Rearrangement Sequence Research Articles

Distribution Patterns of tfdI and tfdII Gene Clusters and New Insights into the Formation of the Architecture of pJP4, a Canonical 2,4-dichlorophenoxyacetic Acid (2,4-D) Degradation Plasmid

Currently, pJP4 is one of the best-known plasmids for the biodegradation of xenobiotics that mediate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), which is associated with serious health and environmental risks. Although the sequencing and proposed theory of pJP4 formation occurred almost 20 years ago (2004), pJP4 is still the model object of many studies focused on the biodegradation of 2,4-D. The uniqueness of this plasmid is due to the presence of two evolutionarily distinct gene clusters, tfdI and tfdII, controlling the degradation of 2,4-D. Recent advances in plasmid biology, especially those concerning the characterization of new IncP-1 plasmids and the systematization of tfd gene cluster findings, serve as a basis for proposing new insights into the formation of the clusters’ architecture of the canonical plasmid, pJP4, and their distribution among other plasmids. In the present work, a comparative genomic and phylogenetic in silico study of plasmids with tfdI and tfdII clusters was carried out. The possible initial distribution patterns of tfdI clusters among plasmids of different incompatibility groups (non-IncP-1) and tfdII clusters among IncP-1 plasmids using the IS1071-based composite transposon were revealed. A new theory on the formation of the architecture of the tfdI and tfdII clusters of pJP4 through sequential internal rearrangements, recombination, and ISJP4 insertion, is proposed. In addition, small gene clusters resulting from internal rearrangements of pJP4 (tfdIISA and ORF31/32) served as fingerprints for exploring the distribution of tfdI and tfdII clusters. The revealed patterns and formulated theory extend the frontiers of plasmid biology and will be beneficial for understanding the role of plasmids in bacterial adaptation to xenobiotic-contaminated environments.

Hepatocyte-derived Igκ promotes HCC progression by stabilizing electron transfer flavoprotein subunit α to facilitate fatty acid β-oxidation

BackgroundLipid metabolism dysregulation is a key characteristic of hepatocellular carcinoma (HCC) onset and progression. Elevated expression of immunoglobulin (Ig), especially the Igκ free light chain with a unique Vκ4-1/Jκ3 rearrangement in cancer cells, is linked to increased malignancy and has been implicated in colon cancer tumorigenesis. However, the role of Igκ in HCC carcinogenesis remains unclear. The aim of this study was to elucidate the pivotal roles of hepatocyte-derived Igκ in HCC development.MethodsThe rearrangement sequence and expression level of hepatocyte-derived Igκ in HCC cells were determined via RT-PCR, Sanger sequencing, immunohistochemistry, and western blot analysis. The function of Igκ in HCC tumorigenesis was assessed by silencing Igκ using siRNA or gRNA in various HCC cell lines. To assess the role of Igκ in HCC pathogenesis in vivo, a mouse model with hepatocyte-specific Igκ knockout and diethylnitrosamine (DEN) and carbon tetrachloride (CCL4)-induced HCC was utilized. The molecular mechanism by which Igκ affects HCC tumorigenesis was investigated through multiomics analyses, quantitative real-time PCR, immunoprecipitation, mass spectrometry, immunofluorescence, and metabolite detection.ResultsWe confirmed that Igκ, especially Vκ4-1/Jκ3-Igκ, is highly expressed in human HCC cells. Igκ depletion inhibited HCC cell proliferation and migration in vitro, and hepatocyte-specific Igκ deficiency ameliorated HCC progression in mice with DEN and CCL4-induced HCC in vivo. Mechanistically, Vκ4-1/Jκ3-Igκ interacts with electron transfer flavoprotein subunit α (ETFA), delaying its protein degradation. Loss of Igκ led to a decrease in the expression of mitochondrial respiratory chain complexes III and IV, resulting in aberrant fatty acid β-oxidation (FAO) and lipid accumulation, which in turn inhibited HCC cell proliferation and migration.ConclusionOur findings indicate that the Igκ/ETFA axis deregulates fatty acid β-oxidation, contributing to HCC progression, which suggests that targeting fatty acid metabolism may be an effective HCC treatment strategy. The results of this study suggest that hepatocyte-derived Vκ4-1/Jκ3-Igκ may serve as a promising therapeutic target for HCC.

