Preparation of 6-(bromomethyl)-2,4-pteridinediamine hydrobromide and its use in improved syntheses of methotrexate and related compounds

Pterin-sulfa conjugates as dihydropteroate synthase inhibitors and antibacterial agents

The sulfonamide class of antibiotics has been in continuous use for over 70years. They are thought to act by directly inhibiting dihydropteroate synthase (DHPS), and also acting as prodrugs that sequester pterin pools by forming dead end pterin-sulfonamide conjugates. In this study, eight pterin-sulfonamide conjugates were synthesized using a novel synthetic strategy and their biochemical and microbiological properties were investigated. The conjugates were shown to competitively inhibit DHPS, and inhibition was enhanced by the presence of pyrophosphate that is crucial to catalysis and is known to promote an ordering of the DHPS active site. The co-crystal structure of Yersinia pestis DHPS bound to one of the more potent conjugates revealed a mode of binding that is similar to that of the enzymatic product analog pteroic acid. The antimicrobial activities of the pterin-sulfonamide conjugates were measured against Escherichia coli in the presence and absence of folate precursors and dependent metabolites. These results show that the conjugates have appreciable antibacterial activity and act by an on target, anti-folate pathway mechanism rather than as simple dead end products.

Facile design of organic-inorganic hybrid gels for molecular recognition of nucleoside triphosphates

We report the molecular recognition for nucleoside triphosphates inside the ligand-modified water-soluble organic-inorganic hybrid gels composed of polyhedral oligomeric silsesquioxane (POSS). The series of ligands were designed to make hydrogen bonds with each nucleobase and introduced into the hybrid gels. From the titration experiments, the binding constants between the ligand inside the gels and nucleosides were evaluated. Accordingly, it was found that the ligands inside the gels can form a stable complex only with the target nucleoside triphosphate which has the complementary pattern of the hydrogen bonds (Ka=G-gel/cytidine triphosphate (CTP), 3.5×10(8)M(-1); U-gel/adenosine triphosphate (ATP), 1.6×10(3)M(-1); A-gel/uridine triphosphate (UTP), 1.9×10(7), respectively). With other nucleoside derivatives which have different numbers of phosphate units or different types of nucleobases, the much weaker interaction was detected. These data indicate that the complex formation only with nucleoside triphosphates should occur inside the hybrid gels, and selective recognition of each nucleoside triphosphate can be accomplished.

Folate pathway disruption leads to critical disruption of methionine derivatives in Mycobacterium tuberculosis

In this study, we identified antifolates with potent, targeted activity against whole-cell Mycobacterium tuberculosis (MTB). Liquid chromatography-mass spectrometry analysis of antifolate-treated cultures revealed metabolic disruption, including decreased pools of methionine and S-adenosylmethionine. Transcriptomic analysis highlighted altered regulation of genes involved in the biosynthesis and utilization of these two compounds. Supplementation with amino acids or S-adenosylmethionine was sufficient to rescue cultures from antifolate treatment. Instead of the "thymineless death" that characterizes folate pathway inhibition in a wide variety of organisms, these data suggest that MTB is vulnerable to a critical disruption of the reactions centered around S-adenosylmethionione, the activated methyl cycle.

Structure-based selectivity optimization of piperidine-pteridine derivatives as potent Leishmania pteridine reductase inhibitors

The upregulation of pteridine reductase (PTR1) is a major contributor to antifolate drug resistance in Leishmania spp., as it provides a salvage pathway that bypasses dihydrofolate reductase (DHFR) inhibition. The structure-based optimization of the PTR1 inhibitor methyl-1-[4-(2,4-diaminopteridin-6-ylmethylamino)benzoyl]piperidine-4-carboxylate (1) led to the synthesis of a focused compound library which showed significantly improved selectivity for the parasite's folate-dependent enzyme. When used in combination with pyrimethamine, a DHFR inhibitor, a synergistic effect was observed for compound 5b. This work represents a step forward in the identification of effective antileishmania agents.

