FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry

Akimoto, Nayumi; Ara, Takeshi; Nakajima, D.; Suda, Kenichi; Ikeda, Chiaki; Takahashi, Sakiko; Muneto, Reiko; Yamada, Manabu; Suzuki, Hideyuki; Shibata, Daisuke; Sakurai, Nozomu

doi:10.1038/s41598-017-01390-3

Cited by 48 publications

(51 citation statements)

References 31 publications

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“…NGS was carried out as previously reported ( 9 , 10 ). Briefly, the quality of total RNA isolated from the UExo fraction by the column-based method (urine 1 mL) was checked using a Bioanalyzer (Agilent; Santa Clara, CA, USA), and the samples from NR and KD animals were pooled as one sample for each group.…”

Section: Methodsmentioning

confidence: 99%

“…We also reported altered levels of miR-26a and miR-146a in the urine of CKD mice, that were mainly associated with glomerular and tubulointerstitial lesions, respectively ( 6 , 7 ). In dogs, we analyzed UExo-derived miRNAs, especially miR-26a, which was significantly decreased in the KD group compared to that in the normal renal function (NR) group, and its decrease in the glomerulus was significantly correlated with the severity of glomerular injuries ( 9 ). Thus, the changes in UExo-derived miRNAs seem to be correlated with the progression of KD in various species.…”

Section: Introductionmentioning

confidence: 99%

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Urinary Exosome-Derived microRNAs Reflecting the Changes in Renal Function in Cats

et al. 2018

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Increased incidence of kidney disease (KD) is a common concern in human and companion animals. Cats, in particular, are highly susceptible to KD. Novel KD biomarkers would help to address these problems. Therefore, we are focusing on microRNA, a highly conserved nucleic acid, as a KD biomarker for various animals. We previously reported that altered levels of urinary exosome (UExo)-derived microRNAs indicate renal pathologies in dogs. This study comprehensively examined UExo-derived microRNAs, which reflected the KD status in cats. The examined cats were divided into two groups: normal renal function (NR) and KD. Based on our previous data in dogs and cats, as well as the present data on UExo-derived microRNAs in cats by next-generation sequencing, let-7b, let-7f, miR-10a, miR-10b, miR-21a, miR-22, miR-26a, miR-27b, miR-146a, miR-181a, miR-191, and miR-486a were identified as biomarker candidates. In summary, the levels of UExo-derived let-7b, miR-22, and miR-26a significantly decreased in cats with KD from the early stages of the disease. UExo-derived miRNA levels normalized to urinary creatinine or total RNA of miR-21a was significantly higher in the KD group. Importantly, the ratio of UExo-derived miR-21a to let-7b showed a significant and strongest correlation with serum creatinine (ρ = 0.751), blood urea nitrogen (ρ = 0.754), and urinary creatinine (ρ = −0.421) among all examined indices. Further, the ratio of miR-181a to let-7b or miR-10b significantly correlated with the progression of renal dysfunction in the KD group. Thus, we identified that UExo-derived microRNAs in cats, and their raw and normalized levels could indicate altered renal function.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Urinary Exosome-Derived microRNAs Reflecting the Changes in Renal Function in Cats

et al. 2018

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“…Herein, we aimed to search for novel compounds that can inhibit DENV at dimeric E protein using several computational tools. Flavonoids were collected from several compound databases and an in-house database based on the core structural similarity of flavonoids [61,62]. In the beginning, the pharmacophore-based screening and molecular docking methods were used for virtual screening of numerous compounds in the dataset.…”

Section: Introductionmentioning

confidence: 99%

Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification Study

et al. 2019

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Dengue infection is caused by a mosquito-borne virus, particularly in children, which may even cause death. No effective prevention or therapeutic agents to cure this disease are available up to now. The dengue viral envelope (E) protein was discovered to be a promising target for inhibition in several steps of viral infection. Structure-based virtual screening has become an important technique to identify first hits in a drug screening process, as it is possible to reduce the number of compounds to be assayed, allowing to save resources. In the present study, pharmacophore models were generated using the common hits approach (CHA), starting from trajectories obtained from molecular dynamics (MD) simulations of the E protein complexed with the active inhibitor, flavanone (FN5Y). Subsequently, compounds presented in various drug databases were screened using the LigandScout 4.2 program. The obtained hits were analyzed in more detail by molecular docking, followed by extensive MD simulations of the complexes. The highest-ranked compound from this procedure was then synthesized and tested on its inhibitory efficiency by experimental assays.

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“…UHPLC-MS has been successfully adopted Table. for flavonoid analyses in many plant species including a number of economically important crops (Cho, Howard, Prior, & Clark, 2004;Farag et al, 2007;Li et al, 2016;Wang et al, 2017). The utility of UHPLC-MS in plant flavonoid analyses is further enhanced by the development of mass spectral libraries as well as informatics tools (Akimoto et al, 2017;Qiu, Fine, Wherritt, Lei, & Sumner, 2016). To date, over 7000 flavonoids have been identified from various plant species and a database of probable mass fragments for 6867 known flavonoids (FsDatabase) was manually constructed (Akimoto et al, 2017).…”

Section: Background Informationmentioning

confidence: 99%

“…The utility of UHPLC-MS in plant flavonoid analyses is further enhanced by the development of mass spectral libraries as well as informatics tools (Akimoto et al, 2017;Qiu, Fine, Wherritt, Lei, & Sumner, 2016). To date, over 7000 flavonoids have been identified from various plant species and a database of probable mass fragments for 6867 known flavonoids (FsDatabase) was manually constructed (Akimoto et al, 2017). This should help improve the identification of flavonoids in complex plant samples using tandem mass spectrometry.…”

Section: Background Informationmentioning

confidence: 99%

UHPLC‐MS Analyses of Plant Flavonoids

et al. 2018

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Flavonoids are a class of specialized metabolites found in many different plant species. They protect against UV radiation, scavenge reactive oxygen species, are involved in plant defense responses, and are associated with plant‐microorganism interactions. They have also been reported to possess health‐promoting effects including anti‐inflammatory, antioxidant, anticancer activity, and antihypertensive effects. Flavonoids encompass >10,000 structures where the types and amounts depend on the plant species, developmental stage, organ, and growth conditions. The diversity of flavonoid structures represents a significant challenge in the analysis of plant flavonoids. Many analytical techniques have been developed to detect and quantify flavonoids, and the most productive of these techniques use liquid chromatography (LC) coupled to mass spectrometry (MS) to analyze flavonoids due to the excellent combination of selectivity and sensitivity of MS. In addition, mass spectral libraries have been constructed to further aid flavonoid identification. Here, the use of ultra‐high pressure liquid chromatography coupled to mass spectrometry (UHPLC‐MS) in plant flavonoid analyses, with an emphasis on sample extraction, flavonoid separation, and MS detection, is described. © 2018 by John Wiley & Sons, Inc.

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FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry

Cited by 48 publications

References 31 publications

Urinary Exosome-Derived microRNAs Reflecting the Changes in Renal Function in Cats

Urinary Exosome-Derived microRNAs Reflecting the Changes in Renal Function in Cats

Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification Study

UHPLC‐MS Analyses of Plant Flavonoids

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