The diversification of virus can be attributed to random mutations leading to the development of drug resistance. The variations can be inherited from one generation to the other rendering the drug ineffective. However, a pharmacologically induced selection pressure can be countered by introducing drugs better adapted to work under rapid mutations. In this study we try to explore the effect of site directed and random substitution mutations simulated in the ligand binding region of SARS-CoV2 protease. Amongst six currently studied anti-protease drugs for COVID-19, Indinavir and Hydroxychloroquine were chosen for the study based on their high binding affinity scores, -6.81, and -4.81 respectively. The effect of mutations in protein-ligand binding was analysed in two steps. Initially, analysis of over 90 homologous protease and 100 SARS-CoV-2 orf1ab regions revealed un-conserved residues in the ligand binding sites. Gly170 and Thr190 were identified and interchanged with polar residues such as ARG, ASN and non-polar residues such as ALA, ILE. The resulting mutants were modelled, minimized and docked with Indinavir and Hydroxychloroquine. A higher binding affinity was observed for Indinavir; however, less variance in the binding affinity was observed for the latter. These results were consistent for random mutations as well. A Bio.seqIO based pipeline was build to simulate changes in the ligand binding site. Under the assumption that the ligand binding region has an equal probability of mutation over a given range for continuous distribution, 200 cycles of mutation was carried out in the nucleotide region corresponding to the ligand binding site. A paired t-test revealed a significant difference between the binding affinity of these mutant Indinavir and Hydroxychloroquine-protease complexes. Further, mean and variance was found to be higher for Indinavir-protease complex but Hydroxychloroquine displayed lesser variance pointing at a constant binding capability towards the mutant. Our study highlights the role of Hydroxychloroquine as a drug that can complement an evolving SARS-CoV2 main protease.