Home About us Contact
|
Home About us Contact | ||
|
|
||
Dihydrofolate Reductase (dihydrofolate + reductase)
Terms modified by Dihydrofolate Reductase Selected AbstractsThe Role of Arginine 28 in Catalysis by Dihydrofolate Reductase from the Hyperthermophile Thermotoga maritimaCHEMBIOCHEM, Issue 16 2009E. Joel Loveridge Dr. Get a grip: Dihydrofolate reductase from Thermotoga maritima (TmDHFR) is unusual in that it has an arginine residue within its active site (ringed residue). Here, we address the role of this residue in catalysis. We find no evidence that Arg28 compromises catalysis in TmDHFR by preventing protonation of the substrate or that it acts as an acid to protonate the substrate. Instead, it appears that this residue plays an important role in binding the substrate tightly to ensure its thermal stability. [source] High Throughput Screening Identifies Novel Inhibitors of Escherichia coli Dihydrofolate Reductase that Are Competitive with Dihydrofolate.CHEMINFORM, Issue 43 2003Michela Zolli-Juran Abstract For Abstract see ChemInform Abstract in Full Text. [source] Substrate and inhibitor specificity of Mycobacterium avium dihydrofolate reductaseFEBS JOURNAL, Issue 13 2007Ronnie A. Böck Dihydrofolate reductase (EC 1.5.1.3) is a key enzyme in the folate biosynthetic pathway. Information regarding key residues in the dihydrofolate-binding site of Mycobacterium avium dihydrofolate reductase is lacking. On the basis of previous information, Asp31 and Leu32 were selected as residues that are potentially important in interactions with dihydrofolate and antifolates (e.g. trimethoprim), respectively. Asp31 and Leu32 were modified by site-directed mutagenesis, giving the mutants D31A, D31E, D31Q, D31N and D31L, and L32A, L32F and L32D. Mutated proteins were expressed in Escherichia coli BL21(DE3)pLysS and purified using His-Bind resin; functionality was assessed in comparison with the recombinant wild type by a standard enzyme assay, and growth complementation and kinetic parameters were evaluated. All Asp31 substitutions affected enzyme function; D31E, D31Q and D31N reduced activity by 80,90%, and D31A and D31L by >,90%. All D31 mutants had modified kinetics, ranging from three-fold (D31N) to 283-fold (D31L) increases in Km for dihydrofolate, and 12-fold (D31N) to 223 077-fold (D31L) decreases in kcat/Km. Of the Leu32 substitutions, only L32D caused reduced enzyme activity (67%) and kinetic differences from the wild type (seven-fold increase in Km; 21-fold decrease in kcat/Km). Only minor variations in the Km for NADPH were observed for all substitutions. Whereas the L32F mutant retained similar trimethoprim affinity as the wild type, the L32A mutation resulted in a 12-fold decrease in affinity and the L32D mutation resulted in a seven-fold increase in affinity for trimethoprim. These findings support the hypotheses that Asp31 plays a functional role in binding of the substrate and Leu32 plays a functional role in binding of trimethoprim. [source] Novel 3-benzoyl-2-piperazinylquinoxaline derivatives as potential antitumor agentsJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 3 2006Sandra Piras A series of new benzoylquinoxaline derivatives (7-26) was synthesized and evaluated for antitumor activity against a panel of 60 human cell lines at the NCI of Bethesda. Among the compounds which have passed the preliminary screening, compound 23 exhibited the best profile and growth inhibition activity at 100 - 10 ,M. The compounds were then tested towards a folate-dependent enzymes bio-library including Thymidylate synthases enzymes and human Dihydrofolate reductase at 10 ,M. The most of compounds exhibited a moderate inhibitory activity towards all or some of the enzymes tested with detectable inhibition constants (Ki) values in the range of 0.6-70 ,M. Compounds 21, 23, 24 showed Ki in the range of 10-38 ,M against both hDHFR and hTS. [source] The Role of Arginine 28 in Catalysis by Dihydrofolate Reductase from the Hyperthermophile Thermotoga maritimaCHEMBIOCHEM, Issue 16 2009E. Joel Loveridge Dr. Get a grip: Dihydrofolate reductase from Thermotoga maritima (TmDHFR) is unusual in that it has an arginine residue within its active site (ringed residue). Here, we address the role of this residue in catalysis. We find no evidence that Arg28 compromises catalysis in TmDHFR by preventing protonation of the substrate or that it acts as an acid to protonate the substrate. Instead, it appears that this residue plays an important role in binding the substrate tightly to ensure its thermal stability. [source] Determination of dissociation constants of folic acid, methotrexate, and other photolabile pteridines by pressure-assisted capillary electrophoresisELECTROPHORESIS, Issue 17 2006Zoltán Szakács Abstract Pressure-assisted CE (PACE) was applied to determine the previously inaccessible complete set of pK values for folic acid and eight related multiprotic compounds. PACE allowed the determination of all acidity macroconstants at low (,0.1,mM) concentration without interferences of selfassociation or photodegradation throughout the pH range. The accuracy of the constants was verified by NMR-pH, UV-pH, and potentiometric titrations and the data could be converted into physiological ionic strength. It was shown that even three overlapping pK values can be determined by CE with good precision (<0.06) and accuracy if an appropriately low sample throughput is used. Experimental aspects of PACE for the quantitation of acid,base properties are analyzed. The site-specific basicity data obtained for folic acid and methotrexate (MTX) reveal that apparently slight constitutional differences between folic acid and MTX carry highly different proton-binding propensities at analogous moieties, especially at the pteridine N1,locus, providing straightforward explanation for the distinctive binding to dihydrofolate reductase at the molecular level. [source] Arsenite induces delayed mutagenesis and transformation in human