Kenji Akahane

Binding specificity of papain and cathepsin B.

In order to obtain useful information for the design of inhibitors of cathepsin B, an important enzyme in both physiological and pathological processes, the modes of interaction between ligands and thiol proteases (papain and cathepsin B) were analyzed. A new and powerful method was developed to quantitatively understand geometrical features of the interaction. Fairly good electrostatic complementarities were found for the oxygen atoms of P1 and P2 amide, and for the hydrogen atom of P2 amide. Electrostatic correlation potentials on the side chains of P1 and P2 were nearly neutral, so that interacting conformations in these regions are anticipated to be stabilized by hydrophobic forces rather than electrostatic ones. A three-dimensional structure of rat liver cathepsin B was deduced based on the assumption that the tertiary structure of cathepsin B is similar to that of actinidin. Furthermore, an inhibitor of the thiol proteases, benzyloxycarbonyl-L-phenylalanyl-L-alanine chloromethyl ketone was model fitted to cathepsin B, in order to investigate its mode of interaction with the enzyme. It was possible to account for some structure-activity relationships in the enzyme-ligand interactions.

Conformational study of a potent human renin inhibitor: X-ray crystal structure of isopropyl (2R,3S)-4-cyclohexyl-2-hydroxy-3-{N-[(2R)-2-morpholinocarbonylmethyl-3-(1-naphthyl)propionyl]-L-histidylamino}butyrate (KRI-1314), a pentapeptide analogue with amino acid sequence corresponding to the cleavage site of angiotensinogen

A potent inhibitor of renin, isopropyl (2R,3S)-4-cyclohexyl-2-hydroxy-3-{N-[(2R)-2-morpholino-carbonylmethyl-3-(1-naphthyl)propionyl]-L-histidylamino}butyrate (KRI-1314), was crystallized as a cinnamic acid salt. The crystal structure of KRI-1314 was determined by X-ray analysis, and the conformation is discussed in relation to the inhibitory activity. The backbone chain of the molecule was largely twisted at the unusual amino acid residue of cyclohexylnorstatine. The observed conformation was compared with that of the model pentapeptide corresponding to the scissile site of angiotensinogen. The stacking interaction was formed between the histidine side-chains related by the crystallographic 2-fold screw axis. The histidine imidazole rings were further fixed by hydrogen bonds with the cinnamic acid. The water molecule of crystallization mediated the hydrogen-bonding bridge of the cinnamic acid with the hydroxy oxygen of the cyclohexylnorstatine. Such interactions appear to be very important in considerations of inhibitor-or substrate-binding mechanisms against renin.

Design and synthesis of an orally potent human renin inhibitor containing a novel amino acid, cyclohexylnorstatine

An orally potent human renin inhibitor (1a) containing a novel amino acid, (2R,3S)-3-amino-4-cyclohexyl-2-hydroxybutyric acid named cyclohexylnorstatine, has been designed from the angiotensinogen transition-state and synthesized.

Drug design based on receptor modeling using a system “BIOCES [E]”

Abstract A computer system BIOCES [E] enables medicinal chemists to study the interaction between biologically active molecules and their receptors. It is capable of building receptor protein models, docking drug molecules into the receptor model, and analyzing their interacting modes. By using BIOCES [E], the three-dimensional structures of human and rat cathepsin H were predicted based on the crystal structure of papain. The binding sites of both enzymes are highly conserved and the only amino acid replacement found was residue 61 (papain numbering scheme). A well-known inhibitor of thiol proteases, benzyloxy-carbonyl-L-phenylalanyl-L-alanyl-methylene, was fitted into the binding site by a Monte Carlo method. Steric, electrostatic and hydrophobic aspects of the interactions of the inhibitor and the enzymes were analyzed.