Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft.
The crystal structure of the inhibitor NS-134 in complex with bovine cathepsin B reveals that functional groups attached to both sides of the epoxysuccinyl reactive group bind to the part of active-site cleft as predicted. The -Leu-Pro-OH side binds to the primed binding sites interacting with the His110 and His111 residues with its C-terminal carboxy group, whereas the -Leu-Gly-Meu (-Leu-Gly-Gly-OMe) part (Meu, methoxycarbonylmethyl) binds along the non-primed binding sites. Comparison with the propeptide structures of cathepsins revealed that the binding of the latter part is least similar to the procathepsin B structure; this result, together with the two-residue shift in positioning of the Leu-Gly-Gly part, suggests that the propeptide structures of the cognate enzymes may not be the best starting point for the design of reverse binding inhibitors.
Stern
Igor
I
Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
Schaschke
Norbert
N
Moroder
Luis
L
Turk
Dusan
D
D000818:Animals; D001665:Binding Sites; D002401:Cathepsin B / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000302:isolation & purification; D002417:Cattle; D018360:Crystallography, X-Ray / Q000379:methods*; D015853:Cysteine Proteinase Inhibitors / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry; D004852:Epoxy Compounds / Q000737:chemistry; D007668:Kidney / Q000201:enzymology; D007930:Leucine / Q000031:analogs & derivatives* / Q000737:chemistry; D008968:Molecular Conformation; D015394:Molecular Structure; D009842:Oligopeptides / Q000138:chemical synthesis / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D011725:Pyridines / Q000737:chemistry; D011758:Pyrroles / Q000138:chemical synthesis / Q000737:chemistry*
C494116:1-(2-((3-(1-(((methoxycarbonylmethyl-carbamoyl)-methyl)-carbamoyl)-3-methyl-butylcarbamoyl)-oxiranecarbonyl)-amino)-4-methyl-pentanoyl)-pyrrolidine-2-carboxylic acid; C402823:CLIK 148; D015853:Cysteine Proteinase Inhibitors; D004151:Dipeptides; D004852:Epoxy Compounds; D009842:Oligopeptides; D011725:Pyridines; D011758:Pyrroles; C068249:N-(3-ethoxycarbonyloxirane-2-carbonyl)-isoleucyl-proline; C068250:N-(3-propylcarbamoyloxirane-2-carbonyl)-isoleucyl-proline; D002401:Cathepsin B; D007930:Leucine; C024974:E 64