Difference in the inhibitory mechanism against TMPRSS2 between camostat and nafamostat: implications for drug design

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), first identified in late 2019 as the causative agent of the COVID-19 pandemic, has triggered a global public health crisis. Transmembrane protease serine 2 (TMPRSS2) is one of the key host factors mediating SARS-CoV-2 infection and invasion. The inhibitors against TMPRSS2 emerge as a promising therapeutic strategy for COVID-19 and other potential viral infections. However, the precise mechanism of action for TMPRSS2 inhibitors remains unclear, with studies on structural optimization being notably scarce. In this work, multiple molecular simulation strategies were employed to systematically compare binding details and conformational changes of the representative inhibitors (i.e., camostat and nafamostat) with those of TMPRSS2 at the atomic level, thereby proposing potential inhibitory mechanisms underlying their activity differences. Compared with camostat, nafamostat is more likely to form a stable covalent enzyme-substrate intermediate. Next, a series of derivatives were designed with the same core structure (i.e., 4-guanidino benzoyl). And finally, the novel TMPRSS2 inhibitor with potentially better performance was identified based on the principle of the lowest binding free energy. This work not only elucidates the inhibitory mechanisms of camostat and nafamostat, showing valuable theoretical insights, but also proposes a viable strategy for future molecular design, thereby exhibiting promising application prospects.