The most common protein lost in urine (proteinuria) is albumin, which is a symptom of the kidney illness focal segmental glomerulosclerosis (FSGS). It causes damage to podocyte foot processes, resulting in effacement of foot processes, and injury to foot processes leads to the leaking of plasma proteins into the urine, resulting in nephrotic syndrome. Alpha actinin (ACTN4) is extensively produced in glomerular podocytes, has a function in non-muscle cytoskeletal activity, and is enhanced early in the course of nephrotic illness in various types. Mutations in ACTN4 induce autosomal and sporadic steroid-resistance nephritic syndrome, which causes disturbance in podocyte foot process and function. All of the FSGS-causing mutations are situated on actin actin-binding domain of the ACTN4 protein. FSGS is typically treated by decreasing dietary salt and using immune-suppressing medications such as glucocorticoids. There is a risk associated with these drugs for cancer patients. Several studies have found that up to 80% of individuals with primary FSGS are resistant to steroid therapy, even though all other therapeutic options have been exhausted. Patients with steroid-resistant FSGS have a higher incidence of end-stage renal failure. Therefore, several new treatment strategies were put forward to cure the disease form of which use of phytochemicals is one such sustainable modality. In addition to this, our study intended to predict the stability of mutant protein’s structure as compared to wild type structure through molecular dynamic simulation analysis. With this, we extend our study to predict the potency of phytochemicals of Boerhaviadiffusa against FSGS by using molecular docking analysis. From our study, we conclude that the actin-binding domain of ACTN4 protein becomes more unstable or loses its stability after the mutation at position W59R among all the studied mutation positions. The boeravinone F phytochemical of the Boerhaviadiffusa plant shows the best inhibitory effect on the mutant actin-binding domain of ACTN4 protein and it confirms a stable binding confirmation at minimum energy of -7.5 kcal/mol. Hence it may be taken into consideration for future research work.