Ligand thermolysin

Any examination of crystal structures of complexes of a series of ligands binding to a protein (the set of complexes of thermolysin with a variety of inhibitors determined in the Brian Mathews lab, for example see references in DePriest et al. [36]) shows clearly a major limitation of the pharmacophore assumption. Ligands do not optimize overlap of similar chemical functionality in complexes but find a way to maintain correct hydrogenbonding geometry, for example, while accommodating other molecular interactions. 

In thermolysin (Matthews et al., 1974 Holmes and Matthews, 1982) zinc is bound approximately tetrahedrally to glutamate (monodentate), two histidines, and water. While zinc in the native enzyme is tetracoord-inate, in some inhibitor complexes it is pentacoordinate. The four calcium ions are bound by six to eight oxygen ligands, as shown in Fig. 35, with Ca 0 distances of 2.23-2.71 A. The RNA polymerase from E. coli contains Zn(II) and Mg(II), which may be substituted by Mn(II) (Chuk-nyhVy et al., 1990). 

Fig. 8. An example of the lack of strong interaction between Ca ions bound to proteins and a-helix dipoles. Shown is the double-Ca -binding site of thermolysin (3TLN), with two associated helices (residues Gly-136 to Asn-181). Side chains are drawn only for Asp-138 and Glu-177 (thick lines), two Ca -ligand residues from the helical regions. Only main-chain atoms are shown for other residues. The Ca ions are circles. The positive amino terminus of the dipole from the first helix passes to one side of the Ca positions. The negative carboxy terminus of the dipole from the second helix bypasses the Ca positions at some distance. The only interaction between the ions and the helices is with the side chains of Asp-138 and Glu-177 that protrude from their respective helix axes.

Zinc proteases carboxypeptidase A and thermolysin have been extensively studied in solution and in the crystal (for reviews, see Matthews, 1988 Christianson and Lipscomb, 1989). Both carboxypeptidase A and thermolysin hydrolyze the amide bond of polypeptide substrates, and each enzyme displays specificity toward substrates with large hydrophobic Pi side chains such as phenylalanine or leucine. The exopeptidase carboxypeptidase A has a molecular weight of about 35K and the structure of the native enzyme has been determined at 1.54 A resolution (Rees et ai, 1983). Residues in the active site which are important for catalysis are Glu-270, Arg-127, (liganded by His-69, His-196, and Glu-72 in bidentate fashion), and the zinc-bound water molecule (Fig. 30). 

Another contrast between the zinc proteases and the carbonic an-hydrases concerns the zinc coordination polyhedron. The carbonic an-hydrases ligate zinc via three histidine residues, whereas the zinc proteases ligate the metal ion through two histidine residues and a glutamate (bidentate in carboxypeptidase A, unidentate in thermolysin). Hence, the fourth ligand on each catalytic zinc ion, a solvent molecule, experiences enhanced electrostatic polarization in carbonic anhydrase II relative to carboxypeptidase A. Indeed, the zinc-bound solvent of carbonic anhydrase II is actually the hydroxide anion [via a proton transfer step mediated by His-64 (for a review see Silverman and Lindskog, 1988)]. 

In particular, in Cd(II)-Thermolysin derivative (a zinc metaUoprotease with proteolytic activity similar to carboxypeptidase A), the X-ray structure has provided evidence for isostructural replacement of Zn(II) by Cd(II). In general, the " Cd chemical shift is very sensitive to the nature, number and coordination type of the amino acid ligands and " Cd resonances are commonly detected by direct observation (/ = V2, and 63% sensitivity compared with C) or by inverse detection of Cd scalar-coupled to H. 

Fig. 7. Co2+ complexes with two oxygen and two nitrogen ligands that are models for the metal ion site of thermolysin.

There also are numerous enzymes that use bound metal ions to form complexes with substrates. In these enzymes, the metal ion usually serves as an electrophilic functional group rather than as a nucleophile. Carbonic anhy-drase, for example, contains a Zn+2 ion that binds one of the substrates, hydroxide ion, as a ligand. The bound OH reacts with the other substrate, C02. In alcohol dehydrogenase, and in the proteolytic enzymes thermolysin and car-boxypeptidase A, a Zn+2 ion forms a complex with a carbonyl oxygen atom of the substrate. The withdrawal of electrons by the Zn+2 increases the partial positive charge on the carbonyl carbon and thus promotes reaction with a nucleophile. 

Zinc proteases are metalloenzymes containing tightly bound zinc examples are carboxypeptidases A and B, collagenase, and thermolysin. The zinc atom is bound to the imidazole moiety of two histidines and the carboxylate of Glu the fourth ligand is a molecule of H20. 

Figure 10-3. The environment of the four structural calcium ions in the enzyme thermolysin isolated from Bacillus thermoproteolyticus. All of the calcium ions are associated with oxygen donor ligands.

Fig. 37. Diagram representing the environment of the catalytic zinc in horse liver alcohol dehydrogenase, human carbonic anhydrase, thermolysin and carboxypeptidase A. Positions occupied by the substrate (S) and proton-abstracting group (PA) are indicated. The angles subtended by the liganding protein atoms at the zinc atom are shown to the right, and their sum (2) is shown extreme right. From the work of Rossmann and colleagues [ 164].

The catalytic zinc site of thermolysin contains His 142 and Hisl46 from the short spacer and Glul66 from the long spacer arm. In this case two other conserved amino acids from the long spacer arm make interactions with the ligands from the short spacer arm. Thus, the carboxamide group of Asnl65... 

Bash et al. (1987) applied the thermodynamic perturbation method to complexes of thermolysin with a phosphonamidate [Cbz-Gly -(NH)-Leu-Leu] and the corresponding phosphonate inhibitor [Cbz-Gly -(0)-Leu-Leu]. The perturbation was carried out by using 20 windows, with 2-psec molecular dynamics simulations in each window. Computations were for the ligand in solution and bound to the enzyme. The solvation of the enzyme was represented by a spherical cap of 168 water molecules about the bound inhibitor. The difference in free energy of binding of the two inhibitors was calculated to be 4.38 kcal/mol, to be compared with the experimental value, 4.10 kcal/mol. These calculations point out the importance of solvation effects, which are seen in the 3.4 kcal/mol difference between the NH and O forms of the inhibitor. 

Wasserman and Hodge (290) used molecular dynamics to dock thermolysin inhibitors to an approximate model of the enzyme, with flexibility in the active site (3 8 of 314 residues) and ligand and with the rest of the enzyme represented by a grid approximation. A solvation model was used to compensate for desolvation in complex formation. To get 22 of 25 runs to orient the hydroxamate function correctly, the hydroxamate oxygens of the starting conformation were initialized within 4 A of the zinc. If they were allowed to vary to 8 A, then only 3 of 24 runs placed the ligand correctly. Obviously, there is a serious sampling problem. 

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