A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems

Surface-functionalized bacteria: Frontier explorations in next-generation live biotherapeutics

Screening robust living bacteria to produce living biotherapeutic products (LBPs) represents a burgeoning research field in biomedical applications. Despite their natural abilities to colonize bio-interfaces and proliferate, harnessing bacteria for such applications is hindered by considerable challenges in unsatisfied functionalities and safety concerns. Leveraging the high degree of customization and adaptability on the surface of bacteria demonstrates significant potential to improve therapeutic outcomes and achieve tailored functionalities of LBPs. This review focuses on the recent laboratory strategies of bacterial surface functionalization, which aims to address these challenges and potentiate the therapeutic effects in biomedicine. Firstly, we introduce various functional materials that are used for bacterial surface functionalization involving organic, inorganic, and biological materials. Secondly, the methodologies for achieving bacterial surface functionalization are categorized into three primary approaches including covalent bonding, non-covalent interactions, and hybrid techniques, while various advantages and limitations of different modification strategies are compared from multiple perspectives. Subsequently, the current status of the applications of surface-functionalized bacteria in bioimaging and disease treatments, especially in the treatment of inflammatory bowel disease (IBD) and cancer is summarized. Finally, challenges and pressing issues in the development of surface-functionalized bacteria as LBPs are presented.

The effects of buffer, pH, and temperature upon SPAAC reaction rates

This study investigates the effects of buffer type, pH, and temperature on the kinetics of strain-promoted alkyne-azide cycloaddition (SPAAC) reactions. Using 3-azido-L-alanine and 1-azido-1-deoxy-β-D-glucopyranoside as model azides and sulfo DBCO-amine as the alkyne, we examined reaction rates in a series of buffers, including PBS, HEPES, MES, borate buffer, and cell culture media (DMEM and RPMI), with pH values ranging from 5 to 10 and temperatures of 25 and 37 °C. Absorbance spectrophotometric data revealed that PBS (pH 7) exhibited among the lowest rate constants (0.32-0.85 M-1 s-1), whereas HEPES (pH 7) had the highest (0.55-1.22 M-1 s-1). Additionally, reactions in DMEM were faster than in RPMI (0.59-0.97 vs. 0.27-0.77 M-1 s-1). We observed that higher pH values generally increased reaction rates, except in HEPES buffer. Notably, 1-azido-1-deoxy-β-D-glucopyranoside reacted faster than 3-azido-L-alanine, highlighting the importance of considering the electron-donating capacity of azides in the optimisation of SPAAC reactions. Additional experiments with DBCO-modified antibodies (DBCO-trastuzumab and DBCO-PEG5-trastuzumab) corroborated the trends related to buffer and azide selection. The presence of a PEG linker notably enhanced reaction rates (0.18-0.37 M-1 s-1) by 31 ± 16%. This study offers useful insights into the factors affecting SPAAC kinetics, facilitating the development of optimised bioconjugation strategies.

Not So Bioorthogonal Chemistry

The advent of bioorthogonal chemistry has transformed scientific research, offering a powerful tool for selective and noninvasive labeling of (bio)molecules within complex biological environments. This innovative approach has facilitated the study of intricate cellular processes, protein dynamics, and interactions. Nevertheless, a number of challenges remain to be addressed, including the need for improved reaction kinetics, enhanced biocompatibility, and the development of a more diverse and orthogonal set of reactions. While scientists continue to search for veritable solutions, bioorthogonal chemistry remains a transformative tool with a vast potential for advancing our understanding of biology and medicine. This Perspective offers insights into reactions commonly classified as "bioorthogonal", which, however, may not always demonstrate the desired selectivity regarding the interactions between their components and the additives or catalysts used under the reaction conditions.

Bio-orthogonal Glycan Imaging of Cultured Cells and Whole Animal C. elegans with Expansion Microscopy

Complex carbohydrates called glycans play crucial roles in regulating cell and tissue physiology, but how they map to nanoscale anatomical features must still be resolved. Here, we present the first nanoscale map of mucin-type O-glycans throughout the entirety of the Caenorhabditis elegans model organism. We constructed a library of multifunctional linkers to probe and anchor metabolically labeled glycans in expansion microscopy (ExM). A flexible strategy was demonstrated for the chemical synthesis of linkers with a broad inventory of bio-orthogonal functional groups, fluorophores, anchorage chemistries, and linker arms. Employing C. elegans as a test bed, metabolically labeled O-glycans were resolved on the gut microvilli and other nanoscale anatomical features. Transmission electron microscopy images of C. elegans nanoanatomy validated the fidelity and isotropy of gel expansion. Whole organism maps of C. elegans O-glycosylation in the first larval stage revealed O-glycan "hotspots" in unexpected anatomical locations, including the body wall furrows. Beyond C. elegans, we validated ExM protocols for nanoscale imaging of metabolically labeled glycans on cultured mammalian cells. Together, our results suggest the broad applicability of the multifunctional reagents for imaging glycans and other metabolically labeled biomolecules at enhanced resolutions with ExM.

Direct organocatalytic chemoselective synthesis of pharmaceutically active benzothiazole/benzoxazole-triazoles

Benzothiazole and benzoxazole heterocyclic ring-containing 1,4,5-trisubstituted-1,2,3-triazoles are well known for their wide range of applications in pharmaceutical and medicinal chemistry, but their high-yielding metal-free selective synthesis has always remained challenging as no comprehensive simple protocol has been outlined to date. Owing to their structural and medicinal importance, herein, we synthesized various benzothiazole and benzoxazole heterocyclic ring-containing 1,4,5-trisubstituted-1,2,3-triazoles in high to excellent yields with chemo-/regioselectivity from the library of benzothiazole/benzoxazole-ketones and aryl/alkyl-azides through an enolate-mediated organocatalytic azide-ketone [3 + 2]-cycloaddition under ambient conditions in a few hours. The commercial availability or quick synthesis of the starting materials and catalysts, a diverse substrate scope, chemo-/regioselectivity, quick synthesis of pharmaceutically active known compounds and their analogues, and numerous medicinal applications of functionalized benzothiazole/benzoxazole-triazoles are the key attractions of this metal-free organo-click reaction.

