Search Results (59)

Our work introduces a facile and efficient metal-free [3+3] annulation approach for the synthesis of polysubstituted pyridines via the reaction between β-enaminonitriles and β,β-dichloromethyl peroxides. This strategy operates under mild conditions, demonstrating broad substrate scope and excellent functional group tolerance. Mechanistic investigations suggest that the reaction proceeds through a Kornblum–De La Mare rearrangement followed by S_NV-type C-Cl bond cleavage and intramolecular cyclization/condensation. By circumventing the need for transition metal catalysts or radical initiators, our method offers practical utility in organic synthesis and provides a new avenue for the rapid construction of complex pyridine scaffolds. Full article

Background/Objectives: Understanding the molecular interactions between small bioactive compounds and serum albumins is essential for drug development and pharmacokinetics. Noraucuparin, a biphenyl-type phytoalexin with promising pharmacological properties, has shown a strong binding affinity to bovine serum albumin (BSA), a model protein for drug transport. This study aims to elucidate the structural and energetic characteristics of the noraucuparin–BSA complex under physiological and slightly elevated temperatures. Methods: Microsecond-scale molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MMGBSA)-binding-free energy calculations were performed to investigate the interaction between noraucuparin and BSA at 298 K and 310 K. Conformational flexibility and per-residue energy decomposition analyses were conducted, along with interaction network mapping to assess ligand-induced rearrangements. Results: Noraucuparin preferentially binds to site II of BSA, near the ibuprofen-binding pocket, with stabilization driven by hydrogen bonding and hydrophobic interactions. Binding at 298 K notably increased the structural mobility of BSA, affecting its global conformational dynamics. Key residues, such as Trp213, Arg217, and Leu237, contributed significantly to complex stability, and the ligand induced localized rearrangements in the protein’s intramolecular interaction network. Conclusions: These findings offer insights into the dynamic behavior of the noraucuparin–BSA complex and enhance the understanding of serum albumin–ligand interactions, with potential implications for drug delivery systems. Full article

The homozygous Leu100Pro amino acid substitution in SPRED2, a protein negatively controlling RAS function, has recently been identified to be causally linked to a recessive form of Noonan syndrome. The amino acid substitution was documented to affect protein stability and cause a decreased and/or less stable interaction with neurofibromin, a RAS-specific GTPase activating protein negatively regulating RAS function. To further investigate the structural and functional impact of Leu100Pro, we structurally characterized the consequences of this change on the interaction of SPRED2 with neurofibromin, by 1 µn-long molecular dynamics (MD) simulations. Our analyses failed in identifying local perturbations predicted to disrupt or dramatically affect SPRED2 binding to neurofibromin, though a rearrangement of their interaction was observed. On the other hand, MD simulations also identified long-range structural rearrangements of the SPRED2 EVH-1 domain, which might be relevant for an aberrant folding of the mutant driving the previously documented accelerated degradation. Overall, the performed MD simulations suggest the occurrence of multiple intramolecular and intermolecular structural perturbations driven by the Leu100Pro change that likely contribute to its LoF behavior. Full article

Lagunamide D is a structurally distinct 26-membered cytotoxic cyclic depsipeptide, originally isolated from a marine cyanobacterium. It exhibits potent antiproliferative activity in the low nanomolar range against A549 human lung adenocarcinoma cells and HCT116 colon cancer cells. A significant challenge associated with lagunamide D is its propensity for intramolecular acyl migration, which leads to the formation of a contracted 24-membered analog, lagunamide D′. This structural rearrangement complicates its isolation, characterization, and synthesis. In this study, the total synthesis of lagunamide D was achieved in a 14-step longest linear sequence, starting from the known intermediate 17, with an overall yield of 4.6%. The synthetic strategy involved several key transformations, including Ghosh’s TiCl₄-promoted anti-aldol reaction, Corey–Bakshi–Shibata reduction (CBS reduction), cross-metathesis, Pinnick oxidation, and Yamaguchi esterification. Furthermore, this synthetic effort unambiguously confirmed the stereochemistry of the natural product. Full article

This research evaluated the effect of fermentation with Lactobacillus plantarum 11122, Lactobacillus casei 23184, and Lactobacillus lactis 1011 on structure, pasting, and in vitro digestion properties of glutinous rice starch varying in TN and HY genotype, respectively. The results showed that fermentation decreased the weight-average molecular weight and increased the radius of gyration. The short chain was increased by degrading the medium chain (B₂, DP 24−35) of amorphous in starch, which directly led to the increase of branching degree and rearrangement of the starch chain. LAB fermentation increases the short-range ordered structure, helix structure, and crystallinity by polymerization or interactions of short chains between intermolecular and intramolecular. Furthermore, the pasting characteristic of the fermented starch sample obtained obvious improvement in terms of hydration capacity, including breakdown and setback value. Fermentation facilitated the forming of both slowly digestible starch (17.1–30.79%) and resistant starch (32.3–46.8%) in TN but caused a decline in the content of rapidly digestible starch (25.47–43.6% in TN, 9.36–17.8% in HY). The result of Pearson’s correlation tests and PCA showed the variety of structural and physicochemical of fermentation-treated starch depend highly on the starter culture and starch resources. These results provided new data support for the potential application of modified starch by fermentation with LABs. Full article

