Flux pinning mechanism in melanin doped MgB2 superconductor has been studied using a scaling law proposed by Dew-Hughes and another method proposed by Eisterer. Our experimental data could be fitted very closely by the aforementioned scaling law. The fitting parameters, the positions of peaks bpeak and k = bpeak/bn confirm a grain-boundary pinning in the 10% melanin doped sample, while the undoped sample consists of mixed pinning. Furthermore, percolation theory was utilized under grain-boundary approximation to investigate the role of Hc2-anisotropy in the critical current density, and its dependence on applied field as well as temperature. The Hc2-anisotropy decreases with melanin doping resulting in the increase of Jc in high field. There is suppression of flux pinning maximum due to melanin doping, which is found to be the main reason for the degradation of low-field Jc.