Residue-Specific Peptide Modification: A Chemist's Guide

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.

Annulative Editing of Peptide Side Chains: N-Pyridination of Lysine via Chichibabin Pyridine Synthesis in Hexafluoroisopropanol

Modifying the lysine side chain through N-heteroaryl annulation offers a unique opportunity to tailor or edit the structure and properties of the parent peptides. Here, we report two new applications of the Chichibabin pyridine synthesis for lysine-specific peptide modification under mild conditions, employing two distinct classes of aldehyde reagents. Reactions with 2-arylacetaldehydes afforded symmetrical 3,5-diarylpyridinium products via an abnormal Chichibabin pathway, whereas reactions with 2-hydroxyacetaldehyde yielded unsymmetrical 3-hydroxy-4-hydroxylmethylpyridiniums (HHMP) products through an unusual, redox-neutral process. The use of a hexafluoroisopropanol (HFIP) solvent was crucial for the reactivity and selectivity in both reactions. Notably, these Lys-specific N-pyridination strategies demonstrated a rare tolerance toward highly nucleophilic cysteine residues.

Late-Stage N-Arylation of Tryptophan-Containing Peptides and Drug Molecules via Arylthianthrenium Salts

We report herein a mild and efficient method for the late-stage N-arylation of tryptophan and tryptophan-containing peptides using readily accessible arylthianthrenium salts through dual photoredox/copper catalysis. Applying this protocol, a library of noncanonical amino acids and N-arylated peptides was facilely prepared. Moreover, this protocol enables efficient peptide ligation and conjugation, offering convenient access to ligated peptides and peptide/drug conjugates. Remarkably, this strategy can also be applied for the late-stage modification of complex drug molecules.

Diacylation of Peptides Enables the Construction of Functional Vesicles for Drug-Carrying Liposomes

Membrane-forming phospholipids are generated in cells by enzymatic diacylation of non-amphiphilic polar head groups. Analogous non-enzymatic processes may have been relevant at the origin of life and could have practical utility in membrane synthesis. However, aqueous head group diacylation is challenging in the absence of enzymes. The use of charged peptides instead of canonical phospholipid head groups offers advantages with respect to ease of acylation and chemical diversity. Here we demonstrate that native chemical ligation (NCL) enables in situ synthesis of diacylated lipopeptides (D-ALPs), which spontaneously self-assemble into micron-sized vesicles resembling cellular membranes. Diacylation occurs between non-amphiphilic peptides possessing an N-terminal cysteine, and acyl thioesters. Peptide head groups endow unique membrane functions, which is demonstrated by incorporation of an arginine-glycine-aspartic acid (RGD) motif, resulting in vesicle targeting to αvβ3 integrin-overexpressing cancer cells. The biocompatibility and functional group programmability of D-ALPs supports their broad utility as membrane mimetics.

Cell-free synthetic biology for natural product biosynthesis and discovery

Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.

Selective Native N(in)-H Bond Activation in Peptides with Metallaphotocatalysis

The development of chemical methods enabling site-selective incorporation of noncanonical amino acids into peptide backbones with precise functional tailoring remains a critical challenge. Particularly compelling is the use of underexplored endogenous amino acid hotspots, such as the N (in) of tryptophan, as versatile anchors for diversification. Herein, we report a chemoselective N(sp2)-H bond activation strategy targeting native tryptophan residues within peptide frameworks, exemplified by GLP-1 (7-37), using nickel metallaphotocatalysis under postsynthetic solid-phase conditions. This selective N (in)-arylation reaction proceeds efficiently within 3 h of light irradiation in highly functionalized heterogeneous environments, employing minimal excesses of electrophile and base, alongside catalytic quantities of nickel, ligand, and photocatalyst. The method affords homogeneous peptide products with high chemoselectivity and operational simplicity. We envision that this strategy could contribute to advancing the design of the next-generation long-acting class II G protein-coupled receptor agonist therapeutics.

Coarctate reaction for synthesis of fluorescent N-heterocycles, late-stage functionalization, and photo-triggered drug delivery

Coarctate reactions, involving the simultaneous formation and cleavage of two bonds at single or multiple atoms, have remained largely unexplored for biomolecular applications. These reactions are characterized by complex helical orbitals in their transition state and produce unique chemical entities unattainable by other methods. This makes coarctate reactions particularly useful for expanding the chemical diversity and properties of biomolecules. In this study, we apply an azo-ene-yne coarctate reaction to synthesize isoindazole-based N-heterocycles and explore their biomolecular applications. The azo-ene-yne coarctate method demonstrates high chemoselectivity, thus enabling the synthesis of unnatural amino acids and drug conjugates, and late-stage peptide functionalization. These isoindazole-based N-heterocycles exhibit inherent fluorescence, which can be enhanced and red-shifted through electronic tuning. Additionally, we discover a photo-triggered cleavage of the isoindazole moiety from 2-amine-isoindazole, enabling the light-triggered selective delivery of secondary amine and hydroxyl-containing drugs, which represent over 70% of current pharmaceuticals. We also employ a light-triggered method for the selective deprotection of secondary amines and the late-stage functionalization of peptides with isoindazole, enabling access to previously unexplored chemical space.

Peptide Multifunctionalization via Modular Construction of Trans-AB2C Porphyrin on Resin

Peptide multifunctionalization is a crucial technique to develop peptide-based agents for various purposes. Porphyrin-peptide conjugates are a class of popular multifunctional peptides renowned for their multifunctional and multimodal properties. However, the tedious synthetic works for porphyrin building blocks are involved in most previous studies. In this work, a modular solid-phase synthetic approach is reported to construct trans-AB2C porphyrin on peptide chains without presynthesized porphyrin building blocks. The products from this approach, which inherit both functionalities from the porphyrins and the modules employed for constructing porphyrins, show potential in biomedical and biomaterial applications. Furthermore, by extending this synthetic approach, the first example of "resin-to-resin" reaction is reported to link two peptides together along the construction of porphyrin motifs to give porphyrin-peptide conjugates with two different peptide chains.