osteosarcoma cells at extremely low concentrationsENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 5 2003Kanae Mure Abstract Arsenite is a human multisite carcinogen, but its mechanism of action is not known. We recently found that extremely low concentrations (,0.1 ,M) of arsenite transform human osteosarcoma TE85 (HOS) cells to anchorage-independence. In contrast to other carcinogens which transform these cells within days of exposure, almost 8 weeks of arsenite exposure are required for transformation. We decided to reexamine the question of arsenite mutagenicity using chronic exposure in a spontaneous mutagenesis assay we previously developed. Arsenite was able to cause a delayed increase in mutagenesis at extremely low concentrations (,0.1 ,M) in a dose-dependent manner. The increase in mutant frequency occurred after almost 20 generations of growth in arsenite. Transformation required more than 30 generations of continuous exposure. We also found that arsenite induced gene amplification of the dihydrofolate reductase (DHFR) gene in a dose-dependent manner. Since HOS cells are able to methylate arsenite at a very low rate, it was possible that active metabolites such as monomethylarsonous acid (MMAIII) contributed to the delayed mutagenesis and transformation in these cells. However, when the assay was repeated with MMAIII, we found no significant increase in mutagenesis or transformation, suggesting that arsenite-induced delayed mutagenesis and transformation are not caused by arsenite's metabolites, but by arsenite itself. Our results suggest that long-term exposure to low concentrations of arsenite may affect signaling pathways that result in a progressive genomic instability. Environ. Mol. Mutagen. 41:322,331, 2003. © 2003 Wiley-Liss, Inc. [source] Substrate and inhibitor specificity of Mycobacterium avium dihydrofolate reductaseFEBS JOURNAL, Issue 13 2007Ronnie A. Böck Dihydrofolate reductase (EC 1.5.1.3) is a key enzyme in the folate biosynthetic pathway. Information regarding key residues in the dihydrofolate-binding site of Mycobacterium avium dihydrofolate reductase is lacking. On the basis of previous information, Asp31 and Leu32 were selected as residues that are potentially important in interactions with dihydrofolate and antifolates (e.g. trimethoprim), respectively. Asp31 and Leu32 were modified by site-directed mutagenesis, giving the mutants D31A, D31E, D31Q, D31N and D31L, and L32A, L32F and L32D. Mutated proteins were expressed in Escherichia coli BL21(DE3)pLysS and purified using His-Bind resin; functionality was assessed in comparison with the recombinant wild type by a standard enzyme assay, and growth complementation and kinetic parameters were evaluated. All Asp31 substitutions affected enzyme function; D31E, D31Q and D31N reduced activity by 80,90%, and D31A and D31L by >,90%. All D31 mutants had modified kinetics, ranging from three-fold (D31N) to 283-fold (D31L) increases in Km for dihydrofolate, and 12-fold (D31N) to 223 077-fold (D31L) decreases in kcat/Km. Of the Leu32 substitutions, only L32D caused reduced enzyme activity (67%) and kinetic differences from the wild type (seven-fold increase in Km; 21-fold decrease in kcat/Km). Only minor variations in the Km for NADPH were observed for all substitutions. Whereas the L32F mutant retained similar trimethoprim affinity as the wild type, the L32A mutation resulted in a 12-fold decrease in affinity and the L32D mutation resulted in a seven-fold increase in affinity for trimethoprim. These findings support the hypotheses that Asp31 plays a functional role in binding of the substrate and Leu32 plays a functional role in binding of trimethoprim. [source] Biogenesis of the yeast frataxin homolog Yfh1pFEBS JOURNAL, Issue 11 2000Tim44-dependent transfer to mtHsp70 facilitates folding of newly imported proteins in mitochondria Tim44 is an essential component of the mitochondrial inner membrane protein import machinery. In this study we asked if Tim44 is of relevance in intramitochondrial protein folding. We investigated the role of Tim44 in the biogenesis of the authentic mitochondrial protein Yfh1p, the yeast homolog of mammalian frataxin, which was recently implicated in Friedreich ataxia. After inactivation of Tim44, binding of mitochondrial heat shock protein (mtHsp)70 to translocating Yfh1p and subsequent folding to the native state was nearly completely blocked. Residual amounts of imported Yfh1p showed an increased tendency to aggregate. To further characterize the functions of Tim44 in the matrix, we imported dihydrofolate reductase (DHFR) as a model protein. Depletion of Tim44 allowed import of DHFR, although folding of the newly imported DHFR was delayed. Moreover, the depletion of Tim44 caused a strongly reduced binding of mtHsp70 and Mge1 to the translocating polypeptide. Subsequent dissociation of mtHsp70 from imported DHFR was delayed, indicating that mtHsp70,substrate complexes formed independently of Tim44 differ from the complexes that form under the control of Tim44. We conclude that Tim44 not only plays a role in protein translocation but also in the pathways of mitochondrial protein folding. [source] The mechanisms of resistance to antimalarial drugs in Plasmodium falciparumFUNDAMENTAL & CLINICAL PHARMACOLOGY, Issue 2 2003Jacques Le Bras Abstract Drug-resistant malaria is primarily caused by Plasmodium falciparum, a species highly prevalent in tropical Africa, the Amazon region and South-east Asia. It causes severe fever or anaemia that leads to more than a million deaths each year. The emergence of chloroquine resistance has been associated with a dramatic increase in malaria mortality among inhabitants of some endemic regions. The rationale for chemoprophylaxis is weakening as multiple-drug resistance develops against well-tolerated drugs. Plasmodium falciparum drug-resistant malaria originates from chromosome mutations. Analysis by molecular, genetic and biochemical approaches has shown that (i) impaired chloroquine uptake by the parasite vacuole is a common characteristic of resistant strains, and this phenotype is correlated with mutations of the Pfmdr1, Pfcg2 and Pfcrt genes; (ii) one to four point mutations of dihydrofolate reductase (DHFR), the enzyme target of antifolates (pyrimethamine and proguanil) produce a moderate to high level of resistance to these drugs; (iii) the mechanism of resistance to sulfonamides and sulfones involves mutations of dihydropteroate synthase (DHPS), their enzyme target; (iv) treatment with sulphadoxine,pyrimethamine selects for DHFR variants Ile(51), Arg(59), and Asn(108) and for DHPS variants Ser(436), Gly(437), and Glu(540); (v) clones that were resistant to some traditional antimalarial agents acquire resistance to new ones at a high frequency (accelerated resistance to multiple drugs, ARMD). The mechanisms of resistance for amino-alcohols (quinine, mefloquine and halofantrine) are still unclear. Epidemiological studies have established that the frequency of chloroquine resistant mutants varies among isolated parasite populations, while resistance to antifolates is highly prevalent in most malarial endemic countries. Established and strong drug pressure combined with low antiparasitic immunity probably explains the multidrug-resistance encountered in the forests of South-east Asia and South America. In Africa, frequent genetic recombinations in Plasmodium originate from a high level of malaria transmission, and falciparum chloroquine-resistant prevalence seems to stabilize at the same level as chloroquine-sensitive malaria. Nevertheless, resistance levels may differ according to place and time. In vivo and in vitro tests do not provide an adequate accurate map of resistance. Biochemical tools at a low cost are urgently needed for prospective monitoring of resistance. [source] Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2002Abstract QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169,176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (,16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 Å) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product,reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute ,40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1314,1322, 2002 [source] Synthesis of 2,6-diamino-5-[(2-substituted phenylamino)ethyl]pyrimidin-4(3h)-one as inhibitors of folate metabolizing enzymes,,JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 6 2006Aleem Gangjee A series of eleven novel 2,6-diamino-5-[(2-substituted phenylamino)ethyl]pyrimidin-4(3H)-one derivatives were synthesized as potential inhibitors of dihydrofolate reductase (DHFR) and thymidylate synthase (TS). The synthesis of analogues 2a-f, 3a and 3e was achieved via an improved method. Commercially available anilines 12a-f were used as starting materials which on reaction with chloroacetaldehyde followed by cyanoacetate and cyclocondensation with guanidine afforded 2,6-diamino-5-[(2-substituted phenylamino)ethyl]pyrimidin-4(3H)-one 2a-f in three steps. The N-methyl analogues 3a-3e were prepared by reductive methylation. These compounds were evaluated against dihydrofolate reductase from Escherichia coli, Toxoplasma gondii, Pneumocystis carinii, human, and rat liver. Few compounds were marginally active against dihydrofolate reductase. The most potent inhibitor, (2c) which has a 1-naphthyl substituent on the side chain, has an IC50 = 150 ,M and 9.1 ,M against Escherichia coli and Toxoplasma gondii DHFR, respectively. [source] Synthesis of 2,4-diaminopyrido[2,3- d]pyrimidines and 2,4-diamino-quinazolines with bulky dibenz[b,f]azepine and dibenzo[a,d]-cycloheptene substituents at the 6-position as inhibitors of dihydrofolate reductases from pneumocystis carinii, toxoplasma gondii, and mycobacterium avium,JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2000Andre Rosowsky The synthesis of four previously undescribed 2,4-diaminopyrido[2,3- d]pyrimidines (3,4) and 2,4-diaminoquinazolines (5,6) with a bulky tricyclic aromatic group at the 6-position is described. Condensation of dibenz[b,f]azepine with 2,4-diamino-6-bromomethylpyrido[2,3- d]pyrimidine (8) and 2,4-diamino-6-bromomethylquinazoline (17) in the presence of sodium hydride afforded N -[(2,4-diaminopyrido[2,3- d]-pyrimidin-6-yl)methyl]dibenz[b,f]azepine (3) and N -[(2,4-diaminoquinazolin-6-yl)methyl]dibenz[b,f]-azepine (4), respectively. Condensation of 5-chlorodibenzo[a,d]cycloheptene (19) and 5-chloro-10,11-dihydrodibenzo[a,d]cycloheptene (20) with 2,4,6-triaminoquinazoline (13) afforded 5-[(2,4-diamino-quinazolin-6-yl)amino]-5H -dibenzo[a,d]cycloheptene (5) and the corresponding 10,11-dihydro derivative (6), respectively. The bromides 8 and 17, as hydrobromic acid salts, were obtained from the corresponding nitriles according to a standard three-step sequence consisting of treatment with Raney nickel in formic acid followed by reduction with sodium borohydride and bromination with dry hydrogen bromide in glacial acetic acid. Compounds 3,6 were evaluated in vitro for the ability to inhibit dihydrofolate reductase from Pneumocystis carinii, Toxoplasma gondii, Mycobacterium avium, and rat liver. Compounds 3 and 4 were potent inhibitors of all four enzymes, with IC50 values in the 0.03,0.1 ,M range, whereas 5 was less potent. However the selectivity of all four compounds for the parasite enzymes relative to the rat enzyme was<10-fold, whereas the recently reported lead compound in this series, N -[(2,4-diaminopteridin-6-yl)methyl]dibenz[b,f]azepine (1) has > 100-fold selectivity for the T. gondii and M. avium enzyme and 21-fold selectivity for the P carinii enzyme. [source] Structure and reactivity of Trypanosoma brucei pteridine reductase: inhibition by the archetypal antifolate methotrexateMOLECULAR MICROBIOLOGY, Issue 6 2006Alice Dawson Summary The protozoan Trypanosoma brucei has a functional pteridine reductase (TbPTR1), an NADPH-dependent short-chain reductase that participates