Conformational Analysis of (+)-Germacrene D-4-ol Using the Crystalline Sponge Method to Elucidate the Origin of its Instability.

Unsaturated cyclic terpenes often exhibit instability due to the proximation of C=C bonds in the cyclic skeleton, leading to nonenzymatic degradation. In this study, the crystalline sponge (CS) method was employed for the X-ray conformational analysis of a minute amount of oily and cyclic terpene compound, (+)-germacrene D-4-ol, which was produced by a terpene synthase OILTS under in vitro conditions.  The CS method revealed a reactive conformation of the cyclic terpene with proximal double bonds. Under weakly acidic in vivo conditions, OILTS gave four pseudo-natural products or artifacts. The CS method also elucidated the structures of these degraded compounds, proposing a degradation mechanism triggered by the transannular reactions.

Functional Plasticity of a Viral Terpene Synthase, OILTS, that Shows Non-Specific Metal Cofactor Binding and Metal-dependent Biosynthesis.

OILTS is a viral class I terpene synthase found from the giant virus Orpheovirus IHUMI-LCC2. It exhibits a unique structure and demonstrates high plasticity to metal cofactors, allowing it to biosynthesize different cyclic terpene frameworks. Notably, while OILTS produces only (+)-germacrene D-4-ol with the most common cofactor, Mg2+, it also biosynthesizes a different cyclic terpene, (+)-cubebol, with Mn2+, Co2+, or Ni2+, presenting a rare instance of cofactor-dependent enzyme catalysis. This is the first report of (+)-cubebol biosynthesis, to our knowledge. In addition, OILTS can uptake Zn2+ as a cofactor, which is uncommon among ordinary terpene synthases. These findings suggest that OILTS's functional plasticity may benefit the virus in diverse host environments, highlighting potential evolutionary implications.

Robotic vs. laparoscopic distal gastrectomy for gastric cancer: A propensity score-matched retrospective comparative study at a single institution.

BACKGROUND: Although robotic surgery is becoming more widespread worldwide, it is still in its infancy. This study aimed to confirm the safety and feasibility of the induction of robotic-assisted gastric surgery at a local hospital. METHODS: For five years, between 2016 and 2020, 42 laparoscopic and 71 robotic distal gastrectomies were performed at the same institution. Patients diagnosed with gastric cancer were retrieved from the database. Propensity score matching was performed based on covariates such as Age, Sex, BMI, the American Society of Anesthesiologists Physical Status, Tumor Location, pT, and pN. Clinicopathological characteristics, surgical performance, postoperative outcomes, and pathological data were retrospectively collected and compared by the Chi-square test, the Fisher's exact test, the Student's t-test, and the Mann-Whitney U test. RESULTS: Billroth II reconstruction was often selected for the robotic group more than the laparoscopic group (59.4% and 15.6%, respectively). In addition, the number of lymph nodes harvested after D2 dissection tended to be more significant in the robotic group than in the laparoscopic group (52.1 ± 7.6 and 29.1 ± 3.7, respectively; p = 0.00934). The mean operative time was 271.4 ± 10.5 min for the robotic group and 220.8 ± 12.3 min for the laparoscopic group (p = 0.00005). There were no differences in short-term clinical outcomes between the two groups. CONCLUSIONS: Although a single-center, small comparative study, the results showed that the robotic surgery group was not inferior to the laparoscopic group in feasibility and safety. Moreover, robotic surgery enables harvesting a higher number of lymph nodes, which may be more advantageous than laparoscopic surgery. This study also showed that as the surgeon gains experience with robotic surgery, its operative time becomes significantly shorter.

Rapid Analysis of Trace Amounts of Amino Acid Derivatives by a Formyl Group-Installed Crystalline Sponge.

The Industries need techniques for the rapid structure analysis of amino acid derivatives. The amino acid derivatives are sometimes produced as impurities in the industrial production processes, and cause toxicity problems. Herein, we report the crystalline sponge (CS) method analysis of variety of amino acids using a formyl group installed CS crystal. Most amino acids possess a primary amino group, which can form Schiff-base with the formyl group under mild conditions. Thus, the formyl group installed CS crystal can efficiently capture the amino acids via Schiff-base formation. We successfully analyzed derivatives of 18 proteogenic amino acids, 6 non-proteogenic amino acids, and 4 dipeptides using the formyl group installed CS. We thus believe that the protocols shown in this study would serve the need of the industries.

Selective Synthesis and Functionalization of an Acyclic Methylene-Bridged-Arene Trimer in a Cage.

