Revealing Comprehensive Food Functionalities and Mechanisms of Action through Machine Learning.

Foods possess a range of unexplored functionalities; however, fully identifying these functions through empirical means presents significant challenges. In this study, we have proposed an in silico approach to comprehensively predict the functionalities of foods, encompassing even processed foods. This prediction is accomplished through the utilization of machine learning on biomedical big data. Our focus revolves around disease-related protein pathways, wherein we statistically evaluate how the constituent compounds collaboratively regulate these pathways. The proposed method has been employed across 876 foods and 83 diseases, leading to an extensive revelation of both food functionalities and their underlying operational mechanisms. Additionally, this approach identifies food combinations that potentially affect molecular pathways based on interrelationships between food functions within disease-related pathways. Our proposed method holds potential for advancing preventive healthcare.

Novel bisthiolane polysulfides from lachrymatory factor synthase-suppressed onion and their in vitro cyclooxygenase-1 inhibitory activity.

Two novel bisthiolane polysulfides (compounds 1 and 2), trivially named thiolanotrisulfide and thiolanotetrasulfide, were isolated from a reaction model of tearless onion (in which lachrymatory factor synthase is suppressed), and the presence of another novel bisthiolane polysulfide (3), trivially named thiolanopentasulfide, was confirmed. On the basis of spectroscopic and mass spectrometric analyses, it was found that these bisthiolane polysulfides were bis(5-hydroxy-3,4-dimethylthiolan-2-yl)-tri/tetra/pentasulfide with the general formulas of C12H22O2S5 (tri-), C12H22O2S6 (tetra-) and C12H22O2S7 (penta-), and they were confirmed to exist in authentic tearless onion juice. Thiolanotrisulfide (1) and thiolanotetrasulfide (2) inhibited cyclooxygenase-1 activity with IC50 values of 720 ± 78 and 464 ± 48 µM respectively, compared with 3282 ± 188 µM for aspirin.

Inhibitory effect of the compounds from the water extract of Curcuma longa on the production of PGE2 and NO in a macrophage cell line stimulated by LPS.

We wished to search for the compounds contributing to the anti-inflammatory effects of the water extract of Curcuma longa (WEC). WEC was fractioned and the fractions were evaluated with regard to their inhibitory effect on the production of nitric oxide (NO) from the macrophage cell line stimulated by lipopolysaccharide. Compounds in the active fractions were isolated and identified. One isolated compound was identified as new: (6S)-2-methyl-5-hydroxy-6-(3-hydroxy-4-methylphenyl)-2-heptene-4-one (1). Four isolated compounds were identified as known: (6S)-2-methyl-6-(4-hydroxyphenyl)-2-heptene-4-one (4), bisabolone-4-one (5), curcumenone (6), and turmeronol A (8). Three isolated compounds were not identified their stereostructures but their planar structures: 2-methyl-6-(4-hydroxymethyl-phenyl)-2-heptene-4-one (2), 2-methyl-6-(2,3-epoxy-4-methyl-4-cyclohexene)-2-heptene (3), and 4-methylene-5-hydroxybisabola-2,10-diene-9-one (7). Compounds 1, 4, 7 and 8 inhibited production of prostaglandin E2 and NO. Others inhibited NO production only. These results (at least in part) show the active compounds contributing to the anti-inflammatory effects of WEC, and may be useful for elucidating its various beneficial physiologic effects.

Changes in trans-S-1-Propenyl-l-cysteine Sulfoxide and Related Sulfur-Containing Amino Acids during Onion Storage.

trans-S-1-Propenyl-l-cysteine sulfoxide (PRENCSO) is the most abundant flavor precursor in onions. The changes in PRENCSO, its biosynthetic precursors, and cycloalliin contents in bulbs stored at 0 °C [i.e., recommended by the Food and Agriculture Organization of the United Nations (FAO)] are investigated. Ion-exchange high-performance liquid chromatography analysis revealed larger amounts of PRENCSO and cycloalliin, which were stoichiometrically balanced by the decrease in the combined amounts of the three biosynthetic precursors. The molar balance of the PRENCSO biosynthesis process during onion storage was explained well by the changes of these five compounds. High-throughput integrated liquid chromatography-tandem mass spectrometry analysis was employed to analyze multiple samples at 5 and 20 °C. The molar concentration data, converted using linear regression equations, showed a similar molar balance for the PRENCSO biosynthesis process comprising these five compounds during storage at all temperatures tested. Furthermore, the content of cycloalliin significantly increased at the expense of that of PRENCSO during storage at 20 °C.

