Bioconjugation

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Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule.

Contents

Overview

Function

Recent advances in the understanding of biomolecules enabled their application to numerous fields like medicine, diagnostics, biocatalysis and materials. Synthetically modified biomolecules can have diverse functionalities, such as tracking cellular events, revealing enzyme function, determining protein biodistribution, imaging specific biomarkers, and delivering drugs to targeted cells. [1] [2] [3] [4] Bioconjugation is a crucial strategy that links these modified biomolecules with different substrates. Besides applications in biomedical research, bioconjugation has recently also gained importance in nanotechnology such as bioconjugated quantum dots.

Types of Conjugated Molecules

The most common types of bioconjugation include coupling of a small molecule (such as biotin or a fluorescent dye) to a protein. Antibody-drug conjugates such as Brentuximab vedotin and Gemtuzumab ozogamicin are examples falling into this category. [5]

Protein-protein conjugations, such as the coupling of an antibody to an enzyme, or the linkage of protein complexes, is also facilitated via bioconjugations. [6] [7]

Other less common molecules used in bioconjugation are oligosaccharides, nucleic acids, synthetic polymers such as polyethylene glycol, [8] and carbon nanotubes. [9]

Common Bioconjugation Reactions

Synthesis of bioconjugates involves a variety of challenges, ranging from the simple and nonspecific use of a fluorescent dye marker to the complex design of antibody drug conjugates. [1] [3] Various bioconjugation reactions have been developed to chemically modify proteins. Common types of bioconjugation reactions on proteins are coupling of lysine, cysteine, and tyrosine amino acid residues, as well as modification of tryptophan residues and of the N- and C- terminus. [1] [3] [4]

However, these reactions often lack chemoselectivity and efficiency, because they depend on the presence of native amino acids, which are present in large quantities that hinder selectivity. There is an increasing need for chemical strategies that can effectively attach synthetic molecules site specifically to proteins. One strategy is to first install a unique functional group onto a protein, and then a bioorthogonal reaction is used to couple a biomolecule with this unique functional group. [1] The bioorthogonal reactions targeting non-native functional groups are widely used in bioconjugation chemistry. Some important reactions are modification of ketone and aldehydes, Staudinger ligation with organic azides, copper-catalyzed Huisgen cycloaddition of azides, and strain promoted Huisgen cycloaddition of azides. [10] [11] [12] [13]

On Natural Amino Acids

Reactions of lysines

The nucleophilic lysine residue is commonly targeted site in protein bioconjugation, typically through amine-reactive N-hydroxysuccinimidyl (NHS) esters. [3] To obtain optimal number of deprotonated lysine residues, the pH of the aqueous solution must be below the pKa of the lysine ammonium group, which is around 10.5, so the typical pH of the reaction is about 8 and 9. The common reagent for the coupling reaction is NHS-ester (shown in the first reaction below in Figure 1), which reacts with nucleophilic lysine through a lysine acylation mechanism. Other similar reagents are isocyanates and isothiocyanates that undergo a similar mechanism (shown in the second and third reactions in Figure 1 below). [1] Benzoyl fluorides (shown in the last reaction below in Figure 1), which allows for lysine modification of proteins under mild conditions (low temperature, physiological pH), were recently proposed as an alternative to classically used lysine specific reagents. [14]

Bioconjugation strategies for lysine residues.tif

Reactions of cysteines

Because free cysteine rarely occurs on protein surface, it is an excellent choice for chemoselective modification. [15] Under basic condition, the cysteine residues will be deprotonated to generate a thiolate nucleophile, which will react with soft electrophiles, such as maleimides and iodoacetamides (shown in the first two reactions in Figure 2 below). As a result, a carbon-sulfur bond is formed. Another modification of cysteine residues involves the formation of disulfide bond (shown in the third reaction in Figure 2). The reduced cysteine residues react with exogenous disulfides, generating new a disulfide bond on the protein. An excess of disulfides is often used to drive the reaction, such as 2-thiopyridone and 3-carboxy-4-nitrothiophenol. [1] [3] Electron-deficient alkynes were demonstrated to selectively react with cysteine residues of proteins in the presence of other nucleophilic amino acid residues. Depending on the alkyne substitution, these reactions can produce either cleavable (when alkynone derivatives are used), [16] or hydrolytically stable bioconjugates (when 3-arylpropiolonitriles are used; the last reaction below in Figure 2). [17]

