ATC-NLSP: Prediction of the Classes of Anatomical Therapeutic Chemicals Using a Network-Based Label Space Partition Method.

Abstract:

:Anatomical Therapeutic Chemical (ATC) classification system proposed by the World Health Organization is a widely accepted drug classification scheme in both academic and industrial realm. It is a multilabeling system which categorizes drugs into multiple classes according to their therapeutic, pharmacological, and chemical attributes. In this study, we adopted a data-driven network-based label space partition (NLSP) method for prediction of ATC classes of a given compound within the multilabel learning framework. The proposed method ATC-NLSP is trained on the similarity-based features such as chemical-chemical interaction and structural and fingerprint similarities of a compound to other compounds belonging to the different ATC categories. The NLSP method trains predictors for each label cluster (possibly intersecting) detected by community detection algorithms and takes the ensemble labels for a compound as final prediction. Experimental evaluation based on the jackknife test on the benchmark dataset demonstrated that our method has boosted the absolute true rate, which is the most stringent evaluation metrics in this study, from 0.6330 to 0.7497, in comparison to the state-of-the-art approaches. Moreover, the community structures of the label relation graph were detected through the label propagation method. The advantage of multilabel learning over the single-label models was shown by label-wise analysis. Our study indicated that the proposed method ATC-NLSP, which adopts ideas from network research community and captures the correlation of labels in a data driven manner, is the top-performing model in the ATC prediction task. We believed that the power of NLSP remains to be unleashed for the multilabel learning tasks in drug discovery. The source codes are freely available at https://github.com/dqwei-lab/ATC.

journal_name

Front Pharmacol

authors

Wang X,Wang Y,Xu Z,Xiong Y,Wei DQ

doi

10.3389/fphar.2019.00971

subject

Has Abstract

pub_date

2019-09-05 00:00:00

pages

971

issn

1663-9812

journal_volume

10

pub_type

杂志文章
  • The Folate Concentration and/or Folic Acid Metabolites in Plasma as Factor for COVID-19 Infection.

    abstract::Pregnant women appear to be more susceptible to infectious diseases than women in reproductive age. According to the California Department of Public Health pregnant women were 9.6-folds more likely to be hospitalized during the 2009 influenza outbreak when compared to non-pregnant women in reproductive age. In contras...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.01062

    authors: Acosta-Elias J,Espinosa-Tanguma R

    更新日期:2020-07-16 00:00:00

  • Targeted Intracellular Delivery of Antibodies: The State of the Art.

    abstract::A dominant area of antibody research is the extension of the use of this mighty experimental and therapeutic tool for the specific detection of molecules for diagnostics, visualization, and activity blocking. Despite the ability to raise antibodies against different proteins, numerous applications of antibodies in bas...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2018.01208

    authors: Slastnikova TA,Ulasov AV,Rosenkranz AA,Sobolev AS

    更新日期:2018-10-24 00:00:00

  • PAI-1 Exacerbates White Adipose Tissue Dysfunction and Metabolic Dysregulation in High Fat Diet-Induced Obesity.

    abstract::Background: Plasminogen activator inhibitor (PAI)-1 levels and activity are known to increase during metabolic syndrome and obesity. In addition, previous studies have implicated PAI-1 in adipose tissue (AT) expansion while also contributing to insulin resistance. As inflammation is also known to occur in AT during ob...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2018.01087

    authors: Wang L,Chen L,Liu Z,Liu Y,Luo M,Chen N,Deng X,Luo Y,He J,Zhang L,Hill MA,Li R,Wu J

    更新日期:2018-09-26 00:00:00

  • Validation and Psychometric Properties of the Arabic Version of the Duke Anticoagulation Satisfaction Scale (DASS).

    abstract::Background: To assess the health-related quality of life (HRQoL) of oral anticoagulant therapy users, different types of instruments are available, either general or specific tools like Duke Anticoagulation Satisfaction Scale (DASS). These tools allow the clinician to adjust the treatment regimen to focus on increasin...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.587489

    authors: AlAmmari M,Sultana K,AlHarbi SN,Marenga AS,AlTuraiki A,Althemery AU,Alfaifi AA,AlShehri A,Aqeel BF

    更新日期:2020-12-17 00:00:00

  • Mitochondrial Defunctionalization Supresses Tim-3-Galectin-9 Secretory Pathway in Human Colorectal Cancer Cells and Thus Can Possibly Affect Tumor Immune Escape.

    abstract::The Tim-3-galectin-9 secretory pathway is known to protect various types of cancer cells against host immune surveillance. We found that pharmacologically induced mitochondrial dysfunction leads to a reduced galectin-9 expression/exocytosis in human colorectal cancer cells and re-distribution of this protein (the effe...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2019.00342

    authors: Sakhnevych SS,Yasinska IM,Fasler-Kan E,Sumbayev VV

    更新日期:2019-04-05 00:00:00

  • The Expiry of Humira® Market Exclusivity and the Entry of Adalimumab Biosimilars in Europe: An Overview of Pricing and National Policy Measures.