in the salvage of pterins, which are essential for parasite growth. PTR1 displays broad-spectrum activity with pterins and folates, provides a metabolic bypass for inhibition of the trypanosomatid dihydrofolate reductase and therefore compromises the use of antifolates for treatment of trypanosomiasis. Catalytic properties of recombinant TbPTR1 and inhibition by the archetypal antifolate methotrexate have been characterized and the crystal structure of the ternary complex with cofactor NADP+ and the inhibitor determined at 2.2 Å resolution. This enzyme shares 50% amino acid sequence identity with Leishmania major PTR1 (LmPTR1) and comparisons show that the architecture of the cofactor binding site, and the catalytic centre are highly conserved, as are most interactions with the inhibitor. However, specific amino acid differences, in particular the placement of Trp221 at the side of the active site, and adjustment of the ,6-,6 loop and ,6 helix at one side of the substrate-binding cleft significantly reduce the size of the substrate binding site of TbPTR1 and alter the chemical properties compared with LmPTR1. A reactive Cys168, within the active site cleft, in conjunction with the C-terminus carboxyl group and His267 of a partner subunit forms a triad similar to the catalytic component of cysteine proteases. TbPTR1 therefore offers novel structural features to exploit in the search for inhibitors of therapeutic value against African trypanosomiasis. [source] The use of folic acid antagonists and the risk of colorectal cancer,PHARMACOEPIDEMIOLOGY AND DRUG SAFETY, Issue 10 2007Patricia F. Coogan Abstract Purpose Since folate is associated with a reduced risk of colorectal cancer, we hypothesized that folic acid antagonists might increase the risk. We used data from a population-based case control study of medication use and colorectal cancer to evaluate the hypothesis. Methods Case patients with adenocarcinoma of the colon or rectum were ascertained from participating hospitals in Massachusetts and the Massachusetts cancer registry (MCR) from January 1, 2001, through November 30, 2004. Age-, sex-, and precinct-matched control subjects were chosen from Massachusetts town lists. Information on folic acid antagonist use and other relevant data were obtained from 1809 cases and 1809 matched controls by telephone interview and by a self-administered dietary questionnaire. We used logistic regression models to estimate odds ratios among 1229 case patients and 1165 control subjects who provided satisfactory dietary information and did not have Crohn's disease or ulcerative colitis. Results The odds ratio for colorectal cancer among regular users of folate-containing supplements was 0.7 (95%CI 0.6,0.9). The odds ratio for regular use of folic acid antagonists was 1.3 (95%CI 0.9,1.9). Contrary to expectation, the odds ratio was reduced in the highest category of alcohol consumption (OR,=,0.5, 95%CI 0.2,1.2). The odds ratio was higher among users of drugs that inhibit dihydrofolate reductase (OR,=,1.6, 95%CI 0.9,2.8) than drugs that work through other mechanisms (OR,=,1.2, 95%CI 0.7,1.9). Conclusions Our data provide little support for the hypothesis that regular folic acid antagonist use increases the risk of colorectal cancer. However, there is a suggestion that dihydrofolate reductase inhibitors specifically may increase the risk. Copyright © 2007 John Wiley & Sons, Ltd. [source] Bis[2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium] dl -malateACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009S. Franklin Racemic malic acid and trimethoprim [5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine] form a 1:2 salt (monoclinic, P21/c), 2C14H19N4O3+·C4H4O52,, in which the malate component is disordered across a centre of inversion. The crystal structure of the salt consists of protonated trimethoprim residues and a malate dianion. The carboxylate group of the malate ion interacts with the trimethoprim cation in a linear fashion through pairs of N,H...O hydrogen bonds to form a cyclic hydrogen-bonded motif. This is similar to the carboxylate,trimethoprim cation interaction observed earlier in the complex of dihydrofolate reductase with trimethoprim. The structure of the salt of trimethoprim with racemic dl -malic acid reported here is the first of its kind. The present study investigates the conformations and the hydrogen-bonding interactions, which are very important for biological functions. The pyrimidine plane makes a dihedral angle of 78.08,(7)° with the benzene ring of the trimethoprim cation. The cyclic hydrogen-bonded motif observed in this structure is self-organized, leading to novel types of hydrogen-bonding motifs in supramolecular patterns. [source] Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureusACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009Christian Oefner Iclaprim is a novel dihydrofolate reductase (DHFR) inhibitor belonging to the 2,4-diaminopyrimidine class of antibiotics, of which trimethoprim (TMP) is the most well known representative. Iclaprim exhibits potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) phenotypes, including TMP-resistant strains. The inhibition properties of racemic iclaprim and of the two enantiomers, termed AR-101 and AR-102, towards S. aureus wild-type DHFR and TMP-resistant F98Y mutant DHFR were determined and compared. Similar to TMP, AR-101, AR-102 and iclaprim are all competitive inhibitors with respect to the substrate dihydrofolate. Iclaprim, AR-101 and AR-102 demonstrated little or no difference in activity towards these enzymes and were significantly more potent than TMP. The crystal structures of S. aureus DHFR and F98Y mutant DHFR were determined as ternary complexes with NADPH and either AR-101, AR-102 or iclaprim. The binding modes of the inhibitors were analysed and compared. The X-ray crystallographic data explain the binding modes of all molecules well and can be used to rationalize the equipotent affinity