Abstract Background β-glucuronidase enzyme is mostly found in plants and animals. It plays a vital role in detoxification of reactive metabolites that are interrelated to several illnesses and the growth of colon cancer. It speeds up the breaking down of β-glucuronosyl-O-bonds. Lack of β-glucuronidase enzyme leads to Sly syndrome in humans, and overexpression of this enzyme leads to many diseases. Therefore, it becomes necessary to mediate the effect of this enzyme.Result Theoretical investigation via QSAR modeling on 30 indole derivatives was performed to build a model which could be used to predict the activity of the indole derivatives. QSAR was carried out using multi-linear regression (MLR) method utilizing genetic function approximation (GFA) to develop the QSAR models. A very high predictive QSAR model was reported based on its statistical fitness with good internal and external validation parameters: R2trng = 0.954942, Qcv2 = 0.925462, R2test = 0.855393, and LOF = 0.042924. Molecular docking on the 30 indole derivatives was also performed to screen and identify the lead compound that would be used as template for designing new indole compounds. The docking investigation reveals that ligand 10 binds very tight in the binding pocket of β-glucuronidase enzyme with binding energy of − 9.5 kcal/mol. The ligand (10) was chosen as a template for designing new β-glucuronidase inhibitors. The four design compounds were found to be better than the template and the standard drug (D-saccharic acid 1, 4-lactone) with binding energies of − 9.6, − 9.7, − 9.8, and − 9.9 kcal/mol.Conclusion A very high predictive QSAR model with good internal and external validation parameters: R2trng = 0.954942, Qcv2 = 0.925462, R2test = 0.855393, and LOF = 0.042924, was built and reported in this study. Molecular docking investigation reveals that the most potent compound among all the data set was compound 10 with binding energy of − 9.5 kcal/mole. It bound to the binding pocket of β-glucuronidase enzyme via hydrophobic, electrostatic, and hydrogen bond, and it was retained as template for designing new indole compounds. The design compound with serial number ID 4 was identified to have the highest binding energy of − 9.9 kcal/mole among the designed compounds. It bound to the binding site of the β-glucuronidase enzyme via halogen, hydrophobic, electrostatic, and hydrogen bond. The design compounds were discovered to be better than the template used in the design and the standard drug.
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