Retrospective assessment of rat liver microsomal stability at NCATS: data and QSAR models.

Abstract:

:Hepatic metabolic stability is a key pharmacokinetic parameter in drug discovery. Metabolic stability is usually assessed in microsomal fractions and only the best compounds progress in the drug discovery process. A high-throughput single time point substrate depletion assay in rat liver microsomes (RLM) is employed at the National Center for Advancing Translational Sciences. Between 2012 and 2020, RLM stability data was generated for ~ 24,000 compounds from more than 250 projects that cover a wide range of pharmacological targets and cellular pathways. Although a crucial endpoint, little or no data exists in the public domain. In this study, computational models were developed for predicting RLM stability using different machine learning methods. In addition, a retrospective time-split validation was performed, and local models were built for projects that performed poorly with global models. Further analysis revealed inherent medicinal chemistry knowledge potentially useful to chemists in the pursuit of synthesizing metabolically stable compounds. In addition, we deposited experimental data for ~ 2500 compounds in the PubChem bioassay database (AID: 1508591). The global prediction models are made publicly accessible ( https://opendata.ncats.nih.gov/adme ). This is to the best of our knowledge, the first publicly available RLM prediction model built using high-quality data generated at a single laboratory.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Siramshetty VB,Shah P,Kerns E,Nguyen K,Yu KR,Kabir M,Williams J,Neyra J,Southall N,Nguyễn ÐT,Xu X

doi

10.1038/s41598-020-77327-0

subject

Has Abstract

pub_date

2020-11-26 00:00:00

pages

20713

issue

1

issn

2045-2322

pii

10.1038/s41598-020-77327-0

journal_volume

10

pub_type

杂志文章
  • Real-time locating and speed measurement of fibre fuse using optical frequency-domain reflectometry.

    abstract::We propose and experimentally demonstrate real-time locating and speed measurement of fibre fuse by analysing the Doppler shift of reflected light using optical frequency-domain reflectometry (OFDR). Our method can detect the start of a fibre fuse within 200 ms which is equivalent to a propagation distance of about 10...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25585

    authors: Jiang S,Ma L,Fan X,Wang B,He Z

    更新日期:2016-05-05 00:00:00

  • Successful selection of mouse sperm with high viability and fertility using microfluidics chip cell sorter.

    abstract::Cell sorting via flow cytometry is a powerful tool to select subpopulations of cells in many biological fields. Selection of fertilisation-prone sperm is a critical step to ensure a stable and high fertilisation rate in in vitro fertilisation (IVF). However, a combination of conventional cell sorting and IVF system ha...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-65931-z

    authors: Nakao S,Takeo T,Watanabe H,Kondoh G,Nakagata N

    更新日期:2020-06-01 00:00:00

  • Outdoor Temperature, Heart Rate and Blood Pressure in Chinese Adults: Effect Modification by Individual Characteristics.

    abstract::We collected data from Kailuan cohort study from 2006 to 2011 to examine whether short-term effects of ambient temperature on heart rate (HR) and blood pressure (BP) are non-linear or linear, and their potential modifying factors. The HR, BP and individual information, including basic characteristics, life style, soci...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep21003

    authors: Madaniyazi L,Zhou Y,Li S,Williams G,Jaakkola JJ,Liang X,Liu Y,Wu S,Guo Y

    更新日期:2016-02-15 00:00:00

  • L290P/V mutations increase ERK3's cytoplasmic localization and migration/invasion-promoting capability in cancer cells.

    abstract::Protein kinases are frequently mutated in human cancers, which leads to altered signaling pathways and contributes to tumor growth and progression. ERK3 is an atypical mitogen-activated protein kinase (MAPK) containing an S-E-G activation motif rather than the conserved T-X-Y motif in conventional MAPKs such as ERK1/2...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-15135-9

    authors: Alsaran H,Elkhadragy L,Shakya A,Long W

    更新日期:2017-11-03 00:00:00

  • High-performance graphene-quantum-dot photodetectors.

    abstract::Graphene quantum dots (GQDs) have received much attention due to their novel phenomena of charge transport and light absorption/emission. The optical transitions are known to be available up to ~6 eV in GQDs, especially useful for ultraviolet (UV) photodetectors (PDs). Thus, the demonstration of photodetection gain wi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05603

    authors: Kim CO,Hwang SW,Kim S,Shin DH,Kang SS,Kim JM,Jang CW,Kim JH,Lee KW,Choi SH,Hwang E

    更新日期:2014-07-07 00:00:00

  • Investigation of thermal energy transport interface of hybrid graphene-carbon nanotube/polyethylene nanocomposites.

