De novo pathway

Figure 24-4. Biosynthesis of ether lipids, including plasmalogens, and platelet-activating factor (PAF). In the de novo pathway for PAF synthesis, acetyl-CoA is incorporated at stage, avoiding the last two steps in the pathway shown here.

Mycophenolate mofetil was approved by the FDA in 1995, and enteric-coated mycophenolic acid was approved in 2004. Both agents are considered to be adjunctive immunosuppressants. Mycophenolic acid acts by inhibiting inosine monophosphate deydrogenase, a vital enzyme in the de novo pathway of purine synthesis. Inhibition of this enzyme prevents the proliferation of most cells that are dependent on the de novo pathway for purine synthesis, including T cells.7,11,26-28... 

L-2 cells (ATCC HTB-149) have been isolated by clonal culture techniques from the adult rat lung. These cells appear to retain differentiated functions that are present in ATII cells of intact rat lungs. L-2 cells are diploid, epithelial cells. They contain osmiophilic lamellar bodies in their cytoplasm and synthesise lecithin by the same de novo pathways as in a whole lung [78], It is not known if L-2 cells are capable to form confluent and electrically tight monolayers. L-2 cells have not been systematically investigated regarding their suitability as a model for absorption studies. 

Both pathways have been shown to be relevant for PCDD/F formation in municipal-waste incinerations. Chlorophenols can be converted to PCDD by copper species known in synthetic chemistry as the Ullmann type II coupling reaction. By use of isotope labeling techniques in competitive concurrent reactions with both reactions performed in laboratory experiments it was shown that precursor theory pathways from chlorophenols may be more important compared to the de novo pathway, but either competing pathway strongly depends on such conditions as temperature, air flow rate, and residence time. It may be difficult to model the complex reahty of large incinerators using relevant laboratory experiments. 

Figure 1-18-1. Nucleotide Synthesis by Salvage and De Novo Pathways...

Mycophenolate sodium (62 Myfortic Norvatis, 2003) is an immunosuppressant drug used to prevent rejection in organ transplantation. It is a selective, noncompetitive, reversible inhibitor of inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme in the de novo pathway of guanosine nucleotide synthesis. Thus, mycophenolic acid (61), originally... 

A number of other purines, purine ring analogues, and their ribonucleosides have been evaluated as feedback inhibitors [13, 173, 294, 297, 297a] by a modification [294] of the method of LePage and co-workers [291,298,299,300]. This method utilizes azaserine to isolate the first few steps of the de novo pathway in whole cells by the specific blockade of the conversion of formylglycinamide... 

In addition to the analogues listed in Table 2.3, cordycepin [302]. 3 -amino-3 -deoxyadenosine [173], and formycin [303] can inhibit the de novo pathway by blocking the phosphoribosylpyrophosphate amidotransferase. Thus, a number ofpurine analogues—after anabolism to nucleoside phosphates—can act as feedback inhibitors, and this inhibition may be the primary cause of their cytotoxicity. 

The mechanism of inhibition of these protozoal infections by the most active drugs, puromycin and the aminonucleoside, is not known. Puromycin and nucleocidin both interfere with protein synthesis, but the aminonucleoside does not. It is known to be demethylated to 3 -amino-3-deoxyadenosine, which is phosphorylated and interferes with nucleic acid metabolism (see above). Whether puromycin must be converted to the aminonucleoside before it can inhibit protozoa has not been established. Some purine analogues known to interfere with nucleic acid metabolism, however, are less effective as antiprotozoal agents, even in vitro, perhaps because their effects are primarily on the de novo pathway which many, if not all, protozoa do not use [406]. 

Mechanism of Action Selectively inhibits inosine monophosphate dehydrogenase in the de novo pathway of purine synthesis, producing potent cytostatic effects on T and B lymphocytes... 

Two types of pathways lead to nucleotides the de novo pathways and the salvage pathways. De novo synthesis of nucleotides begins with their metabolic precursors amino acids, ribose 5-phosphate, C02, and NH3. Salvage pathways recycle the free bases and nucleosides released from nucleic acid breakdown. Both types of... 

The de novo pathways for purine and pyrimidine biosynthesis appear to be nearly identical in all living organisms. Notably, the free bases guanine, adenine, thymine, cytidine, and uracil are not intermediates in these pathways that is, the bases are not synthesized and then attached to ribose, as might be expected. The purine ring structure is built up one or a few atoms at... 

Several important precursors are shared by the de novo pathways for synthesis of pyrimidines and purines. 

Phosphoribosyl pyrophosphate (PRPP) is important in both, and in these pathways the structure of ribose is retained in the product nucleotide, in contrast to its fate in the tryptophan and histidine biosynthetic pathways discussed earlier. An amino acid is an important precursor in each type of pathway glycine for purines and aspartate for pyrimidines. Glutamine again is the most important source of amino groups—in five different steps in the de novo pathways. Aspartate is also used as the source of an amino group in the purine pathways, in two steps. 

DNA contains thymine rather than uracil, and the de novo pathway to thymine involves only deoxyribonu-cleotides. The immediate precursor of thymidylate (dTMP) is dUMP. In bacteria, the pathway to dUMP begins with formation of dUTP, either by deamination of dCTP or by phosphorylation of dUDP (Fig. 22-43). The dUTP is converted to dUMP by a dUTPase. The latter reaction must be efficient to keep dUTP pools low and prevent incorporation of uridylate into DNA. 

