Photochemical Skeletal Editing of Pyridines to Bicyclic Pyrazolines and Pyrazoles.

We present an efficient one-pot photochemical skeletal editing protocol for the transformation of pyridines into diverse bicyclic pyrazolines and pyrazoles under mild conditions. The method requires no metals, photocatalysts, or additives and allows for the selective removal of specific carbon atoms from pyridines, allowing for unprecedented versatility. Our approach offers a convenient and efficient means for the late-stage modification of complex drug molecules by replacing the core pyridine skeleton. Moreover, we have successfully scaled up this procedure in stop-flow and flow-chemistry systems, showcasing its applicability to intricate transformations such as the Diels-Alder reaction, hydrogenation, [3 + 2] cycloaddition, and Heck reaction. Through control experiments and DFT calculations, we provide insights into the mechanistic underpinnings of this skeletal editing protocol.

Comparison of Cyclic and Linear PEG Conjugates.

Bioconjugation of polymers to proteins is a method to impart improved stability and pharmacokinetic properties to biologic systems. However, the precise effects of polymer architecture on the resulting bioconjugates are not well understood. Particularly, cyclic polymers are known to possess unique features such as a decreased hydrodynamic radius when compared to their linear counterparts of the same molecular weight, but have not yet been studied. Here, we report the first bioconjugation of a cyclic polymer, poly(ethylene glycol) (PEG), to a model protein, T4 lysozyme, containing a single engineered cysteine residue (V131C). We compare the stability and activity of this conjugate with those of a linear PEG-T4 lysozyme analogue of similar molecular weight. Furthermore, we used molecular dynamics (MD) simulations to determine the behavior of the polymer-protein conjugates in solution. We introduce cyclic polymer-protein conjugates as potential candidates for the improvement of biologic therapeutics.

Why •CF2H is nucleophilic but •CF3 is electrophilic in reactions with heterocycles.

Radical substitution is a useful method to functionalize heterocycles, as in the venerable Minisci reaction. Empirically observed regiochemistries indicate that the CF2H radical has a nucleophilic character similar to alkyl radicals, but the CF3 radical is electrophilic. While the difference between •CH3 and •CF3 is well understood, the reason that one and two Fs make little difference but the third has a large effect is puzzling. DFT calculations with M06-2X both reproduce experimental selectivities and also lead to an explanation of this difference. Theoretical methods reveal how the F inductive withdrawal and conjugative donation alter radical properties, but only CF3 becomes decidedly electrophilic toward heterocycles. Here, we show a simple model to explain the radical orbital energy trends and resulting nucleophilicity or electrophilicity of fluorinated radicals.

Characterizing Hydroxyl Radical Formation from the Light-Driven Fe(II)-Peracetic Acid Reaction, a Key Process for Aerosol-Cloud Chemistry.

The reaction of peracetic acid (PAA) and Fe(II) has recently gained attention due to its utility in wastewater treatment and its role in cloud chemistry. Aerosol-cloud interactions, partly mediated by aqueous hydroxyl radical (OH) chemistry, represent one of the largest uncertainties in the climate system. Ambiguities remain regarding the sources of OH in the cloud droplets. Our research group recently proposed that the dark and light-driven reaction of Fe(II) with peracids may be a key contributor to OH formation, producing a large burst of OH when aerosol particles take up water as they grow to become cloud droplets, in which reactants are consumed within 2 min. In this work, we quantify the OH production from the reaction of Fe(II) and PAA across a range of physical and chemical conditions. We show a strong dependence of OH formation on ultraviolet (UV) wavelength, with maximum OH formation at λ = 304 ± 5 nm, and demonstrate that the OH burst phenomenon is unique to Fe(II) and peracids. Using kinetics modeling and density functional theory calculations, we suggest the reaction proceeds through the formation of an [Fe(II)-(PAA)2(H2O)2] complex, followed by the formation of a Fe(IV) complex, which can also be photoactivated to produce additional OH. Determining the characteristics of OH production from this reaction advances our knowledge of the sources of OH in cloudwater and provides a framework to optimize this reaction for OH output for wastewater treatment purposes.

