Theoretical Model of EphA2-Ephrin A1 Inhibition

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Wiktoria JedwabnyEdyta Dyguda-Kazimierowicz

Abstract

This work aims at the theoretical description of EphA2-ephrin A1 inhibition by small molecules. Recently proposed ab initio-based scoring models, comprising long-range components of interaction energy, is tested on lithocholic acid class inhibitors of this protein⁻protein interaction (PPI) against common empirical descriptors. We show that, although limited to compounds with similar solvation energy, the ab initio model is able to rank the set of selected inhibitors more effectively than empirical scoring functions, aiding the design of novel compounds.

References

Sep 15, 1973·Journal of Molecular Biology·A Shrake, J A Rupley
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
Jul 7, 1995·Journal of Medicinal Chemistry·A R OrtizR C Wade
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Apr 4, 1997·Journal of Molecular Biology·G JonesR Taylor
Dec 21, 2002·International Journal of Cancer. Journal International Du Cancer·Tatsuya MiyazakiHiroyuki Kuwano
Mar 19, 2004·Journal of Medicinal Chemistry·Richard A FriesnerPeter S Shenkin
Apr 27, 2004·Nature Neuroscience·Juha-Pekka HimanenDimitar B Nikolov
Feb 11, 2005·Journal of the American Chemical Society·Edyta DygudaJerzy Leszczyński
Feb 26, 2005·Journal of Computer-aided Molecular Design·Arthur M Doweyko
Mar 23, 2005·Journal of Molecular Graphics & Modelling·André KrammerMarvin Waldman
Aug 12, 2005·Chemical Reviews·Jacopo TomasiRoberto Cammi
Oct 8, 2005·Journal of Computational Chemistry·Jay L BanksRonald M Levy
Jul 21, 2006·The Journal of Physical Chemistry. B·Robert W GoraVirginia B Pett
Sep 29, 2006·Journal of Medicinal Chemistry·Andrew R LeachCatherine E Peishoff
Sep 29, 2006·Journal of Medicinal Chemistry·Ingo Muegge
Dec 14, 2007·Nature·James A Wells, Christopher L McClendon
Aug 30, 2008·The Journal of Biological Chemistry·Roberta NoberiniElena B Pasquale
Jan 8, 2009·Journal of Chemical Information and Modeling·Oliver KorbThomas E Exner
May 19, 2009·Journal of Chemical Information and Modeling·Pablo Englebienne, Nicolas Moitessier
Apr 7, 2010·Physical Review Letters·Katarzyna PernalKrzysztof Szalewicz
Apr 20, 2010·Journal of Computer-aided Molecular Design·Daniel Seeliger, Bert L de Groot
Apr 12, 2011·PloS One·Carmine GiorgioMassimiliano Tognolini
Feb 10, 2012·Current Pharmaceutical Design·Rachelle J Bienstock
Nov 14, 2012·Journal of Chemical Information and Modeling·K VanommeslaegheA D MacKerell
Nov 14, 2012·Journal of Chemical Information and Modeling·K Vanommeslaeghe, A D MacKerell
Feb 12, 2013·Biochimica Et Biophysica Acta·Jessica E LisleSally-Anne Stephenson
Mar 16, 2013·Journal of Medicinal Chemistry·Matteo IncertiAlessio Lodola
May 1, 2013·Biochimica Et Biophysica Acta·Dimitar B NikolovJuha P Himanen
Oct 25, 2013·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Simonetta RussoAlessio Lodola

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Citations

Jan 20, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Rebecca C Wade, Outi M H Salo-Ahen
Jan 8, 2019·Journal of Molecular Modeling·Wiktoria Jedwabny, Edyta Dyguda-Kazimierowicz
Feb 24, 2021·The Journal of Physical Chemistry. a·Wiktoria JedwabnyKonrad Patkowski

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BETA
surface plasmon resonance

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HVPT
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