The MERS-CoV (Middle East respiratory syndrome coronavirus) is a zoonotic virus with a high mortality rate and a lack of antiviral drugs, underscoring the need for effective therapeutic methods. Viral entry depends on interactions between viral surface proteins and human receptors, with Dipeptidyl Peptidase-4 (DPP4), a transmembrane glycoprotein, acting as the receptor for MERS-CoV. We employed Molecular Dynamics (MD) Simulations to identify critical interface residues under a high-performance computing (HPC) workflow for accelerated results. Target residue pairs were identified through analysis of salt bridge and hydrogen bond occupancy. The stability of these residues was confirmed through three independent MD Simulations at human body temperature and constant pressure. Additionally, binding affinity predictions were calculated to determine the interaction strength between the virus and human receptors. Applying the scientific threshold criteria, we narrowed our results to seven key interaction pairs; two of the identified pairs (Asp510-Arg317, and Arg511-Asp393) are consistent with findings published in previous research studies, and five novel interactions are proposed for future experimental studies with our active collaborators in Pharmacology. The results provide a molecular basis for targeted mutation-based experiments and support the rational design of structure-based inhibitors aimed at disrupting the MERS-CoV-DPP4 complex, thereby facilitating the translation of computational findings into antiviral drug discovery.