Gag HIV-1 Virus-like Particles and Extracellular Vesicles Functionalization with Spike Epitopes of SARS-CoV-2 Using a Copper-Free Click Chemistry Approach

Enveloped nanoparticles such as extracellular vesicles (EVs) and virus-like particles (VLPs) have emerged as promising nanocarriers capable of transporting bioactive molecules for drug delivery and vaccination. Optimized functionalization methodologies are required to increase the functionalization levels of these nanoparticles, enhancing their performance. Here, a bioorthogonal copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) reaction has been optimized to functionalize human immunodeficiency virus type 1 (HIV-1) Gag-based VLPs and EVs. The optimization process has been carried out through reaction kinetics and design of experiments (DoE) using Cy5 as a reporter molecule. The functionalization of both VLPs and EVs has been studied using super-resolution fluorescence microscopy (SRFM), revealing remarkable differences between Gag-VLPs and coproduced EVs. EVs produced by mock transfection and cell growth have been functionalized achieving a mean of 3618.63 ± 48.91 and 6498.75 ± 352.71 Cy5 molecules covalently linked per particle (Cy5cov/particle), respectively. Different nanoparticles have been functionalized with two linear B-cell epitopes from the Spike protein of SARS-CoV-2, S315-338 TSNFRVQPTESIVRFPNITNLCPF and S648-663 GCLIGAEHVNNSYECD, and analyzed by an immunoassay with sera from COVID-19 patients. The obtained results validate the selected B-cell epitopes and highlight the potential of the optimized functionalization approach for the development of nanoparticle-based vaccines.

Organobase-catalyzed efficient synthesis of 4-acyl-5-aryl tri-substituted triazole linked N-glycosides as glycohybrids

Herein, we report a highly efficient organobase-catalyzed method for the synthesis of fully decorated chiral 4-acyl-5-aryl-trisubstituted-1,2,3-triazole-linked N-glycosidic molecular scaffolds as glycohybrids. This process involves a base-catalyzed 1,3 dipolar cycloaddition reaction, where β-ketoesters react with various glycosyl azides in dimethyl sulfoxide at room temperature, furnishing new glycohybrids in good to excellent yields. This intermolecular reaction is metal-free, exceptionally efficient, versatile, and high-yielding, with a broad substrate scope and remarkable regioselectivity.

Click-Based Determination of Accumulation of Molecules in Escherichia coli

Gram-negative bacterial pathogens pose a significant challenge in drug development due to their outer membranes, which impede the permeation of small molecules. The lack of widely adoptable methods to measure the cytosolic accumulation of compounds in bacterial cells has hindered drug discovery efforts. To address this challenge, we developed the CHloroalkane Azide Membrane Permeability (CHAMP) assay, specifically designed to assess molecule accumulation in the cytosol of Gram-negative bacteria. The CHAMP analysis utilizes biorthogonal epitopes anchored within HaloTag-expressing bacteria and measures the cytosolic arrival of azide-bearing test molecules through strain-promoted azide-alkyne cycloaddition. This workflow allows for robust and rapid accumulation measurements of thousands of azide-tagged small molecules. Our approach consistently yields a large number of accumulation profiles, significantly exceeding the scale of previous measurements in Escherichia coli ( E. coli ). We have validated the CHAMP assay across various chemical and biological contexts, including hyperporinated cells, membrane-permeabilized cells, and E. coli strains with impaired TolC function, a key component of the efflux pump. The CHAMP platform provides a simple, high-throughput, and accessible method that enables the analysis of over 1,000 molecules within hours. This technique addresses a critical gap in antimicrobial research, potentially accelerating the development of effective agents against Gram-negative pathogens.

Site-specific activation of the proton pump inhibitor rabeprazole by tetrathiolate zinc centres

Proton pump inhibitors have become top-selling drugs worldwide. Serendipitously discovered as prodrugs that are activated by protonation in acidic environments, proton pump inhibitors inhibit stomach acid secretion by covalently modifying the gastric proton pump. Despite their widespread use, alternative activation mechanisms and potential target proteins in non-acidic environments remain poorly understood. Employing a chemoproteomic approach, we found that the proton pump inhibitor rabeprazole selectively forms covalent conjugates with zinc-binding proteins. Focusing on DENR, a protein with a C4 zinc cluster (that is, zinc coordinated by four cysteines), we show that rabeprazole is activated by the zinc ion and subsequently conjugated to zinc-coordinating cysteines. Our results suggest that drug binding, activation and conjugation take place rapidly within the zinc coordination sphere. Finally, we provide evidence that other proton pump inhibitors can be activated in the same way. We conclude that zinc acts as a Lewis acid, obviating the need for low pH, to promote the activation and conjugation of proton pump inhibitors in non-acidic environments.

Bio-orthogonal Labeling of Chitin in Native Pathogenic Candida Species via the Chitin Scavenge Pathway

The fungal cell wall is essential for the integrity of the cell, providing strength and shape, as well as protection against environmental stimuli. For pathogenic fungi, the cell wall is also the initial point of contact with the host. Specific cell wall features such as hypha tails and smaller glycan components modulate a wide range of fungal interactions with the immune defenses. Here, a bio-orthogonal labeling method utilizing N-acetyl-glucosamine (NAG) probes is developed to fluorescently label native, pathogenic yeast via the chitin scavenging pathway. A panel of NAG probes was assembled, synthesized, and characterized for the ability to label the chitin in pathogenic yeast. Enzymatic data show that the native scavenging biosynthetic enzyme, Hxk1, is promiscuous, permitting the labeling of the native chitin biopolymer. This chitin labeling method was validated via the development of mass spectrometry protocols. When compared to the current available labeling systems for chitin, the probes do not affect the integrity of the cell wall and do not interrupt cell growth. Furthermore, the NAG probes enabled multiple "click" platforms across pathogenic Candida species including Candida albicans and Candida tropicalis. Budding and filamentous hyphal states were observed. The results indicate the probes' utility for in vivo study of the morphological, pathogenic switch, and visualization of growth patterns. Thus, the use of these probes in pathogenic Candida strains is ideal for a variety of future applications including strain specific antifungals, diagnostic tools, and immunomodulators.

Development of Transiently Strainable Benzocycloheptenes for Catalyst-Free, Visible-Light-Mediated [3 + 2]-Cycloadditions

Dynamic photogeneration of ephemeral and reactive species is enabling for chemical reactions, providing spatial and temporal control. A previous study from our group established the ability of 6,7-dihydro-5H-benzo[7]annulene, benzocycloheptene (BC7), to convert photochemical energy into ring strain, enabling the rapid cycloaddition of alkyl azides with the reversibly formed and transient trans-isomer, affording versatile nonaromatic triazolines. Despite the conceptual advances of the previous study, some challenges remained: the fragility of the triazoline products, the low regioselectivity for the cycloaddition, a need for an iridium-based photosensitizer and organic-based solvents, and a lack of convenient linchpin functional group handles. Herein, we communicate the development of a second generation of BC7 molecules that overcome the issues of the first generation. A method to convert fragile triazoline products to stable triazoles was developed. The alkene component was polarized with a carbonyl group, dramatically improving the regioselectivity while simultaneously red-shifting the absorbance of the cycloalkene into the visible region, which was expected to facilitate direct excitation and eliminate the need for photocatalysts. However, experiments indicated that the cycloaddition involved passage through a triplet manifold, complicating the direct excitation strategy. This was successfully overcome by attaching a bromine atom directly to the alkene moiety, which accelerated singlet-to-triplet intersystem crossing by the heavy atom effect. Further exploration identified sites of substitution that can increase the water solubility and provide a handle for the loading of chemical tools and probes.

