Site-Selective Functionalization of Methionine Residues via Photoredox Catalysis

Controlled reversible methionine-selective sulfimidation of peptides

Site-selective chemical peptide manipulation is an effective strategy to understand and regulate structure and function. However, methionine-selective modification remains one of the most difficult challenges in peptide chemistry, with notable limited strategies. In this study, we report a general reversible modification strategy at methionine sites that uses the ruthenium-catalyzed sulfimidation of peptides. This method provides a convenient and effective strategy for late-stage peptide functionalization. The N═S bonds of the conjugates are reduced in the presence of glutathione, resulting the traceless releasing of corresponding peptides and amides. Practical applications are then demonstrated using precise reversible modifications of bioactive peptides, the stapling and linearization of peptides, peptide-drug conjugates, and split-and-pool synthesis. This on/off strategy through methionine-selective and reversible sulfimidation provides a unique tool for peptide chemistry and peptide-based drug discovery.

Direct Photocatalytic Reductive Amidation of Nitroarenes: A Tandem Reduction-Decarboxylation Approach to Amide Bond Construction

We report a photocatalytic strategy for direct amide synthesis from readily available nitroarenes and benzoylformic acids using flavin as an efficient photocatalyst. This one-pot transformation proceeds through a tandem reduction-decarboxylation-amidation sequence under mild blue light irradiation. Preliminary mechanistic studies indicated that nitrosoarene and N-hydroxyamides could be the key intermediates. The method demonstrates a broad substrate scope, excellent functional group tolerance, and remarkable operational simplicity, as it can be conducted under an ambient atmosphere. Notably, this protocol represents a significant advancement in step economy by directly employing diverse nitroarenes as nitrogen sources, avoiding the need for pre-reduced amine intermediates.

Bioinspired Methionine-Selective Desulfurization Editing of Peptides via the Photocatalysis Strategy

S-Adenosylmethionine (SAM) frequently functions as a cofactor or precursor for enzymes, initiating an array of radical reactions in biological systems. In contrast with the conventional 5'-deoxyadenosyl (dAdo) radical pathway, which proceeds via homolytic cleavage of the S-C(5') bond of SAM, the Dph2 enzyme provides an alternative 3-amino-3-carboxypropyl (ACP) radical pathway through breaking the S-C(γ) bond. Inspired by this distinctive bond cleavage mode, we have developed a chemically induced pathway to generate an ACP-type radical intermediate on methionine-based sulfonium. This strategy presents a novel desulfurization conjugation mode for methionine modification, diverging from previous approaches that conjugate onto the sulfur atom or the adjacent methyl group of methionine. The versatility of this strategy is demonstrated by the efficient functionalization of various peptides and peptide macrocyclizations. Density Functional Theory (DFT) calculations provide further insights into the mechanism of this desulfurization reaction, explaining the exceptional selectivity of homolytic cleavage of the S-C(γ) bond of methionine-based sulfonium. The successful implementation of this novel desulfurization strategy represents a substantial advancement in the understanding of sulfonium-based intramolecular radical substitution reactions and provides new opportunities for the functionalization of biomolecules, thereby fostering progress in interdisciplinary research.

Photocatalytic and Chemoselective H/D Exchange at α-Thio C(sp3)-H Bonds

Deuterated compounds used in drug discovery and live-cell imaging have recently gained the attention of various scientific fields. Although hydrogen-deuterium (H/D) exchange reactions are straightforward deuteration methods, achieving perfect chemoselectivity is challenging. We report the highly chemoselective deuteration of α-thio C(sp3)-H bonds using a thioxanthone or anthraquinone organic photocatalyst bearing an aromatic ketone skeleton and D2O as an inexpensive deuterium source under 390 nm irradiation. Notably, incorporation of deuterium at the α-positions of the O/N atoms, benzylic positions, and aromatic rings was not observed. The present chemoselectivity was accomplished via a single electron transfer mechanism between the photocatalyst and S-containing substrates, as proven by laser-induced time-resolved transient absorption spectroscopic measurements. Furthermore, the proposed deuteration method could be applied to various S-containing substrates, including pharmaceuticals and biologically active compounds with high regioselectivities. The available deuterated compounds as novel deuterated alkylation reagents for future drug discovery and materials for Raman imaging were also demonstrated.

Photocatalytic Bilateral Disulfuration of Thioethers Toward α-Sulfide Disulfides With Antibacterial Activity

α-Sulfide disulfides represent valuable motifs in organic and pharmaceutical chemistry. However, the limited availability of synthetic approaches for α-sulfide disulfides has impeded progress in this field. In this study, a photocatalytic approach to synthesizing modifiable α-sulfide disulfides is presented using accessible sulfides and a bilateral disulfurating reagent. The reaction proceeds under mild conditions and demonstrates broad substrate compatibility, accommodating both aromatic and aliphatic sulfides. Moreover, the synthesized α-sulfide disulfides display robust reactivity in subsequent transformations with different electrophiles. Notably, this protocol can also be applied to the modification of polymer matrices. Bioassays further reveal that certain target compounds exhibit significant antibacterial activity against plant pathogens, such as Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas oryzae pathovar oryzicola (Xoc), and Dickeya zeae (D. zeae).

