bbSelect : an open-source tool for performing a 3D pharmacophore-driven diverse selection of R-groups

Rianjongdee, Francesco and Palmer, David and Pickett, Stephen D. and Pogány, Peter and Tomkinson, Nicholas C.O. and Green, Darren V.S. (2024) bbSelect : an open-source tool for performing a 3D pharmacophore-driven diverse selection of R-groups. Journal of Chemical Information and Modeling, 64 (12). pp. 4687-4699. ISSN 1549-9596 (https://doi.org/10.1021/acs.jcim.4c00453)

[thumbnail of Rianjongdee-etal-JCIM-2024-bbSelect-an-open-source-tool-for-performing-a-3D-pharmacophore-driven-diverse-selection-of-R-groups]
Preview
 Text. Filename: Rianjongdee-etal-JCIM-2024-bbSelect-an-open-source-tool-for-performing-a-3D-pharmacophore-driven-diverse-selection-of-R-groups.pdf
Accepted Author Manuscript
License: Creative Commons Attribution 4.0 logo
Download (2MB)| Preview

Abstract

The design of compounds during hit-to-lead often seeks to explore a vector from a core scaffold to form additional interactions with the target protein. A rational approach to this is to probe the region of a protein accessed by a vector with a systematic placement of pharmacophore features in 3D, particularly when bound structures are not available. Herein, we present bbSelect, an open-source tool built to map the placements of pharmacophore features in 3D Euclidean space from a library of R-groups, employing partitioning to drive a diverse and systematic selection to a user-defined size. An evaluation of bbSelect against established methods exemplified the superiority of bbSelect in its ability to perform diverse selections, achieving high levels of pharmacophore feature placement coverage with selection sizes of a fraction of the total set and without the introduction of excess complexity. bbSelect also reports visualizations and rationale to enable users to understand and interrogate results. This provides a tool for the drug discovery community to guide their hit-to-lead activities.

ORCID iDs

Rianjongdee, Francesco, Palmer, David ORCID logoORCID: https://orcid.org/0000-0003-4356-9144, Pickett, Stephen D., Pogány, Peter, Tomkinson, Nicholas C.O. ORCID logoORCID: https://orcid.org/0000-0002-5509-0133 and Green, Darren V.S.;

Persistent Identifier

https://doi.org/10.17868/strath.00089522
CORE (COnnecting REpositories)