The 2022 Nobel Prize in Chemistry for the development of click chemistry and bioorthogonal chemistry

Chemical proteomics for a comprehensive understanding of functional activity and the interactome

Traditional mass spectrometry (MS)-based proteomics aims to detect and measure protein expression on a global scale and elucidate the link between protein function and phenotypic characteristics. Although advances in MS technology have significantly broadened the scope of detectable proteomes, these methodologies primarily provide data on protein abundance and offer limited insights into their functional activities. Phenotypic traits emerge from the interplay between protein abundance and functional activity, making the accurate measurement of activity a critical but challenging task, owing to the complexity of biological systems. Furthermore, the biological function of a protein is strongly linked to its interaction with other molecules within the cellular environment. Chemical proteomics offers a complementary approach that uses a toolkit developed in chemical biology to map the molecular interactome and provide initial insights into the activities of specific target proteins. However, the value of these techniques lies not in isolation, but as part of a broader experimental workflow that includes follow-up biological investigations to validate the findings and elucidate their functional relevance. This tutorial review highlights the design principles of chemical tools and examines their applications in two key areas: (i) functional activity profiling of biomolecules and (ii) molecular proximity profiling for interactome characterization. We also discuss the importance of the experimental context in shaping data interpretation and ensuring the practical adoption of these methods by biologists. Although chemical proteomics is not a standalone solution, it represents a promising step toward next-generation omics technologies and advances our understanding of biological functions at the molecular level.

Sustainable Synthesis of 1,2,3-Triazoles using Cyrene as a Biodegradable Solvent in Click Chemistry

The first successful synthesis of 1,2,3-triazoles using CyreneTM as a biodegradable and non-toxic solvent in click chemistry has been developed. In contrast to previous methods, this sustainable approach allows product isolation by simple precipitation in water, eliminating the need for organic solvent extractions and column chromatography purifications, thus minimizing waste consumption while reducing operational costs. The protocol, performed also at gram scale, has broad applicability and versatility, as shown with complex substrates like biologically active coumarins or triazole-linked bifunctional molecules. Finally, this protocol is also amenable to a three-component reaction involving organic halides, terminal acetylenes and sodium azide, thus avoiding the isolation of organic azides, difficult-to-handle species known for their environmental sensitivity.

Structural Basis for the Catalytic Mechanism of ATP-Dependent Diazotase CmaA6

Although several diazotases have been recently reported, the details of the reaction mechanism are not yet understood. In this study, we investigated the mechanism of CmaA6, an ATP-dependent diazotase, which catalyzes the diazotization of 3-aminocoumaric acid using nitrous acid. X-ray crystallography and cryogenic electron microscopy-single particle analysis revealed CmaA6 structures in the substrate-free and AMP-binding states. Kinetic analysis suggested that CmaA6 catalyzes diazotization via a sequential reaction mechanism in which three substrates (nitrous acid, ATP, and 3-aminocoumaric acid) are simultaneously bound in the reaction pocket. The nitrous acid and 3-aminocoumaric acid binding sites were predicted based on the AMP-binding state and confirmed by site-directed mutagenesis. In addition, computational analysis revealed a tunnel for 3-aminocoumaric acid to enter the reaction pocket, which was advantageous for the sequential reaction mechanism. This study provides important insights into the catalytic mechanism of diazotization in natural product biosynthesis.

