Tumor-Targeting with Novel Non-Benzoyl 6-Substituted Straight Chain Pyrrolo[2,3-d]pyrimidine Antifolates via Cellular Uptake by Folate Receptor α and Inhibition of de novo Purine Nucleotide Biosynthesis

Abstract

A new series of 6-substituted straight side chain pyrrolo[2,3-d]pyrimidines 3a–d with varying chain lengths (n = 5–8) was designed and synthesized as part of our program to provide targeted antitumor agents with folate receptor (FR) cellular uptake specificity and glycinamide ribonucleotide formyltransferase (GARFTase) inhibition. Carboxylic acids 4a–d were converted to the acid chlorides and reacted with diazomethane, followed by 48% HBr to generate the α-bromomethylketones 5a–d. Condensation of 2,4-diamino-6-hydroxypyrimidine 6 with 5a–d afforded the 6-substituted pyrrolo[2,3-d]pyrimidines 7a–d. Hydrolysis and subsequent coupling with diethyl L-glutamate and saponification afforded target compounds 3a–d. Compounds 3b–d showed selective cellular uptake via FRα and -β, associated with high affinity binding and inhibition of de novo purine nucleotide biosynthesis via GARFTase, resulting in potent inhibition against FR-expressing Chinese hamster cells and human KB tumor cells in culture. Our studies establish, for the first time, that a side chain benzoyl group is not essential for tumor-selective drug uptake by FRα.

INTRODUCTION

Folates are essential for cell growth and tissue regeneration. Membrane transport of extracellular folates is required because mammalian cells cannot synthesize folates de novo. Three major folate uptake systems have been reported.^1–5 (i) The reduced folate carrier (RFC or SLC19A1) is an anion antiporter that is ubiquitously expressed in tissues and tumors and is the major membrane transport system for folates in mammalian cells at physiologic pH.¹ (ii) Folate receptors (FRs) α and β are glycosyl phosphatidylinositol-anchored proteins that mediate cellular uptake of folates by receptor-mediated endocytosis.^2,3 High levels of FRs are expressed in a number of malignancies, including ovarian and endometrial cancers (FRα) and in myeloid leukemias (FRβ).^2,3 However, FRs show a more restricted tissue distribution than RFC. In normal tissues where they are expressed, FRs are either inaccessible to circulating folate cofactors (FRα in renal tubules) or are non-functional (FRβ in normal hematopoietic cells).^2,3 (iii) The proton-coupled folate transporter (PCFT; SLC46A1) is a recently discovered proton-folate symporter that functions optimally at acidic pH by coupling the downhill flow of protons to the uphill transport of folates.^4,5 PCFT is widely expressed in human solid tumors⁴ and in modest levels in most normal tissues, although high levels of PCFT are present in the duodenum and jejunum, as well as in the liver and kidney.⁵

Folate-dependent biosynthetic pathways are important therapeutic targets for cancer chemotherapy.^6–8 Clinically relevant antifolate drugs for cancer include potent inhibitors of dihydrofolate reductase [methotrexate (MTX), pralatrexate (PDX)], thymidylate synthase [raltitrexed (RTX), pemetrexed (PMX)], and the purine nucleotide biosynthetic enzymes, β-glycinamide ribonucleotide (GAR) formyltransferase (GARFTase) [PMX] and 5-aminoimidazole-4-carboxamide (AICA) ribonucleotide formyltransferase (AICARFTase) [PMX]^6–8 (Figure 1). Although all these agents are transported by RFC^1,9, the expression of RFC in both normal and tumor cells presents a potential obstacle to antitumor selectivity. Further, loss of RFC is frequently associated with antifolate resistance.^1,8,10 Thus, it is of interest to design tumor-targeted antifolates that are specific substrates for transporters other than RFC with limited expression and/or transport into normal tissues compared with tumors. If these drugs also inhibit targets other than dihydrofolate reductase and thymidylate synthase, this would afford further benefit by circumventing resistance due to increased levels or mutated forms of these enzyme targets. This reasoning was a major impetus to develop novel agents with selective uptake into tumors by FRs or PCFT over RFC, and which specifically target de novo purine nucleotide biosynthesis.^5,6,11–16

Figure 1.