Evaluation of Retro-Aldol vs Retro-Carbonyl-Ene Mechanistic Pathways in a Complexity-Generating C-C Bond Fragmentation.

We report an experimental and computational investigation of the likely mechanism of a cascade reaction. The reaction involves an intramolecular Diels-Alder reaction, followed by a C-C bond cleavage, to afford a complex bridged bicyclic product. As multiple reaction pathways could be envisioned for the latter step, the mechanism of the C-C bond cleavage step was investigated. Two reasonable reaction pathways were evaluated. Both computations and experiments indicate that the C-C bond cleavage step proceeds by a retro-carbonyl-ene pathway rather than a retro-aldol pathway. This report underscores the synergy between computational and experimental studies and establishes the mechanism of an interesting complexity-generating transformation.

Iron Heme Enzyme-Catalyzed Cyclopropanations with Diazirines as Carbene Precursors: Computational Explorations of Diazirine Activation and Cyclopropanation Mechanism.

The mechanism of cyclopropanations with diazirines as air-stable and user-friendly alternatives to commonly employed diazo compounds within iron heme enzyme-catalyzed carbene transfer reactions has been studied by means of density functional theory (DFT) calculations of model systems, quantum mechanics/molecular mechanics (QM/MM) calculations, and molecular dynamics (MD) simulations of the iron carbene and the cyclopropanation transition state in the enzyme active site. The reaction is initiated by a direct diazirine-diazo isomerization occurring in the active site of the enzyme. In contrast, an isomerization mechanism proceeding via the formation of a free carbene intermediate in lieu of a direct, one-step isomerization process was observed for model systems. Subsequent reaction with benzyl acrylate takes place through stepwise C-C bond formation via a diradical intermediate, delivering the cyclopropane product. The origin of the observed diastereo- and enantioselectivity in the enzyme was investigated through MD simulations, which indicate a preferred formation of the cis-cyclopropane by steric control.

Spirostrain-Accelerated Chemiexcitation of Dioxetanes Yields Unprecedented Detection Sensitivity in Chemiluminescence Bioassays.

Chemiluminescence is a fascinating phenomenon that involves the generation of light through chemical reactions. The light emission from adamantyl-phenoxy-1,2-dioxetanes can glow from minutes to hours depending on the specific substituent present on the dioxetane molecule. In order to improve the light emission properties produced by these chemiluminescent luminophores, it is necessary to induce the chemiexcitation rate to a flash mode, wherein the bulk of light is emitted instantly rather than slowly over time. We report the realization of this goal through the incorporation of spirostrain release into the decomposition of 1,2-dioxetane luminophores. DFT computational simulations provided support for the hypothesis that the spiro-cyclobutyl substituent accelerates chemiexcitation as compared to the unstrained adamantyl substituent. Spiro-linking of cyclobutane and oxetane units led to greater than 100-fold and 1000-fold emission enhancement, respectively. This accelerated chemiexcitation rate increases the detection sensitivity for known chemiluminescent probes to the highest signal-to-noise ratio documented to date. A turn-ON probe, containing a spiro-cyclobutyl unit, for detecting the enzyme ß-galactosidase exhibited a limit of detection value that is 125-fold more sensitive than that for the previously described adamantyl analogue. This probe was also able to instantly detect and image ß-gal activity with enhanced sensitivity in E. coli bacterial assays.

A 21st Century View of Allowed and Forbidden Electrocyclic Reactions.

