Learning Subpocket Prototypes for Generalizable Structure-based Drug Design

Zaixi Zhang, Qi Liu
Proceedings of the 40th International Conference on Machine Learning, PMLR 202:41382-41398, 2023.

Abstract

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model’s performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

Cite this Paper

BibTeX
@InProceedings{pmlr-v202-zhang23z, title = {Learning Subpocket Prototypes for Generalizable Structure-based Drug Design}, author = {Zhang, Zaixi and Liu, Qi}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, pages = {41382--41398}, year = {2023}, editor = {Krause, Andreas and Brunskill, Emma and Cho, Kyunghyun and Engelhardt, Barbara and Sabato, Sivan and Scarlett, Jonathan}, volume = {202}, series = {Proceedings of Machine Learning Research}, month = {23--29 Jul}, publisher = {PMLR}, pdf = {https://proceedings.mlr.press/v202/zhang23z/zhang23z.pdf}, url = {https://proceedings.mlr.press/v202/zhang23z.html}, abstract = {Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model’s performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.} }
Endnote
%0 Conference Paper %T Learning Subpocket Prototypes for Generalizable Structure-based Drug Design %A Zaixi Zhang %A Qi Liu %B Proceedings of the 40th International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2023 %E Andreas Krause %E Emma Brunskill %E Kyunghyun Cho %E Barbara Engelhardt %E Sivan Sabato %E Jonathan Scarlett %F pmlr-v202-zhang23z %I PMLR %P 41382--41398 %U https://proceedings.mlr.press/v202/zhang23z.html %V 202 %X Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model’s performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.
APA
Zhang, Z. & Liu, Q.. (2023). Learning Subpocket Prototypes for Generalizable Structure-based Drug Design. Proceedings of the 40th International Conference on Machine Learning, in Proceedings of Machine Learning Research 202:41382-41398 Available from https://proceedings.mlr.press/v202/zhang23z.html.

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