ENZYMES OF THE PYRIMIDINE PATHWAY IN ESCHERICHIA COLI. II. INTRACELLULAR LOCALIZATION AND PROPERTIES OF DIHYDROOROTIC DEHYDROGENASE

The dihydroorotate dehydrogenases: Past and present

The flavoenzyme dihydroorotate dehydrogenase catalyzes the stereoselective oxidation of (S)-dihydroorotate to orotate in the fourth of the six conserved enzymatic reactions involved in the de novo pyrimidine biosynthetic pathway. Inhibition of pyrimidine metabolism by selectively targeting DHODHs has been exploited in the development of new therapies against cancer, immunological disorders, bacterial and viral infections, and parasitic diseases. Through a chronological narrative, this review summarizes the efforts of the scientific community to achieve our current understanding of structural and biochemical properties of DHODHs. It also attempts to describe the latest advances in medicinal chemistry for therapeutic development based on the selective inhibition of DHODH, including an overview of the experimental techniques used for ligand screening during the process of drug discovery.

On dihydroorotate dehydrogenases and their inhibitors and uses

Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.

Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model

Plasmodium falciparum, the causative agent of the most deadly form of human malaria, is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHODH) catalyzes the rate-limiting step in the pyrimidine biosynthetic pathway and represents a potential target for anti-malarial therapy. A high throughput screen and subsequent medicinal chemistry program identified a series of N-alkyl-5-(1H-benzimidazol-1-yl)thiophene-2-carboxamides with low nanomolar in vitro potency against DHODH from P. falciparum, P. vivax, and P. berghei. The compounds were selective for the parasite enzymes over human DHODH, and x-ray structural data on the analog Genz-667348, demonstrated that species selectivity could be attributed to amino acid differences in the inhibitor-binding site. Compounds from this series demonstrated in vitro potency against the 3D7 and Dd2 strains of P. falciparum, good tolerability and oral exposure in the mouse, and ED(50) values in the 4-day murine P. berghei efficacy model of 13-21 mg/kg/day with oral twice-daily dosing. In particular, treatment with Genz-667348 at 100 mg/kg/day resulted in sterile cure. Two recent analogs of Genz-667348 are currently undergoing pilot toxicity testing to determine suitability as clinical development candidates.

Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase

Plasmodium falciparum causes the most deadly form of malaria and accounts for over one million deaths annually. The malaria parasite is unable to salvage pyrimidines and relies on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHOD), a mitochondrially localized flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive antimalarial chemotherapeutic target. Using a target-based high throughput screen, we have identified a series of potent, species-specific inhibitors of P. falciparum DHOD (pfDHOD) that are also efficacious against three cultured strains (3D7, HB3, and Dd2) of P. falciparum. The primary antimalarial mechanism of action of these compounds was confirmed to be inhibition of pfDHOD through a secondary assay with transgenic malaria parasites, and the structural basis for enzyme inhibition was explored through in silico structure-based docking and site-directed mutagenesis. Compound-mediated cytotoxicity was not observed with human dermal fibroblasts or renal epithelial cells. These data validate pfDHOD as an antimalarial drug target and provide chemical scaffolds with which to begin medicinal chemistry efforts.

ENZYMES OF THE PYRIMIDINE PATHWAY IN ESCHERICHIA COLI. I. SYNTHESIS BY CELLS AND SPHEROPLASTS

Taylor, W. Herman (Portland State College, Portland, Ore.), and G. David Novelli. Enzymes of the pyrimidine pathway in Escherichia coli. I. Synthesis by cells and spheroplasts. J. Bacteriol. 88:99-104. 1964.-Upon release from repression, cells and spheroplasts of two mutants of Escherichia coli efficiently synthesized aspartate transcarbamylase and ornithine transcarbamylase, whereas only cells synthesized dihydroorotic dehydrogenase. Ethylenediaminetetraacetate treatment and sucrose incubation of cells were found to be responsible for the loss of dihydroorotic dehydrogenase synthesis. Spheroplasts required the addition of amino acids and an energy source for the synthesis of aspartate transcarbamylase. Uracil repressed synthesis of aspartate transcarbamylase in spheroplasts as well as in cells. Chloramphenicol inhibition and amino acid requirement for increased aspartate transcarbamylase activity in spheroplasts indicated de novo protein synthesis. E. coli 15, R185-482, and E. coli K-12, 496, were used to study the effect of carbon source and stimulation by orotate and dihydroorotate on synthesis of dihydroorotic dehydrogenase. Only E. coli 15, R185-482, showed any stimulation of dihydroorotic dehydrogenase synthesis. When glucose was the carbon source, orotate but not dihydroorotate stimulated; with glycerol as carbon source, dihydroorotate stimulated and orotate acted as a repressor. These results are discussed in terms of induction and pyrimidine supply to the cells.

