction. Overall, we envision the herein presented proof-of-concept studies to lay the foundation for a multifunctional toolbox that allows flexible and broadly applicable functionalization of bacterial membranes.

Transition Metal Catalysis in Living Cells: Progress, Challenges, and Novel Supramolecular Solutions

The importance of transition metal catalysis is exemplified by its wide range of applications, for example in the synthesis of chemicals, natural products, and pharmaceuticals. However, one relatively new application is for carrying out new-to-nature reactions inside living cells. The complex environment of a living cell is not welcoming to transition metal catalysts, as a diverse range of biological components have the potential to inhibit or deactivate the catalyst. Here we review the current progress in the field of transition metal catalysis, and evaluation of catalysis efficiency in living cells and under biological (relevant) conditions. Catalyst poisoning is a ubiquitous problem in this field, and we propose that future research into the development of physical and kinetic protection strategies may provide a route to improve the reactivity of catalysts in cells.

Biodegradable Grubbs-Loaded Artificial Organelles for Endosomal Ring-Closing Metathesis

The application of transition-metal catalysts in living cells presents a promising approach to facilitate reactions that otherwise would not occur in nature. However, the usage of metal complexes is often restricted by their limited biocompatibility, toxicity, and susceptibility to inactivation and loss of activity by the cell's defensive mechanisms. This is especially relevant for ruthenium-mediated reactions, such as ring-closing metathesis. In order to address these issues, we have incorporated the second-generation Hoveyda-Grubbs catalyst (HGII) into polymeric vesicles (polymersomes), which were composed of biodegradable poly(ethylene glycol)-b-poly(caprolactone-g-trimethylene carbonate) [PEG-b-P(CL-g-TMC)] block copolymers. The catalyst was either covalently or non-covalently introduced into the polymersome membrane. These polymersomes were able to act as artificial organelles that promote endosomal ring-closing metathesis for the intracellular generation of a fluorescent dye. This is the first example of the use of a polymersome-based artificial organelle with an active ruthenium catalyst for carbon-carbon bond formation.

Organoiridium Complexes Enhance Cellular Defense Against Reactive Aldehydes Species

Although reactive aldehyde species (RASP) are associated with the pathogenesis of many major diseases, there are currently no clinically approved treatments for RASP overload. Conventional aldehyde detox agents are stoichiometric reactants that get consumed upon reacting with their biological targets, which limits their therapeutic efficiency. To achieve longer-lasting detoxification effects, small-molecule intracellular metal catalysts (SIMCats) were used to protect cells by converting RASP into non-toxic alcohols. It was shown that SIMCats were significantly more effective in lowering cell death from the treatment with 4-hydroxynon-2-enal than aldehyde scavengers over a 72 h period. Studies revealed that SIMCats reduced the aldehyde accumulation in cells exposed to the known RASP inducer arsenic trioxide. This work demonstrates that SIMCats offer unique benefits over stochiometric agents, potentially providing new ways to combat diseases with greater selectivity and efficiency than existing approaches.

Ruthenium-catalyzed intermolecular alkene-alkyne couplings in biologically relevant media

Cationic cyclopentadienyl Ru(ii) catalysts can efficiently promote mild intermolecular alkyne-alkene couplings in aqueous media, even in the presence of different biomolecular components, and in complex media like DMEM. The method can also be used for the derivatization of amino acids and peptides, therefore proposing a new way to label biomolecules with external tags. This C-C bond-forming reaction, based on simple alkene and alkyne reactants, can now be added to the toolbox of bioorthogonal reactions promoted by transition metal catalysts.

Nanosized metal-organic frameworks as unique platforms for bioapplications

Metal-organic frameworks (MOFs) are extremely versatile materials, which serve to create platforms with exceptional porosity and specific reactivities. The production of MOFs at the nanoscale (NMOFs) offers the possibility of creating innovative materials for bioapplications as long as they maintain the properties of their larger counterparts. Due to their inherent chemical versatility, synthetic methods to produce them at the nanoscale can be combined with inorganic nanoparticles (NPs) to create nanocomposites (NCs) with one-of-a-kind features. These systems can be remotely controlled and can catalyze abiotic reactions in living cells, which have the potential to stimulate further research on these nanocomposites as tools for advanced therapies.

