☆ 4.7 Article

Towards Decoding Hepatotoxicity of Approved Drugs through Navigation of Multiverse and Consensus Chemical Spaces

BIOMOLECULES (2023)

Related references

Note: Only part of the references are listed.

Article Biochemical Research Methods

Data Fusion-based Discovery (DAFdiscovery) pipeline to aid compound annotation and bioactive compound discovery across diverse spectral data

Ricardo Moreira Borges et al.

Summary: DAFdiscovery is a pipeline designed to accelerate the annotation and discovery of bioactive compounds by combining mass spectrometry, nuclear magnetic resonance, and bioactivity data and using statistical total correlation spectroscopy and statistical heterospectroscopy calculations. It provides a simple-to-use method for analyzing data from different sources in various situations.

PHYTOCHEMICAL ANALYSIS (2023)

Add to Collection

Article Biotechnology & Applied Microbiology

Super-resolved spatial transcriptomics by deep data fusion

Ludvig Bergenstrahle et al.

Summary: This method improves the low resolution of spatial transcriptomics by integrating gene expression data with histological images, allowing for higher-resolution expression maps to be inferred. The deep generative model used in this method can predict spatial gene expression solely from histology images.

NATURE BIOTECHNOLOGY (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Identification of integrative hepatotoxicity induced by lysosomal phospholipase A2 inhibition of cationic amphiphilic drugs via metabolomics

Hyun-A Oh et al.

Summary: Drug-induced liver injury (DILI) is a condition characterized by abnormal hepatic function caused by drugs. The mechanisms involved in DILI include cellular stress, mitochondrial dysfunction, cell necrosis and apoptosis. Metabolomics has been used to evaluate toxicity mechanisms and has revealed that cationic amphiphilic drugs (CADs) inhibit lysosomal phospholipase A2 (LPLA2) and accumulate phospholipids. Cell-based metabolomics analysis identified changes in various metabolite types, including nucleotide sugars, conjugated bile acids, branched-chain amino acids, polyamine biosynthesis, and long-chain fatty acid and glycerophospholipid metabolism. These findings suggest that metabolomics can provide insights into the integrative molecular mechanisms of DILI.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2022)

Add to Collection

Review Pharmacology & Pharmacy

Yes SIR! On the structure-inactivity relationships in drug discovery

Edgar Lopez-Lopez et al.

Summary: Studying structure-inactivity relationships is crucial for understanding biological activity, but the lack of inactivity data limits the development and application of predictive models. The scientific community should disclose and analyze high-confidence activity data considering both 'active' and 'inactive' compounds.

DRUG DISCOVERY TODAY (2022)

Add to Collection

Review Pharmacology & Pharmacy

Approaches for enhancing the analysis of chemical space for drug discovery

Fernanda Saldivar-Gonzalez et al.

Summary: This article reviews the current state of chemical space in drug design and discovery, discussing advances in efficient navigation and assessment of chemical space diversity, as well as highlighting recent methods for generating visual representations of chemical space.

EXPERT OPINION ON DRUG DISCOVERY (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Progress on open chemoinformatic tools for expanding and exploring the chemical space

Jose L. Medina-Franco et al.

Summary: The concept of chemical space is crucial in chemoinformatics, particularly in drug design and discovery. Molecular representation plays a key role in defining chemical space and exploring structure-property relationships. Freely available tools are important for advancing research and education in this field.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2022)

Add to Collection

Review Chemistry, Medicinal

Chemical Multiverse: An Expanded View of Chemical Space

Jose L. Medina-Franco et al.

Summary: The concept of chemical space, with its technological advances and practical applications, has attracted attention in drug discovery and other research areas. This concept involves a large number of compounds and descriptors encoding molecular structure and properties. This article discusses the definitions of chemical space proposed in literature and highlights the convenience of using complementary descriptors to obtain a comprehensive view of compound data sets. Additionally, the article introduces the concept of chemical multiverse for the comprehensive analysis of compound data sets.

MOLECULAR INFORMATICS (2022)

Add to Collection

Article Chemistry, Multidisciplinary

DrugTax: package for drug taxonomy identification and explainable feature extraction

A. J. Preto et al.

Summary: DrugTax is an easy-to-use Python package for detailed characterization and chemical taxonomy of small molecules, suitable for AI approaches and drug discovery pipelines. It offers a range of features and tools for analysis and visualization.

JOURNAL OF CHEMINFORMATICS (2022)

Add to Collection

Article Computer Science, Artificial Intelligence

Advances in Data Preprocessing for Biomedical Data Fusion: An Overview of the Methods, Challenges, and Prospects

Shuihua Wang et al.

Summary: The advancement of biomedical imaging technologies leads to the daily generation of massive amounts of data, prompting the development of data fusion methods for better understanding. Apart from data generation, factors like noise, missing data, data scarcity, and high dimensionality also need to be considered in the fusion process.

INFORMATION FUSION (2021)

Add to Collection

Article Food Science & Technology

Hepatotoxicity of Pyrrolizidine Alkaloid Compound Intermedine: Comparison with Other Pyrrolizidine Alkaloids and Its Toxicological Mechanism

Ziqi Wang et al.

Summary: This study revealed the hepatotoxic mechanism of herbal medicines containing pyrrolizidine alkaloids, showing that these compounds induce cell apoptosis by generating excessive reactive oxygen species and changing mitochondrial membrane potential. This study provided direct evidence of Intermedine inducing hepatotoxicity through mitochondria-mediated apoptosis, enhancing the understanding of PA toxicity.