Light-induced chemistry for protein functionalisation

Derivatising biomolecules like monoclonal antibodies with drugs or imaging agents, whilst preserving their bioactivity, is a challenging task. Protein functionalisation ideally requires methods that operate under mild conditions, are rapid, efficient (high yielding), chemoselective or site-specific, and importantly, non-denaturing. A broad collection of thermally mediated reagents for direct labelling using protein-based reactivity, or bioorthogonal strategies, has been developed, but arguably the most exciting opportunities lie in the application of photochemistry to create new covalent bioconjugate bonds. With current chemical methods for auxochromic tuning of the spectral features of photoactive groups, and with cheap, high-powered light-emitting diodes with precise emission properties, it has never been easier to explore the use of light-induced chemistry for making protein-based bioactive molecules. In biomedicine, the nature of the covalent bond to the protein can have a dramatic impact on the physicochemical properties and performance of the protein-conjugate. Photochemical methods provide access to new types of covalent linkages on protein with the potential to fine-tune biological interactions, leading to improvements in target uptake, binding specificity, metabolic processing, and washout kinetics in vivo. This perspective/review highlights recent advances in the development of photoactive reagents for protein labelling. We also discuss the experimental conditions and critical requirements to implement light-induced synthesis of functionalised protein-conjugates in aqueous media effectively.

Recent advances of photocatalytic biochemical transformations

The discovery of useful synthetic transformations has made light-mediated catalysis, a widely employed method in chemical synthesis. Since the catalyst, light source, and substrate needed to produce a photoredox reaction are the same as those needed for photosensitization, photoredox reactions are perfect for examining biological surroundings. An attempt has been made to cover the development of future-oriented catalysts and the therapeutic use of photosensitization. New applications of photoredox catalytic techniques for investigating intricate biological environments in living cells and protein bioconjugation is also discussed.

Photocatalyzed elaboration of antibody-based bioconjugates

Antibody-drug conjugates (ADCs) represent a promising class of targeted therapeutics, combining the specificity of antibodies with the potency of cytotoxic drugs to enhance therapeutic efficacy while minimizing off-target effects. The development of new chemical methods for bioconjugation is essential to generate ADCs and to optimize their stability, efficacy, and safety. Traditional conjugation methods often face challenges related to site-selectivity and heterogeneous product mixtures, highlighting the need to develop new, innovative chemical strategies. Photoredox chemistry emerges as a powerful tool in this context, enabling precise, mild, and selective modifications of peptides and proteins. By harnessing light to drive chemical transformations, photoredox techniques can facilitate the synthesis of antibody bioconjugates. This perspective will discuss the drive to develop and empower photoredox methods applied to antibody functionalization.

One-Step Maleimide-Based Dual Functionalization of Protein N-Termini

Maleimide derivatives are privileged reagents for chemically modifying proteins through the Michael addition reaction with cysteine due to their selectivity, operational simplicity, and commercial availability. However, since accessible free cysteine is rarely found in natural proteins, it is highly desirable to find alternative targets to enable direct bioconjugation of proteins with maleimides. In this study, we have developed an operationally simple and straightforward method for the N-terminal modification of proteins without the need for mutagenesis via a copper(II)-mediated [3+2] cycloaddition reaction with maleimides and 2-pyridinecarboxaldehyde (2-PCA) derivatives under non-denaturing conditions at pH 6 and 37 °C in aqueous media. Our method utilizes commercially available maleimides to attach diverse functionalities to various N-terminal amino acids. We demonstrate the preparation of a ternary protein complex cross-linked at the N-termini and dually modified trastuzumab equipped with monomethyl auristatin E (MMAE), a cytotoxic agent, and a Cy5 fluorophore (MMAE-Cy5-trastuzumab). MMAE-Cy5-trastuzumab retained human epidermal growth factor receptor 2 (HER2) recognition activity and exerted cytotoxicity against HER2-positive cells. Furthermore, MMAE-Cy5-trastuzumab allowed successful visualization of HER2-positive cancer cells in mouse tumors. This straightforward method will expand the accessibility of protein conjugates with well-defined structures in a wide range of research fields.

Flavin-Catalyzed, Photochemical Conversion of Dehydroalanine into 4,5-Dihydroxynorvaline

The chemical synthesis of unnatural amino acids (UAA) is a key strategy for preparing designed peptides, including pharmaceutically active compounds. Alterations of existing amino acid residues such as dehydroalanine (Dha) are particularly important since selected positions can be addressed without the necessity of a complete de novo synthesis. The intriguing UAA 4,5-dihydroxynorvaline (Dnv) is found in a variety of naturally occurring peptides and biologically active compounds. However, no method is currently available to modify an existing peptide with this residue. We report the use of flavin catalysts and visible light irradiation for this challenge, which serves as a versatile strategy for converting Dha into Dnv. Our study shows that excited flavins are competent hydrogen atom abstraction catalysts for ethers and acetals, which allows masked 1,2-dihydroxyethylene functionalization from 2,2-dimethyl-1,3-dioxolane. The masked diol was successfully coupled to Dha residues, and a series of Dnv-containing products is reported. A mild and orthogonal protocol for deprotection of the acetal group was also identified, allowing free Dnv-modified peptides to be obtained. This method provides a straightforward strategy for Dnv functionalization, which is envisioned to be crucial for accessing natural products and synthetic analogues with pharmaceutical activity.