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.

Formamidine as an Easy-On and Easy-Off Linker for Reversible Crosslinking of Two Alkyl Amines in Peptide Stapling and Conjugation

Amino groups are abundant in both natural and synthetic molecules, offering highly accessible sites for modifying native biorelevant molecules. Despite significant progress with more reactive thiol groups, methods for ligating two amino groups with reversible linkers for bioconjugation applications remain elusive. Herein, we report the use of oxidative decarboxylative condensation of glyoxylic acid to crosslink or ligate two alkyl amines via a compact formamidine linkage, applicable in both intra- and intermolecular contexts. This linking chemistry exhibits unique hetero-coupling selectivity between primary and secondary alkyl amines. Although the formamidine linkage is stable under pH-neutral buffers and acidic conditions, it can be readily cleaved with ethylenediamine or hydrazine under mild conditions in alcohol solvents or aqueous media, fully restoring the amino groups. This study introduces a rare 'easy-on and easy-off' strategy for connecting two native amines in peptide stapling and biomolecule conjugation.

Site-selective cleavage of peptides and proteins targeting aromatic amino acid residues

The site-selective cleavage of peptides and proteins at specific amino acid residues is an important strategy for the modification of biomolecules as it can potentially transmute the reactivity profile of the whole molecule. Moreover, precise cleavage of a specific amide bond in peptides and proteins has enormous applications in the domains of chemical biology, genetics, and protein engineering. Among the 20 proteinogenic amino acids, tryptophan (Trp, W), tyrosine (Tyr, Y), phenylalanine (Phe, F) and histidine (His, H) are classified as aromatic amino acids that maintain the function of protein folding through hydrophobic and π-π interactions. Thus, scissoring at a specific site of an aromatic amino acid may alter the structure and function of a peptide or protein. In the last 60-70 years, great success has been achieved in the development of methods for the aromatic amino acid (AAA)-selective cleavage of peptides and proteins. Generally, aromatic side chains are derivatized in the presence of specific reagents. Consequently, either the downstream or the upstream amide bond of the aromatic side chain is activated, and hydrolysis of the amide bond splits the peptide. Unfortunately, a systematic review covering this methodological development of the AAA-selective fission of peptide is lacking to date. Thus, in this review, we aim to showcase the up-to-date progress in the site-selective rupture of peptide bonds at aromatic amino acid residues with an emphasis on the postulated mechanisms, enabling future researchers to further drive progress in this research field.

Direct and chemoselective transformation of cysteine to dehydroalanine on peptides

A direct method for the preparation of peptides containing a dehydroalanine residue was developed through the chemoselective transformation of a cysteine residue in peptides, under the influence of cesium carbonate.

Heterogeneous Catalysis Expands the Toolbox for Chemoselective Peptide Derivatization and Labeling

The ability to chemoselectively modify either the peptide backbone or specific side chains is critical to advance the fields of bioconjugation and peptide pharmaceuticals. Transition-metal catalysis has been widely used in peptide and protein derivatization but mostly under homogeneous conditions. Herein, we present a first-in-class heterogeneous catalytic approach for the site-selective functionalization of histidine-containing peptides with aryl and alkenyl moieties bearing fluorescent and affinity tags, lipids, and conjugation handles. This heterogeneous derivatization strategy employs a copper(II) hexacyanometallate to catalyze the Chan-Lam reaction with boronic acids at either the backbone or the histidine imidazole, thus providing novel results that differ from those previously reported for the homogeneous Cu(OAc)2-mediated coupling procedure. A correlation was established between the structural and electronic properties of the copper(II) hexacyanometalate with its ability to catalyze this oxidative cross-coupling. This report expands the toolbox for late-stage peptide derivatization and labeling by unlocking the reactivity of the histidine side chain rather than merely acting as a directing group, thus boosting applications of heterogeneous catalysis in drug discovery and development.

The chemical language of protein glycation

Glycation is a non-enzymatic post-translational modification (PTM) that is correlated with many diseases, including diabetes, cancer and age-related disorders. Although recent work points to the importance of glycation as a functional PTM, it remains an open question whether glycation has a causal role in cellular signaling and/or disease development. In this Review, we contextualize glycation as a specific mechanism of carbon stress and consolidate what is known about advanced glycation end-product (AGE) structures and mechanisms. We highlight the current understanding of glycation as a PTM, focusing on mechanisms for installing, removing or recognizing AGEs. Finally, we discuss challenges that have hampered a more complete understanding of the biological consequences of glycation. The development of tools for predicting, modulating, mimicking or capturing glycation will be essential for interpreting a post-translational glycation network. Therefore, continued insights into the chemistry of glycation will be necessary to advance understanding of glycation biology.

From lead to market: chemical approaches to transform peptides into therapeutics

Peptides are a powerful drug modality with potential to access difficult targets. This recognition underlies their growth in the global pharmaceutical market, with peptides representing ~8% of drugs approved by the FDA over the past decade. Currently, the peptide therapeutic landscape is evolving, with high-throughput display technologies driving the identification of peptide leads with enhanced diversity. Yet, chemical modifications remain essential for improving the 'drug-like' properties of peptides and ultimately translating leads to market. In this review, we explore two recent therapeutic candidates (semaglutide, a peptide hormone analogue, and MK-0616, an mRNA display-derived candidate) as case studies that highlight general approaches to improving pharmacokinetics (PK) and potency. We also emphasize the critical link between advances in medicinal chemistry and the optimisation of highly efficacious peptide therapeutics.

