The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore

Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes

Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-) AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.

Chemogenetic Evolution of Diversified Photoenzymes for Enantioselective [2 + 2] Cycloadditions in Whole Cells

Artificial photoenzymes with novel catalytic modes not found in nature are in high demand; yet, they also present significant challenges in the field of biocatalysis. In this study, a chemogenetic modification strategy is developed to facilitate the rapid diversification of photoenzymes. This strategy integrates site-specific chemical conjugation of various artificial photosensitizers into natural protein cavities and the iterative mutagenesis in cell lysates. Through rounds of directed evolution, prominent visible-light-activatable photoenzyme variants were developed, featuring a thioxanthone chromophore. They successfully enabled the enantioselective [2 + 2] photocycloaddition of 2-carboxamide indoles, a class of UV-sensitive substrates that are traditionally challenging for known photoenzymes. Furthermore, the versatility of this photoenzyme is demonstrated in enantioselective whole-cell photobiocatalysis, enabling the efficient synthesis of enantioenriched cyclobutane-fused indoline tetracycles. These findings significantly expand the photophysical properties of artificial photoenzymes, a critical factor in enhancing their potential for harnessing excited-state reactivity in stereoselective transformations.

Friedel-Crafts reactions for biomolecular chemistry

Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably some of the most well-known and used synthetic methods for the preparation of small molecules but their use in biological and medical fields is relatively less frequent than the other reactions, possibly owing to the notion of their plausible incompatibility with biological systems. This review demonstrates advances in Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or -assisted processes, these reactions have garnered considerable interest in biochemistry, enzymology, and biocatalysis. Despite the challenges of reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated their utility for the construction and functionalization of all the four major biomolecules (i.e., nucleosides, carbohydrates/saccharides, lipids/fatty acids, and amino acids/peptides/proteins), and their diverse applications in biological, medical, and material fields are discussed. As the alkylation and acylation reactions are often fundamental educational components of organic chemistry courses, this review is intended for both experts and nonexperts by discussing their basic reaction patterns (with the depiction of each reaction mechanism in the ESI) and relevant real-world impacts in order to enrich chemical research and education. The significant growth of biomolecular Friedel-Crafts reactions described here is a testament to their broad importance and utility, and further development and investigations of the reactions will surely be the focus in the organic biomolecular chemistry fields.

Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse?

Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.

Ultraviolet Light Debondable Optically Clear Adhesives for Flexible Displays through Efficient Visible-Light Curing

With growing sustainability concerns, the need for products that facilitate easy disassembly and reuse has increased. Adhesives, initially designed for bonding, now face demands for selective removal, enabling rapid assembly-disassembly and efficient maintenance across industries. This need is particularly evident in the display industry, with the rise of foldable devices necessitating specialized adhesives. A novel optically clear adhesive (OCA) is presented for foldable display, featuring a unique UV-stimulated selective removal feature. This approach incorporates benzophenone derivatives into the polymer network, facilitating rapid debonding under UV irradiation. A key feature of this method is the adept use of visible-light-driven radical polymerization for OCA film fabrication. This method shows remarkable compatibility with various monomers and exhibits orthogonal reactivity to benzophenone, rendering it ideal for large-scale production. The resultant OCA not only has high transparency and balanced elasticity, along with excellent resistance to repeated folding, but it also exhibits significantly reduced adhesion when exposed to UV irradiation. By merging this customized formulation with strategically integrated UV-responsive elements, an effective solution is offered that enhances manufacturing efficiency and product reliability in the rapidly evolving field of sustainable electronics and displays. This research additionally contributes to eco-friendly device fabrication, aligning with emerging technology demands.

Tuning the Absorption, Fluorescence, Intramolecular Charge Transfer, and Intersystem Crossing in Spiro[fluorene]acridinone

In this work, we prepared a series of electron donor-acceptor systems based on spiro[fluorene-9,7'-dibenzo[c,h]acridine]-5'-one (SFDBAO). Our SFDBAOs consist of orthogonally positioned fluorenes and aromatic ketones. By fine-tuning the substitution of electron-donating pyrenes, the complex interplay among different excited-state decay channels and the overall impact of solvents on these decay channels were uncovered. Placing pyrene, for example, at the aromatic ketones resulted in a profound solvatochromism in the form of a bright charge-transfer (CT) emission spanning from yellow to red-NIR. In contrast, a dark non-emissive CT was noted upon pyrene substitution at the fluorenes. In apolar solvents, efficient triplet-excited state generation was observed for all SFDBAOs. Either charge transfer was concluded to mediate the intersystem crossing (ISC) in the case of pyrene substitution or the El-Sayed rule was applicable when lacking pyrene substitution as in the case of SFABAO. In polar solvents, charge separation is the sole decay upon pyrene substitution. Moreover, competition between ISC and CT lowered the triplet-excited state generation in SFDBAO.

1,3-Butadiene Dicarbofunctionalization Enabled by the Dual Role of Diaryl Ketone in Photo-HAT/Chromium Catalysis

We report a three-component Nozaki-Hiyama-Kishi type reaction of 1,3-dioxolane, 1,3-butadienes, and aldehydes to access masked aldehyde-incorporated homoallylic alcohols, facilitated by photo-hydrogen atom transfer (HAT)/chromium dual catalysis. The diaryl ketone serves dual roles both in the HAT process and in facilitating the turnover of the chromium catalyst. A range of functional groups are tolerated owing to the mild conditions. Both aromatic and aliphatic aldehydes are suitable substrates for coupling with several 1,3-butadienes and 1,3-dioxolane.