Strain-promoted azide-alkyne cycloaddition enhanced by secondary interactions

Azide-alkyne cycloaddition of cyclooct-2-yn-1-ol and 2-(azidophenyl)boronic acid proceeded rapidly at room temperature with complete regioselectivity to afford a triazole having a boronate ester group. The secondary interaction to form a boronate ion contributed to cycloaddition rate acceleration and the control of regioselectivity. The interaction to form an imine or hemiaminal was also evaluated.

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.

Phosphate triester-based multifunctional handles for post-synthetic oligonucleotide functionalization

The continued advancement of oligonucleotide-based strategies in research and therapeutics relies on expanding the repertoire of chemical modifications to overcome persistent challenges, such as improving cellular uptake and delivery. Addressing these obstacles requires innovative bioconjugation approaches that integrate seamlessly with oligonucleotide modalities. Here, we report the development of a novel phosphotriester trifunctional probe based on the H-phosphonate derivative ammonium (9H-fluoren-9-yl)methyl, introducing significant advancements in synthetic phosphate chemistry. This platform supports robust and versatile chemical transformations, enabling the incorporation of diverse functionalities, such as biotin, fluorescent markers, G4-stabilizing ligands, and azido groups, into oligonucleotide backbones. The resulting multifunctional probes are compatible with different conjugation strategies and phosphorothioate modifications, allowing late-stage functionalization in solution without requiring solid-phase synthesis. We demonstrate the utility of this approach through the synthesis of G4-ligand-conjugated oligonucleotides (GL-Os) designed to target individual G4 structures. However, the strategy's adaptability ensures compatibility with a wide range of oligonucleotide-based applications that benefit from the addition of functional probes. This flexibility broadens accessibility and applicability, facilitating the development of oligonucleotide tools for advanced chemical biology studies, including fluorescence-based imaging and pull-down experiments.

Reaction development: a student's checklist

So you've discovered a reaction. But how do you turn this new discovery into a fully-fledged program that maximises the potential of your novel transformation? Herein, we provide a student's checklist to serve as a helpful guide for synthesis development, allowing you to thoroughly investigate the chemistry in question while ensuring that no key aspect of the project is overlooked. A wide variety of the most illuminating synthetic and spectroscopic techniques will be summarised, in conjunction with literature examples and our own insights, to provide sound justifications for their implementation towards the goal of developing new reactions.

Heterobifunctional cross-linker with dinitroimidazole and azide modules for protein and oligonucleotide functionalization

Dinitroimidazole (DNIm) was recently identified as a powerful bioconjugation agent that could selectively modify thiol over amine on biomolecules at an ultrahigh speed in an aqueous buffer. However, its derivative containing a DNIm module and a terminal alkyne module failed to construct functional agents bearing a DNIm warhead via the CuAAC reaction. To solve this problem, a heterobifunctional cross-linker was designed and synthesized by linking a DNIm module with an azide module via an oxoaliphatic amido bond spacer arm. Its two modules, DNIm and azide, reacted with a thiol and cyclooctyne, respectively, in an orthogonal way. The cross-linker facilitated the preparation of various functional agents bearing a DNIm warhead via SPAAC reaction and was further applied to protein functionalization (including biotinylation and fluorescence labeling) and oligonucleotide functionalization (including PEGylation, oligonucleotide-peptide and oligonucleotide-protein conjugate). Thus, the cross-linker not only provided convenient access to those functional agents bearing a DNIm warhead but also combined DNIm chemistry with click chemistry of SPAAC to enlarge their respective application range in the bioconjugation field.

Nanoscale Cellular Traction Force Quantification: CRISPR-Cas12a Supercharged DNA Tension Sensors in Nanoclustered Ligand Patterns

High-throughput measurement of cellular traction forces at the nanoscale remains a significant challenge in mechanobiology, limiting our understanding of how cells interact with their microenvironment. Here, we present a novel technique for fabricating protein nanopatterns in standard multiwell microplate formats (96/384-wells), enabling the high-throughput quantification of cellular forces using DNA tension gauge tethers (TGTs) amplified by CRISPR-Cas12a. Our method employs sparse colloidal lithography to create nanopatterned surfaces with feature sizes ranging from sub 100 to 800 nm on transparent, planar, and fully PEGylated substrates. These surfaces allow for the orthogonal immobilization of two different proteins or biomolecules using click-chemistry, providing precise spatial control over cellular signaling cues. We demonstrate the robustness and versatility of this platform through imaging techniques, including total internal reflection fluorescence microscopy, confocal laser scanning microscopy, and high-throughput imaging. Applying this technology, we measured the early stage mechanical forces exerted by 3T3 fibroblasts across different nanoscale features, detecting forces ranging from 12 to 56 pN. By integrating the Mechano-Cas12a Assisted Tension Sensor (MCATS) system, we achieved rapid and high-throughput quantification of cellular traction forces, analyzing over 2 million cells within minutes. Our findings reveal that nanoscale clustering of integrin ligands significantly influences the mechanical responses of cells. This platform offers a powerful tool for mechanobiology research, facilitating the study of cellular forces and mechanotransduction pathways in a high-throughput manner compatible with standard cell culture systems.

Conjugation Chemistry Markedly Impacts Toxicity and Biodistribution of Targeted Nanoparticles, Mediated by Complement Activation

Conjugation chemistries are a major enabling technology for the development of drug delivery systems, from antibody-drug conjugates to antibody-targeted lipid nanoparticles inspired by the success of the COVID-19 vaccine. However, here it is shown that for antibody-targeted nanoparticles, the most popular conjugation chemistries directly participate in the activation of the complement cascade of plasma proteins. Their activation of complement leads to large changes in the biodistribution of nanoparticles (up to 140-fold increased uptake into phagocytes of the lungs) and multiple toxicities, including a 50% drop in platelet count. It is founded that the mechanism of complement activation varies dramatically between different conjugation chemistries. Dibenzocyclooctyne, a commonly used click-chemistry, caused aggregation of conjugated antibodies, but only on the surface of nanoparticles (not in bulk solution). By contrast, thiol-maleimide chemistry do not activate complement via its effects on antibodies, but rather because free maleimide bonded to albumin in plasma, and clustered albumin is then attacked by complement. Using these mechanistic insights, solutions are engineered that reduced the activation of complement for each class of conjugation chemistry. These results highlight that while conjugation chemistry is essential for the future of nanomedicine, it is not innocuous and must be designed with opsonins like complement in mind.

