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Identification of ALK5 inhibitor via structure-based virtual screening and ADMET prediction
Aibin Lin1, Zhongqi Cai1, Guoping Hu2
1a Zhejiang Pharmaceutical College , Ningbo , China and.
Abstract:
TGF-β plays a critical role in the initiation and progression of fibrosis in various organ systems such as kidney, heart, lung and liver. TGF-β and its receptors (ALK5 and TβR II) are able to control the cellular growth and promote several biological responses. To date, many pharmaceutical companies have employed virtual screening to identify potent inhibitors against ALK5. Nevertheless, none of these studies had involved the in silico ADMET evaluation and Raccoon filtering. In our experiment, all 57423 molecules were downloaded from TCM database and were filtered and converted to PDBQT formats by Raccoon software. Then 24 189 structures were run through AutoDock Vina in PyRx 0.8, 164 molecules were selected and further evaluated by ADMET Predictor 6.5, and 56 structures were selected and docked by Glide 6.2. Finally, the top 10 hits were identified as promising oral ALK5 inhibitors according to their Glide scores. The Glide scores of the best two compounds, 40686 and 33534, were -10.75 and -10.30 kcal/mol, respectively. This research provides a set of combined and detailed virtual screening protocol and is helpful for explaining the mechanism of receptor-ligand interactions.
Insights
This study identifies promising oral inhibitors for ALK5, a key target in fibrosis, using a novel virtual screening protocol that includes ADMET evaluation and Raccoon filtering. The top compounds show significant potential for therapeutic development.
Area of Science:
- Biochemistry
- Pharmacology
- Computational Chemistry
Background:
- Transforming growth factor-beta (TGF-β) is crucial in initiating and progressing fibrosis across organs like the kidney, heart, lung, and liver.
- TGF-β signaling, involving receptors ALK5 and TβR II, regulates cellular growth and biological responses, making ALK5 a significant drug target.
Purpose of the Study:
- To identify potent oral inhibitors of ALK5 using an integrated virtual screening approach.
- To establish a detailed virtual screening protocol incorporating in silico ADMET evaluation and Raccoon filtering.
Main Methods:
- Utilized Raccoon software for filtering and converting 57,423 molecules from the TCM database to PDBQT format.
- Employed AutoDock Vina (PyRx 0.8) for initial docking, followed by ADMET Predictor 6.5 evaluation and Glide 6.2 docking for refined selection.
- Applied a multi-step virtual screening workflow including molecular docking and ADMET prediction.
Main Results:
- Selected 164 molecules after initial docking, refined to 56 after ADMET evaluation.
- Identified the top 10 potential oral ALK5 inhibitors based on Glide scores.
- Compounds 40686 and 33534 exhibited the highest Glide scores (-10.75 and -10.30 kcal/mol, respectively).
Conclusions:
- The developed virtual screening protocol effectively identifies promising ALK5 inhibitors.
- The identified compounds represent potential therapeutic candidates for treating fibrotic diseases.
- This research aids in understanding receptor-ligand interactions for drug discovery.
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