In this work, we targeted the structure of TMPRSS2 for large-scale library docking of small molecules, seeking new starting points for lead discovery. We explored two distinct, structure-guided strategies to inhibit TMPRSS2 protease activity with covalent and noncovalent small molecule inhibitors (Fig. ). By docking a library of 200 million on-demand, lead-like molecules against both a homology model and the crystal structure of TMPRSS2, an ester-based covalent scaffold and a noncovalent amine scaffold were selected for further biochemical characterization. We identified a readily crystallizable form of TMPRSS2 leading to two novel cocrystal structures and leveraged a suite of biochemical and biophysical assays to validate these inhibitor molecules and understand their potency in terms of noncovalent binding and covalent reactivity. The tools established here will aid future SAR campaigns against TMPRSS2 and other human TTSPs implicated in respiratory virus infections.