    abstract::It is well known the thermal properties of three-dimensional (3-D) hybrid graphene (GR)-carbon nanotube (CNT) structures are not superior to that of the individual GR and CNT, however, the 3-D hybrid GR-CNT structures can effectively improve the thermal properties of polymer matrix. Therefore, understanding the therma...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14710-4

    authors: Liu F,Liu X,Hu N,Ning H,Atobe S,Yan C,Mo F,Fu S,Zhang J,Wang Y,Mu X

    更新日期:2017-10-31 00:00:00

  • Measurement of real pulsatile blood flow using X-ray PIV technique with CO2 microbubbles.

    abstract::Synchrotron X-ray imaging technique has been used to investigate biofluid flows in a non-destructive manner. This study aims to investigate the feasibility of the X-ray PIV technique with CO2 microbubbles as flow tracer for measurement of pulsatile blood flows under in vivo conditions. The traceability of CO2 microbub...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08840

    authors: Park H,Yeom E,Seo SJ,Lim JH,Lee SJ

    更新日期:2015-03-06 00:00:00

  • Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics.

    abstract::The identification of the modes of action of bioactive compounds is a major challenge in chemical systems biology of diseases. Genome-wide expression profiling of transcriptional responses to compound treatment for human cell lines is a promising unbiased approach for the mode-of-action analysis. Here we developed a n...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep40164

    authors: Iwata M,Sawada R,Iwata H,Kotera M,Yamanishi Y

    更新日期:2017-01-10 00:00:00

  • Lewis and AB0 blood group-phenotypes in periodontitis, cardiovascular disease, obesity and stroke.

    abstract::The AB0 blood group has been linked to ischaemic heart disease, stroke, and periodontal disease, while the Lewis blood group has been linked to ischaemic heart disease and obesity, all of which have been associated with periodontitis. AB0 or Lewis blood group phenotype may therefore constitute common hereditary compon...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42594-z

    authors: Enevold C,Nielsen CH,Molbo D,Lund R,Bendtzen K,Fiehn N-,Holmstrup P

    更新日期:2019-04-18 00:00:00

  • Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films.

    abstract::We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be f...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep17557

    authors: Shi X,Li X,Jiang L,Qu L,Zhao Y,Ran P,Wang Q,Cao Q,Ma T,Lu Y

    更新日期:2015-11-30 00:00:00

  • Metabolic output defines Escherichia coli as a health-promoting microbe against intestinal Pseudomonas aeruginosa.

    abstract::Gut microbiota acts as a barrier against intestinal pathogens, but species-specific protection of the host from infection remains relatively unexplored. Although lactobacilli and bifidobacteria produce beneficial lactic and short-chain fatty acids in the mammalian gut, the significance of intestinal Escherichia coli p...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-51058-3

    authors: Christofi T,Panayidou S,Dieronitou I,Michael C,Apidianakis Y

    更新日期:2019-10-08 00:00:00

  • OCT-based label-free in vivo lymphangiography within human skin and areola.

    abstract::Due to the limitations of current imaging techniques, visualization of lymphatic capillaries within tissue in vivo has been challenging. Here, we present a label-free high resolution optical coherence tomography (OCT) based lymphangiography (OLAG) within human skin in vivo. OLAG enables rapid (~seconds) mapping of lym...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep21122

    authors: Baran U,Qin W,Qi X,Kalkan G,Wang RK

    更新日期:2016-02-19 00:00:00

  • Centuries of domestication has not impaired oviposition site-selection function in the silkmoth, Bombyx mori.

    abstract::Oviposition site-selection in insects is mediated through innate recognition templates (IRTs) tuned to specific chemical cues. These cues aid gravid insects in choosing suitable oviposition sites and may even enhance the fitness of their offspring by warding off predators and parasitoids. However, studies on the evolu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep07472

    authors: Damodaram KJ,Kempraj V,Aurade RM,Rajasekhar SB,Venkataramanappa RK,Nandagopal B,Verghese A

    更新日期:2014-12-15 00:00:00

  • Comparison of uric acid reduction and renal outcomes of febuxostat vs allopurinol in patients with chronic kidney disease.

    abstract::Whether the clinical trial treatment effect of urate-lowering therapy (ULT) in patient with chronic kidney disease (CKD) is generalizable to real-word settings is unclear. This study aimed to compare febuxostat with allopurinol for uric acid reduction and renal protection in patients with CKD. Adult CKD patients newly...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67026-1

    authors: Peng YL,Tain YL,Lee CT,Yang YH,Huang YB,Wen YH,Hsu CN

    更新日期:2020-07-01 00:00:00

  • Βeta 2-glycoprotein I protects mice against gram-negative septicaemia in a sexually dimorphic manner.