Structures of clinically relevant antifolates transported by RFC.

We previously reported a series of 6-substituted pyrrolo[2,3-d]pyrimidine phenyl antifolates 2a–d.^11,13 (Figure 2) A highly active compound of this series was the 3- carbon bridge (2a) which was a targeted agent selectively transported into certain tumor cells by FRs and PCFT but not RFC.^11,13 Once intracellular, compound 2a inhibited GARFTase in de novo purine nucleotide biosynthesis, resulting in depletion of purine nucleotides.^11,13 Further, compound 2a was highly active in vitro toward both KB and IGROV1 tumors.¹¹ To further explore the structure-activity relationships (SAR) for GARFTase inhibition and non-RFC targeted transport specificity, we synthesized and tested several series of related analogs with modifications of the aromatic rings and aliphatic linkers.^5,6,12–16

Figure 2.

6-Substituted non-benzoyl straight chain compounds 3a–d, based on lometrexol (LMTX) and compounds 1a–c, showing replacement of the phenyl ring in compounds 2a–2b by 2–5 methylene groups.

Lometrexol (LMTX) is an early generation GARFTase inhibitor¹⁷ that was tested in a phase I clinical trial and was found to be unacceptably toxic.¹⁸ This failure was likely due, at least in part, to its membrane transport into normal cells by RFC. A series of LMTX analogs, 1a–c, was reported in which the phenyl ring in the bridge was replaced by a methylene bridge of variable length^19,20 (Figure 2). Interestingly, replacement of the phenyl ring of LMTX by two, three, or four carbon atom chains substantially preserved both binding to GARFTase¹⁹ and polyglutamylation by folylpolyglutamate synthetase (FPGS).²⁰ However, these analogs were not tested for their membrane transport by the major folate transporters or for their capacities to inhibit cell proliferation.

In the present work, we designed an analogous series of 6-substituted pyrrolo[2,3-d]pyrimidine analogs to examine the impact of an alkyl-for-benzoyl ring replacement on folate transporter specificity, GARFTase inhibition, and anti-proliferative activities. Straight chain compounds 3a–d were designed with replacement of the phenyl ring of the lead compound 2a by methylene bridges of variable lengths (n =2–5) (Figure 2). The precursor acids, 7e–h (Scheme 1), were also biologically evaluated to determine the importance of the L-glutamate moiety to their biological effects. Collectively, our results establish that aliphatic replacement of the benzoyl ring in the 6-substituted pyrrolo[2,3-d]pyrimidine series preserves substantial selective FR-directed cellular uptake and GARFTase inhibition, with potent inhibition of tumor cell proliferation, as long as there is sufficient distance between the bicyclic ring system and the terminal L-glutamate.

Scheme 1.

CHEMISTRY

Compounds 3a–d (n = 5–8) were synthesized using an α-bromomethyl ketone condensation with 2,4-diamino-4-oxo-pyrimidine 6 as the key step outlined in Scheme 1. Commercially available carboxylic acids 4a–d were converted to the acid chlorides and immediately reacted with diazomethane, followed by 48% HBr to give the desired α-bromomethylketones 5a–d.¹¹ Condensation of 2,4-diamino-6-hydroxypyrimidine 6 with 5a–d afforded the 6-substituted pyrrolo[2,3-d]pyrimidines 7a–d. Hydrolysis of 7a–d afforded 7e–h. Subsequent coupling with diethyl L-glutamate using N-methyl morpholine and 2,4-dimethoxy-6-chlorotriazine as the activating agents afforded the diesters 8a–d. Final saponification of the diesters gave the target compounds 3a–d (n = 5–8).