The versatility of peptide hydrogels: From self-assembly to drug delivery applications

Pharmaceuticals often suffer from limitations such as low solubility, low stability, and  short half-life. To address these challenges and reduce the need for frequent drug administrations, a more efficient delivery is required. In this context, the development of controlled drug delivery systems, acting as a protective depot for the drug, has expanded significantly over the last decades. Among these, injectable hydrogels have emerged as a promising platform, especially in view of the rise of biologicals as therapeutics. Hydrogels are functional, solid-like biomaterials, composed of cross-linked hydrophilic polymers and high water content. Their physical properties, which closely mimic the extracellular matrix, make them suitable for various biomedical applications. This review discusses the different types of hydrogel systems and their self-assembly process, with an emphasis on peptide-based hydrogels. Due to their structural and functional diversity, biocompatibility, synthetic accessibility, and tunability, peptides are regarded as promising and versatile building blocks. A comprehensive overview of the variety of peptide hydrogels is outlined, with β-sheet forming sequences being highlighted. Key factors to consider when using peptide hydrogels as a controlled drug delivery system are reviewed, along with a discussion of the main drug release mechanisms and the emerging trend towards affinity-based systems to further refine drug release profiles.

An efficient and flexible approach for local distortion: distortion distribution analysis enabled by fragmentation

Distortion can play crucial roles in influencing structures and properties, as well as enhancing reactivity or selectivity in many chemical and biological systems. The distortion/interaction or activation-strain model is a popular and powerful method for deciphering the origins of activation energies, in which distortion and interaction energies dictate an activation energy. However, decomposition of local distortion energy at the atomic scale remains less clear and straightforward. Knowing such information should deepen our understanding of reaction processes and improve reaction design. Herein, an efficient, general and flexible fragmentation-based approach was proposed to evaluate local distortion energies for various chemical and biological molecules, which can be obtained computationally and/or experimentally. Moreover, our distortion analysis is readily applicable to multiple structures from molecular dynamics (or the minimum energy path) as well as can be evaluated by different computational chemistry methods. Our systematic analysis shows that our approach not only aids computational and experimental chemists in visualizing (relative) distortion distributions within molecules (distortion map) and identifies the key distorted pieces, but also offers deeper understanding and insights into structures, reaction mechanisms and dynamics in various chemical and biological systems. Furthermore, our analysis offers indices of local distortion energy, which can potentially serve as a new descriptor for multi-linear regression (MLR) or machine learning (ML) modelling.

SMAP3-ID for Identification of Endogenous Protein-Protein Interactions Reveals Regulation of Mitochondrial Activity by Lamins

Proteins regulate biological functions through the formation of distinct protein complexes. Identification and characterization of these protein-protein interactions are critical to deciphering their mechanism of action. Different antibody-based or cross-linking-based methods have been developed to identify the protein-protein interactions. However, these methods require genetic engineering or other means to disrupt the native environments. To circumvent this limitation, we introduce here SMAP3-ID (small-molecule-assisted identification of protein-protein interactions through proximity) method to identify protein-protein interactions in native cellular environment. This method combines a selective ligand for binding to a protein of interest for photo-cross-linking, a live-cell-compatible bioorthogonal click reaction with a trifunctional chemical probe, and a final photo-cross-linking reaction to covalently capture the interacting proteins. Using the SMAP3-ID method and nuclear lamins as an example, we identified numerous lamin interactors in native cells. Significantly, we identified a number of mitochondrial enzymes as novel lamin A (LA) interactors. The interactions between mitochondrial enzymes and LA were further validated, which provides mechanistic insights underlying the metabolic alterations caused by mutations in LA. Furthermore, our previously described small-molecule ligand for LA, LBL1, also induced changes in mitochondrial activity and cellular bioenergetic organization. We conclude that SMAP3-ID is a potentially powerful and generalizable method to identify protein-protein interactions in the native cellular environment.

Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability

Hydrogels composed of collagen, the most abundant protein in the human body, are widely used as scaffolds for tissue engineering due to their ability to support cellular activity. However, collagen hydrogels with encapsulated cells often experience bulk contraction due to cell-generated forces, and conventional strategies to mitigate this undesired deformation often compromise either the fibrillar microstructure or cytocompatibility of the collagen. To support the spreading of encapsulated cells while preserving the structural integrity of the gels, we present an interpenetrating network (IPN) of two distinct collagen networks with different crosslinking mechanisms and microstructures. First, a physically self-assembled collagen network preserves the fibrillar microstructure and enables the spreading of encapsulated human corneal mesenchymal stromal cells. Second, an amorphous collagen network covalently crosslinked with bioorthogonal chemistry fills the voids between fibrils and stabilizes the gel against cell-induced contraction. This collagen IPN balances the biofunctionality of natural collagen with the stability of covalently crosslinked, engineered polymers. Taken together, these data represent a new avenue for maintaining both the fiber-induced spreading of cells and the structural integrity of collagen hydrogels by leveraging an IPN of fibrillar and amorphous collagen networks. STATEMENT OF SIGNIFICANCE: Collagen hydrogels are widely used as scaffolds for tissue engineering due to their support of cellular activity. However, collagen hydrogels often undergo undesired changes in size and shape due to cell-generated forces, and conventional strategies to mitigate this deformation typically compromise either the fibrillar microstructure or cytocompatibility of the collagen. In this study, we introduce an innovative interpenetrating network (IPN) that combines physically self-assembled, fibrillar collagen-ideal for promoting cell adhesion and spreading-with covalently crosslinked, amorphous collagen-ideal for enhancing bulk hydrogel stability. Our IPN design maintains the native fibrillar structure of collagen while significantly improving resistance against cell-induced contraction, providing a promising solution to enhance the performance and reliability of collagen hydrogels for tissue engineering applications.