B-227 Customized molecular tests for minimal residual disease: a tool for therapeutic decisions in follicular lymphoma patients

Abstract Background Monitoring of minimal residual disease (MRD) is based on accurate laboratory tests which can recognize a small fraction of malignant cells that survived the course of treatment. Several studies of the B-non-Hodgkin lymphoma group have been presented that MRD positivity at the end of treatment is a negative prognostic index. Follicular lymphoma (FL) is a chronic indolent malignancy, which response highly to immuno-chemotherapy followed by prolonged remissions but with inevitable relapse in most patients. The GALLIUM study showed that immuno-chemotherapy combinations, 6 cycles of bendamustine-obinutuzumab (BO), is the most efficacious treatment, but with severe side effects .In addition, 90% of patients achieved negative MRD from peripheral blood (PB) or bone marrow (BM) after only 3 BO cycles. These findings raise the possibility for MRD based treatment approach, where the duration of chemotherapy could be decided according to MRD status at mid-induction (MI). Identification of a marker in the PB and/or BM of each FL patient which will be use to the design of a sensitive RQ-PCR test for MRD detection for follow-up. Methods Qualitative PCR for translocation 14:18 and for the VDJ rearrangement sequence of the immunoglobulin heavy chain was used for marker identification. MRD monitoring was done by RQ-PCR. MRD monitoring for VDJ was designed specifically to each patients based on his VDJ sequence. MRD was assessed on PB and BM at MI. Results Marker for monitoring was identified at 11/21 patients in this study. After 3 combined therapy cycles, 7 patients were found to have MRD negativity by RQ-PCR therefore continue with immuno-therapy only. MRD positivity was assessed in BM of 3 patients (0.11%, 0.022%, and 0.133%). These 3 patients continued with the combined therapy. RQ-PCR sensitivity was 10-4-10-5. Conclusions This study will reveal the ability to use sensitive and specific MRD that has to be designed for each patient according to his marker and enable the establishment of a treatment with a high safety profile for FL patients. Correlation between MRD status and clinical and safety parameters will be assessed at the end of the study, 30 months after the first treatment, taking into account MRD status from different time point of the follow-up period.

Coronene‐Based 2D Networks by On‐Surface Skeletal Rearrangement of Sumanene Precursors

The design of novel low‐dimensional carbon materials is at the forefront of modern chemistry. Recently, on‐surface covalent synthesis has emerged as a powerful strategy to synthesize previously precluded compounds and polymers. Here, we report a scanning probe microscopy study, complemented by theoretical calculations, about the sequential skeletal rearrangement of sumanene‐based precursors into a coronene‐based organometallic network by stepwise intra‐ and inter‐molecular reactions on Au(111). Interestingly, upon higher annealing, the formed organometallic networks evolve into two‐dimensional coronene‐based covalently‐linked patches through intermolecular homocoupling reactions. A new reaction mechanism is proposed based on the role of C‐Au‐C motifs to promote two stepwise carbon‐carbon couplings to form cyclobutadiene bridges. Our results pave avenues for the conversion of molecular precursors on surfaces, affording the design of unexplored two‐dimensional organometallic and covalent materials.

Lewis Acid‐Catalyzed Tandem Annulation of Propargylic Alcohols with 2‐Allylphenols and Their Anti‐tumor Activities

AbstractA novel bismuth(III) trifluoro‐methanesulfonate‐catalyzed and environmentally benign synthetic strategy for the construction of a wide range of structurally diverse, sophisticated [5,6,5]‐oxygen‐containing tricyclic frameworks with easy‐to handle propargylic alcohols and 2‐allylphenols as substrates in the presence of Bi(OTf)3 and AgOTf is described. This Lewis acid catalyzed [3+2] annulation protocol, which tolerates a great deal of functional groups, proceeds through a sequential Meyer‐Schuster rearrangement, nucleophilic substitution, 5‐exo‐trig cyclization, 5‐endo‐trig cyclization, and proton exchange sequences, affording a versatile approach for accessing oxygen‐containing tricyclic skeletons in moderate‐to‐excellent yields. In addition, most of the obtained compounds exhibited anti‐tumor activities against three types of human cancer cell lines in vitro, including Caco‐2 colon cancer cells, MCF‐7 breast cancer cells, and Hepg‐2 liver cancer cells.

