Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins

Quantitative Protein Labeling in Live Cells by Controlling the Redox State of Encoded Tetrazines

The site-specific attachment of fluorophores, probes, or drugs to proteins in living systems is critical for advancing our understanding of biology and drug development. The site-specific encoding of 1,2,4,5-tetrazine (Tet) residues into target proteins provides the rapid kinetics and stability required for quantitative labeling in living cells, a property that is increasingly desirable as the resolution and specificity of imaging increases. Here, we adapt a common gel-shift assay to create a "PEG Chaser assay" for evaluating labeling completeness in living cells by "chasing" in-cell Tet reactions with an in vitro reaction with a TCO-PEG5000 polymer; then, a gel shift distinguishes proteins that did not react in cells from those that did. We apply this to observe that encoded Tets exist in an equilibrium between oxidized (Tz) and reduced (DHTz) forms in living cells. We further show how a recently developed photooxidation treatment can convert the nonreactive DHTz Tet-protein to the reactive Tz form and enables its rapid, quantitative in-cell labeling. We then develop genetic code expansion machinery for encoding two new Tet ncAAs with different redox potentials and show how the tuning of the Tet redox is a useful variable for controlling the reactivity of Tet ncAAs. Specifically, the new Tet3H ncAA enables photoactivatable labeling and complete protein labeling in living cells in 5 min. This in-depth evaluation of the impact of the intracellular reducing environment on Tet reactivity and the demonstration of controlling Tet redox in living cells expands the utility of encodable Tet in living cells.

Sulfur(IV) Chemistry-Based Peptide and Protein Late-Stage Modification

The development of precise and controllable chemical modification tools for peptides and proteins represents a great challenge in elucidating their structure-activity relationships and regulatory mechanisms, as well as a powerful driver for advancing macromolecular therapeutic strategies. However, current technologies predominantly rely on irreversible covalent labeling or genetic encoding of unnatural amino acids, exhibiting significant limitations in reversible modification, in situ functional regulation, and adaptability to complex physiological environments. In recent years, breakthrough advancements in sulfur(IV) chemistry have provided a paradigm for the late-stage functionalization of peptides and proteins. Through synergistic innovations in sulfur(IV)-based reagent design, intermediate modulation, and bioorthogonal reactions, a more multifaceted modification toolbox has been progressively established, integrating site selectivity, condition responsiveness, and functional rescue. Providing current challenges and future perspectives in this field, this review focuses on sulfur(IV) chemistry-driven strategies for peptide and protein modification, as well as their applications in proximity-labeling strategies and drug delivery/therapeutic interventions.

Reversible Protein Labeling via Genetically Encoded Dithiolane-Containing Amino Acid and Organoarsenic Probes

Conventional protein labeling techniques often rely on irreversible covalent bonds, limiting dynamic control over protein modifications. Here, we present a reversible protein labeling strategy using genetically encoded dithiolane-containing amino acid (dtF) and organoarsenic conjugation chemistry. Using dithiarsolane dicarboxylic acid probe A2, we achieved near-quantitative labeling and ethanedithiol-mediated removal within 1 h at room temperature. A2 exhibited reduced toxicity with a 7-fold higher IC50 compared to arsenoxide, and its fluorescent derivative A2-FB showed no cytotoxicity up to 100 μM, enabling live-cell applications. This is the first demonstration of dithiol-arsenic chemistry at a single amino acid residue, providing a structural alternative to dicysteine motifs. Reversible labeling was validated in purified proteins (sfGFP-Y151dtF and MYO-K99dtF) and live Escherichia coli, offering a versatile tool for dynamic protein modifications and molecular tracking in biological systems.

Linear free energy relationship between reduction potential and photoreduction rate: studies on Drosophila cryptochrome

Cryptochromes are flavin adenine dinucleotide (FAD)-containing blue-light photoreceptors involved in the regulation of the circadian clock and may play a role in magnetic field sensing. The photochemistry of cryptochromes is based on the isoalloxazine moiety, which can be photoreduced and subsequently reoxidized by an electron acceptor such as oxygen, corresponding to a photo-switch between the dark and signaling state. We replaced the FAD cofactor of Drosophila cryptochrome with a series of FAD cofactors modified at the 7α or 8α positions, in order to modulate the chemical properties of the electron acceptor. These modifications were shown to alter the kinetics of the light-dependent reactions. Notably, 7-halogenated FADs form the signaling state more than six times faster compared to the natural FAD cofactor. The more positive reduction potentials as well as the increased intersystem crossing rates due to heavy halogen atoms were identified as reasons for the altered photochemistry. Both parameters show a linear dependence on the reaction kinetics, according to the Hammett relationship. With this knowledge, the photochemistry of cryptochromes may be modified in a defined way without changing its amino acid sequence.

EosinY and copper-catalyzed oxidative [2 + 3] annulation of glycine esters with oxiranes and thiiranes under light free conditions

Herein, we report an oxidative formal [2 + 3] cycloaddition reaction of glycine esters with oxiranes/thiiranes under non-photoredox conditions using the catalytic system consisting of eosin-Y, Cu(OAc)2 and HI. This one-pot protocol delivers an array of oxazolidine-2-carboxylic acids and thiaoxazolidine-2-carboxylic acid derivatives in moderate to good yields under mild reaction conditions. The value of this methodology is demonstrated in preparative scale reactions and downstream synthetic transformations. Based on a series of control experiments, a mechanistic pathway is also proposed.

Site-Selectively Accelerating the Generation of β-Linked Residue Isoaspartate in Proteins

Isoaspartate (isoAsp) is a β-linked residue in proteins spontaneously generated through Asn deamidation or Asp dehydration and significantly affects protein properties. However, the sluggish and site-nonselective generation of isoAsp residues in proteins severely impedes in-depth biological investigations as well as the exploitation of its unique β-linkage features. Herein, we introduce a method that allows site-selective and rapid generation of isoAsp residues in proteins. This method leverages the genetic incorporation of a side-chain-esterified Asp derivative (BnD), which undergoes facile intramolecular arrangement to form the key intermediate, aspartyl succinimide (Suc); subsequent hydrolysis of Suc gives rise to isoAsp as the major product. On native sites of proteins, including Cu/Zn superoxide dismutase and calmodulin, we demonstrate that BnD-mediated isoAsp formation is faster than Asn deamidation generally by three orders of magnitude.