Recent Advances in Smart Linkage Strategies for Developing Drug Conjugates for Targeted Delivery

Targeted drug delivery systems effectively solve the problem of off-target toxicity of chemotherapeutic drugs by combining chemotherapeutic drugs with antibodies or peptides, thereby promoting drug targeting to the tumor site and bringing further hope for cancer treatment. The development of stimulus-responsive smart linkage technologies has led to the emergence of drug conjugates. Linkage technologies play a crucial role in the design, synthesis, and in vivo circulation of drug conjugates, as they determine the release of cytotoxic drugs from the conjugates and their subsequent therapeutic efficacy. This article reviews some of the smart linkage strategies used in designing drug conjugates, with a focus on the tumor microenvironment and exogenous stimuli as conditions influencing controlled drug release. This review introduces linker classifications and cleavage mechanisms, discusses modular linkers that promote the efficient synthesis of conjugates, and discusses the differences between linkage strategies. Furthermore, this article focuses on the implementation of self-assembly in drug conjugates, which is currently of great interest. Related concepts are introduced and relevant examples of their applications are provided. Furthermore, a comprehensive discourse is presented on the challenges that may arise in the research and clinical implementation of diverse linkage strategies, along with the associated enhancement measures. Finally, the factors that should be considered when designing linkage strategies for drug conjugates are summarized, offering strategies and ideas for scientists involved in drug conjugate research. It is particularly noteworthy that appropriate linkage strategies allow for the intracellular release of drugs after internalization of the conjugates, thereby maximizing their tumor cell-killing effect.

Recent Biomedical Applications of Functional Materials Based on Polyhedral Oligomeric Silsesquioxane (POSS)

Polyhedral oligomeric silsesquioxane (POSS) is a 3D, cage-like nanoparticle with an inorganic Si-O-Si core and eight tunable corner functional groups. Its well-defined structure grants it distinctive physical, chemical, and biological properties and has been widely used for preparing high-performance materials. Recently, click chemistry has enabled the synthesis of various functional POSS-based materials for diverse biomedical applications. This article reviews the recent applications of POSS-based materials in the biomedical field, including cancer treatment, tissue engineering, antibacterial use, and biomedical imaging. Representative examples are discussed in detail. Among the various POSS-based applications, cancer treatment and tissue engineering are the most important. Finally, this review presents the current limitations of POSS-based materials and provides guidance for future research.

Nanogels: Smart tools to enlarge the therapeutic window of gene therapy

Gene therapy can potentially treat a great number of diseases, from cancer to rare genetic disorders. Very recently, the development and emergency approval of nucleic acid-based COVID-19 vaccines confirmed its strength and versatility. However, gene therapy encounters limitations due to the lack of suitable carriers to vectorize therapeutic genetic material inside target cells. Nanogels are highly hydrated nano-size crosslinked polymeric networks that have been used in many biomedical applications, from drug delivery to tissue engineering and diagnostics. Due to their easy production, tunability, and swelling properties they have called the attention as promising vectors for gene delivery. In this review, nanogels are discussed as vectors for nucleic acid delivery aiming to enlarge gene therapy's therapeutic window. Recent works highlighting the optimization of inherent transfection efficiency and biocompatibility are reviewed here. The importance of the monomer choice, along with the internal structure, surface decoration, and responsive features are outlined for the different transfection modalities. The possible sources of toxicological endpoints in nanogels are analyzed, and the strategies to limit them are compared. Finally, perspectives are discussed to identify the remining challenges for the nanogels before their translation to the market as transfection agents.

Designing Bioorthogonal Reactions for Biomedical Applications

Bioorthogonal reactions are a class of chemical reactions that can be carried out in living organisms without interfering with other reactions, possessing high yield, high selectivity, and high efficiency. Since the first proposal of the conception by Professor Carolyn Bertozzi in 2003, bioorthogonal chemistry has attracted great attention and has been quickly developed. As an important chemical biology tool, bioorthogonal reactions have been applied broadly in biomedicine, including bio-labeling, nucleic acid functionalization, drug discovery, drug activation, synthesis of antibody-drug conjugates, and proteolysis-targeting chimeras. Given this, we summarized the basic knowledge, development history, research status, and prospects of bioorthogonal reactions and their biomedical applications. The main purpose of this paper is to furnish an overview of the intriguing bioorthogonal reactions in a variety of biomedical applications and to provide guidance for the design of novel reactions to enrich bioorthogonal chemistry toolkits.

