Theoretical Study of Natural Product Biosynthesis Using Computational Chemistry.

The biosynthetic pathways of natural products are complicated, and it is difficult to fully elucidate their details using experimental chemistry alone. In recent years, efforts have been made to elucidate the biosynthetic reaction mechanisms by combining computational and experimental methods. In this review, we will discuss the biosynthetic studies using computational chemistry for various terpene compounds such as cyclooctatin, sesterfisherol, quiannulatene, trichobrasilenol, asperterpenol, preasperterpenoid, spiroviolene, and mangicol.

Long-lasting adverse effects of short-term stress during the suckling-mastication transition period on masticatory function and intraoral sensation in rats.

Early-life stress affects brain development, eventually resulting in adverse behavioral and physical health consequences in adulthood. The present study assessed the hypothesis that short-term early-life stress during infancy before weaning, a period for the maturation of mastication and sleep, poses long-lasting adverse effects on masticatory function and intraoral sensations later in life.Rat pups were exposed to either maternal separation (MS) or intermittent hypoxia (IH-Infancy) for 6 h/day in the light/sleep phase from postnatal day (P)17 to P20 to generate "neglect" and "pediatric obstructive sleep apnea" models, respectively. The remaining rats were exposed to IH during P45-P48 (IH-Adult). Masticatory ability was evaluated based on the rats' ability to chew pellets and bite pasta throughout the growth period (P21-P70). Intraoral chemical and mechanical sensitivities were assessed using two-bottle preference drinking tests, and hind paw pain thresholds were measured in adulthood (after P60).No differences were found in body weight, grip force, and hind paw sensitivity in MS, IH-Infancy, and IH-Adult rats compared with naïve rats. Masticatory ability was lower in MS and IH-Infancy rats from P28 to P70 than in naïve rats. MS and IH-Infancy rats exhibited intraoral hypersensitivity to capsaicin and mechanical stimulations in adulthood. The IH-Adult rats did not display inferior masticatory ability or intraoral hypersensitivity.In conclusion, short-term early-life stress during the suckling-mastication transition period potentially causes a persistent decrease in masticatory ability and intraoral hypersensitivity in adulthood. The period is a "critical window" for the maturation of oral motor and sensory functions.

Physical Stimulation Methods Developed for In Vitro Neuronal Differentiation Studies of PC12 Cells: A Comprehensive Review.

PC12 cells, which are derived from rat adrenal pheochromocytoma cells, are widely used for the study of neuronal differentiation. NGF induces neuronal differentiation in PC12 cells by activating intracellular pathways via the TrkA receptor, which results in elongated neurites and neuron-like characteristics. Moreover, the differentiation requires both the ERK1/2 and p38 MAPK pathways. In addition to NGF, BMPs can also induce neuronal differentiation in PC12 cells. BMPs are part of the TGF-ß cytokine superfamily and activate signaling pathways such as p38 MAPK and Smad. However, the brief lifespan of NGF and BMPs may limit their effectiveness in living organisms. Although PC12 cells are used to study the effects of various physical stimuli on neuronal differentiation, the development of new methods and an understanding of the molecular mechanisms are ongoing. In this comprehensive review, we discuss the induction of neuronal differentiation in PC12 cells without relying on NGF, which is already established for electrical, electromagnetic, and thermal stimulation but poses a challenge for mechanical, ultrasound, and light stimulation. Furthermore, the mechanisms underlying neuronal differentiation induced by physical stimuli remain largely unknown. Elucidating these mechanisms holds promise for developing new methods for neural regeneration and advancing neuroregenerative medical technologies using neural stem cells.

The mechanism for regulating the isometric contraction of masseter muscles is involved in determining the vertical dimension of occlusion.