Intestinal transport of aminopterin enantiomers in dogs and humans with psoriasis is stereoselective: evidence for a mechanism involving the proton-coupled folate transporter

N-[4-[[(2,4-diamino-6-pterdinyl)methyl]amino]benzoyl]-L/D-glutamic acid (L/D-AMT) is an investigational drug in phase 1 clinical development that consists of the L-and D-enantiomers of aminopterin (AMT). L/D-AMT is obtained from a novel process for making the L-enantiomer (L-AMT), a potent oral antiinflammatory agent. The purpose of these studies was to characterize oral uptake and safety in the dog and human of each enantiomer alone and in combination and provide in vitro evidence for a mechanism of intestinal absorption. This is the first report of L /D-AMT in humans. In dogs (n = 40) orally dosed with L-AMT or D-AMT absorption was stereoselective for the L-enantiomer (6- to 12-fold larger peak plasma concentration after oral administration and area under the plasma concentration-time curve at 0-4 h; p < 0.001). D-AMT was not toxic at the maximal dose tested (82.5 mg/kg), which was 100-fold larger than the maximal nonlethal L-AMT dose (0.8 mg/kg). Dogs (n = 10) and humans with psoriasis (n = 21) orally administered L-AMT and L /D-AMT at the same L-enantiomer dose resulted in stereoselective absorption (absent D-enantiomer in plasma), bioequivalent L-enantiomer pharmacokinetics, and equivalent safety. Thus, the D-enantiomer in L/D-AMT did not perturb L-enantiomer absorption or alter the safety of L-AMT. In vitro uptake by the human proton-coupled folate transporter (PCFT) demonstrated minimal transport of D-AMT compared with L-AMT, mirroring the in vivo findings. Enantiomer selectivity by PCFT was attributable almost entirely to decreased binding affinity rather than changes in transport rate. Collectively, our results demonstrate a strong in vitro-in vivo correlation implicating stereoselective transport by PCFT as the mechanism underlying stereoselective absorption observed in vivo.

Discovery of potent pteridine reductase inhibitors to guide antiparasite drug development

Pteridine reductase (PTR1) is essential for salvage of pterins by parasitic trypanosomatids and is a target for the development of improved therapies. To identify inhibitors of Leishmania major and Trypanosoma cruzi PTR1, we combined a rapid-screening strategy using a folate-based library with structure-based design. Assays were carried out against folate-dependent enzymes including PTR1, dihydrofolate reductase (DHFR), and thymidylate synthase. Affinity profiling determined selectivity and specificity of a series of quinoxaline and 2,4-diaminopteridine derivatives, and nine compounds showed greater activity against parasite enzymes compared with human enzymes. Compound 6a displayed a K(i) of 100 nM toward LmPTR1, and the crystal structure of the LmPTR1:NADPH:6a ternary complex revealed a substrate-like binding mode distinct from that previously observed for similar compounds. A second round of design, synthesis, and assay produced a compound (6b) with a significantly improved K(i) (37 nM) against LmPTR1, and the structure of this complex was also determined. Biological evaluation of selected inhibitors was performed against the extracellular forms of T. cruzi and L. major, both wild-type and overexpressing PTR1 lines, as a model for PTR1-driven antifolate drug resistance and the intracellular form of T. cruzi. An additive profile was observed when PTR1 inhibitors were used in combination with known DHFR inhibitors, and a reduction in toxicity of treatment was observed with respect to administration of a DHFR inhibitor alone. The successful combination of antifolates targeting two enzymes indicates high potential for such an approach in the development of previously undescribed antiparasitic drugs.

Optimized design and synthesis of chemical dimerizer substrates for detection of glycosynthase activity via chemical complementation

Glycosynthases catalyze the formation of a glycosidic bond between a glycosyl fluoride donor substrate and a glycosyl acceptor substrate with high yield, thus providing a valuable approach for the synthesis of carbohydrates and glycoconjugates. Chemical complementation can be used to link glycosynthase activity to the transcription of a reporter gene in vivo, providing a selection for the directed evolution of glycosynthase enzymes with improved properties. In this approach, glycosynthase activity is detected as covalent coupling between a small molecule disaccharide acceptor substrate and a small molecule disaccharide alpha-fluoro donor substrate. Here we report the optimized design and synthesis of these small molecule substrates. These optimized substrates are shown to give a robust, glycosynthase-dependent transcriptional read-out in the chemical complementation assay. The full synthesis and characterization of these substrates are reported for the first time. These optimized chemical dimerizer substrates should allow the potential of chemical complementation for the directed evolution of glycosynthases with diverse substrate specificities and improved properties to be fully realized.

Tight binding ligand approach to oligosaccharide-grafted protein

A novel type of artificial glycoprotein was developed, by using dihydrofolate reductase (DHFR) and methotrexate (MTX) as a protein-ligand pair. Various oligosaccharides linked to MTX were shown to bind tightly with DHFR and afforded oligosaccharide-grafted protein, which could be isolated easily by lectin beads.

