Mechanism-based inhibitor

Interactions with metabolic enzymes fluorinated amino acids are peptidomi-metic units or reactive entities used to design either reversible enzyme inhibitors (analogues of substrates) or irreversible enzyme inhibitors (mechanism-based inhibitors). 

Irreversible inhibitors combine or destroy a functional group on the enzyme so that it is no longer active. They often act by covalently modifying the enzyme. Thus a new enzyme needs to be synthesized. Examples of irreversible inhibitors include acetylsal-icyclic acid, which irreversibly inhibits cyclooxygenase in prostaglandin synthesis. Organophosphates (e.g., malathion, 8.10) irreversibly inhibit acetylcholinesterase. Suicide inhibitors (mechanism-based inactivators) are a special class of irreversible inhibitors. They are relatively unreactive until they bind to the active site of the enzyme, and then they inactivate the enzyme. 

Because irreversible inhibitors tend to be reactive electrophiles, they can be difficult to use as drugs. Their reactivity can translate into instability and/or toxicity. A subclass of irreversible inhibitors is the mechanism-based inhibitor. Mechanism-based inhibitors... 

The CYP inhibition assay utilizes the 96-well plate format with a robotic system, where both incubation and analysis are performed in the same plates. The setup of the sample plates is shown in Figure 4.1. For each compound, both direct inhibition and metabolism/mechanism-based inhibition, which is caused by a metabolite of the NCE that is either a more potent direct reversible inhibitor (metabolism-based) or a time-dependent irreversible inhibitor (mechanism-based), are evaluated. Both direct and mechanism-based inhibitors could result in inhibitory DDIs [51,52],... 

The best definition of the third type of irreversible enzyme inhibitor, mechanism-based inactivators, is provided by Dr Richard Silverman, a leading authority on the subject. A mechanism-based inactivator (sometimes, much to my dismay, called a suicide substrate), he writes, is an unreactive compound that has a structural similarity to a substrate or product for an enzyme. Once at the active site of the enzyme, it is converted into a species that generally forms a covalent bond to the enzyme, producing inactivation. Although both quiescent affinity labels and mechanism-based inactivators can be mistaken for... 

Affinity Labels. Active site-directed, irreversible inhibitors or affinity labels are usually substrate analogues that contain a reactive electrophilic functional group. In the first step, they bind to the active site of the target enzyme in a reversible fashion. Subsequentiy, an active site nucleophile in close proximity reacts with the electrophilic group on the substrate to form a covalent bond between the enzyme and the inhibitor, typically via S 2 alkylation or acylation. Affinity labels do not require activation by the catalysis of the enzyme, as in the case of a mechanism-based inhibitor. 

Criteria very similar to those for mechanism-based inactivators apply for the evaluation of pseudoirreversible inhibitors. The kinetics for pseudoirreversible inactivators are as follows ... 

A significant difference between pseudoirreversible inhibitors and mechanism-based inactivators is the reversibiUty of the inactivation. A complete evaluation of the mechanism involved would require evidence not only for the covalent enzyme-inhibitor complex, but also for its decomposition products and its rate of reactivation. It is often difficult to identify the active site amino acid residue covalently linked to the inhibitor because of the instabiUty of the complex. 

Deoxy-2-fluoroglucosides ( ) are mechanism-based glucosidase inhibitors Fluorine at C-2 slows the rate of the acetal C-OR (R = 2,4-dinitrophenyl) bond cleavage in S by destabilizing the proposed oxocarbonium lon-like transition state for glucosidase-catalyzed hydrolyses [28]... 

Rhinoviruses, which represent the single major cause of common cold, belong to the family of picornavimses that harbors many medically relevant pathogens. Inhibitors of the 3C protease, a cysteine protease, have shown good antiviral potential. Several classes of compounds were designed based on the known substrate specificity of the enzyme. Mechanism-based, irreversible Michael-acceptors were shown to be both potent inhibitors of the purified enzyme and to have antiviral activity in infected cells. 

Matthews DA, Dragovich PS, Webber SE, Fuhrman SA, Patick AK, Zalman LS, Hendrickson TF, Love RA, Prins TJ, Marakovits JT, Zhou R, Tikhe J, Ford CE, Meador JW, Ferre RA, Brown EL, Binford SL, Brothers MA, DeLisle DM, Worland ST (1999) Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc Natl Acad Sci USA 96 11000-11007... 

QUINONE METHIDES AND AZA-QUINONE METHIDES AS LATENT ALKYLATING SPECIES IN THE DESIGN OF MECHANISM-BASED INHIBITORS OF SERINE PROTEASES AND p-LACTAMASES... 

The starting point for much of the work described in this article is the idea that quinone methides (QMs) are the electrophilic species that are generated from ortho-hydro-xybenzyl halides during the relatively selective modification of tryptophan residues in proteins. Therefore, a series of suicide substrates (a subtype of mechanism-based inhibitors) that produce quinone or quinonimine methides (QIMs) have been designed to inhibit enzymes. The concept of mechanism-based inhibitors was very appealing and has been widely applied. The present review will be focused on the inhibition of mammalian serine proteases and bacterial serine (3-lactamases by suicide inhibitors. These very different classes of enzymes have however an analogous step in their catalytic mechanism, the formation of an acyl-enzyme intermediate. Several studies have examined the possible use of quinone or quinonimine methides as the latent... 

The functionalized phenaceturates 16 (Fig. 11.10) are substrates of class A and C [3-lactamases, especially the class C enzymes, as observed with the parent unfunctionalized phenaceturates 15. They are also modest inhibitors of these enzymes and the serine DD-peptidase of Streptomyces R61. The inhibition of class C [3-lactamases is turnover dependent, as expected for a mechanism-based inhibitor. Inhibition is not very dependent on the nature of the leaving group, suggesting that the QM is generated in solution after the product phenol has been released from the active site. It therefore... 

Pratt, R. F. On the definition of mechanism-based enzyme inhibitors. Bioorg. Med. Chem. Lett. 1992, 2, 1323-1326. 

Mor, A. Maillard, J. Favreau, C. Reboud-Ravaux, M. Reaction of thrombin and proteinases of the fibrinolytic system with a mechanism-based inhibitor, 3,4-dihydro-3-benzyl-6-chloromethyl-coumarin. Biochim. Biophys. Acta 1990, 1038, 158-163. 

Pochet, L. Doucet, C. Dive, G. Wooters,J. Masereel, B. Reboud-Ravaux,M. Pirotte, B. Coumarinic derivatives as mechanism-based inhibitors of a-chymotrypsin and human leukocyte elastase. Bioorg. Med. Chem. 2000, 8, 1489-1501. 

Frederick, R. Robert, S. Charlier, C. de Ruyck, J. Wouters, J. Masereel, B. Pochet, L. Mechanism-based thrombin inhibitors design, synthesis, and molecular docking of a new selective 2-OXO-2/7- l-benzopyxan derivative. J. Med. Chem. 2007, 50, 3645-3650. 

Wakselman, M. Mazaleyrat, J.-P. Lin, R. C. Xie, J. Vigier, B. Vilain, A. C. Fesquet, S. Boggetto, N. Reboud-Ravaux, M. Design, synthesis and study of a selective cyclopeptidic mechanism-based inhibitor of human thrombin. In Peptides Chemistry, Structure... 

Wade Harper, J. Powers, J. C. Reaction of serine proteases with substituted 3-alkoxy-4-chloroisocoumarins and 3-alkoxy-7-amino-4-chloroisocoumarins new reactive mechanism-based inhibitors. Biochemistry 1985, 24, 7200-7213. 

---