Bioconjugation strategies for cysteine residues.tif

Reactions of tyrosines

Tyrosine residues are relatively unreactive; therefore they have not been a popular targets for bioconjugation. Recent development has shown that the tyrosine can be modified through electrophilic aromatic substitutions (EAS) reactions, and it is selective for the aromatic carbon adjacent to the phenolic hydroxyl group. [1] This becomes particularly useful in the case that cysteine residues cannot be targeted. Specifically, diazonium effectively couples with tyrosine residues (diazonium salt shown as reagent in the first reaction in Figure 3 below), and an electron withdrawing substituent in the 4-position of diazonium salt can effectively increase the efficiency of the reaction. Cyclic diazodicarboxyamide derivative like 4-Phenyl-1,2,4-triazole-3,5-dione (PTAD) were reported for selective bioconjugation on tyrosine residues (the second reaction in Figure 3 below). [18] A three-component Mannich-type reaction with aldehydes and anilines (the last reaction in Figure 3) was also described to be relatively tyrosine-selective under mild optimised reaction conditions. [19]

Bioconjugation strategies for tyrosine residues.tif

Reactions of N- and C- termini

Since natural amino acid residues are usually present in large quantities, it is often difficult to modify one single site. Strategies targeting the termini of protein have been developed, because they greatly enhanced the site selectivity of protein modification. One of the N- termini modifications involves the functionalization of the terminal amino acid. The oxidation of N-terminal serine and threonine residues are able to generate N-terminal aldehyde, which can undergo further bioorthogonal reactions (shown in the first reaction in Figure 4). Another type of modification involves the condensation of N-terminal cysteine with aldehyde, generating thiazolidine that is stable at high pH (second reaction in Figure 4). Using pyridoxal phosphate (PLP), several N-terminal amino acids can undergo transamination to yield N-terminal aldehyde, such as glycine and aspartic acid (third reaction in Figure 4).

Figure 4. Bioconjugation strategies for N-terminus.tif

An example of C-termini modification is the native chemical ligation (NCL), which is the coupling between a C-terminal thioester and a N-terminal cysteine (Figure 5).

Figure 5. Bioconjugation strategies for C-terminus.tif

Bioorthogonal Reactions: On Unique Functional Groups

Modification of ketones and aldehydes

A ketone or aldehyde can be attached to a protein through the oxidation of N-terminal serine residues or transamination with PLP. Additionally, they can be introduced by incorporating unnatural amino acids via the Tirrell method or Schultz method. [10] They will then selectively condense with an alkoxyamine and a hydrazine, producing oxime and hydrazone derivatives (shown in the first and second reactions, respectively, in Figure 6). This reaction is highly chemoselective in terms of protein bioconjugation, but the reaction rate is slow. The mechanistic studies show that the rate determining step is the dehydration of tetrahedral intermediate, so a mild acidic solution is often employed to accelerate the dehydration step. [2]

Figure 6. Bioconjugation strategies for targeting ketones and aldehydes.jpg

The introduction of nucleophilic catalyst can significantly enhance reaction rate (shown in Figure 7). For example, using aniline as a nucleophilic catalyst, a less populated protonated carbonyl becomes a highly populated protonated Schiff base. [20] In other words, it generates a high concentration of reactive electrophile. The oxime ligation can then occur readily, and it has been reported that the rate increased up to 400 times under mild acidic condition. [20] The key of this catalyst is that it can generate a reactive electrophile without competing with desired product.

