283
Views
61
CrossRef citations to date
0
Altmetric
Reviews

Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450

, &
Pages 513-527 | Published online: 18 May 2008

Keep up to date with the latest research on this topic with citation updates for this article.

Read on this site (1)

Paul Czodrowski, Jan M Kriegl, Stefan Scheuerer & Thomas Fox. (2009) Computational approaches to predict drug metabolism. Expert Opinion on Drug Metabolism & Toxicology 5:1, pages 15-27.
Read now

Articles from other publishers (60)

Benjamin Weiser, Jérôme Genzling, Mihai Burai-Patrascu, Ophélie Rostaing & Nicolas Moitessier. (2023) Machine learning-augmented docking. 1. CYP inhibition prediction. Digital Discovery 2:6, pages 1841-1849.
Crossref
Mark A. Ashworth, Elvira Bombino, René M. de Jong, Hein J. Wijma, Dick B. Janssen, Kirsty J. McLean & Andrew W. Munro. (2022) Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin. ACS Catalysis 12:24, pages 15028-15044.
Crossref
Teresa Żołek, Kaori Yasuda, Geoffrey Brown, Toshiyuki Sakaki & Andrzej Kutner. (2022) In Silico Prediction of the Metabolic Resistance of Vitamin D Analogs against CYP3A4 Metabolizing Enzyme. International Journal of Molecular Sciences 23:14, pages 7845.
Crossref
Anne Labarre, Julia K. Stille, Mihai Burai Patrascu, Andrew Martins, Joshua Pottel & Nicolas Moitessier. (2022) Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds─Challenges and Opportunities. Journal of Chemical Information and Modeling 62:4, pages 1061-1077.
Crossref
Annachiara Tinivella, Luca Pinzi & Giulio Rastelli. (2021) Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models. Journal of Cheminformatics 13:1.
Crossref
Dumei Ma, Libo Zhang, Yingwu Yin, Yuxing Gao & Qian Wang. (2021) Spectroscopic studies of the interaction between phosphorus heterocycles and cytochrome P450. Journal of Pharmaceutical Analysis 11:6, pages 757-763.
Crossref
Li Ji. (2020) Synergy between Experiments and Computations: A Green Channel for Revealing Metabolic Mechanism of Xenobiotics in Chemical Toxicology. Chemical Research in Toxicology 33:7, pages 1539-1550.
Crossref
Eko Aditya Rifai, Marc van Dijk & Daan P. Geerke. (2020) Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations. Frontiers in Molecular Biosciences 7.
Crossref
Nico D. Fessner. (2019) P450 Monooxygenases Enable Rapid Late‐Stage Diversification of Natural Products via C−H Bond Activation . ChemCatChem 11:9, pages 2226-2242.
Crossref
Sayada Reemsha Kazmi, Ren Jun, Myeong-Sang Yu, Chanjin Jung & Dokyun Na. (2019) In silico approaches and tools for the prediction of drug metabolism and fate: A review. Computers in Biology and Medicine 106, pages 54-64.
Crossref
Lydia Benkaidali, François André, Gautier Moroy, Bahoueddine Tangour, François Maurel & Michel Petitjean. (2019) Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity. International Journal of Molecular Sciences 20:4, pages 987.
Crossref
Rosa A. Luirink, Stefan J. Dekker, Luigi Capoferri, Laura F.H. Janssen, Cynthia L. Kuiper, Mehmet E. Ari, Nico P.E. Vermeulen, J. Chris Vos, Jan N.M. Commandeur & Daan P. Geerke. (2018) A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants. Journal of Inorganic Biochemistry 184, pages 115-122.
Crossref
Marc van Dijk, Antonius M. ter Laak, Jörg D. Wichard, Luigi Capoferri, Nico P. E. Vermeulen & Daan P. Geerke. (2017) Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. Journal of Chemical Information and Modeling 57:9, pages 2294-2308.
Crossref
Rahim Ghadari. (2017) The role of human CYP2C8 in the metabolizing of montelukast-like compounds: a computational study. Research on Chemical Intermediates 43:8, pages 4781-4794.