Photoclick and Release for Spatiotemporally Localized Theranostics of Single Cells via In Situ Generation of 1,3-Diaryl-1H-benzo[f]indazole-4,9-dione

Bioorthogonal click-release chemistry is a cutting-edge tool for exploring and manipulating biomolecule functions in native biological systems. However, it is challenging to achieve the precise regulation or therapy of individual cells via click-release strategies driven by proximity and thermodynamics. Herein, we propose a novel photoclick-release approach based on a photo-induced cycloaddition between 4,4'-bis(N-arylsydnone) or C-bithienyl-diarylsydnone and 2-arylamino-naphthoquinone via irradiation with 405 or 485 nm light. It constructs 1,3-diaryl-1H-benzo[f]indazole-4,9-dione (BIZON) as a pharmacophore while releases an arylamine for fluorescence turn-on probing. Both photoclick reagents were tailored by connecting to the triphenyl phosphonium delivery motif for enrichment in the mitochondria of live cells. This enables an intracellular photoclick and release under the control of 405 or 485 nm light. We then discovered that the in situ photo-generated BIZON is capable of photosensitizing upon 485 or 520 nm light to produce singlet oxygen inside the mitochondria under aerobic conditions. Therefore, we realized wash-free fluorescence tracking and subsequent anti-cancer efficacy at single-cell resolution using global illumination, which provides a foundation for wavelength-gated single-cell theranostics.

Base-Controlled Synthesis of Heteroatom-Embedded 9-Membered Cycloalkynes and 6-Membered Sultams through Copper-Catalyzed Cyclization

A facile copper-catalyzed, base-controlled cyclization reaction has been developed for the synthesis of 9-membered cycloalkyne and 6-membered heterocycle sultams under mild conditions. This protocol utilizes a copper-catalyzed intramolecular A3 (alkyne-aldehyde-amine) coupling reaction to efficiently synthesize 9-membered cycloalkyne sultams in yields up to 90%. Alternatively, by substituting NaHCO3 with DBU, the protocol achieves selective deprotection of the N-propargyl group, thereby facilitating the formation of 6-membered heterocyclic sultams, also in high yields.

Click Chemistry Methodology: The Novel Paintbrush of Drug Design

Click chemistry is an immensely powerful technique for the synthesis of reliable and efficient covalent linkages. When undertaken in living cells, the concept is thereby coined bioorthogonal chemistry. Used in conjunction with the photo-cross-linking methodology, it serves as a sound strategy in the exploration of biological processes and beyond. Its broad scope has led to widespread use in many disciplines; however, this Review focuses on the use of click and bioorthogonal chemistry within medicinal chemistry, specifically with regards to drug development applications, namely, the use of DNA-encoded libraries as a novel technique for lead compound discovery, as well as the synthesis of antisense oligonucleotides and protein-drug conjugates. This Review aims to provide a critical perspective and a future outlook of this methodology, such as potential widespread use in cancer therapy and personalized medicine.

The right tool for the job: Chemical biology and microbiome science

Microbiomes exist in ecological niches ranging from the ocean and soil to inside of larger organisms like plants and animals. Within these niches, microbes play key roles in biochemical processes that impact larger phenomena, such as biogeochemical cycling or health. By understanding of how these processes occur at the molecular level, it may be possible to develop new interventions to address global problems. The complexity of these systems poses challenges to more traditional techniques. Chemical biology can help overcome these challenges by providing tools that are broadly applicable and can obtain molecular-level information about complex systems. This primer is intended to serve as a brief introduction to chemical biology and microbiome science, to highlight some of the ways that these two disciplines complement each other, and to encourage dialog and collaboration between these fields.

DNA Dendron Tagging as a Universal Way to Deliver Proteins to Cells

The use of proteins as intracellular probes and therapeutic tools is often limited by poor intracellular delivery. One approach to enabling intracellular protein delivery is to transform proteins into spherical nucleic acid (proSNA) nanoconstructs, with surfaces chemically modified with a dense shell of radially oriented DNA that can engage with cell-surface receptors that facilitate endocytosis. However, proteins often have a limited number of available reactive surface residues for DNA conjugation such that the extent of DNA loading and cellular uptake is restricted. Indeed, DNA surface density and sequence have been correlated with scavenger-receptor engagement, the first step of cellular internalization. Here, we report how branched DNA dendrons with dibenzocyclooctyne groups and proteins genetically engineered to include the noncanonical amino acid azido-phenylalanine for click chemistry can be used to synthesize hybrid DNA dendron-protein architectures that exhibit outstanding cellular internalization properties, without the need for extensive surface modification. In a head-to-head comparison, protein-DNA dendron structures (where DNA is concentrated in a local area) are taken up by cells more rapidly and to a greater extent than proSNAs (where the DNA is evenly distributed). Also, protein-G-rich dendron structures show enhanced uptake compared to protein-T-rich dendron structures, highlighting the importance of oligonucleotide sequence on nanoconjugate uptake. Finally, a generalizable method for chemically tagging proteins with dendrons that does not require mutagenesis is described. When a range of proteins, spanning 42 to 464 kDa, were modified through surface lysines with this method, a significant increase in their cellular uptake (up to 17-fold) compared to proteins that are not coupled to a DNA dendron was observed.

Exploring the Utility of Cell-Penetrating Peptides as Vehicles for the Delivery of Distinct Antimalarial Drug Cargoes

The devastating impact of malaria includes significant mortality and illness worldwide. Increasing resistance of the causative parasite, Plasmodium, to existing antimalarial drugs underscores a need for additional compounds with distinct modes of action in the therapeutic development pipeline. Here we showcase peptide-drug conjugates (PDCs) as an attractive compound class, in which therapeutic or lead antimalarials are chemically conjugated to cell-penetrating peptides. This approach aims to enhance selective uptake into Plasmodium-infected red blood cells and impart additional cytotoxic actions on the intraerythrocytic parasite, thereby enabling targeted drug delivery and dual modes of action. We describe the development of PDCs featuring four compounds with antimalarial activity-primaquine, artesunate, tafenoquine and methotrexate-conjugated to three cell-penetrating peptide scaffolds with varied antiplasmodial activity, including active and inactive analogues of platelet factor 4 derived internalization peptide (PDIP), and a cyclic polyarginine peptide. Development of this diverse set of PDCs featured distinct and adaptable conjugation strategies, to produce conjugates with in vitro antiplasmodial activities ranging from low nanomolar to low micromolar potencies according to the drug cargo and bioactivity of the partner peptide. Overall, this study establishes a strategic and methodological framework for the further development of dual mode of action peptide-drug antimalarial therapeutics.