Chemical Assignment of Structural Isomers of Sulfur-Containing Metabolites in Garlic by Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry.

BACKGROUND: The chemical assignment of metabolites is crucial to understanding the relation between food composition and biological activity. OBJECTIVE: This study was designed to detect and chemically assign sulfur-containing metabolites by using LC-Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) in Allium plants. METHODS: Ultrahigh resolution (>250,000 full width at half-maximum) and mass accuracy (<1 mDa) by FTICR-MS allowed us to distinguish ions containing sulfur isotopes ((32)S and (34)S). RESULTS: Putative 69 S-containing monoisotopic ions (S-ions) were extracted from the metabolome data of onion (Allium cepa), green onion (Allium fistulosum), and garlic (Allium sativum) on the basis of theoretical mass differences between (32)S-ions and their (34)S-substituted counterparts and on the natural abundance of (34)S. Eight S-ions were chemically assigned by using the reference data according to the guidelines of the Metabolomics Standards Initiative. Three ions detected in garlic were assigned as derived from the isomers γ-glutamyl-S-1-propenylcysteine and γ-glutamyl-S-2-propenylcysteine and as S-2-propenylmercaptoglutathione on the basis of differences in key product ions identified in reference tandem MS spectra. CONCLUSION: The ability to discriminate between such geometric isomers will be extremely useful for the chemical assignment of unknown metabolites in MS-based metabolomics.

Dill seed extract improves abnormalities in lipid metabolism through peroxisome proliferator-activated receptor-α (PPAR-α) activation in diabetic obese mice.

Dill, a small annual herb, is widely used as a flavoring agent in dishes including salads. It has been demonstrated that dill extract and its essential oil show hypolipidemic effects in rats. However, the mechanism of these effects has not been elucidated yet. We found that dill seed extract (DSE) activated peroxisome proliferator-activated receptor-α (PPAR-α), an indispensable regulator for hepatic lipid metabolism, by luciferase assay. Thus, we performed DSE feeding experiments using diabetic obese model KK-Ay mice to examine the effects of DSE on PPAR-α activation in vivo. A 4-week feeding of DSE contained in a high-fat diet decreased plasma triacylglyceride and glucose levels and increased the mRNA expression levels of fatty acid oxidation-related genes in the liver. In addition, the DSE feeding as well as bezafibrate (a PPAR-α potent agonist) feeding increased oxygen consumption rate and rectal temperature. These results indicate that DSE suppresses high-fat diet-induced hyperlipidemia through hepatic PPAR-α activation.

Proton transfer in a reaction catalyzed by onion lachrymatory factor synthase.

We produced a single deuterated lachrymatory factor (propanthial S-oxide, m/z = 91) in a model reaction system comprising purified alliinase, lachrymatory factor synthase (LFS), and (E)-(+)-S-(1-propenyl)-L-cysteine sulfoxide ((E)-PRENCSO) in D(2)O. Onion LFS reacted with the degraded products of (E)-PRENCSO by alliinase, but not with those of (Z)-PRENCSO. These findings indicate that onion LFS is an (E)-1-propenylsulfenic acid isomerase.

Structure and bioactivity of thiosulfinates resulting from suppression of lachrymatory factor synthase in onion.