Crossref
Shuai-Bing He, Man-Man Li, Bai-Xia Zhang, Xiao-Tong Ye, Ran-Feng Du, Yun Wang & Yan-Jiang Qiao. (2016) Construction of Metabolism Prediction Models for CYP450 3A4, 2D6, and 2C9 Based on Microsomal Metabolic Reaction System. International Journal of Molecular Sciences 17:10, pages 1686.
Crossref
Siddharth S. Kesharwani, Prajwal P. Nandekar, Preeti Pragyan, Vijay Rathod & Abhay T. Sangamwar. (2016) Characterization of differences in substrate specificity among CYP1A1, CYP1A2 and CYP1B1: an integrated approach employing molecular docking and molecular dynamics simulations. Journal of Molecular Recognition 29:8, pages 370-390.
Crossref
Alexander L. Perryman, Thomas P. Stratton, Sean Ekins & Joel S. Freundlich. (2015) Predicting Mouse Liver Microsomal Stability with “Pruned” Machine Learning Models and Public Data. Pharmaceutical Research 33:2, pages 433-449.
Crossref
Junhao Li, Hanwen Du, Zengrui Wu, Haixia Su, Guixia Liu, Yun Tang & Weihua Li. (2016) Interactions of omeprazole-based analogues with cytochrome P450 2C19: a computational study. Molecular BioSystems 12:6, pages 1913-1921.
Crossref
Junhao Li, Jinya Cai, Haixia Su, Hanwen Du, Juan Zhang, Shihui Ding, Guixia Liu, Yun Tang & Weihua Li. (2016) Effects of protein flexibility and active site water molecules on the prediction of sites of metabolism for cytochrome P450 2C19 substrates. Molecular BioSystems 12:3, pages 868-878.
Crossref
Yufeng J. Tseng, Bo-Han Su, Ming-Tsung Hsu & Olivia A. Lin. 2016. Frontiers in Molecular Design and Chemical Information Science - Herman Skolnik Award Symposium 2015: Jürgen Bajorath. Frontiers in Molecular Design and Chemical Information Science - Herman Skolnik Award Symposium 2015: Jürgen Bajorath 283 329 .
Lars Olsen, Flemming Steen Jørgensen & Chris Oostenbrink. 2015. New Horizons in Predictive Drug Metabolism and Pharmacokinetics. New Horizons in Predictive Drug Metabolism and Pharmacokinetics 66 78 .
Luigi Capoferri, Marlies C. A. Verkade-Vreeker, Danny Buitenhuis, Jan N. M. Commandeur, Manuel Pastor, Nico P. E. Vermeulen & Daan P. Geerke. (2015) Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation. PLOS ONE 10:11, pages e0142232.
Crossref
Alexander V. LyubimovRodolpho C. Braga, Vinicius M. Alves, Flavia C. Silva & Carolina H. Andrade. 2011. Encyclopedia of Drug Metabolism and Interactions. Encyclopedia of Drug Metabolism and Interactions 1 28 .
Zi-Ru Dai, Chun-Zhi Ai, Guang-Bo Ge, Yu-Qi He, Jing-Jing Wu, Jia-Yue Wang, Hui-Zi Man, Yan Jia & Ling Yang. (2015) A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4. International Journal of Molecular Sciences 16:12, pages 14677-14694.
Crossref
Hannu Raunio, Mira Kuusisto, Risto O. Juvonen & Olli T. Pentikäinen. (2015) Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes. Frontiers in Pharmacology 6.
Crossref
Lars Olsen, Chris Oostenbrink & Flemming Steen Jørgensen. (2015) Prediction of cytochrome P450 mediated metabolism. Advanced Drug Delivery Reviews 86, pages 61-71.
Crossref
Urban Bren, Julian E. Fuchs & Chris Oostenbrink. (2014) Cooperative Binding of Aflatoxin B 1 by Cytochrome P450 3A4: A Computational Study . Chemical Research in Toxicology 27:12, pages 2136-2147.
Crossref
Siddharth S. Kesharwani, Prajwal P. Nandekar, Preeti Pragyan & Abhay T. Sangamwar. (2014) Comparative Proteomics Among Cytochrome P450 Family 1 for Differential Substrate Specificity. The Protein Journal 33:6, pages 536-548.
Crossref