De novo synthesis of pyrimidine nucleotides by Helicobacter pylori

The incorporation of pyrimidine nucleotide precursors into Helicobacter pylori and the activities of enzymes involved in their synthetic pathways were investigated by radioactive tracer analysis and 31P nuclear magnetic resonance spectroscopy. The bacterium was found to take up aspartate and bicarbonate and to incorporate carbon atoms from these precursors into its genomic DNA. Orotate, an intermediate of de novo pyrimidine biosynthesis, and uracil and uridine, precursors for pyrimidine pathways, were also incorporated by the micro-organism. Radiolabelled substrates were used to assess the activities of aspartate transcarbamoylase, orotate phosphoribosyltransferase, orotidylate decarboxylase, CTP synthetase, uracil phosphoribosyltransferase, thymidine kinase and deoxycytidine kinase in bacterial lysates. The study provided evidence for the presence in H. pylori of an operational de novo pathway, and a less active salvage pathway for the biosynthesis of pyrimidine nucleotides.

Cloning, nucleotide sequence and regulation of the Salmonella typhimurium pyrD gene encoding dihydroorotate dehydrogenase

The Salmonella typhimurium pyrD gene encoding dihydroorotate dehydrogenase was cloned and sequenced. In total, a sequence of 1286 nucleotide pairs was determined wherein a single open-reading-frame of 1011 bp, encoding a polypeptide of 336 amino acids having 95% similarity with the Escherichia coli pyrD gene product, was identified. A region of hyphenated-dyad symmetry exists within the leader region affording the potential for the formation of a stable secondary structure in the 5' end of the transcript. Mutations from several regulatory mutants were located within the region of dyad symmetry which would impart changes in the transcript within the putative secondary structure, implicating the secondary structure in regulation. Primer extension analysis revealed multiple transcriptional start sites located six to nine nucleotides downstream from the Pribnow box, with the primary initiation site differing in repressing and derepressing growth conditions. The results are discussed in terms of a translational attenuation model for regulation of pyrD expression.

A Salmonella typhimurium mutant dependent upon carbamyl aspartate for resistance to 5-fluorouracil is specifically affected in ubiquinone biosynthesis

The isolation and properties of a mutant dependent upon exogenous carbamyl aspartate for resistance to 5-fluorouracil are described. The mutant was deficient in the synthesis of ubiquinone and accumulated a quinone provisionally identified as the ubiquinone precursor 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone. The mutation resulted in an alteration in the regulation of synthesis of enzymes involved in de novo pyrimidine biosynthesis but did not establish a functional block in dihydroorotate dehydrogenase activity in vivo. Conditional resistance to 5-fluorouracil apparently occurred through an inhibition of the conversion of the analog to the nucleotide level.

A mutation in Salmonella typhimurium imparting conditional resistance to 5-fluorouracil and a bioenergetic defect: mapping of cad

The position of the genetic locus allelic with the cad-2 mutation has been located between units 14 and 15 of the linkage map of S. typhimurium. Fine structure mapping established the gene order as cad flrB nag. The genetic evidence coupled with biochemical evidence indicates that this cad locus is homologous to the ubiF gene of Escherichia coli.

The anaerobic oxidation of dihydroorotate by Escherichia coli K-12

The oxidation of dihydroorotate under anaerobic conditions has been examined using various mutant strains of Escherichia coli K-12. This oxidation in cells grown anaerobically in a glucose minimal medium is linked via menaquinone to the fumarate reductase enzyme coded for by the frd gene and is independent of the cytochromes. The same dihydroorotate dehydrogenase protein functions in both the anaerobic and aerobic oxidation of dihydroorotate. Ferricyanide can act as an artificial electron acceptor for dihydroorotate dehydrogenase and the dihydroorotate-menaquinone-ferricyanide reductase activity can be solubilised by 2 M guanidine-HCl with little loss of activity.

