Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening

• Published in: Journal of cheminformatics 2019-11, Vol.11 (1), p.67-14, Article 67
• Main Authors: Lovrics, Anna, Pape, Veronika F. S., Szisz, Dániel, Kalászi, Adrián, Heffeter, Petra, Magyar, Csaba, Szakács, Gergely
• Format: Article
• Language: English
• Subjects: Analogies; Antineoplastic agents; Biological activity; Chemistry; Chemistry and Materials Science; Comparative analysis; Computational Biology/Bioinformatics; Computer Applications in Chemistry; Cytotoxicity; DNA topoisomerase (ATP-hydrolysing); Documentation and Information in Chemistry; Drug development; Drug screening; Mathematical analysis; Mitoxantrone; NCI60 cell panel; Organic chemistry; Research Article; Scaffold hopping; Scaffolds; Similarity; Theoretical and Computational Chemistry; Topoisomerase II poisons; Toxicity; Tumors; Virtual screening
• ISSN: 1758-2946; 1758-2946
• DOI: 10.1186/s13321-019-0390-3

Molecular descriptor (2D) and three dimensional (3D) shape based similarity methods are widely used in ligand based virtual drug design. In the present study pairwise structure comparisons among a set of 4858 DTP compounds tested in the NCI60 tumor cell line anticancer drug screen were computed using chemical hashed fingerprints and 3D molecule shapes to calculate 2D and 3D similarities, respectively. Additionally, pairwise biological activity similarities were calculated by correlating the 60 element vectors of pGI50 values corresponding to the cytotoxicity of the compounds across the NCI60 panel. Subsequently, we compared the power of 2D and 3D structural similarity metrics to predict the toxicity pattern of compounds. We found that while the positive predictive value and sensitivity of 3D and molecular descriptor based approaches to predict biological activity are similar, a subset of molecule pairs yielded contradictory results. By simultaneously requiring similarity of biological activities and 3D shapes, and dissimilarity of molecular descriptor based comparisons, we identify pairs of scaffold hopping candidates displaying characteristic core structural changes such as heteroatom/heterocycle change and ring closure. Attempts to discover scaffold hopping candidates of mitoxantrone recovered known Topoisomerase II (Top2) inhibitors, and also predicted new, previously unknown chemotypes possessing in vitro Top2 inhibitory activity.