Endothiapepsin inhibitors

The active-site cleft has a less open arrangement in renins than in the other aspartic proteinases. Many loops as well as the helix hc (residues 224-236) belonging to the C-domain (residues 190-302) are significantly closer to the active site in the renin structures compared to those of endothiapepsin-inhibitor complexes. This is partly due to a difference in relative position of the rigid body comprising the C-domain. For instance, there is a domain rotation of 4° and translation of 0.1 A in the human renin complex with respect to the endothiapepsin-difluorostatone complex. 

Incorporation of glycol or vicinal diol analogs of the peptide bond (-CH(OH)-CH(OH)-) has led to potent inhibitors and the x-ray structure for one such compound complexed with endothiapepsin is available [27]. The first hydroxyl in... 

The catalytic mechanism proposed by Veerapandian et al. [31] based on the x-ray structure of a difluoroketone (geminal-diol) inhibitor bound to endothiapepsin. A water molecule tightly bound to the aspartates in the native enzyme is proposed to nucleophilically attack the scissile-bond carbonyl. The resulting geminal-diol intermediate is stabilised by hydrogen bonds with the negatively charged carboxyl of aspartate 32. 

There is also great similarity between aspartic proteinases in terms of interactions with the transition-state analog inhibitors at the catalytic center. The catalytic aspartyl side chains and the inhibitor hydroxyl group are essentially superimposable in both renin complexes. The isostere C-OH bonds lie at identical positions when the structures of inhibitor complexes of several aspartic proteinases are superposed, in spite of the differences in the sequence and secondary structure. Most of the complex array of hydrogen bonds found in endothiapepsin complexes are formed in renin with the exception of that to the threonine or serine at 218, which is replaced by alanine in human renin. The similarity can be extended to all other pepsin-like aspartic proteinases and even to the retroviral proteinases [44,45]. This implies that the recognition of the transition state is conserved in evolution, and the mechanisms of this divergent group of proteinases must be very similar. 

Cooper J, Quail W, Frazao C, Foundling SI, Blundell TL. X-ray crystallographic analysis of inhibition of endothiapepsin by cyclohexyl renin inhibitors. Biochemistry 1992 31 8142-8150. 

Scheme 1. Hydrogen bonding scheme observed in five X-ray structures of endothiapepsin bound with renin inhibitors [17], (llll) Non-conserved hydrogen bond (—) conserved hydrogen bonds.

Figure 4. Stereoview of the X-ray crystal structure of a renin inhibitor, Smo-Phe-Ets-ACDMH (yellow), bound in endothiapepsin [17]. The hydrogen bond between the PI hydroxyl and Gly76(NH) (magenta) is shown by a white dotted line. The catalytic aspartic acids are shown in red.

Figure 8. Stereoview of renin inhibitors extracted from the X-ray crystal structures of three different aspartic proteases. The yellow inhibitor, 20, is from an HIV-1 protease structure (unpublished), the cyan inhibitor is from an endothiapepsin structure [17] and the green inhibitor is from a renin structure [43],...

Figure 28. A schematic representation of the extensive backbone hydrogen bonding between (a) compound 32 and (b) compound 31 with the enzyme endothiapepsin. These inhibitors displace waters bound to Asp-32 and Asp-215 in the uncomplexed enzyme.

In the work of Aqvist et al., a was taken to be 0.5, which has an approximate theoretical basis. No firm theoretical framework has yet been worked out to guide the choice of 7, so this parameter was treated as an empirical parameter. Promising results for the binding energies of a number of inhibitors to the protein endothiapepsin were obtained by these authors. This... 

In this paper, we treat various molecular similarity problems through the study of six different families of molecules, as already detailed in the literature. The selected families are the TOMI and DFKi elastase ligands [26-29], inhibitors of endothiapepsins [16, 20, 30], trypsins [16, 18, 31, 32], thermolysins [16, 17, 30-32], human rhinovirus HRV14 [16, 18, 32], and of p38 mitogen-activated proteins (MAP) [18, 32]. 

Endothiapepsin is a single-chain proteinase of 330 amino acids. The structure is largely of / -sheet type and consists of two related lobes of approximately 170 amino acids each. The active site resides in a pronounced cleft between the lobes. Inhibitors have been shown, by X-ray crystallography, to bind in the active site cleft in extended conformations. A detailed comparison of the X-ray structures of 21 inhibitor complexes is given by Bailey and Cooper [50]. The hydrogen bonds that position the inhibitor main chain in the active site cleft are largely conserved from one... 

In the present work, a Monte Carlo/Simulated Annealing rigid superposition algorithm was applied to six families of drug molecules, that is, elastase inhibitors, and ligands of endothiapepsins, trypsins, thermolysins, p38 MAP kinases, and rhinovirus, for which various alignment problems were reported in the literature. 

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