    abstract::The immune responses of males and females to bacterial infections display differences. The mechanisms that underlie this sexual dimorphism are multifactorial. Lipopolysaccharide (LPS) contributes to the pathogenesis of endotoxaemia. We have previously demonstrated that the plasma protein beta-2 glycoprotein-1 (β2GPI) ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07945-8

    authors: El-Assaad F,Qi M,Gordon AK,Qi J,Dong S,Passam F,Weaver JC,Giannakopoulos B,Krilis SA

    更新日期:2017-08-15 00:00:00

  • Acute Heart Failure developed as worsening of Chronic Heart Failure is associated with increased mortality compared to de novo cases.

    abstract::Acute heart failure (AHF) emerges either de novo or from worsening of chronic heart failure (CHF). The aim of the present study was to evaluate the association between worsening of CHF and mortality in AHF patients. Out of 152 included AHF patients, 47 (30.9%) were de novo AHF patients and 105 (69%) were AHF patients ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28027-3

    authors: Degoricija V,Trbušić M,Potočnjak I,Radulović B,Terešak SD,Pregartner G,Berghold A,Tiran B,Frank S

    更新日期:2018-06-25 00:00:00

  • Expresser phenotype determines ABO(H) blood group antigen loading on platelets and von Willebrand factor.

    abstract::ABO blood group is associated with cardiovascular disease, with significantly lower risk in blood group O individuals. ABO(H) blood group determinants are expressed on different glycoproteins on platelet surfaces. In addition, ABO(H) structures are also present on VWF glycans. These ABO(H) carbohydrates influence both...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-75462-2

    authors: O'Donghaile D,Jenkins PV,McGrath RT,Preston L,Field SP,Ward SE,O'Sullivan JM,O'Donnell JS

    更新日期:2020-10-27 00:00:00

  • Exosome surface glycans reflect osteogenic differentiation of mesenchymal stem cells: Profiling by an evanescent field fluorescence-assisted lectin array system.

    abstract::Extracellular vesicles (EVs) carry information between cells in the form of biomolecules. Such molecules have been found to serve as biomarkers. Glycans attached to surface molecules on EVs are involved in their cellular uptake. In this study, we examined glycan profiles of small EVs which are generally termed exosome...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-47760-x

    authors: Shimoda A,Sawada SI,Sasaki Y,Akiyoshi K

    更新日期:2019-08-08 00:00:00

  • A Novel Mechanism for Nitrosative Stress Tolerance Dependent on GTP Cyclohydrolase II Activity Involved in Riboflavin Synthesis of Yeast.

    abstract::The biological functions of nitric oxide (NO) depend on its concentration, and excessive levels of NO induce various harmful situations known as nitrosative stress. Therefore, organisms possess many kinds of strategies to regulate the intracellular NO concentration and/or to detoxify excess NO. Here, we used genetic s...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-62890-3

    authors: Anam K,Nasuno R,Takagi H

    更新日期:2020-04-07 00:00:00

  • Calcium binding and voltage gating in Cx46 hemichannels.

    abstract::The opening of connexin (Cx) hemichannels in the membrane is tightly regulated by calcium (Ca2+) and membrane voltage. Electrophysiological and atomic force microscopy experiments indicate that Ca2+ stabilizes the hemichannel closed state. However, structural data show that Ca2+ binding induces an electrostatic seal p...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-15975-5

    authors: Pinto BI,Pupo A,García IE,Mena-Ulecia K,Martínez AD,Latorre R,Gonzalez C

    更新日期:2017-11-20 00:00:00

  • A different vision of dyslexia: Local precedence on global perception.

    abstract::Individuals perceive the wor(l)d hierarchically. Firsty, the global visual scene is processed by the right hemisphere, and later, the local features are perceived by the left hemisphere. Based on this hierarchical analysis, humans evolved unique communication ability: reading. However, for about 10% of people reading ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17626-1

    authors: Franceschini S,Bertoni S,Gianesini T,Gori S,Facoetti A

    更新日期:2017-12-12 00:00:00

  • Investigating the validity and reliability of Electrovestibulography (EVestG) for detecting post-concussion syndrome (PCS) with and without comorbid depression.

    abstract::Features from Electrovestibulography (EVestG) recordings have been used to classify and measure the severity of both persistent post-concussion syndrome (PCS) and major depressive disorder. Herein, we examined the effect of comorbid depression on the detection of persistent PCS using EVestG. To validate our previously...