Macrocycles bridge the gap between conventional small molecules and polymers. Drawing inspiration from successful carbon heteroatom-containing macrocycles, peroxide-containing macrocycles are gaining attention for enhanced bioactivity, potential chelating properties, and applications in energetic materials. This review presents the following strategies for the construction of cyclic peroxides with 10- to 36-membered frameworks: (1) the intramolecular iodocyclization of hydroperoxides, (2) the intermolecular cyclization of hydroperoxides with alkyl dihalides or carbonyls, (3) the acid-catalyzed rearrangements of ozonides or 11-membered cyclic triperoxides via oxy- or peroxycarbenium ions, and (4) the peroxidation of carbonyls targeting macrocyclic peroxides. The specific agents that allow for the selective construction of the medium and large cycles are also analyzed. Full article

Ethyl maltol was investigated using matrix isolation infrared spectroscopy and DFT calculations. In an argon matrix (14.5 K), the compound was found to exist in a single conformer (form I), characterized by an intramolecular hydrogen bond with an estimated energy of ~17 kJ mol⁻¹. The IR spectrum of this conformer was assigned, and the molecule’s potential energy landscape was explored to understand the relative stability and isomerization dynamics of the conformers. Upon annealing the matrix to 41.5 K, ethyl maltol was found to predominantly aggregate into a centrosymmetric dimer (2× conformer I) bearing two intermolecular hydrogen bonds with an estimated energy of ca. 28 kJ mol⁻¹ (per bond). The UV-induced (λ > 235 nm) photochemistry of the matrix-isolated ethyl maltol was also investigated. After 1 min of irradiation, band markers of two rearrangement photoproducts formed through the photoinduced detachment-attachment (PIDA) mechanism, in which the ethyl maltol radical acts as an intermediate, were observed: 1-ethyl-3-hydroxy-6-oxibicyclo [3.1.0] hex-3-en-2-one and 2-ethyl-2H-pyran-3,4-dione. The first undergoes subsequent reactions, rearranging to 4-hydroxy-4-propanoylcyclobut-2-en-1-one and photofragmenting to cyclopropenone and 2-hydroxybut-1-en-1-one. Other final products were also observed, specifically acetylene and CO (the expected fragmentation products of cyclopropenone), and CO₂. Overall, the study demonstrated ethyl maltol’s high reactivity under UV irradiation, with significant photochemical conversion occurring within minutes. The rapid photochemical conversion, with complete consumption of the compound in 20 min, should be taken into account in designing practical applications of ethyl maltol. Full article

CO₂ geological sequestration in coal seams can be carried out to achieve the dual objectives of CO₂ emission reduction and enhanced coalbed methane production, making it a highly promising carbon capture and storage technology. However, the injection of CO₂ into coal reservoirs in the form of supercritical fluid (ScCO₂) leads to complex physicochemical reactions with the coal seam, altering the properties of the coal reservoir and impacting the effectiveness of CO₂ sequestration and methane production enhancement. In this paper, theoretical calculations based on ReaxFF-MD were conducted to study the interaction mechanism between ScCO₂ and the macromolecular structures of both low-rank and high-rank coal, to address the limitations of experimental methods. The reaction of ScCO₂ with low-rank coal and high-rank coal exhibited significant differences. At the swelling stage, the low-rank coal experienced a decrease in aromatic structure and aliphatic structure, and high-rank coal showed an increase in aromatic structure and a decrease in aliphatic structure, while the swelling phenomenon was more pronounced in high-rank coal. At the dissolution stage, low-rank coal was initially decomposed into two secondary molecular fragments, and then these recombined to form a new molecular structure; the aromatic structure increased and the aliphatic structure decreased. In contrast, high-rank coal showed the occurrence of stretches–breakage–movement–reconnection, a reduction in aromatic structure, and an increase in aliphatic structure. The primary reasons for these variations lie in the distinct molecular structure compositions and the properties of ScCO₂, leading to different reaction pathways of the functional group and aromatic structure. The reaction pathways of functional groups and aromatic structures in coal can be summarized as follows: the breakage of the O–H bond in hydroxyl groups, the breakage of the C–OH bond in carboxyl groups, the transformation of aliphatic structures into smaller hydrocarbon compounds or the formation of long-chain alkenes, and various pathways involving the breakage, rearrangement, and recombination of aromatic structures. In low-rank coal, there is a higher abundance of oxygen-containing functional groups and aliphatic structures. The breakage of O–H and C–OH chemical bonds results in the formation of free radical ions, while some aliphatic structures detach to produce hydrocarbons. Additionally, some of these aliphatic structures combine with carbonyl groups and free radical ions to generate new aromatic structures. Conversely, in high-rank coal, a lower content of oxygen-containing functional groups and aliphatic structures, along with stronger intramolecular forces, results in fewer chemical bond breakages and makes it less conducive to the formation of new aromatic structures. These results elucidate the specific deformations of different chemical groups, offering a molecular-level understanding of the interaction between CO₂ and coal. Full article