Monitoring SARS-CoV-2 Nsp13 helicase binding activity using expanded genetic code techniques

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 13 (Nsp13) helicase is a multi-functional protein that can unwind dsDNA and dsRNA in an NTP-dependent manner. Given that this viral helicase is essential for viral replication and highly conserved among coronaviruses, a thorough understanding of the helicase's unwinding and binding activity may allow for the development of more effective pan-coronavirus therapeutics. Herein, we describe the use of genetic code expansion techniques to site-specifically incorporate the non-canonical amino acid (ncAA) p-azido-l-phenylalanine (AzF) into Nsp13 for fluorescent labelling of the enzyme with a conjugated Cy5 fluorophore. This Cy5-labelled Nsp13-AzF can then be used in Förster resonance energy transfer (FRET) experiments to investigate the dynamics of enzyme translocation on its substrate during binding and unwinding. Five sites (F81, F90, Y205, Y246, and Y253) were identified for AzF incorporation in Nsp13 and assessed for fluorescent labelling efficiency. The incorporation of AzF was confirmed to not interfere with the unwinding activity of the helicase. Subsequently, FRET-based binding assays were conducted to monitor the binding of Cy5-labelled Nsp13-AzF constructs to a series of fluorescently-labelled nucleic acid substrates in a distance-dependent manner. Overall, this approach not only allows for the direct monitoring of Nsp13's binding activity on its substrate, it may also introduce a novel method to screen for compounds that can inhibit this essential enzymatic activity during viral replication.

A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity

Attaching enzymes to nanostructures has proven useful to the study of enzyme functionality under controlled conditions and has led to new technologies. Often, the utility and interest of enzyme-tethered nanostructures lie in how the enzymatic activity is affected by how the enzymes are arranged in space. Therefore, being able to conjugate enzymes to nanostructures while preserving the enzymatic activity is essential. In this paper, we present a method to conjugate single-stranded DNA to the enzyme urease while maintaining enzymatic activity. We show evidence of successful conjugation and quantify the variables that affect the conjugation yield. We also show that the enzymatic activity is unchanged after conjugation compared to the enzyme in its native state. Finally, we demonstrate the tethering of urease to nanostructures made using DNA origami with high site-specificity. Decorating nanostructures with enzymatically-active urease may prove to be useful in studying, or even utilizing, the functionality of urease in disciplines ranging from biotechnology to soft-matter physics. The techniques we present in this paper will enable researchers across these fields to modify enzymes without disrupting their functionality, thus allowing for more insightful studies into their behavior and utility.

A modular click ligand-directed approach to label endogenous dopamine D1 receptors in live cells

Most luminescence-based technologies to determine the pharmacological properties of G Protein-Coupled Receptors (GPCRs) rely on the overexpression of genetically modified receptors. However, it is essential to develop approaches allowing the specific labelling of native receptors. Here we report an innovative approach based on the use of molecular modules to build fluorescent ligand-directed probes that can label aminergic GPCRs. Such probes are readily prepared with a click reaction between a ligand that may include nucleophilic groups and a fluorescent electrophilic linker. The rapidity of click reaction before receptor labelling prevents a side reaction between the nucleophilic ligand and the electrophile. This approach allowed us to label D1 receptor in transfected cells and native receptors in neural cell lines, leaving the receptor fully functional. This approach will pave the way to develop new reagents and assays with which to monitor endogenous GPCRs' distribution, trafficking, activity or binding properties in their native environment.

Advances in the chemical synthesis of human proteoforms

Access to structurally-defined human proteoforms is essential to the biochemical studies on human health and medicine. Chemical protein synthesis provides a bottom-up and atomic-resolution approach for the preparation of homogeneous proteoforms bearing any number of post-translational modifications of any structure, at any position, and in any combination. In this review, we summarize the development of chemical protein synthesis, focusing on the recent advances in synthetic methods, product characterizations, and biomedical applications. By analyzing the chemical protein synthesis studies on human proteoforms reported to date, this review demonstrates the significant methodological improvements that have taken place in the field of human proteoform synthesis, especially in the last decade. Our analysis shows that although further method development is needed, all the human proteoforms could be within reach in a cost-effective manner through a divide-and-conquer chemical protein synthesis strategy. The synthetic proteoforms have been increasingly used to support biomedical research, including spatial-temporal studies and interaction network analysis, activity quantification and mechanism elucidation, and the development and evaluation of diagnostics and therapeutics.

Design and application of a fluorescent probe for imaging of endogenous Bruton's tyrosine kinase with preserved enzymatic activity

Fluorophore integration into proteins within living cells is essential for exploring proteins in their natural environment. Bruton's tyrosine kinase (BTK), is a validated oncology target and is crucial for B cell proliferation and activation. Developing BTK-labelling probes is key to understand BTK's dynamic signalling pathway. In this work, we aimed to develop a novel fluorescent labelling probe for endogenous BTK imaging while preserving its enzymatic activity. Evobrutinib, a second-generation BTK inhibitor with high selectivity, was chosen as the scaffold. We designed two probes, Evo-1 and Evo-2, with a BODIPY fluorescent group, guided by molecular modelling. The synthesis was achieved using optimised Suzuki-Miyaura cross-coupling and amide coupling reactions. Biochemical assays confirmed covalent binding to Cys481 of BTK while preserving its enzymatic activity. Labelling of endogenous BTK with Evo-2 with reduced off-target effects in Ramos cells was validated in cellular assays. The dynamic signalling pathway of BTK in its native environment was investigated by confocal microscopy with Evo-2. This methodology is a valuable asset in the chemical biology toolbox for studying protein dynamics and interactions in real time without interfering with the protein activity.