    journal_title:Scientific reports

    pub_type: 临床试验,杂志文章

    doi:10.1038/s41598-018-32808-1

    authors: Suleiman A,Lithgow B,Mansouri B,Moussavi Z

    更新日期:2018-09-27 00:00:00

  • AutoFoci, an automated high-throughput foci detection approach for analyzing low-dose DNA double-strand break repair.

    abstract::Double-strand breaks (DSBs) are the most lethal DNA damages induced by ionising radiation (IR) and their efficient repair is crucial to limit genomic instability. The cellular DSB response after low IR doses is of particular interest but its examination requires the analysis of high cell numbers. Here, we present an a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-35660-5

    authors: Lengert N,Mirsch J,Weimer RN,Schumann E,Haub P,Drossel B,Löbrich M

    更新日期:2018-11-23 00:00:00

  • A Multiwell-Based Detection Platform with Integrated PDMS Concentrators for Rapid Multiplexed Enzymatic Assays.

    abstract::We report an integrated system for accelerating assays with concentrators in a standard 12-well plate (ISAAC-12) and demonstrate its versatility for rapid detection of matrix metalloproteinase (MMP)-9 expression in the cell culture supernatant of breast cancer cell line MDA-MB-231 by accelerating the enzymatic reactio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-29065-7

    authors: Wei X,Do VQ,Pham SV,Martins D,Song YA

    更新日期:2018-07-17 00:00:00

  • Determination of the optimal location for constructing solar photovoltaic farms based on multi-criteria decision system and Dempster-Shafer theory.

    abstract::Considering environmental concerns regarding air pollution which is induced by burning fossil fuels to generate electrical power, utilizing solar energy as a green and sustainable energy source is of great interest. This study proposes a novel framework to determine the optimal location for constructing solar photovol...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-65165-z

    authors: Mokarram M,Mokarram MJ,Khosravi MR,Saber A,Rahideh A

    更新日期:2020-05-18 00:00:00

  • Impact of 12-month cryopreservation on endogenous DNA damage in whole blood and isolated mononuclear cells evaluated by the comet assay.

    abstract::The comet assay is an electrophoretic technique used to assess DNA damage, as a marker of genotoxicity and oxidative stress, in tissues and biological samples including peripheral blood mononuclear cells (PBMCs) and whole blood (WB). Although numerous studies are performed on stored samples, the impact of cryopreserva...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-79670-8

    authors: Marino M,Gigliotti L,Møller P,Riso P,Porrini M,Del Bo C

    更新日期:2021-01-11 00:00:00

  • No evidence for after-effects of noisy galvanic vestibular stimulation on motion perception.

    abstract::Noisy galvanic vestibular stimulation (nGVS) delivered at imperceptible intensities can improve vestibular function in health and disease. Here we evaluated whether nGVS effects on vestibular function are only present during active stimulation or may exhibit relevant post-stimulation after-effects. Initially, nGVS amp...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59374-9

    authors: Keywan A,Badarna H,Jahn K,Wuehr M

    更新日期:2020-02-13 00:00:00

  • The effect of cold priming on the fitness of Arabidopsis thaliana accessions under natural and controlled conditions.

    abstract::Priming improves an organism's performance upon a future stress. To test whether cold priming supports protection in spring and how it is affected by cold acclimation, we compared seven Arabidopsis accessions with different cold acclimation potentials in the field and in the greenhouse for growth, photosynthetic perfo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep44055

    authors: Cvetkovic J,Müller K,Baier M

    更新日期:2017-03-09 00:00:00

  • Anthropogenic effects on a tropical forest according to the distance from human settlements.

    abstract::The protection of tropical forests is one of the most urgent issues in conservation biology because of the rapid deforestation that has occurred over the last 50 years. Even in protected forests, the anthropogenic effects from newly expanding villages such as harvesting of medicinal plants, pasturing cattle and forest...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep14689

    authors: Popradit A,Srisatit T,Kiratiprayoon S,Yoshimura J,Ishida A,Shiyomi M,Murayama T,Chantaranothai P,Outtaranakorn S,Phromma I

    更新日期:2015-10-05 00:00:00

  • The cellular and molecular determinants of emphysematous destruction in COPD.

    abstract::The introduction of microCT has made it possible to show that the terminal bronchioles are narrowed and destroyed before the onset of emphysematous destruction in COPD. This report extends those observations to the cellular and molecular level in the centrilobular phenotype of emphysematous destruction in lungs donate...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10126-2

    authors: Suzuki M,Sze MA,Campbell JD,Brothers JF 2nd,Lenburg ME,McDonough JE,Elliott WM,Cooper JD,Spira A,Hogg JC

    更新日期:2017-08-25 00:00:00