Biosynthetic dihydroorotate dehydrogenase from Lactobacillus bulgaricus: partial characterization of the enzyme

Some of the catalytic properties of the biosynthetic dihydroorotate dehydrogenase purified from an anaerobic bacterium, Lactobacillus bulgaricus, are described. Studies with p-hydroxymercuribenzoate, N-ethylmaleimide, and mercuric chloride showed that sulfhydryl groups are necessary for transfer of electrons from dihydroorotate to a variety of electron acceptors. Protection studies with substrates for the enzyme indicated that free sulfhydryl groups at or near the active center are required for catalytic activity. Evidence is presented for the production of superoxide free radicals during reaction of the enzyme with molecular oxygen. Inhibitor studies with Tiron indicated that reduction of cytochrome c by the enzyme may involve the superoxide free radical as an intermediate. Orotate, one of the substrates for the enzyme, has been found to be a competitive inhibitor for the dihydroorotate site. The K(i) for orotate as estimated by several techniques is 0.1 mM. The K(m) for dihydroorotate with ferricyanide as the electron acceptor is estimated to be 0.5 mM.

Repression of enzyme synthesis of the pyrimidine pathway in Salmonella typhimurium

It has been reported by other workers that a uridine and probably also a cytidine nucleotide are required for maximal repression of aspartate transcarbamylase encoded by the gene pyrB in Salmonella typhimurium. We have identified the repressing metabolites for three more biosynthetic enzymes, namely, dihydroorotate dehydrogenase (encoded by pyrD), orotidine-5'-monophosphate pyrophosphorylase (encoded by pyrE), and orotidine-5'-monophosphate decarboxylase (encoded by pyrF), as well as examining the repression profiles of aspartate transcarbamylase in more detail. Using a specially constructed strain of S. typhimurium (JL1055) which lacks the enzymes for the interconversion of cytidine and uridine compounds, thus allowing the independent manipulation of endogenous cytidine and uridine nucleotides, we found that a cytidine compound is the primary effector of repression in all cases except for aspartate transcarbamylase where little repression is observed in excess cytidine. For aspartate transcarbamylase, we found that the primary repressing metabolite is a uridine compound.

Isolation and partial characterization of regulatory mutants of the pyrimidine pathway in Salmonella typhimurium

Mutants of Salmonella typhimurium affected in the regulation of pyrimidine biosynthesis were isolated by two methods. The first involved screening for bacteria able to feed a pyrimidine-requiring indicator strain, and the second involved selection for bacteria simultaneously resistant to two pyrimidine analogues, 5-fluorouracil and 5-fluorouridine, in a S. typhimurium strain unable to degrade 5-fluorouridine. Among the mutants isolated by these methods are constitutive mutants, producing high levels of pyrimidine biosynthetic enzymes in the presence or absence of pyrimidines, and feedback modified mutants, in which aspartate transcarbamylase is partially desensitized to its inhibitor, cytidine triphosphate. No fully desensitized mutant has been found. The partially desensitized character cotransduces with the pyrB locus, that of aspartate transcarbamylase. The constitutive character has been determined in a few cases to be localized in the region of leu and pro on the Salmonella map.

Biosynthetic dihydroorotate dehydrogenase from Lactobacillus bulgaricus

This paper describes the first detailed study on a dihydroorotate dehydrogenase involved in pyrimidine biosynthesis. In most organisms the enzyme is membrane-bound; however, a soluble dihydroorotate dehydrogenase was produced in relatively high levels when the anaerobe, Lactobacillus bulgaricus, was released from repression. The enzyme was purified 213-fold over derepressed levels with a 39% recovery of enzyme units. The enzyme showed only one minor protein contaminant when analyzed by polyacrylamide electrophoresis. It was characterized as a flavoprotein containing only flavine mononucleotide as the prosthetic group. Molecular weight estimations by gel filtration gave a value of approximately 55,000, which is one-half that of the degradative enzyme described by others. During aerobic oxidation of dihydroorotate, the rates of oxygen consumption, orotate formation, and hydrogen peroxide formation were equal, as would be expected in a flavoprotein-catalyzed reaction. The enzymatic activity with ferricyanide as acceptor was optimum around pH 7.7. The stimulation of enzymatic activity over a wide pH range by ammonium sulfate was attributed to an effect on the maximum velocity of the reaction. As analyzed by polyacrylamide electrophoresis, inactivation of the enzyme by visible light resulted in the appearance of a second protein band with lowered specific activity. The purified enzyme used redox dyes, oxygen, or cytochrome c as electron acceptors but was not active with pyridine nucleotides. Flavine adenine dinucleotide has been implicated at the active site for pyridine nucleotide reduction in the degradative enzyme. The biosynthetic enzyme lacks this flavine and the associated activity.

