A series of nitro-based compounds were synthesized and evaluated as inhibitors against thermolysin (TLN). The binding modes of the nitro group at the active site of TLN were characterized based on the structural analysis of TLN-(R)-2-benzyl-3-nitropropionic amide complex, which was suggested as a pseudo-transition state analogue. Further structure–activity relationship studies disclosed that both the stereochemistry of the P1 chains and the bulkiness of the P2′ substituents were crucial to the potent inhibition of TLN.