One-pot dual protein labeling for simultaneous mechanical and fluorescent readouts in optical tweezers

Optical tweezers are widely used in the study of biological macromolecules but are limited by their one-directional probing capability, potentially missing critical conformational changes. Combining fluorescence microscopy with optical tweezers, employing Förster resonance energy transfer (FRET) pairs, addresses this issue. When integrating fluorescence microscopy with optical tweezers, orthogonal protein conjugation methods are needed to enable simultaneous, site-specific attachment of fluorophores and DNA handles, commonly used to apply force to molecules of interest. In this study, we utilized commercially available reagents for dual site-specific labeling of the homodimeric heat shock protein 90 (Hsp90) using thiol-maleimide and inverse electron demand Diels-Alder cycloaddition (IEDDAC) bioorthogonal reactions. In a one-pot approach, Hsp90 modified with a cysteine mutation and the non-canonical amino acid cyclopropene-L-lysine (CpK) was labeled with the FRET pair maleimide-Atto 550 and maleimide-Atto 647N, alongside single-stranded methyltetrazine-modified DNA oligonucleotide. Optical tweezers experiments with this labeled Hsp90 construct revealed structural transitions consistent with previous studies, validating the approach. Fluorescence measurements confirmed the proximity of FRET pairs in the N-terminally closed state of Hsp90 in this experimental setup. This integrative method provides a powerful tool for probing complex protein conformational dynamics beyond the limitations of traditional optical tweezers.

Substrate recognition by a peptide-aminoacyl-tRNA ligase

The continuing discovery of new peptide-aminoacyl-tRNA ligases (PEARLs) has unveiled a diverse array of enzymes with the unique potential to append amino acids to the C terminus of substrate peptides in an aminoacyl-tRNA-dependent manner. To date, PEARLs have been reported that can conjugate Cys, Ala, Trp, Gly, Leu, Asn, and Thr residues, but the basis of peptide substrate and aminoacyl-tRNA recognition is not known. Cell-free expression (CFE) has emerged as a powerful tool to rapidly assay activity of substrate variants, and we used the technique in this study to investigate the peptide substrate specificity of the PEARL [Formula: see text]. This enzyme that adds Trp was discovered previously during genome mining for ribosomally synthesized and posttranslational modified peptides (RiPPs). The enzyme is remarkably tolerant of changes to the C-terminal amino acid of the peptide substrate, and truncation and replacement experiments suggest a minimal sequence requirement. An AlphaFold3 model provided insights into binding interactions of the substrate peptide BhaA-Ala to [Formula: see text] and also generated predictions for tRNA, ATP, and Mg2+ binding modes that were tested by site-directed mutagenesis. The data suggest that several highly conserved residues in PEARLs recognize the 3'-CCA sequence present in all tRNAs. The minimal sequence required for Trp incorporation by [Formula: see text] was employed as a protein tag for C-terminal labeling of eGFP, lysozyme, and MBP with Trp and 5-Br-Trp.

Metal-Mediated Protein Engineering within Live Cells

Metal mediated several organic reactions are known which can be used inside the cellular medium for protein modifications, eventually for targeting diseases. Indeed, due to their ease of handling, rapid solubility, and effective cell penetration, metals are superior than any other competitor as a stimulus/mediator in organic reactions relevant with protein modifications. Metal mediated most effective reactions as a chemical biology tool are Cu(I)-catalyzed azide-alkyne cycloaddition(CuAAC)/click reactions or Pd mediated multiple chemical reactions for intra/extra cellular protein modifications etc. A few examples of Au(III), Ru(III) are also known. Among these, the click reaction has high potential for the management of biomolecules within cells, and thus this methodology is adopted broadly in chemistry, biology towards therapeutic applications in pharmacology. Fast kinetics in aqueous medium at ambient to normal temperature with specificity between precursors (e. g., azide and alkyne for click reactions which are bio-orthogonal to cells) are essential aspects behind the success of metal mediated intracellular reactions. This review dealt with specifically metal mediated protein modifications within live cells, the achievements and challenges.

Design strategies for tetrazine fluorogenic probes for bioorthogonal imaging

Tetrazine fluorogenic probes play a critical role in bioorthogonal chemistry, selectively activating fluorescence upon reaction to enhance precision in imaging and sensing within complex biological environments. Recent structural innovations-such as varied fluorophore choices, spacer optimization, and direct tetrazine integration within a fluorophore's π-conjugated system-have expanded their spectral range from visible to NIR, enhancing adaptability across various applications. This review examines advancements in the rational design and synthesis of these probes. We examine key fluorogenic mechanisms, such as energy transfer, internal conversion, and electron/charge transfer, that significantly influence fluorescence activation. We also highlight representative applications in live-cell imaging, super-resolution microscopy, and therapeutic monitoring, underscoring the expanding role of tetrazine probes in biomedical research and diagnostics. Collectively, these insights provide a strategic foundation for developing next-generation tetrazine probes with tailored properties to address evolving diagnostic and therapeutic challenges.

Synthesis of Fluorescent Dibenzofuran α-Amino Acids: Conformationally Rigid Analogues of Tyrosine

We report two synthetic strategies for the preparation of dibenzofuran α-amino acids, expanding the structural toolbox of fluorescent probes. The strategies involved dibenzofuran synthesis via a Pd(II)-catalyzed C-O cyclization, alongside an efficient Negishi coupling approach for faster access to analogues. These rigid tyrosine mimics possess enhanced fluorescent properties compared to proteinogenic amino acids as demonstrated by application of the lead compound as a FRET donor for monitoring peptide hydrolysis by a serine protease.

Chemical tools for probing histidine modifications

Histidine is a unique amino acid with critical roles in protein structure and function, ranging from metal ion binding to enzyme catalysis. Histidine residues in proteins also undergo diverse posttranslational modifications, including methylation, phosphorylation and hydroxylation, by various enzymes, some of them being only recently identified and characterised. In this review, we describe the development of chemical tools for understanding the role of histidine residues in chemical and biological systems. We spotlight the application of histidine analogues in probing biomedically important posttranslational modifications of histidine residues in proteins, and we highlight novel bioconjugation methods that enable chemoselective modifications of histidine residues in peptides and proteins.

Optogenetics with Atomic Precision─A Comprehensive Review of Optical Control of Protein Function through Genetic Code Expansion

Conditional control of protein activity is important in order to elucidate the particular functions and interactions of proteins, their regulators, and their substrates, as well as their impact on the behavior of a cell or organism. Optical control provides a perhaps optimal means of introducing spatiotemporal control over protein function as it allows for tunable, rapid, and noninvasive activation of protein activity in its native environment. One method of introducing optical control over protein activity is through the introduction of photocaged and photoswitchable noncanonical amino acids (ncAAs) through genetic code expansion in cells and animals. Genetic incorporation of photoactive ncAAs at key residues in a protein provides a tool for optical activation, or sometimes deactivation, of protein activity. Importantly, the incorporation site can typically be rationally selected based on structural, mechanistic, or computational information. In this review, we comprehensively summarize the applications of photocaged lysine, tyrosine, cysteine, serine, histidine, glutamate, and aspartate derivatives, as well as photoswitchable phenylalanine analogues. The extensive and diverse list of proteins that have been placed under optical control demonstrates the broad applicability of this methodology.