Figure 7. Nucleophilic catalysis of oxime ligation.jpg

Recent developments that exploit proximal functional groups have enabled hydrazone condensations [21] to operate at 20 M−1s−1 at neutral pH while oxime condensations have been discovered which proceed at 500-10000 M−1s−1 at neutral pH without added catalysts. [22] [23]

Staudinger ligation with azides

The Staudinger ligation of azides and phosphine has been used extensively in field of chemical biology. Because it is able to form a stable amide bond in living cells and animals, it has been applied to modification of cell membrane, in vivo imaging, and other bioconjugation studies. [24] [25] [26] [27]


Figure 8. Staudinger Ligation with Azides.jpg

Contrasting with the classic Staudinger reaction, Staudinger ligation is a second order reaction in which the rate-limiting step is the formation of phosphazide (specific reaction mechanism shown in Figure 9). The triphenylphosphine first reacts with the azide to yield an azaylide through a four-membered ring transition state, and then an intramolecular reaction leads to the iminophosphorane intermediate, which will then give the amide-linkage under hydrolysis. [28]

Figure 9. Mechanism of Staudinger Ligation.jpg

Huisgen cyclization of azides

Copper catalyzed Huisgen cyclization of azides

Azide has become a popular target for chemoselective protein modification, because they are small in size and have a favorable thermodynamic reaction potential. One such azide reactions is the [3+2] cycloaddition reaction with alkyne, but the reaction requires high temperature and often gives mixtures of regioisomers.

Figure 10. Copper-catalyzed cyclization of Azides.jpg

An improved reaction developed by chemist Karl Barry Sharpless involves the copper (I) catalyst, which couples azide with terminal alkyne that only give 1,4 substituted 1,2,3 triazoles in high yields (shown below in Figure 11). The mechanistic study suggests a stepwise reaction. [13] The Cu (I) first couples with acetylenes, and then it reacts with azide to generate a six-membered intermediate. The process is very robust that it occurs at pH ranging from 4 to 12, and copper (II) sulfate is often used as a catalyst in the presence of a reducing agent. [13]

Figure 11. Mechanism for Copper-catalyzed cyclization of Azides.jpg

Strain promoted Huisgen cyclization of azides

Even though Staudinger ligation is a suitable bioconjugation in living cells without major toxicity, the phosphine's sensitivity to air oxidation and its poor solubility in water significantly hinder its efficiency. The copper(I) catalyzed azide-alkyne coupling has reasonable reaction rate and efficiency under physiological conditions, but copper poses significant toxicity and sometimes interferes with protein functions in living cells. In 2004, chemist Carolyn R. Bertozzi's lab developed a metal free [3+2] cycloaddition using strained cyclooctyne and azide. Cyclooctyne, which is the smallest stable cycloalkyne, can couple with azide through [3+2] cycloaddition, leading to two regioisomeric triazoles (Figure 12). [11] The reaction occurs readily at room temperature and therefore can be used to effectively modify living cells without negative effects. It has also been reported that the installation of fluorine substituents on a cyclic alkyne can greatly accelerate the reaction rate. [2] [29]

Figure 12. Strain promoted cycloaddition of azides and cyclooctynes.jpg

Transition Metal-Mediated Bioconjugation Reactions

Transition metal-based bioconjugation had been challenging due to the nature of biological conditions – aqueous solution, room temperature, mild pH, and low substrate concentrations – which are generally challenging for organometallic reactions. However, recently, besides copper-catalyzed [3 + 2] azide alkyne cycloaddition reaction, more and more diverse transition metal-mediated chemical transformations have been applied for bioconjugation reactions, introducing olefin metathesis, alkylation, C–H arylation, C–C, C–S, and C–N cross-coupling reactions. [30] [31]

Alkylation

On Natural Amino Acids

  • Rh-catalyzed Trp and Cys alkylation [32] [33]

Using in situ generated RhII-carbenoid by activation of vinyl-substituted diazo compounds with Rh2(OAc)4, tryptophans and cysteines were shown to be selectively alkylated in aqueous media.

However, this method is limited to surface tryptophans and cysteines possibly because of steric constraints. [34]

Rh-carbenoid 2.png

  • Ir-catalyzed Lys and N-terminus (reductive) alkylation [35]

Imines formed from the condensation of aldehydes with lysines or the N-terminus can be reduced efficient by an water-stable [Cp*Ir(bipy)(H2O)]SO4 complex in the presence of formate ions (serving as the hydride source). The reaction happens readily under physiologically relevant conditions and results in high conversion for various aromatic aldehydes.