of AR-101, AR-102 and iclaprim, which is also reflected in their antibacterial properties. [source] Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexateACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Olga Senkovich The flagellate protozoan parasite Trypanosoma cruzi is the pathogenic agent of Chagas disease (also called American trypanosomiasis), which causes approximately 50,000 deaths annually. The disease is endemic in South and Central America. The parasite is usually transmitted by a blood-feeding insect vector, but can also be transmitted via blood transfusion. In the chronic form, Chagas disease causes severe damage to the heart and other organs. There is no satisfactory treatment for chronic Chagas disease and no vaccine is available. There is an urgent need for the development of chemotherapeutic agents for the treatment of T. cruzi infection and therefore for the identification of potential drug targets. The dihydrofolate reductase activity of T. cruzi, which is expressed as part of a bifunctional enzyme, dihydrofolate reductase,thymidylate synthase (DHFR-TS), is a potential target for drug development. In order to gain a detailed understanding of the structure,function relationship of T. cruzi DHFR, the three-dimensional structure of this protein in complex with various ligands is being studied. Here, the crystal structures of T. cruzi DHFR-TS with three different compositions of the DHFR domain are reported: the folate-free state, the complex with the lipophilic antifolate trimetrexate (TMQ) and the complex with the classical antifolate methotrexate (MTX). These structures reveal that the enzyme is a homodimer with substantial interactions between the two TS domains of neighboring subunits. In contrast to the enzymes from Cryptosporidium hominis and Plasmodium falciparum, the DHFR and TS active sites of T. cruzi lie on the same side of the monomer. As in other parasitic DHFR-TS proteins, the N-terminal extension of the T. cruzi enzyme is involved in extensive interactions between the two domains. The DHFR active site of the T. cruzi enzyme shows subtle differences compared with its human counterpart. These differences may be exploited for the development of antifolate-based therapeutic agents for the treatment of T. cruzi infection. [source] High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2 -symmetric active siteACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2006Narendra Narayana R67 plasmid-encoded dihydrofolate reductase (R67 DHFR) is an NADPH-dependent homotetrameric enzyme that catalyzes the reduction of dihydrofolate to tetrahydrofolate. The amino-acid sequence and molecular architecture of R67 DHFR and its inhibitory properties toward folate analogues are different from those of chromosomal DHFR. Here, the crystal structure of R67 DHFR refined using 1.1,Å resolution data is presented. Blocked full-matrix least-squares refinement without restraints resulted in a final R factor of 11.4%. The anisotropic atomic displacement parameters analyzed by Rosenfield matrices and translation,libration,screw validation suggested four quasi-rigid domains. A total of ten C,,HO hydrogen bonds were identified between the ,-strands. There is reasonable structural evidence that His62 is not protonated in the tetramer, which is in accord with previous pH-profile studies. The side chain of Gln67 that protrudes into the active site exhibits dual conformation, a feature noticed for the first time owing to the availability of atomic resolution data. The R67 DHFR active site is unique: it has D2 symmetry and is a large active site with a pentagonal network of water molecules and exposure of backbone atoms to solvent; the central pore is favorable for planar ring-stacking interactions. The geometrical shape, overall symmetry, local asymmetry and waters appear to dominate the binding of ligands, catalysis and inhibition. [source] Characterization, crystallization and preliminary X-ray analysis of bifunctional dihydrofolate reductase,thymidylate synthase from Plasmodium falciparumACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Penchit Chitnumsub The full-length pfdhfr-ts genes of the wild-type TM4/8.2 and the double mutant K1CB1 (C59R+S108N) from the genomic DNA of the corresponding Plasmodium falciparum parasite have been cloned into a modified pET(17b) plasmid and expressed in Escherichia coli BL21 (DE3) pLysS. Conditions for the expression and purification of the P. falciparum dihydrofolate reductase,thymidylate synthase (PfDHFR-TS) have been established that yield ,1,mg of the soluble active enzyme per litre of culture. The purified enzymes have been crystallized using a modified microbatch method with PEG 4000 as the primary precipitating agent. X-ray diffraction data were collected to 2.50 and 2.64,Å resolution under cryogenic conditions from single crystals of the two PfDHFR-TS proteins in complex with NADPH, dUMP and either Pyr30 or Pyr39. Preliminary X-ray analysis indicated that the crystals belong to the orthorhombic space group P212121, with two molecules per asymmetric unit and ,52% solvent content (VM, 2.6,Å3,Da,1). The use of a particular type of baby oil in the microbatch setup appeared to be beneficial to PfDHFR-TS crystallization and a preliminary comparison with another commonly used oil is described. [source] Analysis of quinazoline and pyrido[2,3- d]pyrimidine N9,C10 reversed-bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2002Vivian Cody Structural studies of two ternary complexes of Pneumocystis carinii dihydrofolate reductase (pcDHFR) with the cofactor NADP+ and potent antifolates, the N9,C10 reversed-bridge inhibitor 2,4-diamino-6-[N -(2,,5,-dimethoxybenzyl)- N -methylamino]quinazoline (1) and its 3,,5,-dimethoxypyrido[2,3- d]pyrimidine analog (2), were carried out. Data for the monoclinic crystals were refined to 1.90,Å resolution for the complex with (1) (R = 0.178) and to 2.1,Å resolution for the complex with (2) (R = 0.193). The effect