Cyclization Research Articles

Structural basis of the T4 bacteriophage primosome assembly and primer synthesis

The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome to couple DNA unwinding with RNA primer synthesis for DNA replication. How the primosome is assembled and how the primer length is defined are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates. We show that gp41 alone is an open spiral, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the ring closure and activates the helicase. Helicase activation exposes a cryptic hydrophobic surface to recruit the gp61 primase. The primase binds the helicase in a bipartite mode in which the N-terminal Zn-binding domain and the C-terminal RNA polymerase domain each contain a helicase-interacting motif that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Our study reveals the T4 primosome assembly process and sheds light on the RNA primer synthesis mechanism.

Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis

Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis

Palladium-catalyzed ring-closing reaction of enynols with aminals via methylene transfer and C–N bond activation

The aminomethyl cyclopalladated complex is identified as a key intermediate for promoting the C–N bond activation of tertiary amines via reductive elimination and oxidative addition sequence. This strategy has enabled a palladium-catalyzed ring-closing reaction of enynols with aminals via methylene transfer and C–N bond activation, which provides rapid access to densely functionalized O-heterocycle containing allenic amines. The dual roles of the cyclopalladated complex, first as an aminomethylene-carrying reagent and then as a catalyst for C–N bond activation, have enabled a rare cascade redox-neutral methylene transfer and cyclization process that can simultaneously construct O-heterocycle framework and allenic amine functionality.

Synthesis, characterization, molecular docking studies, and in vitro elucidation of protein aggregation inhibition potential of 3β-acetoxy steroidal pyrazolines

Protein misfolding and amyloid fibril deposition may lead to several neurodegenerative disorders like Alzheimer's, Parkinson's, Huntington's, and similar amyloid polyneuropathies. Inhibition of fibril formation and disaggregation of mature fibrils by some chemical compounds could be a therapeutic approach toward such chronic diseases. In this study, we synthesized a series of novel steroidal pyrazolines and tested the effects of the series on the in vitro inhibition of human lysozyme aggregation. The effect of synthesized steroidal compounds on the kinetics of protein aggregation inhibition was elucidated by Tryptophan (Trp), 8-anilino-1-naphthalenesulfonic acid (ANS), and Congo red (CR) spectral analysis. Further, we examined that the ring closure reaction in the later step produced a mixture of two steroidal pyrazoline epimers that could only be separated in their acetylated form. The (5’S)-3β-acetoxy steroidal pyrazolines (5a-i) were found as the major product and their structures were examined using NMR techniques. The efficacy of various acid catalysts to catalyze the condensation reaction was also evaluated to obtain better yield in lesser time. In addition, molecular docking studies were also performed to understand the receptor-ligand binding interactions.

3-(4-(Benzyloxy)-3-methoxyphenyl)-[1,2,4]triazolo[4,3-a]pyridine

The [1,2,4]triazolo[4,3-a]pyridine derivative 3-(4-(benzyloxy)-3-methoxyphenyl)-[1,2,4]triazolo[4,3-a]pyridine was prepared in a 73% isolated yield by means of an oxidative ring closure of a hydrazine intermediate. Sodium hypochlorite was used as the oxidant and ethanol as a solvent, making the process a clean, green approach. The reaction was performed at room temperature for 3 h, and then the heterocycle was isolated in an analytically pure form by extraction, followed by passing the crude product mixture through a small plug of alumina.

Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing

Eukaryotic DNA replication must occur exactly once per cell cycle to maintain cell ploidy. This outcome is ensured by temporally separating replicative helicase loading (G1 phase) and activation (S phase). In budding yeast, helicase loading is prevented outside of G1 by cyclin-dependent kinase (CDK) phosphorylation of three helicase-loading proteins: Cdc6, the Mcm2-7 helicase, and the origin recognition complex (ORC). CDK inhibition of Cdc6 and Mcm2-7 is well understood. Here we use single-molecule assays for multiple events during origin licensing to determine how CDK phosphorylation of ORC suppresses helicase loading. We find that phosphorylated ORC recruits a first Mcm2-7 to origins but prevents second Mcm2-7 recruitment. The phosphorylation of the Orc6, but not of the Orc2 subunit, increases the fraction of first Mcm2-7 recruitment events that are unsuccessful due to the rapid and simultaneous release of the helicase and its associated Cdt1 helicase-loading protein. Real-time monitoring of first Mcm2-7 ring closing reveals that either Orc2 or Orc6 phosphorylation prevents Mcm2-7 from stably encircling origin DNA. Consequently, we assessed formation of the MO complex, an intermediate that requires the closed-ring form of Mcm2-7. We found that ORC phosphorylation fully inhibits MO complex formation and we provide evidence that this event is required for stable closing of the first Mcm2-7. Our studies show that multiple steps of helicase loading are impacted by ORC phosphorylation and reveal that closing of the first Mcm2-7 ring is a two-step process started by Cdt1 release and completed by MO complex formation.

Regioselectivity of CH activation in cytochrome P450‐catalyzed intramolecular cyclization of alkylamine compounds

AbstractThe reaction mechanism of cytochrome P450‐mediated intramolecular cyclization of 2‐aminoamide compounds to imidazolinone was studied by density functional theory. The cyclization reaction involves three steps: hydrogen abstraction, dehydration of intermediates to zwitterions and final ring closure. Interestingly, high spin (HS) state P450‐catalyzed dehydration exhibits a mechanism distinct from conventional processes such as in low spin state. In HS pathways, the hydroxyl group after hydrogen abstraction does not rebound but produce an intermediate, which makes the second hydrogen abstraction regioselective. Regioselectivity leads to diverse intermediates and mechanisms to zwitterion, which implies different functions of the high and low spin states P450. The alkylamine nitrogen and amide group are key groups to enables regioselectivity of in HS pathway. Small changes of molecular structure can affect the molecular transformation process, indicating the complex regulation of electronic state to reaction process. The results lay the theoretical basis for the regioselectivity determined by P450 enzyme and substrate structure together. The research establishes a foundation for the drug design, drug metabolite, and synthesis of nitrogen‐containing heterocyclic drugs.

Rilmazafone: A designer benzodiazepine pro-drug involved in fatal intoxications.

Rilmazafone is a pro-drug that can be prescribed in Japan to treat insomnia. Rilmazafone metabolizes into active compounds by a ring closure resulting in a triazolo benzodiazepine structure similar to alprazolam. In mid-2022, the National Board of Forensic Medicine in Sweden were requested to investigate two separate deaths with the suspected use of pagoclone. Packages labelled "Pagoclone" were found at each scene that was suspected to contain rilmazafone based on website information. During screening by high resolution mass spectrometry, rilmazafone metabolites were presumptively identified. Due to the lack of reference material for the active metabolites, the metabolites were synthesized in house and quantification of the compounds identified in the two autopsy cases was prompted. In Case 1, femoral blood concentrations of 7.9, 65, and 170 ng/g of the metabolites rilmazolam, N-desmethyl rilmazolam and di-desmethyl rilmazolam, respectively, were detected. Additional toxicological findings included the medications haloperidol, alimemazine, fluoxetine, olanzapine, and acetaminophen. In Case 2, femoral blood concentrations of 1.7, 1.4 and 70 ng/g of rimazolam, N-desmethyl rilmazolam and di-desmethyl rilmazolam, respectively, were detected. Additional toxicological findings included loperamide, alimemazine, and pregabalin. The intake of rilmazafone was determined as the cause of death in Case 1 and contributed in the Case 2.

Cyclic Polymers: Controlled Synthesis, Properties and Perspectives.