Ir-catalyzed Lys (reductive) alkylation.png

  • Pd-catalyzed Tyr O-alkylation [36]

By using a pre-formed electrophilic π-allylpalladium(II) reagent derived from allylic acetate or carbamate precursors, selective allylic alkylation of tyrosines can be achieved in aqueous solution at room temperature and in the presence of cysteines.

Pd-catalyzed Tyr O-alkylation.png

  • Au-catalyzed Cys alkylation [37]

Cysteine-containing peptides have been shown to undergo 1,2-addition to allenes in the presence of gold(I) and/or silver(I) salts, producing hydroxyl substituted vinyl thioethers. The reaction with peptides proceeds with high yields and is selective for cysteines over other nucleophilic residues.

However, the reactivity towards proteins is much decreased, potentially due to the coordination of gold to the protein backbone.

Au-catalyzed Cys alkylation.png

Arylation

On Natural Amino Acids

  • Trp arylation

Multiple methods have been reported to achieve tryptophan C–H arylation, where diverse electrophiles such as aryl halides [38] [39] and aryl boronic acids [40] (an example shown below) have been used to transfer the aryl groups.

However, current tryptophan C–H arylation reaction conditions remain relatively harsh, requiring organic solvents, low pH and/or high temperatures.

Trp arylation.png

  • Cys arylation

Free thiols has been considered unfavorable for Pd-mediated reactions due to Pd-catalyst decomposition. [41] However, PdII oxidative addition complexes (OACs) supported by dialkylbiaryl phosphine ligands have shown to work efficiently towards cysteine S-arylation.

The first example is the use of PdII OAC with RuPhos: [42] The PdII complex resulting from the oxidative addition of aryl halides or trifluoromethanesulfonates and using RuPhos as the ligand could chemoselectively modify cysteines in various buffer with 5% organic co-solvent under neutral pH. This method has been shown to modify peptides and proteins, achieve peptide macrocyclization (by using bis-palladium reagent and peptides with two unprotected cysteines) [43] and synthesizing antibody-drug conjugates (ADCs). Changing the ligand to sSPhos supports the PdII complex to be sufficiently water soluble to achieve cysteine S-arylation under cosolvent-free aqueous conditions. [44]

Cys arylation (RuPhos) -2.png

There are other applications of this method where the PdII complexes were generated as PdII-peptide OACs by introducing 4-halophenylalanine into peptides during SPPS to achieve peptide-peptide or peptide-protein ligation. [45]

Pd-peptide OAC 2.png

Alternate to directly oxidative addition to the peptide, the Pd OACs could also be transferred to the protein through amine-selective acylation reaction via NHS ester. The latter has been applied to selectively label surface lysine residues of a protein (forming PdII-protein OACs) and oligonucleotides (forming PdII-oligonucleotide OACs), which could then be linked to cysteine-containing peptides or proteins. [46]

Pd-biomolecule OAC 2.png

Another example of protein-protein cross-coupling is achieved through converting cysteine residues into an electrophilic S-aryl–Pd–X OAC by utilizing an intramolecular oxidative addition strategy. [47]

Similar to cysteine, lysine N-arylation could be achieved through Pd OACs with different dialkylbiaryl phosphine ligands. Due to weaker nucleophilicity and slower reductive elimination rate compared to cysteine, the selection of supporting ligands is shown to be critical. The bulky BrettPhos and t-BuBrettPhos ligands in conjunction with mildly basic sodium phenoxide have been used as the strategy to functionalize lysines on peptide substrates. The reaction happens in mild conditions and is selective over most other nucleophilic amino acid residues.

Lys arylation.png

On Unnatural Amino Acids

Pd-mediated Sonogashira, Heck, and Suzuki-Miyaura cross-coupling reactions have been applied widely to modify peptides and proteins, where diverse Pd reagents have been developed for the application in aqueous solutions. [49] Those reactions require the protein or peptide substrate bearing unnatural functional groups such as alkyne, [50] [51] [52] aryl halides, [53] [54] [55] [56] and aryl boronic acids, [57] which can be achieved through genetic code expansion or post-translational modifications.

