Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse

BackgroundPredicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive.ResultsHere a fast and reliable method to analyse ligands and visualise potential metabolic sites is presented which is based on annotated metabolic data, described by circular fingerprints. The method is available via the graphical workbench Bioclipse, which is equipped with advanced features in cheminformatics.ConclusionsDue to the speed of predictions (less than 50 ms per molecule), scientists can get real time decision support when editing chemical structures. Bioclipse is a rich client, which means that all calculations are performed on the local computer and do not require network connection. Bioclipse and MetaPrint2D are free for all users, released under open source licenses, and available from http://www.bioclipse.net.

• Publication year

  2010

• Venue

  BMC Bioinformatics

• Publication date

  2010-07-01

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-11-362PMID 20594327PMCID 2912884
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Bioclipse: an open source workbench for chemo- and bioinformatics

  2007cited by this paper
• Reaction Site Mapping of Xenobiotic Biotransformations

  2007cited by this paper
• State-of-the-art Tools for Computational Site of Metabolism Predictions: Comparative Analysis, Mechanistical Insights, and Future Applications

  2007cited by this paper
• MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist.

  2005cited by this paper
• New methods in predictive metabolism

  2004cited by this paper
• The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics

  2003influential reference
• Predicting pKa by Molecular Tree Structured Fingerprints and PLS

  2003cited by this paper
• Novel Methods for the Prediction of logP, pKa, and logD

  2002cited by this paper

• Green Contributions to the Chemistry of Perezone and Oxidation of the Double Bond of the Side Chain: A Theoretical Study and Cytotoxic Evaluation in MDA-MB231 Cells

  2025cites this paper
• Improving the Efficiency and the Validity of Molecular Transformers

  2025cites this paper
• Artificial intelligence and computational methods in human metabolism research: A comprehensive survey

  2025cites this paper
• Structure-based drug design for Protein Arginine Deiminase Type IV (PAD4) receptor: Chemoinformatics Approach

  2024cites this paper
• ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation

  2024cites this paper
• Combining predictive and analytical methods to elucidate pharmaceutical biotransformation in activated sludge.

  2023cites this paper
• Bioaccumulation and biotransformation of simvastatin in probiotic bacteria: A step towards better understanding of drug-bile acids-microbiome interactions

  2023cites this paper
• Machine learning for metabolomics research in drug discovery

  2023cites this paper
• A Practical Strategy for Exploring the Pharmacological Mechanism of Chrysophanol Against Obesity Asthma/Childhood Asthma

  2023cites this paper
• Molecular modeling approaches to address drug-metabolizing enzymes (DMEs) mediated chemoresistance: a review

  2021cites this paper
• A rapid RP-HPLC method for the simultaneous estimation of Ivacaftor and Tezacaftor and in silico study of their metabolitic products

  2021cites this paper
• Phenanthridine derivatives as promising new anticancer agents: synthesis, biological evaluation and binding studies.

  2020cites this paper
• A Simplistic Approach for Preparation of Alkylidenemalononitrile Derivatives: Characterization, In silico Studies, Quantum Chemical Evaluation, Molecular Docking, and In vitro Biological Activity Evaluation

  2020cites this paper
• Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy

  2020cites this paper
• Evaluation of pyrrole-2,3-dicarboxylate derivatives: Synthesis, DFT analysis, molecular docking, virtual screening and in vitro anti-hepatic cancer study

  2019cites this paper
• Computational Drug Designing and Prediction Of Important Parameters Using in silico Methods- A Review.

  2019cites this paper
• 4-Hydroxy-2-pyridone Derivatives and the δ-pyrone Isostere as Novel Agents Against Mycobacterium smegmatis Biofilm Inhibitors.

  2019cites this paper
• Computational Prediction of the Site(s) of Metabolism and Binding Modes of Protein Kinase Inhibitors Metabolized by CYP3A4

  2019cites this paper
• Redesigning hazardous chemicals by learning from structure-based drug discovery

  2019cites this paper
• Transport and Biotransformation of Gliclazide and the Effect of Deoxycholic Acid in a Probiotic Bacteria Model

  2019cites this paper
• Potent antibacterial activity of Dihydydropyrimidine-1,3,5-triazines via inhibition of DNA gyrase and antifungal activity with favourable metabolic profile.

  2019cites this paper
• Prediction of UGT-mediated Metabolism Using the Manually Curated MetaQSAR Database.

  2019cites this paper
• Potential Deoxycytidine Kinase Inhibitory Activity of Amaryllidaceae Alkaloids: An In Silico Approach

  2018cites this paper
• Structure–Activity Relationship and Molecular Docking of Natural Product Library Reveal Chrysin as a Novel Dipeptidyl Peptidase-4 (DPP-4) Inhibitor: An Integrated In Silico and In Vitro Study

  2018cites this paper
• Re-Designing Hazardous Chemicals with Target-Specific Toxicities by Learning from Structure-Based Drug Design

  2018cites this paper
• Computer-aided drug design and virtual screening of targeted combinatorial libraries of mixed-ligand transition metal complexes of 2-butanone thiosemicarbazone

  2018cites this paper
• Design, synthesis, and pharmacological evaluation of fluorinated azoles as anti‐tubercular agents

  2018cites this paper
• Synthesis, characterization, computational studies and biological activity evaluation of Cu, Fe, Co and Zn complexes with 2-butanone thiosemicarbazone and 1,10-phenanthroline ligands as anticancer and antibacterial agents

  2018cites this paper
• Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift

  2018cites this paper
• In silico approach to study the metabolism and biological activities of oligomeric proanthocyanidin complexes

  2018influential citation
• Molecular docking analysis of curcumin analogues against kinase domain of ALK5

  2017cites this paper
• The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

  2017cites this paper
• Predicting the Metabolic Sites by Flavin-Containing Monooxygenase on Drug Molecules Using SVM Classification on Computed Quantum Mechanics and Circular Fingerprints Molecular Descriptors

  2017cites this paper
• Towards Predicting the Cytochrome P450 Modulation: From QSAR to Proteochemometric Modeling.