of the N9,C10 reversed-bridge geometry is to distort the bridge from coplanarity with the pyrido[2,3- d]pyrimidine or quinazoline ring system and to twist the C10 methylene conformation toward a gauche conformation. This change also influences the conformation of the methoxybenzyl ring, moving it away from a trans position. This change places the 5,-methoxy group deeper within the hydrophobic pocket made by Ile65, Pro66 and Phe69 of the pcDHFR active site. These results also revealed the first observation of an unusual conformation for the reversed-bridge geometry (C5,C6,N9,C10 torsion angle) in antifolate (2). The electron density is consistent with the presence of two models (conformers 2-1 and 2-2) that result from inversion of the geometry at N9. The four examples of N9,C10 reversed-bridge antifolates cluster in two conformations, with the structure of quinazoline (1) similar to that previously reported for its 2,,5,-dimethoxypyrido[2,3- d]pyrimidine analog (3). The two conformers of (2) differ from these and each other by a twisted-bridge geometry that results in the dimethoxybenzyl ring occupying the same conformational space. Conformer 2-2 also has the N9,C10 reversed bridge perpendicular to the pyrido[2,3- d]pyrimidine plane, in contrast to the gauche,trans conformation normally observed. As a result of these changes, the N9 methyl probes conformational space in the active site not normally occupied by antifolate structures. The N9 methyl of conformer 2-2 makes close contacts to the conserved Leu25 as well as the hydroxyl O atoms of the nicotinamide ribose and Ser64, whereas the other three reversed-bridge conformers make weak hydrophobic contacts with Ile123, Thr61 and Ile65. These antifolates are ten times more selective for pcDHFR than the C9,N10 bridge parent trimetrexate. However, pyrido[2,3- d]pyrimidines (2) and (3) are three times more selective for pcDHFR than quinazoline (1) is for rat liver DHFR. These data suggest that the loss of hydrogen-bonding interactions with N8 is more important to potency than the interactions of the methoxybenzyl substituents. [source] Folate deficiency followed by ionizing radiation perturbs hepatic dihydrofolate reducatse activityBIOFACTORS, Issue 4 2008Vipen Batra Abstract There is lot of interest in the folate metabolism because of the essential role of folate coenzymes in nucleic acid synthesis. Gamma (,) radiation is well known for inducing damage in the DNA. To counteract these damage, a variety of DNA repair pathways have evolved that require regular supply of DNA bases whose biosynthesis in turn depends on sufficient pools of folate dependent enzymes like dihydrofolate reductase (DHFR). In the present study, we examined the ionizing radiation mediated perturbation of DHFR activity in folate deficient and folate sufficient conditions. In folate deficient animals a potent inhibition of liver DHFR activity was observed. Our results showed that combination of folate starvation and ionizing radiation might adversely affect the DHFR activity, compared to their individual treatments. Measurement of apurinic/apyrimidinic sites (AP sites), a major type of DNA damage generated by radiation induced loss of purine and/or pyrimidine base, indicated a dose dependent DNA damage in folate deficient animals. In conclusion our data suggest an interactive role of folate deficiency and radiation injury in inhibiting DHFR activity. [source] The Z isomer of 2,4-diaminofuro[2,3- d]pyrimidine antifolate promotes unusual crystal packing in a human dihydrofolate reductase ternary complexACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Vivian Cody The crystal structure of the ternary complex of human dihydrofolate reductase (hDHFR) with NADPH and the Z isomer of 2,4-diamino-5-[2-(2,-methoxyphenyl)propenyl]-furo[2,3- d]pyrimidine (Z1) shows that the Z isomer binds in the normal antifolate orientation in which the furo oxygen occupies the 8-amino position observed in the binding of 2,4-diaminopteridine antifolates such as methotrexate and with the methoxyphenyl moiety cis to and coplanar with the furo[2,3- d]pyrimidine ring. The hDHFR ternary complex crystallized in the orthorhombic space group P212121 and its structure was refined to 1.7,Å resolution. Although other hDHFR complexes crystallize in this space group, these data provide only the second example of an unusual packing arrangement in which the conserved active-site Arg70 forms a salt bridge to the side chain of Glu44 from a symmetry-related molecule. As a result, the conformations of Phe31 and Gln35 shift with respect to those observed in the structure of mouse DHFR bound to Z1, which crystallizes in the monoclinic space group P21 and shows that Gln35 interacts with Arg70. [source] Folinic acid protects against suppression of growth by Methotrexate in miceBIOPHARMACEUTICS AND DRUG DISPOSITION, Issue 4 2001M. Perwaiz Iqbal Abstract The objective of this study was to investigate whether folinic acid supplementation would protect young mice against suppression of growth by methotrexate (MTX). Four equal groups of Balb/c young male mice (5 animals in each group; mean±SD body weight 9.64±0.85 g, in their rapid growth phase) were subjected to the following drug treatment: One group was given MTX (3.5 mg/kg body weight) intraperitoneally on every 2nd day, another received folinic acid (7.0 mg/kg body weight) intraperitoneally every 2nd day. The third group was given both of these drugs (MTX on every 2nd day and folinic acid 8 h post-MTX injection). The fourth group was injected with physiological saline every other day to serve as a control group. Total body weight, food and water consumption by animals in each group were monitored every second day for a period of 3 weeks. After this period mice were sacrificed and liver, spleen and kidneys were excised, weighed and analyzed for MTX and dihydrofolate reductase activity. A small segment of the proximal part of small intestine and small pieces of liver and