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PLoS Comput Biol. 2017 Nov 10;13(11):e1005813. doi: 10.1371/journal.pcbi.1005813. eCollection 2017 Nov.

Are there physicochemical differences between allosteric and competitive ligands?

Author information

1
Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States of America.
2
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States of America.

Abstract

Previous studies have compared the physicochemical properties of allosteric compounds to non-allosteric compounds. Those studies have found that allosteric compounds tend to be smaller, more rigid, more hydrophobic, and more drug-like than non-allosteric compounds. However, previous studies have not properly corrected for the fact that some protein targets have much more data than other systems. This generates concern regarding the possible skew that can be introduced by the inherent bias in the available data. Hence, this study aims to determine how robust the previous findings are to the addition of newer data. This study utilizes the Allosteric Database (ASD v3.0) and ChEMBL v20 to systematically obtain large datasets of both allosteric and competitive ligands. This dataset contains 70,219 and 9,511 unique ligands for the allosteric and competitive sets, respectively. Physically relevant compound descriptors were computed to examine the differences in their chemical properties. Particular attention was given to removing redundancy in the data and normalizing across ligand diversity and varied protein targets. The resulting distributions only show that allosteric ligands tend to be more aromatic and rigid and do not confirm the increase in hydrophobicity or difference in drug-likeness. These results are robust across different normalization schemes.

PMID:
29125840
PMCID:
PMC5699844
DOI:
10.1371/journal.pcbi.1005813
[Indexed for MEDLINE]
Free PMC Article

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