In normal onion (Allium cepa), trans-S-1-propenyl-L-cysteine sulfoxide is transformed via 1-propenesulfenic acid into propanethial S-oxide, a lachrymatory factor, through successive reactions catalyzed by alliinase and lachrymatory factor synthase (LFS). A recent report showed that suppression of the LFS activity caused a dramatic increase in thiosulfinates previously reported as "zwiebelane isomers". After purification by recycle high-performance liquid chromatography and subsequent analyses, we established the planar structure of the putative "zwiebelane isomers" as S-3,4-dimethyl-5-hydroxythiolane-2-yl 1-propenethiosulfinate, in which two of the three molecules of 1-propenesulfenic acid involved in the formation gave the thiolane backbone, and the third molecule gave the thiosulfinate structure. Of at least three stereoisomers observed, one in the (2'R,3'R,4'R,5'R)-configuration was collected as an isolated fraction, and the other isomers were collected as a combined fraction because spontaneous tautomerization prevented further purification. Both fractions showed inhibitory activities against cyclooxygenase-1 and α-glucosidase in vitro.

Using synthesized onion lachrymatory factor to measure age-related decreases in reflex-tear secretion and ocular-surface sensation.

PURPOSE: To use synthesized onion lachrymatory factor (SOLF) to investigate age-related changes in reflex-tear secretion and ocular-surface sensation. METHODS: We separated 91 healthy volunteers into four groups: groups A, age 20-29 years; B, 30-39; C, 40-49; and D, older than 50 years. We exposed one eye of each subject to SOLF and measured the elapsed time until the subject's limit of irritation tolerance (TLI) was reached and an increase in the tear meniscus radius (DeltaR). After the SOLF stimulus, corneal sensitivity was examined by Cochet-Bonnet esthesiometry (CB), and reflex-tear secretion was examined by the Schirmer I-test (ST). RESULTS: TLI was significantly shorter in group A than in the other groups (P < 0.0001), and the groups B and D also differed significantly from each other (P = 0.0013). The increase in DeltaR was significantly greater in group A than in group C (P = 0.0306) or D (P < 0.0001), and groups B (P = 0.0002) and C (P = 0.0308) also differed significantly from group D. There were no significant intergroup differences in the CB and ST results. CONCLUSIONS: An age-related decrease in reflex-tear secretion and ocular-surface sensation was revealed by the SOLF test but could not be detected by either CB or the ST.

Chemically stabilized phenylboranylidene groups having a dimethoxytrityl group as a colorimetrically detectable protecting group designed for cis-1,2-diol functions of ribonucleosides in the solid-phase synthesis of m2(2,2)G5'ppT.

To not only improve the inherently poor stability of the phenylboranylidene group as a protecting group of the 2',3'-cis-diol function of ribonucleosides but also introduce a colorimetrically detectable function into its mother structure, various 2-[(dialkylamino)methyl]phenylboronic acid derivatives having a [(4,4'-dimethoxytrityl)oxy]methyl group were synthesized. The reaction of uridine with these substituted phenylboronic acid derivatives gave the corresponding 2',3'-O-phenylboranylideneuridine derivatives. The stability of these phenylboranylidene groups was examined. As a result, it was shown that the steric hindrance around the amino group greatly influenced the stability of the 2-substituted phenylboranylidene groups. The 2-aminomethyl-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group was the most stable. Its 2-dimethylamino counterpart, the 2-[(dimethylamino)methyl]-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group, was the second most stable. When the most and second stable protecting groups were applied to the synthesis of m(2)(2,2)G(5)(')ppT on controlled pore glass, the second stable protecting group showed the best result. The use of this DMTr-containing protecting group enabled us to estimate colorimetrically the amount of the m(2)(2,2)G residue that was incorporated into the reactive site of the pT-loaded CPG resin.

A new 2',3'-cis diol protecting group required for the solid-phase synthesis of capped oligonucleotide derivatives.

New 2',3'-cis-diol protecting groups of methylated G-capping reagents required for the solid-phase synthesis of capped oligonucleotide derivatives were designed so as to have a phenylborate skeleton with an alkylaminomethyl substituent and a DMTr group. The former can stabilize the boronic ester function. The latter led to significant enhancement of the solubility of the capping building units and the spectrometric assay of the DMTr cation generated upon acid treatment of capped products on solid supports enabled us to estimate easily the coupling yield of the 5'-capping reaction. The utility of these protecting groups are discussed.