    abstract::Background: From October 2018, adalimumab biosimilars could enter the European market. However, in some countries, such as Netherlands, high discounts reported for the originator product may have influenced biosimilar entry. Objectives: The aim of this paper is to provide a European overview of (list) prices of origin...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.591134

    authors: Moorkens E,Godman B,Huys I,Hoxha I,Malaj A,Keuerleber S,Stockinger S,Mörtenhuber S,Dimitrova M,Tachkov K,Vončina L,Palčevski VV,Achniotou G,Slabý J,Popelková L,Kohoutová K,Bartels D,Laius O,Martikainen JE,Selke GW,

    更新日期:2021-01-08 00:00:00

  • Repeated Administration of Norbinaltorphimine Produces Cumulative Kappa Opioid Receptor Inactivation.

    abstract::Kappa receptor activation by dynorphins contributes to the anxiogenic, dysphoric, and cognitive disrupting effects of repeated stress, suggesting that kappa receptor antagonists might have therapeutic utility in the treatment of stress disorders. Three classes of kappa antagonists have been distinguished: non-selectiv...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2019.00088

    authors: Chavkin C,Cohen JH,Land BB

    更新日期:2019-02-06 00:00:00

  • First-Line Interactive Wound Dressing Update: A Comprehensive Review of the Evidence.

    abstract::Wound management is a significant and growing issue worldwide. Knowledge of dressing products and clinical expertise in dressing selection are two major components in holistic wound management to ensure evidence-based wound care. With expanding global market of dressing products, there is need to update clinician know...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2020.00155

    authors: Weller CD,Team V,Sussman G

    更新日期:2020-02-28 00:00:00

  • Animal-Free Chemical Safety Assessment.

    abstract::The exponential growth of the Internet of Things and the global popularity and remarkable decline in cost of the mobile phone is driving the digital transformation of medical practice. The rapidly maturing digital, non-medical world of mobile (wireless) devices, cloud computing and social networking is coalescing with...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2016.00218

    authors: Loizou GD

    更新日期:2016-07-21 00:00:00

  • Calenduloside E Analogues Protecting H9c2 Cardiomyocytes Against H2O2-Induced Apoptosis: Design, Synthesis and Biological Evaluation.

    abstract::Modulation of apoptosis is therapeutically effective in cardiomyocytes damage. Calenduloside E (CE), a naturally occurring triterpenoid saponin, is a potent anti-apoptotic agent. However, little is known about its synthetic analogues on the protective effects in apoptosis of cardiomyocytes. The present research was pe...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2017.00862

    authors: Tian Y,Du YY,Shang H,Wang M,Sun ZH,Wang BQ,Deng D,Wang S,Xu XD,Sun GB,Sun XB

    更新日期:2017-11-23 00:00:00

  • A Novel Catecholopyrimidine Based Small Molecule PDE4B Inhibitor Suppresses Inflammatory Cytokines in Atopic Mice.

    abstract::Degradation of cyclic adenosine mono phosphate (cAMP) by phosphodiesterase-4B (PDE-4B) in the inflammatory cells leads to elevated expression of inflammatory cytokines in inflammatory cells. Suppression of cytokines has proved to be beneficial in the treatment of atopic dermatitis (AD). Henceforth, application of PDE4...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2018.00485

    authors: Purushothaman B,Arumugam P,Song JM

    更新日期:2018-05-11 00:00:00

  • microRNA-155 Modulates Hepatic Stellate Cell Proliferation, Apoptosis, and Cell Cycle Progression in Rats With Alcoholic Hepatitis via the MAPK Signaling Pathway Through Targeting SOCS1.

    abstract::The aim of this study was to investigate the regulatory function of the non-coding microRNA-155 (miR-155) and suppressor of cytokine signaling 1 (SOCS1) in alcoholic hepatitis (AH) and its potential mechanism associated with the mitogen-activated protein kinase (MAPK) signaling pathway. Levels of alanine aminotransfer...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.00270

    authors: Liu D,Han P,Gao C,Gao W,Yao X,Liu S

    更新日期:2020-04-07 00:00:00

  • Mechanistic Study of Bakuchiol-Induced Anti-breast Cancer Stem Cell and in Vivo Anti-metastasis Effects.

    abstract::Cancer stem cells are involved in cancer establishment, progression, and resistance to current treatments. We demonstrated the in vitro and in vivo anti-breast cancer effect of bakuchiol in a previous study. However, the ability of bakuchiol to target breast cancer stem cells (BCSCs) and inhibit breast cancer metastas...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2017.00746

    authors: Li L,Liu CC,Chen X,Xu S,Hernandez Cortes-Manno S,Cheng SH

    更新日期:2017-10-18 00:00:00

  • Long Non-Coding RNA in Drug Resistance of Non-Small Cell Lung Cancer: A Mini Review.