Arene-formaldehyde condensation is a versatile reaction for producing various oligomeric/polymeric materials. However, the precise control of oligomerization degree is still challenging because the starting materials and intermediates have similar reactivities. Here, we demonstrate the selective synthesis of a methylene-bridged arene trimer using the confined cavity of a coordination cage. The limited space of the cavity prevents unregulated polymerization. The confinement effect for the kinetic protection is also demonstrated by the subsequent site-selective iodination of the trimer product within the cage.

Chemical Site-Differentiation of Calix[4]arenes through Enforced Conformations by Confinement in a Cage.

Desymmetrization of a symmetric skeleton enables late-stage functionalization of molecules. However, reagent-controlled desymmetrization by site-selective reactions of symmetric molecules remains a difficult synthetic strategy. Here, we found that complete confinement of a symmetric molecule within a coordination cage can desymmetrize the guest conformation, making it possible to site-selectively activate or protect the otherwise equivalent reaction sites of calix[4]arene derivatives. Multistep, one-cage reactions also demonstrated the transformation of an AAAA-type calix[4]arene into a lower symmetry ABAC-type one.

Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome.

Giant viruses are nonstandard viruses with large particles and genomes. While previous studies have shown that their genomes contain various sequences of interest, their genes related specifically to natural product biosynthesis remain unexplored. Here we analyze the function and structure of a terpene synthase encoded by the gene of a giant virus. The enzyme is phylogenetically separated from the terpene synthases of cellular organisms; however, heterologous gene expression revealed that it still functions as a terpene synthase and produces a cyclic terpene from a farnesyl diphosphate precursor. Crystallographic analysis revealed its protein structure, which is relatively compact but retains essential motifs of the terpene synthases. We thus suggest that like cellular organisms, giant viruses produce and utilize natural products for their ecological strategies.

Tetradehydro-Diels-Alder Reactions of Flexible Arylalkynes via Folding Inside a Molecular Cage.

The tetradehydro-Diels-Alder (TDDA) reaction is a useful transformation for the rapid assembly of polycyclic scaffolds from simple linear precursors in a single synthetic step. However, the reaction requires careful substrate design and harsh reaction conditions to overcome the inherent entropic cost for this transformation. Herein we report an efficient site-selective TDDA transformation within a self-assembled Pd6L4 cage. Despite the large size, the flexibility of the employed substrates allows for efficient encapsulation within the host cavity. The rate of thermal cyclization of the encapsulated guest was found to be greatly enhanced, and high product selectivity for an unsymmetrical substrate was observed. The efficiency of this system relies on the precise conformational control of the substrate within the confined space of the host cage.

X-ray and Electron Diffraction Observations of Steric Zipper Interactions in Metal-Induced Peptide Cross-ß Nanostructures.

The steric zipper is a common hydrophobic packing structure of peptide side chains that forms between two adjacent ß-sheet layers in amyloid and related fibrils. Although previous studies have revealed that peptide fragments derived from native protein sequences exhibit steric zipper structures, their de novo designs have rarely been studied. Herein, steric zipper structures were artificially constructed in the crystalline state by metal-induced folding and assembly of tetrapeptide fragments Boc-3pa-X1-3pa-X2-OMe (3pa: ß-(3-pyridyl)-l-alanine; X1 and X2: hydrophobic amino acids). Crystallographic studies revealed two types of packing structures, interdigitation and hydrophobic contact, that result in a class 1 steric zipper geometry when the X1 and X2 residues contain alkyl side chains. Furthermore, a class 3 steric zipper geometry was also observed for the first time among any reported steric zippers when using tetrapeptide fragments with (X1, X2) = (Thr, Thr) and (Phe, Leu). The system could also be extended to a knob-hole-type zipper using a pentapeptide sequence.

Synthetic Modulation of an Unstable Dehydrosecodine-type Intermediate and Its Encapsulation into a Confined Cavity Enable Its X-ray Crystallographic Observation.

Numerous indole alkaloids such as the iboga- and aspidosperma-type are believed to be biosynthesized via a common hypothetical intermediate, dehydrosecodine. The highly reactive nature of dehydrosecodine-type compounds has hampered their isolation and structural elucidation. In this study, we achieved the first X-ray structural determination of a dehydrosecodine-type compound by integrating synthetic optimization of the reactivity and stabilizing the fragile molecule by encapsulation into a supramolecular host. Formation of a 1 : 1 complex of the dehydrosecodine-type labile guest bearing both vinyl indole and dihydropyridine units with the host was observed. This integrated approach not only provides insights into the biosynthetic conversions but also allows stabilization and storage of the reactive and otherwise short-lived intermediate within the confined hydrophobic cavity.

[M8L4]8+-Type Squares Self-Assembled by Dipalladium Corners and Bridging Aromatic Dipyrazole Ligands for Iodine Capture.