Siderophore-Linked Ruthenium Catalysts for Targeted Allyl Ester Prodrug Activation within Bacterial Cells

Due to rising resistance, new antibacterial strategies are needed, including methods for targeted antibiotic release. As targeting vectors, chelating molecules called siderophores that are released by bacteria to acquire iron have been investigated for conjugation to antibacterials, leading to the clinically approved drug cefiderocol. The use of small-molecule catalysts for prodrug activation within cells has shown promise in recent years, and here we investigate siderophore-linked ruthenium catalysts for the activation of antibacterial prodrugs within cells. Moxifloxacin-based prodrugs were synthesised, and their catalyst-mediated activation was demonstrated under anaerobic, biologically relevant conditions. In the absence of catalyst, decreased antibacterial activities were observed compared to moxifloxacin versus Escherichia coli K12 (BW25113). A series of siderophore-linked ruthenium catalysts were investigated for prodrug activation, all of which displayed a combinative antibacterial effect with the prodrug, whereas a representative example displayed little toxicity against mammalian cell lines. By employing complementary bacterial growth assays, conjugates containing siderophore units based on catechol and azotochelin were found to be most promising for intracellular prodrug activation.

Metal complexes for catalytic and photocatalytic reactions in living cells and organisms

The development of organometallic catalysis has greatly expanded the synthetic chemist toolbox compared to only exploiting "classical" organic chemistry. Although more widely used in organic solvents, metal-based catalysts have also emerged as efficient tools for developing organic transformations in water, thus paving the way for further development of bio-compatible reactions. However, performing metal-catalysed reactions within living cells or organisms induces additional constraints to the design of reactions and catalysts. In particular, metal complexes must exhibit good efficiency in complex aqueous media at low concentrations, good cell specificity, good cellular uptake and low toxicity. In this review, we focus on the presentation of discrete metal complexes that catalyse or photocatalyse reactions within living cells or living organisms. We describe the different reaction designs that have proved to be successful under these conditions, which involve very few metals (Ir, Pd, Ru, Pt, Cu, Au, and Fe) and range from in cellulo deprotection/decaging/activation of fluorophores, drugs, proteins and DNA to in cellulo synthesis of active molecules, and protein and organelle labelling. We also present developments in bio-compatible photo-activatable catalysts, which represent a very recent emerging area of research and some prospects in the field.

In Vivo Biocatalytic Cascades Featuring an Artificial-Enzyme-Catalysed New-to-Nature Reaction

Artificial enzymes utilizing the genetically encoded non-proteinogenic amino acid p-aminophenylalanine (pAF) as a catalytic residue are able to react with carbonyl compounds through an iminium ion mechanism to promote reactions that have no equivalent in nature. Herein, we report an in vivo biocatalytic cascade that is augmented with such an artificial enzyme-catalysed new-to-nature reaction. The artificial enzyme in this study is a pAF-containing evolved variant of the lactococcal multidrug-resistance regulator, designated LmrR_V15pAF_RMH, which efficiently converts benzaldehyde derivatives produced in vivo into the corresponding hydrazone products inside E. coli cells. These in vivo biocatalytic cascades comprising an artificial-enzyme-catalysed reaction are an important step towards achieving a hybrid metabolism.

Bioorthogonal nanozymes: an emerging strategy for disease therapy

Transition metal catalysts (TMCs), capable of performing bioorthogonal reactions, have been engineered to trigger the formation of bioactive molecules in a controlled manner for biomedical applications. However, the widespread use of TMCs based biorthogonal reactions in vivo is still largely limited owing to their toxicity, poor stability, and insufficient targeting properties. The emergence of nanozymes (nanomaterials with enzyme-like activity), especially bioorthogonal nanozymes that combine the bioorthogonal catalytic activity of TMCs, the physicochemical properties of nanomaterials, and the enzymatic properties of classical nanozymes potentially provide opportunities to address these challenges. Thus, they can be used as multifunctional catalytic platforms for disease treatment and will be far-reaching. In this review, we first briefly recall the classical TMC-based bioorthogonal reactions. Furthermore, this review highlights the diverse strategies for manufacturing bioorthogonal nanozymes and their potential for therapeutic applications, with the goal of facilitating bioorthogonal catalysis in the clinic. Finally, we present challenges and the prospects of bioorthogonal nanozymes in bioorthogonal chemistry.