Pyrimidine synthesis in Neurospora crassa: gene-enzyme relationships

A new series of pyrimidine-requiring mutants of Neurospora has been isolated and all enzymes involved in pyrimidine biosynthesis are represented by at least one mutant. Among these mutants is included a single isolate for a new locus, pyr-6. This mutant is deficient in dihydroorotase (DHOase) and represents the only enzymatic step in orotate synthesis for which no mutant previously had been found. This mutant, which mapped genetically on the right arm of linkage group V, is unlinked to any of the other pyrimidine mutants. The DHOase-deficient mutant is also characterized by an unexpected growth behavior. The pyr-1 locus has been specifically associated with a lack of dihydroorotate dehydrogenase (DHOdehase). Mutants isolated in this series for other pyrimidine loci have been related to previously isolated mutants by allelism, recombination, and accumulation studies.

Particulate dihydroorotate oxidase system from a pseudomonad. Linkage with the respiratory chain

A particulate dihydroorotate oxidase system was prepared from a soil pseudomonad. Components of the respiratory chain participating in electron transport from dihydroorotate to molecular oxygen are bound non-heme iron, ubiquinone, cytochromes b and c, and cytochrome oxidase. Alternate pathways to oxygen are also operative. Inhibition by conventional respiratory inhibitors was incomplete. Dyes and added cytochrome c were readily reduced by dihydroorotate. Pyridine–adenine dinucleotide coenzymes were not reduced by the substrate. However, oxidase activities for these cofactors may have prevented any net reduction. The primary site of reaction with dihydroorotate probably consists of a dehydrogenase which is linked to the respiratory chain and is reactive with various dyes.In the absence of external electron acceptors or inhibitors, 0.5 mole of oxygen was consumed per mole of dihydroorotate oxidized. The anaerobic rate of reduction of bound cytochrome c, as studied by the stopped–flow technique, was slower than the maximum initial rates of orotate production.

Two functionally different dihydroorotic dehydrogenases in bacteria

Taylor, W. H. (Portland State College, Portland, Ore.), M. L. Taylor, and D. F. Eames. Two functionally different dihydroorotic dehydrogenases in bacteria. J. Bacteriol. 91:2251-2256. 1966.-We have investigated the relationship between the two kinds of dihydroorotic dehydrogenases produced by bacteria. A pseudomonad, capable of growth on a salts medium with glucose, aspartate, glycerol, or orotate as the carbon source, was isolated from lake bank mud. A particle-bound dihydroorotic dehydrogenase, similar to the biosynthetic enzyme in Escherichia coli, was formed by the pseudomonad when the carbon source was orotate, glucose, glycerol, or aspartate. A soluble, degradative nicotinamide adenine dinucleotide phosphate-linked dihydroorotic dehydrogenase, as well as the particle-bound biosynthetic enzyme, was formed when the pseudomonad was cultivated on orotate. The biosynthetic enzyme links to oxygen or ferricyanide, but not to pyridine nucleotides. Zymobacterium oroticum, when cultivated on glucose, contained only the biosynthetic type of dihydroorotic dehydrogenase. The presence of two functionally different dihydroorotic dehydrogenases in the pseudomonad was suggested on the basis of the following observations: (i) the two enzyme activities were separated by centrifugation; (ii) the pyridine nucleotide-linked activity was formed only when orotate was present in the growth medium; and (iii) the biosynthetic enzyme was stable to storage at -20 C for 4 months, whereas the degradative enzyme activity was destroyed by storage under these conditions.