AI Model for Predicting Binding Affinity of Antidiabetic Compounds Targeting PPAR
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866929651141574656 |
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| author | Aman, La Ode Asnawi, Aiyi |
| author_facet | Aman, La Ode Asnawi, Aiyi |
| contents | This study aims to develop a deep learning model for predicting the binding affinity of ligands targeting the Peroxisome Proliferator-Activated Receptor (PPAR) family, using 2D molecular descriptors. A dataset of 3,764 small molecules with known binding affinities, sourced from the ChEMBL database, was preprocessed by eliminating duplicates and incomplete data. Molecular docking simulations using AutoDock Vina were performed to predict binding affinities for the PPAR receptor family. 2D molecular descriptors were computed from the SMILES notation of each ligand, capturing essential structural and physicochemical features. These descriptors, along with the predicted binding affinities, were used to train a deep learning model to predict binding affinity as a regression task. The model was evaluated using metrics such as Mean Squared Error (MSE), Mean Absolute Error (MAE), and R-squared. Results indicated strong performance with an R squared value of 0.861 for the training set and 0.655 for the test set, suggesting good model generalization. The model shows promise for predicting ligand-receptor interactions and can be applied in drug discovery efforts targeting PPAR-related diseases. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2412_20011 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | AI Model for Predicting Binding Affinity of Antidiabetic Compounds Targeting PPAR Aman, La Ode Asnawi, Aiyi Biomolecules 68T01, 92E10, 68Q25, 68U99 I.2.7; I.5.2; I.6.8; D.2.8 This study aims to develop a deep learning model for predicting the binding affinity of ligands targeting the Peroxisome Proliferator-Activated Receptor (PPAR) family, using 2D molecular descriptors. A dataset of 3,764 small molecules with known binding affinities, sourced from the ChEMBL database, was preprocessed by eliminating duplicates and incomplete data. Molecular docking simulations using AutoDock Vina were performed to predict binding affinities for the PPAR receptor family. 2D molecular descriptors were computed from the SMILES notation of each ligand, capturing essential structural and physicochemical features. These descriptors, along with the predicted binding affinities, were used to train a deep learning model to predict binding affinity as a regression task. The model was evaluated using metrics such as Mean Squared Error (MSE), Mean Absolute Error (MAE), and R-squared. Results indicated strong performance with an R squared value of 0.861 for the training set and 0.655 for the test set, suggesting good model generalization. The model shows promise for predicting ligand-receptor interactions and can be applied in drug discovery efforts targeting PPAR-related diseases. |
| title | AI Model for Predicting Binding Affinity of Antidiabetic Compounds Targeting PPAR |
| topic | Biomolecules 68T01, 92E10, 68Q25, 68U99 I.2.7; I.5.2; I.6.8; D.2.8 |
| url | https://arxiv.org/abs/2412.20011 |