Proceedings of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS

Human tissue information processing

JELENKA SAVKOVIC-STEVANOVIC Faulty of Technology and Metallury, Belgrade University,Karnegijeva 4, 11000 Belgrade SERBIA, [email protected]

Abstract:-In this paper the metabolisms of the and and their and have examined. The biomedical important is de novo synthesis which is permiting and analogs with potential as anticancer drugs to be incorporated into DNA. The synthesis rates of purine and pyrimidine oxyribonucleotides and are subject to precise regulation. The obtained results of investigation in this paper have shown human tissue information processing incorporating nucleic acids. Keywords: Purine bases, pyrimidine bases, physicochemical properties, DNA,RNA, tissue.

as enzyme inhibitors and can replace 1 Introduction the naturally occurring nucleotides in nucleic acids. The nucleotides participate in a wide variety of Therapeutic attempts to inhibit the growth of biochemical processes. Perhaps the best known role cancer cells or certain viruses have often employed of purine and pyrmidine nucleotides is to serve as administration of analogs of bases, nucleosides, or the monomeric precursors of RNA and DNA[1-4]. nucleotides that inhibit the synthesis of either DNA However, the purine serve also as or RNA.Such compounds include 5-, the ubiquitous high energy source, ATP, as 5’-iodo-2’-, 6-thioguanine,6- regulatory signals (cycle AMP [cAMP] and GMP mercaptopurine, 6- azauridine, and arabinosyl [cGMP]), and as components of the coenzymes . as azauridine. Allopurinol, a purine and of the methyl group donor S adenosil analog, is widely used in the treatment of gout. methionine. The pyrimidine nucleotides in Neither nucleotides nor their parent purine and addition to providing monomeric precursors for pyrimidine bases in the diet are incorporated into synthesis, also serve as high energy human tissue nucleic acids or into purine or intermediates, such as UDP - glucose and UDP- pyrimidine coenzymes such as ATP or NAD. Even galactose in carbohydrate metabolism and CDP- when a diet rich in nucleoproteins is ingested, acylglycerol in lipid synthesis. human subjects form the constituents of tissue The heterocyclic bases purine and pyrimidine nucleic acids from amphibolic intermediates. This are the parent molecules of nucleosides and de novo synthesis permits purine and pyrimidine nucleotides. Nucleotides are ubiquitous in living analogs with potential as anticancer drugs to be cells, where they perform numerous key functions. incorporated into DNA. The rates of synthesis of Examples include incorporation, as their ribose purine and pyrimidine oxy- and (RNA) or (DNA) monophosfates, into deoxyribonucleotides are subject to precise nucleic acids, energy transduction (ATP) , parts of regulation. Mechanisms have evolved to ensure coenzymes (AMP) acceptors for oxidative production of these compounds in quantities and at phosphorylation (ADP) allosteric regulators of times appropriate to meet varying physiologic enzyme activity, and second messengers (cAMP), demand. In addition to de novo synthesis, these cGMP). include “salvage” pathways for reutilization of purine or pyrimidine bases released by degradation The structure and function of the purines and of nucleic acids in vivo. Human diseases that pyrimidines and their nucleosides and nucleotides involve abnormalities in purine or pyrimidine were studied in numerous literature. metabolism include gout, Lesch-Nyhan syndrome, In this paper the metabolism of the purines and Reye’s syndrome, deaminase deficiency, pyrimidines and their nucleosides and nucleotides and purine phosphorylase deficiency. have examined. 3 Structure and properties of purine and pyrimidine base 2 Biomedical important Purine and pyrimidine bases that occur in the Synthetic analogs of naturally occurring nucleotides are derived by substitution on the ring nucleotides find application in cancer

ISSN: 1790-5125 64 ISBN: 978-960-474-110-6 Proceedings of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS

structures of the parent substances, purine and attached at N9 . consists of pyrimidine. with with D-ribose attached at N9 . ytidine is cytosine with ribose attached at its N position. The three major pyrimidine bases present in 1 consists of ribose attached at the position the nucleotides of both procaryotes and eukaryotes of . are cytosine, , and uracil. The purine bases and guanine are the two major purines The 2’- consist of 2- found in living organisms. Two other purine bases, deoxyribose attached to purine or pyrimidine bases. and , occur as intermediates Attachment of the ribose or 2-deoxyribose to the in the metabolism of adenine and guanine. In ring structuresis through an glycosidic bond, which humans, a completely oxidizes purine base, uric is relatively acid labile. Although, theoretically, acid, is formed as the end product catabolism. free rotation of the moiety and the purine or pyrimidine In natural materials, unusual bases occur in he addition to the 5 major described bases. Some of Ring structure occurs about this N-glycosidic these unusual substituted bases are present only in bond, steric hindrance in fact hinders free rotation. the nucleic acids of bacteria and viruses, but many In the naturally occurring nucleosides, the anti are also found in the DNA and transfer of conformation is strongly favored over the syn both prokaryotes and eukaryotes. For example, form. The anti form is necessary for the proper both bacterial and human DNA contain significant positioning of the complementary purine and quantities of 5-methylcytosine, bacteriophages pyrimidine bases in the double stranded B-form of contain 5- hydroxyl-methyl-cytosine. Unusual deoxyribonucleic acid. bases presenting the messenger RNA molecules of Nucleotides are nucleosides phophotylated on mammalian cells include N6, N6-dimethyladenine, one or more of the hydroxyl groups of the sugar and N7-methylguanine. An uracil modified at theN 3 (ribose or deoxyribose). Thus, adenosine position by the attachment of an (α-amino, α- monophosphate(AMP or adenylate) is adenine + carboxyl)-propyl group has also been detected in ribose +. 2’- mono- bacteria. phosphate (dAMP or deoxyadenylate) consists of In plants, a series of purine bases ontaining 2-deoxyribose + phosphate. The only sugar methyl occurs. Many hve commonly found attached to uracil is ribose, and pharmacologic properties. Examples are coffee, that commonly found attached to thymine is 2- which contains caffeine (1,3,7 –trimethylxanthine), deoxyribose. Therefore, thymidic acid (TMP) is tea, which contains theophylline (1,3- thymine +2-deoxyribose +phosphate, and uridylic dimethylxanthine). acid (UMP) is uracil +phosphate. DNA is a polymer of thymidilic acid, 2’-deoxycytidilic acid, Because of keto-enol tautomerism, thses 2’-deoxyadenylic acid, and 2’-deoxyguanylic acid. aromatic molecules can exist in a lactim or lactam RNA is a polymer containing uridylate, citydilate, form, the latter is by far the predominant tautomer adenylate, and guanylate. of guanine or thymine under physiologic conditions. There areexpectations to the above structures of nucleotides. For example, in tRNA riboeis At neutral pH, guanine is the least soluble of occasionally attached to uracil at the 5 position, the bases, followed in thi respect y xanthyne. establishing a carbon-to-carbon linkage instead of Although uric acid as urate is relatively soluble at the usual nitrogen –to-carbon linkage. This a neutral pH, it is highly insoluble in solutions unusually compound is called pseudo uridine (ψ). with a lower pH, such as urine. Guanine is not a tRNA molecules contain another unusual normal constituent of human urine, but xanthyne structure, i.e. thymine attached to ribose and uric acid do occur in human urine. These latter monophosphate. Pseudurydilic acid (ψMP) is 2 purines frequently occur as constituents of similarly rearranged from urydilic acid after the t urinary tract stones. RNA molecule has been synthesized.

The abbervations A,G,C,T, and U may be used to designate the nucleosides that contain adenine, 4 Nucleosides and nucleotides guanine, cytosine thymine, or uracil, respectively. The free bases are much less abundant in nature For example, guanosine containing 2’-deoxyribose than are their nucleosides and nucleotides. The would be designated dG () and the nucleoside is composed of a purine or a pyramidine corresponding monophosphate with the pphosphate base to which a sugar (usually either D-ribose or esterified to the carbon 3 of the deoxyribose moiety 2-deoxyribose) is attached in β –linkage at N9 or designated dG-3’-MP. Generally, when the N1, respectively. Thus, the adenine ribonucleside phosphate is esterified to the carbon 5 of the ribose adenosine consists of adenine with D-ribose or deoxyribose moiety, the prefixed primed (5’) is omitted. For example, gunosine 5’- monophosphate