Square-like metallamacrocyclic palladium(II) complexes [M8L4]8+ (1-7) were synthesized by reacting aromatic dipyrazole ligands (H2L1-H2L3 with pyromellitic arylimide-, 1,4,5,8-naphthalenetetracarboxylic arylimide-, and anthracene-based aromatic groups, respectively) with dipalladium corners ([(bpy)2Pd2(NO3)2](NO3)2, [(dmbpy)2Pd2(NO3)2](NO3)2, or [(phen)2Pd2(NO3)2](NO3)2, where bpy = 2,2'-bipyridine, dmbpy = 4,4'-dimethyl-2,2'-bipyridine, and phen = 1,10-phenanthroline) in aqueous solutions via metal-directed self-assembly. Metallamacrocycles 1-7 were fully characterized by 1H and 13C nuclear magnetic resonance spectroscopy and electrospray ionization mass spectrometry, and the square structure of 7·8NO3- was further confirmed via single crystal X-ray diffraction. These square-like metallamacrocycles exhibit effective performance for iodine adsorption.

Interconversion of Highly Entangled Polyhedra into Concave Polyhedra by Nitrate-Induced Ternary Coordination.

Entangled (M3 L2 )n polyhedral complexes represent a unique class of supramolecular architectures that are stabilized by relatively weak metal-acetylene interactions in cooperation with conventional metal-pyridyl coordination. Counter-anion exchange of these complexes with a nitrate (NO3 - ) ion triggered formal metal insertion between the metal centers, and a heteroleptic ternary coordination mode with acetylenic, pyridyl, and nitrate donors was generated on the metal centers. As a result, the main frameworks of the polyhedral complexes M18 L12 and M12 L8 were formally extended into a new series of concave polyhedra having the compositions M21 L12 and M13 L8 , respectively. This transformation also resulted in the local disconnection of the highly entangled trifurcate topology of the framework, providing clues toward the skeletal editing of extended and complex three-dimensional (3D) architectures.

A case of recurrent epiphrenic esophageal diverticulum treated with lower esophagogastric resection and interstitial jejunal reconstruction.

The patient is a 60-year-old female with a history of multiple times of recurrences of an esophageal diverticulum. She was referred for a diagnosis of persistent dysphagia and vomiting. Balloon dilation did not improve the symptoms; thus, she was referred for surgery. Esophageal fluoroscopy revealed a 5 cm diverticulum. There was no significant change in the size before and after dilation. Gastrointestinal endoscopy revealed a diverticulum in the lower esophagus, with a residue accumulation. The esophagus directly below the diverticulum was narrowed. The patient was diagnosed with recurrent lower esophageal diverticulum and underwent surgery. The operative findings showed poor coloration of the gastric fundus surrounding operated before by Nissen's method, so the patient underwent lower esophagogastric resection and interstitial jejunal reconstruction. The postoperative course was uneventful and discharged on the 19th day. She is 6 years postoperatively and gained six kg compared to her preoperative weight. She has remained in excellent health.

Hysteresis behavior in the unfolding/refolding processes of a protein trapped in metallo-cages.

Confinement of molecules in a synthetic host can physically isolate even their unstable temporary structures, which has potential for application to protein transient structure analysis. Here we report the NMR snapshot observation of protein unfolding and refolding processes by confining a target protein in a self-assembled coordination cage. With increasing acetonitrile content in CD3CN/H2O media (50 to 90 vol%), the folding structure of a protein sharply denatured at 83 vol%, clearly revealing the regions of initial unfolding. Unfavorable aggregation of the protein leading to irreversible precipitation is completely prevented because of the spatial isolation of the single protein molecule in the cage. When the acetonitrile content reversed (84 to 70 vol%), the once-denatured protein started to regain its original folded structure at 80 vol%, showing that the protein folding/unfolding process can be referred to as a phase transition with hysteresis behavior.

[A Case of Primary Liver Cancer and Gastric Glomus Tumor Diagnosed Preoperatively and Treated with Liver Segmentectomy and Local Gastrectomy].

A man in his 70s was concurrently suspected of having a submucosal tumor(SMT)of the stomach and a liver tumor during a medical examination. Abdominal contrast-enhanced CT scan revealed S8 hepatocellular carcinoma(HCC)and an SMT of the stomach, which was strongly enhanced from the early to the later phase. Upper gastrointestinal endoscopy revealed a 20 mm SMT in the antrum of the stomach. Endoscopic ultrasonography showed a hyperechoic tumor in the fourth layer of the gastric wall. T2-weighted MRI showed a 25 mm SMT in the antrum of the stomach with a faint high signal intensity compared with that of the gastric wall. The patient was diagnosed with HCC and gastric glomus tumor, and a liver segmentectomy and a local gastrectomy were performed. Immunohistochemistry of the SMT revealed the expression of α-SMA but no expression of desmin, c-kit, CD34, or S-100. Therefore, a diagnosis of a Glomus tumor of the stomach was made. Gastric Glomus tumors are very rare; therefore, we have reviewed some citations and would like to discuss our case.