Previously Published Phosphatase Probes have Limited Utility Due to their Unspecific Reactivity

This study explores the use of activity-based protein profiling to study protein tyrosine phosphatases. With the discovery of allosteric SHP2 inhibitors, this enzyme family has resurfaced as interesting drug targets. Therefore, we envisioned that previously described direct electrophiles and quinone methide-based traps targeting phosphatases could be applied in competitive activity-based protein profiling assays. This study evaluates three direct electrophiles, specifically, a vinyl sulfonate, a vinyl sulfone, and an α-bromobenzylphosphonate as well as three quinone methide-based traps as activity-based probes. For all these moieties it was previously shown that they could selectively engage in assays with purified or overexpressed phosphatases in bacterial lysates. However, this study demonstrates that probes based on these moieties all suffer from unspecific labelling. Direct electrophiles were either unspecific or not activity-based, while quinone methide-based traps showed dependence on phosphatase activity but also resulted in unspecific labelling due to diffusion after activation. This phenomenon, termed 'bystander' labelling, occurred even with catalytically inactive SHP2 mutants. We concluded that alternative strategies or chemistries are needed to apply activity-based protein profiling in phosphatase research. Moreover, this study shows that quinone methide-based designs have limited potential in probe and inhibitor development strategies due to their intrinsic reactivity.

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.

Chemical Synthesis of Human Proteoforms and Application in Biomedicine

Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.

Synthesis of Sulfilimines via Visible-Light-Mediated Triplet Energy Transfer to Sulfonyl Azides

Sulfilimines and their derivatives have garnered considerable interest in both synthetic and medicinal chemistry. Photochemical nitrene transfer to sulfides is known as a conventional synthetic approach to sulfilimines. However, the existing methods have a limited substrate scope stemming from the incompatibility of singlet nitrene intermediates with nucleophilic functional groups. Herein, we report the synthesis of N-sulfonyl sulfilimines via visible-light-mediated energy transfer to sulfonyl azides, uncovering the previously overlooked reactivity of triplet nitrenes with sulfides. This reaction features broad functional group tolerance, water compatibility, and amenability to the late-stage functionalization of drugs. Thus, this work represents an important example of energy transfer chemistry that overcomes challenges in traditional synthetic methods.

Unimolecular Chemiexcited Oxygenation of Pathogenic Amyloids

Pathogenic protein aggregates, called amyloids, are etiologically relevant to various diseases, including neurodegenerative Alzheimer disease. Catalytic photooxygenation of amyloids, such as amyloid-β (Aβ), reduces their toxicity; however, the requirement for light irradiation may limit its utility in large animals, including humans, due to the low tissue permeability of light. Here, we report that Cypridina luciferin analogs, dmCLA-Cl and dmCLA-Br, promoted selective oxygenation of amyloids through chemiexcitation without external light irradiation. Further structural optimization of dmCLA-Cl led to the identification of a derivative with a polar carboxylate functional group and low cellular toxicity: dmCLA-Cl-acid. dmCLA-Cl-acid promoted oxygenation of Aβ amyloid and reduced its cellular toxicity without photoirradiation. The chemiexcited oxygenation developed in this study may be an effective approach to neutralizing the toxicity of amyloids, which can accumulate deep inside the body, and treating amyloidosis.

Copper(I)-nitrene platform for chemoproteomic profiling of methionine

Methionine plays a critical role in various biological and cell regulatory processes, making its chemoproteomic profiling indispensable for exploring its functions and potential in protein therapeutics. Building on the principle of rapid oxidation of methionine, we report Copper(I)-Nitrene Platform for robust, and selective labeling of methionine to generate stable sulfonyl sulfimide conjugates under physiological conditions. We demonstrate the versatility of this platform to label methionine in bioactive peptides, intact proteins (6.5-79.5 kDa), and proteins in complex cell lysate mixtures with varying payloads. We discover ligandable proteins and sites harboring hyperreactive methionine within the human proteome. Furthermore, this has been utilized to profile oxidation-sensitive methionine residues, which might increase our understanding of the protective role of methionine in diseases associated with elevated levels of reactive oxygen species. The Copper(I)-Nitrene Platform allows labeling methionine residues in live cancer cells, observing minimal cytotoxic effects and achieving dose-dependent labeling. Confocal imaging further reveals the spatial distribution of modified proteins within the cell membrane, cytoplasm, and nucleus, underscoring the platform's potential in profiling the cellular interactome.

