SynLethDB-Recon3D-A549
Description
The datasets associated with the article “Metabolic Synthetic Lethality–Guided Drug Repurposing for Non-Small Cell Lung Cancer: An Integrated Systems Biology and Molecular Modeling Study” are provided in three separate files, each corresponding to a distinct stage of the study.
Files
Steps to reproduce
The SL pairs were obtained in an Excel file from SynLethDB v3. By using MATLAB, the Recon3D metabolic genes and GPR rules were demonstrated. The final metabolic SL pairs resulted from the integration of these steps and were analyzed by their expression in one of the famous lung cancer cell lines (A-549). This filter reduced the SL pairs to 4 pairs and 6 unique genes. The approved drugs were obtained from the DrugBank database, and the VSW was done for all 6 enzymes in a structure-based drug discovery. From the XP results, three enzymes that make two SL pairs (FDPS-FH and FDPS-RRM1) had acceptable docking scores compared to the control drugs. Also, the MM-GBSA was checked for the top three candidate drugs from the XP results. The MD simulation and analysis of parameters such as RMSD, RMSF, and interaction fractions were done for the top 3 drug candidates of the final 3 enzymes. Finally, approved iohexol and iobitridol were obtained for hitting these two SL pairs.
Institutions
- Shiraz UniversityFars, Shiraz