A self-assembled coordination cage enhances the reactivity of confined amides via mechanical bond-twisting.

Self-assembled coordination cages composed of metal cations and ligands can enhance the hydrolysis of non-covalently trapped amides in mild conditions as demonstrated in recent experiments. Here, we reveal the mechanism that accelerates base-catalyzed amide hydrolysis inside the octahedral coordination cage, by means of a quantum mechanics/molecular mechanics/polarizable continuum model. The calculated activation barrier of the nucleophilic OH- addition to a planar diaryl amide drastically decreases in the cage because of mechanical bond-twisting due to host-guest π-stacking. By contrast, the OH- addition to an N-acylindole, which possesses a twisted amide bond in bulk water, is not enhanced in the cage. Even though the cage hinders OH- collisions with the confined amide, the cage can twist the dihedral angle of the planar amide so as to mimic the transition state of OH- addition.

Selective Confinement of Rare-Earth-Metal Hydrates by a Capped Metallo-Cage under Aqueous Conditions.

The properties of rare-earth-metal ions in aqueous media often depend on their various hydration modes, which allow them to exist as monomeric or oligomeric species with different coordination numbers. Capturing rare-earth-metal ions in a confined cavity can fix their hydration modes and thus enable their intrinsic properties to be distinguished. However, the isolation of ionic species from bulk aqueous media is not an easy task due to competitive interaction with bulk water. Here, we report the encapsulation of hydrated rare-earth-metal ions in a hydrophobic cavity of a synthetic cage. Cap-like counter anions located at the cage's portals play an important role in capturing the rare-earth metals at a fixed position via electrostatic interactions. Preferential encapsulation of early lanthanoid (III) ions was observed even though all the rare-earth metals have the same hydration number and geometry, as visualized by the competitive inclusion of a dye molecule. Accordingly, the early lanthanoid ion was selectively extracted from a mixture of two rare-earth-metal ions.

A case report of anaplastic carcinoma with osteoclast-like giant cells arising in the pancreatic body.

The patient is a 58-year-old woman. She was referred to our hospital following a computed tomography scan that revealed a 2-cm tumor-like lesion in the pancreatic body. Endoscopic ultrasound fine-needle aspiration examination revealed a suspected undifferentiated carcinoma with pleomorphic type. The patient was diagnosed with anaplastic carcinoma of the pancreas (ACP) and underwent distal pancreatectomy with lymph nodes dissection. The resected body and tail of the pancreas had a nodular tumor measuring 30 mm in diameter. Histologically, the main lesion of the tumor showed well-differentiated adenocarcinoma, and diffuse proliferation of atypical short spindle cells and round cells accompanied by multinucleated giant cells aggregation was observed around the tubular structure; hence, it was diagnosed with ACP. The postoperative course was uneventful, and the patient was discharged 14 days after the operation. It has already been about 5 years since the surgery, and although the tumor has recurred, the patient is still alive and undergoing chemotherapy.

Amplification of weak chiral inductions for excellent control over the helical orientation of discrete topologically chiral (M3L2) n polyhedra.

Superb control over the helical chirality of discrete (M3L2) n polyhedra (n = 2,4,8, M = CuI or AgI) created from the self-assembly of propeller-shaped ligands (L) equipped with chiral side chains is demonstrated here. Almost perfect chiral induction (>99 : 1) of the helical orientation of the framework was achieved for the largest (M3L2)8 cube with 48 small chiral side chains (diameter: ∼5 nm), while no or moderate chiral induction was observed for smaller polyhedra (n = 2, 4). Thus, amplification of the weak chiral inductions of each ligand unit is an efficient way to control the chirality of large discrete nanostructures with high structural complexity.

Electrophilic Spirocyclization of a 2-Biphenylacetylene via Conformational Fixing within a Hollow-Cage Host.

A 2-biphenylacetylene was fixed into a specific conformation within the confined cavity of a hollow cage, where it underwent a regioselective spirocyclization in the presence of an electrophile. A 5-endo-dig cyclization proceeded selectively in the cage, which stands in sharp contrast to the 6-endo-dig cyclization that normally occurs in common organic media. The folded conformation adopted by the substrate within the cage was examined by 1 H NMR spectroscopy and X-ray crystallographic analysis.