Photocatalytic Functionalization of Dehydroalanine-Derived Peptides in Batch and Flow

Unnatural amino acids, and their synthesis by the late-stage functionalization (LSF) of peptides, play a crucial role in areas such as drug design and discovery. Historically, the LSF of biomolecules has predominantly utilized traditional synthetic methodologies that exploit nucleophilic residues, such as cysteine, lysine or tyrosine. Herein, we present a photocatalytic hydroarylation process targeting the electrophilic residue dehydroalanine (Dha). This residue possesses an α,β-unsaturated moiety and can be combined with various arylthianthrenium salts, both in batch and flow reactors. Notably, the flow setup proved instrumental for efficient scale-up, paving the way for the synthesis of unnatural amino acids and peptides in substantial quantities. Our photocatalytic approach, being inherently mild, permits the diversification of peptides even when they contain sensitive functional groups. The readily available arylthianthrenium salts facilitate the seamless integration of Dha-containing peptides with a wide range of arenes, drug blueprints, and natural products, culminating in the creation of unconventional phenylalanine derivatives. The synergistic effect of the high functional group tolerance and the modular characteristic of the aryl electrophile enables efficient peptide conjugation and ligation in both batch and flow conditions.

Non-symmetric stapling of native peptides

Stapling has emerged as a powerful technique in peptide chemistry. It enables precise control over peptide conformation leading to enhanced properties such as improved stability and enhanced binding affinity. Although symmetric stapling methods have been extensively explored, the field of non-symmetric stapling of native peptides has received less attention, largely as a result of the formidable challenges it poses - in particular the complexities involved in achieving the high chemo-selectivity and site-selectivity required to simultaneously modify distinct proteinogenic residues. Over the past 5 years, there have been significant breakthroughs in addressing these challenges. In this Review, we describe the latest strategies for non-symmetric stapling of native peptides, elucidating the protocols, reaction mechanisms and underlying design principles. We also discuss current challenges and opportunities this field offers for future applications, such as ligand discovery and peptide-based therapeutics.

Sulfur in Waste-Free Sustainable Synthesis: Advancing Carbon-Carbon Coupling Techniques

This review explores the pivotal role of sulfur in advancing sustainable carbon-carbon (C-C) coupling reactions. The unique electronic properties of sulfur, as a soft Lewis base with significant mesomeric effect make it an excellent candidate for initiating radical transformations, directing C-H-activation, and facilitating cycloaddition and C-S bond dissociation reactions. These attributes are crucial for developing waste-free methodologies in green chemistry. Our mini-review is focused on existing sulfur-directed C-C coupling techniques, emphasizing their sustainability and comparing state-of-the-art methods with traditional approaches. The review highlights the importance of this research in addressing current challenges in organic synthesis and catalysis. The innovative use of sulfur in photocatalytic, electrochemical and metal-catalyzed processes not only exemplifies significant advancements in the field but also opens new avenues for environmentally friendly chemical processes. By focusing on atom economy and waste minimization, the analysis provides broad appeal and potential for future developments in sustainable organic chemistry.

Site-Selective Protein Conjugation by a Multicomponent Ugi Reaction

The chemical bioconjugation of proteins has seen tremendous applications in the past decades, with the booming of antibody-drug conjugates and their use in oncology. While genetic engineering has permitted to produce bespoke proteins featuring key (un-)natural amino acid residues poised for site-selective modifications, the conjugation of native proteins is riddled with selectivity issues. Chemoselective strategies are plentiful and enable the precise modification of virtually any residue with a reactive side-chain; site-selective methods are less common and usually most effective on small and medium-sized proteins. In this context, we studied the application of the Ugi multicomponent reaction for the site-selective conjugation of amine and carboxylate groups on proteins, and antibodies in particular. Through an in-depth mechanistic methodology work supported by peptide mapping studies, we managed to develop a set of conditions allowing the highly selective modification of antibodies bearing N-terminal glutamate and aspartate residues. We demonstrated that this strategy did not alter their affinity toward their target antigen and produced an antibody-drug conjugate with subnanomolar potency. Excitingly, we showed that the high site selectivity of our strategy was maintained on other protein formats, especially on anticalins, for which directed mutagenesis helped to highlight the key importance of a single lysine residue.

Selenium chemistry for spatio-selective peptide and protein functionalization

The ability to construct a peptide or protein in a spatio-specific manner is of great interest for therapeutic and biochemical research. However, the various functional groups present in peptide sequences and the need to perform chemistry under mild and aqueous conditions make selective protein functionalization one of the greatest synthetic challenges. The fascinating paradox of selenium (Se) - being found in both toxic compounds and also harnessed by nature for essential biochemical processes - has inspired the recent exploration of selenium chemistry for site-selective functionalization of peptides and proteins. In this Review, we discuss such approaches, including metal-free and metal-catalysed transformations, as well as traceless chemical modifications. We report their advantages, limitations and applications, as well as future research avenues.

