Benchmark set for relative free energy calculations

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