Hein J. Wijma, Siewert J. Marrink & Dick B. Janssen. (2014) Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 54:7, pages 2079-2092.
Crossref
Chris Oostenbrink. 2014. Drug Metabolism Prediction. Drug Metabolism Prediction 243 264 .
C. Ruben Vosmeer, René Pool, Mariël van Stee, Lovorka Perić-Hassler, Nico Vermeulen & Daan Geerke. (2014) Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach. International Journal of Molecular Sciences 15:1, pages 798-816.
Crossref
Karl‐Heinz Baringhaus, Gerhard Hessler, Hans Matter & Friedemann Schmidt. 2013. Chemoinformatics for Drug Discovery. Chemoinformatics for Drug Discovery 245 265 .
Gabriele Cruciani, Massimo Baroni, Paolo Benedetti, Laura Goracci & Cosimo Gianluca Fortuna. (2013) Exposition and reactivity optimization to predict sites of metabolism in chemicals. Drug Discovery Today: Technologies 10:1, pages e155-e165.
Crossref
Mariana C. Sousa, Rodolpho C. Braga, Bertilha A.S. Cintra, Valéria de Oliveira & Carolina H. Andrade. (2013) In silico metabolism studies of dietary flavonoids by CYP1A2 and CYP2C9. Food Research International 50:1, pages 102-110.
Crossref
Sabina Berne, Barbara Podobnik, Neja Zupanec, Metka Novak, Nada Kraševec, Samo Turk, Branka Korošec, Ljerka Lah, Erika Šuligoj, Jure Stojan, Stanislav Gobec & Radovan Komel. (2012) Virtual Screening Yields Inhibitors of Novel Antifungal Drug Target, Benzoate 4-Monooxygenase. Journal of Chemical Information and Modeling 52:11, pages 3053-3063.
Crossref
Valérie Campagna-Slater, Joshua Pottel, Eric Therrien, Louis-David Cantin & Nicolas Moitessier. (2012) Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s. Journal of Chemical Information and Modeling 52:9, pages 2471-2483.
Crossref
Michael Widmann, Jürgen Pleiss & Anne K. Samland. (2012) COMPUTATIONAL TOOLS FOR RATIONAL PROTEIN ENGINEERING OF ALDOLASES. Computational and Structural Biotechnology Journal 2:3, pages e201209016.
Crossref
Urban Bren & Chris Oostenbrink. (2012) Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations. Journal of Chemical Information and Modeling 52:6, pages 1573-1582.
Crossref
Rodolpho C. Braga, Vinícius M. Alves, Carlos A. M. Fraga, Eliezer J. Barreiro, Valéria de Oliveira & Carolina H. Andrade. (2011) Combination of docking, molecular dynamics and quantum mechanical calculations for metabolism prediction of 3,4-methylenedioxybenzoyl-2-thienylhydrazone. Journal of Molecular Modeling 18:5, pages 2065-2078.
Crossref
Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender & Robert C. Glen. (2012) Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms. Journal of Chemical Information and Modeling 52:3, pages 617-648.
Crossref
Antony J. Williams, Sean Ekins, Ola Spjuth & Egon L. Willighagen. 2012. Computational Toxicology. Computational Toxicology 221 241 .
Samuel L. C. Moors, Ann M. Vos, Maxwell D. Cummings, Herman Van Vlijmen & Arnout Ceulemans. (2011) Structure-Based Site of Metabolism Prediction for Cytochrome P450 2D6. Journal of Medicinal Chemistry 54:17, pages 6098-6105.
Crossref
Matthew L. Danielson, Prashant V. Desai, Michael A. Mohutsky, Steven A. Wrighton & Markus A. Lill. (2011) Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures. European Journal of Medicinal Chemistry 46:9, pages 3953-3963.
Crossref
Carolina Horta Andrade, Lenis Medeiros de Freitas & Valéria de Oliveira. (2011) Twenty-six years of HIV science: an overview of anti-HIV drugs metabolism. Brazilian Journal of Pharmaceutical Sciences 47:2, pages 209-230.
Crossref
Friederike Stoll, Andreas H. Göller & Alexander Hillisch. (2011) Utility of protein structures in overcoming ADMET-related issues of drug-like compounds. Drug Discovery Today 16:11-12, pages 530-538.