Directed Evolution and Unusual Protonation Mechanism of Pyridoxal Radical C-C Coupling Enzymes for the Enantiodivergent Photobiocatalytic Synthesis of Noncanonical Amino Acids

Visible light-driven pyridoxal radical biocatalysis has emerged as a new strategy for the stereoselective synthesis of valuable noncanonical amino acids in a protecting-group-free fashion. In our previously developed dehydroxylative C-C coupling using engineered PLP-dependent tryptophan synthases, an enzyme-controlled unusual α-stereochemistry reversal and pH-controlled enantiopreference were observed. Herein, through high-throughput photobiocatalysis, we evolved a set of stereochemically complementary PLP radical enzymes, allowing the synthesis of both l- and d-amino acids with enhanced enantiocontrol across a broad pH window. These newly engineered l- and d-amino acid synthases permitted the use of a broad range of organoboron substrates, including boronates, trifluoroborates, and boronic acids, with excellent efficiency. Mechanistic studies unveiled unexpected PLP racemase activity with our earlier PLP enzyme variants. This promiscuous racemase activity was abolished in our evolved amino acid synthases, shedding light on the origin of enhanced enantiocontrol. Further mechanistic investigations suggest a switch of proton donor to account for the stereoinvertive formation of d-amino acids, highlighting an unusual stereoinversion mechanism that is rare in conventional two-electron PLP enzymology.

Investigating protein degradability through site-specific ubiquitin ligase recruitment

We report targeted protein degradation through the site-specific recruitment of native ubiquitin ligases to a protein of interest via conjugation of E3 ligase ligands. Direct comparison of degradation ability of proteins displaying the corresponding bioconjugation handle at different regions of protein surfaces was explored. We demonstrate the benefit of proximal lysine residues and investigate flexibility in linker length for the design of optimal degraders. Two proteins without known small molecule ligands, EGFP and DUSP6, were differentially degraded when modified at different locations on their protein surfaces. Further, the cereblon-mediated degradation of the known PROTAC target ERRα was improved through the recruitment of the E3 ligase to regions different from the known ligand binding site. This new methodology will provide insight into overall protein degradability, even in the absence of a known small molecule ligand and inform the process of new ligand and PROTAC development to achieve optimal protein degradation. Furthermore, this approach represents a new, small molecule-based conditional OFF switch of protein function with complete genetic specificity. Importantly, the protein of interest is only modified with a minimal surface modification (<200 Da) and does not require any protein domain fusions.

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.

Genetic Code Expansion: Recent Developments and Emerging Applications

The concept of genetic code expansion (GCE) has revolutionized the field of chemical and synthetic biology, enabling the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins, thus opening new avenues in research and applications across biology and medicine. In this review, we cover the principles of GCE, including the optimization of the aminoacyl-tRNA synthetase (aaRS)/tRNA system and the advancements in translation system engineering. Notable developments include the refinement of aaRS/tRNA pairs, enhancements in screening methods, and the biosynthesis of noncanonical amino acids. The applications of GCE technology span from synthetic biology, where it facilitates gene expression regulation and protein engineering, to medicine, with promising approaches in drug development, vaccine production, and gene editing. The review concludes with a perspective on the future of GCE, underscoring its potential to further expand the toolkit of biology and medicine. Through this comprehensive review, we aim to provide a detailed overview of the current state of GCE technology, its challenges, opportunities, and the frontier it represents in the expansion of the genetic code for novel biological research and therapeutic applications.

Toolbox of Clickable Benzylguanines for Labeling of HoxB8-Derived Macrophages via SNAP-Tag and Bioorthogonal Chemistry

Inflammation is a dynamic process which importantly involves migration of immune cells. Understanding the onset, acute phase and resolution of inflammation is greatly facilitated by their in vivo imaging. However, immune cells are sensitive, difficult to genetically manipulate and prone to changes in response to contact, hindering the application of well-established cell labeling methods. We generated the first reported SNAP-tag expressing conditionally immortalized early hematopoietic progenitor cells (ER-HoxB8) and synthesized benzylguanine (BG) analogs with bioorthogonal groups for SNAP-tag mediated cell surface labeling. Comparative investigation of SNAP-tag positive HeLa cells, ER-HoxB8 progenitor cells and ER-HoxB8-derived macrophages as well as neutrophiles revealed remarkable differences in labeling depending on the bioorthogonal group and fluorescent reporter used. HeLa cells and ER-HoxB8 progenitor cells were efficiently labeled with BG analogs bearing an azide and a dioxolan-fused trans-cyclooctene (dTCO). When we differentiated ER-HoxB8 cells into macrophages, labeling was less bright due to lower SNAP-tag expression and only the tetrazine ligation of dTCO proved suitable for cell-type specific labeling. These results show that exploring different reactions and bioorthogonal groups is important to address the challenge of labeling differentiated immune cells. Combining the SNAP-tag with click chemistry provides a modular approach for cell-specific labeling and the combination of SNAP-tag and dTCO presents an improved system for labeling ER-HoxB8-derived macrophages.

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.