Spiro[2.3]hexane‐ and Spiro[3.3]heptane‐derived α‐Amino Acids: Synthesis and Isoelectric Point Evaluation

AbstractAn efficient synthesis of spiro[2.3]hexane‐ and spiro[3.3]heptane‐derived α‐amino acids is reported. The used methods are divided on two different approaches. First of them involves modification of commercially available spirocyclic diesters via monohydrolysis, Curtius rearrangement and functional groups deprotection sequence. Alternative approach was based on Bucherer ‐ Bergs hydantoine synthesis with its subsequent cleavage to the target amino acid fragment. The proposed synthetic schemes offer the desired product in 31–52 % overall yield on up to 22.5 g scale. Acid‐base titration of the obtained spirocyclic amino acids revealed lowered pI values compared to the parent 1‐amino‐cyclohexane‐ and ‐cycloheptanecarboxylic acids.

Biosynthesis of the Non-canonical C17 Sesquiterpenoids Chlororaphen A and B from Pseudomonas chlororaphis.

Chlororaphens A and B are structurally unique non-canonical C17 sesquiterpenoids from Pseudomonas chlororaphis that are made by two SAM-dependent methyltransferases and a type I terpene synthase. This study addresses the mechanism of their formation in isotopic labelling experiments and DFT calculations. The results demonstrate an astonishing complexity with distribution of labellings within a cyclopentane core that is reversely connected to two acyclic fragments in chlororaphen A and B. In addition, the uptake of up to 14 deuterium atoms from D2O was observed. These findings are explainable by a repeated late stage multistep rearrangement sequence. The absolute configurations of the chlororaphens and their biosynthetic intermediates were elucidated in stereoselective labelling experiments.

Modular Synthesis of Tetrasubstituted Vinyl Sulfides via One-Pot Sequential Carbene Transfer Reaction from Thiols with α-Diazo Carbonyl Compounds.

We present a one-pot reaction that offers an efficient approach to synthesizing tetrasubstituted vinyl sulfides with high stereoselectivity. This method involves the sequential Wolff rearrangement, ylide formation, and [1,4]-aryl transfer by utilizing aryl and alkyl thiols and α-diazo carbonyl compounds as substrates. Notably, this reaction features commercially available materials, straightforward operation, atom economy, and broad substrate scope. Moreover, the primary photophysical properties (aggregation-induced emission effect) of the products were also investigated, which might be useful in functional materials via structural modification.

Divergent synthesis of complex withanolides enabled by a scalable route and late-stage functionalization.

Withanolides are a group of naturally occurring C28 steroids based on an ergostane skeleton. They have a high degree of polyoxygenation, and the abundance of O-functional groups has enabled various natural alterations to both the carbocyclic skeleton and the side chain. Consequently, these molecules have intricate structural features that lead to their highly varied display of biological activities including anticancer, anti-inflammatory, and immunomodulating properties. Despite being intriguing leads for further discovery research, synthetic access to the withanolides remains highly challenging-compounds for current biological research are mainly isolated from plants, often inefficiently. Here, we report the divergent synthesis of 11 withanolides in 12 to 20 steps, enabled by a gram-scale route and a series of late-stage functionalizations, most notably a bioinspired photooxygenation-allylic hydroperoxide rearrangement sequence. This approach enables further biological research disconnected from a reliance on minute quantities of the parent natural products or their simple derivatives.

Synthesis of Cyclic β-Amino Acid Derivatives by Desymmetrization and Lossen Rearrangement of N-Sulfoxy Meso-Succinimides.

Bifunctional thiourea-based organocatalysts facilitate an enantioselective desymmetrization and Lossen rearrangement cascade reaction of N-sulfoxy meso-succinimides, resulting in the synthesis of cyclic β-amino acid derivatives. This catalytic system was optimized for bicyclic and tricyclic succinimide substrates affording yields from 61-91% and up to 96:4 er. This reaction proceeds via the group selective addition of the primary alcohol nucleophile to an enantiotopic carbonyl group with sequential rearrangement of the intermediate O-sulfonyl hydroxamate ester.