BIOLOGICAL EVALUATION AND DISCUSSION

Non-benzoyl 6-carbon chain pyrrolo[2,3-d]pyrimidine antifolates are inhibitors of cell proliferation, correlating with expression of folate receptors

Our goal was to examine the role of the side chain phenyl ring and the terminal L-glutamate of the pyrrolo[2,3-d]pyrimidine antifolates as determinants of folate transporter selectivity, GARFTase inhibitory activity and anti-proliferative activity, based on prior studies of compounds 2a–d. We previously showed that the intramolecular distance between the bicyclic scaffold and the L-glutamate moiety of the latter series was an important determinant of inhibitory potency toward FR-expressing cell lines,^{10,11,13–15} so this was also examined.

Compounds 3a–d (Figure 2) and 7e–h (Scheme 1) were tested in cell proliferation assays with a well-characterized cohort of isogenic Chinese hamster ovary (CHO) sublines previously engineered to individually express the major (anti)folate cellular uptake systems including RFC (PC43-10)²¹, FRα and β (RT16 and D4, respectively) ¹¹, or PCFT (R2/PCFT4).^12,13 Additional testing was performed with KB human nasopharengeal carcinoma cells which express RFC, FRα, and PCFT.^11,12 Experiments were performed in standard RPMI 1640/10% dialyzed fetal bovine serum (dFBS) (PC43-10), and in folate-defined media {folate-free RPMI1640/10% dFBS, supplemented with 2 nM (RT16, D4, KB) or 25 nM leucovorin [(6R,S)5-formyl tetrahydrofolate (LCV)] (R2/PCFT4)}. The impact of the drug treatments on cell proliferation was measured after 96 h and results were compared to negative controls including RFC-, FR- and PCFT-null MTXRIIOua^R2-4 (R2) CHO cells^11,12,21 [either the parental R2 subline or vector control R2(VC) cells]. For FR-expressing CHO and KB cells, parallel cultures were treated with drugs along with excess folic acid (200 nM) to block drug binding and cellular uptake by FRs. Internalization of exogenous folic acid by FRs would also increase intracellular folate pools. Results were compared with those for the lead 6-substituted pyrrolo[2,3-d]pyrimidine benzoyl analogs 2a–d and are summarized in Table 1.

Table 1. IC₅₀s (in nM) for 6-substituted pyrrolo[2,3-d]pyrimidine antifolates and classical antifolates in RFC-, PCFT-, and FR-expressing cell lines.

Growth inhibition assays were performed for CHO sublines engineered to express human RFC (PC43-10), FRs α and β (RT16 and D4, respectively), or PCFT (R2/PCFT4), for comparison with transporter-null [R2, R2(VC)] CHO cells, and for the KB human tumor subline (expresses RFC, FRα, and PCFT), as described in the Experimental Section. For the FR experiments, growth inhibition assays were performed in the presence and the absence of 200 nM folic acid (FA). The data shown are mean values from 3–10 experiments (plus/minus SEM in parentheses). Results are presented as IC₅₀ values, corresponding to the concentrations that inhibit growth by 50% relative to cells incubated without drug. Data for MTX, PMX, RTX, and LMTX, and for compounds 2a–d were previously published.^11,13 The structures for the classical antifolate drugs are shown in Figure 1 and those for compounds 7e–h and 3a–d are shown in Figure 2 and Scheme 1.