Phosphinic acid pseudopeptides analogous to glutamyl-gamma-glutamate: synthesis and coupling to pteroyl azides leads to potent inhibitors of folylpoly-gamma-glutamate synthetase

Several routes to a complex phosphinate phosphapeptide analogous to the gamma-glutamyl peptide Glu-gamma-Glu have been investigated. Formation of gamma-phosphono glutamate derivatives via addition of a phosphorus-based radical to protected vinylglycine was found to be of limited value because of the elevated temperatures required. Alkylation and conjugate addition reactions of trivalent phosphorus (P(III)) species were investigated. In situ generation of bis-trimethylsilyl esters of phosphinous acids proved to be an effective route to phosphinates of modest structural complexity. However, this chemistry could not be extended to the incorporation of an amino acid moiety at the N-terminal side of the desired phosphinate. A successful synthesis of the target phosphinate phosphapeptide was effected using P(III) chemistry and dehydrohalogenation to yield an alpha,beta-unsaturated phosphinic acid ester, following which conjugate addition of diethylacetamido malonate and acid-mediated hydrolysis afforded the desired phosphinate phosphapeptide. Coupling of the unprotected phosphinate phosphapeptide with two acyl azides derived from folic acid and methotrexate led to the corresponding pteroylphosphapeptides of interest as possible mimics of tetrahedral intermediates in the reaction catalyzed by folylpolyglutamate synthetase.

Synthesis and antifolate evaluation of the aminopterin analogue with a bicyclo

N-[4-[[2,4-diamino-6-pteridinyl)methyl]amino]bicyclo[2.2.2]octane-1-carbonyl]-L-glutamic acid (1) was synthesized and tested for antifolate activity. N-(4-Aminobicyclo[2.2.2]octane-1-carbonyl-L-glutamic acid dimethyl ester (6), the side chain precursor to subject compound 1, was synthesized readily via reported bicyclo[2.2.2]octane-1,4-dicarboxylic acid monoethyl ester (2). The side chain precursor 6 was alkylated by 6-(bromomethyl)-2,4-pteridinediamine (7). Subsequent ester hydrolysis then afforded 1. Antifolate and antitumor evaluation of 1 verses L1210 dihydrofolate reductase (DHFR) and three tumor cell lines (L1210, S180, and HL60) showed it to be ineffective. Although compound 1 was very similar to aminopterin structurally, the bicyclo[2.2.2]octane ring system in place of the phenyl ring in the p-aminobenzoate moiety effectively negates the stoichiometric binding displayed by many classical DHFR inhibitors bearing appropriate aromatic ring systems in the side chain.

The structure-based design and synthesis of selective inhibitors of Trypanosoma cruzi dihydrofolate reductase

This paper describes the design and synthesis of potential inhibitors of Trypanosoma cruzi dihydrofolate reductase using a structure-based approach. A model of the structure of the T. cruzi enzyme was compared with the structure of the human enzyme. The differences were used to design modifications of methotrexate to produce compounds which should be selective for the parasite enzyme. The derivatives of methotrexate were synthesised and tested against the enzyme and intact parasites.

15N NMR studies of the conformation of E. coli dihydrofolate reductase in complex with folate or methotrexate

We have employed 15N NMR to characterize the conformations of Escherichia coli dihydrofolate reductase (ECDHFR) in complex with [5-15N]folate or [5-15N]methotrexate (MTX). Two 15N resonances were observed for DHFR/MTX binary complex. The relative population of these two conformations is pH dependent. Addition of NADP+ or NADPH results in the disappearance of the low field resonance. In contrast, only one conformation was observed for both the DHFR/folate and DHFR/folate/NADP+ complexes. However, the 15N chemical shift of [5-15N]folate in the binary DHFR/folate complex is 7.28 ppm upfield from that of the ternary complex, suggesting the possible loss of a hydrogen bonding to N5 of folate in the ternary complex.

Mobility of the spin-labeled side chains of some novel antifolate inhibitors in their complexes with dihydrofolate reductase

Four spin-labeled inhibitors of dihydrofolate reductase (DHFR) have been synthesized, each of which has the 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) reporting group at a different distance from the 2,4-diaminopyrimidine moiety by which the inhibitors are anchored and oriented in the active site. Inhibitors in which the TEMPO group is attached by a short side chain are weakly bound to DHFR from bacteria (Streptococcus faecium and Lactobacillus casei), to the bovine enzyme and to recombinant human DHFR. However, binding is sufficiently tight, especially in the ternary complexes with NADPH, for recording of the EPR spectra of the bound ligands. The spectra indicate that when these inhibitors are bound to the enzyme the TEMPO group is highly immobilized with correlation time, tau c, 4-20ns. Inhibitors that have the reporter group attached to the glutamate moiety of methotrexate bind to all four DHFRs more tightly than the inhibitors with shorter side chains by factors of up to 10(6). However, in most complexes formed by the inhibitors with longer side chains immobilization of the TEMPO group is slight (tau c 0.2-4 ns). These results are in general agreement with predictions from X-ray crystallographic results including thermal factors but there are some unanticipated differences between some results for bacterial and eukaryotic enzymes. Three of the splin-labeled inhibitors would provide good probes for distance measurements in and around the active site of mammalian DHFR.