Recent Advances in Photoinduced Modification of Amino Acids, Peptides, and Proteins

The chemical modification of biopolymers like peptides and proteins is a key technology to access vaccines and pharmaceuticals. Similarly, the tunable derivatization of individual amino acids is important as they are key building blocks of biomolecules, bioactive natural products, synthetic polymers, and innovative materials. The high diversity of functional groups present in amino acid-based molecules represents a significant challenge for their selective derivatization Recently, visible light-mediated transformations have emerged as a powerful strategy for achieving chemoselective biomolecule modification. This technique offers numerous advantages over other methods, including a higher selectivity, mild reaction conditions and high functional-group tolerance. This review provides an overview of the most recent methods covering the photoinduced modification for single amino acids and site-selective functionalization in peptides and proteins under mild and even biocompatible conditions. Future challenges and perspectives are discussed beyond the diverse types of photocatalytic transformations that are currently available.

Flavin-Mediated Photocatalysis Provides a General Platform for Sulfide C-H Functionalization

Functionalized sulfides are important in many areas of science, ranging from chemical biology through drug discovery to organic materials chemistry. Sulfides bearing pendant reactive groups in the α-position are particularly useful; however, methods for the selective valorization of simple sulfides or the late-stage functionalization of complex sulfides by the convenient addition of valuable functionality are underexplored. Here we exemplify a general reaction platform for sulfide functionalization by showcasing three modes of α-sulfur C-H functionalization; cyanation, alkenylation, and alkynylation. Using inexpensive and commercially available riboflavin tetraacetate and visible light, decoration of both feedstock and complex sulfides proceeds in a good yield and with high selectivity. Methionine-containing peptides can also be selectively functionalized and a tolerance screen using amino-acid dopants suggests that the platform is compatible with most amino-acid side chains and thus is a potential tool for bioconjugation.

Chemical technology principles for selective bioconjugation of proteins and antibodies

Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.

Covalent fragment approaches targeting non-cysteine residues

Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.

Site-Specific 68Ga Radiolabeling of Trastuzumab Fab via Methionine for ImmunoPET Imaging

Bioconjugates of antibodies and their derivatives radiolabeled with β+-emitting radionuclides can be utilized for diagnostic PET imaging. Site-specific attachment of radioactive cargo to antibody delivery vectors provides homogeneous, well-defined immunoconjugates. Recent studies have demonstrated the utility of oxaziridine chemistry for site-specific labeling of methionine residues. Herein, we applied this approach to site-specifically radiolabel trastuzumab-derived Fab immunoconjugates with 68Ga, which can be used for in vivo PET imaging of HER2-positive breast cancer tumors. Initially, a reactive azide was introduced to a single solvent-accessible methionine residue in both the wild-type Fab and an engineered derivative containing methionine residue M74, utilizing the principles of oxaziridine chemistry. Subsequently, these conjugates were functionalized with a modified DFO chelator incorporating dibenzocyclooctyne. The resulting DFO-WT and DFO-M74 conjugates were radiolabeled with generator-produced [68Ga]Ga3+, to yield the novel PET radiotracers, [68Ga]Ga-DFO-WT and [68Ga]Ga-DFO-M74. In vitro and in vivo studies demonstrated that [68Ga]Ga-DFO-M74 exhibited a higher affinity for HER2 receptors. Biodistribution studies in mice bearing orthotopic HER2-positive breast tumors revealed a higher uptake of [68Ga]Ga-DFO-M74 in the tumor tissue, accompanied by rapid renal clearance, enabling clear delineation of tumors using PET imaging. Conversely, [68Ga]Ga-DFO-WT exhibited lower uptake and inferior image contrast compared to [68Ga]Ga-DFO-M74. Overall, the results demonstrate that the highly facile methionine-oxaziridine modification approach can be simply applied to the synthesis of stable and site-specifically modified radiolabeled antibody-chelator conjugates with favorable pharmacokinetics for PET imaging.

Ordered Porous Layer Interferometry for Dynamic Observation of Non-Specific Adsorption Induced by 1-Ethyl-3-(3-(dimethylamino)propyl) Carbodiimide

Nonspecific adsorption (NSA) seems to be an impregnable obstacle to the progress of the biomedical, diagnostic, microelectronic, and material fields. The reaction path of bioconjugation can alter the surface charge distribution on products and the interaction of bioconjugates, an ignored factor causing NSA. We monitored exacerbated NSA introduced by a 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide (EDC) addition reaction, which cannot be resistant to bovine serum albumin (BSA) or polyethylene glycol (PEG) antifouling coating and Tween-20. And the negative effects can be minimized by adding as low as 7.5 × 10-6 M N-hydroxysulfosuccinimide (sulfo-NHS). We applied ordered porous layer interferometry (OPLI) to sensitively evaluate the NSA that is difficult to measure on individual particles. Using the silica colloidal crystal (SCC) film with Fabry-Perot fringes as in situ and real-time monitoring for the NSA, we optimized the surface chemistry to yield a conjugate surface without variational charge distribution. In this work, we propose a novel approach from the perspective of the reaction pathway to minimize the NSA of solely EDC-induced chemistry.