Copper adorned magnetic nanoparticles as a heterogeneous catalyst for Sonogashira coupling reaction in aqueous media

A nanomagnetic hydrophilic heterogeneous copper catalyst, termed γ-Fe₂O₃@PEG@PAMAM G₀-Cu, has been successfully prepared and characterized using FT-IR, XRD, FE-SEM, TEM, EDX, mapping, TGA/DTG, VSM and ICP analyses. The catalyst displayed excellent activity for the palladium-free Sonogashira cross coupling reaction of various aryl iodides and bromides with phenylacetylene derivatives in pure water. The presence of polyethylene glycol coupled with hydrophilic character of the Cu-catalyst adorned on γ-Fe₂O₃ MNPs provides the ready dispersion of the catalyst particles in water, leading to higher catalytic performance as well as facile catalyst recovery via simple magnetic decantation. The recovered catalyst was reused for at least six successive runs with little reduction in its catalytic activity and any noticeable changes in its structure. The use of water as a green solvent, without requiring any additive or organic solvent, as well as the exploitation of abundant and low-cost copper catalyst instead of expensive Pd catalyst along with the catalyst recovery and scalability, make this method favorable from environmental and economic points of view for the Sonogashira coupling reaction.

Evaluation of acute toxicity of cancer-targeting albumin-based artificial metalloenzymes

Recently, the development of abiotic metal-mediated drug delivery has been significant growth in the fields of anticancer approach and biomedical application. However, the intrinsic toxicity of abiotic metal catalysts makes in vivo use difficult. Our group developed a system of cancer-targeting albumin-based artificial metalloenyzmes (ArMs) capable of performing localized drug synthesis and selective tagging therapy in vivo for cancer therapy. The toxicity of the system at higher concentrations was investigated in vitro and in vivo in the study to demonstrate its safety for potential application in clinical trials. In cell-based experiments, the study revealed that the cytotoxicity of metal catalysts anchored within the binding cavity of the cancer-targeting ArMs could be significantly reduced compared to free-in-solution metal catalysts. Moreover, the in vivo data demonstrated that the cancer-targeting ArMs did not cause considerable damage in organs or change in the hematological parameters in a single-dose (160 mg/Kg) toxicity study in rats. Therefore, the system is safe, highlighting that it could be used in clinical trials for cancer treatment.

Exporting Homogeneous Transition Metal Catalysts to Biological Habitats

The possibility of performing designed transition-metal catalyzed reactions in biological and living contexts can open unprecedented opportunities to interrogate and interfere with biology. However, the task is far from obvious, in part because of the presumed incompatibly between organometallic chemistry and complex aqueous environments. Nonetheless, in the past decade there has been a steady progress in this research area, and several transition-metal (TM)-catalyzed bioorthogonal and biocompatible reactions have been developed. These reactions encompass a wide range of mechanistic profiles, which are very different from those used by natural metalloenzymes. Herein we present a summary of the latest progress in the field of TM-catalyzed bioorthogonal reactions, with a special focus on those triggered by activation of multiple carbon-carbon bonds.

Organometallic catalysis in aqueous and biological environments: harnessing the power of metal carbenes

Translating the power of transition metal catalysis to the native habitats of enzymes can significantly expand the possibilities of interrogating or manipulating natural biological systems, including living cells and organisms. This is especially relevant for organometallic reactions that have shown great potential in the field of organic synthesis, like the metal-catalyzed transfer of carbenes. While, at first sight, performing metal carbene chemistry in aqueous solvents, and especially in biologically relevant mixtures, does not seem obvious, in recent years there has been a growing number of reports demonstrating the feasibility of the task. Either using small molecule metal catalysts or artificial metalloenzymes, a number of carbene transfer reactions that tolerate aqueous and biorelevant media are being developed. This review intends to summarize the most relevant contributions, and establish the state of the art in this emerging research field.