13C and 15N nuclear magnetic resonance evidence of the ionization state of substrates bound to bovine dihydrofolate reductase

The state of protonation of substrates bound to mammalian dihydrofolate reductase (DHFR) has significance for the mechanism of catalysis. To investigate this, dihydrofolate and dihydropteroyl-pentaglutamate have been synthesized with 15N enrichment at N-2. 15N NMR studies have been performed on the binary complexes formed by bovine DHFR with these compounds and with [5-15N]dihydrobiopterin. The results indicate that there is no protonation at N-5 in the binary complexes, and this was confirmed by 13C NMR studies with folate and dihydrofolate synthesized with 13C enrichment at C-6. The chemical shift displacements produced by complex formation are in the same direction as those which result from deprotonation of the N-3/C-4-O "amide" group and are consistent with at least partial loss of the proton from N-3. This would be possible if, as crystallographic data indicate, there is interaction of N-3 and the 2-amino group of the bound ligands with the carboxylate of the active site glutamate residue (Glu30).

Liposome-mediated delivery of pteridine antifolates to cells in vitro: potency of methotrexate, and its alpha and gamma substituents

We have examined the growth-inhibitory potency of several pteridines encapsulated in negatively charged liposomes, including methotrexate, methotrexate-gamma-methylamide, methotrexate-gamma-dimethylamide, methotrexate-alpha-aspartate, and a lipophilic methotrexate-phosphatidylethanolamine conjugate. The potency of encapsulated methotrexate is greater than the potency of the free drug for CV1-P cells, but not for other cell lines. The potency of methotrexate-gamma-methylamide and methotrexate-gamma-dimethylamide is only minimally improved by encapsulation. The potency of methotrexate-alpha-aspartate is increased by encapsulation. In addition, the lipophilic methotrexate derivative has demonstrable potency when incorporated in liposomes. We have also examined the potency of several pteridines under conditions where the cells are exposed to the drug for periods shorter than the entire growth assay. Reduction of the exposure time decreases the potency of both encapsulated and free drugs. However, the difference in potency between the encapsulated and free drug is increased, because the potency of the encapsulated drug is affected less. Consequently, encapsulated methotrexate-gamma-aspartate is 300-fold more potent than free drug, if CV1-P cells are exposed to drug for 4 h. Moreover, encapsulated methotrexate is more potent than free methotrexate for growth inhibition of L929 fibroblasts, if the term of exposure is less than 8 h. Potency is least affected by reduction of exposure length for the lipophilic methotrexate derivative.

gamma-Fluoromethotrexate: synthesis and biological activity of a potent inhibitor of dihydrofolate reductase with greatly diminished ability to form poly-gamma-glutamates

A methotrexate (MTX) analog containing fluorine at the gamma-carbon of the glutamate moiety, gamma-fluoromethotrexate (FMTX), has been synthesized and evaluated for its biochemical and pharmacological properties. FMTX inhibition of dihydrofolate reductase from several sources is nearly equivalent to that shown by MTX. Most important, FMTX is an exceedingly poor substrate for folylpoly (gamma-glutamate) synthetase, the enzyme that catalyzes the biosynthesis of the highly-retained, cytotoxic MTX polyglutamates. Uptake experiments in H35 hepatoma cells show that FMTX accumulates to approximately the same extent as MTX at steady state. The rapid efflux of both derivatives is also very similar. The major difference detected in cells between the two compounds is the meager glutamylation of FMTX, due to the electronegative properties of the fluorine adjacent to the potential amide-forming carboxyl group. Exposure of dividing cells to 50 microM MTX for 2 and 6 hr results in the formation of 55 and 130 nmol, respectively, of the polyglutamates (more than two glutamate residues)/g of cell protein. With FMTX these values were reduced by 98% and 93%, respectively. Growth inhibition studies show that MTX is only 12-fold more toxic than FMTX when the cells are exposed to each derivative continuously for 72 hr. When the exposure time is reduced, a greater disparity between the inhibitory effects is observed; with a 2-hr pulse, MTX is 2300-fold more effective than FMTX. These data correlate with the effects of pulses of FMTX and MIX on de novo thymidylate biosynthesis in intact cells. The results indicate that of the parameters examined, the vastly reduced toxicity of FMTX after its removal from the culture medium is best correlated with impaired glutamylation. The data strongly suggest that prolonged toxicity of MTX is a result of metabolic conversion to MTX polyglutamates and that these effects are far more dramatic in short-term than in long-term exposure to the antifolates.

