Cleavage Reaction Research Articles

Kinetic Resolution of Helicenols via Palladium-Catalyzed Atroposelective C-C Bond Cleavage/Ring-Opening Reaction.

Helicenes represent a class of inherently chiral structures that lack conventional chiral elements, such as stereogenic centers, chiral axes, or plane. The asymmetric synthesis of these helical compounds can be particularly challenging as a result of their pronounced molecular strain. In this study, we report a palladium-catalyzed atroposelective carbon-carbon bond cleavage reaction of helical tertiary alcohols. Because the helical alcohols are configurationally stable, the reaction proceeded through a kinetic resolution pathway, resulting in achieving optically active helicenols alongside the sterically hindered axially chiral products.

Masters of Mediation: MN(SiMe3)2 in Functionalization of C(sp3)-H Latent Nucleophiles.

Organoalkali compounds have undergone a far-reaching transformation being a coupling partner to a mediator in unusual organic conversions which finds its spot in the field of sustainable synthesis. Transition-metal catalysis has always been the priority in C(sp3)-H bond functionalization, however alternatively, in recent times this has been seriously challenged by earth-abundant alkali metals and their complexes arriving at new sustainable organometallic reagents. In this line, the importance of MN(SiMe3)2 (M=Li, Na, K & Cs) reagent revived in C(sp3)-H bond functionalization over recent years in organic synthesis is showcased in this minireview. MN(SiMe3)2 reagent with higher reactivity, enhanced stability, and bespoke cation-π interaction have shown eye-opening mediated processes such as C(sp3)-C(sp3) cross-coupling, radical-radical cross-coupling, aminobenzylation, annulation, aroylation, and other transformations to utilize readily available petrochemical feedstocks. This article also emphasizes the unusual reactivity of MN(SiMe3)2 reagent in unreactive and robust C-X (X=O, N, F, C) bond cleavage reactions that occurred alongside the C(sp3)-H bond functionalization. Overall, this review encourages the community to exploit the untapped potential of MN(SiMe3)2 reagent and also inspires them to take up this subject to even greater heights.

Production of native recombinant proteins using a novel split intein affinity technology

Affinity tags are frequently engineered into recombinant proteins to facilitate purification. Although this technique is powerful, removal of the tag is desired because the tag can interfere with biological activity and can potentially increase the immunogenicity of therapeutic proteins. Tag removal is complex, as it requires adding expensive protease enzymes. To overcome this limitation, split intein based affinity purification systems have been developed in which a CC-intein tag is engineered into a protein of interest for binding to a NC-intein peptide ligand fixed to a chromatographic support. Tag removal in these systems is achieved by creating an active intein-complex during protein capture, which triggers a precise self-cleavage reaction. In this work, we show applications of a new split intein system, Cytiva™ ProteinSelect™. One advantage of the new system is that the NC-intein ligand can be robustly produced and conjugated to large volumes of resin for production of gram scale proteins. SARS-CoV-2 spike protein receptor binding domain and a Bispecific T Cell Engager in this work were successfully captured on the affinity resin and scaled 10-fold. Another advantage of this system is the ability to sanitize the resin with sodium hydroxide without loosing the 10–20 g/L binding capacity. Binding studies with IL-1b and IFNAR-1 ECD showed that the resin can be regenerated and sanitized for up to 50 cycles without loosing binding capacity. Additionally, after several cycles of sanitization, binding capacity was retained for the SARS-CoV-2 spike protein receptor binding domain and a Bispecific T Cell Engager. As with other split intein systems, optimization was needed to achieve ideal expression and recovery. The N-terminal amino acid sequence of the protein of interest required engineering to enable the cleavage reaction. Additionally, ensuring the stability of the CC-intein tag was important to prevent premature cleavage or truncation. Controlling the hold time of the expression product and the prevention of protease activity prior to purification was needed. These results demonstrate the feasibility of the Cytiva™ ProteinSelect™ system to be used in academic and industrial research and development laboratories for the purification of novel proteins expressed in either bacterial or mammalian systems.

Metal‐Free and NBS‐Mediated C(sp3)−S Bond Cleavage of Thioethers to Access Alkyl Bromides

AbstractA selective C(sp3)−S bond cleavage of thioethers mediated by NBS is developed. Various alkyl bromides have been obtained in good yields using N‐aryl‐3‐(methylthio)propanamides and arylmethylene alkylthioethers. Mechanistic studies suggest that the formation of 3‐bromo‐N‐arylpropanamides may involve sulfoxide intermediates, while the arylmethylene bromides are formed through direct bromination process mediated by NBS. The significance of this strategy lies in its pioneering use of NBS for C−S bond cleavage and subsequent bromination reaction.

