2011
DOI: 10.1021/ci2004779
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Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery

Abstract: As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster,… Show more

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Cited by 48 publications
(70 citation statements)
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References 57 publications
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“…[28,29] From the visual analysis of the predicted TS for A370I (Figure 3), aw eak interaction between the newly introduced Ile370 and the bicyclic moiety of the ligand seems to be taking place, causing the latter to assumeamore vertical positioni n the active site, in agreement with our initial model (Figure 1). In practice, the desired substrate was docked by forcingo xidation at the desired sites of reaction.…”
supporting
confidence: 81%
“…[28,29] From the visual analysis of the predicted TS for A370I (Figure 3), aw eak interaction between the newly introduced Ile370 and the bicyclic moiety of the ligand seems to be taking place, causing the latter to assumeamore vertical positioni n the active site, in agreement with our initial model (Figure 1). In practice, the desired substrate was docked by forcingo xidation at the desired sites of reaction.…”
supporting
confidence: 81%
“…All DFT computations were performed with Jaguar 7.0 (Schrodinger LLC). An in-house drug discovery program suite forecaster [53] including prepare, process, smart and fitted was used to prepare structures and carry out the docking experiments. In order to probe the entire structure for potential binding locations, the complete G-quadruplex structure was set as the "binding site".…”
Section: Methodsmentioning
confidence: 99%
“…Following on the earlier work of Verdonk et al, where the reasons of docking failures were compared for fragments and small molecules, [105] Vass et al used Glide to further investigate factors affecting success rates for the placement of linked fragments in sequential fragment docking. [82,110] Using 129 protein-ligand complexes, they tested three sampling protocols [124] AMMOS www.mti.univ-paris-diderot.fr/en/downloads.html [216] AutoMap ligmap.sourceforge.net [142] Cell-Dock mmb.pcb.ub.es/~cpons/Cell-Dock [217] CovalentDock code.google.com/p/covalentdock [102] CRDOCK ub.cbm.uam.es [101] cudock code.google.com/p/cudock [218] DecoyFinder URVnutrigenomica-CTNS.github.com/DecoyFinder [219] DockoMatic sourceforge.net/projects/dockomatic [103] Dolina by request [13] eSimDock www.brylinski.org/esimdock [64] GalaxyDock galaxy.seoklab.org/softwares/galaxydock.html [4,5] FIPSDock by request [104] Fleksy www.cmbi.ru.nl/software/fleksy [21] MMPBSA.py ambermd.org [220] RDKit www.rdkit.org [221] RosettaLigand www.rosettacommons.org/software/ [7,144] S4MPLE infochim.u-strasbg.fr [50] VinaMPI cmb.ornl.gov/~sek/ [222] WaterDock sbcb.bioch.ox.ac.uk/waterdock [81] Servers, platforms, and web interfaces BSP-SLIM zhanglab.ccmb.med.umich.edu/BSP-SLIM [212] ChemBioServer bioserver-3.bioacademy.gr/Bioserver/ChemBioServer [223] CovalentDock Cloud docking.sce.ntu.edu.sg [224] FORECASTER fitted.ca [175] FTMap ftmap.bu.edu [225,226] FTSite ftsite.bu.edu [227] idTarget idtarget.rcas.sinica.edu.tw [228] pyDockWEB life.bsc.es/servlet/pydock [229] Robetta robe...…”
Section: Fragment Dockingmentioning
confidence: 99%