Purine bases from ingested foods, or formed by catabolism of nucleic acids, are able to react with PRPP under the influence of phosphoribosyltransferases.3063 Two such enzymes are known to act on purines. One converts adenine to AMP (Fig. 25-17, step b) and also acts upon 5-aminoimidazole-4-carboxamide. This enzyme may be especially important to parasitic protozoa such as Leishmania, which lack the de novo pathway of purine synthesis (Fig. 25-15).278/306b... 

Figure 25-18 Pathways of catabolism of purine nucleotides, nucleosides, and free bases. Spiders excrete xanthine while mammals and birds excrete uric acid. Spiders and birds convert all of their excess nitrogen via the de novo pathway of Fig. 25-15 into purines. Many animals excrete allantoin, urea, or NH4+. Some legumes utilize the pathway marked by green arrows in their nitrogen transport via ureides.

In view of the central importance of amino acids in proteins, we might expect that all organisms would possess the necessary enzymes to synthesize the protein amino acids. Surprisingly, only eight protein amino acids can be synthesized by the standard de novo pathways (fig. 22.1). The remainder are synthesized by alternative pathways (sometimes referred to as salvage pathways) or supplied by nutrients. 

The inability of mammals to synthesize all of the amino acids they require has led to the classification of amino acids as essential and nonessential. Conceptually this distinction seems clear. Practically speaking, it turns out to be more complex to designate essential amino acids. An essential amino acid, in this classification, means one that must be supplied in the diet if the organism is to maintain a positive nitrogen balance. As we will see, the absence of a de novo pathway for the biosynthesis of an amino acid does... 

Synthesis of arginine by the salvage pathway found in vertebrates and by the de novo pathway found in plants and bacteria. The final steps from ornithine to arginine are also part of the urea cycle (see fig. 22.7). 

Another form of detoxified ammonia that is used in nitrogen excretion is uric acid. Uric acid is the predominant nitrogen excretory product in birds and terrestrial reptiles (turtles excrete urea, whereas alligators excrete ammonia unless they are dehydrated, in which case they, too, excrete uric acid). Uric acid formed as a product of amino acid catabolism involves the de novo pathway of purine biosynthesis therefore, its formation from NH3 liberated in amino acid catabolism is described elsewhere (see chapter 23). In mammals, uric acid is exclusively an intermediate in purine... 

Only eight of the de novo pathways for amino acid biosynthesis can be found in humans. These amino acids are all related by a small number of steps to glycolytic or TCA cycle intermediates. A number of additional amino acids can be formed from these amino acids. Essential amino acids are those that must be supplied in the diet. 

The A-acetyl groups in the de novo pathway prevent the spontaneous cyclization of the semialdehyde intermediate. 

De novo pathway. A biochemical pathway that starts from elementary substrates and ends in the synthesis of a biochemical. 

Moussavi M, Assi K, Gomez-Munoz A, Salh B. 2006. Curcumin mediates ceramide generation via the de novo pathway in colon cancer cells. Carcinogenesis 27 1636-1644. 

The endogenously synthesised dTTP dilutes the specific activity of the [3H]dTTP formed from the added [3H]thymidine. Thus on adding tritiated thymidine at 3 X 10 8M most of the DNA thymine is synthesised by the endogenous or de novo pathway, but when the [3H]thymidine concentration in the medium is raised to 0.3 mM it contributes 90% or more of the DNA thymine (Cleaver and Holford, 1965 Cooper et al., 1966 Cleaver, 1967). As the specific activity of [3H]dTTP is one of the factors which determine the amount of radioactivity incorporated into DNA (either total counts/min or grain counts) and as this varies (a) with external thymidine concentration and (b) with the state of the cells, the quantitative estimation of rates of DNA synthesis is full of pitfalls. 

Understand the purine and pyrmidine de novo biosynthetic pathways, with special attention to enzymes controlling pathway rates and the properties of such enzymes the positive and negative effectors steps inhibited by the various antitumor agents and their mechanisms final products of the de novo pathways and how the various nucleotides are generated from them and the biosynthesis of deoxyribonucleotides and the attendant mechanisms. 

The so-called salvage pathways are available in many cells to scavenge free purine and pyrimidine bases, nucleosides, and mononucleotides and to convert these to metabolically useful di- and trinucleotides. The function of these pathways is to avoid the costly (energy) and lengthy de novo purine and pyrimidine biosynthetic processes. In some cells, in fact, the salvage pathways yield a greater quantity of nucleotides than the de novo pathways. The substrates for salvage reactions may come from dietary sources or from normal nucleic acid turnover processes. 

A serious genetic disorder is associated with the salvage pathways, the Lesch-Nyhan syndrome. It is believed that it is caused by a failure to control the de novo purine biosynthetic pathway. In the Lesch-Nyhan syndrome, the enzyme HGPRTase is severely depressed. Because the de novo pathway is controlled largely via feedback effects of purine nucleotides, the pathway is derepressed and excessive quantities of purine nucleotides and their degradation product, uric acid, are accumulated. This results is neurologic effects, self-mutilation, and mental retardation. 

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