Recently, cyclic polymers have attracted increasing interest due to their unique topologies, properties, and functions compared to the linear analogues. This mini-review focuses on the recent advances in the synthesis and applications of cyclic polymers. First, the main synthetic methods for cyclic polymers, namely ring closure and ring expansion methods, are presented and discussed, followed by a review on the exploration of the properties and applications of synthetic cyclic polymers. Finally, a critical assessment of the preliminary studies exploring the efficient synthesis and potential applications of cyclic polymers are presented, and the remaining challenges in the field as well as ideas for solving these challenges will be discussed.

Catalyst-Free Synthesis of Functionalized 4-Substituted-4H-Benzo[d][1,3]oxazines via Intramolecular Cyclization of ortho-Amide-N-tosylhydrazones.

Functionalized 4-aryl-4H-benzo[d][1,3]oxazines are synthesized under transition-metal-free conditions using ortho-amide-N-tosylhydrazones. This synthetic method uses readily available N-tosylhydrazones as the diazo compound precursors and involves an intramolecular ring closure reaction mediated by a protic polar additive (iPrOH). A wide range of functionalized oxazines are obtained by this straightforward method in good to excellent yields. Furthermore, the viability of our strategy is illustrated by the gram-scale elaboration of a bromo-substituted 4H-benzo[d][1,3]oxazine and its post-functionalization by palladium-catalyzed cross-couplings.

Investigation of the Model-Dependent Reactivity of the Char-Bound Nitrogen Surface: A DFT Study.

The concern of energy and the environment provides great inducement for fundamental research on the mechanisms of oxidation of char-bound nitrogen (char(N)). In the present study, based on the armchair(N) model, we investigated its reaction mechanism at an atomistic level and with a comprehensive study of the effect of the model surface. Several pathways are found by density functional theory (DFT) calculations for the oxidation of armchair(N). The main gaseous species released during the oxidation are NO, HCN, CO, and CO2. The evaluated optimal reaction pathways are selected to investigate the model-dependent reactivity. According to our calculations, the oxidation of the simplified top armchair(N) model (TM) will be much more competitive than that of the simplified edge armchair(N) model (EM). In the route giving NO, the decreased stability of the intermediates makes the reaction of TM more favorable. In the route giving HCN, the described reduced mechanism and the larger exothermicity and lower highest-energy transition state will be responsible for the priority. Further analysis of the kinetics gives the evidence for the competitiveness: the rate constants for most of the steps of the TM, such as HCN desorption, surface bond dissociation, ring closure and opening, and oxygen insertion and migration, are higher than that of the EM. Therefore, a conclusion can be drawn that the oxidation of the armchair(N) will mainly take place from the top surface rather than the edge surface. The results can be used to supplement present understanding of the oxidation of armchair structure, which is extremely crucial for the development of the kinetics model to better predict the NOx emissions during the air-staged combustion.

Cesium Carbonate-Promoted Reaction of Nitro-Substituted Donor-Acceptor Cyclopropanes with Salicylaldehydes in Water: Access to Chromane Derivatives.

Nitro-substituted donor-acceptor cyclopropanes react with salicylaldehydes in the presence of cesium carbonate in water to give new chromane derivatives. The reaction takes place through in situ formation of allene intermediates from the cyclopropanes and subsequent Michael-initiated ring closure of the intermediates with salicylaldehydes.

Visible-Light-Promoted 6π Photocyclization of ortho-Biaryl-Appended β-Ketoesters.

A photocatalyst- and additive-free visible-light-induced 6π-photocyclization of ortho-biaryl-appended β-ketoesters has been developed. Upon irradiation with visible light, substrates undergo 6-endo-trig cyclization/1,5-H shift to 9,10-dihydrophenanthren-9-ols with high efficiency and selectivity. The reaction proceeds via conrotatory ring closure followed by a suprafacial 1,5-hydrogen shift leading to the observed single trans-fused products. Preliminary mechanistic studies reveal the feasibility of both 1,5-H shift and intersystem crossing of the diradical intermediate.