Total Syntheses of (±)-Acetoxymarsupellone and (±)-Marsupellins A, B, and D Enabled by a Reductive Cyclization and Semipinacol Rearrangement Strategy.

We report herein the total syntheses of three marsupellin-family sesquiterpenoids, (±)-acetoxymarsupellone and (±)-marsupellins B and D, in 14-19 steps from our known precursor, making marsupellin A also accessible from marsupellin B through a known procedure. The critical tricyclic framework bearing the challenging C7 bridgehead all-carbon quaternary center is strategically constructed through a Ti-mediated reductive cyclization and semipinacol rearrangement sequence. This study provides a general approach to the syntheses of (ent-)longipinane-type molecules.

Inside Back Cover: Stereoselective Synthesis of Polysubstituted Conjugated Dienes Enabled by Photo‐Driven Sequential Sigmatropic Rearrangement (Angew. Chem. Int. Ed. 24/2024)

Inside Back Cover: Stereoselective Synthesis of Polysubstituted Conjugated Dienes Enabled by Photo‐Driven Sequential Sigmatropic Rearrangement (Angew. Chem. Int. Ed. 24/2024)

Innenrücktitelbild: Stereoselective Synthesis of Polysubstituted Conjugated Dienes Enabled by Photo‐Driven Sequential Sigmatropic Rearrangement (Angew. Chem. 24/2024)

Innenrücktitelbild: Stereoselective Synthesis of Polysubstituted Conjugated Dienes Enabled by Photo‐Driven Sequential Sigmatropic Rearrangement (Angew. Chem. 24/2024)

Stereoselective Synthesis of Polysubstituted Conjugated Dienes Enabled by Photo‐Driven Sequential Sigmatropic Rearrangement

AbstractWe here reported a highly stereoselective method for the synthesis of polysubstituted conjugated dienes from α‐aryl α‐diazo alkynyl ketones and pyrazole‐substituted unsymmetric aminals under mild conditions, which was promoted by photo‐irridation and involved with 1,6‐dipolar intermediate and quadruple sigmatropic rearrangements, was successfully developed. In this transformation, the cleavage of four bonds and the recombination of five bonds were implemented in one operational step. This protocol provided a modular tool for constructing dienes from amines, pyrazoles and α‐alkynyl‐α‐diazoketones in one‐pot manner. The results of mechanistic investigation indicated that the plausible reaction path underwent the 1,6‐sigmatropic rearrangement instead of the 1,5‐sigmatropic rearrangement.

Stereoselective Synthesis of Polysubstituted Conjugated Dienes Enabled by Photo-Driven Sequential Sigmatropic Rearrangement.

We here reported a highly stereoselective method for the synthesis of polysubstituted conjugated dienes from α-aryl α-diazo alkynyl ketones and pyrazole-substituted unsymmetric aminals under mild conditions, which was promoted by photo-irridation and involved with 1,6-dipolar intermediate and quadruple sigmatropic rearrangements, was successfully developed. In this transformation, the cleavage of four bonds and the recombination of five bonds were implemented in one operational step. This protocol provided a modular tool for constructing dienes from amines, pyrazoles and α-alkynyl-α-diazoketones in one-pot manner. The results of mechanistic investigation indicated that the plausible reaction path underwent the 1,6-sigmatropic rearrangement instead of the 1,5-sigmatropic rearrangement.

PIII/PV-Catalyzed Beckmann Reaction and Sequential [2,3]-Sigmatropic Rearrangement to Construct 2-Amidopyridines.

An organophosphorus catalytic method for the synthesis of substituted 2-amidopyridines is reported. The method employs a small-ring organophosphorus-based catalyst and a hydrosilane reductant to drive the conversion of ketoximes and pyridine-N-oxides into 2-amidopyridines through sequential Beckmann rearrangement followed by [2,3]-sigmatropic rearrangement. The readily available ketoximes could be activated to nitrilium ions in PIII/PV redox catalysis and could efficiently participate in the domino reaction of pyridine-N-oxides, thus providing various substituted 2-amidopyridines in moderate to excellent yields. This presented strategy features excellent functional group tolerance and a broad substrate scope.