Direct Click Bonding of Dissimilar Solid Materials Based on the Catalyst-Free Huisgen 1,3-Dipolar Cycloaddition

Here, "direct click bonding" of solid materials is proposed, which is the direct bonding of solid surfaces via the formation of covalent bonds without any adhesive. The present study shows that the Cu-free Huisgen 1,3-dipolar cycloaddition reaction proceeds between solid surfaces displaying cyclooctyne and azide groups, and it achieved the strong bonding of dissimilar solid materials as a macroscopic reaction. The bonding strength obtained is sufficiently high for practical use, and the strength can be controlled by the surface density of the cyclooctyne groups. The click bonding reaction proceeds at ambient temperature in water, an organic solvent, air, and vacuum without a catalyst or a byproduct. The bonding strength is kept more than 2 years. The click bonding works for different types of substrate materials as long as alkyne and azide groups are displayed on their surfaces. The X-ray photoelectron spectroscopy (XPS) measurements provide an evidence that the Cu-free Huisgen 1,3-dipolar cycloaddition reaction proceeds between the solid surfaces through the click bonding.

Facets of click-mediated triazoles in decorating amino acids and peptides

Decorating biomolecular building blocks, such as amino acids, to afford desired and tuneable photophysical/biophysical properties would allow chemical biologists to use them for several biotechnological and biosensing applications. While many synthetic methodologies have been explored in this direction, advantages provided by click-derived triazole moieties are second to none. However, since their discovery, click-mediated triazoles have been majorly utilised as linkers for conjugating biomolecules, creating materials with novel properties, such as polymers or drug conjugates. Despite exploring their profound role as linkers, click-mediated triazoles as an integral part of biomolecular building blocks have not been addressed. 1,2,3-Triazole, a transamide mimic, exhibits high aromatic stacking propensity, high associability with biomolecules through H-bonding, and high stability against enzymatic hydrolysis. Furthermore, triazoles can be considered donors useable for installation/modulation of the photophysics of a fluorophore. Therefore, triazole with a chromophoric unit may rightly be utilised as an integral part of biomolecular building blocks to install microenvironment-sensitive solvofluorochromic properties suitable for biological sensing, studying inter-biomolecular interactions and introducing novel physicochemical properties in a biomolecule. This review mainly focuses on the facets of click-derived triazole in designing novel fluorescent amino acids and peptides with a particular emphasis on those wherein triazole acts as an integral part of amino acids, i.e. the side chain, generating a new class of fluorescent unnatural triazolyl amino acids. Thus, fluorescent triazolyl unnatural amino acids, peptidomimetics with such amino acids and aliphatic/aromatic triazolyl amino acids as scaffolds for peptidomimetics are the central part. However, to start with, a brief history, followed by a discussion on various other relevant facets of triazoles as linkers in various fields ranging from therapeutics, materials science, diagnostics, and bioconjugation to peptidomimetics, is cited. Additionally, the possible roles of CuAAC-mediated triazoles in shaping the future of bioorganic chemistry, medicinal chemistry, diagnostics, nucleoside chemistry and protein engineering are briefly discussed.

TPDYs: strained macrocyclic diynes for bioconjugation processes

A terphenyl diyne (TPDY) macrocycle, 3,5-TPDY, has been developed incorporating a bent 1,3-diyne that is active in SPAAC processes affording atropoisomeric triazole products, as well as cycloadditions with diazoacetates and tetrazines. A pendant amine allowed bioconjugation of TPDY to two proteins in a microbial transglutaminase-catalyzed reaction. In contrast to many cycloalkyne SPAAC reagents, the TPDY stabilization occurs via interactions of π and π* orbitals of the adjacent alkynes.

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.

Bioorthogonally activated probes for precise fluorescence imaging

Over the past two decades, bioorthogonal chemistry has undergone a remarkable development, challenging traditional assumptions in biology and medicine. Recent advancements in the design of probes tailored for bioorthogonal applications have met the increasing demand for precise imaging, facilitating the exploration of complex biological systems. These state-of-the-art probes enable highly sensitive, low background, in situ imaging of biological species and events within live organisms, achieving resolutions comparable to the size of the biomolecule under investigation. This review provides a comprehensive examination of various categories of bioorthogonally activated in situ fluorescent labels. It highlights the intricate design and benefits of bioorthogonal chemistry for precise in situ imaging, while also discussing future prospects in this rapidly evolving field.

Insights into biomimetic system-ligand interaction of substituted isophthalic acid: A functionality induced photophysical study

The present article attempts to interpret the modulation of photophysical properties of isophthalic acid (IPA) through its amino [5-amino isophthalic acid (5-amino IPA)] and azido [5-azido isophthalic acid (5-azido IPA)] substituted derivatives which are chemically potent organic ligands. The ground state structure-reactivity correlation of 5-amino IPA and 5-azido IPA has been deciphered through computational studies. The computed energetics show significant interaction feasibility of the substituted ligand systems with the biomimetic systems which is further validated experimentally. The binding interaction of the probes with oppositely polarized functionalization is studied to be significant with cetyltrimethylammonium bromide (CTAB) and bovine serum albumin (BSA) with the amino functionalized derivative having a comparatively stronger binding constant value. The steady-state absorption and fluorescence study establish significant modification of polarity of the heteronuclear probes. The micro polarity study in water-dioxane mixtures enables determination of polarity of 5-amino IPA in CTAB and BSA unlike 5-azido IPA. Presence of an overlapping region between the emission spectrum of BSA and the absorption spectrum of the probes as probable donor-acceptor pair are also scrutinized via the steady-state fluorescence studies. The photophysical behavior of 5-amino IPA is observed to be somewhat dissimilar to that of 5-azido IPA.

Synthesis and Investigation of Peptide-Drug Conjugates Comprising Camptothecin and a Human Protein-Derived Cell-Penetrating Peptide

Drug targeting strategies, such as peptide-drug conjugates (PDCs), have arisen to combat the issue of off-target toxicity that is commonly associated with chemotherapeutic small molecule drugs. Here we investigated the ability of PDCs comprising a human protein-derived cell-penetrating peptide-platelet factor 4-derived internalization peptide (PDIP)-as a targeting strategy to improve the selectivity of camptothecin (CPT), a topoisomerase I inhibitor that suffers from off-target toxicity. The intranuclear target of CPT allowed exploration of PDC design features required for optimal potency. A suite of PDCs with various structural characteristics, including alternative conjugation strategies (such as azide-alkyne cycloaddition and disulfide conjugation) and linker types (non-cleavable or cleavable), were synthesized and investigated for their anticancer activity. Membrane permeability and cytotoxicity studies revealed that intact PDIP-CPT PDCs can cross membranes, and that PDCs with disulfide- and protease-cleavable linkers liberated free CPT and killed melanoma cells with nanomolar potency. However, selectivity of the PDIP carrier peptide for melanoma compared to noncancerous epidermal cells was not maintained for the PDCs. This study emphasizes the distinct role of the peptide, linker, and drug for optimal PDC activity and highlights the need to carefully match components when assembling PDCs as targeted therapies.