Photoredox-Catalyzed Labeling of Hydroxyindoles with Chemoselectivity (PhotoCLIC) for Site-Specific Protein Bioconjugation

We have developed a novel visible-light-catalyzed bioconjugation reaction, PhotoCLIC, that enables chemoselective attachment of diverse aromatic amine reagents onto a site-specifically installed 5-hydroxytryptophan residue (5HTP) on full-length proteins of varied complexity. The reaction uses catalytic amounts of methylene blue and blue/red light-emitting diodes (455/650 nm) for rapid site-specific protein bioconjugation. Characterization of the PhotoCLIC product reveals a unique structure formed likely through a singlet oxygen-dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and its compatibility with strain-promoted azide-alkyne click reaction, enables site-specific dual-labeling of a target protein.

Acyl Azolium-Photoredox-Enabled Synthesis of β-Keto Sulfides

α-Heteroatom functionalization is a key strategy for C-C bond formation in organic synthesis, as exemplified by the addition of a nucleophile to electrophilic functional groups, such as iminium ions; oxocarbenium ions; and their sulfur analogues, sulfenium ions. We envisioned a photoredox-enabled radical Pummerer-type reaction realized through the single-electron oxidation of a sulfide. Following this oxidative event, α-deprotonation would afford α-thio radicals that participate in radical-radical coupling reactions with azolium-bound ketyl radicals, thereby accessing a commonly proposed mechanistic intermediate of the radical-radical coupling en route to functionalized additive Pummerer products. This system provides a complementary synthetic approach to highly functionalized sulfurous products, including modification of methionine residues in peptides, and beckons further exploration in C-C bond formations previously limited in the standard two-electron process.

Aqueous Flavin Photoredox Catalysis Drives Exclusive C3-Alkylation of Indolyl Radical Cations in Route to Unnatural Tryptophan Mimetics

One way to build chemical diversity into indoles is to oxidize them to indolyl radical cations (Ind•+). These intermediates can accept new functional groups across C2-C3 bonds or independently at C2. Less encountered is selective diversification at C3, a position plagued by competing dearomative side reactions. We disclose an aqueous photoredox-catalyzed method for transforming Ind•+ into C3-substituted tryptophan mimetics that uses water as a transient protecting group to guide site-selective C3 alkylation.

An update on late-stage functionalization in today's drug discovery

INTRODUCTION

Late-stage functionalization (LSF) allows for the introduction of new chemical groups toward the end of a synthetic sequence, which means new molecules can be rapidly accessed without laborious de novo chemical synthesis. Over the last decade, medicinal chemists have begun to implement LSF strategies into their drug discovery programs, affording benefits such as efficient access to diverse libraries to explore structure-activity relationships and the improvement of physicochemical and pharmacokinetic properties.

AREAS COVERED

An overview of the key advancements in LSF methodology development from 2019 to 2022 and their applicability to drug discovery is provided. In addition, several examples from both academia and industry where LSF methodologies have been applied by medicinal chemists to their drug discovery programs are presented.

EXPERT OPINION

Utilization of LSF by medicinal chemists is on the rise, both in academia and in industry. The maturation of the LSF field to produce methodologies bearing increased regioselectivity, scope, and functional group tolerance is envisaged to narrow the gap between methodology development and medicinal chemistry research. The authors predict that the sheer versatility of these techniques in facilitating challenging chemical transformations of bioactive molecules will continue to increase the efficiency of the drug discovery process.

Carbon-Centered Radicals in Protein Manipulation

Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.

Photo-induced defluorination acyl fluoride exchange as a fluorogenic photo-click reaction for photo-affinity labeling

Photo-click chemistry has emerged as a powerful tool for revolutionizing bioconjugation technologies in pharmacological and various biomimetic applications. However, enriching the photo-click reactions to expand the bioconjugation toolkit remains challenging, especially when focusing on spatiotemporal control endowed by light activation. Herein, we describe a photo-induced defluorination acyl fluoride exchange (photo-DAFEx) as a novel type of photo-click reaction that is mediated through acyl fluorides produced by the photo-defluorination of m-trifluoromethylaniline to covalently conjugate with primary/secondary amines and thiols in an aqueous environment. (TD)-DFT calculations, together with experimental discovery, indicate that the m-NH2PhF2C(sp3)-F bond in the excited triplet state is cleaved by water molecules, which is key to inducing defluorination. Intriguingly, the benzoyl amide linkages built by this photo-click reaction exhibited a satisfactory fluorogenic performance, which allowed visualization of its formation in situ. Accordingly, this photo-controlled covalent strategy was exploited not only for the decoration of small molecules, peptide cyclization and functionalization of proteins in vitro, but also for designing photo-affinity probes targeting endogenous carbonic anhydrase II (hCA-II) in living cells.