Creating a Defined Chirality in Amino Acids and Cyclic Dipeptides by Photochemical Deracemization

2,5-Diketopiperazines are cyclic dipeptides displaying a wide range of applications. Their enantioselective preparation has now been found possible from the respective racemates by a photochemical deracemization (53 examples, 74 % to quantitative yield, 71-99 % ee). A chiral benzophenone catalyst in concert with irradiation at λ=366 nm enables to establish the configuration at the stereogenic carbon atom C6 at will. If other stereogenic centers are present in the diketopiperazines they remain unaffected and a stereochemical editing is possible at a single position. Consecutive reactions, including the conversion into N-aryl or N-alkyl amino acids or the reduction to piperazines, occur without compromising the newly created stereogenic center. Transient absorption spectroscopy revealed that the benzophenone catalyst processes one enantiomer of the 2,5-diketopiperazines preferentially and enables a reversible hydrogen atom transfer that is responsible for the deracemization process. The remarkably long lifetime of the protonated ketyl radical implies a yet unprecedented mode of action.

A New Strategy of Chemical Photo Grafting Metal Organic Framework to Construct NH2-UiO-66/BiOBr/PVDF Photocatalytic Membrane for Synergistic Separation and Self-Cleaning Dyes

Photocatalytic membranes are typical multifunctional membranes that have emerged in recent years. The lack of active functional groups on the surface of membranes made of inert materials such as polyvinylidene fluoride(PVDF) makes it difficult to have a stable binding interaction with photocatalysts directly. Therefore, in this study, we developed a simple method to prepare NH2-UiO-66/BiOBr/PVDF(MUB) membranes for efficient dye treatment by grafting benzophenolic acid-functionalized NH2-UiO-66 onto the surface of membranes with photocatalytic properties under visible light irradiation using benzophenolic acid with photoinitiating ability as an anchor. The structural characteristics, photocatalytic properties, antifouling properties, and reusability of the composite membranes were investigated in subsequent experiments using a series of experiments and characterizations. The results showed that the benzophenone acid grafting method was stable and the nanoparticles were not easily dislodged. The MUB composite membrane achieved a higher dye degradation efficiency (99.2%) than the pristine PVDF membrane at 62.9% within a reaction time of 180 min. In addition, the composite membranes exhibited higher permeate fluxes for both pure and mixed dyes and also demonstrated outstanding water flux recovery (>96%) after the light self-cleaning cycle operation. This combination proved to improve the performance of the membranes instead of reducing them, increasing their durability and reusability, and helping to broaden the application areas of membrane filtration technology.

Solvatochromic and Aggregation-Induced Emission Active Nitrophenyl-Substituted Pyrrolidinone-Fused-1,2-Azaborine with a Pre-Twisted Molecular Geometry

Boron-nitrogen-containing heterocycles with extended conjugated π-systems such as polycyclic aromatic 1,2-azaborines, hold the fascination of organic chemists due to their unique optoelectronic properties. However, the majority of polycyclic aromatic 1,2-azaborines aggregate at high concentrations or in the solid-state, resulting in aggregation-caused quenching (ACQ) of emission. This practical limitation poses significant challenges for polycyclic aromatic 1,2-azaborines' use in many applications. Additionally, only a few solvatochromic polycyclic aromatic 1,2-azaborines have been reported and they all display minimal solvatochromism. Therefore, the scope of available polycyclic 1,2-azaborines needs to be expanded to include those displaying fluorescence at high concentration and in the solid-state as well as those that exhibit significant changes in emission intensity in various solvents due to different polarities. To address the ACQ issue, we evaluate the effect of a pre-twisted molecular geometry on the optoelectronic properties of polycyclic aromatic 1,2-azaborines. Specifically, three phenyl-substituted pyrrolidinone-fused 1,2-azaborines (PFAs) with similar structures and functionalized with diverse electronic moieties (-H, -NO2, -CN, referred to as PFA 1, 2, and 3, respectively) were experimentally and computationally studied. Interestingly, PFA 2 displays two distinct emission properties: 1) solvatochromism, in which its emission and quantum yields are tunable with respect to solvent polarity, and 2) fluorescence that can be completely "turned off" and "turned on" via aggregation-induced emission (AIE). This report provides the first example of a polycyclic aromatic 1,2-azaborine that displays both AIE and solvatochromism properties in a single BN-substituted backbone. According to time-dependent density function theory (TD-DFT) calculations, the fluorescence properties of PFA 2 can be explained by the presence of a low-lying n-π* charge transfer state inaccessible to PFA 1 or PFA 3. These findings will help in the design of future polycyclic aromatic 1,2-azaborines that are solvatochromic and AIE-active as well as in understanding how molecular geometry affects these compounds' optoelectronic properties.

Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides

Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity peptides. To overcome these problems, we established a scheme for ribosome display selection of peptide epitopes bound to monoclonal antibodies and then applied genetic code expansion with synthetic X-tRNAUAG reprogramming of the UAG codons (X = Tyr, Trp, or p-benzoyl-l-phenylalanine (pBzo-Phe)) to the scheme. Based on the assessment of the efficiency of in vitro translation with X-tRNAUAG, we carried out ribosome display selection with genetic code expansion using Trp-tRNAUAG, and we verified that affinity peptides could be identified efficiently regardless of the presence of UAG codons in the peptide coding sequences. Additionally, after evaluating the photo-cross-linking reactions of pBzo-Phe-incorporated peptides, we performed ribosome display selection of low-affinity peptides in combination with genetic code expansion using pBzo-Phe-tRNAUAG and photo-irradiation. The results demonstrated that sub-micromolar low-affinity peptide epitopes could be identified through the formation of photo-induced covalent bonds with monoclonal antibodies. Thus, the developed ribosome display techniques could contribute to the promotion of diverse peptide-based research.

