Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes.

Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.

An indicator color chart for quick detection of Pigment Red 53 in cosmetic products in Indonesia.

BACKGROUND: Pigment Red 53 is a dangerous synthetic dye that is often added to cosmetics, even though its use in cosmetic products has been prohibited because of possible impacts on health. Faster and more sensitive detection of Pigment Red 53 is needed for onsite analysis to protect the community from illegal cosmetics that contain the dye. Indicator color charts are a kind of analytical method that can be used to detect Pigment Red 53 in cosmetic products, including lipstick, rouge, and eyeshadow. Such charts are practical, fast, and can be used for onsite analysis. METHODS: In this study, an indicator for Pigment Red 53 detection was obtained through a reagent reaction that caused a specific color change. An indicator color chart was then produced by setting out in paper form the series of colors which resulted from the reaction of specific chemical reagents and Pigment Red 53 solutions at concentrations of 10, 20, 40, 60, 80, and 100 ppm. RESULTS: The testing results showed that the indicator color chart may be used as an initial screening method for the detection of Pigment Red 53 in cosmetic products with a detectable minimum concentration of 10 ppm. Out of nine samples, only one (Eyeshadow 3) tested positive for Pigment Red 53. Further analysis was carried out on the indicator color chart and the results showed good agreement with TLC and UV-Vis spectrophotometry methods. CONCLUSION: The results reported in this paper demonstrate that the indicator color chart is a good prospective method for onsite analysis to detect Pigment Red 53 in cosmetic samples, with a lower detection limit compared to polymer-based indicators.

Wearable Sensing Device Integrated with Prestored Reagents for Cortisol Detection in Sweat.

Wearable sweat sensors have achieved rapid development since they hold great potential in personalized health monitoring. However, a typical difficulty in practical processes is the control of working conditions for biorecognition elements, e.g., pH level and ionic strength in sweat may decrease the affinity between analytes and recognition elements. Here, we developed a wearable sensing device for cortisol detection in sweat using an aptamer as the recognition element. The device integrated functions of sweat collection, reagent prestorage, and signal conversion. Especially, the components of prestored reagents were optimized according to the inherent characteristics of sweat samples and electrodes, which allowed us to keep optimal conditions for aptamers. The sweat samples were transferred from the inlet of the device to the reagent prestored chamber, and the dry preserved reagents were rehydrated with sweat and then arrived at the aptamer-modified electrodes. Sweat samples of volunteers were analyzed by the wearable sensing device, and the results showed a good correlation with those of the ELISA kit. We believe that this convenient and reliable wearable sensing device has significant potential in self-health monitoring.

A new derivatizing reagent for the determination of 5-nitro-2-furaldehyde in trout muscle by liquid chromatography-tandem mass spectrometry.

The 5-nitro-2-furaldehyde (5-NF) is an aldehyde aromatic organic compound that has been envisaged as an alternative marker for detecting nitrofurazone treatment abuse and to avoid the false positive results induced by the semicarbazide. Analyzing 5-NF presents challenges, and its derivatization reaction with hydrazine reagents is required to enhance the capability of its detection and its identification. This study aims at developping an analytical method for 5-NF determination in trout muscle samples based on chemical derivatization prior to analysis by liquid chromatography-tandem mass spectrometry. Four commercially available hydrazine reagents, namely: N,N-Dimethylhydrazine (DMH), 4-Hydrazinobenzoic acid (HBA), 2,4-Dichlorophenylhydrazine (2,4-DCPH) and 2,6-Dichlorophenylhydrazine (2,6-DCPH) were proposed for the first time as derivatizing reagents in the analysis of 5-NF. The derivatization reaction was simultaneously performed along with the extraction method in acidic condition using ultrasonic assistance and followed by liquid extraction using acetonitrile. The efficiency of the chemical reaction with 5-NF was examined and the reaction conditions including the concentration of hydrochloric acid, pH, temperature, reaction time and the concentration of the derivatizing reagents were optimized. Experiments with fortified samples demonstrated that 2,4-DCPH derivatizing reagent at 20 mM for 20 min of ultrasonic treatment under acidic condition (pH 4) gave an effective sample derivatization method for 5-NF analysis. Under the optimized conditions, the calibration curves were linear from 0.25 to 2 µg kg-1 with coefficient of determination >0.99. The recoveries ranged from 89 % to 116 % and precision was less than 13 %. The limit of detection and quantification were 0.1 and 0.2 µg kg-1, respectively.

Harnessing alcohols as sustainable reagents for late-stage functionalisation: synthesis of drugs and bio-inspired compounds.