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.

Click chemistry-based dual nanosystem for microRNA-122 detection with single-base specificity from tumour cells

MicroRNAs (miRNAs) have been recognised as potential biomarkers due to their specific expression patterns in different biological tissues and their changes in expression under pathological conditions. MicroRNA-122 (miR-122) is a vertebrate-specific miRNA that is predominantly expressed in the liver and plays an important role in liver metabolism and development. Dysregulation of miR-122 expression is associated with several liver-related diseases, including hepatocellular carcinoma and drug-induced liver injury (DILI). Given the potential of miR-122 as a biomarker, its effective detection is important for accurate diagnosis. However, miRNA detection methods still face challenges, particularly in terms of accurately identifying miRNA isoforms that may differ by only a single base. Here, with the aim of advancing accessible methods for the detection of miRNAs with single-base specificity, we have developed a robust dual nanosystem that leverages the simplicity of click chemistry reactions. Using the dual nanosystem, we successfully detected miR-122 at single-base resolution using flow cytometry and analysed its expression in various tumour cell lines with high specificity and strong correlation with TaqMan assay results. We also detected miR-122 in serum and identified four single nucleotide variations in its sequence. The chemistry employed in this dual nanosystem is highly versatile and offers a promising opportunity to develop nanoparticle-based strategies that incorporate click chemistry and bioorthogonal chemistry for the detection of miRNAs and their isoforms.

Site-Specific Immobilization Boosts the Performance of a Galectin-1 Biosensor

The analysis of protein-bound glycans has gained significant attention due to their pivotal roles in physiological and pathological processes like cell-cell recognition, immune response, and disease progression. Routine methods for glycan analysis are challenged by the very similar physicochemical properties of their carbohydrate components. As an alternative, lectins, which are proteins that specifically bind to glycans, have been integrated into biosensors for glycan detection. However, the effectiveness of protein-based biosensors depends heavily on the immobilization of proteins on the sensor surface. To enhance the sensitivity and/or selectivity of lectin biosensors, it is crucial to immobilize the lectin in an optimal orientation for ligand binding without compromising its function. Random immobilization methods often result in arbitrary orientation and reduced sensitivity. To address this, we explored a directed immobilization strategy relying on a reactive noncanonical amino acid (ncAA) and bioorthogonal chemistry. In this study, we site-specifically incorporated the reactive noncanonical lysine derivative, Nε-((2-azidoethoxy)carbonyl)-l-lysine, into a cysteine-less single-chain variant of human galectin-1 (scCSGal-1). The reactive bioorthogonal azide group allowed the directed immobilization of the lectin on a biosensor surface using strain-promoted azide-alkyne cycloaddition. Biolayer interferometry data demonstrated that the controlled, directed attachment of scCSGal-1 to the biosensor surface enhanced the binding sensitivity to glycosylated von Willebrand factor by about 12-fold compared to random immobilization. These findings emphasize the importance of controlled protein orientation in biosensor design. They also highlight the power of single site-specific genetic encoding of reactive ncAAs and bioorthogonal chemistry to improve the performance of lectin-based diagnostic tools.

Synthesis and Preliminary Evaluation of Tanshinone Mimic Conjugates for Mechanism of Action Studies

Human antigen R (HuR) is an RNA binding protein (RBP) belonging to the ELAV (Embryonic Lethal Abnormal Vision) family, which stabilizes mRNAs and regulates the expression of multiple genes. Its altered expression or localization is related to pathological features such as cancer or inflammation. Dihydrotanshinone I (DHTS I) is a naturally occurring, tetracyclic ortho-quinone inhibitor of the HuR-mRNA interaction. Our earlier efforts led to the identification of a synthetic Tanshinone Mimic (TM) 2 with improved affinity for HuR. Here we report five new TM probes 3-5 bearing a detection-promoting moiety (either photo affinity probe - PAP or biotin) as a para-substituent on the phenyl-sulphonamide for mechanism of action (MoA) studies. Biological and biochemical assays were used to characterize the novel TM conjugates 3-5. They showed similar toxic activity in HuR-expressing triple-negative breast cancer MDA-MB-231 cells, with micromolar CC50s. REMSAs revealed that photoactivatable groups (4 a and 4 b), but not biotin (5 a and 5 b), prevented conjugates' ability to disrupt rHuR-RNA complexes. Further biochemical studies confirmed that biotinylated probes, in particular 5 a, can be used to isolate rM1 M2 from solutions, taking advantage of streptavidin-coated magnetic beads, thus being the most promising HuR inhibitor to be used for further MoA studies in cell lysates.

Click-ready iridium(iii) complexes as versatile bioimaging probes for bioorthogonal metabolic labeling

Herein, we report the synthesis, photophysical characterization and validation of iridium(iii)-polypyridine complexes functionalized for click chemistry and bioorthogonal chemistry, as well as their versatile applications as probes in bioimaging studies exploiting metabolic labeling. The designed dyes are conjugated to chemical reporters in a specific manner within cells by CuAAC ligation and display attractive photophysical properties in the UV-visible range. They are indeed highly photostable and emit in the far-red to near-IR region with long lifetimes and large Stokes shifts. We demonstrate that they can be efficiently used to monitor nascent intracellular sialylated glycoconjugates in bioorthogonal MOE studies with a varied panel of optical and non-optical techniques, namely conventional UV-vis laser scanning confocal microscopy (for routine purposes), UV-vis time-resolved luminescence imaging (for specificity and facilitated multiplexing with nano-environment sensitivity), synchrotron radiation based X-ray fluorescence nanoimaging (for high resolution, elemental mapping and quantification in situ) and inductively coupled plasma mass spectrometry (for routine quantification on cell populations with high statistical confidence). The synthesized Ir(iii) complexes were utilized in single labeling experiments, as well as in dual click-labeling experiments utilizing two distinct monosaccharide reporters relevant to the same metabolic pathway.

Chemical proteomics accelerates the target discovery of natural products

More than half of the global novel drugs are directly or indirectly derived from natural products (NPs) because of their better selectivity towards proteins. Traditional medicines perform multiple bioactivities through various NPs binding to drug targets, which highlights the opportunities of target discovery for drug development. However, detecting the binding relationship between NPs and targets remains challenging. Chemical proteomics, an interdisciplinary field of chemistry, proteomics, biology, and bioinformatics, has emerged as a potential approach for uncovering drug-target interactions. This review summarizes the principles and characteristics of the current widely applied chemical proteomic technologies, while delving into their latest applications in the target discovery of natural medicine. These endeavours demonstrate the potential of chemical proteomics for target discovery to supply dependable methodologies for the target elucidation of NPs.