Hydrodechlorination of Aryl Chlorides Under Biocompatible Conditions

Developing nonenzymatic chemistry that is nontoxic to microbial organisms creates the potential to integrate synthetic chemistry with metabolism and offers new remediation strategies. Chlorinated organic compounds known to bioaccumulate and cause harmful environmental impact can be converted into less damaging derivatives through hydrodehalogenation. The hydrodechlorination of substituted aryl chlorides using Pd/C and ammonium formate in biological media under physiological conditions (neutral pH, moderate temperature, and ambient pressure) is reported. The reaction conditions were successful for a range of aryl chlorides with electron-donating and -withdrawing groups, limited by the solubility of substrates in aqueous media. Soluble substrates gave good yields (60-98%) of the reduction product within 48 h. The relative toxicities of each reaction component were tested separately and together against bacteria, and the reaction proceeded in bacterial cultures containing an aryl chloride with robust cell growth. This work offers an initial step toward the removal of aryl chlorides from waste streams that currently use bacterial degradation to remove pollutants.

Deactivation of a dimeric DNA-binding peptide through a palladium-mediated self-immolative cleavage

Herein, we describe an approach for the on-demand disassembly of dimeric peptides using a palladium-mediated cleavage of a designed self-immolative linker. The utility of the strategy is demonstrated for the case of dimeric basic regions of bZIP transcription factors. While the dimer binds designed DNA sequences with good affinities, the peptide-DNA complex can be readily dismounted by addition of palladium reagents that trigger the cleavage of the spacer, and the release of unfunctional monomeric peptides.

Truly-Biocompatible Gold Catalysis Enables Vivo-Orthogonal Intra-CNS Release of Anxiolytics

Being recognized as the best-tolerated of all metals, the catalytic potential of gold (Au) has thus far been hindered by the ubiquitous presence of thiols in organisms. Herein we report the development of a truly-catalytic Au-polymer composite by assembling ultrasmall Au-nanoparticles at the protein-repelling outer layer of a co-polymer scaffold via electrostatic loading. Illustrating the in vivo-compatibility of the novel catalysts, we show their capacity to uncage the anxiolytic agent fluoxetine at the central nervous system (CNS) of developing zebrafish, influencing their swim pattern. This bioorthogonal strategy has enabled -for the first time- modification of cognitive activity by releasing a neuroactive agent directly in the brain of an animal.

Truly-Biocompatible Gold Catalysis Enables Vivo-Orthogonal Intra-CNS Release of Anxiolytics

Being recognized as the best-tolerated of all metals, the catalytic potential of gold (Au) has thus far been hindered by the ubiquitous presence of thiols in organisms. Herein we report the development of a truly-catalytic Au-polymer composite by assembling ultrasmall Au-nanoparticles at the protein-repelling outer layer of a co-polymer scaffold via electrostatic loading. Illustrating the in vivo-compatibility of the novel catalysts, we show their capacity to uncage the anxiolytic agent fluoxetine at the central nervous system (CNS) of developing zebrafish, influencing their swim pattern. This bioorthogonal strategy has enabled -for the first time- modification of cognitive activity by releasing a neuroactive agent directly in the brain of an animal.

Plasmonic-Assisted Thermocyclizations in Living Cells Using Metal-Organic Framework Based Nanoreactors

We describe a microporous plasmonic nanoreactor to carry out designed near-infrared (NIR)-driven photothermal cyclizations inside living cells. As a proof of concept, we chose an intramolecular cyclization that is based on the nucleophilic attack of a pyridine onto an electrophilic carbon, a process that requires high activation energies and is typically achieved in bulk solution by heating at ∼90 °C. The core-shell nanoreactor (NR) has been designed to include a gold nanostar core, which is embedded within a metal-organic framework (MOF) based on a polymer-stabilized zeolitic imidazole framework-8 (ZIF-8). Once accumulated inside living cells, the MOF-based cloak of NRs allows an efficient diffusion of reactants into the plasmonic chamber, where they undergo the transformation upon near-IR illumination. The photothermal-driven reaction enables the intracellular generation of cyclic fluorescent products that can be tracked using fluorescence microscopy. The strategy may find different type of applications, such as for the spatio-temporal activation of prodrugs.