Catalytic Serine Labeling in Nonaqueous, Acidic Media

Chemoselective modification of alkyl alcohols (e. g., serine residues) on proteins has been a daunting challenge especially in aqueous media. Herein, we report chemical modification of alkyl alcohols in protein and cell lysate samples using carboxylic acid-based bioconjugation media. The acidic medium is not only useful to suppress reactivity of other nucleophiles in proteins, but the medium also serves as a potentially biomolecule-compatible solvent. The acid-catalyzed acylation strategy has a unique selectivity paradigm compared to the common active-serine-targeted method and would act as a new strategy for studying biological roles of serine residues.

Trp31 Residue of Trx-1 Is Essential for Maintaining Antioxidant Activity and Cellular Redox Defense Against Oxidative Stress

Thioredoxin-1 (Trx-1) is an important redox protein found in almost all prokaryotic and eukaryotic cells, which has a highly conserved active site sequence: Trp-Cys-Gly-Pro-Cys. To investigate whether the Trp31 residue is essential for the antioxidant activity of human Trx-1 (hTrx-1), we mutated Trx-1 by replacing Trp31 with Ala31 (31Ala) or deleting Trp31 residue (31Del). We introduced 31Ala and 31Del mutations into prokaryotic cells for hTrx-1 protein expression, protein purification and evaluation of antioxidant activity. The results showed that neither the replacing mutation to Ala31 nor the deletion of Trp31 residue affected the efficient expression of hTrx-1 protein in prokaryotic cells, indicating that neither form of Trp31 mutation would disrupt the folded structure of the Trx-1 protein. Comparison of the antioxidant activity of purified hTrx-1 proteins of wild-type, 31Ala and 31Del forms revealed that both mutant forms significantly decreased the antioxidant capacity of hTrx-1. Further investigations on eukaryotic cells showed that H2O2 treatment caused massive cell death in EA.Hy926 human endothelial cells with 31Ala and 31Del mutations compared to wild-type cells, which was associated with increased ROS production and downregulation of antioxidant Nrf2 and HO-1 expression in the mutant cells. These results suggested that mutations in the Trp31 residue of hTrx-1 remarkably disrupted cellular redox defense against oxidative stress. The antioxidant activity of hTrx-1 relies on the thiol-disulfide exchange reaction, in which the content of thiol groups forming disulfide bonds in hTrx-1 is critical. We found that the content of free thiol groups specifically participating in disulfide bond formation was significantly lower in Trp31 mutant hTrx-1 than in wild-type hTrx-1; that was speculated to affect the formation of disulfide bonds between Cys32 and Cys35 by virtual analysis, thus abolishing the antioxidant activity of hTrx-1 in cleaving oxidized groups and defending against oxidative stress. The present study provided valuable insights towards understanding the importance of Trp31 residue of hTrx-1 in maintaining the correct conformation of the Trx fold structure, the antioxidant functionality of hTrx-1 and the cellular redox defense capability against oxidative stress.

Tryptophan-specific modification and diversification of peptides and proteins

In spite of being the second-lowest abundant proteinogenic amino acid, approximately 90% of proteins contain at least one tryptophan residue. Hence, the chemoselective functionalization of tryptophan residue can provide access to site-selective bioconjugation of almost all known proteins. With the increase in the utility of bioconjugated proteins and peptides as drugs and therapeutic agents, the development of smart protocols to fabricate and modulate biomolecules has flourished. This review provides a comprehensive summary of the latest advances in tryptophan-specific modification and diversification of peptides and proteins that exhibit significant applications in proteomics, protein engineering, living cell imaging, drug discovery, etc. The article also highlights literature gaps and new opportunities for the sake of future innovation in the field.

Late-stage installation and functionalization of alkyl pyridiniums: a general HTE amenable strategy to access diverse aryl alanine containing macrocyclic peptides

This manuscript describes a strategy to readily access diverse aryl and homoaryl alanine-containing pharmaceutically relevant macrocyclic peptides. A two-step sequence involving the late-stage installation of the pyridinium functionality on macrocyclic peptides followed by reductive couplings was implemented. These transformations are amenable to microscale high-throughput experimentation (HTE) and enable rapid access to aryl alanine-containing macrocyclic peptides that would otherwise be inaccessible via solid-phase peptide synthesis using commercially available amino acids. Numerous aryl and heteroaryl derivatives can be effectively used in these reactions. In addition, a systematic investigation was undertaken using an "informer" set of macrocyclic peptides which revealed the compatibility of the late-stage diversification with peptides containing diverse side chain functionalities.

Light-Activated Reactivity of Nitrones with Amino Acids and Proteins

Controlled modifications of amino acids are an indispensable tool for advancing fundamental and translational research based on peptides and proteins. Yet, we still lack methods to chemically modify each naturally occurring amino acid sidechain. To help address this gap, we show that N,α-diaryl oxaziridines expand the scope of bioconjugation methods to chemically modify cysteine, methionine, and tryptophan residues with evidence for additional tyrosine labelling in a proteomic context. Conjugation primarily at tryptophan sites can be accessed by selective cleavage of modifications at other sidechains. The N,α-diaryl oxaziridine reagents are accessed through photoisomerization of nitrones, which serve as photocaged reagents, thus providing an additional level of control over reactivity. Initial guiding principles for the design of nitrone reagents are developed by exploring the impact of structure on UV/Vis absorption, photoisomerization, and reactivity. We identify a nitrone structure that maximizes photoisomerization efficiency, the aqueous stability of the oxaziridine, the extent of amino acid modification, and the stability of the resulting amino acid conjugates. We then translate nitrone reagents to modify proteins in aqueous conditions. Finally, we use nitrones to profile reactive residues across the proteome of a mammalian cell line and find that they expand the proteome coverage.