UAA arylation.png

Examples of Applied Bioconjugation Techniques

Growth Factors

Bioconjugation of TGF-β to iron oxide nanoparticles and its activation through magnetic hyperthermia in-vitro has been reported. [58] This was done by using 1-(3-dimethylaminopropyl)ethylcarbodiimide combined with N-Hydroxysuccinimide to form primary amide bonds with the free primary amines on the growth factor. Carbon nanotubes have been successfully used in conjunction with bioconjugation to link TGF-β followed by an activation with near-infrared light. [59] Typically, these reactions have involved the use of a crosslinker, but some of these add molecular space between the compound of interest and base material and in turn causes higher degrees of non-specific binding and unwanted reactivity. [60]

See also

Related Research Articles

<span class="mw-page-title-main">Protein primary structure</span> Linear sequence of amino acids in a peptide or protein

Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences.

<span class="mw-page-title-main">Post-translational modification</span> Biological processes

Post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes translating mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.

Native Chemical Ligation (NCL) is an important extension of the chemical ligation concept for constructing a larger polypeptide chain by the covalent condensation of two or more unprotected peptides segments. Native chemical ligation is the most effective method for synthesizing native or modified proteins of typical size.

<span class="mw-page-title-main">Protein sequencing</span> Sequencing of amino acid arrangement in a protein

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The Heck reaction is the chemical reaction of an unsaturated halide with an alkene in the presence of a base and a palladium catalyst to form a substituted alkene. It is named after Tsutomu Mizoroki and Richard F. Heck. Heck was awarded the 2010 Nobel Prize in Chemistry, which he shared with Ei-ichi Negishi and Akira Suzuki, for the discovery and development of this reaction. This reaction was the first example of a carbon-carbon bond-forming reaction that followed a Pd(0)/Pd(II) catalytic cycle, the same catalytic cycle that is seen in other Pd(0)-catalyzed cross-coupling reactions. The Heck reaction is a way to substitute alkenes.

<span class="mw-page-title-main">Peptide synthesis</span> Production of peptides

In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another. Protecting group strategies are usually necessary to prevent undesirable side reactions with the various amino acid side chains. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide (C-terminus), and proceeds toward the amino-terminus (N-terminus). Protein biosynthesis in living organisms occurs in the opposite direction.

<span class="mw-page-title-main">Chemical biology</span> Scientific discipline

Chemical biology is a scientific discipline between the fields of chemistry and biology. The discipline involves the application of chemical techniques, analysis, and often small molecules produced through synthetic chemistry, to the study and manipulation of biological systems. Although often confused with biochemistry, which studies the chemistry of biomolecules and regulation of biochemical pathways within and between cells, chemical biology remains distinct by focusing on the application of chemical tools to address biological questions.

In chemical synthesis, click chemistry is a class of simple, atom-economy reactions commonly used for joining two molecular entities of choice. Click chemistry is not a single specific reaction, but describes a way of generating products that follow examples in nature, which also generates substances by joining small modular units. In many applications, click reactions join a biomolecule and a reporter molecule. Click chemistry is not limited to biological conditions: the concept of a "click" reaction has been used in chemoproteomic, pharmacological, biomimetic and molecular machinery applications. However, they have been made notably useful in the detection, localization and qualification of biomolecules.

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The Negishi coupling is a widely employed transition metal catalyzed cross-coupling reaction. The reaction couples organic halides or triflates with organozinc compounds, forming carbon-carbon bonds (C-C) in the process. A palladium (0) species is generally utilized as the metal catalyst, though nickel is sometimes used. A variety of nickel catalysts in either Ni0 or NiII oxidation state can be employed in Negishi cross couplings such as Ni(PPh3)4, Ni(acac)2, Ni(COD)2 etc.