Postsynthetic Photochemical Modification and 2D Structuring of Zr-MOF Thin Films Containing Benzophenone Linker Molecules

For the fabrication of next-generation MOF-based devices the availability of highly adaptable materials in suitable shapes is crucial. Here, we present thin films of a metal-organic framework (MOF) containing photoreactive benzophenone units. Crystalline, oriented and porous films of the zirconium-based bzpdc-MOF (bzpdc=benzophenone-4-4'-dicarboxylate) are prepared by direct growth on silicon or glass substrates. Via a subsequent photochemical modification of the Zr-bzpdc-MOF films, various properties can be tuned postsynthetically by covalent attachment of modifying agents. Apart from the modification with small molecules, also grafting-from polymerization reactions are possible. In a further extension, 2D structuring and photo-writing of defined structures is also possible, for example by using a photolithographic approach, paving the way towards micro-patterned MOF surfaces.

A genetically encodable and fluorogenic photo-crosslinker via photo-induced defluorination acyl fluoride exchange

We report a genetically encodable m-trifluoromethylaniline modified L-lysine (m-TFMAK) which defluorinates upon light activation and covalently conjugates to native residues via acyl fluoride exchange. The encoded m-TFMAK photo-crosslinks with temporal controllability, residue selectivity, and fluorogenic tracking features, making it suitable for identifying protein interactions in living systems.

Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin-Deubiquitylating Enzyme Interactions

Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C-terminal electrophiles (Ub-E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub-Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p-benzoyl-L-phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub-based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine-based chemistries.

Identification of photocrosslinking peptide ligands by mRNA display

Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.

Site-directed biochemical analyses reveal that the switchable C-terminus of Rpc31 contributes to RNA polymerase III transcription initiation

Rpc31 is a subunit in the TFIIE-related Rpc82/34/31 heterotrimeric subcomplex of Saccharomyces cerevisiae RNA polymerase III (pol III). Structural analyses of pol III have indicated that the N-terminal region of Rpc31 anchors on Rpc82 and further interacts with the polymerase core and stalk subcomplex. However, structural and functional information for the C-terminal region of Rpc31 is sparse. We conducted a mutational analysis on Rpc31, which uncovered a functional peptide adjacent to the highly conserved Asp-Glu-rich acidic C-terminus. This C-terminal peptide region, termed 'pre-acidic', is important for optimal cell growth, tRNA synthesis, and stable association of Rpc31 in the pre-initiation complex (PIC). Our site-directed photo-cross-linking to map protein interactions within the PIC reveal that this pre-acidic region specifically targets Rpc34 during transcription initiation, but also interacts with the DNA entry surface in free pol III. Thus, we have uncovered a switchable Rpc31 C-terminal region that functions in an initiation-specific protein interaction for pol III transcription.

Chitosan modified with bio-extract as an antibacterial coating with UV filtering feature

Benzophenone-3 grafted chitosan (CS-BP-3) was successfully synthesized and applied as an antibacterial coating for the first time. The grafting mechanism is based on the reaction between ketone and primary amine to form imine derivatives and the chemical structure of grafted chitosan was studied by Fourier transform infrared (FT-IR) spectroscopy. Water solubility of BP-3 is enhanced after covalently grafted on chitosan and consequently renders the chitosan coating with UV blocking property. Results of thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) further confirmed the thermal stability of BP-3 modified chitosan is enhanced. The CS-BP-3 coating was applied on a variety of substrates of glass, plastics, wood, and metal. The surface features of the coatings such as morphology, water contact angle (WCA), and surface roughness were investigated. The optical and thermal stabilities of the coatings under UV irradiation were studied for 16 h. Antibacterial activity of CS-BP-3 was evaluated against both Gram-negative and Gram-positive bacteria. And the results of bacterial inhibition by CS-BP-3 coating indicate its potential for future application in food packaging.

One-step fabrication of three-dimensional macropore copolymer-modified polycarbonate array by photo-crosslinking for protein immunoassay

A photocross-linked copolymer was prepared, and could rapidly form a macropore structure in phosphate buffer solution (PBS) without the addition of porogen. The photo-crosslinking process contained the crosslinking of the copolymer itself and that with the polycarbonate substrate. The three-dimensional (3D) surface was achieved through one-step photo-crosslinking of the macropore structure. The macropore structure can be finely regulated by multiple dimensions, including monomer structure of the copolymer, PBS and copolymer concentration. Compared with the two-dimensional (2D) surface, the 3D surface has a controllable structure, a high loading capacity (59 μg cm^-2) and immobilization efficiency (92%), and the effect of inhibiting the coffee ring for protein immobilization. Immunoassay results show that a 3D surface immobilized by IgG has high sensitivity (LOD value of 5 ng mL^-1) and broader dynamic range (0.005-50 μg mL^-1). This simple and structure-controllable method for preparing 3D surfaces modified by macropore polymer has great potential applications in the fields of biochips and biosensing.

