Structure of human α-thrombin complexed with RWJ-51438 at 1.7 Å: unusual perturbation of the 60A–60I insertion loop

Abstract

The three-dimensional structure of the ternary complex consisting of human -thrombin, hirugen and the active-site inhibitor RWJ-51438 has been determined at 1.7 A Ê resolution. The crystals of the complex belong to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 62.98, b = 117.52, c = 47.99 A Ê . The re®ned R and R free values are 0.196 and 0.232, respectively. The ketone carbonyl group of the inhibitor is covalently linked to the hydroxyl O atom of Ser195, forming a tetrahedral intermediate hemiketal structure; the benzothiazole ring N atom of RWJ-51438 forms a hydrogen bond with His57. Surprisingly, the carboxylate substituent on the benzothiazole group forms salt bridges with Lys60F NZ and the NZ of the symmetry-related residues Lys236 and Lys240, which introduces steric effects that perturb the 60A±60I insertion loop, especially at residues Trp60D and Phe60H.

Inhibitors of Serine Proteases as Potential Therapeutic Agents: The Road from Thrombin to Tryptase to Cathepsin G

“…This heterocycle-activated ketone approach provided potent thrombin inhibitors, some with subnanomolar K i values, as first reported in our preliminary publication . In detailed articles, we have highlighted the advanced leads RWJ-50353 ( 6a ), RWJ-51438 ( 6b ), and RWJ-51439 ( 6c ), which exhibit potent antithrombotic activity. , The X-ray crystal structures of thrombin complexes of 6a and 6b have also been discussed. ,,

2 Strategy for the design of novel thrombin inhibitors with a heterocycle-activated ketone.

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“…The X-ray crystal structure of Ac-Val-Pro-Val-(2-benzoxazole) complexed with porcine pancreatic elastase (PPE) depicted hemiketal formation with Ser-195 and a hydrogen-bonding interaction between the benzoxazole nitrogen and Nε of His-57 ,, Since our 1996 report, and follow-up reports by Edwards et al, there have been numerous papers on peptide-based α-ketoheterocycles as inhibitors of thrombin, other serine proteases, and cysteine proteases …”

Sparse Topological Pharmacophore Graphs for Interpretable Scaffold Hopping

“…The surrounding six molecules help interpret the SPhG in Figure b. Through the investigation of PDB, we found these types of molecules bound to Thr., e.g., 1DOJ and 1A61. , Ligands in both the complexes had the carbonyl part interacting with Gly193 and a nitrogen atom in an aromatic ring interacting with the residue of Hys57. , …”

“…Through the investigation of PDB, 37 we found these types of molecules bound to Thr., e.g., 1DOJ and 1A61. 40,41 Ligands in both the complexes had the carbonyl part interacting with Gly193 and a nitrogen atom in an aromatic ring interacting with the residue of Hys57. 40,41 Likewise, for the other two targets, typical top-ranked SPhGs were shown along with typical active compounds in Figures S2 and S3 in the Supporting Information.…”

Application of EMBM to Structure‐Based Design of Warheads for Protease Inhibitors

“…PDB crystal structures of covalent tetrahedral complexes formed by thrombin (1DOJ), [25] fatty acid amide hydrolase (2VYA), [26] and cathepsin K (2BDL) [27] were used as initial templates. The CS fragments in the crystal structures were changed manually by molecular modeling tools according to the sets of examined inhibitors (see below).…”