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Amidst the unprecedented 2019 coronavirus outbreak and the substantial loss of lives due to the scarcity of information about the virus and lack of viable drugs, understanding the impact of the nCoV Main Protease (Mpro) on the endocrine system has emerged as a critical topic to pursue. This study explores the potential interactions between four key hormones (cortisol, cortisone, estradiol, and estrone) and the Mpro of nCoV using various in‐silico methodologies. Density Functional Theory (DFT) calculations scrutinized the electron density delocalization of these hormones. Through molecular docking, the molecular‐level binding of Mpro of nCoV with these hormones was studied, revealing cortisol as the hormone exhibiting the most promising binding affinity (−100.05 kcal/mol). Furthermore, molecular dynamics (MD) simulations, emulating human body conditions at distinct temperatures, were employed to study the implications of these interactions. The study analysed the various trajectories such as root mean square deviation (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg), and H‐bond trajectories to understand the potential impact on biological systems. The findings demonstrate the binding potential of the Mpro of nCoV with these hormones, raising plausible concerns regarding consequential physiological changes within the human body. [ABSTRACT FROM AUTHOR]