We previously demonstrated that accurate regulation of isometric contraction (IC) of jaw-closing muscles to counteract the ramp load applied to the jaw in the jaw-opening direction is achieved through the calibration between the two sensations arising from muscle spindles (MSs) and periodontal mechanoreceptors (PMRs). However, it remains unclear whether this calibration mechanism accurately works at any jaw positions, i.e., any vertical dimensions of occlusion (VDO). In the present study, we examined the effects of altering VDO on the IC of the masseter muscles in complete dentulous and edentulous subjects. At a VDO higher than the original VDO (O-VDO), the root mean square (RMS) of masseter EMG activity increased more steeply with a load increase, resulting in an over-counteraction. The regression coefficient of the load-RMS relationship significantly increased as the VDO was increased, suggesting that the overestimation became more pronounced with the VDO increases. Consistently also in the edentulous subjects, at a higher VDO than the O-VDO, a steeper increase in the RMS emerged with a delay in response to the same ramp load whereas a similar steeper increase was seen surprisingly even at a lower VDO. Thus, the edentulous subjects displayed a delayed overestimation of the ramp load presumably due to less and slowly sensitive mucous membrane mechanoreceptor (MMR) in alveolar ridge compared with the PMR. Taken together, the accurate calibration between the two sensations arising from MSs and PMRs/MMRs can be done only at the O-VDO, suggesting that the O-VDO is the best calibration point for performing accurate IC.NEW & NOTEWORTHY Since 1934, the vertical dimension of occlusion (VDO) in edentulous individuals has been anatomically determined mostly by referring to the resting jaw position. However, such a static method is not always accurate. Considering the dynamic nature of clenching/mastication, it is desirable to determine VDO dynamically. We demonstrate that VDO can be accurately determined by measuring masseter EMG during the voluntary isometric contraction of jaw-closing muscles exerted against the ramp load in the jaw-opening direction.

Concertedness and Activation Energy Control by Distal Methyl Group during Ring Contraction/Expansion in Scalarane-Type Sesterterpenoid Biosynthesis.

Salmahyritisol A, similan A, and hippospongide A, which are scalarane-type sesterterpenoids, feature 6/6/5/7/5 pentacyclic skeletons. Although their biosyntheses have been previously proposed to involve a unique skeletal rearrangement reaction, the detailed reaction mechanism remains unclear as none of the corresponding biosynthetic enzymes for this reaction have been reported. Herein, this skeletal rearrangement reaction was investigated using computational techniques, which revealed the following four key features: (i) the distal 24-Me substituent controls both the concertedness and activation energy of this transformation, (ii) enzymes are not responsible for the observed regioselectivity of C12-C20 bond formation, (iii) stereoselectivity is enzyme-regulated, and (iv) protonation is a key step in this skeletal rearrangement process. These new findings provide insight into the C-ring-contraction and D-ring-expansion mechanisms in scalarane-type sesterterpenoid biosyntheses.

Mechanistic Investigation of the Degradation Pathways of α-ß/α-α Bridged Epipolythiodioxopiperazines (ETPs).

Epipolythiodioxopiperazines (ETPs) make up a class of biologically active fungal metabolites with a transannular disulfide bridge. In this work, we used DFT calculations to examine in detail the degradation (desulfurization) pathways of α-ß/α-α bridged ETPs. The chemical stability of ETPs is influenced by the type of sulfur bridge, the structural features, and the storage conditions. Our results suggest appropriate protection of the phenolic OH of ETPs would improve various pharmaceutically relevant properties, including bioavailability.

Theoretical study of the rearrangement reaction in bisorbicillinoid biosynthesis: insights into the molecular mechanisms involved.

Bisorbibutenolide and bisorbicillinolide are polyketide compounds with complex skeletons that are formed by the dimerization of sorbicillin. These compounds have long been of interest, with several reports of their biosynthesis, biological activity, and total synthesis. In this study, we theoretically investigated the detailed biosynthetic mechanism of the rearrangement reaction to form bisorbicillinolide. We showed that the presence of water molecules facilitates the intramolecular aldol reaction, determined the rate-limiting steps, and revealed that a cyclopropane intermediate is formed during the rearrangement process. Although computational chemistry has been widely applied to the carbocation chemistry present in terpene biosynthesis, it has seldom been used to investigate the carbonyl chemistry responsible for polyketide biosynthesis. This study shows that computational chemistry is a useful tool for studying anionic skeletal rearrangement reactions.

Long-term changes in oral feeding behaviors of growing rats.

Oral feeding is critical for survival in both humans and animals. However, few studies have reported quantitative behavioral measures associated with the development of oral feeding behaviors. Therefore, the present study investigated developmental changes in the oral feeding behaviors of rats by quantitatively assessing pasta eating and licking behaviors. In the pasta eating test, the time to finish pasta sticks of three different thicknesses (Φ = 0.9, 1.4, and 1.9 mm, 4 cm long) was recorded between postnatal day 29 (P29) and P49, because all rats were able to finish eating these pasta sticks on P29. A developmental decrease in the time to finish pasta sticks of all thicknesses was observed during the initial period of recordings and plateaued before P35. The extent of this decrease was dependent on the thickness of pasta sticks. In the licking test, the number of licks per 10 s and the total intake volume during the test were recorded between P19 and P49, because all rats were able to access and lick the solution on P19. The time courses of developmental increases in the number of licks and the total intake volume were similar to the results obtained in the pasta eating test. Collectively, these results suggest that developmental changes in pasta eating and licking behaviors markedly differed between the weanling and periadolescent periods. The present study also demonstrated the applicability of the pasta eating and licking tests to the quantification of developmental changes in the oral feeding behaviors of rats.

