10.5281/zenodo.3459811
https://zenodo.org/records/3459811
oai:zenodo.org:3459811
Schindler, Christina
Christina
Schindler
Merck KGaA, Darmstadt, Germany
Kuhn, Daniel
Daniel
Kuhn
Merck KGaA, Darmstadt, Germany
Benchmark set for relative free energy calculations
Zenodo
2019
free energy calculations
drug discovery
binding affinity prediction
benchmark
2019-08-05
eng
10.5281/zenodo.3360435
2.0
MIT License
Created by Christina Schindler and Daniel Kuhn, Merck KGaA, Darmstadt, Germany.
December 2018
Manuscript in preparation.
Previously presented at Alchemical Free Energy Workshop 2019 in Goettingen, Germany.
DOI: 10.5281/zenodo.3258925
References for datasets used in benchmark
CDK8
Schiemann, Kai, et al. "Discovery of potent and selective CDK8 inhibitors from an HSP90 pharmacophore." Bioorganic & medicinal chemistry letters 26.5 (2016): 1443-1451.
DOI: 10.1016/j.bmcl.2016.01.062
c-Met
Dorsch, Dieter, et al. "Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors." Bioorganic & medicinal chemistry letters 25.7 (2015): 1597-1602.
DOI: 10.1016/j.bmcl.2015.02.002
Eg5
Schiemann, Kai, et al. "The discovery and optimization of hexahydro-2H-pyrano [3, 2-c] quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5." Bioorganic & medicinal chemistry letters 20.5 (2010): 1491-1495.
DOI: 10.1016/j.bmcl.2010.01.110
Hif2a
Wallace, Eli M., et al. "A small-molecule antagonist of HIF2α is efficacious in preclinical models of renal cell carcinoma." Cancer research 76.18 (2016): 5491-5500.
DOI: 10.1158/0008-5472.CAN-16-0473
Dixon, Darryl David, et al. "Aryl ethers and uses thereof." U.S. Patent No. 9,908,845. 6 Mar. 2018.
URL: Google Patents
PFKFB3
Boutard, Nicolas, et al. "Discovery and Structure–Activity Relationships of N-Aryl 6-Aminoquinoxalines as Potent PFKFB3 Kinase Inhibitors." ChemMedChem 14.1 (2019): 169-181.
DOI: 10.1002/cmdc.201800569
SHP2
Chen, Ying-Nan P., et al. "Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases." Nature 535.7610 (2016): 148.
DOI:10.1038/nature18621
Garcia Fortanet, Jorge, et al. "Allosteric inhibition of SHP2: identification of a potent, selective, and orally efficacious phosphatase inhibitor." Journal of medicinal chemistry 59.17 (2016): 7773-7782.
DOI: 10.1021/acs.jmedchem.6b00680
Chen, Christine Hiu-tung, et al. "1-pyridazin-/triazin-3-yl-piper (-azine)/idine/pyrolidine derivatives and compositions thereof for inhibiting the activity of shp2." U.S. Patent Application No. 15/110,498.
URL: Google Patents
SYK
Currie, Kevin S., et al. "Discovery of GS-9973, a selective and orally efficacious inhibitor of spleen tyrosine kinase." Journal of medicinal chemistry 57.9 (2014): 3856-3873.
DOI: 10.1021/jm500228a
TNKS2
Buchstaller, Hans-Peter, et al. "Discovery and Optimization of 2-Arylquinazolin-4-ones into a Potent and Selective Tankyrase Inhibitor Modulating Wnt Pathway Activity." Journal of medicinal chemistry 62.17 (2019): 7897-7909.
DOI: 10.1021/acs.jmedchem.9b00656