In 1965, Woodward and Hoffmann proposed a theory to predict the stereochemistry of electrocyclic reactions, which, after expansion and generalization, became known as the Woodward-Hoffmann Rules. Subsequently, Longuet-Higgins and Abrahamson used correlation diagrams to propose that the stereoselectivity of electrocyclizations could be explained by the correlation of reactant and product orbitals with the same symmetry. Immediately thereafter, Hoffmann and Woodward applied correlation diagrams to explain the mechanism of cycloadditions. We describe these discoveries and their evolution. We now report an investigation of various electrocyclic reactions using DFT and CASSCF. We track the frontier molecular orbitals along the intrinsic reaction coordinate and modeled trajectories and examine the correlation between HOMO and LUMO for thermally forbidden systems. We also investigate the electrocyclizations of several highly polarized systems for which the Houk group had predicted that donor-acceptor substitution can induce zwitterionic character, thereby providing low-energy pathways for formally forbidden reactions. We conclude with perspectives on the field of pericyclic reactions, including a refinement as the meaning of Woodward and Hoffmann's "Violations. There are none!" Lastly, we comment on the burgeoning influence of computations on all fields of chemistry.

A Synergistic Antibacterial Study of Copper-Doped Polydopamine on Ti3C2Tx Nanosheets with Enhanced Photothermal and Fenton-like Activities.

In response to the trend of drug-resistant and super bacteria, the existing single antibacterial methods are not sufficient to kill bacteria, and the development of multifunctional antibacterial nanomaterials is urgent. Our study aims to construct copper-doped polydopamine-coated Ti3C2Tx (CuPDA@Ti3C2Tx) with an enhanced photothermal property and Fenton-like activity. The nanocomposite hydrogel consisting of CuPDA@Ti3C2Tx and alginate can improve the antioxidant activity of two-dimensional MXene nanosheets by coating them with a thin layer of PDA nanofilm. Meanwhile, Cu ions are adsorbed through the coordination of PDA-rich oxygen-containing functional groups and amino groups. Calcium ions were further used to crosslink sodium alginate to obtain antibacterial hydrogel materials with combined chemotherapy and photothermal therapy properties. The photothermal conversion efficiency of CuPDA@Ti3C2Tx is as high as 57.7% and the antibacterial rate of Escherichia coli reaches 96.12%. The photothermal effect leads to oxidative stress in bacteria, increases cell membrane permeability, and a high amount of ROS and copper ions enter the interior of the bacteria, causing protein denaturation and DNA damage, synergistically leading to bacterial death. Our study involves a multifunctional synergistic antibacterial nanodrug platform, which is conducive to the development of high-performance antibacterial agents and provides important research ideas for solving the problem of drug-resistant bacteria.

Genome Mining from Agriculturally Relevant Fungi Led to a d-Glucose Esterified Polyketide with a Terpene-like Core Structure.

Comparison of biosynthetic gene clusters (BGCs) found in devastating plant pathogens and biocontrol fungi revealed an uncharacterized and conserved polyketide BGC. Genome mining identified the associated metabolite to be treconorin, which has a terpene-like, trans-fused 5,7-bicyclic core that is proposed to derive from a (4 + 3) cycloaddition. The core is esterified with d-glucose, which derives from the glycosidic cleavage of a trehalose ester precursor. This glycomodification strategy is different from the commonly observed glycosylation of natural products.

Computational Exploration of the Thermal Rearrangement of Basketene: One Forbidden versus Two Allowed Pericyclic Reactions.

The thermal rearrangement of basketene to Nenitzescu's hydrocarbon has been explored using density functional theory (M06-2X and ωB97X-D) and DLPNO-CCSD(T) quantum mechanics. Both the sequential thermally allowed retro Diels-Alder followed by Cope rearrangement and the thermally forbidden retro-[2 + 2] cycloaddition were studied. The controlling role of orbital symmetry rather than reaction thermodynamics is demonstrated.

Experimental and Theoretical Exploration of the Kinetics and Thermodynamics of the Nucleophile-Induced Fragmentation of Ylidenenorbornadiene Carboxylates.