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B.

Terpene cyclization reactions involve a number of carbocation intermediates. In some cases, these carbocations are stabilized by through-space interactions with π orbitals. Several terpene/terpenoids, such as sativene, santalene, bergamotene, ophiobolin and mangicol, possess prenyl side chains that do not participate in the cyclization reaction. The role of these prenyl side chains has been partially investigated, but remains elusive in the cyclization cascade. In this study, we focus on variexenol B that is synthesized from iso-GGPP, as recently reported by Dickschat and co-workers, and investigate the possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation-π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner.

Elucidation of Late-Stage Biosynthesis of Phomoidride: Proposal of Cyclization Mechanism Affording Characteristic Nine-Membered Ring of Fungal Dimeric Anhydride.

Antihypercholesterolemic agent phomoidride (PMD) B has a highly elaborated bicyclo[4.3.1]deca-1,6-diene core scaffold derived from dimeric anhydride with a nine-membered ring. This report elucidated the late stage transformation from an anhydride monomer to PMD B through the heterologous expression of three enzyme genes, TstC, TstK, and TstE. Additional in vitro studies of TstK and TstE provided evidence on the formation of PMD via dimerization, three-step oxidation, and unusual methylation-triggered bicyclic ketal formation. Elucidation of the function of cyclase TstC prompts us to examine the cyclization mechanism of TstC by using a computational approach. Computational analytical data on PMD and structurally related glaucanic acid indicated that the initial decarboxylation of monomer results in enolate and subsequent double Michael reactions of another monomer, followed by an optional aldol reaction proceeding in an endo-selective manner to give cycloadducts, supporting the fact that the starting orientation of two monomers is directly transferred to the product configurations.

DFT Study on the Biosynthesis of Asperterpenol and Preasperterpenoid Sesterterpenoids: Exclusion of Secondary Carbocation Intermediates and Origin of Structural Diversification.

The biosynthetic pathway to asperterpenol, a sesterterpenoid featuring a 6/6/8/5 tetracyclic ring system, was proposed to involve three secondary (2°) carbocation intermediates (B, D, and I), but it remains controversial whether or not these are viable. Further, the proposed 11/6/5 tricyclic intermediate C has the same "ChemDraw" structure as an intermediate in the biosynthesis of preasperterpenoid, which has a very different 5/7/(3)6/5 pentacyclic skeleton. Here, we present a detailed scrutiny of the asperterpenol/preasperterpenoid biosynthetic pathways based on comprehensive DFT calculations.

Molecular and Computational Bases for Spirofuranone Formation in Setosusin Biosynthesis.

The 3(2H)-furanone unit is observed in many biologically active natural products, as represented by the antifungal medication griseofulvin. Setosusin (1) is a fungal meroditerpenoid featuring a unique spiro-fused 3(2H)-furanone moiety; however, the biosynthetic basis for spirofuranone formation has not been investigated since its isolation. Therefore, in this study we identified the biosynthetic gene cluster of 1 in the fungus Aspergillus duricaulis CBS 481.65 and elucidated its biosynthetic pathway by heterologous reconstitution of related enzyme activities in Aspergillus oryzae. To understand the reaction mechanism to afford spirofuranone, we subsequently performed a series of in vivo and in vitro isotope-incorporation experiments and theoretical calculations. The results indicated that SetF, the cytochrome P450 enzyme that is critical for spirofuranone synthesis, not only performs the epoxidation of the polyketide portion of the substrate but also facilitates the protonation-initiated structural rearrangement to yield 1. Finally, a mutagenesis experiment using SetF identified Lys303 as one of the potential catalytic residues that are important for spirofuranone synthesis.

Changes in cortical, cardiac, and respiratory activities in relation to spontaneous rhythmic jaw movements in ketamine-anesthetized guinea pigs.