kidney were also removed to study morphological changes. Compared to the groups, which received folinic acid alone, folinic acid plus MTX or physiological saline, mean increase in body weight (6.8±0.8 g) of mice over a period of 3 weeks was minimal in the group receiving MTX alone (one-way ANOVA p=0.0001). The mean weights of liver and kidney in this group receiving MTX alone were also found to be significantly less than the mean weights of these organs in the 3 groups (p<0.001). The negative effect on growth of animals appears not only due to malabsorption but inhibition of pathway of de novo DNA synthesis may also be involved. This is supported by loss of villous pattern in small intestine of mice treated with MTX alone and increased accumulation of free MTX and decreased dihydrofolate reductase in the liver of the group receiving MTX alone as compared with the group receiving MTX plus folinic acid. The data indicate that the administration of folinic acid protects mice against suppression of growth by MTX. On the basis of these observations it can be deduced that patients suffering from juvenile rheumatoid arthritis or acute lymphoblastic leukaemia receiving MTX over a long period of time might be at a risk of experiencing short-term suppression of growth, however they could benefit from supplementation with folinic acid. Copyright © 2001 John Wiley & Sons, Ltd. [source] Bacterial artificial chromosome library for genome-wide analysis of Chinese hamster ovary cellsBIOTECHNOLOGY & BIOENGINEERING, Issue 5 2009Takeshi Omasa Abstract Chinese hamster ovary (CHO) cell lines are widely used for scientific research and biotechnology. A CHO genomic bacterial artificial chromosome (BAC) library was constructed from a mouse dihydrofolate reductase (DHFR) gene-amplified CHO DR1000L-4N cell line for genome-wide analysis of CHO cell lines. The CHO BAC library consisted of 122,281 clones and was expected to cover the entire CHO genome five times. A CHO chromosomal map was constructed by fluorescence in situ hybridization (FISH) imaging using BAC clones as hybridization probes (BAC-FISH). Thirteen BAC-FISH marker clones were necessary to identify all the 20 individual chromosomes in a DHFR-deficient CHO DG44 cell line because of the aneuploidy of the cell line. To determine the genomic structure of the exogenous Dhfr amplicon, a 165-kb DNA region containing exogenous Dhfr was cloned from the BAC library using high-density replica (HDR) filters and Southern blot analysis. The nucleotide sequence analysis revealed a novel genomic structure in which the vector sequence containing Dhfr was sandwiched by long inverted sequences of the CHO genome. Biotechnol. Bioeng. 2009; 104: 986,994. © 2009 Wiley Periodicals, Inc. [source] A study of monoclonal antibody-producing CHO cell lines: What makes a stable high producer?,BIOTECHNOLOGY & BIOENGINEERING, Issue 4 2009Janet Chusainow Abstract Generating stable, high-producing cell lines for recombinant protein production requires an understanding of the potential limitations in the cellular machinery for protein expression. In order to increase our understanding of what makes a stable high producer, we have generated a panel of 17 recombinant monoclonal antibody expressing Chinese hamster ovary subclones (CHO-mAb) with specific productivities ranging between 3 and 75 pg,cell,1,day,1 using the dihydrofolate reductase (dhfr) expression system and compared the molecular features of these high- and low-producer clones. The relative heavy chain (HC) and light chain (LC) transgene copy numbers and mRNA levels were determined using real-time quantitative PCR (RT qPCR). We observed that not only higher transgene copy numbers and mRNA levels of both HC and LC were characteristic for the high-producer clones as compared to the low-producer clones but also a more favorable HC to LC transgene copy numbers ratio. By studying the long-term stability of the CHO-mAb subclones in the absence of methotrexate (MTX) selective pressure over 36 passages we observed a 35,92% decrease in volumetric productivity, primarily caused by a significant decrease in HC and LC mRNA levels with little change in the transgene copy numbers. Using Southern blot hybridization we analyzed the HC and LC transgene integration patterns in the host chromosome and their changes in course of gene amplification and long-term culturing. We observed that MTX-induced gene amplification caused chromosomal rearrangements resulting in clonal variability in regards to growth, productivity, and stability. No further obvious DNA rearrangements occurred during long-term culturing in the absence of MTX, indicating that other mechanisms were responsible for the decreased transcription efficiency. Our results implicate that the amplified transgene sequences were arranged in tandem repeats potentially triggering repeat-induced gene silencing. We hypothesize that the decline in transgene mRNA levels upon long-term culturing without MTX was mainly caused by transgene silencing consequently leading to a loss in mAb productivity. The exact molecular mechanisms causing production instability are not yet fully understood. The herein described extensive characterization studies could help understand the limitations to high-level, stable recombinant protein production and find ways to improving and accelerating the process for high-producer cell line generation and selection. Biotechnol. Bioeng. 2009;102: 1182,1196. © 2008 Wiley Periodicals, Inc. [source] Characterization of gene localization and accessibility in DHFR-amplified CHO cellsBIOTECHNOLOGY PROGRESS, Issue 1 2009Zhou Jiang Abstract Efficient transcription is critical for high yields of recombinant proteins by mammalian cells. We previously reported that dihydrofolate reductase (DHFR)-mediated gene amplification can augment transcriptional rates as well as increasing gene copy numbers in Chinese hamster ovary (CHO) cells.1 In an attempt to elucidate the mechanisms involved, we have employed several approaches to identify the epigenetic differences between cell clones with varying transcriptional rates. Transgene placement and accessibility varies between unrelated parental cell clones with differential transcriptional rates. However, we did not observe any apparent epigenetic differences between parental clones and their amplified progeny, indicating undiscovered regulatory mechanisms are responsible for the augmentation of transcriptional rates upon DHFR-mediated amplification. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Schedule-dependent Synergism and Antagonism between Raltitrexed ("Tomudex") and Methotrexate in Human Colon Cancer Cell Lines in vitroCANCER SCIENCE, Issue 1 2001Yasuhiko Kano The folate-dependent enzymes are attractive targets for cancer chemotherapy. Methotrexate (MTX), which inhibits dihydrofolate reductase, has been widely used for the treatment of solid tumors and hematological cancers. Raltitrexed ("Tomudex"), which inhibits thymidylate synthase, is a novel anticancer agent active against colorectal cancer and some other solid tumors. We studied the optimal schedule of raltitrexed and MTX in combination against four human colon cancer cell lines Colo201, Colo320, LoVo, and WiDr. These cells were simultaneously exposed to raltitrexed and MTX for 24 h, or sequentially exposed to raltitrexed for 24 h followed by MTX for 24 h, or vice versa. Cell growth inhibition after 5 days was determined by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The effects of drug combinations at the concentrations of drug that produced 80% and 50% cell growth inhibition (Icg80 and IC50) were analyzed by the isobologram method (Steel and Peckham, 1979). Cytotoxic interactions between raltitrexed and MTX were schedule-dependent. The simultaneous exposure to raltitrexed and MTX showed additive effects in Colo201, LoVo and WiDr cells and antagonistic effects in Colo320 cells. The sequential exposure to raltitrexed followed by MTX produced additive effects in all four cell lines. The sequential exposure to MTX followed by raltitrexed produced synergistic effects in Colo201, LoVo and WiDr cells and additive effects in Colo320 cells. These findings suggest that the sequential administration of MTX followed by raltitrexed produces more than the expected cytotoxicity and may be the optimal schedule at the cellular level. Further in vivo and clinical studies will be necessary to determine the toxicity and to test the antitumor effects of sequential administration of MTX followed by raltitrexed proposed on the basis of the in vitro synergism. [source] 7-Methyl Trimethoprim Analogues as Inhibitors of the Folate Metabolizing Enzymes,JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 3 2003Aleem Gangjee A series of 5-(1-phenylethyl)pyrimidines 2,10 (Table I) were designed and synthesized as potent and selective inhibitors of Pneumocystis carinii (P. carinii), Toxoplasma gondii (T. gondii) and Mycobacterium avium (M. avium) dihydrofolate reductases (DHFR). The structure of 2,10 incorporates a 7-methyl group to increase the potency of monocyclic trimethoprim (TMP). The target compounds were synthesized by an acid catalyzed condensation of ethyl cyanoacetate and appropriately substituted benzaldehydes followed by a Michael addition using methyl copper-lithium. The resulting adduct was cyclocondensed with guanidine to afford 2,6-diamino-4-hydroxy-5-(1-phenylethyl)pyrimidines 2,7. Both amino moieties of 2,4 were protected with pivaloyl groups and their 4-hydroxy group chlorinated with phosphorus oxychloride. The resulting intermediates were subjected to hydrogenation and deprotection to afford 8,10. Compound 7 was a good inhibitor of DHFR, however the other compounds were poor inhibitors of P. carinii, T. gondii and M. avium DHFR. [source] Synthesis of 2,4-diaminopyrido[2,3- d]pyrimidines and 2,4-diamino-quinazolines with bulky dibenz[b,f]azepine and dibenzo[a,d]-cycloheptene substituents at the 6-position as inhibitors of dihydrofolate reductases from pneumocystis carinii, toxoplasma gondii, and mycobacterium avium,JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2000Andre Rosowsky The synthesis of four previously undescribed 2,4-diaminopyrido[2,3- d]pyrimidines (3,4) and 2,4-diaminoquinazolines (5,6) with a bulky tricyclic aromatic group at the 6-position is described. Condensation of dibenz[b,f]azepine with 2,4-diamino-6-bromomethylpyrido[2,3- d]pyrimidine (8) and 2,4-diamino-6-bromomethylquinazoline (17) in the presence of sodium hydride afforded N -[(2,4-diaminopyrido[2,3- d]-pyrimidin-6-yl)methyl]dibenz[b,f]azepine (3) and N -[(2,4-diaminoquinazolin-6-yl)methyl]dibenz[b,f]-azepine (4), respectively. Condensation of 5-chlorodibenzo[a,d]cycloheptene (19) and 5-chloro-10,11-dihydrodibenzo[a,d]cycloheptene (20) with 2,4,6-triaminoquinazoline (13) afforded 5-[(2,4-diamino-quinazolin-6-yl)amino]-5H -dibenzo[a,d]cycloheptene (5) and the corresponding 10,11-dihydro derivative (6), respectively. The bromides 8 and 17, as hydrobromic acid salts, were obtained from the corresponding nitriles according to a standard three-step sequence consisting of treatment with Raney nickel in formic acid followed by reduction with sodium borohydride and bromination with dry hydrogen bromide in glacial acetic acid. Compounds 3,6 were evaluated in vitro for the ability to inhibit dihydrofolate reductase from Pneumocystis carinii, Toxoplasma gondii, Mycobacterium avium, and rat liver. Compounds 3 and 4 were potent inhibitors of all four enzymes, with IC50 values in the 0.03,0.1 ,M range, whereas 5 was less potent. However the selectivity of all four compounds for the parasite enzymes relative to the rat enzyme was<10-fold, whereas the recently reported lead compound in this series, N -[(2,4-diaminopteridin-6-yl)methyl]dibenz[b,f]azepine (1) has > 100-fold selectivity for the T. gondii and M. avium enzyme and 21-fold selectivity for the P carinii enzyme. [source] | ||||||||||||||||||||||||||||