Ylidenenorbornadienes (YNDs), prepared by [4 + 2] cycloadditions between fulvenes and acetylene carboxylates, react with thiol nucleophiles to yield mixtures of four to eight diastereomers depending on the symmetry of the YND substrate. The mixtures of diastereomers fragment via a retro-[4 + 2] cycloaddition with a large variation in rate, with half-lives ranging from 16 to 11,000 min at 80 °C. The diastereomer-enriched samples of propane thiol adducts [YND-propanethiol (PTs)] were isolated and identified by nuclear Overhauser effect spectroscopy (NOESY) correlations. Simulated kinetics were used to extrapolate the rate constants of individual diastereomers from the observed rate data, and it correlated well with rate constants measured directly and from isolated diastereomer-enriched samples. The individual diastereomers of a model system fragment at differing rates with half-lives ranging from 5 to 44 min in CDCl3. Density functional theory calculations were performed to investigate the mechanism of fragmentation and support an asynchronous retro-[4 + 2] cycloaddition transition state. The computations generally correlated well with the observed free energies of activation for four diastereomers of the model system as a whole, within 2.6 kcal/mol. However, the observed order of the fragmentation rates across the set of diastereomers deviated from the computational results. YNDs display wide variability in the rate of fragmentation, dependent on the stereoelectronics of the ylidene substituents. A Hammett study showed that the electron-rich aromatic rings attached to the ylidene bridge increase the fragmentation rate, while electron-deficient systems slow fragmentation rates.

Enzymatic Benzofuranoindoline Formation in the Biosynthesis of the Strained Bridgehead Bicyclic Dipeptide (+)-Azonazine A.

We uncovered and reconstituted a concise biosynthetic pathway of the strained dipeptide (+)-azonazine A from marine-derived Aspergillus insulicola. Formation of the hexacyclic benzofuranoindoline ring system from cyclo-(l-Trp-N-methyl-l-Tyr) is catalyzed by a P450 enzyme through an oxidative cyclization. Supplementing the producing strain with various indole-substituted tryptophan derivatives resulted in the generation of a series of azonazine A analogs.

New score models for assessing disease activity in Crohn's disease based on bowel ultrasound and biomarkers: Ideal surrogates for endoscopy or imaging.

Disease activity evaluation is important in Crohn's disease (CD). We aimed to establish new disease activity indices for CD based on noninvasive parameters. The data of 110 patients with CD were retrospectively analyzed. Parameters from bowel ultrasound and biomarkers were measured to select the variables included in the models by univariate analysis. Logistic regression analysis was performed to predict mucosal and transmural activities defined by ileocolonoscopy or computed tomography enterography, respectively. The models' performance was measured by the area under the receiver operating characteristic (ROC) curve (AUC). Leave-one-out cross validation (LOOCV) was applied to adjust for overconfidence in the newly established score models. To predict mucosal activity, erythrocyte sedimentation rate (ESR) and (LimG × BWT)-SUM (the sum of the product of Limberg grade [LimG] and bowel wall thickness [BWT] of each bowel segment) were selected for model A, and the equation was A = 2 × ESR + 9.3 × (LimG × BWT)-SUM. The AUC of ROC, sensitivity, and specificity were 0.927%, 89.8%, and 86.4%, respectively. The AUC of the ROC curve verified by LOOCV was 0.913. To predict transmural activity, albumin (ALB) and LimG-SUM (the sum of the LimG of all the bowel segments) were selected for model B, which was established as B = -1.3 × ALB +1.7 × LimG-SUM. The AUC of ROC, sensitivity, and specificity were 0.851%, 78.0%, and 84.2%, respectively. The AUC of the ROC curve verified by LOOCV was 0.833. Nomograms were developed for two score models. New score models based on noninvasive parameters established in this study showed good abilities in detecting active disease and performed well in the validation phase.

Tandem intermolecular [4 + 2] cycloadditions are catalysed by glycosylated enzymes for natural product biosynthesis.

