Enzymes problems with

The problem with most quantum mechanical methods is that they scale badly. This means that, for instance, a calculation for twice as large a molecule does not require twice as much computer time and resources (this would be linear scaling), but rather 2" times as much, where n varies between about 3 for DFT calculations to 4 for Hartree-Fock and very large numbers for ab-initio techniques with explicit treatment of electron correlation. Thus, the size of the molecules that we can treat with conventional methods is limited. Linear scaling methods have been developed for ab-initio, DFT and semi-empirical methods, but only the latter are currently able to treat complete enzymes. There are two different approaches available. 

Toxicological studies have demonstrated that there are no important problems with fluconazole. Therapeutic doses of fluconazole may cause enzyme induction in the Hver. This suggests that interactions with other dmgs cannot be excluded. The side effects are similar to those of itraconazole and include nausea, headache, and vertigo. Occasionally, increased Hver enzymes may be noted. Like itraconazole, fluconazole is contraindicated during pregnancy. 

The biggest limitation of the CoMFA method is the alignment step. The algorithm superimposes the portions of the inhibitors that are of similar stmcture, assuming that they bind with similar orientations in the active site of the enzyme, which is not necessarily the case. Also, because of a problem with alignment, a CoMFA may fail when a few molecules are very dissimilar from all others in the series. Like QSAR, CoMFA does not require a stmcture of the relevant biological receptor, but does require knowledge about a series of inhibitory compounds. 

Clearly, proximity and orientation play a role in enzyme catalysis, but there is a problem with each of the above comparisons. In both cases, it is impossible to separate true proximity and orientation effects from the effects of entropy loss when molecules are brought together (described the Section 16.4). The actual rate accelerations afforded by proximity and orientation effects in Figures 16.14 and 16.15, respectively, are much smaller than the values given in these figures. Simple theories based on probability and nearest-neighbor models, for example, predict that proximity effects may actually provide rate increases of only 5- to 10-fold. For any real case of enzymatic catalysis, it is nonetheless important to remember that proximity and orientation effects are significant. 

One of the problems with cycloserine (57) as an antibacterial agent is its tendency to dimenze In an attempt to overcome this, the prodrug penti/idone (59) has been prepared The primary amino group essential for the dimenzation reacnon is reversibly blocked to prevent this Penti/idone is synthesized conveniently from cycloserine (57) by merely mixing it with acetyl acetone (58) and storing for two days to achieve the dehydration The resulting pentizidone apparently requires enzymic assistance to release cycloserine in vivo [20]... 

The search for inhibitors of this pathway began with the first key regulatory enzyme, HMG CoA reductase. Several clinically useful inhibitors of HMG CoA reductase are now known. One of the most successful, Mevacor, produced by Merck, is one of the pharmaceutical industry s best selling products. However, the problem with inhibiting a branched biosynthetic pathway at an early point is that the biosynthesis of other crucial biomolecules may also be inhibited. Indeed, there is some evidence that levels of ubiquinone and the dolichols are affected by some HMG CoA reductase inhibitors. Consequently, efforts have recently been directed towards finding inhibitors of squalene synthase, the enzyme controlling the first step on the route to cholesterol after the FPP branch point. 

Many procedures have been suggested to achieve efficient cofactor recycling, including enzymatic and non-enzymatic methods. However, the practical problems associated with the commercial application of coenzyme dependent biocatalysts have not yet been generally solved. Figure A8.18 illustrates the continuous production of L-amino adds in a multi-enzyme-membrane-reactor, where the enzymes together with NAD covalently bound to water soluble polyethylene glycol 20,000 (PEG-20,000-NAD) are retained by means of an ultrafiltration membrane. 

Neotame is an artificial sweetener designed to overcome some of the problems with aspartame. The dimethylbutyl part of the molecule was added to block the action of peptidases, enzymes that break the peptide bond between the two amino acids aspartic acid and phenylalanine. This reduces the availability of phenylalanine, eliminating the need for a warning on labels directed at people who cannot properly metabolize phenylalanine. 

The main problems with early, irreversible MAOIs were adverse interactions with other drugs (notably sympathomimetics, such as ephedrine, phenylpropanolamine and tricyclic antidepressants) and the infamous "cheese reaction". The cheese reaction is a consequence of accumulation of the dietary and trace amine, tyramine, in noradrenergic neurons when MAO is inhibited. Tyramine, which is found in cheese and certain other foods (particularly fermented food products and dried meats), is normally metabolised by MAO in the gut wall and liver and so little ever reaches the systemic circulation. MAOIs, by inactivating this enzymic shield, enable tyramine to reach the bloodstream and eventually to be taken up by the monoamine transporters on serotonergic and noradrenergic neurons. Fike amphetamine, tyramine reduces the pH gradient across the vesicle membrane which, in turn, causes the vesicular transporter to fail. Transmitter that leaks out of the vesicles into the neuronal cytosol cannot be metabolised because... 

Under certain circumstances DNA has both primer and template activities. For example, the addition of mononucleotides is to the 3 end of the growing DNA primer. This presents a problem with regard to how the other strand is synthesized. Biochemists have looked hard but unsuccessfully for an enzyme that can add deoxyribonucleotides onto the 5 end of DNA primers. Such a primer should contain a triphosphate on the hydroxyl group of the 5 end. Although a very active 5 -exonuclease, actually part of DNA polymerase I, has made the search for such an activated 5 end extremely difficult, investigators conclude that a polymerase able to use such a primer probably does not exist. On the contrary, good evidence suggests that the synthesis of both strands is by the known DNA poly-merases. 

Phytate (myo-inositol hexaphosphate Fig. 15.3, structure 33) is found in many food species and can be considered as a phytochemical. Its role in the plant is primarily as a phosphate store in seeds, but it is found in other tissues as well, for example, tubers (Harland et al., 2004). Phytate and its hydrolysis products are anti-nutrients that chelate metal ions and thus reduce their bioavailability (Persson et al., 1998 House, 1999). This is particularly a problem with cereal grains, but pre-processing can improve mineral absorption from these foods (Agte and Joshi, 1997). There is some concern that high phytate foods could also contain higher levels of toxic heavy metals caused by natural accumulation. Plants also contain phytate-degrading enzymes that can also influence metal ion bioavailability (Viveros et al., 2000). 

One problem with the ATP assay in aqueous media is that the enzyme requires hydrophobic media the reaction rate of luciferase-catalyzed reactions is variously affected by the presence of detergents [117, 118]. The presence of cationic liposomes improves sensitivity by a factor of five times compared to that in water alone [119]. 

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