Dual-Performing Vinyltetrazine for Rapid, Selective Bioconjugation and Functionalization of Cysteine Proteins

Although methods for Cys-specific bioconjugation and functionalization of proteins have been developed and widely utilized in biomolecule engineering and therapeutic development, reagents for this purpose are generally designed to accomplish bioconjugation only. Consequently, additional clickable groups must be attached to these reagents to accomplish functionalization. Herein, we describe a new, simple, dual-performing bioconjugation-functionalization reagent, VMeTz, which possesses an electron-withdrawing tetrazine (Tz) substituted vinyl (V) moiety to serve as both a Michael receptor for selective conjugation with Cys and a site for click with TCO derivatives to introduce functionality. Critically, VMeTz contains a methyl group that prevents the formation of multiple Tz-containing Cys-adducts. Reactions of VMeTz with Cys-containing peptides and proteins both in vitro and in live cells produce single stable Michael adducts with high selectivity. Moreover, the Cys-VMeTz peptide and protein conjugates undergo facile click reactions with TCO-functionalized reagents for labeling and protein profiling. Furthermore, VMeTz selectively activates and delivers the TCO-caged toxic substances Dox and PROTAC ARV-771 to cancer cells to produce therapeutic effects that are comparable to those of the parent drugs. Collectively, the studies demonstrate that VMeTz is a useful reagent for therapeutically significant Cys-specific protein bioconjugation and functionalization.

Rh(III)-Catalyzed Double C-H Activation toward Peptide-Benzazepine Conjugates

We herein report the efficient synthesis of peptide-benzazepine conjugates from Lys-based peptides and acroleins via Rh(III)-catalyzed double C-H activation. This reaction features mild reaction conditions, broad scope, high atom and step economies, and excellent chemo- and site selectivity. The synthetic utility of this strategy is further demonstrated by scale-up experiments and product derivatizations, including diverse late-stage ligations based on the aldehyde moiety. The preliminary biological activity studies show that peptide-benzazepine conjugates have good antifungal activities toward crop and forest pathogenic fungi.

Unconventional Synthetic Approaches to Unusual Peptide Derivatives

Peptides that contain unusual motifs, such as non-proteinogenic amino acids (AAs) and/or macrocyclic substructures, have recently attracted great attention as a new modality in medium-sized-molecule drug discovery. Therefore, it is highly important to develop methods for the chemical synthesis of a wide variety of such unusual peptide derivatives, which are often difficult to prepare via conventional synthetic approaches. In this review, the development of unconventional approaches for the synthesis of unusual peptide derivatives is discussed. Specifically, a novel external-oxidant-mediated decarboxylative condensation of α-ketoacids that can be applied to the synthesis of a wide variety of unusual peptide derivatives is reported. Moreover, an organocatalytic asymmetric Mannich-type addition is discussed that provides chiral β-amino-α-ketoacids, which are required as starting materials for the decarboxylative condensation. In this reaction, the adducts corresponding to various unusual AA side chains are obtained in high yield and excellent stereoselectivity. Furthermore, the "N-chloropeptide strategy" is proposed as a new method for the chemical modification of peptides without the need for a reactive AA residue.

Triple C-H Activation/Annulation: In Situ Construction of Fluorescent Peptides

Herein, we report a Rh(III)-catalyzed triple C-H activation-annulation of Phe-based peptides with alkynes for the preparation of fluorescent peptides. The robustness of this protocol is reflected by a broad substrate scope, high atom- and step-economy, and excellent chemo- and site-selectivity. An in situ generated polycyclic aromatic hydrocarbon carbocation as a fluorophore exhibits good fluorescence properties (maximum emission wavelength up to 628 nm) and low cell cytotoxicity. The synthetic utility of this method is further demonstrated by versatile product applications in bioconjugation with the protein BSA and specifically targeting lysosomes and mitochondria of live mammalian cells.

Triflic Acid-Mediated Chemoselective Indole C2-Heteroarylation of Peptide Tryptophan Residues by Triazine

Peptide modification provides opportunities to afford peptides with designed functions. Among the proteogenic amino acids, tryptophan represents an ideal and attractive target for peptide modification because of the exclusive chemical reactivity of its unique indole structure. Herein, we reported an indole C2 position-selective and transition-metal-free modification approach for indole derivatives and tryptophan-containing peptides by triazine derivatives via triflic acid activation and that the incorporated functional group could act as an orthogonal handle for further bioconjugation via an inverse electron demand Diels-Alder reaction.

Target Bioconjugation of Protein Through Chemical, Molecular Dynamics, and Artificial Intelligence Approaches

Covalent modification of proteins at specific, predetermined sites is essential for advancing biological and biopharmaceutical applications. Site-selective labeling techniques for protein modification allow us to effectively track biological function, intracellular dynamics, and localization. Despite numerous reports on modifying target proteins with functional chemical probes, unique organic reactions that achieve site-selective integration without compromising native functional properties remain a significant challenge. In this review, we delve into site-selective protein modification using synthetic probes, highlighting both chemical and computational methodologies for chemo- and regioselective modifications of naturally occurring amino acids, as well as proximity-driven protein-selective chemical modifications. We also underline recent traceless affinity labeling strategies that involve exchange/cleavage reactions and catalyst tethering modifications. The rapid development of computational infrastructure and methods has made the bioconjugation of proteins more accessible, enabling precise predictions of structural changes due to protein modifications. Hence, we discuss bioconjugational computational approaches, including molecular dynamics and artificial intelligence, underscoring their potential applications in enhancing our understanding of cellular biology and addressing current challenges in the field.

Functionalized DNA secondary structures and nanostructures for specific protein modifications

The development of non-biological applications of DNA has not only resulted in delicately shaped DNA-based nano-objects with complex functions but also spawned their use for novel catalytic applications. From the multitude of applications of DNAzymes that operate on a relatively simple substrate, we have witnessed the emergence of multifunctional catalytically active DNA-based nanostructures for one of the most challenging tasks known to a chemist: the controlled and precise modification of a wild-type protein in its natural environment. By incorporating various elements associated with post-translational modification (PTM) writer enzymes into complex nanostructures, it is now possible to chemically modify a specific protein in cell lysates under the influence of an externally added trigger, clearly illustrating the promising future for this approach.