Antifolate	hRFC		hFRα		hFRβ		hPCFT		hRFC/FRα/hPCFT
	PC43-10	R2	RT16	RT16 (+FA)	D4	D4 (+FA)	R2/hPCFT4	R2(VC)	KB	KB (+FA)
2a	648.6(38.1)	>1000	4.1(1.6)	>1000	5.6(1.2)	>1000	23.0(3.3)	>1000	1.7(0.4)	>1000
2b	>1000	>1000	6.3 (1.6)	>1000	10 (2)	>1000	213 (28)	>1000	1.9 (0.7)	>1000
2c	>1000	>1000	54(21)	>1000	80(9)	>1000	>1000	>1000	13(7.2)	>1000
2d	>1000	>1000	162(18)	>1000	198(34)	>1000	>1000	>1000	23(12)	>1000
7e	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000
7f	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000
7g	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000	>1000
7h	>1000	>1000	>10000	>100	>1000	>1000	>1000	>1000	>1000	>1000
3a	>1000	>1000	>1000	>1000	214(62)	>1000	>1000	>1000	200.3(34.6)	>10000
3b	>1000	>1000	47.1(16.5)	>1000	10.55(3.69)	>1000	>1000	>1000	7.9 (0.72)	>1000
3c	>1000	>1000	8.54(1.53)	>1000	0.87(0.12)	>1000	>1000	>1000	1.10(0.88)	>1000
3d	>1000	>1000	12.31 (3.14)	>10000	3.99(0.57)	>1000	>1000	>1000	1.48(0.04)	>1000
LMTX	12(2.3)	>1000	12(8)	188(41)	2.6(1.0)	275(101)	38.0(5.3)	>1000	1.2(0.6)	31(7)
MTX	12(1.1)	216(8.7)	114(31)	461(62)	106(11)	211(43)	121(17)	>1000	6.0(0.6)	20(2.4)
PDX	0.69(0.07)	819(94)	168(50)	>1000	ND	ND	57(12)	>1000	0.47(0.20)	1.94(0.28)
PMX	138(13)	894(93)	42(9)	388(68)	60(8)	254(78)	13.2(2.4)	974.0(18.1)	68(12)	327(103)
RTX	6.3(1.3)	>1000	15(5)	>1000	22(10)	746(138)	99.5(11.4)	>1000	5.9(2.2)	22(5)

ND: not determined.

The data in Table 1 clearly establish that the compounds (7e–h) lacking the L-glutamate are not inhibitory, regardless of the cell line model tested. Compounds 3a–d were also inactive up to 1000 nM toward RFC-expressing PC43-10 cells and PCFT-expressing R2/PCFT4 CHO cells. Compounds 3a–d were inhibitory toward CHO cells engineered to express FRα and FRβ, as well as FRα-expressing KB tumor cells. Growth inhibition was abolished in the presence of excess (200 nM) folic acid. The most potent inhibitor was 3c (7-carbon atom chain), followed by 3d (8-carbon chain) and 3b (6-carbon chain). The 5-carbon chain analog, 3a, was a much poorer inhibitor of cell proliferation. Growth inhibitions, as reflected in the IC₅₀ values, were similar with FRα-expressing sublines (KB, RT16) for compounds 2a, 2b, 3c and 3d. Whereas sensitivities of FRα-expressing RT16 cells were similar to those for FRβ-expressing D4 cells for compounds 2a and 2b, D4 cells were distinctly more sensitive to the non-benzoyl compounds 3b–3d. The FR specificity for the active analogs of this series contrasts with results with classic antifolates including MTX, RTX, PMX, PDX, and LMTX, for which anti-proliferative activities for RFC- and PCFT-expressing cells exceeded those for FR-expressing cells (Table 1).

Binding of non-benzoyl pyrrolo[2,3-d]pyrimidine antifolates to FRα and β

Compounds 3a–d are all inhibitors of proliferation for cell lines that express FRα (RT16, KB) and FRβ (D4) (Table 1). The inhibitory effects of these active compounds were blocked by excess folic acid, consistent with their surface binding and internalization by FRs.