A synthetic approach to poly-gamma-glutamyl analogs of methotrexate

Methotrexate poly-gamma-glutamates bearing two and three glutamate units above that present in methotrexate have been synthesized by extension of a previously described route by which the lower congener bearing one added glutamate unit was synthesized. Key steps in the sequence are the peptide coupling of N-[4-[[(benzyloxy)-carbonyl]methylamino]benzoyl]-L-glutamic acid alpha-benzyl ester (5) with oligo-gamma-L-glutamate benzyl esters, removal of blocking groups by catalytic hydrogenolysis, and introduction of the (2,4-diamino-6-pteridinyl)methyl grouping by alkylation with (6-bromomethyl)-2,4-pteridinediamine hydrobromide. Elaboration of the required oligo-gamma-L-glutamate chain was achieved one unit at a time beginning with the coupling of L-glutamic acid dibenzyl ester with t-butyloxycarbonyl-L-glutamic acid alpha-benzyl ester (7) followed by selective removal of the t-butyloxycarbonyl grouping and another coupling step with 5 or 7 as required. Diphenylphosphoryl azide was used as the coupling reagent in each conversion producing a peptide linkage. Intermediates were obtained in pure form according to thin-layer chromatography and elemental analysis results, and the final target compounds were obtained in high purity as judged by thin-layer chromatography, high-performance liquid chromatography, 1H NMR and mass spectral data, and elemental analysis results.

Purity profiles of pteroylglutamate reference substances by high-performance liquid chromatography

High-performance liquid chromatography (HPLC) in the reversed-phase mode was used for the purity analysis of three pteroylglutamic acid-type reference substances (folic acid, leucovorin calcium, and methotrexate). The influence of the pH of the mobile phase on the separation of an artificial mixture of six pteroylglutamic acid derivatives and three potential impurities was studied. Results of purity analysis of current lots of USP reference standards are reported. A better separation of methotrexate from its major impurities was achieved by using a standard buffer, rather than an ion-pairing mobile phase. A separation of methotrexate and its biologically inactive 7-isomer is reported.

Diazoketone and chloromethylketone analogs of methotrexate as potential antitumor agents

The synthesis of 4-amino-4-deoxy-N10-methylpteroyl-(6-diazo-5-oxo)-L-norleucine and 4-amino-4-deoxy-N10-methylpteroyl-(6-chloro-5-oxo)-L-norleucine, analogs of methotrexate in which the gamma-carboxyl group is replaced by a diazoketone and a chloromethylketone, respectively, was carried out. The analogs inhibited the growth of leukemia L-1210 cells in culture by 50% at 4 X 10(-7) M and 2 X 10(-7) M, respectively, and were effective inhibitors of the synthesis of thymidylate in L-1210 cells in vitro (I50 = 3 X 10(-6) M), exhibiting significant antifolate activity. The results demonstrated the feasibility of introducing chemically reactive groups at the gamma-position of pteroyl glutamates with retention of biological activity. However, in the systems investigated thus far, there was no evidence of covalent bond formation due to these reactive groups at the active sites of the enzymes.

Carbon-13 nuclear magnetic resonance study of protonation of methotrexate and aminopterin bound to dihydrofolate reductase

Methotrexate, aminopterin, and folate have been synthesized with 90% enrichment of C-2 with 13C. 13C nuclear magnetic resonance has been used to examine the state of protonation of the pteridine ring of these compounds under various conditions and gives much more clear-cut results than most other methods. For the free compounds the following pK values were obtained: methotrexate, 5.73 +/- 0.02 (N-1); aminopterin, 5.70 +/- 0.03 (N-1); folic acid, 2.40 (N-1) and 8.25 +/- 0.05 (N-3, O-4 amide group). The state of protonation of these compounds when complexed to dihydrofolate reductase (isoenzyme 2 from Streptococcus faecium) was also studied over the pH range 6--10. The resonance from bound methotrexate showed a constant chemical shift over the whole pH range studied, and it is inferred that in the complex the pteridine ring remains protonated to at least pH 10. The same result was obtained for the binary complex of aminopterin with the reductase and for either methotrexate or aminopterin in ternary complex with reductase and NADPH4. The latter is an inhibitor of the reductase competitive with NADPH. However, folate bound to the reductase in either the binary or the ternary complex shows the same protonation behavior as in the free state. The data indicate that the association constant for binding of methotrexate is increased enough when protonation of N-1 occurs to account for the enhanced binding of methotrexate as compared with folate.