Alkynylated and triazole-linked aroyl-S,N-ketene acetals: one-pot synthesis of solid-state emissive dyes with aggregation-induced enhanced emission characteristics

Alkynylated aroyl-S,N-ketene acetals are readily synthesized in mostly excellent yields by a Sonogashira reaction resulting in a substance library of more than 20 examples. Upon expansion of the reaction sequence by deprotection and concatenating of the copper-click reaction in a one-pot fashion, a library of 11 triazole-ligated aroyl-S,N-ketene acetals is readily accessible. All derivatives show pronounced solid-state emission and aggregation-induced emission properties depending on the nature of the alkynyl or the triazole substituents.

Fluorine-Containing Functional Group-Based Energetic Materials

Molecules featuring fluorine-containing functional groups exhibit outstanding properties with high density, low sensitivity, excellent thermal stability, and good energetic performance due to the strong electron-withdrawing ability and high density of fluorine. Hence, they play a pivotal role in the field of energetic materials. In light of current theoretical and experimental reports, this review systematically focuses on three types of energetic materials possessing fluorine-containing functional groups F- and NF2 - substituted trinitromethyl groups (C(NO2 )2 F, C(NO2 )2 NF2 ), trifluoromethyl group (CF3 ), and difluoroamino and pentafluorosulfone groups (NF2 , SF5 ) and investigates the synthetic methods, physicochemical parameters, and energetic properties of each. The incorporation of fluorine-containing functional moieties is critical for the development of novel high energy density materials, and is rapidly being adopted in the design of energetic materials.

Novel Oleanolic Acid-Phtalimidines Tethered 1,2,3 Triazole Hybrids as Promising Antibacterial Agents: Design, Synthesis, In Vitro Experiments and In Silico Docking Studies

As part of the valorization of agricultural waste into bioactive compounds, a series of structurally novel oleanolic acid ((3β-hydroxyolean-12-en-28-oic acid, OA-1)-phtalimidines (isoindolinones) conjugates 18a-u bearing 1,2,3-triazole moieties were designed and synthesized by treating an azide 4 previously prepared from OA-1 isolated from olive pomace (Olea europaea L.) with a wide range of propargylated phtalimidines using the Cu(I)-catalyzed click chemistry approach. OA-1 and its newly prepared analogues, 18a-u, were screened in vitro for their antibacterial activity against two Gram-positive bacteria, Staphylococcus aureus and Listeria monocytogenes, and two Gram-negative bacteria, Salmonella thyphimurium and Pseudomonas aeruginosa. Attractive results were obtained, notably against L. monocytogenes. Compounds 18d, 18g, and 18h exhibited the highest antibacterial activity when compared with OA-1 and other compounds in the series against tested pathogenic bacterial strains. A molecular docking study was performed to explore the binding mode of the most active derivatives into the active site of the ABC substrate-binding protein Lmo0181 from L. monocytogenes. Results showed the importance of both hydrogen bonding and hydrophobic interactions with the target protein and are in favor of the experimental data.

Development and Recent Advances in Lysine and N-Terminal Bioconjugation for Peptides and Proteins

The demand for creation of protein diversity and regulation of protein function through native protein modification and post-translational modification has ignited the development of selective chemical modification methods for peptides and proteins. Chemical bioconjugation offers selective functionalization providing bioconjugates with desired properties and functions for diverse applications in chemical biology, medicine, and biomaterials. The amino group existing at the lysine residue and N-terminus of peptides and proteins has been extensively studied in bioconjugation because of its good nucleophilicity and high surface exposure. Herein, we review the development of chemical methods for modification of the amino groups on lysine residue and N-terminus featuring excellent selectivity, mild reaction conditions, short reaction time, high conversion, biocompatibility, and preservation of protein integrity. This review is organized based on the chemoselectivity and site-selectivity of the chemical bioconjugation reagents to the amino acid residues aiming to provide guidance for the selection of appropriate bioconjugation methods.