Surface FR binding of cytotoxic folate analogs is an essential step for drug internalization by this mechanism and for inhibition of intracellular enzyme targets.^{11,12,14–16} To establish a SAR for FRα and –β binding of this series, in particular the impact of alkyl chain length (5–8 carbons) for the 6-substituted analogs and of the terminal L-glutamate on FR binding, we performed competitive binding assays with compounds 3a–d and 7e–h at pH 7.4. In these experiments, unlabeled pyrrolo[2,3-d]pyrimidine compounds were tested for their abilities to compete for surface FR binding with [³H]folic acid. FR binding of unknown ligands was compared to those for positive (compounds 2a and 2b, also folic acid) and negative (MTX) controls, with documented FR-binding characteristics. The CHO sublines expressing FRα (RT16) or FRβ (D4) were initially rinsed with acid-buffered saline to release FR-bound folates, followed by incubation with [³H]folic acid (at pH 7.4), in the presence of unlabeled (anti)folate competitors over a range of concentrations.^{11,12,14–16} After further washing the cells (pH 7.4), FR-bound [³H]folic acid was quantitated and normalized to cell protein and results calculated as pmol [³H]folic acid bound to FRs per mg cell protein. Relative affinities were expressed as inverse molar ratios of (anti)folates required to decrease bound [³H]folic acid by 50% normalized to the affinity for unlabeled folic acid in each experiment (assigned a value of 1.0).^{11,12,14–16} The results are expressed as mean values +/− standard errors and are presented in Figure 3.

Figure 3. Binding of non-benzoyl 5- and 6-substituted pyrrolo[2,3-d]pyrimidine analogs (3a–d and 7e–h) to FRα (RT16) and FRβ (D4), compared to compounds 2a and 2b.

Data are shown for the effects of the unlabeled ligands with FRα-expressing RT16 and FRβ-expressing D4 CHO cells. Binding affinities for assorted folate/antifolate substrates were determined over a range of ligand concentrations and were calculated as the inverse molar ratios of unlabeled ligands required to inhibit [³H]folic acid binding by 50%. Relative binding affinities for individual experiments were normalized to that for unlabeled folic acid which was assigned a value of 1.0. For the various ligands, results are presented as mean values +/− standard errors from 3 experiments. Details for the binding assays are provided in the Experimental Section. Undefined abbreviations: FA, folic acid. The results for compounds 2a and 2b were previously published.¹¹

With the 6-substituted analogs that included terminal L-glutamates (3a–d), FR binding increased with increasing substituent chain length (3d > 3c > 3b > 3a) for both FRα and –β, with compound 3d exhibiting relative binding affinities approximating those for compounds 2a and 2b, and slightly less than for folic acid (Figure 3). The lack of a terminal L-glutamate (compounds 7e–h) had a deleterious effect on FR binding, consistent with the results for the cell proliferation experiments (Table 1). For FRα (but not FRβ), compound 7h with the 8-carbon chain showed detectable binding. Interestingly, binding of the active linear analogs (compounds 3b, 3c, and 3d) was consistently reduced for FRβ compared to FRα, in spite of their increased inhibitory effects toward FRβ-expressing D4 cells over FRα-expressing RT16 cells (Table 1).

These results demonstrate that the presence of a phenyl side chain ring system for the 6-substituted pyrrolo[2,3-d]pyrimidine analogs is not obligatory for binding to FRα or -β. Further, whereas FR binding is clearly critical to cellular uptake of cytotoxic folate analogs, this parameter shows at best an inexact correlation with anti-proliferative activities of the non-benzoyl pyrrolo[2,3-d]pyrimidine series of analogs. Nonetheless, FR binding for both FR α and β was greatest for the compounds (3c and 3d) with the most potent anti-proliferative effects.

Determination that GARFTase is the major cellular target for compounds 3b, 3c and 3d

Previous reports of non-benzoyl analogs of LMTX, 1a–c, in which the phenyl ring was replaced by 2–4 methylene groups (Figure 2) established that the aromatic B ring is not essential for binding to the GARFTase active site, as these novel antifolate compounds were potently inhibitory toward purified murine GARFTase.¹⁹ Further, compounds 1a–c were all excellent substrates for polyglutamylation by murine FPGS.²⁰ By analogy to compounds 1a–c and the parent 6-substituted pyrrolo[2,3-d]pyrimidines 2a and 2b, we hypothesized that the non-benzoyl analogs 3b–d were also GARFTase inhibitors. To establish the targeted pathway for compounds 3b–d (i.e., de novo thymidylate versus de novo purine nucleotide biosynthesis), exogenous thymidine and adenosine were tested for their capacities to reverse their growth inhibitory effects toward KB cells (Figure 4).^11–17 AICA, a precursor of the AICARFTase substrate was added to circumvent the step catalyzed by GARFTase so as distinguish inhibition of GARFTase from AICARFTase.^11–17