Comparison of Laparoscopic Percutaneous Extraperitoneal Internal Ring Closure by Two-Hook Hernia Needle and Open Repair for Pediatric Inguinal Hernia.

Purpose: In children, pediatric inguinal hernia (PIH) is a prevalent condition. PIH is currently more frequently managed by laparoscopic closure of the hernia sac. We improved this minimally invasive technique; that is, laparoscopic two-hook hernia needle percutaneous extraperitoneal internal ring closure. Safety and effectiveness were evaluated by comparing the differences between laparoscopic repair (LR) and open repair (OR) in terms of operation time, surgical complications, contralateral metachronous hernia incidence, and recurrence rate. Methods: A retrospective clinical data analysis was performed on pediatric patients who had hernia surgery utilizing the LR or OR method between June 2019 and June 2021. Medical records of all of the children were gathered, and clinical traits, information about the procedure, and follow-up were all analyzed. Results: A total of 370 patients' inguinal hernias were repaired. For 136 patients undergoing OR and 234 patients undergoing LR, all procedures were completed satisfactorily. There were 98 cases of bilateral hernias and 272 cases of unilateral hernias (180 on the right side and 92 on the left). In the LR group, 58 patients who had been initially diagnosed with unilateral hernias developed contralateral occult hernias intraoperatively. Inguinal hernia operations took an average of 13.82 (LR) and 32.07 (OR) minutes for unilateral cases, and 21.00 (LR) and 54.85 (OR) minutes for bilateral cases. For LR and OR, the average follow-up time was 22.41 months and 23.10 months, respectively. The perioperative complications included peritoneal rupture in 3 patients, scrotal edema or hematoma in 5, hydrocele in 3, and groin pain in 6. In the LR group, 1 patient experienced the postoperative recurrence, whereas 8 individuals in the OR group did. Conclusions: Our initial research showed that laparoscopic two-hook hernia needle percutaneous extraperitoneal internal ring closure inguinal hernia repair is a safe and effective procedure. The LR method has the benefits of concealing the incision, a quicker procedure, having a lower risk of complications, and finding contralateral patent processus vaginalis. Therefore, promoting and using this surgical technique in clinical practice are merited. Clinical Trial Registration number: Medical Association of Xiangtan (2022-xtyx-28).

General Access to Acenaphthene-FusedN-Heterocyclic Carbene Ligands

We communicate a general method for the syntheses of acenaphthene-fused imidazolinium salts that are direct precursors to augmented N-heterocyclic carbenes with a fixed cis geometry. Reduction of bis(imino)acenaphthene ligands with a LiAlH4/AlCl3 reagent mix initially produced the corresponding 1,2-diamines which, upon ring-closing reaction with triethyl orthoformate in acidic solution, gave the requisite ionic intermediates. Formation of the carbenes was then shown by preparation of selected [Cu(NHC)] complexes that were obtained via treatment of the respective imidazolinium salt with base in the presence of a Cu(I) source.

Physical UV-blocker TiO2 nanocomposites elevated toxicity of chemical sunscreen BP-1 under UV irradiation

Physical UV-blocker TiO2 nanocomposites and chemical sunscreen benzophenones (BPs) have been frequently detected in the aquatic environment, their combined fates and potential risk should be concerned. In this study, the typical cosmetic grade UV-blocker TiO2 nanocomposites (labeled as CG-TiO2) and 2,4-dihydroxy benzophenone (BP-1) were targeted, and the effects of CG-TiO2 on the transformation of BP-1 during UV irradiation were explored. It was found that CG-TiO2 destruction did not form toxic products, while they could promote the chemical reactions of BP-1 that will lead to highly toxic products during UV irradiation. More importantly, UV irradiation could break the organic coatings on CG-TiO2, the broken CG-TiO2 exhibited stronger catalytic activity on BP-1 and form highly toxic products during UV irradiation. Total of 24 transformation products were tentatively identified, including hydroxyl BPs, hydroxyl dibenzo-p-dioxins, hydroxyl benzoyl benzoquinones, etc. The main transforamtion mechanisms of BP-1 included hydroxylation, radical coupling, oxidation, decarboxylation, Norrish type I reaction, and ring closure through electrophilic substitution. This study highlighted that physical UV-blocker CG-TiO2 promoted the transformation of chemical sunscreen BP-1 and generated higher toxicity during UV irradiation. It was expected that these results would provide scientific data for evaluating the fates and potential risk of sunscreens in the environment.

Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli

Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli

Synthesis of 2-Difluoroethylated 2H-1,3-Benzoxazines via Proton-Mediated Ring Opening/Interrupted Ritter Reaction of 1,1-Difluorocyclopropanes.

2-(1,1-Difluoroethyl)-2H-1,3-benzoxazines were synthesized by (i) the regioselective ring opening of 1,1-difluorocyclopropanes bearing an aryloxy group and (ii) the Ritter reaction followed by a Friedel-Crafts-type ring closure. When 2-aryloxy-1,1-difluorocyclopropanes were treated with triflic acid, the C-C bond distal to the CF2 moiety was cleaved regioselectively via protonation to generate the corresponding oxocarbenium ions. These intermediates readily underwent nucleophilic attack by nitriles, followed by a carbocationic cyclization to afford the 2-difluoroethylated benzoxazines.

Preprint Highlight: Contractile ring mechanosensation and its anillin-dependent tuning during early embryogenesis

Dividing cells assemble and constrict a contractile ring made up of actin and myosin anchored to the cell cortex. How the contractile ring senses the mechanics of the cell cortex is not known. With asymmetric ring closure in C. elegans as a model, the authors used novel 4D imaging and image segmentation methods to carefully track ring closure over time. They found that ring-directed cortical flow underlies mechanosensation and supports a positive feedback loop between ring closure, cortical flow, and myosin accumulation. These findings suggest that differences in cell cortex stiffness may determine the orientation and type of cell division–i.e., asymmetric vs. symmetric ring closure. As tissue morphogenesis often relies on specifically oriented cell divisions, defining mechanisms of ring closure is essential for understanding multicellular development. This preprint has been assigned the following badges: New Methods, New Hypothesis. Read the preprint on bioRxiv ( Hsu et al., 2023 ): https://doi.org/10.1101/2022.09.09.506560 .

Stable β-form zinc phthalocyanine cathodes for flexible Zn-ion hybrid supercapacitors with ultra-long cycling life

Metal phthalocyanine with a unique π-conjugated structure, has shown extraordinary promise for electrocatalysis, batteries and supercapacitors. High-performance Zn-ion hybrid supercapacitors make high demands on the energy storage mechanisms of metal phthalocyanine. We propose a β-form zinc phthalocyanine (ZnPc) molecular crystal as a cathode material for flexible Zn-ion hybrid supercapacitors. The β-ZnPc is facilely synthesized through the annealing treatment of the original ZnPc, which is previously fabricated through a ring-closure reaction assisted by catalysis of sodium methanol and ultrasonic treatment. The structural transformation of ZnPc from α-ZnPc to β-ZnPc is demonstrated at the annealing temperature from 200 °C to 300 °C, probably attributed to the short-range neighbor interaction between the adjacent ZnPc molecular layers. The β-ZnPc electrode exhibits the higher specific capacitance and the better rate capability than those of the α-ZnPc electrode, mainly due to its higher specific surface area and more abundant pore structure. The electron density and adsorption energy of ZnPc are theoretically calculated, revealing the active N sites for the reversible adsorption/desorption of Zn2+. The flexible Zn-ion hybrid supercapacitor provides the maximum energy density of 86.2 Wh kg−1 at 0.22 kW kg−1, and maintains the capacitance retention of 73.4% after 100,000 cycles, opening up a new avenue for developing high-energy and long-life Zn-ion hybrid supercapacitors.