CLigOpt: controllable ligand design through target-specific optimization

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CLigOpt: controllable ligand design through target-specific optimization
Title:
CLigOpt: controllable ligand design through target-specific optimization
Journal Title:
Bioinformatics
Keywords:
Publication Date:
02 September 2024
Citation:
Li, Y., Avelar, P. H. da C., Chen, X., Zhang, L., Wu, M., & Tsoka, S. (2024). CLigOpt: controllable ligand design through target-specific optimization. Bioinformatics, 40(Supplement_2), ii62–ii69. https://doi.org/10.1093/bioinformatics/btae396
Abstract:
Abstract Motivation A key challenge in deep generative models for molecular design is to navigate random sampling of the vast molecular space, and produce promising molecules that strike a balance across multiple chemical criteria. Fragment-based drug design (FBDD), using fragments as starting points, is an effective way to constrain chemical space and improve generation of biologically active molecules. Furthermore, optimization approaches are often implemented with generative models to search through chemical space, and identify promising samples which satisfy specific properties. Controllable FBDD has promising potential in efficient target-specific ligand design. Results We propose a controllable FBDD model, CLigOpt, which can generate molecules with desired properties from a given fragment pair. CLigOpt is a variational autoencoder-based model which utilizes co-embeddings of node and edge features to fully mine information from molecular graphs, as well as a multi-objective Controllable Generation Module to generate molecules under property controls. CLigOpt achieves consistently strong performance in generating structurally and chemically valid molecules, as evaluated across six metrics. Applicability is illustrated through ligand candidates for hDHFR and it is shown that the proportion of feasible active molecules from the generated set is increased by 10%. Molecular docking and synthesizability prediction tasks are conducted to prioritize generated molecules to derive potential lead compounds. Availability and implementation The source code is available via  https://github.com/yutongLi1997/CLigOpt-Controllable-Ligand-Design-through-Target-Specific-Optimisation.
License type:
Attribution 4.0 International (CC BY 4.0)
Funding Info:
This research / project is supported by the A*STAR - Decentralised Gap funding
Grant Reference no. : I23D1AG081
Description:
This article has been accepted for publication in [Bioinformatics] Published by Oxford University Press.
ISSN:
1367-4803
1367-4811