Figure 4. Protection of KB cells from growth inhibition by non-benzoyl 6-substituted pyrrolo[2,3-d]pyrimidine analogs 3b–d, in the presence of nucleosides and 5-aminoimidazole-4-carboxamide (AICA).

Proliferation inhibition was measured for KB cells over a range of concentrations of compounds 3b–d, as shown, in complete folate-free RPMI1640 with 2 nM LCV in the absence of other additions (labeled “No additions”), or in the presence of 200 nM folic acid (labeled “Folate Added”), adenosine (60 μM), thymidine (10 μM), adenosine plus thymidine, or AICA (320 μM). Cell densities were measured with CellTiter Blue^™ fluorescence dye and a fluorescence plate reader. Results were normalized to cell densities in the absence of drug. Results shown are representative data of experiments performed in triplicate.

For non-benzoyl pyrrolo[2,3-d]pyrimidine analogs 3b–d, thymidine (10 μM) had no impact on the extent of inhibition of cellular proliferation, indicating that thymidylate biosynthesis (i.e., thymidylate synthase) was not being targeted. Conversely, both adenosine (60 μM) and AICA (320 μM) completely reversed the inhibitory effects of this series, establishing that de novo purine nucleotide biosynthesis in general, and GARFTase in particular were the likely intracellular targets (Figure 4). Essentially identical results were previously published for compounds 2a and 2b.¹¹ In addition, in experiments with recombinant DHFR and TS, compounds 3b–3d were not inhibitory (data not shown).

We used an in situ activity assay to directly measure cellular GARFTase activity in KB cells treated with the novel antifolates.^11–17 Cells were incubated with [¹⁴C]glycine as a radiotracer for 15 h in the presence of compounds 3b–d under conditions and at concentrations approximating those used in the cell proliferation experiments (Table 1). In this metabolic assay, [¹⁴C]glycine is incorporated into the GARFTase substrate [¹⁴C] GAR and subsequently into [¹⁴C]formyl GAR (by GARFTase) which accumulates in the presence of azaserine. Following protein precipitation with trichloroacetic acid, the acid-soluble metabolites are extracted and fractionated by ion-exchange chromatography, permitting quantitation of [¹⁴C]formyl GAR normalized to cellular protein.

The results show that in KB cells, compounds 3b–d were all potent GARFTase inhibitors at extracellular drug concentrations approximating those required to inhibit cell proliferation (Figure 5). Calculated IC₅₀ values for GARFTase inhibition varied within a 3-fold range from 2.89 for compound 3b to 9.62 nM for compound 3d. By comparison, the IC₅₀s for the 3- and 4-carbon benzoyl analogs 2a and 2b were 18 and 6.8 nM, respectively.¹¹

Figure 5. In situ GARFTase inhibition assay.

For the in situ assays, incorporation of [¹⁴C]glycine into [¹⁴C]formyl GAR was measured in KB tumor cells cultured for 15 h in complete folate-free RPMI 1640 plus 2 nM LCV. Details are described in the Experimental Section. Results are presented as a percent of control treated without drugs for KB cells treated with nanomolar concentrations of 3b–d. Results are presented as mean IC₅₀ values +/− standard errors. Mean IC₅₀s (+/− SEs) were calculated as 2.89 (+/−0.62) nM for 3b, 5.49 (+/−1.36) nM for 3c, and 9.62 (+/−0.98) nM for 3d. For comparison, IC₅₀s for compounds 2a and 2b were 18 (+/− 2) nM and 6.8 (+/−0.9) nM, respectively.¹¹

These results unambiguously demonstrate that the absence of a side chain benzoyl ring system in the 6-substituted pyrrolo[2,3-d]pyrimidine series is not required to potently inhibit intracellular GARFTase, analogous to results for the non-benzoyl analogs of LMTX 1a–c (Figure 1).

