Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks
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| Main Authors: | , , , , , , , , , , |
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| Format: | Preprint |
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2023
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| _version_ | 1866913858397929472 |
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| author | Ünlü, Atabey Çevrim, Elif Yiğit, Melih Gökay Sarıgün, Ahmet Çelikbilek, Hayriye Bayram, Osman Kahraman, Deniz Cansen Olğaç, Abdurrahman Rifaioğlu, Ahmet Sureyya Banoğlu, Erden Doğan, Tunca |
| author_facet | Ünlü, Atabey Çevrim, Elif Yiğit, Melih Gökay Sarıgün, Ahmet Çelikbilek, Hayriye Bayram, Osman Kahraman, Deniz Cansen Olğaç, Abdurrahman Rifaioğlu, Ahmet Sureyya Banoğlu, Erden Doğan, Tunca |
| contents | Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, offer a high potential for designing de novo molecules. However, to be utilisable in real life drug development pipelines, these models should be able to design drug like and target centric molecules. In this study, we propose an end to end generative system, DrugGEN, for the de novo design of drug candidate molecules that interact with intended target proteins. The proposed method represents molecules as graphs and processes them via a generative adversarial network comprising graph transformer layers. The system is trained using a large dataset of drug like compounds and target specific bioactive molecules to design effective inhibitory molecules against the AKT1 protein, which is critically important in developing treatments for various types of cancer. We conducted molecular docking and dynamics to assess the target centric generation performance of the model, as well as attention score visualisation to examine model interpretability. In parallel, selected compounds were chemically synthesised and evaluated in the context of in vitro enzymatic assays, which identified two bioactive molecules that inhibited AKT1 at low micromolar concentrations. These results indicate that DrugGEN's de novo molecules have a high potential for interacting with the AKT1 protein at the level of its native ligands. Using the open access DrugGEN codebase, it is possible to easily train models for other druggable proteins, given a dataset of experimentally known bioactive molecules. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2302_07868 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks Ünlü, Atabey Çevrim, Elif Yiğit, Melih Gökay Sarıgün, Ahmet Çelikbilek, Hayriye Bayram, Osman Kahraman, Deniz Cansen Olğaç, Abdurrahman Rifaioğlu, Ahmet Sureyya Banoğlu, Erden Doğan, Tunca Machine Learning Biomolecules Quantitative Methods Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, offer a high potential for designing de novo molecules. However, to be utilisable in real life drug development pipelines, these models should be able to design drug like and target centric molecules. In this study, we propose an end to end generative system, DrugGEN, for the de novo design of drug candidate molecules that interact with intended target proteins. The proposed method represents molecules as graphs and processes them via a generative adversarial network comprising graph transformer layers. The system is trained using a large dataset of drug like compounds and target specific bioactive molecules to design effective inhibitory molecules against the AKT1 protein, which is critically important in developing treatments for various types of cancer. We conducted molecular docking and dynamics to assess the target centric generation performance of the model, as well as attention score visualisation to examine model interpretability. In parallel, selected compounds were chemically synthesised and evaluated in the context of in vitro enzymatic assays, which identified two bioactive molecules that inhibited AKT1 at low micromolar concentrations. These results indicate that DrugGEN's de novo molecules have a high potential for interacting with the AKT1 protein at the level of its native ligands. Using the open access DrugGEN codebase, it is possible to easily train models for other druggable proteins, given a dataset of experimentally known bioactive molecules. |
| title | Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks |
| topic | Machine Learning Biomolecules Quantitative Methods |
| url | https://arxiv.org/abs/2302.07868 |