N-Acyl-N-alkyl/aryl Sulfonamide Chemistry Assisted by Proximity for Modification and Covalent Inhibition of Endogenous Proteins in Living Systems

Selective chemical modification of endogenous proteins in living systems with synthetic small molecular probes is a central challenge in chemical biology. Such modification has a variety of applications important for biological and pharmaceutical research, including protein visualization, protein functionalization, proteome-wide profiling of enzyme activity, and irreversible inhibition of protein activity. Traditional chemistry for selective protein modification in cells largely relies on the high nucleophilicity of cysteine residues to ensure target-selectivity and site-specificity of modification. More recently, lysine residues, which are more abundant on protein surfaces, have attracted attention for the covalent modification of proteins. However, it has been difficult to efficiently modify the ε-amino groups of lysine side-chains, which are mostly (∼99.9%) protonated and thus exhibit low nucleophilicity at physiological pH. Our group revealed that N-acyl-N-alkyl sulfonamide (NASA) moieties can rapidly and efficiently acylate noncatalytic (i.e., less reactive) lysine residues in proteins by leveraging a reaction acceleration effect via proximity. The excellent reaction kinetics and selectivity for lysine of the NASA chemistry enable covalent modification of natural intracellular and cell-surface proteins, which is intractable using conventional chemistries. Moreover, recently developed N-acyl-N-aryl sulfonamide (ArNASA) scaffolds overcome some problems faced by the first-generation NASA compounds. In this Account, we summarize our recent works in the development of NASA/ArNASA chemistry and several applications reported by ourselves and other groups. First, we characterize the basic properties of NASA/ArNASA chemistry, including the labeling kinetics, amino acid preference, and biocompatibility, and compare this approach with other ligand-directed chemistries. This section also describes the principles of nucleophilic organocatalyst-mediated protein acylation, another important protein labeling strategy using the NASA reactive group, and its application to neurotransmitter receptor labeling in brain slices. Second, we highlight various recent examples of protein functionalization using NASA/ArNASA chemistry, such as visualization of membrane proteins including therapeutically important G-protein coupled receptors, gel-based ligand screening assays, photochemical control of protein activity, and targeted protein degradation. Third, we survey covalent inhibition of proteins by NASA/ArNASA-based lysine-targeting. The unprecedented reactivity of NASA/ArNASA toward lysine allows highly potent, irreversible inhibition of several drug targets for the treatment of cancer, including HSP90, HDM2-p53 protein-protein interaction, and a Bruton's tyrosine kinase mutant that has developed resistance to cysteine-targeted covalent-binding drugs. Finally, current limitations of, and future perspectives on, this research field are discussed. The new chemical labeling techniques offered by NASA/ArNASA chemistry and its derivatives create a valuable molecular toolbox for studying numerous biomolecules in living cells and even in vivo.

Molecular Matchmakers: Bioconjugation Techniques Enhance Prodrug Potency for Immunotherapy

Cancer patients suffer greatly from the severe off-target side effects of small molecule drugs, chemotherapy, and radiotherapy─therapies that offer little protection following remission. Engineered immunotherapies─including cytokines, immune checkpoint blockade, monoclonal antibodies, and CAR-T cells─provide better targeting and future tumor growth prevention. Still, issues such as ineffective activation, immunogenicity, and off-target effects remain primary concerns. "Prodrug" therapies─classified as therapies administered as inactive and then selectively activated to control the time and area of release─hold significant promise in overcoming these concerns. Bioconjugation techniques (e.g., natural linker conjugation, bioorthogonal reactions, and noncanonical amino acid incorporation) enable the rapid and homogeneous synthesis of prodrugs and offer selective loading of immunotherapeutic agents to carrier molecules and protecting groups to prevent off-target effects after administration. Several prodrug activation mechanisms have been highlighted for cancer therapeutics, including endogenous activation by hypoxic or acidic conditions common in tumors, exogenous activation by targeted bioorthogonal cleavage, or stimuli-responsive light activation, and dual-stimuli activation, which adds specificity by combining these mechanisms. This review will explore modern prodrug conjugation and activation options, focusing on how these strategies can enhance immunotherapy responses and improve patient outcomes. We will also discuss the implications of computational methodology for therapy design and recommend procedures to determine how and where to conjugate carrier systems and "prodrug" groups onto therapeutic agents to enhance the safety and control of these delivery platforms.

Investigation of protein post-translational modifications with site-specifically incorporated non-canonical amino acids

Despite the important functions of protein post-translational modifications (PTMs) in numerous cellular processes, understanding the biological roles of PTMs remains quite challenging. Here, we summarize our efforts in recent years to incorporate a variety of non-canonical amino acids (ncAAs) to study the biological functions of protein PTMs in mammalian cells, with a focus on the use of ncAA tools to probe the biological functions of various protein PTMs. We design length-tunable lipidation mimics for studying lipidation function and designing protein drugs. We highlight the use of genetically encoded lysine aminoacylations as chemical baits to identify aminoacylated lysine ubiquitination. Finally, we discuss the use of genetically encoded electron-rich Trp derivatives to design binding affinity-enhancing histone methylations readers.

Advances in Natural-Product-Based Fluorescent Agents and Synthetic Analogues for Analytical and Biomedical Applications

Fluorescence is a remarkable property exhibited by many chemical compounds and biomolecules. Fluorescence has revolutionized analytical and biomedical sciences due to its wide-ranging applications in analytical and diagnostic tools of biological and environmental importance. Fluorescent molecules are frequently employed in drug delivery, optical sensing, cellular imaging, and biomarker discovery. Cancer is a global challenge and fluorescence agents can function as diagnostic as well as monitoring tools, both during early tumor progression and treatment monitoring. Many fluorescent compounds can be found in their natural form, but recent developments in synthetic chemistry and molecular biology have allowed us to synthesize and tune fluorescent molecules that would not otherwise exist in nature. Naturally derived fluorescent compounds are generally more biocompatible and environmentally friendly. They can also be modified in cost-effective and target-specific ways with the help of synthetic tools. Understanding their unique chemical structures and photophysical properties is key to harnessing their full potential in biomedical and analytical research. As drug discovery efforts require the rigorous characterization of pharmacokinetics and pharmacodynamics, fluorescence-based detection accelerates the understanding of drug interactions via in vitro and in vivo assays. Herein, we provide a review of natural products and synthetic analogs that exhibit fluorescence properties and can be used as probes, detailing their photophysical properties. We have also provided some insights into the relationships between chemical structures and fluorescent properties. Finally, we have discussed the applications of fluorescent compounds in biomedical science, mainly in the study of tumor and cancer cells and analytical research, highlighting their pivotal role in advancing drug delivery, biomarkers, cell imaging, biosensing technologies, and as targeting ligands in the diagnosis of tumors.