Alcohol is ubiquitous with unparalleled structural diversity and thus has wide applications as a native functional group in organic synthesis. It is highly prevalent among biomolecules and offers promising opportunities for the development of chemical libraries. Over the last decade, alcohol has been extensively used as an environmentally friendly chemical for numerous organic transformations. In this review, we collectively discuss the utilisation of alcohol from 2015 to 2023 in various organic transformations and their application toward intermediates of drugs, drug derivatives and natural product-like molecules. Notable features discussed are as follows: (i) sustainable approaches for C-X alkylation (X = C, N, or O) including O-phosphorylation of alcohols, (ii) newer strategies using methanol as a methylating reagent, (iii) allylation of alkenes and alkynes including allylic trifluoromethylations, (iv) alkenylation of N-heterocycles, ketones, sulfones, and ylides towards the synthesis of drug-like molecules, (v) cyclisation and annulation to pharmaceutically active molecules, and (vi) coupling of alcohols with aryl halides or triflates, aryl cyanide and olefins to access drug-like molecules. We summarise the synthesis of over 100 drugs via several approaches, where alcohol was used as one of the potential coupling partners. Additionally, a library of molecules consisting over 60 fatty acids or steroid motifs is documented for late-stage functionalisation including the challenges and opportunities for harnessing alcohols as renewable resources.

Unrevealing the influence of reagent properties on disruption and digestibility of lignocellulosic biomass during alkaline pretreatment.

Beyond the conventional consideration of pretreatment severity (PS) responsible for biomass disruption, the influence of reagent properties on biomass (LCB) disruption is often overlooked. To investigate the LCB disruption as a function of reagent properties, reagents with distinct cations (NaOH and KOH) and significantly higher delignification potential were chosen. NaOH solution (3 % w/v) with a measured pH of 13.05 ± 0.01 is considered the reference, against which a KOH solution (pH = 13.05 ± 0.01) was prepared for LCB pretreatment under the same PS. Despite comparable lignin content, varying glucose yield of NaOH (68.76 %) and KOH (46.88 %) pretreated residues indicated the presence of heterogeneously disrupted substrate. Holocellulose extracted from raw poplar (ASC, control) and alkaline pretreated residues (C-NaOH and C-KOH) were analyzed using HPLC, XRD, SEM, TGA/DTG, XPS, and 13CP MAS NMR to investigate the pretreatment-induced structural modification. Results revealed that, despite the same pretreatment severity, better disruption in C-NaOH (higher accessible fibril surface and less-ordered region) leading to higher digestibility than C-KOH, likely due to the smaller ionic radius of Na+, facilitates better penetration into dense LCB matrix. This study elucidates the importance of considering the reagent properties during LCB pretreatment, eventually enhancing consciousness while selecting reagents for efficient LCB utilization.

Oxidative cyclization reagents reveal tryptophan cation-π interactions.

Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.

Fluorescence-Polarization-Based Assaying of Lysozyme with Chitooligosaccharide Tracers.

Lysozyme is a well-known enzyme found in many biological fluids which plays an important role in the antibacterial protection of humans and animals. Lysozyme assays are used for the diagnosis of a number of diseases and utilized in immunohistochemistry, genetic and cellular engineering studies. The assaying methods are divided into two categories measuring either the concentration of lysozyme as a protein or its activity as an enzyme. While the first category of methods traditionally uses an enzyme-linked immunosorbent assay (ELISA), the methods for the determination of the enzymatic activity of lysozyme use either live bacteria, which is rather inconvenient, or natural peptidoglycans of high heterogeneity and variability, which leads to the low reproducibility of the assay results. In this work, we propose the use of a chemically synthesized substrate of a strictly defined structure to measure in a single experiment both the concentration of lysozyme as a protein and its enzymatic activity by means of the fluorescence polarization (FP) method. Chito-oligosaccharides of different chain lengths were fluorescently labeled and tested leading to the selection of the pentasaccharide as the optimal size tracer and the further optimization of the assay conditions for the accurate (detection limit 0.3 µM) and rapid (<30 min) determination of human lysozyme. The proposed protocol was applied to assay human lysozyme in tear samples and resulted in good correlation with the reference assay. The use of synthetic fluorescently labeled tracer, in contrast to natural peptidoglycan, in FP analysis allows for the development of a reproducible method for the determination of lysozyme activity.

Divinylpyrimidine reagents generate antibody-drug conjugates with excellent in vivo efficacy and tolerability.

