Dataset of drugs, their molecular scaffolds and medical indications with interactive visualization

Georgii Malakhov; Pavel Pogodin

doi:10.1016/j.dib.2024.110417

Dataset of drugs, their molecular scaffolds and medical indications with interactive visualization

Data Brief. 2024 Apr 14:54:110417. doi: 10.1016/j.dib.2024.110417. eCollection 2024 Jun.

Authors

Georgii Malakhov^{1

2}, Pavel Pogodin¹

Affiliations

¹ Institute of Biomedical Chemistry, Pogodinskaya Street, 10, 119121, Moscow, Russia.
² Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 1-73, 119991, Moscow, Russia.

Abstract

Bemis-Murcko scaffolding [1] is a powerful tool for compound clustering and subsequent analysis. Here, using ChEMBL database [2] and RDKit library [3], we have compiled the dataset of known small molecule drugs, their molecular scaffolds and associated medical indications augmented with the interactive interface. We present these data, which can be used by medicinal chemists to find most promising scaffolds for their tasks using an interactive visualization that can help to evaluate both the diversity of known drugs and pharmacological promiscuity of each particular scaffold visually. Our scripts, that are freely available, can help to carry out such scaffold-based analysis and to visualize a compound library in a similar way.

Keywords: Bemis-Murcko scaffolds; Computational medicinal chemistry; Drug diversity; Interactive visualization; Pharmacological promiscuity.