Real-Time Observation of Clickable Cyanotoxin Synthesis in Bloom-Forming Cyanobacteria Microcystis aeruginosa and Planktothrix agardhii

Recently, the use of click chemistry for localization of chemically modified cyanopeptides has been introduced, i.e., taking advantage of promiscuous adenylation (A) domains in non-ribosomal peptide synthesis (NRPS), allowing for the incorporation of clickable non-natural amino acids (non-AAs) into their peptide products. In this study, time-lapse experiments have been performed using pulsed feeding of three different non-AAs in order to observe the synthesis or decline of azide- or alkyne-modified microcystins (MCs) or anabaenopeptins (APs). The cyanobacteria Microcystis aeruginosa and Planktothrix agardhii were grown under maximum growth rate conditions (r = 0.35-0.6 and 0.2-0.4 (day-1), respectively) in the presence of non-AAs for 12-168 h. The decline of the azide- or alkyne-modified MC or AP was observed via pulse-feeding. In general, the increase in clickable MC/AP in peptide content reached a plateau after 24-48 h and was related to growth rate, i.e., faster-growing cells also produced more clickable MC/AP. Overall, the proportion of clickable MC/AP in the intracellular fraction correlated with the proportion observed in the dissolved fraction. Conversely, the overall linear decrease in clickable MC/AP points to a rather constant decline via dilution by growth instead of a regulated or induced release in the course of the synthesis process.

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.

Recent advances in the expanding genetic code

For over a billion years, the central dogma of biology has been limited largely to 20 canonical amino acids with relatively simple functionalities. The ability to rationally add new building blocks to the genetic code has enabled the site-specific incorporation of hundreds of noncanonical amino acids (ncAAs) with novel properties into proteins in living organisms. Recent technological advances have enabled high level mammalian expression of proteins containing ncAAs, the use of unique codons to direct ncAA incorporation, extension of this methodology to a range of eukaryotic organisms, and the ability to encode building blocks beyond α-amino acids. These ncAAs have been used to study and control proteins in their native cellular context and to engineer enzymes and biotherapeutics with improved or novel properties. Herein we discuss recent developments in the field and potential future research directions.

Noncanonical Amino Acid Tools and Their Application to Membrane Protein Studies

Methods rooted in chemical biology have contributed significantly to studies of integral membrane proteins. One recent key approach has been the application of genetic code expansion (GCE), which enables the site-specific incorporation of noncanonical amino acids (ncAAs) with defined chemical properties into proteins. Efficient GCE is challenging, especially for membrane proteins, which have specialized biogenesis and cell trafficking machinery and tend to be expressed at low levels in cell membranes. Many eukaryotic membrane proteins cannot be expressed functionally in E. coli and are most effectively studied in mammalian cell culture systems. Recent advances have facilitated broader applications of GCE for studies of membrane proteins. First, AARS/tRNA pairs have been engineered to function efficiently in mammalian cells. Second, bioorthogonal chemical reactions, including cell-friendly copper-free "click" chemistry, have enabled linkage of small-molecule probes such as fluorophores to membrane proteins in live cells. Finally, in concert with advances in GCE methodology, the variety of available ncAAs has increased dramatically, thus enabling the investigation of protein structure and dynamics by multidisciplinary biochemical and biophysical approaches. These developments are reviewed in the historical framework of the development of GCE technology with a focus on applications to studies of membrane proteins.

SIRT3 differentially regulates lysine benzoylation from SIRT2 in mammalian cells

Lysine benzoylation (Kbz), a new type of protein post-translational modification (PTM) we discovered, has garnered significant attention. While we initially identified SIRT2 as a debenzoylase in mammalian cells, recent findings suggest its exclusivity may be questioned. However, other debenzoylases in mammalian cells remain underexplored. Here, our study reveals SIRT3 as an additional debenzoylase. Through quantitative analysis, we identified 1,075 Kbz sites in mammalian cells, with 44 specifically mediated by SIRT3 and 66 influenced by SIRT2. Notably, SIRT3 and SIRT2 regulate distinct Kbz substrates, indicating involvement in different cellular processes. Functional investigations demonstrated SIRT3's regulation of benzoylated protein peptidyl-prolyl cis-trans isomerase F (PPIF), where K73bz and K197bz markedly diminished interactions with the tumor suppressor p53. Additionally, K978bz on ATP-citrate lyase (ACLY) notably inhibited its enzymatic activity. This study not only identifies a debenzoylase and its Kbz substrates but also enhances our understanding of Kbz's biological functions.

Palladium-Mediated Bioorthogonal System for Prodrug Activation of N-Benzylbenzamide-Containing Tubulin Polymerization Inhibitors for the Treatment of Solid Tumors

Bioorthogonal cleavage reactions have been developed as an intriguing strategy to enhance the safety of chemotherapeutics. Aiming to reduce the toxicity and improve the targeted release properties of the colchicine binding site inhibitors (CBSIs) based on previous work, a series of biologically inert prodrugs were further designed and synthesized through a bioorthogonal prodrug strategy. The therapeutic effects of prodrugs could be "turned-on" once combined with palladium resins. Particularly, prodrug 2b was 68.3-fold less cytotoxic compared to the parent compound, while its cytotoxicity was recovered in situ in the presence of palladium resins. Mechanism studies confirmed that 2b inhibited cell growth in the same manner as CBSIs. More importantly, in vivo efficacy studies demonstrated the efficient activation of 2b by palladium resins, resulting in significant inhibition of tumor growth (63.2%). These results suggest that prodrug 2b with improved safety and targeted release property catalyzed by a Pd-mediated bioorthogonal cleavage reaction deserves further investigation.

Investigating Protein Degradability through Site-Specific Ubiquitin Ligase Recruitment

We report targeted protein degradation through the site-specific recruitment of native ubiquitin ligases to a protein of interest via conjugation of E3 ligase ligands. Direct comparison of degradation ability of proteins displaying the corresponding bioconjugation handle at different regions of protein surfaces was explored. We demonstrate the benefit of proximal lysine residues and investigate flexibility in linker length for the design of optimal degraders. Two proteins without known small molecule ligands, EGFP and DUSP6, were differentially degraded when modified at different locations on their protein surfaces. Further, the cereblon-mediated degradation of the known PROTAC target ERRα was improved through the recruitment of the E3 ligase to regions different from the known ligand binding site. This new methodology will provide insight into overall protein degradability, even in the absence of a known small molecule ligand and inform the process of new ligand and PROTAC development to achieve optimal protein degradation. Furthermore, this approach represents a new, small molecule-based conditional OFF switch of protein function with complete genetic specificity. Importantly, the protein of interest is only modified with a minimal surface modification (< 200 Da) and does not require any protein domain fusions.