The development of divinylpyrimidine (DVP) reagents for the synthesis of antibody-drug conjugates (ADCs) with in vivo efficacy and tolerability is reported. Detailed structural characterisation of the synthesised ADCs was first conducted followed by in vitro and in vivo evaluation of the ADCs' ability to safely and selectively eradicate target-positive tumours.

Minimal Information about MHC Multimers (MIAMM).

With the goal of improving the reproducibility and annotatability of MHC multimer reagent data, we present the establishment of a new data standard: Minimal Information about MHC Multimers (https://miamm.lji.org/). Multimers are engineered reagents composed of a ligand and a MHC, which can be represented in a standardized format using ontology terminology. We provide an online Web site to host the details of the standard, as well as a validation tool to assist with the adoption of the standard. We hope that this publication will bring increased awareness of Minimal Information about MHC Multimers and drive acceptance, ultimately improving the quality and documentation of multimer data in the scientific literature.

Multifunctional Probes with High Utilization Rates: Self-Assembled Merocyanine Nanoparticles in Water as Acid-Base Indicators and Mitochondrion-Targeting Chemotherapeutic Agents.

Multifunctional probes with high utilization rates have great value in practical applications in various fields such as cancer diagnosis and therapy. Here we have synthesized two organic molecules based on merocyanine. They can self-assemble in water to form ∼1.5 nm nanoparticles. Both of them have good application potential in fluorescent anticounterfeit printing ink and pH detection. More importantly, they have excellent mitochondrial targeting ability, intracellular red light and near-infrared dual-channel imaging ability, strong antiphotobleaching ability, and in vivo and in vitro near-infrared imaging capabilities, showing superior chemotherapy capabilities and biocompatibility in the 4T1 tumor-bearing mouse model.

Statistical optimization of medium components for biosurfactant production by Pseudomonas guguanensis D30.

Biosurfactant production by Pseudomonas guguanensis D30 was reported using mineral oil in submerged condition. Twelve medium components were tested at two levels by Plackett-Burman design, among them, mineral oil, yeast extract, peptone, MgSO4, and CaCl2 found significant on the basis of emulsification index. These five significant components were further optimized through central composite design (CCD). The experimental design was successfully used for regression analysis and the significant model suggested the solution of 10% (v/v) mineral oil, 3.0 g/L (w/v) yeast extract and 0.2 g/L (w/v) peptone for 13.14 g/L predicted biosurfactant production. We kept the suggested concentrations of medium components and got 13.34 ± 0.08 g/L biosurfactant production, which is almost double the conventional one-factor-at-a-time production (7.126 ± 0.12 g/L). It reduced the surface tension of the medium up to 28 ± 1.2 mN/m. We found ethyl acetate a suitable solvent for biosurfactant extraction amongst methanol, chloroform, and methanol:chloroform. The partially purified biosurfactant was chemically characterized as lipopeptide by Fourier transform infrared spectroscopy (FT-IR).

Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps.

BACKGROUND: High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment. METHODS: We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem. RESULTS: Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples. CONCLUSIONS: Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.

Resazurin rapid screening for antibacterial activities of organic and inorganic nanoparticles: Potential, limitations and precautions.

Nanoparticles have been used as antibacterial agents in several products. To optimize their effectiveness, synthesis processes and particle modifications have been developed, creating the need for a rapid screening method to investigate their potencies. Owing to the opacity and insolubility of nanoparticles, a classical method to determine antibacterial activity-such as the minimum inhibitory concentration (MIC), which relies on turbidimetry-might not apply to them. In this study, we demonstrate the potential of a dye (resazurin)-based assay as an indicator of bacterial growth to rapidly screen the antibacterial activities of both organic and inorganic nanomaterials against both gram-negative (E. coli) and gram-positive (S. aureus) bacteria. The results indicate that the resazurin-based assay successfully determine the MIC of organic lipid nanocarriers, and several inorganic nanoparticles. However, the use of resazurin require a precaution for nanoparticles with photocatalytic properties, which may cause dye degradation at higher concentrations. In this study, resazurin bleaching was observed at approximately >50 mg/ml of TiO2. In summary, the modified MIC assay with resazurin can evaluate antibacterial activity of nanomaterials, whose turbidity interferer conventional MIC assay. This modification conserves an advantage of MICs assay which are simple and reliable. This would be useful for screening of antibacterial nanomaterials.

Directing-group-free catalytic dicarbofunctionalization of unactivated alkenes.

