1-trans-Epoxysuccinyl-L-leucylamido(4-guanidino)butane (E-64) was shown to inhibit β-trypsin by a reversible competitive mechanism; this contrasts with the widely held view that E-64 is a class-specific inhibitor of the cysteine proteinases and reports in the literature that it does not inhibit a number of other enzymes including, notably, trypsin. The Ki value (3×10-5 M) determined by kinetic analysis of the hydrolysis of Nα-benzoyl-L-arginine 4-nitroanilide in Tris/HCl buffer, pH 7.4, at 25 °C, I = 0.1, catalysed by β-trypsin is comparable with those for the inhibition of trypsin by benzamidine and 4-aminobenzamidine, which are widely regarded as the most effective low Mr inhibitors of this enzyme. Computer modelling of the β-trypsin–E-64 adsorptive complex, by energy minimization, molecular dynamics simulation and Poisson–Boltzmann electrostatic-potential calculations, was used to define the probable binding mode of E-64; the ligand lies parallel to the active-centre cleft, anchored principally by the dominant electrostatic interaction of the guanidinium cation at one end of the E-64 molecule with the carboxylate anion of Asp-171 (β-trypsin numbering from Ile-1) in the S1-subsite, and by the interaction of the carboxylate substituent on C-2 of the epoxide ring at the other end of the molecule with Lys-43; the epoxide ring of E-64 is remote from the catalytic site serine hydroxy group. The possibility that E-64 might bind to the cysteine proteinases clostripain (from Clostridium histolyticum) and α-gingivain (one of the extracellular enzymes from Porphyromonas gingivalis) in a manner analogous to that deduced for the β-trypsin–E-64 complex is discussed.

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