It has been reported that rhythmic jaw movements (RJMs) spontaneously occur in ketamine-anesthetized animals. The present study investigated the physiological processes that occur during the cortical, cardiac, and respiratory events which contribute to the genesis of RJMs in animals after supplemental ketamine injections. Fourteen guinea pigs were prepared to allow electroencephalographic, electrocardiographic, and electromyographic activities to be recorded from the digastric muscle, measurement of jaw movements, and nasal expiratory airflow under ketamine-xylazine anesthesia. Rhythmic jaw movements spontaneously occurred with rhythmic digastric muscle contractions, 23-29 minutes after injection of supplemental ketamine (12.5 and 25.0 mg kg-1 , intravenously). The cycle length of RJMs did not differ significantly between the two doses of ketamine (mean±SD: 12.5 mg kg-1 , 326.5 ± 60.0 ms; 25 mg kg-1 , 278.5 ± 45.1 ms). Following injection of ketamine, digastric muscle activity, heart and respiratory rates, and cortical beta power significantly decreased, while cortical delta and theta power significantly increased. These changes were significantly larger in animals given 25.0 mg kg-1 of ketamine than in those given 12.5 mg kg-1 . With the onset of RJMs, the levels of these variables returned to pre-injection levels, regardless of the dose of ketamine administered. These results suggest that, following supplemental ketamine injections, spontaneous RJMs occur during a specific period when the pharmacological effects of ketamine wear off, and that these RJMs are characterized by stereotypical changes in cardiac, respiratory, and cortical activities.

Knowledge, Experience, and Perceptions of Generic Drugs among Middle-Aged Adults and their Willingness-to-Pay: A Nationwide Online Survey in Japan.

Promoting generic drugs can reduce the financial burden on patients and improve healthcare finances. The insurers have been conducting promotional efforts, such as direct-mail campaigns, but little is known about the public's perception of generic drugs and effective message strategies for promotion. In 2018, we conducted a web-based survey of middle-aged Japanese men and women that investigated: (i) their perceptions of generic drugs, (ii) the association between perceptions and willingness-to-pay for brand-name drugs relative to generic drugs, and (iii) potentially effective forms of information provision to alter individuals' perceptions. Of the 1,005 respondents, over half perceived generic drugs as having the same level of efficacy and safety as brand-name drugs. While willingness-to-pay was dispersed among respondents, two factors were associated with small willingness-to-pay: (a) perceiving generic drugs as having the same level of efficacy and safety as brand-name drugs and (b) perceiving that promoting the use of generic drugs is important for controlling medical expenditures. Moreover, presenting potential savings over five years by choosing generic drugs was a potentially effective tool for altering perceptions, relative to showing monthly savings. Our findings suggest that certain parts of the population still have high willingness-to-pay for brand-name drugs, and strategic communication to alter perception could be effective in promoting the use of generic drugs among those who are price-inelastic.

Elemental diet therapy plays a significant role in preventing surgical recurrence of Crohn's disease in the era of biologics.

PURPOSE: Most patients with Crohn's disease (CD) experience surgical recurrence. In this era of novel therapies, we conducted this study to clarify which treatments effectively decrease the risk of surgical recurrence in patients with CD. METHODS: The subjects of this retrospective study were 37 patients with CD. We created cumulative surgery rate curves and performed univariate and multivariate analyses. RESULTS: Univariate analysis revealed that patients who consumed an elemental diet (ED; ≥ 900 kcal/day), anti-tumor necrosis factor-alpha, and thiopurines had a significantly better prognosis than those who did not (p = 0.011, p = 0.025, and p = 0.0080, respectively). Multivariate analysis revealed that ED therapy and thiopurines were independent significant factors for controlling surgical recurrence (p = 0.046 and p = 0.032, respectively). Additional analyses showed that the most promising ED therapeutic dose was ≥ 1200 kcal/day, while an ED therapeutic dose of ≥ 900 kcal/day was acceptable. CONCLUSIONS: Although univariate analyses revealed that all three treatment strategies had significant effects on surgical recurrence in patients with CD, multivariate analysis revealed that only ED therapy was significantly associated with surgical recurrence rates. Thus, ED therapy plays an important role in the management of CD, even in the era of biological therapies.

Theoretical Study on the Mechanism of Spirocyclization in Spiroviolene Biosynthesis.