Molecular modeling: docking studies of compound 3c with human GARFTase

Figure 6 shows the docked pose of 3c (n=7) in the human GARFTase (PDB ID: 1NJS)²² active site. The cofactor binding pocket of GARFTase is located at the interface between the N-terminal mononucleotide binding domain and the C-terminal half of the structure. The binding site for the folate cofactor moiety consists of three parts: the pteridine binding cleft, the benzoylglutamate region, and the formyl transfer region.²² The docked pose shows the pyrrolo[2,3-d]pyrimidine scaffold of 3c to be buried deep in the active site and occupies the same location as the diaminopyrimidone ring in the native crystal structure ligand 10-trifluoroacetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid (10-CF₃CO-DDACTHF). This orientation of the scaffold permits the 2-amino moiety of 3c to form hydrogen bonds to Glu141 and the backbone of Leu92. The N1 nitrogen interacts with the backbone of Leu92 to form a hydrogen bond. The 4-oxo moiety forms a hydrogen bond with Asp144 and forms water-mediated hydrogen bonds with Asp142 and Ala140. The molecule is oriented in a manner that aids the N7-nitrogen to form a hydrogen bond with Arg90. As is shown with 10-CF₃CO-DDACTHF (Figure 6), several hydrophobic residues flank the pocket which holds the pyrrolo[2,3-d]pyrimidine scaffold. The hydrophobic pocket consists of Leu85, Ile91, Leu92, Val97 (not shown), and the folate binding loop residues 141–146. The amide NH of the L-glutamate forms a hydrogen bond with Met89. The 7-carbon side chain of 3c shifts the glutamate side chain away from the corresponding glutamate side chain of 10-CF₃CO-DDACTHF. The carbonyl group of the glutamate side chain of 3c interacts with Arg64, which is not seen with the corresponding carbonyl group of the side chain of 10-CF₃CO-DDACTHF. The γ-carboxylic acid of 3c interacts with Arg64. The α-carboxylic acid of the glutamate side chain of 3c interacts with Arg90. Thus, the interaction pattern of the α- and γ-carboxylic acid moieties of 3c are reversed compared to the corresponding α- and γ-carboxylic acids of 10-CF₃CO-DDACTHF and could represent an alternate conformation of the side chain. These interactions could easily permit binding and potent inhibition of 3c against GARFTase, as demonstrated by the results of our in situ GARFTase assays (Figure 5).

Figure 6.

Stereoview. Overlay of the docked pose of 3c (white) with 10-CF₃CO-DDACTHF (purple) in human GARFTase (PDB ID: 1NJS).²²

Molecular modeling: docking studies of compound 3c with human FRα

The X-ray crystal structure of human FRα with folic acid was recently published.²³ Accordingly, we determined the docked structure of 3c (a prototype of the nonbenzoyl series of 6-substituted pyrrolo-[2,3-d]pyrimidine analogs) with FRα.

Figure 7 shows the docked pose of compound 3c in the human FRα (PDB ID: 4LRH)²³ binding site. The long and open folate-binding pocket of FRα contains a predominantly negatively charged pocket where the pteroate group of folic acid binds, and a positively charged entrance of the binding pocket which is occupied by the glutamate moiety of folic acid. In its docked pose, the pyrrolo[2,3-d]pyrimidine scaffold of 3c binds similar to the pterin scaffold of folic acid. The 2-NH₂ moiety of 3c interacts with the side chain carboxylic acid of Asp81. Additional hydrogen bonds are formed between N3 and the side chain hydroxyl of Ser174 and between the 4-oxo group and the side chain NH of Arg103 and His135. The pyrrolo[2,3-d]pyrimidine scaffold is sandwiched between the side chains of Tyr60 and Tyr171, similar to the pteridine ring seen in the bound conformation of folic acid. The pyrrole NH of 3c does not interact with the binding pocket. The flexible C6-substituted chain in 3c enables the glutamate moiety to be oriented similarly to the corresponding groups in folic acid. The α-carboxylic acid of 3c can form hydrogen bonds with the backbone NH of Gly137 and Trp138 while the γ-carboxylic acid interacts with the backbone NH of Lys136 and the side chain NH of Trp102. The hydrophobic C6-linker of 3c can interact in the linker region with surrounding hydrophobic amino acids such as Tyr60, Phe62, Trp102, Trp134 and His135. The docking score of 3c with FRα was -46.4850.