ISSN: 1790-5125 65 ISBN: 978-960-474-110-6 Proceedings of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS

would be abbreviated GMP , while the 5’- conversion of ribose 5-posphate and ATP to AMP monophosphate of 2’-deoxyguanosine would be +PRPP is not however unique to the synthesis of designated dGMP. When 2 or 3 are purine nucleotides. PRPP also serves as a attached to the sugar moiety in the acid anhydride precursors of the pyrimidine nucleotides and form, the abbervations DP (diphosphate) and TP required for the synthesis of NAD and NADP, 2 (triphosphate) are added to the abbervations for the coenzymes derived from niacin. corresponding purine or pyrimidine nucleoside. PRPP then react with glutamine in a reaction Because the phosphate are in the acid anhydride catalyzed by phosphor ribosylpyrophosphate form - a low entropy situation-the phosphates are amidotransferase to form 5-phosphoribosyl amine. said to be high energy ones, i.e., high potential The reaction is accompanied by the displacement energy. The hydrolysis of 1 mol ATP to ADP of pyrophosphate and the formation of glutamate. releases about 7 x 4,16 kJ of potential energy. Although other mechanism have been proposed for Free nucleotides also perform important the synthesis of 5- phosphoribosylamine, the functions in tissues. physiological important reaction in mammalian tissues is that catalyzed by the amidotransferase. 5- The functional moieties of many vitamins are phosphoribosylamine, then reacts with glycine to coenzyme nucleotides with structures analogous to produce glycinamide ribosylphosphate. Synthesis purine and pyramidine nucleotides. of purine and pyramidine deoxyribonucleptides Mammals and most lower vertebrates are occurs by direct reduction at the 2’-carbon in the prototrophic for purines and pyrimidines, i.e., they ribose moiety of the corresponding nucleotide, not synthesize purine and pyrimidine nucleotides de by synthesis of the entire nucleotide utilizing 2’- novo. deoxy analog of PRPP. Several antimetabolites that are glutamine analogs are effective inhibitors of purine 5 Metabolism . Mammals and most lower vertebrates are Conversion of AMP and GMP to their prototrophic for purines and pyrimidines, i.e., they respective nucleoside diphosphates and nucleoside synthesize purine and pyrimidine nucleotides de triphosphates occurs in 2 successive steps. The novo. successive transfers of phosphate groups from ATP are catalysed by nucleoside monophosphate In human and other mammals, purine and nucleoside diphosphate kinase, nucleotides are synthesized to meet the needs of the respectively. The enzyme that phosphorylates organism for the monomeric precursors of nucleic adenalyte is also called myokinase. acids and for those other functions. Formation of purine deoxyribonucleotides is In some organisms (birds, amphibians, and performed by synthesis of purine and pyramidine reptiles), the synthesis of purine nucleotides has an deoxyribonucleotides which occurs by direct additional function, which is to serve as the reduction at the 2’-carbon in the ribose moiety of chemical vehicle to excrete nitrogen waste products the corresponding nucleotide, not by synthesis of as uric acid. Such organisms are referred to as the entire nucleotide utilizing a 2’-deoxy analog of uricotelic, whereas those organisms which dispose PRPP. Reduction at the 2’- carbon occurs only after of nitrogenous waste products in the form of urea, the purine and pyramidine nucleotides have been as humans do, are referred to as ureotelic. Because converted to their respective nucleoside the uricotelic organisms must dispose of their diphosphates. In some bacteria, cobalamin (vitamin nitrogenous wastes in the form of uric acid., they B12) is required for this reductive process, although synthesize purine nucleotides at a relatively greater it is not required for the same reaction in mammals. rate than do ureotelic organisms. However the steps Reduction of diphosphates to involved in de novo purine nucleotide synthesis in diphosphates is catalysed by mammals (ureotelic) are analogous of those in reductase and requires thioredoxin birds (uricotelic). (a protein cofactor), thioredoxin reductase (a Information on the source of the various atoms flavoprotein), and NADPH as cofactor.The of the purine base obtained by tracer studies in immediate electron donor to the nucleotide is birds, rats, and humans. thioredoxin that has been reduced by NADPH. The reversibile oxidation-reduction of thioredoxinis The biosynthetic pathway for the synthesis of catalyzed by thioredoxin reductase. Reduction of purine nucleotides can be summarized in the ribonucleoside diphosphates by reduced following steps. The first step in the synthesis of thioredoxins only when they are actively purine nucleotides is the formation of 5- synthesizing DNA and dividing. phosphoribosyl-1-pyrophosphate (PRPP). The

ISSN: 1790-5125 66 ISBN: 978-960-474-110-6 Proceedings of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS

6 Tissue specify of purine biosynthesis Not all human tissues catalyze the de novo Ribose 5-phosphate + ATP synthesis of purine nucleotides. Erytrocites and polymorphonuclear leukocites are incapable of synthesizing 5-phpsphoribosilamine and therefore PRPP SYNTHETASE are independent upon exogenous purines for the formation of purine nucleotides (Fig.1). Peripheral lymphocytes do possess some ability to synthesize PRPP purines de novo. Mammalian brain appears to have - a reduced content of PRPP amidotransferase, ideed, it has been suggested that the human brain is 5- Phosphoribosylamine dependent upon exogenous purines for the formation of purine nucleoptides. Mammalian liver is a major site of purine nucleotide synthesis and . provides purines in the form of bases or - - nucleosides to be salvaged and utilized by those tissues incapable of synthesizing purines de novo. IMP The most important regulator of de novo purine biosynthesis is the intracellular concentration of PRPP. AMP GMP 7 Biosynthesis of pyrimidine

Although the pyramidine nucleus is simpler and its synthetic pathway briefer than that of the purine ADP GDP structure, the share several common precursors.

PRPP, glutamine, CO2, and aspartate are required for the synthesis of all pyramidine and purine ATP GTP nucleotides. For the thymidne nucleotides and for all purine nucleotides, tetrahydrofolate derivates Chemical flow are also necessary. There is one striking difference ------feedback inhibition between the syntesis of pyrimidine nucleotides and end products pathway that of purine nucleotides, namely, that the - synthesis of the purine nucleotides commences with ribose phosphate as an integral part of the earliest precursor molecule, whereas the pyrimidine Fig.1 De novo synthesis purine control base is formed and attachment of the ribose In a subsequent dehydrogenation step catalyzed phosphate moiety delayed until the later steps of by dihydroorotate dehydrogenase and utilizing the pathway. NAD as a cofactor, orotic acid is formed. Then a Synthesis of the pyrimidine ring commences ribose phosphate moiety is aidded to orotic acid to with the formation of carbamoyl phosphate from form orotidylate (orotidine monophosphate, OMP). This reaction is catalyzed by orotate glutamine, ATP, and CO2, in a reaction catalyzed by the carbamoyl phosphate synthase in the phosphoribosyltransferase, an enzyme analogous to cytosol. The carbamoyl phosphate synthase the hypoxanthine-guanine phosphoribosyl- enzyme responsible for the early steps in urea transferase, and the adenine phosphoribosyl- synthesis resides in the mitochondria. transferase, involved in the phosphoribosylation of performed purine rings. The first step uniquely committed to the biosynthesis of pyrimidines is the formation of The first true pyrimidine ribonucleotide is carbamoyl aspartate by the condensation of formed by the decarboxylation of orotidylate to carbamoyl phosphate and aspartate, a reaction form uridilate (UMP-). catalyzed by the enzyme aspartate Dihydroorotate dehydrogenase is transcarbamoylase. mitochondrial, all the other enzymes in the de novo A ring structure can then be formed from pyrimidine nucleotide pathway are in the cytosol. carbamoyl aspartate by loss of H2O catalyzed by By mechanisms analogous to those desribed the enzyme dihydroorotase. for the further phosphorylaton of the purine nucleoside

ISSN: 1790-5125 67 ISBN: 978-960-474-110-6 Proceedings of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS

8.1.1 Lesch-Nyhan syndrome and Von Gerke’s disease monophosphates, the pyrimidine nucleoside monophosphates are converted to their diphosphate Some individuals with urate overexctretion greater and triphosphate derivatives. UTP is aminated to than 600mg/uric acid per 24 hours can be CTP by glutamine and ATP. The reduction of the categorized as having secondary hyperuricemia. pyrimidine nucleoside diphosphates occurs by a They have other diease processes such as cancer or mechanism also analogous to that described for the psoriasis that lead enhanced tissue turnover. purine nucleotides. Finally, there are persons with identifiable The formation of thymidylate (TMP- enzyme defects, including abnormalities of PRPP monophosphate)is the one reaction in pyrimidine synthetase, the HGPRT ase (hypoxanthine-guanine nucleotide biosynthesis that requires a phosphoribosyl- transferase ) deficiencies, both the tetrahydrofolate donor of a single carbon complete Lesch-Nyhan syndrome and incomplete compound. In order to continue to use the deficiencies and glucose-6-phosphatase deficiency carrier, the cell must reduce dihydrofolate to von Gierke’s disease. There exists also a group of tetrahydrofolate, a reaction carried out by the patients exhibiting idiopathic overproduction enzyme . Thus, dividing hyperuricemia, which will certainly be regarded as cells that by necessity are generaling TMP and a heterogeneous group of disease ons the molecular dihydrofolate are especially sensitive to inhibitors bases for their metabolic defects are recognized. of dihydrofolate reductase. An example of such an 7.2 Clinical disorders of pyrimidine metabolism inhibitor is (amethopterin, a widely used anticancer drug. The end products of pyrimidine metabolism, unlike those of purine metabolism, are highly water Futhermore, carbamyl phosphate synthase is soluble compounds such as CO , ammonia, β – sensitive to feedback inhibition by both purine and 2 alanine, and propionate. Thus, in circumstances pyramidine nucleotides and activation by PRPP. where pyrimidine overproduction occurs, clinically Thus, there several sites at which there is detectable abnormalities are rarely evident. In in significant cross-regulation between purine and cases of hyperuricemia associated with severe pyramidine nucleotide synthesis. PRPP overproduction, there is concomitant overproduction of pyrimidine nucleotides with increased excretion of compounds such as β – 8 Clinical disorders alanine. 8.1 Clinical disorders of purine metabolism In specific liver mitochondrial failure, such as The predominant form of uric acid is determined in Reye’s syndrome, there is a secondary orotic by the pH of its milieu (eg, blood, urine, acid-urea. cerebrospinal fluid).Thus, under physiologic conditions ie, at the usual pH of physiologic fluids, 8 Conclusions only uric acid and its monosodium salt, sodium This paper illustrated purine and pyrimidine urate, are found. In a fluid where the pH is less than metabolisms. The biosynthesis was control by 5.75, the predominant molecular species will be enzymes. Enzymes were demonstrated successfully uric acid. In a fluid at pH 5.75, the concentration of control and deficiencies recognition. sodium urate will equal that of uric acid. At a pH greater than 5.75, sodium urate will predominate The obtained results in the frame of this in the solution. investigation show metabolisms information processing in the human body. The miscible urate pool in the body is reflected by the sodium urate concentration in the serum. Results of this investigation can be applied in When this level exceeds the solubility of sodium the other domain in biomedical engineering. urate in serum (hyperuricemia), crystals of sodium urate may precipitate. The solubility of sodium Acknowledgment. The author wishes to express her urate in serum at 37 ˚C is 7 mg/dl. Crystals of gratitude to the Fund of Serbia for financial support. sodium urate can collect and deposit in soft tissues, particularly in or about joints. These urates Notation deposits are referred to as tophi. Accumulation of sodium urate crystals in the tissues including AMP- adenine monophosphate phagocytosis of the crystals by polymorphonuclear ADP- adenine diphosphate leukocytesin joint spaces, can lead to an acute inflammatory reaction called acute gouty arthritis. ATP- adenine triphosphate CTP- cytosine triphosphate

ISSN: 1790-5125 68 ISBN: 978-960-474-110-6 Proceedings of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS

DP-diphosphate GDP- guanine diphosphate GMP-guanine monophosphate GTP- guanine triphosphate HGPRTase-hypoxanthine-guanine phosphoribosyl- transferase IMP- monophosphate MP-monnophosphate NADPH-cofactor OMP- orotidine monophosphate PRPP- phosphoribosyl-pyrophosphate TMP-thymidine monophosphate TP- triphosphate UMP- uridine monophosphate UTP-

9 References [1] J.Savkovic-Stevanovic, Informational macromolecule in biological systems, MCBC2009-Mathematics and Computers in Biology and Chemistry, Prague,March,23- 25,2009. [2] J.F.Henderson, A.R.P. Paterson, Nucleotide metabolism:An introduction, Academic Press,1973. [3] Michelson A.M. The chemistry of nucleosides and nucleotides, Academic Press,1963. [4] W.H., Prusoff, D.C.Ward, Nucleoside analogs with antivirial activity, Biochem. Pharmacol. 25,1233,1976. [5] B.N.Ames, et al., Uric acid provides an antioxidant defense in humans against oxidant- and radical –caused aging and cancer: A hypothesis. Proc. Natl. Acad. Sci USA,78,6858,1981. [6] M.Jones Pyrimidine nucleotide biosynthesis in animal cells, Annu Rev.Biochem. 49,523,1980.

ISSN: 1790-5125 69 ISBN: 978-960-474-110-6