    abstract::Lung cancer is one of main causes of cancer mortality and 83% of lung cancer cases are classified as non-small cell lung cancer (NSCLC). Patients with NSCLC usually have a poor prognosis and one of the leading causes is drug resistance. With the progress of drug therapy, the emergence and development of drug resistanc...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2019.01457

    authors: Sun R,Wang R,Chang S,Li K,Sun R,Wang M,Li Z

    更新日期:2019-12-18 00:00:00

  • Potential Targeting of Renal Fibrosis in Diabetic Kidney Disease Using MicroRNAs.

    abstract::Diabetic kidney disease (DKD) is a major health problem and one of the leading causes of end-stage renal disease worldwide. Despite recent advances, there exists an urgent need for the development of new treatments for DKD. DKD is characterized by the excessive synthesis and deposition of extracellular matrix proteins...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2020.587689

    authors: Sakuma H,Hagiwara S,Kantharidis P,Gohda T,Suzuki Y

    更新日期:2020-11-13 00:00:00

  • Corrigendum: Safety Profiles of Tripterygium wilfordii Hook F: A Systematic Review and Meta-Analysis.

    abstract::[This corrects the article on p. 402 in vol. 7, PMID: 27877128.]. ...

    journal_title:Frontiers in pharmacology

    pub_type: 已发布勘误

    doi:10.3389/fphar.2017.00059

    authors: Zhang C,Sun PP,Guo HT,Liu Y,Li J,He XJ,Lu AP

    更新日期:2017-02-15 00:00:00

  • Endocannabinoids: A Promising Impact for Traumatic Brain Injury.

    abstract::The endogenous cannabinoid (endocannabinoid) system regulates a diverse array of physiological processes and unsurprisingly possesses considerable potential targets for the potential treatment of numerous disease states, including two receptors (i.e., CB1 and CB2 receptors) and enzymes regulating their endogenous liga...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2017.00069

    authors: Schurman LD,Lichtman AH

    更新日期:2017-02-17 00:00:00

  • Chymase Inhibitor as a Novel Therapeutic Agent for Non-alcoholic Steatohepatitis.

    abstract::Non-alcoholic steatohepatitis (NASH) is characterized by inflammation and fibrosis, in addition to steatosis, of the liver, but no therapeutic agents have yet been established. The mast cell protease chymase can generate angiotensin II, matrix metalloproteinase-9 and transforming growth factor-β, all of which are asso...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2018.00144

    authors: Takai S,Jin D

    更新日期:2018-02-21 00:00:00

  • Type I PRMT Inhibition Protects Against C9ORF72 Arginine-Rich Dipeptide Repeat Toxicity.

    abstract::Repeat expansion mutations in the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-associated non-AUG translation of this expansion produces dipeptide repeat proteins (DRPs). The arginine containing DRPs, polyGR and polyPR, are consistently...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.569661

    authors: Premasiri AS,Gill AL,Vieira FG

    更新日期:2020-09-08 00:00:00

  • A Prognostic Model Based on Immune-Related Long Non-Coding RNAs for Patients With Cervical Cancer.

    abstract::Objectives: The study is performed to analyze the relationship between immune-related long non-coding RNAs (lncRNAs) and the prognosis of cervical cancer patients. We constructed a prognostic model and explored the immune characteristics of different risk groups. Methods: We downloaded the gene expression profiles and...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.585255

    authors: Chen P,Gao Y,Ouyang S,Wei L,Zhou M,You H,Wang Y

    更新日期:2020-11-30 00:00:00

  • An Update on in Vivo Imaging of Extracellular Vesicles as Drug Delivery Vehicles.

    abstract::Extracellular vesicles (EVs) are currently being considered as promising drug delivery vehicles. EVs are naturally occurring vesicles that exhibit many characteristics favorable to serve as drug delivery vehicles. In addition, EVs have inherent properties for treatment of cancers and other diseases. For research and c...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2018.00169

    authors: Gangadaran P,Hong CM,Ahn BC

    更新日期:2018-02-28 00:00:00

  • Dual Behavior of Long-Chain Fatty Acids and Their Cyclooxygenase/Lipoxygenase Metabolites on Human Intestinal Caco-2 Cell Growth.

