Protease inhibitors transition state analogs

The requirements of protease inhibitors as drugs in terms of potency, pharmacokinetics, and toxicity will vary depending on the nature of the infection and the goals of therapy. At one extreme is treatment of HlV-1, a chroific infection that requires life-long therapy and full suppression of viral replication. At the other extreme is the treatment of human rhinovirus (i.e., the cold virus), where short-term treatment to blunt viremia will likely be sufficient to reduce the unwanted symptoms of a cold. In all cases, viral proteases represent very attractive targets with familiar mechanisms of catalysis that frequently allow for the design of transition state analogs and with distinct specificities from host proteases. 

E. Dufour, A. C. Storer, R. Menard, Peptide Aldehydes and Nitriles as Transition State Analog Inhibitors of Cysteine Proteases , Biochemistry 1995, 34, 9136 - 9143. 

The strategy of designing saquinavir was based on the transition-state mimetic concept, an approach that has been used successfully in the design of potent inhibitors of renin and other aspartic proteases [10]. From the variety of nonscissile transition-state analogs of a dipeptide, the hydroxyethylamine mimetic was selected because it most readily accommodates the amino acid moiety characteristic of the Phe-Pro and Tyr-Pro cleavage sequence of the... 

HIV protease inhibitors are transition-state analogs (Chapter 9, Section 9.2.6) HIV protease binds them much more tightly than the natural substrate because the substrate must be distorted to assume its transition-state configuration. Thus, HIV protease inhibitors are competitive enzyme inhibitors and thereby prevent the maturation and infectivity of the viral particle. They offer advantages over RTIs with respect to efficacy, safety, and occurrence of resistance. However, just like RTIs, HIV protease inhibitors are most often offered in combination with therapies based on another mode of action. Structures and data for the five approved HIV protease inhibitors are shown in Figure 13.14 and in Table 13.5. 

Phosphonates and phosphonamidates were selected as transition-state analogs for carbonate and ester hydrolysis they are relatively stable molecules, they are known inhibitors of acyl transfer enzymes and they imitate the initial negative charge of the tetrahedral oxyanion of acyl transfer enzymes (such as serine proteases) in the dipole of the P=0 bond. 

Phosphonopeptides containing a transition state analog of the hydrolysis of the amide bond represent another attractive approach for the preparation of proteolitically stable peptides (10,30,31). In addition to increased stability, incorporation of a phosphonate moiety into the peptide sequence provides access to additional binding interactions within the transition-state conformation of the enzyme/substrate complex (13). This peptidomimetic approach is used to design very effective protease inhibitors (31-34). As in the case... 

Transition-state inhibitors stably mimic the transition state of the enzymatic reaction, and thereby interact with the substrate-bin-ding and catalytic machinery of the enzyme in a low-energy conformation. Transition-state analogs are competitive, reversible inhibitors, although some have extremely low Kj s and very slow off-rates. All proteases activate a nucleophile to attack a carbonyl, which leads to the formation of a tetrahedral intermediate that then collapses to form the enzyme products—two peptides. Thus, synthetic small molecules that mimic the tetrahedral intermediate of the protease reaction are attractive transition-state analogs. A classic class of protease transition-state inhibitors uses a boronic acid scaffold (4, 10). Boronic acid adopts a stable tetrahedral conformation in the protease active site that is resistant to nucleophilic attack. Boronic acid inhibitors, which are derivatized with different specificity elements, have been developed against every class of protease... 

Figure 7 Various transition-state protease inhibitors. Bortezomib is an approved drug for the treatment of multiple myeloma. It is a boronic acid analog that inhibits the proteosome, a threonine protease. The boronic acid moiety can adopt a tetrahedral conformation in the active site. Pepstatin is a peptidyl aspartic acid inhibitor. The reactive statine group binds to the catalytic machinery, and the chiral hydroxyl group of the statine mimics the tetrahedral geometry of the transition state. Idinavir is an approved HIV 1 Protease inhibitor that binds to the active site via a hydroxyethylene transition state isostere. Aldehydes are also transition state analogs, which are susceptible to nucleophilic attack. In cysteine, serine and threonine proteases, this results in a covalent, reversible inhibition mechanism.

Transition-state inhibitors, especially those with peptidyl or peptidomimetic extensions, are slow-binding inhibitors, and the protease-inhibitor binding mechanism includes one or more weakly bound intermediates before the formation of the tightly bound E I complex. This slow-binding inhibition is a hallmark of inhibitors that bind in the active site in a substrate-like manner. In this way, transition-state analogs mimic the association... 

Phosphonates (Fig. 8) and sulfonates represent a third class of covalent irreversible inhibitors. These inhibitors adopt a stable tetrahedral geometry and are covalently bound transition-state analogs. They often have a peptide-like specificity element, and the electrophilicity of the leaving groups can be modified to mne the reactivity of the inhibitor. These inhibitors are specific for serine proteases, because the serine protease active site has a well-defined oxyanion hole, which stabilizes the transition-state mimic. 

Stowasser B, Budt K-H, Jian-Qi L, Peyman A, Ruppert D. New hybrid transition state analog inhibitors of HIV protease with peripheric C2-symmetry. Tetrahedron Lett. 1992 33 6625-6628. 

From Transition-State Analog Inhibitors to Non-Peptide Inhibitors Examples in Protease Inhibitors, 646... 

FROM TRANSITION-STATE ANALOG INHIBITORS TO NON-PEPTIDE INHIBITORS EXAMPLES IN PROTEASE INHIBITORS... 

A stable structure that mimics this tetrahedral Intermediate would be a transition state analog inhibitor. A silicon diol structure, in which the C(OH)2NH group of the transition state is replaced by an Si(OH)2CH2 moiety, mimics that tetrahedral transition state, and it has recently been shown that incorporating silicon diol moieties into peptide mimetics results in potent and selective inhibitors for metallo and aspartyl proteases [1 - 3] (1 and 2, Fig. 2). 

Chen, C. A., Sieburth, S. M., Glekas, A., Hewitt, G. W, Trainor, G. L., Erickson-Viitanen, S., Garber, S. S., Cordova, B., Jeffry, S., Klabe, R. M. Drug design with a new transition state analog of the hydrated carbonyl sihcon-based inhibitors of the HIV protease. Chem. Biol. 2001, S(12), 1161-1166. 

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