We have explored two distinct chemistries that target the TMPRSS2 active site and identified a novel scaffold that noncovalently engages the protease within the S1 region. We have built a set of kinetic and biophysical assays that allow compounds of distinct mechanisms to be accurately compared. Furthermore, we have identified a highly crystallizable form of TMPRSS2 that provides high resolution co-crystal structures. The noncovalent scaffold (and potentially the ester-based scaffold) may be amenable to structure-guided medicinal chemistry campaigns that further improve TMPRSS2 binding potency and selectivity, paving the way for new antiviral therapeutics.