Genetic Code Expansion Approaches to Decipher the Ubiquitin Code

The covalent attachment of Ub (ubiquitin) to target proteins (ubiquitylation) represents one of the most versatile PTMs (post-translational modifications) in eukaryotic cells. Substrate modifications range from a single Ub moiety being attached to a target protein to complex Ub chains that can also contain Ubls (Ub-like proteins). Ubiquitylation plays pivotal roles in most aspects of eukaryotic biology, and cells dedicate an orchestrated arsenal of enzymes to install, translate, and reverse these modifications. The entirety of this complex system is coined the Ub code. Deciphering the Ub code is challenging due to the difficulty in reconstituting enzymatic machineries and generating defined Ub/Ubl-protein conjugates. This Review provides a comprehensive overview of recent advances in using GCE (genetic code expansion) techniques to study the Ub code. We highlight strategies to site-specifically ubiquitylate target proteins and discuss their advantages and disadvantages, as well as their various applications. Additionally, we review the potential of small chemical PTMs targeting Ub/Ubls and present GCE-based approaches to study this additional layer of complexity. Furthermore, we explore methods that rely on GCE to develop tools to probe interactors of the Ub system and offer insights into how future GCE-based tools could help unravel the complexity of the Ub code.

Fast and Selective Cysteine Conjugation Using para-Quinone Methides

An efficient and selective method for cysteine conjugation utilizing para-quinone methides (p-QMs) was developed. p-QM labeling exhibits high specificity toward the cysteine residue, as evidenced by its reactivity with various amino acid derivatives, peptides, and proteins. Notably, the p-QM-cysteine reactions display robust kinetics with rate constants up to 1.67 × 104 M-1·s-1. Furthermore, p-QM conjugation enables us to attach a fluorescent probe to a HER2 nanobody, resulting in selective labeling of HER2-positive SK-BR-3 cells.

Biosynthesis of Halogenated Tryptophans for Protein Engineering Using Genetic Code Expansion

Genetic Code Expansion technology offers significant potential in incorporating noncanonical amino acids into proteins at precise locations, allowing for the modulation of protein structures and functions. However, this technology is often limited by the need for costly and challenging-to-synthesize external noncanonical amino acid sources. In this study, we address this limitation by developing autonomous cells capable of biosynthesizing halogenated tryptophan derivatives and introducing them into proteins using Genetic Code Expansion technology. By utilizing inexpensive halide salts and different halogenases, we successfully achieve the selective biosynthesis of 6-chloro-tryptophan, 7-chloro-tryptophan, 6-bromo-tryptophan, and 7-bromo-tryptophan. These derivatives are introduced at specific positions with corresponding bioorthogonal aminoacyl-tRNA synthetase/tRNA pairs in response to the amber codon. Following optimization, we demonstrate the robust expression of proteins containing halogenated tryptophan residues in cells with the ability to biosynthesize these tryptophan derivatives. This study establishes a versatile platform for engineering proteins with various halogenated tryptophans.

Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming

Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.

Visible-Light-Driven Synthesis of N-Alkyl α-Amino Acid Derivatives from Unactivated Alkyl Bromides and In Situ Generated Imines

One-pot, multicomponent reactions are known for their green and efficient nature. We report a novel three-component reaction of alkyl amines, alkyl glyoxylates, and unactivated alkyl bromides under visible-light-induced palladium catalysis, yielding N-alkyl unnatural α-amino acid derivatives. This method offers mild conditions, broad substrate scope, and excellent functional group tolerance without requiring stoichiometric organometallic reagents. The approach has promising applications in protein engineering and drug discovery.

Selective fluorescent labeling of cellular proteins and its biological applications

Proteins, which are ubiquitous in cells and critical to almost all cellular functions, are indispensable for life. Fluorescence imaging of proteins is key to understanding their functions within their native milieu, as it provides insights into protein localization, dynamics, and trafficking in living systems. Consequently, the selective labeling of target proteins with fluorophores has emerged as a highly active research area, encompassing bioorganic chemistry, chemical biology, and cell biology. Various methods for selectively labeling proteins with fluorophores in cells and tissues have been established and are continually being developed to visualize and characterize proteins. This review highlights research findings reported since 2018, with a focus on the selective labeling of cellular proteins with small organic fluorophores and their biological applications in studying protein-associated biological events. We also discuss the strengths and weaknesses of each labeling approach for their utility in living systems.

Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids

Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.

Genetic Code Expansion in Shewanella oneidensis MR-1 Allows Site-Specific Incorporation of Bioorthogonal Functional Groups into a c-Type Cytochrome

Genetic code expansion has enabled cellular synthesis of proteins containing unique chemical functional groups to allow the understanding and modulation of biological systems and engineer new biotechnology. Here, we report the development of efficient methods for site-specific incorporation of structurally diverse noncanonical amino acids (ncAAs) into proteins expressed in the electroactive bacterium Shewanella oneidensis MR-1. We demonstrate that the biosynthetic machinery for ncAA incorporation is compatible and orthogonal to the endogenous pathways of S. oneidensis MR-1 for protein synthesis, maturation of c-type cytochromes, and protein secretion. This allowed the efficient synthesis of a c-type cytochrome, MtrC, containing site-specifically incorporated ncAA in S. oneidensis MR-1 cells. We demonstrate that site-specific replacement of surface residues in MtrC with ncAAs does not influence its three-dimensional structure and redox properties. We also demonstrate that site-specifically incorporated bioorthogonal functional groups could be used for efficient site-selective labeling of MtrC with fluorophores. These synthetic biology developments pave the way to expand the chemical repertoire of designer proteins expressed in S. oneidensis MR-1.