A rapid and selective methionine oxidative modification strategy

Considering the fact that site-selective late-stage diversification of peptides and proteins remains a challenge for biochemistry, strategies targeting low-abundance natural amino acids need to be further developed. As an extremely oxidation-sensitive and low-abundance amino acid, methionine emerges as a promising target for chemo- and site-selective modification. Herein we report an efficient and highly selective modification on methionine residues by one-pot O- and N-transfer reaction, generating sulfoximine-modified peptides with near-perfect conversion within 10 min. Moreover, the great tolerance to other natural amino acids has been demonstrated in reactions with various peptide substrates. To demonstrate the generality of this protocol, we have modified natural peptides and obtained sulfoximination products with high conversion rates. This methodology provides a novel strategy as the expansion of the methionine-based peptide functionalization toolbox.

pH-Triggered Recovery of Organic Polymer Photocatalytic Particles for the Production of High Value Compounds and Enhanced Recyclability

Pseudo-homogeneous polymeric photocatalysts are an emerging class of highly efficient and tunable photocatalytic materials, where the photocatalytic centers are easily accessible. The creation of highly efficient photocatalytic materials that can be rapidly separated and recovered is one of the critical challenges in photocatalytic chemistry. Here, we describe pH-responsive photocatalytic nanoparticles that are active and well-dispersed under acidic conditions but aggregate instantly upon elevation of pH, enabling easy recovery. These responsive photocatalytic polymers can be used in various photocatalytic transformations, including Cr^VI reduction and photoredox alkylation of indole derivative. Notably, the cationic nature of the photocatalyst accelerates reaction rate of an anionic substrate compared to uncharged species. These photocatalytic particles could be readily recycled allowing multiple successive photocatalytic reactions with no clear loss in activity.

Chemical modification of proteins - challenges and trends at the start of the 2020s

Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.

Photocatalytic Late-Stage C-H Functionalization

The emergence of modern photocatalysis, characterized by mildness and selectivity, has significantly spurred innovative late-stage C-H functionalization approaches that make use of low energy photons as a controllable energy source. Compared to traditional late-stage functionalization strategies, photocatalysis paves the way toward complementary and/or previously unattainable regio- and chemoselectivities. Merging the compelling benefits of photocatalysis with the late-stage functionalization workflow offers a potentially unmatched arsenal to tackle drug development campaigns and beyond. This Review highlights the photocatalytic late-stage C-H functionalization strategies of small-molecule drugs, agrochemicals, and natural products, classified according to the targeted C-H bond and the newly formed one. Emphasis is devoted to identifying, describing, and comparing the main mechanistic scenarios. The Review draws a critical comparison between established ionic chemistry and photocatalyzed radical-based manifolds. The Review aims to establish the current state-of-the-art and illustrate the key unsolved challenges to be addressed in the future. The authors aim to introduce the general readership to the main approaches toward photocatalytic late-stage C-H functionalization, and specialist practitioners to the critical evaluation of the current methodologies, potential for improvement, and future uncharted directions.

The thiol-sulfoxonium ylide photo-click reaction for bioconjugation

Visible-light-mediated methods were heavily studied as a useful tool for cysteine-selective bio-conjugation; however, many current methods suffer from bio-incompatible reaction conditions and slow kinetics. To address these challenges, herein, we report a transition metal-free thiol-sulfoxonium ylide photo-click reaction that enables bioconjugation under bio-compatible conditions. The reaction is highly cysteine-selective and generally finished within minutes with naturally occurring riboflavin derivatives as organic photocatalysts. The catalysts and substrates are readily accessible and bench stable and have satisfactory water solubility. As a proof-of-concept study, the reaction was smoothly applied in chemo-proteomic analysis, which provides efficient tools to explore the druggable content of the human proteome.

Recent Advances towards the Reversible Chemical Modification of Proteins

Proteins are intriguing biomacromolecules for all living systems, not only as essential building blocks of organisms, but also as participants in almost every aspect of cellular activity such as metabolism and gene transcription/expression. Developing chemical biology tools that are capable of labeling/modifying proteins is a powerful method for decoding their detailed structures and functions. However, most current approaches heavily rely on the installation of permanent tags or genetic engineering of unnatural amino acids. There has been slow development in reversible chemical labeling using small organic probes and bioorthogonal transformations to construct site-selectively modified proteins and conditionally restore their activities or structures. This review summarizes recent advances in the field of chemical regulation of proteins with reversible transformations towards distinct motifs, including amino acid residues, amide backbones and native post-translational lysine. Finally, current challenges and future perspectives are discussed.

A Vitamin B2 -Photocatalysed Approach to Methionine Analogues

Access to new non-canonical amino acid residues is crucial for medicinal chemistry and chemical biology. Analogues of the amino acid methionine have been far less explored-despite their use in biochemistry, pharmacology and peptide bioconjugation. This is largely due to limited synthetic access. Herein, we exploit a new disconnection to access non-natural methionines through the development of a photochemical method for the radical α-C-H functionalization of sulfides with alkenes, in water, using inexpensive and commercially-available riboflavin (vitamin B2 ) as a photocatalyst. Our photochemical conditions allow the two-step synthesis of novel methionine analogues-by radical addition to unsaturated amino acid derivatives-and the chemoselective modification of peptide side-chains to yield non-natural methionine residues within small peptides. The mechanism of the bio-inspired flavin photocatalysis has been probed by experimental, DFT and TDDFT studies.