Crystalline poly-para-xylylene (parylene) has the potential for use as a protective membrane to delay the nucleation of explosives by separating the explosives and their decomposition products to decrease the explosive sensitivity. Here, molecular dynamics (MD) and density functional theory (DFT) techniques were used to calculate the dissociative adsorption configurations of 1,1-diamino-2,2-dinitroethylene (FOX-7) on (001)- and (101)-oriented crystalline parylene membranes. Based on the results of the calculations, this work demonstrates that the -NO₂–π electrostatic interactions are the dominant passivation mechanism of FOX-7 on these oriented surfaces. FOX-7 can dissociatively adsorb on oriented parylene membranes due to the interactions between the LUMO of the toluene (or methyl) groups on parylene and the HOMO of the -NO₂ (or -NH₂) groups on FOX-7. The formation of a new intermolecular H-bond with the ONO group leads to FOX-7 decomposition via intramolecular C-NO₂ bond fission and nitro-to-nitrite rearrangement. The most likely adsorption configurations are described in terms of the decomposition products, surface active groups of parylene, binding behaviors, and N charge transfer. Importantly, the (001)-oriented parylene AF8 membrane is promising for use as a protective membrane to passivate the high-energy -NO₂ bonds during the dissociative adsorption of FOX-7. This study offers a new perspective on the development of protective membranes for explosives. Full article

In this study, the total synthesis of osajin, scandenone and their analogues have been accomplished. The key synthetic steps include aldol/intramolecular iodoetherification/elimination sequence reactions and a Suzuki coupling reaction to assemble the tricyclic core, chemoselective propargylation and Claisen rearrangement reactions to obtain natural compounds. In addition, we also designed and synthesized twenty-five natural product analogues. All synthetic compounds were screened for anti-inflammatory activity against tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. Collectively, Compound 39e and 39d were considered as promising lead compounds for further development. Full article

In the present work, the bond breaking/forming events along the intramolecular Diels–Alder (IMDA) reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one have been revealed within bonding evolution theory (BET) at the density functional theory level, using the M05-2X functional with the cc-pVTZ basis set. Prior to achieving this task, the energy profiles and stationary points at the potential energy surface (PES) have been characterized. The analysis of the results finds that this rearrangement can proceed along three alternative reaction pathways (a–c). Paths a and b involve two steps, while path c is a one-step process. The first step in path b is kinetically favored, and leads to the formation of an intermediate step, Int-b. Further evolution from Int-b leads mainly to 3-b1. However, 2 is the thermodynamically preferred product and is obtained at high temperatures, in agreement with the experimental observations. Regarding the BET analysis along path b, the breaking/forming process is described by four structural stability domains (SSDs) during the first step, which can be summarized as follows: (1) the breaking of the C–O bond with the transfer of its population to the lone pair (V(O)), (2) the reorganization of the electron density with the creation of two V(C) basins, and (3) the formation of a new C–C single bond via the merger of the two previous V(C) basins. Finally, the conversion of Int-b (via TS2-b1) occurs via the reorganization of the electron density during the first stage (the creation of different pseudoradical centers on the carbon atoms as a result of the depopulation of the C–C double bond involved in the formation of new single bonds), while the last stage corresponds to the non-concerted formation of the two new C–C bonds via the disappearance of the population of the four pseudoradical centers formed in the previous stage. On the other hand, along path a, the first step displays three SSDs, associated with the depopulation of the V(C2,C3) and V(C6,C7) basins, the appearance of the new monosynaptic basins V(C2) and V(C7), and finally the merging of these new monosynaptic basins through the creation of the C2–C7 single bond. The second step is described by a series of five SSDs, that account for the reorganization of the electron density within Int-a via the creation of four pseudoradical centers on the C12, C13, C3 and C6 carbon atoms. The last two SSDs deal with the formation of two C-C bonds via the merging of the monosynaptic basins formed in the previous domains. Full article

