Heat shock protein 90 (HSP90) is known as one of the most potential target in cancer therapy. In this context, we have demonstrated that marine fungi derivatives can play as possible inhibitors for preventing the biological activity of HSP90 using a combination of molecular docking and fast pulling of ligand (FPL) simulations. In particular, the computational approaches were validated since compared with the respective experiments. Based on a benchmark on available inhibitors of HsP90, GOLD docking package using ChemPLP scoring function was found to be dominated over both Autodock Vina and Autodock4 in preliminary estimation the ligand binding affinity and binding pose with the Pearson correlation, R=-0.62. Moreover, FPL calculations were also indicated to be a suitable approach to refine docking simulations with a correlation coefficient with the respective experimental data of R=-0.81. Therefore, the binding affinity of marine fungi derivatives to Hsp90 was evaluated. Docking and FPL calculations suggested that five compounds including 23, 40, 46, 48, and 52 are as highly potential inhibitors for HSP90. The obtained results probably enhance the cancer therapy.