Between Descriptors and Properties: Understanding the Ligand Efficiency Trends for G Protein-Coupled Receptor and Kinase Structure-Activity Data Sets

Journal of Chemical Information and Modeling

Volumn 57, Issue 6, 2017, Pages 1321-1329

  Polanski, Jaroslaw ^a   Tkocz, Aleksandra ^a  

^a UNIVERSITY OF SILESIA   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; EFFICIENCY; ENZYMES; MOLECULES;

BINDING PROPERTIES; G-PROTEIN COUPLED RECEPTORS; HYPERBOLIC MODELS; MATHEMATICAL VALIDITY; MOLECULAR DESCRIPTORS; SINGLE MOLECULE; STATISTICAL PROPERTIES; STRUCTURE ACTIVITY;

LIGANDS;

G PROTEIN COUPLED RECEPTOR; LIGAND; PROTEIN KINASE;

BIOLOGY; IC50; METABOLISM; PROTEIN DATABASE; STRUCTURE ACTIVITY RELATION;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; INHIBITORY CONCENTRATION 50; LIGANDS; PROTEIN KINASES; RECEPTORS, G-PROTEIN-COUPLED; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 85021290874     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.7b00116     Document Type: Article

References (14)

1. Hopkins, A. L.; Keseru, G. M.; Leeson, P. D.; Rees, D. C.; Reynolds, C. H. The Role of Ligand Efficiency Metrics in Drug Discovery Nat. Rev. Drug Discovery 2014, 13, 105-121 10.1038/nrd4163
2. Cortes-Ciriano, I. Benchmarking the Predictive Power of Ligand Efficiency Indices in QSAR J. Chem. Inf. Model. 2016, 56, 1576-1587 10.1021/acs.jcim.6b00136
3. Sugaya, N. Training Based on Ligand Efficiency Improves Prediction of Bioactivities of Ligands and Drug Target Proteins J. Chem. Inf. Model. 2013, 53, 2525-2537 10.1021/ci400240u
4. 50 as QSAR Activities J. Chem. Inf. Model. 2016, 56, 2253-2262 10.1021/acs.jcim.6b00431
5. Kenny, P. W.; Leitao, A.; Montanari, C. A. Ligand Efficiency Metrics Considered Harmful J. Comput.-Aided Mol. Des. 2014, 28, 699-710 10.1007/s10822-014-9757-8
6. Zhou, H. X.; Gilson, M. K. Theory of Free Energy and Entropy in Noncovalent Binding Chem. Rev. 2009, 109, 4092-4107 10.1021/cr800551w
7. Matta, C. F.; Massa, L.; Gubskaya, A. V.; Knoll, E. Can One Take the Logarithm or the Sine of a Dimensioned Quantity or a Unit? Dimensional Analysis Involving Transcendental Functions J. Chem. Educ. 2011, 88, 67-70 10.1021/ed1000476
8. Shultz, M. D. Improving the Plausibility of Success with Inefficient Metrics ACS Med. Chem. Lett. 2014, 5, 2-5 10.1021/ml4004638
9. Murray, C. W.; Erlanson, D. A.; Hopkins, A. L.; Keseru, G. M.; Leeson, P. D.; Rees, D. C.; Reynolds, C. H.; Richmond, N. J. Validity of Ligand Efficiency Metrics ACS Med. Chem. Lett. 2014, 5, 616-618 10.1021/ml500146d
10. Hann, M. M. Molecular Obesity, Potency and Other Addictions in Drug Discovery MedChemComm 2011, 2, 349-355 10.1039/c1md00017a
11. Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. The Maximal Affinity of Ligands Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 9997-10002 10.1073/pnas.96.18.9997
12. Polanski, J.; Gasteiger, J. In Handbook of Computational Chemistry; Leszczynski, J.; Puzyn, T., Eds.; Springer: Dordrecht, The Netherlands, 2016.
13. Abad-Zapatero, C.; Metz, J. T. Ligand Efficiency Indices as Guideposts for Drug Discovery Drug Discovery Today 2005, 10, 464-469 10.1016/S1359-6446(05)03386-6
14. Aldrich, C.; Bertozzi, C.; Georg, G. I.; Kiessling, L.; Lindsley, C.; Liotta, D.; Merz, K. M.; Schepartz, A.; Wang, S. The Ecstasy and Agony of Assay Interference Compounds ACS Cent. Sci. 2017, 3, 143-147 10.1021/acscentsci.7b00069