Role of galacturonic acid in acrylamide formation: Insights from structural analysis

Acrylamide (AA) is a neoformed compound in heated foods, mainly produced between asparagine (Asn) and glucose (Glc) during the Maillard reaction. Galacturonic acid (GalA), the major component of pectin, exhibits high activity in AA formation. This study investigated the pathway for AA formation between GalA and Asn. Three possible pathways were proposed: 1) The carbonyl group of GalA directly interacts with Asn to produce AA; 2) GalA undergoes an oxidative cleavage reaction to release α-dicarbonyl compounds, which subsequently leads to AA production; 3) 5-formyl-2-furancarboxylic acid, the thermal degradation product of GalA, reacts with Asn to generate AA. Structural analysis revealed that the COOH group in GalA accelerated intramolecular protonation and electron transfer processes, thereby increasing the formation of AA precursors such as decarboxylated Schiff base and α-dicarbonyl compounds, promoting AA formation. This study provides a theoretical basis and new insights into the formation and control of AA.

An all-in-one tetrazine reagent for cysteine-selective labeling and bioorthogonal activable prodrug construction

The prodrug design strategy offers a potent solution for improving therapeutic index and expanding drug targets. However, current prodrug activation designs are mainly responsive to endogenous stimuli, resulting in unintended drug release and systemic toxicity. In this study, we introduce 3-vinyl-6-oxymethyl-tetrazine (voTz) as an all-in-one reagent for modular preparation of tetrazine-caged prodrugs and chemoselective labeling peptides to produce bioorthogonal activable peptide-prodrug conjugates. These stable prodrugs can selectively bind to target cells, facilitating cellular uptake. Subsequent bioorthogonal cleavage reactions trigger prodrug activation, significantly boosting potency against tumor cells while maintaining exceptional off-target safety for normal cells. In vivo studies demonstrate the therapeutic efficacy and safety of this prodrug design approach. Given the broad applicability of functional groups and labeling versatility with voTz, we foresee that this strategy will offer a versatile solution to enhance the therapeutic range of cytotoxic agents and facilitate the development of bioorthogonal activatable biopharmaceuticals and biomaterials.

An isothermal CRISPR- based lateral flow assay for detection of Neisseria meningitidis

BackgroundNeisseria meningitidis can cause life-threatening meningococcal meningitis and meningococcemia. Old standard microbiological results from CSF/blood cultures are time consuming. This study aimed to combine the sensitivity of loop-mediated isothermal nucleic acid amplification (LAMP) with the specificity of CRISPR/Cas12a cleavage to demonstrate a reliable diagnostic assay for rapid detection of N. meningitidis.MethodsA total of n = 139 samples were collected from patients with suspected meningococcal disease and were used for evaluation. The extracted DNA was subjected to qualitative real-time PCR, targeting capsular transporter gene (ctrA) of N. meningitidis. LAMP-specific primer pairs, also targeting the ctrA, were designed and the LAMP products were subjected to CRISPR/Cas12 cleavage reaction. the readout was on a lateral flow strip. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of LAMP-CRISPR/Cas was compared with real-time PCR assays. The limit of detection (LOD) was established with serial dilutions of the target N. meningitidis DNA and calculated by Probit regression analysis.ResultsSix LAMP assay-specific primers were developed targeting the ctrA gene of N. meningitidis, which is conserved in all meningococcal serogroups. The LAMP primers did not amplify DNA from other bacterial DNA tested, showing 100% specificity. The use of 0.4 M betaine increased the sensitivity and stability of the reaction. LAMP-CRISPR/Cas detected meningococcal serogroups (B, C, W). The assay showed no cross-reactivity and was specific for N. meningitidis. The LOD was 74 (95% CI: 47–311) N. meningitidis copies. The LAMP-CRISPR/Cas performed well compared to the gold standard. In the 139 samples from suspected patients, the sensitivity and specificity of the test were 91% and 99% respectively.ConclusionThis developed and optimized method can complement for the available gold standard for the timely diagnosis of meningococcal meningitis and meningococcemia.

