Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.

Autor: Luigi Capoferri, Marlies C A Verkade-Vreeker, Danny Buitenhuis, Jan N M Commandeur, Manuel Pastor, Nico P E Vermeulen, Daan P Geerke

Publikováno v: PLoS ONE, Vol 10, Iss 11, p e0142232 (2015)

Prediction of human Cytochrome P450 (CYP) binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards diffe

Externí odkaz: https://doaj.org/article/3ed89fa3fa634a258200e17253a8f53b

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors

Autor: Luigi Capoferri, Antonius Ter Laak, Daan P. Geerke, Marc van Dijk, Jörg Wichard, Nico P. E. Vermeulen

Publikováno v: Journal of Chemical Information and Modeling
Journal of Chemical Information and Modeling, 57(9), 2294-2308. American Chemical Society
van Dijk, M, Ter Laak, A M, Wichard, J D, Capoferri, L, Vermeulen, N P E & Geerke, D P 2017, ' Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors ', Journal of Chemical Information and Modeling, vol. 57, no. 9, pp. 2294-2308 . https://doi.org/10.1021/acs.jcim.7b00222

Cytochrome P450 aromatase (CYP19A1) plays a key role in the development of estrogen dependent breast cancer, and aromatase inhibitors have been at the front line of treatment for the past three decades. The development of potent, selective and safer

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e23bdeaf214b05cf8cdb014ff82282bb
https://doi.org/10.1021/acs.jcim.7b00222

A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants

Autor: Jan N. M. Commandeur, Luigi Capoferri, Cynthia L. Kuiper, Laura F.H. Janssen, J. Chris Vos, Nico P. E. Vermeulen, Rosa A. Luirink, Mehmet E. Ari, Daan P. Geerke, Stefan J. Dekker

Publikováno v: Journal of Inorganic Biochemistry, 184, 115-122. Elsevier Inc.
Luirink, R A, Dekker, S J, Capoferri, L, Kuiper, C L, Janssen, L F H, Ari, M E, Vermeulen, N P E, Vos, J C, Commandeur, J N M & Geerke, D P 2018, ' A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants ', Journal of Inorganic Biochemistry, vol. 184, pp. 115-122 . https://doi.org/10.1016/j.jinorgbio.2018.04.013

The 5′-hydroxymethyl metabolite of the penicillin based antibiotic flucloxacillin (FLX) is considered to be involved in bile duct damage occurring in a small number of patients. Because 5′-hydroxymethyl FLX is difficult to obtain by organic synth

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9937dc44bef21fac6bfe5f63344427bb
https://research.vu.nl/en/publications/9e064fb2-79b8-46f2-8281-8dc89356a4a2

Quantum Mechanics/Molecular Mechanics Modeling of Covalent Addition between EGFR–Cysteine 797 and N-(4-Anilinoquinazolin-6-yl) Acrylamide

Autor: Luigi Capoferri, Silvia Rivara, Marco Mor, Alessio Lodola

Publikováno v: Journal of Chemical Information and Modeling. 55:589-599

Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer. They covalently bind a noncatalytic cysteine (Cys797) at the surfa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::85860e4254fbc9ebf105a07bbad87fc6
https://doi.org/10.1021/ci500720e

Improving the iterative linear interaction energy approach using automated recognition of configurational transitions

Autor: Luigi Capoferri, Daan P. Geerke, Derk P. Kooi, C. Ruben Vosmeer, Nico P. E. Vermeulen, Margreet M. Terpstra

Publikováno v: Journal of Molecular Modeling, 1:31. Springer Verlag
Vosmeer, C R, Kooi, D P, Capoferri, L, Terpstra, M M, Vermeulen, N P E & Geerke, D P 2016, ' Improving the iterative linear interaction energy approach using automated recognition of configurational transitions. ', Journal of Molecular Modeling, vol. 1, 31 . https://doi.org/10.1007/s00894-015-2883-y
Journal of Molecular Modeling

Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was sho

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3e76eb8c0d075d8248f4ae8ef2b5b008
https://research.vu.nl/en/publications/68d814af-97bd-4c5b-9720-d68fca3e2c30