Hydro- and deutero-deamination of primary amines using O-diphenylphosphinylhydroxylamine

While selective defunctionalizations are valuable in organic synthesis, hydrodeamination of primary amines poses challenges. Deuterodeamination, analogous to hydrodeamination, presents even greater difficulties due to its frequently slower deuteration rate, interference by hydrogenation and constraints in deuterated sources. This study introduces a reliable, robust, and scalable hydro- and deuterodeamination method capable of handling various primary amines. Defined by its mild reaction conditions, rapid completion, simplified purification facilitated by water-soluble byproducts, the method leverages deuterium oxide as a deuterium source and employs commercialized O-diphenylphosphinylhydroxylamine for deamination. Applied to a diverse range of biologically active molecules, it has consistently achieved high yields and efficient deuterium incorporation. By synergizing with site-selective C-H functionalization of primary aliphatic amines, our method reveals synthetic strategies utilizing nitrogen atom as a traceless directing group, encompassing deaminative alkylation, 1,1-deuteroalkylation, 1,1-dialkylation, 1,1,1-deuterodialkylation, C-H arylation, and 1,3-deuteroarylation. Emphasizing this innovation, the processes of deaminative degree-controlled deuteration have been developed.

N-Substituted Iminothiolane (NIT): A Promising Strategy for Protecting Lysine Side Chains for Solid-Phase Peptide Chemistry

In this study, we introduce N-substituted iminothiolane (NIT) as a robust protecting group for lysine side chains. NIT is compatible with Fmoc-SPPS and can be efficiently removed under mild nucleophilic conditions. Notably, NIT offers enhanced hydrophilicity compared to traditional orthogonal lysine-protecting groups and does not undergo intramolecular migration. Additionally, the synthesis of NIT in aqueous media highlights its eco-friendly nature, positioning it as a promising alternative to protect lysine side chains.

Appendage- and Scaffold-Diverse Electrophilic and Photoreactive Probes for Integrated Phenotypic Screening-Target Identification Campaigns via a Minimalist Bifunctional Isocyanide

One of the grand challenges in chemical biology is identifying a small-molecule modulator for all proteins within a proteome. To expand the variety and number of ligandable proteins for drug discovery, the objective of this study was to synthesize and evaluate the protein target profiles of electrophilic and photoreactive fully functionalized small-molecule probes (FFSMPs) featuring increased scaffold-, appendage-, and protein-reactive functional group (PRFG) diversity. FFSMPs contain: (1) a protein-binding motif, (2) an electrophilic or photoreactive PRFG for target protein capture, and (3) a terminal alkyne for click chemistry-based proteomic applications. These compounds can be directly applied in phenotypic screening programs to identify ligand-protein pairs in cells unbiasedly. Herein, we highlight 17 examples from 34 structurally diverse FFSMPs featuring five electrophiles, three photoreactive groups, and 15 chemical scaffolds. Essential to the synthesis of the FFSMPs was a new minimalist bifunctional isocyanide in an "isocyanide-based multicomponent reaction-Boc deprotection-arming" synthetic sequence. To the best of our knowledge, this is the first report concerning the preparation of appendage- and scaffold-diverse FFSMPs for integrated phenotypic screening-target identification campaigns with the ability to examine either electrophilic or photoreactive PRFGs. In contrast, the status quo for such studies has been appendage-diverse FFSMPs comprised of a single chemical scaffold and a single PRFG, which limits efficient target protein capture and/or chemical space sampling significantly in the quest for discovering new drug targets and/or compounds with novel mechanisms of action. Phenotypic screening of the electrophilic members of our library identified several FFSMPs with potent antiproliferative activity against MCF10CA1a breast cancer cells. One of these FFSMPs (Compound 4a) covalently targeted and potently inhibited protein disulfide isomerase A1 (PDIA1). This study supports the continued use of minimalist bifunctional isocyanides as valuable building blocks for preparing structurally diverse FFSMPs for integrated phenotypic screening-target identification campaigns.

Synthesis of non-canonical amino acids through dehydrogenative tailoring

Amino acids are essential building blocks in biology and chemistry. Whereas nature relies on a small number of amino acid structures, chemists desire access to a vast range of structurally diverse analogues1-3. The selective modification of amino acid side-chain residues represents an efficient strategy to access non-canonical derivatives of value in chemistry and biology. While semisynthetic methods leveraging the functional groups found in polar and aromatic amino acids have been extensively explored, highly selective and general approaches to transform unactivated C-H bonds in aliphatic amino acids remain less developed4,5. Here we disclose a stepwise dehydrogenative method to convert aliphatic amino acids into structurally diverse analogues. The key to the success of this approach lies in the development of a selective catalytic acceptorless dehydrogenation method driven by photochemical irradiation, which provides access to terminal alkene intermediates for downstream functionalization. Overall, this strategy enables the rapid synthesis of new amino acid building blocks and suggests possibilities for the late-stage modification of more complex oligopeptides.

Introducing Chemoselective Peptide Conjugation via N-Alkylation of Pyridyl-alanine: Solution and Solid Phase Applications

A novel chemoselective peptide conjugation via late-stage N-alkylation of pyridyl-alanine (PAL) in the solution and solid phase, namely, NAP, is demonstrated. The method constructs functionally diverse and highly stable N-alkylated conjugates with various peptides. Notably, conjugations in the solid phase offered a more economical process. The method can provide the opportunity for dual labeling along with a cysteine handle in a peptide chain. Finally, we showcased that the antiproliferative activities of the p53 peptide (MDM2 inhibitor) could be 2-fold enhanced via NAP conjugation with the RGD peptide (selective integrin binder).