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<span class="mw-page-title-main">PEPPSI</span> Group of chemical compounds

PEPPSI is an abbreviation for pyridine-enhanced precatalyst preparation stabilization and initiation. It refers to a family of commercially available palladium catalysts developed around 2005 by Prof. Michael G. Organ and co-workers at York University, which can accelerate various carbon-carbon and carbon-heteroatom bond forming cross-coupling reactions. In comparison to many alternative palladium catalysts, Pd-PEPPSI-type complexes are stable to air and moisture and are relatively easy to synthesize and handle.

The term bioorthogonal chemistry refers to any chemical reaction that can occur inside of living systems without interfering with native biochemical processes. The term was coined by Carolyn R. Bertozzi in 2003. Since its introduction, the concept of the bioorthogonal reaction has enabled the study of biomolecules such as glycans, proteins, and lipids in real time in living systems without cellular toxicity. A number of chemical ligation strategies have been developed that fulfill the requirements of bioorthogonality, including the 1,3-dipolar cycloaddition between azides and cyclooctynes, between nitrones and cyclooctynes, oxime/hydrazone formation from aldehydes and ketones, the tetrazine ligation, the isocyanide-based click reaction, and most recently, the quadricyclane ligation.

An aldehyde tag is a short peptide tag that can be further modified to add fluorophores, glycans, PEG chains, or reactive groups for further synthesis. A short, genetically-encoded peptide with a consensus sequence LCxPxR is introduced into fusion proteins, and by subsequent treatment with the formylglycine-generating enzyme (FGE), the cysteine of the tag is converted to a reactive aldehyde group. This electrophilic group can be targeted by an array of aldehyde-specific reagents, such as aminooxy- or hydrazide-functionalized compounds.

<span class="mw-page-title-main">Dehydroamino acid</span>

In biochemistry, a dehydroamino acid or α,β-dehydroamino acid is an amino acids, usually with a C=C double bond in its side chain. Dehydroamino acids are not coded by DNA, but arise via post-translational modification.

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<span class="mw-page-title-main">3-Arylpropiolonitriles</span> Chemical compound

3-Arylpropiolonitriles (APN) belong to a class of electron-deficient alkyne derivatives substituted by two electron-withdrawing groups – a nitrile and an aryl moieties. Such activation results in improved selectivity towards highly reactive thiol-containing molecules, namely cysteine residues in proteins. APN-based modification of proteins was reported to surpass several important drawbacks of existing strategies in bioconjugation, notably the presence of side reactions with other nucleophilic amino acid residues and the relative instability of the resulting bioconjugates in the blood stream. The latter drawback is especially important for the preparation of targeted therapies, such as antibody-drug conjugates.

Bradley Lether Pentelute is currently a professor of chemistry at the Massachusetts Institute of Technology (MIT). His research program lies at the intersection of chemistry and biology and develops bioconjugation strategies, cytosolic delivery platforms, and rapid flow synthesis technologies to optimize the production, achieve site-specific modification, enhance stability, and modulate function of a variety of bioactive agents. His laboratory successfully modified proteins via cysteine-containing “pi-clamps” made up of a short sequence of amino acids, and delivered large biomolecules, such as various proteins and drugs, into cells via the anthrax delivery vehicle. Pentelute has also made several key contributions to automated synthesis technologies in flow. These advances includes the invention of the world's fastest polypeptide synthesizer. This system is able to form amide bonds at a more efficient rate than standard commercial equipment and has helped in the process of understanding protein folding and its mechanisms. This automated flow technology was recently used to achieve total chemical synthesis of protein chains up to 164 amino acids in length that retained the structure and function of native variants obtained by recombinant expression. The primary goal of his endeavor is to use these processes to create designer biologics that can be used to treat diseases and solve the manufacturing problem for on-demand personalized therapies, such as cancer vaccines.

An artificial metalloenzyme (ArM) is a metalloprotein made in the laboratory which cannot be found in the nature and can catalyze certain desired chemical reactions. Despite fitting into classical enzyme categories, ArMs also have potential in chemical reactivity like catalyzing Suzuki coupling, metathesis and so on, which are never reported in natural enzymatic reaction. With the progress in organometallic synthesis and protein engineering, more and more new kind of design of ArMs came out, showing promising future in both academia and industrial aspects.

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