Literature DB >> 25907346

Predicting drug metabolism: experiment and/or computation?

Johannes Kirchmair1, Andreas H Göller2, Dieter Lang3, Jens Kunze4, Bernard Testa5, Ian D Wilson6, Robert C Glen7, Gisbert Schneider4.   

Abstract

Drug metabolism can produce metabolites with physicochemical and pharmacological properties that differ substantially from those of the parent drug, and consequently has important implications for both drug safety and efficacy. To reduce the risk of costly clinical-stage attrition due to the metabolic characteristics of drug candidates, there is a need for efficient and reliable ways to predict drug metabolism in vitro, in silico and in vivo. In this Perspective, we provide an overview of the state of the art of experimental and computational approaches for investigating drug metabolism. We highlight the scope and limitations of these methods, and indicate strategies to harvest the synergies that result from combining measurement and prediction of drug metabolism.

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Year:  2015        PMID: 25907346     DOI: 10.1038/nrd4581

Source DB:  PubMed          Journal:  Nat Rev Drug Discov        ISSN: 1474-1776            Impact factor:   84.694


  117 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules.

Authors:  Suresh B Singh; Lucy Q Shen; Matthew J Walker; Robert P Sheridan
Journal:  J Med Chem       Date:  2003-04-10       Impact factor: 7.446

3.  The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies.

Authors:  Jean-Loup Faulon; Donald P Visco; Ramdas S Pophale
Journal:  J Chem Inf Comput Sci       Date:  2003 May-Jun

Review 4.  Host-gut microbiota metabolic interactions.

Authors:  Jeremy K Nicholson; Elaine Holmes; James Kinross; Remy Burcelin; Glenn Gibson; Wei Jia; Sven Pettersson
Journal:  Science       Date:  2012-06-06       Impact factor: 47.728

Review 5.  The role of drug metabolizing enzymes in clearance.

Authors:  Li Di
Journal:  Expert Opin Drug Metab Toxicol       Date:  2014-01-07       Impact factor: 4.481

Review 6.  P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations.

Authors:  Sason Shaik; Shimrit Cohen; Yong Wang; Hui Chen; Devesh Kumar; Walter Thiel
Journal:  Chem Rev       Date:  2010-02-10       Impact factor: 60.622

7.  Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations.

Authors:  Tereza Hendrychova; Karel Berka; Veronika Navratilova; Pavel Anzenbacher; Michal Otyepka
Journal:  Curr Drug Metab       Date:  2012-02       Impact factor: 3.731

8.  Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

Authors:  Richard Lonsdale; Simon Hoyle; Daniel T Grey; Lars Ridder; Adrian J Mulholland
Journal:  Biochemistry       Date:  2012-02-10       Impact factor: 3.162

9.  Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants.

Authors:  Stephanie B A de Beer; Harini Venkataraman; Daan P Geerke; Chris Oostenbrink; Nico P E Vermeulen
Journal:  J Chem Inf Model       Date:  2012-07-19       Impact factor: 4.956

10.  Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations.

Authors:  Gabor Nagy; Chris Oostenbrink
Journal:  Eur Biophys J       Date:  2012-10-20       Impact factor: 1.733

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  89 in total

1.  Use of big data in drug development for precision medicine.

Authors:  Rosa S Kim; Nicolas Goossens; Yujin Hoshida
Journal:  Expert Rev Precis Med Drug Dev       Date:  2016-04-28

2.  Validation strategies for target prediction methods.

Authors:  Neann Mathai; Ya Chen; Johannes Kirchmair
Journal:  Brief Bioinform       Date:  2020-05-21       Impact factor: 11.622

3.  Prediction of UGT-mediated Metabolism Using the Manually Curated MetaQSAR Database.

Authors:  Angelica Mazzolari; Avid M Afzal; Alessandro Pedretti; Bernard Testa; Giulio Vistoli; Andreas Bender
Journal:  ACS Med Chem Lett       Date:  2019-02-12       Impact factor: 4.345

Review 4.  Scaffold-hopping as a strategy to address metabolic liabilities of aromatic compounds.

Authors:  Phillip R Lazzara; Terry W Moore
Journal:  RSC Med Chem       Date:  2019-12-16

Review 5.  The genetics of drug efficacy: opportunities and challenges.

Authors:  Matthew R Nelson; Toby Johnson; Liling Warren; Arlene R Hughes; Stephanie L Chissoe; Chun-Fang Xu; Dawn M Waterworth
Journal:  Nat Rev Genet       Date:  2016-03-14       Impact factor: 53.242

Review 6.  Counting on natural products for drug design.

Authors:  Tiago Rodrigues; Daniel Reker; Petra Schneider; Gisbert Schneider
Journal:  Nat Chem       Date:  2016-04-25       Impact factor: 24.427

Review 7.  From Classical Toxicology to Tox21: Some Critical Conceptual and Technological Advances in the Molecular Understanding of the Toxic Response Beginning From the Last Quarter of the 20th Century.

Authors:  Supratim Choudhuri; Geoffrey W Patton; Ronald F Chanderbhan; Antonia Mattia; Curtis D Klaassen
Journal:  Toxicol Sci       Date:  2018-01-01       Impact factor: 4.849

Review 8.  Automating drug discovery.

Authors:  Gisbert Schneider
Journal:  Nat Rev Drug Discov       Date:  2017-12-15       Impact factor: 84.694

9.  WhichP450: a multi-class categorical model to predict the major metabolising CYP450 isoform for a compound.

Authors:  Peter A Hunt; Matthew D Segall; Jonathan D Tyzack
Journal:  J Comput Aided Mol Des       Date:  2018-02-20       Impact factor: 3.686

10.  New Proluciferin Substrates for Human CYP4 Family Enzymes.

Authors:  Jingyao Liu; David Machalz; Gerhard Wolber; Erik J Sorensen; Matthias Bureik
Journal:  Appl Biochem Biotechnol       Date:  2020-09-01       Impact factor: 2.926

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