Enzyme mechanisms structure-activity relationships

Kalgutkar, A. S., Obach, R. S., and Maurer, T. S. (2007). Mechanism-based inactivation of cytochrome p450 enzymes Chemical mechanisms, structure-activity relationships and relationship to clinical drug-drug interactions and idiosyncratic adverse drug reactions. Curr. Drug. Metab. 8 407 -447. 

In 1985, it was reported by Hsiang et al. [43] that the cytotoxic activity of 20-(S)-camptothecin (CPT III) was attributed to a novel mechanism of action involving the nuclear enzyme topo I, and this discovery of unique mechanism of action revived the interest in CPT and its analogues as anticancer agents. CPT stabilizes the covalent, reversible topo I-DNA complex leading to the inhibition of DNA synthesis in mammalian cells and interferes with the topo I breakage-reunion reaction [44]. Clinical trials and structure-activity relationships have demonstrated the requirement of the a-hydroxy group, the... 

In this chapter, a short introduction to DFT and to its implementation in the so-called ab initio molecular dynamics (AIMD) method will be given first. Then, focusing mainly on our own work, applications of DFT to such fields as the definition of structure-activity relationships (SAR) of bioactive compounds, the interpretation of the mechanism of enzyme-catalyzed reactions, and the study of the physicochemical properties of transition metal complexes will be reviewed. Where possible, a case study will be examined, and other applications will be described in less detail. 

In this section several recently published studies on the interaction of nonionic surfactants with a variety of biological systems, including enzymes, bacteria, erythrocytes, leukocytes, membrane proteins, low density lipoproteins and membranes controlling absorption from the gastrointestinal tract, nasal and rectal cavities, will be assessed. This is a selective account, work having been reviewed that throws light on structure-activity relationships and on mechanisms of surfactant action. 

Flavonoids, especially flavones and flavonols, also directly bind to several CYP isoforms (lAl, 1A2, IBl, 3A4) involved in xenobiotics metabolism and inhibit enzyme activity. Structure-activity relationships show rather high isoform selectivities depending on the flavonoid substitution pattern and contrasted inhibition mechanisms. For instance, inhibition by flavonoids of 7-methoxyresorufin O-demethylation in microsomes enriched in CYP lAl and 1A2 reveals that galangin (3,5,7-trihydroxyflavone) is a mixed inhibitor of CYP 1A2 (.ST = 8 nM) and a five times less potent inhibitor of CYP 1A1. By contrast, 7-hydroxy flavone is a competitive inhibitor of CYP lAl (Aii = 15 nM) and a six times less potent inhibitor of CYP 1A2. In addition, fairly selective inhibition of CYP IBl (specifically detected in cancer cells) by some flavonoids has been reported. For example, 5,7-dihydroxy-4 -methoxyflavone inhibits IBl, 1 Al, and 1A2 with IC50 values of 7, 80, and 80 nM, respectively. ... 

As a class of compounds, the two main toxicity concerns for nitriles are acute lethality and osteolathyrsm. A comprehensive review of the toxicity of nitriles, including detailed discussion of biochemical mechanisms of toxicity and structure-activity relationships, is available (12). Nitriles vary broadly in their ability to cause acute lethality and subtle differences in structure can greatly affect toxic potency. The biochemical basis of their acute toxicity is related to their metabolism in the body. Following exposure and absorption, nitriles are metabolized by cytochrome p450 enzymes in the liver. The metabolism involves initial hydrogen abstraction resulting in the formation of a carbon radical, followed by hydroxylation of the carbon radical. Metabolism at the carbon atom adjacent (alpha) to the cyano group would yield a cyanohydrin metabolite, which decomposes readily in the body to produce cyanide. Hydroxylation at other carbon positions in the nitrile does not result in cyanide release. 

Further structure-activity relationship (S AR) analyses of other cytoprotective enzyme inducers revealed the fact that all inducers can react with thiol/disulfide groups by alkylation, oxidoreduction, or thiol-disulfide interchange [Dinkova-Kostova and Talalay, 1999]. In fact, the capability of enzyme inducers to induce cytoprotective enzymes is well correlated with their reactivity with thiols. These results suggested a cellular sensor of inducers with highly reactive sulfhydryl groups, possibly reactive thiols in cysteine residues of a sensor protein. Nevertheless, the initial search for the sensor protein by using radioactively labeled inducers was not successful due to the abundance of thiol groups presented in many proteins in cells [Holtzclaw et al., 2004]. The molecular mechanism by which cytoprotective enzymes are induced remained to be elucidated. 

The interest in catechol oxidase, as well as in other copper proteins with the type 3 active site, is to a large extent due to their ability to process dioxygen from air at ambient conditions. While hemocyanin is an oxygen carrier in the hemolymph of some arthropods and mollusks, catechol oxidase and tyrosinase utilize it to perform the selective oxidation of organic substrates, for example, phenols and catechols. Therefore, establishment of structure-activity relationships for these enzymes and a complete elucidation of the mechanisms of enzymatic conversions through the development of synthetic models are expected to contribute greatly to the design of oxidation catalysts for potential industrial applications. 

I have been pursuing enzyme mimics, artificial enzymes that perform biomimetic chemistry, since starting my independent career in 1956. In the first work [52-59] my co-workers and I studied models for the function of thiamine pyrophosphate 1 as a coenzyme in enzymes such as carboxylase. We discovered the mechanism by which it acts, by forming an anion 2 that we also described as a stabilized carbene, one of its resonance forms. We examined the related anions from imidazolium cations and oxazolium cations, which produce anions 3 and 4 that can also be described as nucleophilic carbenes. We were able to explain the structure-activity relationships in this series, and the reasons why the thiazolium ring is best suited to act as a biological... 

Presently, some information is available on the structure of the active site of PAL and its mechanism of action. This knowledge was advanced with an aim of studies on PAL mutants obtained by site-directed mutagenesis, 100-102 comparison of its structure with the recently determined three-dimensional structure of histidine ammonia-lyase io3,i°4 as wejj as (fog detailed analysis of structure-activity relationship found for its inhibitors.105-108 Despite a recent knowledge of PAL three-dimensional structure, 109 110 the detailed mechanism of this particular enzyme action remains unresolved. 

The effect of gastric HVK -ATPase inhibitors on enzyme activity (ATP cleavage) can be studied in vitro with partly purified HVK -ATPase preparations [27]. This assay has been used more effectively to study the mechanism of action of H /K -ATPase inhibitors in detail than to study the structure-activity relationship of such inhibitors [28]. Since HVK -ATPase inhibitors of the omeprazole-type need acid activation and the enzyme assay should be performed at neutral pH values, a pre-incubation period at the lowest possible pH of about 6 was used to initiate the acidic conversion of the test compound into its active principle. This reflects more the chemical instability of the test compound at neutral pH values than its effect during conditions of much higher acidity within the secretory cannaliculus of the parietal cell during acid secretion. Many chemically labile inhibitors are therefore very active in this test system. However, they do not cause an inhibition in more complex test systems and, therefore, are without any practical usefulness [28]. 

The effect of gastric PPIs on ATPase activity (ATP-induced phosphorylation) can be studied in vitro with partially purified H /K -ATPase preparations Ifom pig gastric mucosa (36). Given that the enzyme assay needs to be performed at neutral pH, this system has been most effectively used to study the mechanism of action of PPIs rather thmi the structure-activity relationship (SAR)... 

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