Sortase-Mediated Site-Specific Conjugation to Prepare Fluorine-18-Labeled Nanobodies

Single-domain antibodies, or nanobodies (Nbs), are promising biomolecules for use in molecular imaging due to their excellent affinity, specificity, and fast clearance from the blood. Given their short blood half-life, pairing Nbs with short-lived imaging radioisotopes is desirable. Because fluorine-18 (18F) is routinely used for clinical imaging, it is an attractive radioisotope for Nbs. We report a novel sortase-based, site-specific 18F-labeling method applied to three nanobodies. Labeled nanobodies were synthesized either by a two-step indirect radiolabeling method in one pot or by a one-step direct labeling method using a sortase-mediated conjugation of either the radiolabeled chelator (H-GGGK((±)-Al[18F]FH3RESCA)-NH2) or the unlabeled chelator (H-GGGK((±)-H3RESCA)-NH2) followed by labeling with Al[18F]F, respectively. The overall radiochemical yields were 15-43% (n = 22, decay-corrected) in 70 min (indirect labeling) and 23-58% (n = 12, decay-corrected) in 50 min (direct labeling). The radiochemical purities of the labeled nanobodies prepared by both methods were >98% with a specific activity of 400-600 Ci/mmol (n = 22) for each of the three Nbs tested and exhibited excellent stability profiles under physiological conditions. This simple, site-specific, reproducible, and generalizable 18F-labeling method to prepare nanobodies (Nb-Al[18F]F-RESCA) or other low molecular weight biomolecules can easily be adopted in various settings for preclinical and clinical studies.

A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins

Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and nitration. Despite the biological and physiological importance of Tyr-PTMs, our current understanding of the mechanisms by which these modifications contribute to human health and disease remains incomplete. This knowledge gap arises from the absence of natural amino acids that can mimic these PTMs and the lack of synthetic tools for the site-specific introduction of aromatic PTMs into proteins. Herein, we describe a facile method for the site-specific chemical installation of aromatic PTMs into proteins through palladium-mediated S-C(sp2) bond formation under ambient conditions. We demonstrate the incorporation of novel PTMs such as Tyr-nitration and phosphorylation analogs to synthetic and recombinantly expressed Cys-containing peptides and proteins within minutes and in good yields. To demonstrate the versatility of our approach, we employed it to prepare 10 site-specifically modified proteins, including nitrated and phosphorylated analogs of Myc and Max proteins. Furthermore, we prepared a focused library of site-specifically nitrated and phosphorylated α-synuclein (α-Syn) protein, which enabled, for the first time, deciphering the role of these competing modifications in regulating α-Syn conformation aggregation in vitro. Our strategy offers advantages over synthetic or semisynthetic approaches, as it enables rapid and selective transfer of rarely explored aromatic PTMs into recombinant proteins, thus facilitating the generation of novel libraries of homogeneous posttranslationally modified proteins for biomarker discovery, mechanistic studies, and drug discovery.

DNA-modulated dimerization and oligomerization of cell membrane receptors

DNA-based nanostructures and nanodevices have recently been employed for a broad range of applications in modulating the assemblies and interaction patterns of different cell membrane receptors. These versatile nanodevices can be rationally designed with modular structures, easily programmed and tweaked such that they may act as smart chemical biology and cell biology tools to reveal insights into complicated cellular signaling processes. Their outstanding in vitro and cellular features have also begun to be further validated for some in vivo applications and demonstrated their great biomedical potential. In this review, we will highlight some key current advances in the molecular engineering and biological applications of DNA-based functional nanodevices, with a focus on how these tools have been used to respond and modulate membrane receptor dimerizations and/or oligomerizations, as a way to control cellular signaling processes. Some current challenges and future directions to further develop and apply these DNA nanodevices will also be discussed.

Designing Michaelases: exploration of novel protein scaffolds for iminium biocatalysis

Biocatalysis is becoming a powerful and sustainable alternative for asymmetric catalysis. However, enzymes are often restricted to metabolic and less complex reactivities. This can be addressed by protein engineering, such as incorporating new-to-nature functional groups into proteins through the so-called expansion of the genetic code to produce artificial enzymes. Selecting a suitable protein scaffold is a challenging task that plays a key role in designing artificial enzymes. In this work, we explored different protein scaffolds for an abiological model of iminium-ion catalysis, Michael addition of nitromethane into E-cinnamaldehyde. We studied scaffolds looking for open hydrophobic pockets and enzymes with described binding sites for the targeted substrate. The proteins were expressed and variants harboring functional amine groups - lysine, p-aminophenylalanine, or N6-(D-prolyl)-L-lysine - were analyzed for the model reaction. Among the newly identified scaffolds, a thermophilic ene-reductase from Thermoanaerobacter pseudethanolicus was shown to be the most promising biomolecular scaffold for this reaction.

Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics

Many cellular processes are governed by protein-protein interactions that require tight spatial and temporal regulation. Accordingly, it is necessary to understand the dynamics of these interactions to fully comprehend and elucidate cellular processes and pathological disease states. To map de novo protein-protein interactions with time resolution at an organelle-wide scale, we developed a quantitative mass spectrometry method, time-resolved interactome profiling (TRIP). We apply TRIP to elucidate aberrant protein interaction dynamics that lead to the protein misfolding disease congenital hypothyroidism. We deconvolute altered temporal interactions of the thyroid hormone precursor thyroglobulin with pathways implicated in hypothyroidism pathophysiology, such as Hsp70-/90-assisted folding, disulfide/redox processing, and N-glycosylation. Functional siRNA screening identified VCP and TEX264 as key protein degradation components whose inhibition selectively rescues mutant prohormone secretion. Ultimately, our results provide novel insight into the temporal coordination of protein homeostasis, and our TRIP method should find broad applications in investigating protein-folding diseases and cellular processes.

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.

Quantitative analysis of electroporation-mediated intracellular delivery via bioorthogonal luminescent reaction

Efficient intracellular delivery is crucial for biotherapeutics, such as proteins, oligonucleotides, and CRISPR/Cas9 gene-editing systems, to achieve their efficacy. Despite the great efforts of developing new intracellular delivery carriers, the lack of straightforward methods for intracellular delivery quantification limits further development in this area. Herein, we designed a simple and versatile bioorthogonal luminescent reaction (BioLure assay) to analyze intracellular delivery. Our results suggest that BioLure can be used to estimate the amount of intracellularly delivered molecules after electroporation, and the estimation by BioLure is in good correlation with the results from complementary methods. Furthermore, we used BioLure assay to correlate the intracellularly-delivered RNase A amount with its tumoricidal activity. Overall, BioLure is a versatile tool for understanding the intracellular delivery process on live cells, and establishing the link between the cytosolic concentration of intracellularly-delivered biotherapeutics and their therapeutic efficacy.