Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft

Abstract

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.

Novel Mechanism of Cathepsin B Inhibition by Antibiotic Nitroxoline and Related Compounds

“…The structures of the two cathepsin B molecules in the asymmetric unit are closely related, with a root mean square distance (RMSD) value of 0.44 . The crystal structure is also closely related to previously published structures 1CSB [14] and 1GMY, [15] with an RMSD value of equipositioned CA atom (a atom in the amino acid) smaller than 0.5 .…”

“…The negatively charged nitro group interacts with His 110 and His 111, similarly to the carboxylate of the epoxysuccinyl-based irreversible inhibitors CA-030 [14] and NS134. [15] In these structures, the carboxylic group of the terminal proline residue binds between the two histidines with one oxygen atom, while the other oxygen atom binds asymmetrically to His111 only. The nitro group of nitroxoline, on the other hand, lies more symmetrically between the two histidines and each oxygen atom interacts with one histidine.…”

Cysteine cathepsins: From structure, function and regulation to new frontiers

“…On the primed binding side, there is still a limited structural insight into the substrate binding. Data are provided by the synthetic epoxysuccinyl-based inhibitors CA030, CA074 and NS134 complexes with cathepsin B [76][77][78]. Their binding revealed the position of the P1′ and P2′ residues.…”

Solid‐Phase Synthesis of Double‐Headed Epoxysuccinyl Activity‐Based Probes for Selective Targeting of Papain Family Cysteine Proteases

“…[8] Thus, we reasoned that development of a method that would allow facile attachment of diverse peptide sequences on both sides of the epoxide moiety would facilitate the synthesis of probes with increased selectivity compared to the general DCG-04 probe. Here we report our preliminary results involving the solid-phase synthesis of cathepsin B-specific ABPs.…”