Intermolecular sulfur atom transfer cascade enabled late-stage introduction of sulfilimines into peptides

Sulfilimines, a privileged class of -S(iv)[double bond, length as m-dash]N- functional groups found in nature, have been exploited as valuable building blocks in organic synthesis and as pharmacophores in drug discovery, and have aroused significant interest in the chemical community. Nevertheless, strategies for late-stage introduction of sulfilimines into peptides and proteins have still met with limited success. Herein, we have developed a method of introducing biological sulfilimine fragments into peptides by an intermolecular sulfur atom transfer cascade reaction, utilizing hydroxylamine condensed with the acid moieties of peptides and varied diaryl disulfides. It provides a convenient, efficient, metal-free and widely applicable method for late-stage modification and functionalization of peptides at their acid sites both in the homogeneous phase and on-resins in SPPS. Moreover, the modified peptides with sulfilimines have been demonstrated as cleavable linkers for peptide conjugates under reducible conditions, providing unique opportunities in peptide therapeutics development and drug discovery.

Late-Stage Glycosylation of Peptides by Methionine-Directed β-C(sp3)-H Functionalization with 1-Iodoglycals

Using l-methionine (Met) as the endogenous directing group, we developed Pd-catalyzed β-C(sp3)-H glycosylation of peptides with 1-iodoglycals. A wide range of tri- to hexapeptides containing the Ala-Met motifs underwent Ala C-H glycosylation under the standard conditions to give the glycopeptides smoothly. 15 proteinogenic amino acids (with easily removable protecting groups) were well tolerated. Control experiments indicated that Met acted as a N,S-bidentate directing group and exhibited an effect superior to other amino acid residues such as l-aspartic acid (Asp), l-asparagine (Asn), and S-protected l-cysteine (Cys). In addition, further transformation by HFIP-promoted 1,4-elimination furnished another type of glycopeptide with the 1,3-diene motif, which provides a handle for further derivatization.

Strategies for Making High-Performance Artificial Spider Silk Fibers

Artificial spider silk is an attractive material for many technical applications since it is a biobased fiber that can be produced under ambient conditions but still outcompetes synthetic fibers (e.g., Kevlar) in terms of toughness. Industrial use of this material requires bulk-scale production of recombinant spider silk proteins in heterologous host and replication of the pristine fiber's mechanical properties. High molecular weight spider silk proteins can be spun into fibers with impressive mechanical properties, but the production levels are too low to allow commercialization of the material. Small spider silk proteins, on the other hand, can be produced at yields that are compatible with industrial use, but the mechanical properties of such fibers need to be improved. Here, the literature on wet-spinning of artificial spider silk fibers is summarized and analyzed with a focus on mechanical performance. Furthermore, several strategies for how to improve the properties of such fibers, including optimized protein composition, smarter spinning setups, innovative protein engineering, chemical and physical crosslinking as well as the incorporation of nanomaterials in composite fibers, are outlined and discussed.

Discovery and development of tyrosine-click (Y-click) reaction for the site-selective labelling of proteins

With the versatile utility of bio-conjugated peptides and proteins in the fields of agriculture, food, cosmetics and pharmaceutical industry, the design of smart protocols to conjugate and modulate biomolecules becomes highly desirable. During this process, the most important consideration for biochemists is the retention of configurational integrity of the biomolecules. Moreover, this type of bioconjugation of peptide and protein becomes frivolous if the reaction is not performed with precise amino acid residues. Hence, chemo-selective, as well as site-selective reactions, that are biocompatible and possess an appropriate level of reactivity are necessary. Based on click chemistry, there are so many tyrosine (Y) conjugation strategies, such as sulfur-fluoride exchange (SuFEx), sulfur-triazole exchange (SuTEx), coupling with π-allyl palladium complexes, diazonium salts, diazodicarboxyamide-based reagents etc. Among these techniques, diazodicarboxyamide-based Y-conjugation, which is commonly known as the "tyrosine-click (Y-click) reaction", has met the expectations of synthetic and biochemists for the tyrosine-specific functionalization of biomolecules. Over the past one and a half decades, significant progress has been made in the classical organic synthesis approach, as well as its biochemical, photochemical, and electrochemical variants. Despite such progress and increasing importance, the Y-click reaction has not been reviewed to document variations in its methodology, applications, and broad utility. The present article aims to provide a summary of the approaches for the modulation of biomolecules at the hotspot of tyrosine residue by employing the Y-click reaction. The article also highlights its application for the mapping of proteins, imaging of living cells, and in the fields of analytical and medicinal chemistry.

Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization

Ethynylbenziodoxol(on)es (EB(X)xs) reagents have emerged as useful reagents for peptide/protein modification due to their versatile reactivity and high selectivity. Herein, we report the successful introduction of ethynylbenziodoxoles (EBxs) on different amino acid building blocks (Lys/Orn/Dap), and show their compatibility with both solid phase peptide synthesis (SPPS) and solution phase peptide synthesis (SPS). The selective incorporation of the EBx core into peptide sequences enable efficient macrocyclizations under mild conditions for the synthesis of topologically unique cyclic and bicyclic peptides.