TOXINS (2021)

Add to Collection

Article Environmental Sciences

Acetaminophen metabolism revisited using non-targeted analyses: Implications for human biomonitoring

Arthur David et al.

Summary: This study aimed to address the issue of potential underestimation of APAP use by identifying overlooked metabolites with delayed formation and excretion rates in a controlled longitudinal exposure study. These metabolites, formed via the thiomethyl shunt after the enterohepatic circulation, were found to have delayed peak levels in blood and urine compared to other APAP metabolites, potentially extending the window of exposure assessment and providing important information regarding metabolic pathways of interest from a toxicological perspective.

ENVIRONMENT INTERNATIONAL (2021)

Add to Collection

Article Biochemistry & Molecular Biology

Tubulin Inhibitors: A Chemoinformatic Analysis Using Cell-Based Data

Edgar Lopez-Lopez et al.

Summary: This manuscript discusses the activity and structure relationship of Tub-Mts system inhibitors, and identifies promising analog series with high biological activities through constellations plots.

MOLECULES (2021)

Add to Collection

Article Biology

NFnetFu: A novel workflow for microbiome data fusion

Vartika Bisht et al.

Summary: Microbiome data analysis faces challenges such as collinearity, sparsity, and effect size, with the need for interpretable models integrating data and background knowledge. A multimodal framework has been developed to address these challenges and provide candidate taxa/OTUs for future validation experiments.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

Add to Collection

Review Chemistry, Analytical

Data handling in data fusion: Methodologies and applications

Silvana M. Azcarate et al.

Summary: The use of data fusion methodologies has increased as the modern analytical laboratories' capability to measure samples from multiple sources has improved. Understanding the data structure obtained from a particular instrument is essential for the success of data fusion methods, which is sometimes overlooked in the literature. This manuscript focuses on explaining data fusion based on the structure of data obtained from different analytical platforms, with special attention to the nature of the data and the relationships between samples and variables, as well as within variables.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2021)

Add to Collection

Review Pharmacology & Pharmacy

Drug-induced liver injury severity and toxicity (DILIst): binary classification of 1279 drugs by human hepatotoxicity

Shraddha Thakkar et al.

DRUG DISCOVERY TODAY (2020)

Add to Collection

Proceedings Paper Computer Science, Artificial Intelligence

Measuring Distances Among Graphs En Route To Graph Clustering

Ivan Kyosev et al.

2020 IEEE INTERNATIONAL CONFERENCE ON BIG DATA (BIG DATA) (2020)

Add to Collection

Article Neurosciences

Organophosphorus flame retardant induced hepatotoxicity and brain AChE inhibition on zebrafish (Danio rerio)

Mathan Ramesh et al.

NEUROTOXICOLOGY AND TERATOLOGY (2020)

Add to Collection

Review Biochemistry & Molecular Biology

On fusion methods for knowledge discovery from multi-omics datasets

Edwin Baldwin et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Add to Collection

Review Pharmacology & Pharmacy

DataWarrior: an evaluation of the open-source drug discovery tool

Edgar Lopez-Lopez et al.

EXPERT OPINION ON DRUG DISCOVERY (2019)

Add to Collection

Article Biochemistry & Molecular Biology

An In Silico Model for Predicting Drug-Induced Hepatotoxicity

Shuaibing He et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Add to Collection

Article Chemistry, Medicinal

Predicting pKa for Small Molecules on Public and In-house Datasets Using Fast Prediction Methods Combined with Data Fusion

Tuomo Kalliokoski et al.

MOLECULAR INFORMATICS (2019)

Add to Collection

Article Environmental Sciences

Contamination of organohalogen chemicals and hepatic steatosis in common kingfisher (Alcedo atthis) breeding at a nature reserve near e-waste recycling sites in South China

Jiang-Ping Wu et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2019)

Add to Collection

Article Toxicology

Intestinal and hepatic biotransformation of pyrrolizidine alkaloid N-oxides to toxic pyrrolizidine alkaloids

Mengbi Yang et al.

ARCHIVES OF TOXICOLOGY (2019)

Add to Collection

Review Pharmacology & Pharmacy

Reaching for the bright StARs in chemical space

Jose L. Medina-Franco et al.

DRUG DISCOVERY TODAY (2019)

Add to Collection

Article Medicine, Research & Experimental

Three-Level Hepatotoxicity Prediction System Based on Adverse Hepatic Effects

Lu Liu et al.

MOLECULAR PHARMACEUTICS (2019)

Add to Collection

Article Chemistry, Multidisciplinary

BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification

Yannick Djoumbou-Feunang et al.

JOURNAL OF CHEMINFORMATICS (2019)

Add to Collection

Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Add to Collection

Article Chemistry, Medicinal

Impact of Physicochemical Properties on Dose and Hepatotoxicity of Oral Drugs

Paul D. Leeson

CHEMICAL RESEARCH IN TOXICOLOGY (2018)

Add to Collection

Article Pharmacology & Pharmacy

Safety data and withdrawal of hepatotoxic drugs

Samy Babai et al.

THERAPIE (2018)

Add to Collection

Article Biochemistry & Molecular Biology

Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery

Jaak Simm et al.

CELL CHEMICAL BIOLOGY (2018)

Add to Collection

Article Chemistry, Medicinal

Data Warrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis

Thomas Sander et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)

Add to Collection

Article Chemistry, Multidisciplinary

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

Aaron M. Virshup et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Add to Collection

© Peeref 2019-2024. All rights reserved.