A Vitamin B2-Photocatalysed Approach to Methionine Analogues

Access to new non-canonical amino acid residues is crucial for medicinal chemistry and chemical biology. Analogues of the amino acid methionine have been far less explored-despite their use in biochemistry, pharmacology and peptide bioconjugation. This is largely due to limited synthetic access. Herein, we exploit a new disconnection to access non-natural methionines through the development of a photochemical method for the radical α-C-H functionalization of sulfides with alkenes, in water, using inexpensive and commercially-available riboflavin (vitamin B2) as a photocatalyst. Our photochemical conditions allow the two-step synthesis of novel methionine analogues-by radical addition to unsaturated amino acid derivatives-and the chemoselective modification of peptide side-chains to yield non-natural methionine residues within small peptides. The mechanism of the bio-inspired flavin photocatalysis has been probed by experimental, DFT and TDDFT studies.

An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4

Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. By identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.

Direct formation and site-selective elaboration of methionine sulfoximine in polypeptides

Sulfoximines are emerging moieties for medicinal and biological chemistry, due in part to their efficacy in selective inhibition of amide-forming enzymes such as γ-glutamylcysteine synthetase. While small-molecule sulfoximines such as methionine sulfoximine (MSO) and its derivatives are well studied, structures with methionine sulfoximine residues within complex polypeptides have been generally inaccessible. This paper describes a straightforward means of late-stage one-step oxidation of methionine residues within polypeptides to afford NH-sulfoximines. We also present chemoselective subsequent elaboration, most notably by copper(ii)-mediated N-H cross-coupling at methionine sulfoximine residues with arylboronic acid reagents. This development serves as a strategy to incorporate diverse sulfoximine structures within natural polypeptides, and also identifies the methionine sulfoximine residue as a new site for bioorthogonal, chemoselective bioconjugation.

Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine

The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.

Tyrosine bioconjugation with hypervalent iodine

Hypervalent iodine reagents have recently emerged as powerful tools for late-stage peptide and protein functionalization. Herein we report a tyrosine bioconjugation methodology for the introduction of hypervalent iodine onto biomolecules under physiological conditions. Tyrosine residues were engaged in a selective addition onto the alkynyl bond of ethynylbenziodoxolones (EBX), resulting in stable vinylbenziodoxolones (VBX) bioconjugates. The methodology was successfully applied to peptides and proteins and tolerated all other nucleophilic residues, with the exception of cysteine. The generated VBX were further functionalized by palladium-catalyzed cross-coupling and azide-alkyne cycloaddition reactions. The method could be successfully used to modify bioactive natural products and native streptavidin to enable thiol-mediated cellular uptake.

Protein C-Terminal Tyrosine Conjugation via Recyclable Immobilized BmTYR

Protein modification plays an essential role in biological and pharmaceutical research. Due to the ordinary selectivity and inevitable damage to proteins of chemical synthetic methods, increased efforts were focused on biocatalysts which exhibited high regioselectivity and mild reaction conditions. However, separation of the biocatalysts and modified proteins remained a problem, especially when scaling up. Here, we developed a simple method for site-specific protein modification with a recyclable biocatalyst. The immobilizing tyrosinase (BmTYR) on magnetic beads can oxidize C-terminal tyrosine residues of the target protein to o-quinone, followed by the spontaneous addition of different nucleophiles (e.g., aniline derivatives), resulting in a C-terminal modified protein. Compared to the homogeneous biocatalytic system reported before, this heterogeneous system leads to an easier separation. Furthermore, the solid-phase biocatalyst can be regenerated during separation, providing reusability and lower costs.

C(sp3)-H/C(sp3)-H Dehydrogenative Radical Coupling of Glycine Derivatives

Here we report a general C(sp³)-H/C(sp³)-H dehydrogenative coupling strategy for the preparation of various natural or unnatural amino acids from readily available glycine derivatives and hydrocarbons through a combination of SET and HAT process.

Chemical Conjugation to Less Targeted Proteinogenic Amino Acids

Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.

A Toolkit for Engineering Proteins in Living Cells: Peptide with a Tryptophan-Selective Ru-TAP Complex to Regioselectively Photolabel Specific Proteins

Using a chemical approach to crosslink functionally versatile bioeffectors (such as peptides) to native proteins of interest (POI) directly inside a living cell is a useful toolbox for chemical biologists. However, this goal has not been reached due to unsatisfactory chemoselectivity, regioselectivity, and protein selectivity in protein labeling within living cells. Herein, we report the proof of concept of a cytocompatible and highly selective photolabeling strategy using a tryptophan-specific Ru-TAP complex as a photocrosslinker. Aside from the high selectivity, the photolabeling is blue light-driven by a photoinduced electron transfer (PeT) and allows the bioeffector to bear an additional UV-responsive unit. The two different photosensitivities are demonstrated by blue light-photocrosslinking a UV-sensitive peptide to POI. Our visible light photolabeling can generate photocaged proteins for subsequent activity manipulation by UV light. Cytoskeletal dynamics regulation is demonstrated in living cells via the unprecedented POI photomanipulation and proves that our methodology opens a new avenue to endogenous protein modification.