Artificial metalloenzymes in a nutshell: the quartet for efficient catalysis

Artificial metalloenzymes combine the inherent reactivity of transition metal catalysis with the sophisticated reaction control of natural enzymes. By providing new opportunities in bioorthogonal chemistry and biocatalysis, artificial metalloenzymes have the potential to overcome certain limitations in both drug discovery and green chemistry or related research fields. Ongoing advances in organometallic catalysis, directed evolution, and bioinformatics are enabling the design of increasingly powerful systems that outperform conventional catalysis in a growing number of cases. Therefore, this review article collects challenges and opportunities in designing artificial metalloenzymes described in recent review articles. This will provide an equitable insight for those new to and interested in the field.

Exporting Metal-Carbene Chemistry to Live Mammalian Cells: Copper-Catalyzed Intracellular Synthesis of Quinoxalines Enabled by N-H Carbene Insertions

Implementing catalytic organometallic transformations in living settings can offer unprecedented opportunities in chemical biology and medicine. Unfortunately, the number of biocompatible reactions so far discovered is very limited, and essentially restricted to uncaging processes. Here, we demonstrate the viability of performing metal carbene transfer reactions in live mammalian cells. In particular, we show that copper (II) catalysts can promote the intracellular annulation of alpha-keto diazocarbenes with ortho-amino arylamines, in a process that is initiated by an N-H carbene insertion. The potential of this transformation is underscored by the in cellulo synthesis of a product that alters mitochondrial functions, and by demonstrating cell selective biological responses using targeted copper catalysts. Considering the wide reactivity spectrum of metal carbenes, this work opens the door to significantly expanding the repertoire of life-compatible abiotic reactions.

In vivo organic synthesis by metal catalysts

The metal-catalyzed reactions have given various chemical modifications that could not be achieved through basic organic chemistry reactions. In the past decade, many metal-mediated catalytic systems have carried out different transformations in cellulo, such as decaging of fluorophores, drug release, and protein conjugation. However, translating abiotic metal catalysts for organic synthesis in vivo, including bacteria, zebrafish, or mice, could encounter numerous challenges regarding their biocompatibility, stability, and reactivity in the complicated biological environment. In this review, we categorize and summarize the relevant advances in this research field by emphasizing the system's framework, the design of each transformation, and the mode of action. These studies disclose the massive potential of the emerging field and the significant applications in synthetic biology.

Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein

Artificial metalloenzymes (ArMs) combine characteristics of both homogeneous catalysts and enzymes. Merging abiotic and biotic features allows for the implementation of new-to-nature reactions in living organisms. Here, we present the directed evolution of an artificial metalloenzyme based on Escherichia coli surface-displayed streptavidin (SavSD hereafter). Through the binding of a ruthenium-pianostool cofactor to SavSD, an artificial allylic deallylase (ADAse hereafter) is assembled, which displays catalytic activity toward the deprotection of alloc-protected 3-hydroxyaniline. The uncaged aminophenol acts as a gene switch and triggers the overexpression of a fluorescent green fluorescent protein (GFP) reporter protein. This straightforward readout of ADAse activity allowed the simultaneous saturation mutagenesis of two amino acid residues in Sav near the ruthenium cofactor, expediting the screening of 2762 individual clones. A 1.7-fold increase of in vivo activity was observed for SavSD S112T-K121G compared to the wild-type SavSD (wt-SavSD). Finally, the best performing Sav isoforms were purified and tested in vitro (SavPP hereafter). For SavPP S112M-K121A, a total turnover number of 372 was achieved, corresponding to a 5.9-fold increase vs wt-SavPP. To analyze the marked difference in activity observed between the surface-displayed and purified ArMs, the oligomeric state of SavSD was determined. For this purpose, crosslinking experiments of E. coli cells overexpressing SavSD were carried out, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot. The data suggest that SavSD is most likely displayed as a monomer on the surface of E. coli. We hypothesize that the difference between the in vivo and in vitro screening results may reflect the difference in the oligomeric state of SavSD vs soluble SavPP (monomeric vs tetrameric). Accordingly, care should be applied when evolving oligomeric proteins using E. coli surface display.

Epoc group: transformable protecting group with gold(iii)-catalyzed fluorene formation

This study presents the novel concept of a transformable protecting group, which changes its properties through structural transformation. Based on this concept, we developed a 2-(2-ethynylphenyl)-2-(5-methylfuran-2-yl)-ethoxycarbonyl (Epoc) group. The Epoc group was transformed into an Fmoc-like structure with gold(iii)-catalyzed fluorene formation and was removable under Fmoc-like mild basic conditions post-transformation even though it was originally stable under strongly basic conditions. As an application for organic synthesis, the Epoc group provides the novel orthogonality of gold(iii)-labile protecting groups in solid-phase peptide synthesis. In addition, the high turnover number of fluorene formation in aqueous media is suggestive of the applicability of the Epoc group to biological systems.