Tandem Diels-Alder reactions are frequently used in the construction of polycyclic ring systems in complex organic compounds. Unlike the many Diels-Alderases (DAases) that catalyse a single cycloaddition, enzymes for multiple Diels-Alder reactions are rare. Here we demonstrate that two calcium-ion-dependent glycosylated enzymes, EupfF and PycR1, independently catalyse sequential, intermolecular Diels-Alder reactions in the biosynthesis of bistropolone-sesquiterpenes. We elucidate the origins of catalysis and stereoselectivity within these DAases through analysis of enzyme co-crystal structures, together with computational and mutational studies. These enzymes are secreted as glycoproteins with diverse N-glycans. The N-glycan at N211 in PycR1 significantly increases the affinity to the calcium ion, which in turn regulates the active cavity, making it specifically interact with substrates to accelerate the tandem [4 + 2] cycloaddition. The synergistic effect of the calcium ion and N-glycan on the catalytic centre of enzymes involved in secondary metabolism, especially for complex tandem reactions, can extend our understanding of protein evolution and improve the artificial design of biocatalysts.

Vitamin D Status Is Associated With Immune Checkpoint Inhibitor Efficacy and Immune-related Adverse Event Severity in Lung Cancer Patients: A Prospective Cohort Study.

Vitamin D (VitD) is potentially immunomodulatory, so here we aimed to explore the relationships between serum VitD levels, immune checkpoint inhibitor (ICI) efficacy, and immune-related adverse events (irAEs). Serum 25-hydroxyvitamin D [25(OH)D] levels were quantified before and after ICI treatment in prospectively enrolled patients with advanced lung cancers. Of 77 enrolled patients, 29 developed 42 irAEs. Baseline 25(OH)D levels of partial response (PRs) patients were significantly higher than non-PR patients (19.39±7.16 vs. 16.28±5.99 ng/mL, P =0.04). The area under the curve of 25(OH)D >15.73 ng/mL to identify PR was 0.63 (95% CI, 0.51-0.76, P =0.047), and baseline 25(OH)D levels >15.73 ng/mL (odds ratio: 2.93, 95% CI, 1.10-7.79, P =0.03) and prior targeted therapy (odds ratio: 0.30, 95% CI, 0.10-0.92, P =0.04) were independent predictors of PR as best efficacy by multivariable logistic regression. With respect to irAEs, baseline 25(OH)D levels were higher in grade 1 irAE patients than in grade 2/3/4 irAE patients (20.07±8.64 vs. 15.22±2.30 ng/mL, P =0.02). However, the area under the curve was only 0.56 (95% CI, 0.42-0.70, P =0.39) for a baseline 25(OH)D of 20.99 ng/mL for predicting irAE occurrence. There was a direct monotonic relationship and U-shaped relationship between baseline 25(OH)D levels and ICI efficacy and irAE occurrence, respectively. Overall survival was significantly different between VitD sufficient, insufficient, and deficient patients (log-rank P =0.01), which remained after adjustment in Cox proportional hazards regression models. Baseline 25(OH)D levels seem to be associated with ICI efficacy and prognosis, it might be helpful to assess the baseline VitD status, and supplementation with VitD might bring some benefit to enhance ICI efficacy and reduce moderate-severe irAEs.

Dynamic gut microbiota changes in patients with advanced malignancies experiencing secondary resistance to immune checkpoint inhibitors and immune-related adverse events.

