Consensus Models of Activity Landscapes with Multiple Chemical, Conformer, and Property Representations

Authors

Austin B. Yongye, Torrey Pines Institute for Molecular Studies
Kendall Byler, Torrey Pines Institute for Molecular Studies
Radleigh Santos, Torrey Pines Institute for Molecular StudiesFollow
Karina Martinez-Mayorga, Torrey Pines Institute for Molecular Studies
Gerald M. Maggiora, University of Arizona; United States and Translational Genomics Research Institute
Jose L. Medina-Franco, Torrey Pines Institute for Molecular Studies

Document Type

Article

Publication Date

5-24-2011

Publication Title

Journal of Chemical Information and Modeling

ISSN

1549-9596

Volume

51

Issue/No.

6

First Page

1259

Last Page

1270

Abstract

We report consensus Structure–Activity Similarity (SAS) maps that address the dependence of activity landscapes on molecular representation. As a case study, we characterized the activity landscape of 54 compounds with activities against human cathepsin B (hCatB), human cathepsin L (hCatL), and Trypanosoma brucei cathepsin B (TbCatB). Starting from an initial set of 28 descriptors we selected ten representations that capture different aspects of the chemical structures. These included four 2D (MACCS keys, GpiDAPH3, pairwise, and radial fingerprints) and six 3D (4p and piDAPH4 fingerprints with each including three conformers) representations. Multiple conformers are used for the first time in consensus activity landscape modeling. The results emphasize the feasibility of identifying consensus data points that are consistently formed in different reference spaces generated with several fingerprint models, including multiple 3D conformers. Consensus data points are not meant to eliminate data, disregarding, for example, “true” activity cliffs that are not identified by some molecular representations. Instead, consensus models are designed to prioritize the SAR analysis of activity cliffs and other consistent regions in the activity landscape that are captured by several molecular representations. Systematic description of the SARs of two targets give rise to the identification of pairs of compounds located in the same region of the activity landscape of hCatL and TbCatB suggesting similar mechanisms of action for the pairs involved. We also explored the relationship between property similarity and activity similarity and found that property similarities are suitable to characterize SARs. We also introduce the concept of structure–property-activity (SPA) similarity in SAR studies.

Comments

Copyright © 2011 American Chemical Society

NSUWorks Citation

Yongye, Austin B.; Byler, Kendall; Santos, Radleigh; Martinez-Mayorga, Karina; Maggiora, Gerald M.; and Medina-Franco, Jose L., "Consensus Models of Activity Landscapes with Multiple Chemical, Conformer, and Property Representations" (2011). Mathematics Faculty Articles. 220.
https://nsuworks.nova.edu/math_facarticles/220

DOI

10.1021/ci200081k