A protecting group removable with gold(iii)-catalyzed fluorene formation and the subsequent addition of piperidine was developed.

Iridium-Triggered Allylcarbamate Uncaging in Living Cells

Designing a metal catalyst that addresses the major issues of solubility, stability, toxicity, cell uptake, and reactivity within complex biological milieu for bioorthogonal controlled transformation reactions is a highly formidable challenge. Herein, we report an organoiridium complex that is nontoxic and capable of the uncaging of allyloxycarbonyl-protected amines under biologically relevant conditions and within living cells. The potential applications of this uncaging chemistry have been demonstrated by the generation of diagnostic and therapeutic agents upon the activation of profluorophore and prodrug in a controlled fashion within HeLa cells, providing a valuable tool for numerous potential biological and therapeutic applications.

Bioorthogonal strategies for the in vivo synthesis or release of drugs

The site-specific delivery of antitumor agents is a rapidly developing field that relies on prodrug activation and uncaging strategies. For this purpose, a wide range of homogeneous and heterogeneous biocompatible activators/catalysts have been developed to convert caged drugs with low toxicity and high stability in physiological settings into active substances in a bioorthogonal manner. The current methods allow for the site-specific delivery of activators and prodrugs to organelles, target cells, or tumors in living organisms. Here, we present an overview of the latest advances in catalytic drugs, highlighting the expanding toolbox of bioorthogonal activation strategies made possible by transition metals acting as activators or catalysts.

Bioorthogonal Azide-Thioalkyne Cycloaddition Catalyzed by Photoactivatable Ruthenium(II) Complexes

Tailored ruthenium sandwich complexes bearing photoresponsive arene ligands can efficiently promote azide-thioalkyne cycloaddition (RuAtAC) when irradiated with UV light. The reactions can be performed in a bioorthogonal manner in aqueous mixtures containing biological components. The strategy can also be applied for the selective modification of biopolymers, such as DNA or peptides. Importantly, this ruthenium-based technology and the standard copper-catalyzed azide-alkyne cycloaddition (CuAAC) proved to be compatible and mutually orthogonal.

Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells

Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.

In Vivo Assembly of Artificial Metalloenzymes and Application in Whole-Cell Biocatalysis*

We report the supramolecular assembly of artificial metalloenzymes (ArMs), based on the Lactococcal multidrug resistance regulator (LmrR) and an exogeneous copper(II)-phenanthroline complex, in the cytoplasm of E. coli cells. A combination of catalysis, cell-fractionation, and inhibitor experiments, supplemented with in-cell solid-state NMR spectroscopy, confirmed the in-cell assembly. The ArM-containing whole cells were active in the catalysis of the enantioselective Friedel-Crafts alkylation of indoles and the Diels-Alder reaction of azachalcone with cyclopentadiene. Directed evolution resulted in two different improved mutants for both reactions, LmrR_A92E_M8D and LmrR_A92E_V15A, respectively. The whole-cell ArM system required no engineering of the microbial host, the protein scaffold, or the cofactor to achieve ArM assembly and catalysis. We consider this a key step towards integrating abiological catalysis with biosynthesis to generate a hybrid metabolism.

Harnessing the power of transition metals in solid-phase peptide synthesis and key steps in the (semi)synthesis of proteins

Peptides and proteins can be either synthesized using solid-phase peptide synthesis (SPPS) or by applying a combination of SPPS and ligation approaches to address fundamental questions related to human health and disease, among others. The demand for their production either by chemical or biological methods continues to raise significant interests from the synthetic community. In this context, transition metals such as Pd, Ag, Hg, Tl, Au, Zn, Ni, and Cu have also contributed to the field of peptide and protein synthesis such as in peptide conjugation, extending native chemical ligation (NCL), and for regioselective disulfide bonds formation. In this review, we highlight, summarize, and evaluate the use of various transition metals in the chemical synthesis of peptides and proteins with emphasis on recent developments in this exciting research area.