Multifaceted View on the Mechanism of a Photochemical Deracemization Reaction

Upon irradiation in the presence of a chiral benzophenone catalyst (5 mol %), a racemic mixture of a given chiral imidazolidine-2,4-dione (hydantoin) can be converted almost quantitatively into the same compound with high enantiomeric excess (80-99% ee). The mechanism of this photochemical deracemization reaction was elucidated by a suite of mechanistic experiments. It was corroborated by nuclear magnetic resonance titration that the catalyst binds the two enantiomers by two-point hydrogen bonding. In one of the diastereomeric complexes, the hydrogen atom at the stereogenic carbon atom is ideally positioned for hydrogen atom transfer (HAT) to the photoexcited benzophenone. Detection of the protonated ketyl radical by transient absorption revealed hydrogen abstraction to occur from only one but not from the other hydantoin enantiomer. Quantum chemical calculations allowed us to visualize the HAT within this complex and, more importantly, showed that the back HAT does not occur to the carbon atom of the hydantoin radical but to its oxygen atom. The achiral enol formed in this process could be directly monitored by its characteristic transient absorption signal at λ ≅ 330 nm. Subsequent tautomerization leads to both hydantoin enantiomers, but only one of them returns to the catalytic cycle, thus leading to an enrichment of the other enantiomer. The data are fully consistent with deuterium labeling experiments and deliver a detailed picture of a synthetically useful photochemical deracemization reaction.

Multifunctional Photo-Cross-Linking Probes: From Target Protein Searching to Imaging Applications

Despite advances in genome sequencing technology, the complete molecular interaction networks reflecting the biological functions of gene products have not been fully elucidated due to the lack of robust molecular interactome profiling techniques. Traditionally, molecular interactions have been investigated in vitro by measuring their affinity. However, such a reductionist approach comes with throughput constraints and does not depict an intact living cell environment. Therefore, molecular interactions in live cells must be captured to minimize false-positive results. The photo-cross-linking technique is a promising tool because the production of a temporally controlled reactive functional group can be induced using light exposure. Photoaffinity labeling is used in biochemistry and medicinal chemistry for bioconjugation, including drug and antibody conjugation, target protein identification of bioactive compounds, and fluorescent labeling of target proteins. This Account summarizes recent advances in multifunctional photo-cross-linkers for drug target identification and bioimaging. In addition to our group's contributions, we reviewed the most notable examples from the last few decades to provide a comprehensive overview of how this field is evolving. Based on cross-linking chemistry, photo-cross-linkers are classified as either (i) reactive intermediate-generating or (ii) electrophile-generating. Reactive intermediates generating photoaffinity tags have been extensively modified to target a molecule of interest using aryl azide, benzophenone, diazirine, diazo, and acyl silanes. These species are highly reactive and can form covalent bonds, irrespective of residue. Their short lifetime is ideal for the instant capture and labeling of biomolecules. Recently, photocaged electrophiles have been investigated to take advantage of their residue selectivity and relatively high yield for adduct formation with tetrazole, nitrobenzyl alcohol, o-nitrophenylethylene, pyrone, and pyrimidone. Multifunctional photo-cross-linkers for two parallel practical applications have been developed using both classes of photoactivatable groups. Unbiased target interactome profiling of small-molecule drugs requires a challenging structure-activity relationship study (SAR) step to retain the nature or biological activity of the lead compound, which led to the design of a multifunctional "minimalist tag" comprising a bio-orthogonal handle, a photoaffinity labeling group, and functional groups to load target molecules. In contrast, fluorogenic photo-cross-linking is advantageous for bioimaging because it does not require an additional bio-orthogonal reaction to introduce a fluorophore to the minimalist tag. Our group has made progress on minimalist tags and fluorogenic photo-cross-linkers through fruitful collaborations with other groups. The current range of photoactivation reactions and applications demonstrate that photoaffinity tags can be improved. We expect exciting days in the rational design of new multifunctional photo-cross-linkers, particularly clinically interesting versions used in photodynamic or photothermal therapy.

Unraveling Structural Information of Multi-Domain Nonribosomal Peptide Synthetases by Using Photo-Cross-Linking Analysis with Genetic Code Expansion

Nonribosomal peptide synthetases (NRPSs) are large, multifunctional enzymes that facilitate the stepwise synthesis of modified peptides, many of which serve as important pharmaceutical products. Typically, NRPSs contain one module for the incorporation of one amino acid into the growing peptide chain. A module consists of the domains required for activation, covalent binding, condensation, termination, and optionally modification of the aminoacyl or peptidyl moiety. We here describe a protocol using genetically encoded photo-cross-linking amino acids to probe the 3D architecture of NRPSs by determining spatial proximity constraints. p-benzoyl-L-phenylalanine (BpF) is incorporated at positions of presumed contact interfaces between domains. The covalent cross-link products are visualized by SDS-PAGE-based methods and precisely mapped by tandem mass spectrometry. Originally intended to study the communication (COM) domains, a special pair of docking domains of unknown structure between two interacting subunits of one NRPS system, this cross-linking approach was also found to be useful to interrogate the spatial proximity of domains that are not connected on the level of the primary structure. The presented photo-cross-linking technique thus provides structural insights complementary to those obtained by protein crystallography and reports on the protein in solution.

Repurposing Photosensitizer Proteins Through Genetic Code Expansion to Facilitate Photo-Biocatalysis

Artificial photoenzymes with noncanonical photo-redox cofactors have paved the way for enzyme rational design and the creation of new-to-nature biocatalysts. Genetically encoded photo-redox cofactors endow photoenzymes with enhanced or novel activities that catalyze numerous transformations with high efficiency. Herein, we describe a protocol of repurposing photosensitizer proteins (PSP) through genetic code expansion to facilitate multiple photocatalytic conversions including photo-activated dehalogenation of aryl halides, CO₂ to CO and CO₂ to formic acid reduction. The methods for expression, purification, and characterization of the PSP are detailed. The installation of the catalytic modules and the utilization of PSP-based artificial photoenzymes for photoenzymatic CO₂ reduction and dehalogenation are also described.