Crossref
Poongavanam Vasanthanathan, Jeroen Lastdrager, Chris Oostenbrink, Jan N. M. Commandeur, Nico P. E. Vermeulen, Flemming S. Jørgensen & Lars Olsen. (2011) Identification of CYP1A2 ligands by structure-based and ligand-based virtual screening. MedChemComm 2:9, pages 853.
Crossref
Tereza Hendrychová, Eva Anzenbacherová, Jiří Hudeček, Josef Skopalík, Reinhard Lange, Peter Hildebrandt, Michal Otyepka & Pavel Anzenbacher. (2011) Flexibility of human cytochrome P450 enzymes: Molecular dynamics and spectroscopy reveal important function-related variations. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1814:1, pages 58-68.
Crossref
Giulio Vistoli, Alessandro Pedretti, Angelica Mazzolari & Bernard Testa. (2010) Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0. Journal of Computer-Aided Molecular Design 24:9, pages 771-787.
Crossref
Guosheng Wu, Sarvesh C. Vashishtha & John C. L. Erve. (2010) Characterization of Glutathione Conjugates of Duloxetine by Mass Spectrometry and Evaluation of in Silico Approaches to Rationalize the Site of Conjugation for Thiophene Containing Drugs . Chemical Research in Toxicology 23:8, pages 1393-1404.
Crossref
Poongavanam Vasanthanathan, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen & Chris Oostenbrink. (2010) Computational Prediction of Binding Affinity for CYP1A2-Ligand Complexes Using Empirical Free Energy Calculations. Drug Metabolism and Disposition 38:8, pages 1347-1354.
Crossref
Patrik Rydberg, David E. Gloriam, Jed Zaretzki, Curt Breneman & Lars Olsen. (2010) SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism. ACS Medicinal Chemistry Letters 1:3, pages 96-100.
Crossref
Eva Stjernschantz & Chris Oostenbrink. (2010) Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes. Biophysical Journal 98:11, pages 2682-2691.
Crossref
Rita Santos, Jozef Hritz & Chris Oostenbrink. (2009) Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. Journal of Chemical Information and Modeling 50:1, pages 146-154.
Crossref
Giulio Vistoli, Alessandro Pedretti, Angelica Mazzolari & Bernard Testa. (2010) In silico prediction of human carboxylesterase-1 (hCES1) metabolism combining docking analyses and MD simulations. Bioorganic & Medicinal Chemistry 18:1, pages 320-329.
Crossref
Chad L. Stoner, Michael R. Wester & Benjamin J. Burke. 2010. Enzyme- and Transporter-Based Drug-Drug Interactions. Enzyme- and Transporter-Based Drug-Drug Interactions 151 168 .
Edward L. Lecluyse, Michael W. Sinz, Nicola Hewitt, Stephen S. Ferguson & Jasminder Sahi. 2009. Enzyme Inhibition in Drug Discovery and Development. Enzyme Inhibition in Drug Discovery and Development 265 314 .
Felix Hammann, Heike Gutmann, Ulli Baumann, Christoph Helma & Juergen Drewe. (2009) Classification of Cytochrome P 450 Activities Using Machine Learning Methods . Molecular Pharmaceutics 6:6, pages 1920-1926.
Crossref
Patrik Rydberg, Poongavanam Vasanthanathan, Chris Oostenbrink & Lars Olsen. (2009) Fast Prediction of Cytochrome P450 Mediated Drug Metabolism. ChemMedChem 4:12, pages 2070-2079.
Crossref
Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen & Chris Oostenbrink. (2008) Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. Journal of Chemical Information and Modeling 49:1, pages 43-52.
Crossref
Jozef Hritz, Anita de Ruiter & Chris Oostenbrink. (2008) Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking. Journal of Medicinal Chemistry 51:23, pages 7469-7477.
Crossref

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.