title: Activity cliffs and activity cliff generators based on chemotype-related activity landscapes.
abstract: Activity cliffs have large impact in drug discovery; therefore, their detection and quantification are of major importance. This work introduces the metric activity cliff enrichment factor and expands the previously reported activity cliff generator concept by adding chemotype information to representations of the activity landscape. To exemplify these concepts, three molecular databases with multiple biological activities were characterized. Compounds in each database were grouped into chemotype classes. Then, pairwise comparisons of structure similarities and activity differences were calculated for each compound and used to construct chemotype-based structure-activity similarity (SAS) maps. Different landscape distributions among four major regions of the SAS maps were observed for different subsets of molecules grouped in chemotypes. Based on this observation, the activity cliff enrichment factor was calculated to numerically detect chemotypes enriched in activity cliffs. Several chemotype classes were detected having major proportion of activity cliffs than the entire database. In addition, some chemotype classes comprising compounds with smooth structure activity relationships (SAR) were detected. Finally, the activity cliff generator concept was applied to compounds grouped in chemotypes to extract valuable SAR information.
authors.affiliation: División de Ciencias Biológicas y de la Salud, Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana Unidad Xochimilco (UAM-X), 04960, Mexico, DF, Mexico. jpvillanueva@correo.xoc.uam.mx.
authors.forename: Jaime
authors.identifier: http://orcid.org/0000-0001-5777-2536
authors.initials: J
authors.lastname: Pérez-Villanueva
authors.affiliation: Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, DF, Mexico.|Unilever Centre for Molecular Science Informatics Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
authors.forename: Oscar
authors.initials: O
authors.lastname: Méndez-Lucio
authors.affiliation: División de Ciencias Biológicas y de la Salud, Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana Unidad Xochimilco (UAM-X), 04960, Mexico, DF, Mexico.
authors.forename: Olivia
authors.initials: O
authors.lastname: Soria-Arteche
authors.affiliation: Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico, DF, Mexico.
authors.forename: José L
authors.initials: JL
authors.lastname: Medina-Franco
mesh_terms: D062126:Databases, Chemical; D015195:Drug Design; D008958:Models, Molecular; D015394:Molecular Structure; D013329:Structure-Activity Relationship
keywords: Activity cliff enrichment factor; Activity cliff generators; Chemotype; SAS maps; Structure–activity relationships