  2017cites this paper
• Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors

  2017influential citation
• Antileishmanial potential of fused 5-(pyrazin-2-yl)-4H-1,2,4-triazole-3-thiols: Synthesis, biological evaluations and computational studies.

  2017cites this paper
• RD-Metabolizer: an integrated and reaction types extensive approach to predict metabolic sites and metabolites of drug-like molecules

  2017cites this paper
• In silico pharmacodynamics, toxicity profile and biological activities of the Saharan medicinal plant Limoniastrum feei

  2017cites this paper
• Recent advances in the prediction of non‐CYP450‐mediated drug metabolism

  2017cites this paper
• CHEMINFORMATICS TOOLS FOR ENABLING METABOLOMICS

  2017cites this paper
• Introduction to Cheminformatics

  2016cites this paper
• Urinary excretion and metabolism of miglustat and valproate in patients with Niemann-Pick type C1 disease: One- and two-dimensional solution-state (1)H NMR studies.

  2016cites this paper
• Discovery of Two Diacetylene Glycosides as Human Uridine-Cytidine Kinase 2 Inhibitors: an in Silico Approach

  2016cites this paper
• Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40

  2016cites this paper
• The Importance of Bioactivation in Computer-Guided Drug Repositioning. Why the Parent Drug is Not Always Enough.

  2016cites this paper
• XMetDB: an open access database for xenobiotic metabolism

  2016cites this paper
• In silico pharmacokinetic and molecular docking studies of small molecules derived from Indigofera aspalathoides Vahl targeting receptor tyrosine kinases

  2015cites this paper
• Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane

  2015cites this paper
• Development of in silico models for the prediction of toxicity incorporating ADME information

  2015cites this paper
• Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge

  2015cites this paper
• Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy 200 Ligand-based Methods for Data Management and Modelling

  2015cites this paper
• In silico methods for predicting drug-drug interactions with cytochrome P-450s, transporters and beyond.

  2015cites this paper
• Advances in methods for predicting phase I metabolism of polyphenols.

  2014cites this paper
• Predicting drug metabolism by CYP1A1, CYP1A2, and CYP1B1: insights from MetaSite, molecular docking and quantum chemical calculations

  2014cites this paper
• Online Databases and Web Servers for Drug Metabolism Research

  2014cites this paper
• Predicting Toxic Effects of Metabolites

  2014cites this paper
• Reactivity‐Based Approaches and Machine Learning Methods for Predicting the Sites of Cytochrome P450‐Mediated Metabolism

  2014cites this paper
• Polypharmacology and Adverse Bioactivity Profiles Predict Potential Toxicity and Drug‐Related Adrs

  2014cites this paper
• Progress in computational toxicology.

  2014cites this paper
• Preliminary hazard evaluation of androgen receptor-mediated endocrine-disrupting effects of thioxanthone metabolites through structure-based molecular docking.

  2014cites this paper
• Defining molecular initiating events in the adverse outcome pathway framework for risk assessment.

  2014cites this paper
• QSAR modeling: where have you been? Where are you going to?

  2014cites this paper
• In silico metabolism studies of dietary flavonoids by CYP1A2 and CYP2C9

  2013cites this paper
• CHEMOINFORMATICS AND BEYOND

  2013cites this paper
• The contribution of atom accessibility to site of metabolism models for cytochromes P450.

  2013cites this paper
• On mechanisms of reactive metabolite formation from drugs.

  2013cites this paper
• Pragmatic Approaches to Using Computational Methods To Predict Xenobiotic Metabolism

  2013cites this paper
• WhichCyp: prediction of cytochromes P450 inhibition

  2013cites this paper
• Structural basis and SAR for G007-LK, a lead stage 1,2,4-triazole based specific tankyrase 1/2 inhibitor.

  2013cites this paper
• Computational approaches for preclinical ADMET optimization

  2013cites this paper
• How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted?

  2013cites this paper
• Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software.

  2012cites this paper
• Open source drug discovery with bioclipse.

  2012cites this paper
• Accessing, using, and creating chemical property databases for computational toxicology modeling.

  2012cites this paper
• The challenges involved in modeling toxicity data in silico: a review.

  2012cites this paper
• Redefining Cheminformatics with Intuitive Collaborative Mobile Apps

  2012cites this paper
• Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms

  2012cites this paper
• Technology Review Special FocuS: compuTaTional chemiSTRy

  2012cites this paper
• Combination of docking, molecular dynamics and quantum mechanical calculations for metabolism prediction of 3,4-methylenedioxybenzoyl-2-thienylhydrazone

  2012cites this paper
• Brunn: An open source laboratory information system for microplates with a graphical plate layout design process

  2011cites this paper
• In silico site of metabolism prediction of cytochrome P450-mediated biotransformations

  2011cites this paper
• The Future of Computational Models for Predicting Human Toxicities

  year unknowncites this paper