    abstract::Etiology of colorectal cancer (CRC) is related, at least in part, with nutritional profile and epidemiological data indicating a key role of dietary fat on CRC pathogenesis. Moreover, inflammation and eicosanoids produced from arachidonic acid might have a pivotal role in CRC development. However, the effect of specif...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.529976

    authors: Storniolo CE,Cabral M,Busquets MA,Martín-Venegas R,Moreno JJ

    更新日期:2020-09-04 00:00:00

  • A Comprehensive Strategy to Evaluate Compatible Stability of Chinese Medicine Injection and Infusion Solutions Based on Chemical Analysis and Bioactivity Assay.

    abstract::Stability of traditional Chinese medicine injection (TCMI) is an important issue related with its clinical application. TCMI is composed of multi-components, therefore, when evaluating TCMI stability, several marker compounds cannot represent global components or biological activities of TCMI. Till now, when evaluatin...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2017.00833

    authors: Li JP,Liu Y,Guo JM,Shang EX,Zhu ZH,Zhu KY,Tang YP,Zhao BC,Tang ZS,Duan JA

    更新日期:2017-11-15 00:00:00

  • Mifepristone for Treatment of Metabolic Syndrome: Beyond Cushing's Syndrome.

    abstract::A growing body of research indicates that cortisol, the glucocorticoid product of the activation of the hypothalamic-pituitary-adrenal axis, plays a role in the pathophysiology of metabolic syndrome. In this regard, chronic exposure to cortisol is associated with risk factors related to metabolic syndrome like weight ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2020.00429

    authors: Díaz-Castro F,Monsalves-Álvarez M,Rojo LE,Del Campo A,Troncoso R

    更新日期:2020-04-24 00:00:00

  • Critical Role of Hepatic Cyp450s in the Testis-Specific Toxicity of (5R)-5-Hydroxytriptolide in C57BL/6 Mice.

    abstract::Low solubility, tissue accumulation, and toxicity are chief obstacles to developing triptolide derivatives, so a better understanding of the pharmacokinetics and toxicity of triptolide derivatives will help with these limitations. To address this, we studied pharmacokinetics and toxicity of (5R)-5-hydroxytriptolide (L...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2017.00832

    authors: Yu C,Li Y,Liu M,Gao M,Li C,Yan H,Li C,Sun L,Mo L,Wu C,Qi X,Ren J

    更新日期:2017-11-21 00:00:00

  • Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods.

    abstract::Scoring functions play an important role in structure-based virtual screening. It has been widely accepted that target-specific scoring functions (TSSFs) may achieve better performance compared with universal scoring functions in actual drug research and development processes. A method that can effectively construct T...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2019.00924

    authors: Wang D,Cui C,Ding X,Xiong Z,Zheng M,Luo X,Jiang H,Chen K

    更新日期:2019-08-22 00:00:00

  • Novel Anti-fibrotic Therapies.

    abstract::Fibrosis is a major player in cardiovascular disease, both as a contributor to the development of disease, as well as a post-injury response that drives progression. Despite the identification of many mechanisms responsible for cardiovascular fibrosis, to date no treatments have emerged that have effectively reduced t...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2017.00318

    authors: McVicker BL,Bennett RG

    更新日期:2017-05-31 00:00:00

  • UPLC-QTOF/MSE and Bioassay Are Available Approaches for Identifying Quality Fluctuation of Xueshuantong Lyophilized Powder in Clinic.

    abstract::Xueshuantong Lyophilized Powder (XST), consisting of a series of saponins extracted from Panax notoginseng, is widely applied to treat acute cerebral infarction, stroke, and coronary heart disease in China. However, most adverse drug reactions (ADR) in clinic are caused by quality problems of XST. In this study, six b...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2018.00633

    authors: Yang ZR,Wang ZH,Tang JF,Yan Y,Yue SJ,Feng WW,Shi ZY,Meng XT,Peng C,Wang CY,Meng DL,Yan D

    更新日期:2018-06-15 00:00:00

  • Cannabidiol as a Potential New Type of an Antipsychotic. A Critical Review of the Evidence.

    abstract::There is urgent need for the development of mechanistically different and less side-effect prone antipsychotic compounds. The endocannabinoid system has been suggested to represent a potential new target in this indication. While the chronic use of cannabis itself has been considered a risk factor contributing to the ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审

    doi:10.3389/fphar.2016.00422

    authors: Rohleder C,Müller JK,Lange B,Leweke FM

    更新日期:2016-11-08 00:00:00

  • DeCoST: A New Approach in Drug Repurposing From Control System Theory.

    abstract::In this paper, we propose DeCoST (Drug Repurposing from Control System Theory) framework to apply control system paradigm for drug repurposing purpose. Drug repurposing has become one of the most active areas in pharmacology since the last decade. Compared to traditional drug development, drug repurposing may provide ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章

    doi:10.3389/fphar.2018.00583

    authors: Nguyen TM,Muhammad SA,Ibrahim S,Ma L,Guo J,Bai B,Zeng B

    更新日期:2018-06-05 00:00:00