A Photochemical Macrocyclization Route to Asymmetric Strained [3.2] Paracyclophanes

The intricate frameworks of paracyclophanes are an important target for synthesis since they are found in various chiral auxiliaries, solar cells, high-performance plastics, pharmaceuticals, and molecular machines. Whereas numerous methods exist for the preparation of symmetric paracyclophanes, protocols for the efficient synthesis of strained asymmetric scaffolds are limited. Here we report a remarkably simple photochemical route to strained [3.2]paracyclophanes starting from readily available educts. By way of NMR and X-ray analyses, we discovered that UV-irradiation of an aromatic carboxylic ester tethered to a toluene moiety leads to the intramolecular formation of a new C-C bond, with loss of an alcohol. A systematic evaluation of the reaction conditions and substituents, as well as radical starter and triplet quenching experiments, point to a reaction mechanism involving an excited triplet state and hydrogen atom transfer. The new method proved to be robust and versatile enabling the synthesis of a range of cyclophanes with different substitutions, including an unusual diastereoisomer with two planar chiral centers, and thus proved to be a valuable addition to the synthetic toolbox.

Light-empowered contra-thermodynamic stereochemical editing

Creating, conserving and modifying the stereochemistry of organic compounds has been the subject of significant research efforts in synthetic chemistry. Most synthetic routes are designed according to the stereoselectivity-determining step. Stereochemical editing is an alternative strategy, wherein the chiral-defining or geometry-defining steps are independent of the construction of the major scaffold or complexity. It enables late-stage alterations of stereochemistry and can generate isomers from a single compound. However, in many instances, stereochemical editing processes are contra-thermodynamic, meaning the transformation is unfavourable. To overcome this barrier, photocatalysis uses photogenerated radical species and introduces thermochemical biases. A range of synthetically valuable contra-thermodynamic stereochemical editing processes have been invented, including deracemization of chiral molecules, positional alkene isomerization and dynamic epimerization of sugars and diols. In this Review, we highlight the fundamental mechanisms of visible-light photocatalysis and the general reactivity modes of the photogenerated radical intermediates towards contra-thermodynamic stereochemical editing processes.

Dual role of benzophenone enables a fast and scalable C-4 selective alkylation of pyridines in flow

The efficient C-4 selective modification of pyridines is a major challenge for the synthetic community. Current strategies are plagued with at least one drawback regarding functional group-tolerant electronic activation of the heteroarene, mild generation of the required alkyl radicals, regioselectivity, safety and/or scalability. Herein, we describe a fast, safe and scalable flow process which allows preparation of said C-4 alkylated pyridines. The process involves a photochemical hydrogen atom transfer (HAT) event to generate the carbon-centered radicals needed to alkylate the C-2 blocked pyridine. In a two-step streamlined flow process, this light-mediated alkylation step is combined with a nearly instantaneous inline removal of the blocking group. Notably, cheap benzophenone plays a dual role in the pyridine alkylation mechanism by activating the hydrocarbon feedstock reagents via a HAT mechanism, and by acting as a benign, terminal oxidant. The key role of benzophenone in the operative reaction mechanism has also been revealed through a combination of experimental and computational studies.

Direct patterning of colloidal quantum dots with adaptable dual-ligand surface

Colloidal quantum dots (QDs) stand at the forefront of a variety of photonic applications given their narrow spectral bandwidth and near-unity luminescence efficiency. However, integrating luminescent QD films into photonic devices without compromising their optical or transport characteristics remains challenging. Here we devise a dual-ligand passivation system comprising photocrosslinkable ligands and dispersing ligands to enable QDs to be universally compatible with solution-based patterning techniques. The successful control over the structure of both ligands allows the direct patterning of dual-ligand QDs on various substrates using commercialized photolithography (i-line) or inkjet printing systems at a resolution up to 15,000 pixels per inch without compromising the optical properties of the QDs or the optoelectronic performance of the device. We demonstrate the capabilities of our approach for QD-LED applications. Our approach offers a versatile way of creating various structures of luminescent QDs in a cost-effective and non-destructive manner, and could be implemented in nearly all commercial photonics applications where QDs are used.

Photochemical Ring Contraction of 5,5-Dialkylcyclopent-2-enones and in situ Trapping by Primary Amines

If substituted in the 5,5-position, cyclopent-2-enones undergo a smooth photochemical rearrangement to ketenes. A concomitant cyclopropane formation occurs due to a 1,3-shift of the C5 carbon atom from the carbonyl carbon atom (C1) to carbon atom C3. In this study, the cyclopropyl-substituted ketene intermediates were trapped in situ by primary amines providing an efficient entry into 2,2-disubstituted cyclopropaneacetic amides (24 examples, 49-95% yield). A remarkable feature of the reaction is the fact that the photochemical rearrangement can occur from either the first excited singlet (S₁) or the respective triplet state (T₁). In line with experimental results (triplet quenching, sensitization), XMS-CASPT2 calculations support the existence of efficient reaction pathways to the intermediate ketene both on the singlet and on the triplet hypersurface.