Small Scale, Big Impact: Nanotechnology-Enhanced Drug Delivery for Brain Diseases

Central nervous system (CNS) diseases, ranging from brain cancers to neurodegenerative disorders like dementia and acute conditions such as strokes, have been heavily burdening healthcare and have a direct impact on patient quality of life. A significant hurdle in developing effective treatments is the presence of the blood-brain barrier (BBB), a highly selective barrier that prevents most drugs from reaching the brain. The tight junctions and adherens junctions between the endothelial cells and various receptors expressed on the cells make the BBB form a nonfenestrated and highly selective structure that is crucial for brain homeostasis but complicates drug delivery. Nanotechnology offers a novel pathway to circumvent this barrier, with nanoparticles engineered to ferry drugs across the BBB, protect drugs from degradation, and deliver medications to the designated area. After years of development, nanoparticle optimization, including sizes, shapes, surface modifications, and targeting ligands, can enable nanomaterials tailored to specific brain drug delivery settings. Moreover, smart nano drug delivery systems can respond to endogenous and exogenous stimuli that control subsequent drug release. Here, we address the importance of the BBB in brain disease treatment, summarize different delivery routes for brain drug delivery, discuss the cutting-edge nanotechnology-based strategies for brain drug delivery, and further offer valuable insights into how these innovations in nanoparticle technology could revolutionize the treatment of CNS diseases, presenting a promising avenue for noninvasive, targeted therapeutic interventions.

Fluoroalcohols for chemical modification of biomolecules

While their broad utility in various chemistry fields were well recognized for decades, fluoroalcohols have recently emerged as a unique solvent system for bioconjugation development. This review describes examples and roles of fluoroalcohols such as trifluoroethanol (TFE) and hexafluoroisopropanol (HFIP) for chemical modification of biomolecules such as polypeptides, nucleic acids, and saccharides. Many chemical modification processes were facilitated by notable functions of those fluoroalcohols such as a proton shuttle, reversible adduct formation with reactive species, and compatibility with electrochemistry/photochemistry. The usefulness of the fluoroalcohol solvents can be even promoted by its combination with a different solvent system for reaction enhancement and protein stabilization. The collection of the various chemical transformations in this review is an indication of the rapid growth of the solvent-assisted bioconjugation field.

Methionine-enabled peptide modification through late-stage Pd-catalyzed β-C(sp3)-H olefination/cyclization

We present a method for site-selective diversification of peptides via Pd-catalyzed β-C(sp3)-H olefination/cyclization. In this protocol, the native methionine residue acts as a directing group, enabling site-specific olefination/cyclization of peptides. This chemistry demonstrates broad substrate scope, offering a versatile tool for peptide ligation.

Late-stage peptide modification and macrocyclization enabled by tertiary amine catalyzed tryptophan allylation

Late-stage modification of peptides could potentially endow peptides with significant bioactivity and physicochemical properties, and thereby provide novel opportunities for peptide pharmaceutical studies. Since tryptophan (Trp) bears a unique indole ring residue and plays various critical functional roles in peptides, the modification methods for tryptophan were preliminarily developed with considerable progress via transition-metal mediated C-H activation. Herein, we report an unprecedented tertiary amine catalyzed peptide allylation via the SN2'-SN2' pathway between the N1 position of the indole ring of Trp and Morita-Baylis-Hillman (MBH) carbonates. Using this method that proceeds under mild conditions, we demonstrated an extremely broad scope of Trp-containing peptides and MBH carbonates to prepare a series of peptide conjugates and cyclic peptides. The reaction is amenable to either solid-phase (on resin) or solution-phase conditions. In addition, the modified peptides can be further conjugated with other biomolecules at Trp, providing a new handle for bioconjugation.

Organometallic Oxidative Addition Complexes for S-Arylation of Free Cysteines

Development of bioconjugation strategies to efficiently modify biomolecules is of key importance for fundamental and translational scientific studies. Cysteine S-arylation is an approach which is becoming more popular due to generally rapid kinetics and high chemoselectivity, as well as the strong covalently bonded S-aryl linkage created in these processes. Organometallic approaches to cysteine S-arylation have been explored that feature many advantages compared to their more traditional organic counterparts. In this Viewpoint, progress in the use of Au(III) and Pd(II) oxidative addition (OA) complexes for stoichiometric cysteine S-arylation is presented and discussed. A focus is placed on understanding the rapid kinetics of these reactions under mild conditions, as well as the ability to generate biomolecular heterostructures. Potential avenues for further exploration are addressed and usefulness of these methods to the practitioner are emphasized in the discussion.

Electrochemical Bioconjugation of Tryptophan Residues: A Strategy for Peptide Modification

Interest in electrocatalytic bioconjugation reactions has surged, particularly for modifying tryptophan and tyrosine residues in proteins. We used a cost-effective graphite felt electrode and low-current methodology to achieve selective bioconjugation of tryptophan with thiophenols, yielding up to 92%. This method exclusively labeled tryptophan residues and incorporated fluorinated tryptophan for NMR analysis. Eight polypeptides, including lanreotide and leuprorelin, were effectively coupled, demonstrating the method's versatility and potential for novel diagnostic and therapeutic agents.

Amplifiable protein identification via residue-resolved barcoding and composition code counting

Ultrasensitive protein identification is of paramount importance in basic research and clinical diagnostics but remains extremely challenging. A key bottleneck in preventing single-molecule protein sequencing is that, unlike the revolutionary nucleic acid sequencing methods that rely on the polymerase chain reaction (PCR) to amplify DNA and RNA molecules, protein molecules cannot be directly amplified. Decoding the proteins via amplification of certain fingerprints rather than the intact protein sequence thus represents an appealing alternative choice to address this formidable challenge. Herein, we report a proof-of-concept method that relies on residue-resolved DNA barcoding and composition code counting for amplifiable protein fingerprinting (AmproCode). In AmproCode, selective types of residues on peptides or proteins are chemically labeled with a DNA barcode, which can be amplified and quantified via quantitative PCR. The operation generates a relative ratio as the residue-resolved 'composition code' for each target protein that can be utilized as the fingerprint to determine its identity from the proteome database. We developed a database searching algorithm and applied it to assess the coverage of the whole proteome and secretome via computational simulations, proving the theoretical feasibility of AmproCode. We then designed the residue-specific DNA barcoding and amplification workflow, and identified different synthetic model peptides found in the secretome at as low as the fmol/L level for demonstration. These results build the foundation for an unprecedented amplifiable protein fingerprinting method. We believe that, in the future, AmproCode could ultimately realize single-molecule amplifiable identification of trace complex samples without further purification, and it may open a new avenue in the development of next-generation protein sequencing techniques.