Discovery and characterization of l-DOPA 2,3-dioxygenase from Streptomyces hygroscopicus jingganensis

The largest natural reservoir of untapped carbon can be found in the cell-wall strengthening, plant woody-tissue polymer, lignin - a polymer of catechols or 1,2-dihydroxybenzene monomers. The catecholic carbon of lignin could be valorized into feedstocks and natural products by way of catabolic and biosynthetic transformations, including the oxygen-dependent cleavage reaction of extradiol dioxygenase (EDX) enzymes. The EDX l-DOPA 2,3-dioxygenase was first discovered as part of a biosynthetic gene cluster to the natural product antibiotic, lincomycin, and also contributes to the biosyntheses of anthramycin, sibiromycin, tomaymycin, porothramycin and hormaomycin. Using these l-DOPA 2,3-dioxygenases as a starting point, we searched sequence space in order to identify new sources of dioxygenase driven natural product diversity. A “vicinal-oxygen-chelate (VOC) family protein” from Streptomyces hygroscopicus jingganensis was identified using bioinformatic methods and biochemically investigated for dioxygenase activity against a suite of natural and synthetic catechols. Steady-state oxygen consumption assays were used to screen and identify substrates, and a steady-state kinetic model of oxygen consumption was developed to evaluate activity of the S. hygroscopicus jingganensis VOC-family-protein with respect to activity of l-DOPA 2,3-dioxygenases from Streptomyces lincolnensis and Streptomyces sclerotialus. Lastly, these data were integrated with steady-state kinetic methods to observe the formation of the EDX cleavage product with UV–visible spectroscopy. The genomic context and enzymatic activity of the S. hygroscopicus jingganensis VOC family protein are consistent with a l-DOPA 2,3-dioxygenase contained within a cryptic biosynthetic pathway.

An Enzymatic Carbon‐Carbon Bond Cleavage and Aldol Reaction Cascade Converts an Angular Scaffold into the Linear Tetracyclic Core of Ochraceopones

AbstractMeroterpenoids of the ochraceopones family featuring a linear tetracyclic scaffold exhibit exceptional antiviral and anti‐inflammatory activities. The biosynthetic pathway and chemical logic to generate this linear tetracycle, however, remain unknown. In this study, we identified and characterized all biosynthetic enzymes to afford ochraceopones and elucidated the complete biosynthetic pathway. We demonstrated that the linear tetracyclic scaffold of ochraceopones was derived from an angular tetracyclic precursor. A multifunctional cytochrome P450 OchH was validated to catalyze the free‐radical‐initiated carbon‐carbon bond cleavage of the angular tetracycle. Then, a new carbon‐carbon bond was verified to be constructed using a new aldolase OchL, which catalyzes an intramolecular aldol reaction to form the linear tetracycle. This carbon‐carbon bond fragmentation and aldol reaction cascade features an unprecedented strategy for converting a common angular tetracycle to a distinctive linear tetracyclic scaffold in meroterpenoid biosynthesis.

An Enzymatic Carbon-Carbon Bond Cleavage and Aldol Reaction Cascade Converts an Angular Scaffold into the Linear Tetracyclic Core of Ochraceopones.

Meroterpenoids of the ochraceopones family featuring a linear tetracyclic scaffold exhibit exceptional antiviral and anti-inflammatory activities. The biosynthetic pathway and chemical logic to generate this linear tetracycle, however, remain unknown. In this study, we identified and characterized all biosynthetic enzymes to afford ochraceopones and elucidated the complete biosynthetic pathway. We demonstrated that the linear tetracyclic scaffold of ochraceopones was derived from an angular tetracyclic precursor. A multifunctional cytochrome P450 OchH was validated to catalyze the free-radical-initiated carbon-carbon bond cleavage of the angular tetracycle. Then, a new carbon-carbon bond was verified to be constructed using a new aldolase OchL, which catalyzes an intramolecular aldol reaction to form the linear tetracycle. This carbon-carbon bond fragmentation and aldol reaction cascade features an unprecedented strategy for converting a common angular tetracycle to a distinctive linear tetracyclic scaffold in meroterpenoid biosynthesis.

Smart Free-Standing Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film-Based Sensing System Using Changes in Bending Angles as a Visual Signal Readout.