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.

Chemically engineered exogenous organic reactions in living cells for in situ fluorescence imaging and biomedical applications

The unique microenvironment within living cells, characterized by high glutathione levels, reactive oxygen species concentrations, and active enzymes, facilitates the execution of chemical reactions. Recent advances in organic chemistry and chemical biology have leveraged living cells as reactors for chemical synthesis. This review summarizes recent reports on key intracellular in situ synthesis processes, including the synthesis of near-infrared fluorescent dyes, intracellular oxidative cross-linking, bioorthogonal reactions, and intracellular polymerization reactions. These methods have been applied to fluorescence imaging, tumor treatment, and the enhancement of biological functions. Finally, we discuss the challenges and opportunities in the field of in situ intracellular synthesis. We aim to guide the design of chemical molecules for in situ synthesis, improving the efficiency and control of artificial reactions in living cells, and ultimately achieving cell factory-like exogenous biological synthesis, biological function enhancement, and biomedical applications.

Revolutionizing DNA: advanced modification techniques for next-gen nanotechnology

The comprehensive advancement in DNA modification and coupling is driving DNA nanotechnology to new heights, paving the way for groundbreaking innovations in healthcare, materials science, and beyond. The ability to engineer DNA with tailored properties and functionalities underscores its immense potential in creating novel materials and devices. Utilizing a spectrum of techniques-such as amino handles, thiol groups, alkynes, azides, Diels-Alder reactions, hydrazides, and aminooxy functions-enables diverse coupling strategies, including Palladium-Catalyzed Couplings, to construct intricate DNA nanostructures. Further coupling modifications encompass hydrophobic alterations, redox-active moieties, chemical crosslinking agents, and Biotinylation. These modifications significantly broaden DNA's functional repertoire, offering precise control over interactions, structures, and features. By leveraging these advanced techniques, alongside next-generation sequencing (NGS)-based DNA modifications, researchers can design and implement DNA nanostructures with specific capabilities and applications, showcasing DNA's versatility as a programmable biomaterial. Through meticulous design and strategic implementation, DNA nanotechnology achieves unprecedented levels of precision and functionality, ushering in a new era of technological advancements and applications. These advanced DNA modification techniques hold great potential for transformative applications in nanotechnology, paving the way for innovations in drug delivery, diagnostics, and bioengineering.

Suspension Bead Loading (SBL): An Economical Protein Delivery Platform to Study URM1's Behavior in Live Cells

Uniquely modified synthetic proteins are difficult to produce in large quantities, which could limit their use in various in vitro settings and in cellular studies. In this study, we developed a method named "suspension bead loading" (SBL), to deliver protein molecules into suspended living cells using glass beads, which significantly reduces the amount of protein required for effective delivery. We investigated the delivery efficiency of functionally different proteins and evaluated the cytotoxic effect of our method and the chemical and functional integrity of the delivered protein. We utilized SBL to address questions related to ubiquitin-related modifier 1 (URM1). Employing minimal protein quantities, SBL has enabled us to study its behavior within live cells under different redox conditions, including subcellular localization and conjugation patterns. We demonstrate that oxidative stress alters both the localization and conjugation pattern of URM1 in cells, highlighting its possible role in cellular response to such extreme conditions.

A Diketopinic Reagent for the Reversible Bioconjugation to Arginine Residues on Native Antibodies

Arginine is one of the less commonly targeted amino acids in protein bioconjugation, despite its unique reactivity and abundance on the surface of proteins. In this work, a molecule containing diketopinic acid and an azide handle was developed for the chemo-selective bioconjugation to arginine. This compound proved to be efficient for bioconjugation to IgG1 and IgG4 antibodies, achieving mono- and double-label conversion rates of 37-44 and 12-30%, respectively. Mass spectrometry analysis confirmed the antibody modification at two conserved regions. The compound was also applied for the labeling of other proteins such as transferrin, BSA, and an EgA1 nanobody. The conjugation was shown to be reversible using an o-phenylenediamine-based alkaline solution. This novel conjugation method offers precise and stable bioconjugation to proteins, enhancing the potential for various biomedical applications.

Sugar Highs: Recent Notable Breakthroughs in Glycobiology

Glycosylation is biochemically complex and functionally critical to a wide range of processes and disease states, making it a vibrant area of contemporary research. Here, we highlight a selection of notable recent advances in the glycobiology of SARS-CoV-2 infection and immunity, cancer biology and immunotherapy, and newly discovered glycosylated RNAs. Together, these studies illustrate the significance of glycosylation in normal biology and the great promise of manipulating glycosylation for therapeutic benefit in disease.

A concise synthesis of anti-bicyclo[6.1.0]nonyne carboxylic acid

Bicyclo[6.1.0]nonyne carboxylic acid (BCN-COOH) is a valuable intermediate for the development of bioorthogonal click reagents. A convenient three-step synthesis of pure diastereomer anti-BCN-COOH is reported here, with an overall yield of 32% starting from 1,5-cyclooctadiene. To the best of our knowledge, this is the shortest route to anti-BCN-COOH known to date. The new method compares favourably with the optimised four-step synthesis based on previously reported data.

Deciphering the Cell Surface Sugar-Coating via Biochemical Pathways

Cell surface components, specifically glycans, play a significant role in several biological functions like cell structure, crosstalk between cells, and eventual target recognition of the cells for therapeutics. The dense layer of glycans, i. e., glycocalyx, could differ in taxon, species, and cell type. Glycans are coupled with lipids and proteins to form glycolipids, glycoproteins, proteoglycans, and glycosylphosphatidylinositol-anchored proteins, making their study challenging. However, understanding glycosylation at the cellular level is vital for fundamental research and advancing glycan-targeted therapy. Among different pathways, metabolic glycan labelling uses the natural metabolic processes of the cell to introduce abiotic functionality into glycan residues. The Bertozzi group pioneered metabolic oligosaccharide engineering using glycan salvage pathways to convert monosaccharides with unnatural modifications. This eventually results in the probe becoming part of the complex cellular glycan structures via click chemistry using copper. On the other hand, the boronic acid-based probe can recognise carbohydrates in a single step without any chemical modification of the surface. This review discusses the significance of glycans as biomarkers for different diseases and the necessity to evaluate them in situ within the physiological environment. The review also discusses the prospect of this field and its potential applications.