A Photo-Crosslinking Approach to Identify Class II SUMO-1 Binders

The small ubiquitin-like modifier (SUMO) is involved in various cellular processes and mediates known non-covalent protein-protein interactions by three distinct binding surfaces, whose interactions are termed class I to class III. While interactors for the class I interaction, which involves binding of a SUMO-interacting motif (SIM) to a hydrophobic groove in SUMO-1 and SUMO-2/3, are widely abundant, only a couple of examples have been reported for the other two types of interactions. Class II binding is conveyed by the E67 loop region on SUMO-1. Many previous studies to identify SUMO binders using pull-down or microarray approaches did not strategize on the SUMO binding mode. Identification of SUMO binding partners is further complicated due to the typically transient and low affinity interactions with the modifier. Here we aimed to identify SUMO-1 binders selectively enriched for class II binding. Using a genetically encoded photo-crosslinker approach, we have designed SUMO-1 probes to covalently capture class II SUMO-1 interactors by strategically positioning the photo-crosslinking moiety on the SUMO-1 surface. The probes were validated using known class II and class I binding partners. We utilized the probe with p-benzoyl-phenylalanine (BzF, also termed BpF or Bpa) at the position of Gln69 to identify binding proteins from mammalian cell extracts using mass spectrometry. By comparison with results obtained with a similarly designed SUMO-1 probe to target SIM-mediated binders of the class I type, we identified 192 and 96 proteins specifically enriched by either probe, respectively. The implicated preferential class I or class II binding modes of these proteins will further contribute to unveiling the complex interplay of SUMO-1-mediated interactions.

Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins

Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.

Chemo-Enzymatic Modification of the 5' Cap To Study mRNAs

The central dogma of molecular biology hinges on messenger RNA (mRNA), which presents a blueprint of the genetic information encoded in the DNA and serves as a template for translation into proteins. In addition to its fundamental importance in basic research, this class of biomolecules has recently become the first approved Covid vaccine, underscoring its utility in medical applications.Eukaryotic mRNA is heavily processed, including the 5' cap as the primary hallmark. This 5' cap protects mRNA from degradation by exoribonucleases but also interacts specifically with several proteins and enzymes to ensure mRNA turnover and processing, like splicing, export from the nucleus to the cytoplasm, and initiation of translation. The absence of a 5' cap leads to a strong immune response, and the methylation status contributes to distinguishing self from non-self RNA.Non-natural modifications of the 5' cap provide an avenue to label mRNAs and make them accessible to analyses, which is important to study their cellular localization, trafficking, and binding partners. They bear potential to engineer mRNAs, e.g., more stable or immunogenic mRNAs that are still translated, by impacting select interactions in a distinct manner. The modification of the 5' cap itself is powerful as it can be applied to make long mRNAs (∼1000 nt, not directly accessible by solid-phase synthesis) by in vitro transcription.This Account describes our contribution to the field of chemo-enzymatic modification of mRNA at the 5' cap. Our approach relies on RNA methyltransferases (MTases) with promiscuous activity on analogues of their natural cosubstrate S-adenosyl-L-methionine (AdoMet). We will describe how RNA MTases in combination with non-natural cosubstrates provide access to site-specific modification of different positions of the 5' cap, namely, the N² and N7 position of guanosine and the N⁶ position of adenosine as the transcription start nucleotide (TSN) and exemplify strategies to make long mRNAs with modified 5' caps.We will compare the chemical and enzymatic synthesis of the AdoMet analogues used for this purpose. We could overcome previous limitations in methionine adenosyltransferase (MAT) substrate scope by engineering variants (termed PC-MATs) with the ability to convert methionine analogues with benzylic and photocaging groups at the sulfonium ion.The final part of this Account will highlight applications of the modified mRNAs. Like in many chemo-enzymatic approaches, a versatile strategy is to install small functional groups enzymatically and use them as handles in subsequent bioorthogonal reactions. We showed fluorescent labeling of mRNAs via different types of click chemistry in vitro and in cells. In a second line of applications, we used the handles to make mRNAs amenable for analyses, most notably next-generation sequencing. In the case of extremely promiscuous enzymes, the direct installation of photo-cross-linking groups was successful also and provided a way to covalently bind protein-interaction partners. Finally, the non-natural modifications of mRNAs can also modulate the properties of mRNAs. Propargylation of A_m as the transcription start nucleotide at its N⁶ position maintained the translation of mRNAs but increased their immunogenicity. The installation of photocaging groups provides a way to revert these effects and control interactions by light.

Charting the Chemical and Mechanistic Scope of Light-Triggered Protein Ligation

The creation of discrete, covalent bonds between a protein and a functional molecule like a drug, fluorophore, or radiolabeled complex is essential for making state-of-the-art tools that find applications in basic science and clinical medicine. Photochemistry offers a unique set of reactive groups that hold potential for the synthesis of protein conjugates. Previous studies have demonstrated that photoactivatable desferrioxamine B (DFO) derivatives featuring a para-substituted aryl azide (ArN₃) can be used to produce viable zirconium-89-radiolabeled monoclonal antibodies (⁸⁹Zr-mAbs) for applications in noninvasive diagnostic positron emission tomography (PET) imaging of cancers. Here, we report on the synthesis, ⁸⁹Zr-radiochemistry, and light-triggered photoradiosynthesis of ⁸⁹Zr-labeled human serum albumin (HSA) using a series of 14 different photoactivatable DFO derivatives. The photoactive groups explore a range of substituted, and isomeric ArN₃ reagents, as well as derivatives of benzophenone, a para-substituted trifluoromethyl phenyl diazirine, and a tetrazole species. For the compounds studied, efficient photochemical activation occurs inside the UVA-to-visible region of the electromagnetic spectrum (∼365-450 nm) and the photochemical reactions with HSA in water were complete within 15 min under ambient conditions. Under standardized experimental conditions, photoradiosynthesis with compounds 1-14 produced the corresponding ⁸⁹ZrDFO-PEG₃-HSA conjugates with decay-corrected isolated radiochemical yields between 18.1 ± 1.8% and 62.3 ± 3.6%. Extensive density functional theory (DFT) calculations were used to explore the reaction mechanisms and chemoselectivity of the light-induced bimolecular conjugation of compounds 1-14 to protein. The photoactivatable DFO-derivatives operate by at least five distinct mechanisms, each producing a different type of bioconjugate bond. Overall, the experimental and computational work presented here confirms that photochemistry is a viable option for making diverse, functionalized protein conjugates.