Stimuli-responsive DNA hydrogels have shown great potential in sensing applications due to their attractive properties such as programmable target responsiveness, excellent biocompatibility, and biodegradability. In contrast to the extensively developed DNA hydrogel sensing systems based on the stimuli-responsive hydrogel-to-solution phase transition of the hydrogel matrix, the quantitative sensing application of DNA hydrogels exhibiting smart shape deformations has rarely been explored. Moreover, bulk DNA hydrogel-based sensing systems also suffer from high material cost and slow response. Herein, free-standing bilayer polyacrylamide/DNA hybrid hydrogel films with programmable responsive properties directed by the sequence of functional DNA units have been constructed. Compared with bulk DNA hydrogels, these DNA hydrogel films with a thickness at the micrometer scale not only greatly reduce the consumption of DNA materials but also facilitate the mass transfer of biomacromolecular substances within the hydrogel network, thus favoring their sensing applications. Therefore, a target-responsive smart DNA hydrogel film-based sensor system is further demonstrated based on the large amplitude macroscopic shape deformation of the film as a visual signal readout. As a proof of concept, Pb2+ or UO22+ ion-responsive DNA units were introduced into the active layer of the bilayer hydrogel films. In the presence of Pb2+ or UO22+ ions, the occurrence of a cleavage reaction within the DNA units leads to the release of DNA segments from the hydrogel film, inducing a dramatic shape deformation of the film, and thus sensing of Pb2+ or UO22+ ions with high specificity is achieved based on measuring the bending angle changes of these smart free-standing films. These smart DNA hydrogel film sensors with target-programmable responsiveness, simple operation, and ease of storage may hold promise for future rapid on-site testing applications.

In-Depth Profiling of 4-Hydroxy-2-nonenal Modification via Reversible Thiazolidine Chemistry.

Protein modification by lipid-derived electrophiles (LDEs) is associated with various signaling pathways. Among these LDEs, 4-hydroxy-2-nonenal (HNE) is the most toxic, and protein modified with HNE has been linked to various diseases, including Alzheimer's and Parkinson's. However, due to their low abundance, in-depth profiling of HNE modifications still presents challenges. This study introduces a novel strategy utilizing reversible thiazolidine chemistry to selectively capture HNE-modified proteins and a palladium-mediated cleavage reaction to release them. Thousands of HNE-modified sites in different cell lines were identified. Combined with ABPP, we discovered a set of HNE-sensitive sites that offer a new tool for studying LDE modifications in proteomes.

Acrylate‐derived RAFT Polymers for Enzyme Hyperactivation – Boosting the α‐Chymotrypsin Enzyme Activity Using Tailor‐Made Poly(2‐Carboxyethyl)acrylate (PCEA)

AbstractWe study the hyperactivation of α‐chymotrypsin (α‐ChT) using the acrylate polymer poly(2‐carboxyethyl) acrylate (PCEA) in comparison to the commonly used poly(acrylic acid) (PAA). The polymers are added during the enzymatic cleavage reaction of the substrate N‐glycyl‐L‐phenylalanine p‐nitroanilide (GPNA). Enzyme activity assays reveal a pronounced enzyme hyperactivation capacity of PCEA, which reaches up to 950 % activity enhancement, and is significantly enhanced to PAA (revealing an activity enhancement of approx. 450 %). In a combined experimental and computational study, we investigate α‐ChT/polymer interactions to elucidate the hyperactivation mechanism of the enzyme. Isothermal titration calorimetry reveals a pronounced complexation between the polymer and the enzyme. Docking simulations reveal that binding of polymers significantly improves the binding affinity of GPNA to α‐ChT. Notably, a higher binding affinity is found for the α‐ChT/PCEA compared to the α‐ChT/PAA complex. Further molecular dynamics (MD) simulations reveal changes in the size of the active site in the enzyme/polymer complexes, with PCEA inducing a more pronounced alteration compared to PAA, facilitating an easier access for the substrate to the active site of α‐ChT.

Electronic structure modulation of iron sites with fluorine coordination enables ultra-effective H2O2 activation

Electronic structure modulation of active sites is critical important in Fenton catalysis as it offers a promising strategy for boosting H2O2 activation. However, efficient generation of hydroxyl radicals (•OH) is often limited to the unoptimized coordination environment of active sites. Herein, we report the rational design and synthesis of iron oxyfluoride (FeOF), whose iron sites strongly coordinate with the most electronegative fluorine atoms in a characteristic moiety of F-(Fe(III)O3)-F, for effective H2O2 activation with potent •OH generation. Results demonstrate that the fluorine coordination plays a pivotal role in lowering the local electron density and optimizing the electronic structures of iron sites, thus facilitating the rate-limiting H2O2 adsorption and subsequent peroxyl bond cleavage reactions. Consequently, FeOF exhibits a significant and pH-adaptive •OH yield (~450 µM) with high selectivity, which is 1 ~ 3 orders of magnitude higher than the state-of-the-art iron-based catalysts, leading to excellent degradation activities against various organic pollutants at neutral condition. This work provides fundamental insights into the function of fluorine coordination in boosting Fenton catalysis at atomic level, which may inspire the design of efficient active sites for sustainable environmental remediation.

Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity.

Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.

Abstract 2115 SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction

Abstract 2115 SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction

Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions.

A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+ ) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.

Zirconium and hafnium catalyzed C–C single bond hydroboration

Selective cleavage and subsequent functionalization of C−C single bonds present a fundamental challenge in synthetic organic chemistry. Traditionally, the activation of C−C single bonds has been achieved using stoichiometric transition-metal complexes. Recently, examples of catalytic processes were developed in which use is made of precious metals. However, the use of inexpensive and Earth-abundant group IV metals for catalytic C−C single-bond cleavage is largely underdeveloped. Herein, the zirconium-catalyzed C−C single-bond cleavage and subsequent hydroboration reactions is realized using Cp2ZrCl2 as a catalytic system. A series of structures of various γ-boronated amines are readily obtained, which are otherwise difficult to obtain. Mechanistic studies disclose the formation of a N–ZrIV species, and then a β-carbon elimination route is responsible for C–C single bond activation. Besides zirconium, hafnium exhibits a similar performance for this transformation.

XUV Absorption Spectroscopy and Photoconversion of a Tin-Oxo Cage Photoresist.

Extreme ultraviolet lithography has recently been introduced in high-volume production of integrated circuits for manufacturing the smallest features in high-end computer chips. Hybrid organic/inorganic materials are considered as the next generation of photoresists for this technology, but detailed knowledge about the response of such materials to the ionizing radiation used (13.5 nm, 92 eV) is still scarce. In the present work, we use broadband high-harmonic radiation in the energy range 22-70 eV for absorption spectroscopy and photobleaching (that is, the decrease of absorbance) of thin films of an n-butyltin oxo-cage, a representative of the class of metal-based EUV photoresist. The shape of the absorption spectrum in the range 22-92 eV matches well with the spectrum predicted using tabulated atomic cross sections. The photobleaching results are consistent with loss of the butyl side groups due to the breaking of Sn-C bonds following photoionization. Bleaching is strongest in the low-energy range (<40 eV), where the absorption is largely due to the carbon atoms in the organic groups. At higher energies (42-70 eV), absorption is dominated by the tin atoms, and since these remain in the film after photoconversion, the absorption change in this region is smaller. It is estimated that after prolonged irradiation (up to ∼3 J cm-2 in the range 22-40 eV) about 70% of the hydrocarbon groups are removed from the film. The rate of bleaching is high at the beginning of exposure, but it rapidly decreases with increasing conversion. We rationalize this using density functional theory calculations: the first Sn-C bonds are efficiently cleaved (quantum yield Φ ≈ 0.9), because the highest occupied molecular orbitals (HOMOs) (from which an electron is removed after photoionization) are located on Sn-C sigma bonds. In the photoproducts, the HOMO is localized on tin atoms that have lost their hydrocarbon group (formally reduced to the Sn(II) oxidation state), and holes formed on those tin atoms lead to less efficient cleavage reactions. Our results reveal the primary reaction steps following excitation with ionizing radiation of tin-oxo cages. Our methodology represents a systematic approach of studying and quantitatively assessing the performance of new photoresists and as such enables the development of future EUV photoresists.

Synthesis and Deconstruction of Polyethylene-type Materials.

Polyethylene deconstruction to reusable smaller molecules is hindered by the chemical inertness of its hydrocarbon chains. Pyrolysis and related approaches commonly require high temperatures, are energy-intensive, and yield mixtures of multiple classes of compounds. Selective cleavage reactions under mild conditions (<ca. 200 °C) are key to improve the efficacy of chemical recycling and upcycling approaches. These can be enabled by introduction of low densities of predetermined breaking points in the polyethylene chains during the step-growth or chain-growth synthetic construction of designed-for-recycling polyethylene-type materials. Alternatively, they can be accomplished by postpolymerization functionalization of postconsumer polyethylene waste via dehydrogenation and follow-up reactions or through oxidation to long-chain dicarboxylates. Deconstruction of litter under environmental conditions via the aforementioned break points can alleviate plastics' persistency, as a backstop to closed-loop recycling.