Background: Immune checkpoint inhibitors (ICIs) have been a breakthrough in cancer immunotherapy, but secondary resistance (SR) and immune-related adverse events (irAEs) are significant clinical dilemmas. Although the gut microbiota is associated with ICI efficacy and irAEs, the knowledge of longitudinal gut microbiota dynamics during SR and irAE development is still quite limited. Methods: This was a prospective observational cohort study of cancer patients initially receiving anti-programmed cell death-1 (PD-1) treatment between May 2020 and October 2022. Clinical information was collected to evaluate therapy response and AEs. Patients were divided into a secondary resistance (SR) group, a non-secondary resistance (NSR) group, and an irAE group. Fecal samples were longitudinally obtained from baseline across multiple timepoints and analyzed with 16S rRNA sequencing. Results: Thirty-five patients were enrolled, and 29 were evaluable. After a median follow-up of 13.3 months, NSR patients had a favorable progression-free survival (PFS) compared with SR (457.9 IQR 241.0-674.0 days vs. 141.2 IQR 116.9-165.4 days, P=0.003) and irAE patients (457.9 IQR 241.0-674.0 days vs. 269.9, IQR 103.2-436.5 days, P=0.053). There were no significant differences in the microbiota between groups at baseline. Several previously reported beneficial microbiomes for ICI efficacy including Lachnospiraceae, Ruminococcaceae, Agathobacter, and Faecalibacterium showed decreasing trends as secondary resistance developed, yet not achieved significance (P>0.05). Significant changes in butyrate-producing bacteria were also presented in the SR cohort (P=0.043) with a decreasing trend upon secondary resistance occurrence (P=0.078). While the abundance of IgA-coated bacteria was stable in the SR cohort, there was a temporary decrease upon ICI treatment initiation and reestablishment after continuation of ICI treatment in the NSR cohort (primary ICI response: 0.06, IQR 0.04-0.10; durable ICI response: 0.11, IQR 0.07-0.14; P=0.042). Bacteroides contributed most to the difference between baseline and irAE occurrence, which decreased after irAE occurrence (Baseline: 0.10 IQR 0.07-0.36; irAE occurrence: 0.08 IQR 0.06-0.12) and was restored upon irAE remission to a comparable level as baseline (irAE remission: 0.10 IQR 0.09-0.18). Conclusions: The development of SR and irAEs is related to the longitudinal dynamics of the intestinal microbiota. The investigation into the preventative and protective effects of enteric microbe manipulation strategies is further required.

Improving the Performance of a Triboelectric Nanogenerator by Using an Asymmetric TiO2/PDMS Composite Layer.

To improve the output power of the polydimethylsiloxane (PDMS)-based triboelectric nanogenerators (TENGs), we fabricated an asymmetric TiO2/PDMS composite film in which a pure PDMS thin film was deposited as a capping layer on a TiO2 nanoparticles (NPs)-embedded PDMS composite film. Although in the absence of the capping layer, the output power decreased when the content of TiO2 NPs exceeded a certain value, the asymmetric TiO2/PDMS composite films showed that the output power increased with increasing content. The maximum output power density was approximately 0.28 W/m2 at a TiO2 content of 20 vol.%. The capping layer could be responsible not only for maintaining the high dielectric constant of the composite film but also for suppressing interfacial recombination. To further improve the output power, we applied a corona discharge treatment to the asymmetric film and measured the output power at a measurement frequency of 5 Hz. The maximum output power density was approximately 78 W/m2. The idea of the asymmetric geometry of the composite film should be applicable to various combinations of materials for TENGs.

Gut microbiota composition in patients with advanced malignancies experiencing immune-related adverse events.

Introduction: The gut microbiota is implicated in the occurrence and severity of immune-related adverse events (irAEs), but the role it plays as well as its causal relationship with irAEs has yet to be established. Methods: From May 2020 to August 2021, 93 fecal samples were prospectively collected from 37 patients with advanced thoracic cancers treated with anti-PD-1 therapy, and 61 samples were collected from 33 patients with various cancers developing different irAEs. 16S rDNA amplicon sequencing was performed. Antibiotic-treated mice underwent fecal microbiota transplantation (FMT) with samples from patients with and without colitic irAEs. Results: Microbiota composition was significantly different in patients with and without irAEs (P=0.001) and with and without colitic-type irAEs (P=0.003). Bifidobacterium, Faecalibacterium, and Agathobacter were less abundant and Erysipelatoclostridium more abundant in irAE patients, while Bacteroides and Bifidobacterium were less abundant and Enterococcus more abundant in colitis-type irAE patients. Major butyrate-producing bacteria were also less abundant in patients with irAEs than those without (P=0.007) and in colitic vs. non-colitic irAE patients (P=0.018). An irAE prediction model had an AUC of 86.4% in training and 91.7% in testing. Immune-related colitis was more common in colitic-irAE-FMT (3/9) than non-irAE-FMT mice (0/9). Conclusions: The gut microbiota is important in dictating irAE occurrence and type, especially for immune-related colitis, possibly by modulating metabolic pathways.