Photochemical modifications for DNA/RNA oligonucleotides

Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.

Electrotransfer of Immunoprobes through Thin-Layer Polyacrylamide Gels

Hydrogels are important structural and operative components of microfluidic systems, finding diverse utility in biological sample preparation and interrogation. One inherent challenge for integrating hydrogels into microfluidic tools is thermodynamic molecular partitioning, which reduces the in-gel concentration of molecular solutes (e.g., biomolecular regents), as compared to the solute concentration in an applied solution. Consequently, biomolecular reagent access to in-gel scaffolded biological samples (e.g., encapsulated cells, microbial cultures, target analytes) is adversely impacted in hydrogels. Further, biomolecular reagents are typically introduced to the hydrogel via diffusion. This passive process requires long incubation periods compared to active biomolecular delivery techniques. Electrotransfer is an active technique used in Western blots and other gel-based immunoassays that overcomes limitations of size exclusion (increasing the total probe mass delivered into gel) and expedites probe delivery, even in millimeter-thick slab gels. While compatible with conventional slab gels, electrotransfer has not been adapted to thin gels (50-250 μm thick), which are of great interest as components of open microfluidic devices (vs enclosed microchannel-based devices). Mechanically delicate, thin gels are often mounted on rigid support substrates (glass, plastic) that are electrically insulating. Consequently, to adapt electrotransfer to thin-gel devices, we replace rigid insulating support substrates with novel, mechanically robust, yet electrically conductive nanoporous membranes. We describe grafting nanoporous membranes to thin-polyacrylamide-gel layers via silanization, characterize the electrical conductivity of silane-treated nanoporous membranes, and report the dependence of in-gel immunoprobe concentration on transfer duration for passive diffusion and active electrotransfer. Alternative microdevice component layers─including the mechanically robust, electrically conductive nanoporous membranes reported here─provide new functionality for integration into an increasing array of open microfluidic systems.

Thermal Response and Thermochromism of Methyl Red-Based Copolymer Systems - Coupled Responsiveness in Critical Solution Behaviour and Optical Absorption Properties

Until now, only limited experimental knowledge and sparse theoretical treatment about the mechanisms of thermochromism of azo dyes in solution has been available. Especially the coupling of thermoresponsiveness of polymers...

Photo-crosslinking and surface-attachment of polyvinyl alcohol nanocoatings by C,H insertion to customize their swelling behavior and stability in polar media

Benzophenone-modified polyvinyl alcohol is synthesized, processed to nanocoatings and converted to UV-crosslinked surface-bound polymer networks.

Photochemical Deracemization at sp3-Hybridized Carbon Centers via a Reversible Hydrogen Atom Transfer

A photochemical deracemization of 5-substituted 3-phenylimidazolidine-2,4-diones (hydantoins) is reported (27 examples, 69%-quant., 80-99% ee). The reaction is catalyzed by a chiral diarylketone which displays a two-point hydrogen bonding site. Mechanistic evidence (DFT calculations, radical clock experiments, H/D labeling) suggests the reaction to occur by selective hydrogen atom transfer (HAT). Upon hydrogen binding, one substrate enantiomer displays the hydrogen atom at the stereogenic center to the photoexcited catalyst allowing for a HAT from the substrate and eventually for its conversion into the product enantiomer. The product enantiomer is not processed by the catalyst and is thus enriched in the photostationary state.

One-Step Synthesis of Photoaffinity Probes for Live-Cell MS-Based Proteomics

We present a one-step Ugi reaction protocol for the expedient synthesis of photoaffinity probes for live-cell MS-based proteomics. The reaction couples an amine affinity function with commonly used photoreactive groups, and a variety of handle functionalities. Using this technology, a series of pan-BET (BET: bromodomain and extra-terminal domain) selective bromodomain photoaffinity probes were obtained by parallel synthesis. Studies on the effects of photoreactive group, linker length and irradiation wavelength on photocrosslinking efficiency provide valuable insights into photoaffinity probe design. Optimal probes were progressed to MS-based proteomics to capture the BET family of proteins from live cells and reveal their potential on- and off-target profiles.

