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Abstract Oxidative stress–induced dopaminergic neurodegeneration plays a crucial role in the pathogenesis of Parkinson’s disease. Natural antioxidants such as Vitamin E and Rutin have exhibited promising neuroprotective potential. The present study aimed to evaluate the protective effects of Vitamin E and Rutin, individually and in combination, against Paraquat-induced neurotoxicity using in silico and in vivo approaches. The results show that Rutin has a higher binding affinity (− 9.3 kcal/mol) than Vitamin E (− 7.3 kcal/mol) and the standard drug Levodopa (− 7.6 kcal/mol) in molecular docking studies (PyRx) against MAO-B (PDB ID: 2V5Z). In vivo, the combination-treated group (Group VI: Vitamin E 60 mg/kg + Rutin 10 mg/kg, p.o.) showed highly considerable improvements (***p
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