FAVOR: Full-Body AR-Driven Virtual Object Rearrangement Guided by Instruction Text

Rearrangement operations form the crux of interactions between humans and their environment. The ability to generate natural, fluid sequences of this operation is of essential value in AR/VR and CG. Bridging a gap in the field, our study introduces FAVOR: a novel dataset for Full-body AR-driven Virtual Object Rearrangement that uniquely employs motion capture systems and AR eyeglasses. Comprising 3k diverse motion rearrangement sequences and 7.17 million interaction data frames, this dataset breaks new ground in research data. We also present a pipeline FAVORITE for producing digital human rearrangement motion sequences guided by instructions. Experimental results, both qualitative and quantitative, suggest that this dataset and pipeline deliver high-quality motion sequences. Our dataset, code, and appendix are available at https://kailinli.github.io/FAVOR.

Sequential rearrangement and stereochemical reorganization to design an antimicrobial peptide with enhanced stability

Antimicrobial peptides (AMPs) are natural molecules that function within the innate immune system to counteract pathogenic invasion and minimize the detrimental consequences of infection. However, utilizing these molecules for medical applications has been challenging. In this study, we selected a model AMP with poor stability, Tilapia Piscidin 4 (TP4), and modified its sequence and chirality (TP4-γ) to improve its potential for clinical application. The strategy of chirality inversion was inspired by the cereulide peptide, which has a DDLL enantiomer pattern and exhibits exceptional stability. Sequential substitution of key residues and selective chirality inversion yielded a less toxic peptide with enhanced stability and notable antimicrobial activity. In addition to its superior stability profile and antimicrobial activity, TP4-γ treatment reduced the level of LPS-induced nitric oxide (NO) release in a macrophage cell line. This reduction in NO release may reflect anti-inflammatory properties, as NO is widely known to promote inflammatory processes. Hence, our heterochiral peptide construct shows a more suitable pharmacokinetic profile than its parental compound, and further studies are warranted to develop the molecule for potential clinical application.

Alternative Approach to Access 5-Hydroxy-1H-pyrrol-2-(5H)-ones from Base-Induced Tandem Intramolecular Cyclization of Sulfur Ylide with Ketones and 1,3-Hydroxy Rearrangement.

An easily adaptable protocol for the preparation of 5-hydroxy-1H-pyrrol-2(5H)-ones from readily available starting materials has been reported. The reaction of sulfur ylides with carbonyl compounds is a common approach to synthesizing epoxides. Alternatively, we have developed a method with mild reaction conditions wherein sulfur ylide underwent an intramolecular cyclization with a ketonic carbonyl group in a highly efficient way and was followed by 1,3-hydroxy rearrangement to produce 5-hydroxy-1H-pyrrol-2(5H)-ones in excellent yields. The present method offers a straightforward approach to synthesize 5-hydroxy-1H-pyrrol-2(5H)-ones from sulfur ylides without the aid of transition metal in one-pot operation, which involves sequential cyclization and rearrangement reaction. The formation of 5-hydroxy-1H-pyrrol-2(5H)-ones is supported by different spectroscopic techniques, including X-ray crystallographic data and 2D NMR studies (COSY, HSQC, HMBC, and DEPT).

Total Syntheses of Rhodomollins A and B.

The first and asymmetric total syntheses of rhodomollins A and B, two rhodomollane type grayanoids featuring a d-homograyanane carbon skeleton and an oxa-bicyclo[3.2.1] core, were accomplished via a convergent strategy. A Stille coupling and a lithium-halogen exchange/intramolecular nucleophilic addition to the aldehyde sequence were employed to assemble two enantioenriched fragments. The oxa-bicyclo[3.2.1] core was achieved through an intramolecular SN2 substitution of cyclic sulfate of 1,2-diols (Williamson ether synthesis). The A ring oxidation states were adjusted by a Payne/Meinwald rearrangement sequence and subsequent redox transformations.