In the absence of directing auxiliaries, the catalytic addition of carbogenic groups to unactivated alkenes with control of regioselectivity remains an ongoing challenge in organic chemistry. Here we describe a directing-group-free, nickel-catalysed strategy that couples a broad array of unactivated and activated olefins with aryl-substituted triflates and organometallic nucleophiles to afford diarylation adducts in either regioisomeric form, in up to 93% yield and >98% site selectivity. By switching the reagents involved, the present strategy may be extended to other classes of dicarbofunctionalization reactions. Mechanistic and computational investigations offer insights into the origin of the observed regiochemical outcome and the utility of the method is highlighted through the concise syntheses of biologically active molecules. The catalyst control principles reported are expected to advance efforts towards the development of general site-selective alkene functionalizations, removing the requirement for neighbouring activating groups.

A novel design of multiple ligands for ultrasensitive colorimetric chemosensor of glutathione in plasma sample.

In this study, we developed a novel colorimetric chemosensor for selective and sensitive recognition of Glutathione (GSH) using a simple binary mixture of commercially accessible and inexpensive metal receptors with names, Bromo Pyrogallol Red (BPR) and Xylenol Orange (XO). This procedure is based on the synergistic coordination of BPR and XO with cerium ion (Ce3+) for the recognition of GSH over other available competitive amino acids (AAs) especially thiol species in aqueous media. Generally, cysteine (Cys) and homocysteine (hCys) can seriously interfere with the detection of GSH among common biological species because they possess similar chemical behavior. Using all the information from 1HNMR and FT-IR studies, the proposed interaction is presented in which GSH acts as a tri-dentate ligand with three N donor atoms in conjunction with BPR and XO as mono and bi-dentate ligands respectively. This approach opens a path for selective detection of other AAs by argumentatively selecting the ensemble of mixed organic ligands from commercially available reagents, thereby eliminating the need for developing synthetic receptors, sample preparation, organic solvent mixtures, and expensive equipment. Evaluating the feasibility of the existing method was led to the determination of GSH in human plasma samples.

Advanced graphene oxide-based paper sensor for colorimetric detection of miRNA.

MicroRNAs (miRNAs), found in blood and body fluids, have emerged as potential non-invasive biomarkers for disease and injury. miRNAs are quantitatively evaluated using typical RNA analysis methods such as the quantitative reverse transcription polymerase chain reaction, microarrays, and Northern blot, all of which require complex procedures and expensive reagents. To utilize miRNAs as practical biomarkers, it will be helpful to develop simple and user-friendly sensors. In this study, a paper-based miRNA sensor was developed by combining two methods: (1) target-recycled DNAzyme (Dz) amplification and (2) graphene oxide-assisted Dz blotting on paper. The Dz spots on paper caused a miRNA-dependent color change in presence of colorimetric reagents and facilitated the quantification of absolute amount of the target miRNA, irrespective of the volume, with high reproducibility. This approach is technologically straightforward and enables quantification of as low as 7.75 fmol miRNA using a portable smartphone.

Olefination via Cu-Mediated Dehydroacylation of Unstrained Ketones.

The dehydroacylation of ketones to olefins is realized under mild conditions, which exhibits a unique reaction pathway involving aromatization-driven C-C cleavage to remove the acyl moiety, followed by Cu-mediated oxidative elimination to form an alkene between the α and ß carbons. The newly adopted N'-methylpicolinohydrazonamide (MPHA) reagent is key to enable efficient cleavage of ketone C-C bonds at room temperature. Diverse alkyl- and aryl-substituted olefins, dienes, and special alkenes are generated with broad functional group tolerance. Strategic applications of this method are also demonstrated.

Synthesis of a TNF inhibitor, flurbiprofen and an i-Pr analogue in enantioenriched forms by copper-catalyzed propargylic substitution with Grignard reagents.

The copper-catalyzed substitution reaction of diethyl phosphate derived from TMSCCCH(OH)CH2CH2OTBDPS with 3-c-C5H9-4-MeOC6H3MgBr, followed by several transformations, afforded a tumor necrosis factor inhibitor possessing a Ph-acetylene moiety. The inhibitor was also synthesized from phenylacetylene phosphate PhCCCH(OP(O)(OEt)2)CH2CH2OTBDPS. Furthermore, the substitution of phosphates derived from TMSCCCH(OH)CH3 and TMSCCCH(OH)-i-Pr with 3-F-4-PhC6H3MgBr gave the corresponding substitution products, which were transformed to flurbiprofen and its i-Pr analogue, respectively. The copper-catalyzed substitutions in these syntheses proceeded in a regio- and stereoselective manner.