Iron-Catalyzed C-H Alkylamination of Tyrosine Derivatives

An efficient method for the direct alkylamination of tyrosine derivatives via iron-catalyzed C-H amination has been developed. The method, using O-benzoyl-N,N-dialkylhydroxylamines as aminating agents, provides various C-amino-functionalized tyrosine derivatives in up to 77% yield. The utility of this method is showcased by its application to the direct introduction of drug molecules into tyrosine, facilitating access to structurally diverse amino-functionalized tyrosine derivatives.

Production of constrained L-cyclo-tetrapeptides by epimerization-resistant direct aminolysis

The synthesis of constrained 12-membered rings is notably difficult. The main challenges result from constraints during the linear peptide cyclization. Attempts to overcome constraints through excessive activation frequently cause peptidyl epimerization, while insufficient activation of the C-terminus hampers cyclization and promotes intermolecular oligomer formation. We present a β-thiolactone framework that enables the synthesis of cyclo-tetrapeptides via direct aminolysis. This tactic utilizes a mechanism that restricts C-terminal carbonyl rotation while maintaining high reactivity, thereby enabling efficient head-to-tail amidation, reducing oligomerization, and preventing epimerization. A broad range of challenging cyclo-tetrapeptides ( > 20 examples) are synthesized in buffer and exhibits excellent tolerance toward nearly all proteinogenic amino acids. Previously unattainable macrocycles, such as cyclo-L-(Pro-Tyr-Pro-Val), have been produced and identified as μ-opioid receptor (MOR) agonists, with an EC50 value of 2.5 nM. Non-epimerizable direct aminolysis offers a practical solution for constrained peptide cyclization, and the discovery of MOR agonist activity highlights the importance of overcoming synthetic challenges for therapeutic development.

Targeting and Manipulating Tryptophan Interactions on Proteins

Tryptophan, commonly regarded as buried within the interior cores of proteins to maintain secondary structures, is now being recognized for its significant contributions to protein functionality. However, investigating functional tryptophan-involved interactions across the proteome and manipulating these interactions in live cells are considerable challenges. In this In Focus article, we summarize emerging advances in the field, describing innovative chemistries that leverage distinctive biochemical properties of the indole moiety for targeting and functionally manipulating tryptophan interactions.

Efficient synthetic methods for α,β-dehydroamino acids as useful and environmentally benign building blocks in biological and materials science

Both natural and unnatural amino acids, peptides, and proteins are widely recognized as green and sustainable organic chemicals, not only in the field of biological sciences but also in materials science. It has been discovered that artificially designed unnatural peptides and proteins exhibit advanced properties in medical and materials science. In this context, the development of precise chemical modification methods for amino acids and peptides is acknowledged as an important research project in the field of organic synthesis. While a wide variety of modification methods for amino acid residues have been developed to artificially modify peptides and proteins, the representative methods for modifying amino acid residues have traditionally relied on the nucleophilic properties of the functionalities on the residues. In this context, the development of different modification methods using an umpolung-like approach by utilizing the electrophilic nature of amino acid derivatives appears to be very attractive. One of the promising electrophilic amino acid compounds for realizing important modification methods of amino acid derivatives is α,β-dehydroamino acids, which possess an α,β-unsaturated carbonyl structure. This review article summarizes methods for the preparation of α,β-dehydroamino acids derived from natural and unnatural amino acid derivatives. The utilities of α,β-dehydroamino acid derivatives, including peptides and proteins containing dehydroalanine units, in bioconjugations are also discussed.

Cysteine-Specific Multifaceted Bioconjugation of Peptides and Proteins Using 5-Substituted 1,2,3-Triazines

Peptide and protein postmodification have gained significant attention due to their extensive impact on biomolecule engineering and drug discovery, of which cysteine-specific modification strategies are prominent due to their inherent nucleophilicity and low abundance. Herein, the study introduces a novel approach utilizing multifunctional 5-substituted 1,2,3-triazine derivatives to achieve multifaceted bioconjugation targeting cysteine-containing peptides and proteins. On the one hand, this represents an inaugural instance of employing 1,2,3-triazine in biomolecular-specific modification within a physiological solution. On the other hand, as a powerful combination of precision modification and biorthogonality, this strategy allows for the one-pot dual-orthogonal functionalization of biomolecules utilizing the aldehyde group generated simultaneously. 1,2,3-Triazine derivatives with diverse functional groups allow conjugation to peptides or proteins, while bi-triazines enable peptide cyclization and dimerization. The examination of the stability of bi-triazines revealed their potential for reversible peptide modification. This work establishes a comprehensive platform for identifying cysteine-selective modifications, providing new avenues for peptide-based drug development, protein bioconjugation, and chemical biology research.

A Method for Rigorously Selective Capture and Simultaneous Fluorescent Labeling of N-Terminal Glycine Peptides

Although chemical methods for the selective derivatization of amino acid (AA) side chains in peptides and proteins are available, selective N-terminal labeling is challenging, especially for glycine, which has no side chain at the α-carbon position. We report here a double activation at glycine's α-methylene group that allows this AA to be differentiated from the other 19 AAs. A condensation reaction of dibenzoylmethane with glycine results in the formation of an imine, and subsequent tautomerization is followed by intramolecular cyclization, leading to the formation of a fluorescent pyrrole ring. Additionally, the approach exhibits compatibility with AAs possessing reactive side chains. Further, the method allows for selective pull-down assays of N-terminal glycine peptides from mixtures without prior knowledge of the N-terminal peptide distribution.