Spiroviolene is a spirocyclic triquinane diterpene produced by Streptomyces violens. Recently, a biosynthetic pathway that includes secondary carbocation intermediates and a complicated concerted skeletal rearrangement was proposed for spiroviolene, based upon careful labeling experiments. On the basis of density functional theory (DFT) calculations, we propose a revised pathway for spiroviolene biosynthesis, involving a multistep carbocation cascade that bypasses the formation of unstable secondary carbocations by breaking the adjacent C-C bond to form a more stable tertiary carbocation (IM3) and by Wagner-Meerwein 1,2-methyl rearrangement (IM7).

[Malignant Pleural Mesothelioma with High Serum Granulocyte Coronary Stimulating Factor].

A 38-year-old man was admitted to our hospital because of right chest pain and high fever. Chest X-ray and computed tomography scan revealed right pleural effusion and pleural thickness. Diagnosis of malignant mesothelioma was established by pleural biopsy. Serum level of granulocyte colony stimulating factor (G-CSF) was high. We performed extrapleural pneumonectomy which improved high fever and inflammation, however the patient died three months after surgery.

DFT Study of a Missing Piece in Brasilane-Type Structure Biosynthesis: An Unusual Skeletal Rearrangement.

Brasilane-type sesquiterpenes have been known for a long time, but their biosynthetic pathways and mechanisms remain elusive. Recently, two groups independently characterized a Trichoderma terpene cyclase that produces trichobrasilenol, a brasilane-type sesquiterpene, and a plausible biosynthetic pathway was proposed based on isotopic labeling experiments. In the proposed mechanism, the characteristic brasilane-type 5/6 bicyclic skeleton is synthesized from a 5/7/3 tricyclic intermediate via a complicated concerted reaction, including six chemical events of C-C σ bond metathesis and rearrangements, ring-contraction, π bond formation, and regioselective hydroxylation. However, our density functional theory (DFT) calculations do not support this mechanism. On the basis of DFT calculations, we propose a new pathway for trichobrasilenol biosynthesis, involving a multistep carbocation cascade in which cyclopropylcarbinyl cations in equilibrium with homoallyl cations play a pivotal role. This pathway and mechanism is in good agreement with previous biosynthetic studies on brasilane-type compounds and related terpenoids, including isotope-labeling experiments and byproducts analysis.

Association Between Helicobacter pylori Infection and Short-segment/Long-segment Barrett's Esophagus in a Japanese Population: A Large Cross-Sectional Study.

GOAL: The goal of this study was to investigate the relationship between Helicobacter pylori (H. pylori) infection and short-segment and long-segment Barrett's esophagus (SSBE and LSBE). BACKGROUND: H. pylori infection is reported to be inversely associated with Barrett's esophagus (BE) in western countries. However, the impact of BE segment length on the association between BE and H. pylori infection has scarcely been investigated. MATERIALS AND METHODS: The study subjects were 41,065 asymptomatic Japanese individuals who took medical surveys between October 2010 and September 2017. Using this large database of healthy Japanese subjects, we investigated the association between H. pylori infection and SSBE/LSBE. We used multivariable logistic regression analysis to estimate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS: Among the study subjects, 36,615 were eligible for the analysis. H. pylori seropositivity was significantly associated with a lower rate of LSBE (OR: 0.42; 95% CI: 0.16-0.91) and a higher rate of SSBE (OR: 1.66; 95% CI: 1.56-1.78) after multivariate adjustment. In the subgroup analysis, H. pylori seropositivity was significantly associated with a high rate of SSBE in subjects without reflux esophagitis (RE) (OR: 1.73; 95% CI: 1.61-1.85). However, H. pylori seropositivity was not associated with SSBE in subjects with RE (OR: 1.07; 95% CI: 0.84-1.37). CONCLUSION: In a Japanese population, H. pylori infection was inversely associated with LSBE but significantly associated with SSBE only in subjects without RE. H. pylori may be a risk factor for SSBE, especially in individuals without RE.

DFT Study on the Biosynthesis of Preasperterpenoid A: Role of Secondary Carbocations in the Carbocation Cascade.

Preasperterpenoid A, featuring a 5/7/(3)6/5 pentacyclic structure, is a C25 sesterterpenoid produced by Penicillium verruculosum. The results of density functional calculations on putative biosynthetic carbocation cyclization/rearrangements leading to preasperterpenoid A revealed a highly concerted four-step cyclization mechanism. Interestingly, two secondary carbocation structures were obtained as minima, but appeared almost as shoulders in the energy profile, and may represent essentially transient structures during the highly concerted reaction.