Numerous observations have supported the idea that various types of noncoding RNAs, including tRNA fragments (tRFs), are involved in communications between the host and its microbial community. The possibility of using their signaling function has stimulated the study of secreted RNAs, potentially involved in the interspecies interaction of bacteria. This work aimed at identifying such RNAs and characterizing their maturation during transport. We applied an approach that allowed us to detect oligoribonucleotides secreted by Prevotella copri (Segatella copri) or Rhodospirillum rubrum inside Escherichia coli cells. Four tRFs imported by E. coli cells co-cultured with these bacteria were obtained via chemical synthesis, and all of them affected the growth of E. coli. Their successive modifications in the culture medium and recipient cells were studied by high-throughput cDNA sequencing. Instead of the expected accidental exonucleolysis, in the milieu, we observed nonrandom cleavage by endonucleases continued in recipient cells. We also found intramolecular rearrangements of synthetic oligonucleotides, which may be considered traces of intermediate RNA circular isomerization. Using custom software, we estimated the frequency of such events in transcriptomes and secretomes of E. coli and observed surprising reproducibility in positions of such rare events, assuming the functionality of ring isoforms or their permuted derivatives in bacteria. Full article

Triazolo[4,3-a]pyrimidine is one of the promising structural fragments for the development of drugs, including anticancer drugs. This work is devoted to the synthesis of a number of new 2-arylhydrazone derivatives of thiazolo[3,2-a]pyrimidine, which are synthetic precursors for triazolo[4,3-a]pyrimidines. The crystal structure of 6-acetyl-7-methyl-5-phenyl-2-(2-phenylhydrazineylidene)-5H-thiazolo[3,2-a]pyrimidin-3(2H)-one was established by SCXRD. In the reduction reaction of the compound, the following system was used: vanadium(V) oxide, and sodium borohydride in ethanol at room temperature, which led to the formation of only one pair of diastereomers (1R*)-1-((5S*,6R*,7R*)-(1-(hydroxymethyl)-7-methyl-1,5-diphenyl-1,5,6,7-tetrahydro[1,2,4]triazolo[4,3-a]pyrimidin-6-yl)ethan-1-ol. Full article

Imine or Schiff base formation is considered as a key event in the catalytic mechanisms of many enzymes and in certain biological transformations, including glycation. In this process, less stable amino-acid-derived Schiff bases rearrange into more stable ketoamines or Amadori products. Schiff bases are also stipulated to be stabilized through complexation with metal ions, or through intramolecular cyclization to form more stable and reversible cyclic isomers, such as oxazolidin-5-ones. These intermediates can be easily detected relative to Schiff bases due to their higher stability. In this study, high-resolution mass spectrometry and isotope labeling techniques were used to identify labile imines as their oxazolidin-5-one derivatives in heated reaction systems of glucose/alanine/FeCl₂, including their ¹³C-labeled counterparts. The reaction mixtures were heated for 2h at 110 °C and were analyzed by high resolution qTOF/MS for the presence of masses corresponding to Schiff bases of α-alanine with short chain aldehydes that can be generated from glucose degradation and also for the incorporation of ¹³C-labeled atoms from ¹³C-3 alanine and ¹³C-U glucose. Analysis of the data has indicated that Schiff bases can indeed be detected in the form of oxazolidin-3-ones, when methanol is used as the solvent. Furthermore, it was discovered that metal-ion-stabilized Schiff bases, in addition to forming oxazolidin-3-ones, can also undergo aldol addition with short chain sugars and initiate oligomerization reactions, leading to the formation of dimeric or trimeric oxazolidin-3-one oligomers, as demonstrated by their characteristic MS/MS fragmentations. Full article

In multidomain proteins, individual domains connected by flexible linkers are dynamically rearranged upon ligand binding and sensing changes in environmental factors, such as pH and temperature. Here, we characterize dynamic domain rearrangements of Lys48-linked ubiquitin (Ub) chains as models of multidomain proteins in which molecular surfaces mediating intermolecular interactions are involved in intramolecular domain–domain interactions. Using NMR and other biophysical techniques, we characterized dynamic conformational interconversions of diUb between open and closed states regarding solvent exposure of the hydrophobic surfaces of each Ub unit, which serve as binding sites for various Ub-interacting proteins. We found that the hydrophobic Ub-Ub interaction in diUb was reinforced by cysteine substitution of Lys48 of the distal Ub unit because of interaction between the cysteinyl thiol group and the C-terminal segment of the proximal Ub unit. In contrast, the replacement of the isopeptide linker with an artificial ethylenamine linker minimally affected the conformational distributions. Furthermore, we demonstrated that the mutational modification allosterically impacted the exposure of the most distal Ub unit in triUb. Thus, the conformational interconversion of Ub chains offers a unique design framework in Ub-based protein engineering not only for developing biosensing probes but also for allowing new opportunities for the allosteric regulation of multidomain proteins. Full article