Clinical Antiviral Drug Arbidol Inhibits Infection by SARS-CoV-2 and Variants through Direct Binding to the Spike Protein

Arbidol (ARB) is a broad-spectrum antiviral drug approved in Russia and China for the treatment of influenza. ARB was tested in patients as a drug candidate for the treatment at the early onset of COVID-19 caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite promising clinical results and multiple ongoing trials, preclinical data are lacking and the molecular mechanism of action of ARB against SARS-CoV-2 remains unknown. Here, we demonstrate that ARB binds to the spike viral fusion glycoprotein of the SARS-CoV-2 Wuhan strain as well as its more virulent variants from the United Kingdom (strain B.1.1.7) and South Africa (strain B.1.351). We pinpoint the ARB binding site on the S protein to the S2 membrane fusion domain and use an infection assay with Moloney murine leukemia virus (MLV) pseudoviruses (PVs) pseudotyped with the S proteins of the Wuhan strain and the new variants to show that this interaction is sufficient for the viral cell entry inhibition by ARB. Finally, our experiments reveal that the ARB interaction leads to a significant destabilization and eventual lysosomal degradation of the S protein in cells. Collectively, our results identify ARB as the first clinically approved small molecule drug binder of the SARS-CoV-2 S protein and place ARB among the more promising drug candidates for COVID-19.

Solvent Effects on Ultrafast Photochemical Pathways

Photochemical reactions are increasingly being used for chemical and materials synthesis, for example, in photoredox catalysis, and generally involve photoexcitation of molecular chromophores dissolved in a liquid solvent. The choice of solvent influences the outcomes of the photochemistry because solute-solvent interactions modify the energies of and crossings between electronic states of the chromophores, and they affect the evolving structures of the photoexcited molecules. Ultrafast laser spectroscopy methods with femtosecond to picosecond time resolution can resolve the dynamics of these photoexcited molecules as they undergo structural and electronic changes, relax back to the ground state, dissipate their excess internal energy to the surrounding solvent, or undergo photochemical reactions. In this Account, we illustrate how experimental studies using ultrafast lasers can reveal the influences that different solvents or cosolutes exert on the photoinduced nonadiabatic dynamics of internal conversion and intersystem crossing in nonradiative relaxation pathways. Although the environment surrounding a solute molecule is rapidly changing, with fluctuations in the coordination to neighboring solvent molecules occurring on femtosecond or picosecond time scales, we show that it is possible to photoexcite selectively only those molecular chromophores transiently experiencing specific solute-solvent interactions such as intermolecular hydrogen bonding.The effects of different solvation environments on the photodynamics are illustrated using four selected examples of photochemical processes in which the solvent has a marked effect on the outcomes. We first consider two aromatic carbonyl compounds, benzophenone and acetophenone, which are known to undergo fast intersystem crossing to populate the first excited triplet state on time scales of a few picoseconds. We show that the nonadiabatic excited-state dynamics are modified by transient hydrogen bonding of the carbonyl group to a protic solvent or by coordination to a metal cation cosolute. We then examine how different solvents modify the competition between two alternative relaxation pathways in a photoexcited UVA-sunscreen molecule, diethylamino hydroxybenzoyl hexyl benzoate (DHHB). This relaxation back to the ground electronic state is an essential part of the effective operation of the sunscreen compound, but the dynamics are sensitive to the surrounding environment. Finally, we consider how solvents of different polarity affect the energies and lifetimes of excited states with locally excited or charge-transfer character in heterocyclic organic compounds used as excited-state electron donors for photoredox catalysis. With these and other examples, we seek to develop a molecular level understanding of how the choice of solution environment might be used to control the outcomes of photochemical reactions.

A Metal-Free Visible-Light Photoredox Construction and Direct C-H Functionalization of Pyridines: Green Synthesis of Polysubstituted Picolinaldehydes

The development of a novel environmental benign and sustainable synthetic method for highly efficient construction and direct C-H functionalization of N-heterocycles remains a pivotal central research topic for organic and medicinal chemistry. Herein, a novel visible-light-enabled biomimetic aza-6π electrocyclization for efficient assembly of diverse pyridines and further tandem Minisci-type reaction were developed. A broad spectrum of polysubstituted picolinaldehydes were readily constructed with high efficacy and good functional group tolerance under metal- and oxidant-free conditions.

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Colicins are protein antibiotics deployed by Escherichia coli to eliminate competing strains. Colicins frequently exploit outer membrane (OM) nutrient transporters to penetrate the selectively permeable bacterial cell envelope. Here, by applying live-cell fluorescence imaging, we were able to monitor the entry of the pore-forming toxin colicin B (ColB) into E. coli and localize it within the periplasm. We further demonstrate that single-stranded DNA coupled to ColB can also be transported to the periplasm, emphasizing that the import routes of colicins can be exploited to carry large cargo molecules into bacteria. Moreover, we characterize the molecular mechanism of ColB association with its OM receptor FepA by applying a combination of photoactivated cross-linking, mass spectrometry, and structural modeling. We demonstrate that complex formation is coincident with large-scale conformational changes in the colicin. Thereafter, active transport of ColB through FepA involves the colicin taking the place of the N-terminal half of the plug domain that normally occludes this iron transporter. IMPORTANCE Decades of excessive use of readily available antibiotics has generated a global problem of antibiotic resistance and, hence, an urgent need for novel antibiotic solutions. Bacteriocins are protein-based antibiotics produced by bacteria to eliminate closely related competing bacterial strains. Bacteriocin toxins have evolved to bypass the complex cell envelope in order to kill bacterial cells. Here, we uncover the cellular penetration mechanism of a well-known but poorly understood bacteriocin called colicin B that is active against Escherichia coli. Moreover, we demonstrate that the colicin B-import pathway can be exploited to deliver conjugated DNA cargo into bacterial cells. Our work leads to a better understanding of the way bacteriocins, as potential alternative antibiotics, execute their mode of action as well as highlighting how they might even be exploited in the genomic manipulation of Gram-negative bacteria.