Figure 7.

Stereoview. Overlay of the docked pose of compound 3c (white) with folic acid (blue) in human FRα (PDB ID: 4LRH).²³

Conclusions

There is growing interest in tumor targeting of cytotoxic folate-based therapeutics via their selective cellular uptake by FRs or PCFT over RFC.^5,6,11–16 Specific uptake by FRs or PCFT but not RFC would afford these analogs selectivity for tumor cells expressing FRα and –β and/or PCFT and significant advantages over classical antifolates such as RTX or PMX that are transported by all systems.^1,5

In previous studies, we began establishing a SAR for FR and PCFT binding and cellular uptake vis á vis RFC, and of GARFTase inhibition in de novo purine nucleotide biosynthesis.^5,6,11–16 Hence, (i) the 6-substituted pyrrolo[2,3-d]pyrimidine ring system, (ii) a thienoyl-for-benzoyl B ring replacement, and (iii) optimal spacing between the pyrrolo[2,3-d]pyrimidine system and the terminal L-glutamate all favored FR and PCFT cellular uptake and GARFTase inhibition, resulting in potent anti-proliferative activity.^5,6,11–16

In this report, we continued our systematic study of structural determinants of cellular uptake by RFC, PCFT, and FRs α and β. A novel series of classical 6-substituted straight chain pyrrolo[2,3-d]pyrimidine antifolates 3a–d was designed and synthesized as analogs of 2a with replacement of the phenyl ring by a linear carbon chain of variable lengths (n = 2–5) with or without the terminal L-glutamate. Our results demonstrate, for the first time, that the presence of the phenyl side chain ring is not essential for binding and cellular uptake by FRs. There is an absolute requirement for a terminal L-glutamate and there is an optimal distance for the alkyl linker separating the pyrrolo[2,3-d]pyrimidine ring system and the L-glutamate moiety. The lack of a requirement of the phenyl side chain for FR-mediated cellular uptake is consistent with structural data for FRα²³ and our docking results with compound 3c and FRα which show that this region of the molecule interacts with FRα only via hydrophobic interactions.

There were modest differences in surface binding to FRα and –β at neutral pH between the active analogs, 3b–d, with binding to FRα exceeding that for FR–β. However, this did not translate into corresponding differences in in vitro drug efficacies toward isogenic CHO cell line models expressing one or the other transport system. Rather, inhibition of proliferation of FRβ-expressing CHO cells exceeded that for FRα-expressing CHO cells. This apparent discrepancy may reflect differences in relative affinities of bound substrates at the acidic pH conditions of the endosome for FR α and β. FRβ but not FRα was found to show (by isothermal titration calorimetry) a pH-dependent decrease in binding affinities for number of classic antifolates (MTX, aminopterin, PMX) at acidic versus neutral pH.²⁴ By analogy, for the linear 6-substituted pyrrolo[2,3-d]pyrimidine analogs, in spite of their slightly decreased binding affinities for FRβ at pH 7.4, bound drugs may be more effectively released in the endosome than drugs bound to FRα.

For both FRα and –β, the most active compounds of the present series, compounds 3c and 3d, bound with the highest affinities and inhibited proliferation of FR-expressing CHO and KB tumor cells with nanomolar potencies approaching those of compounds 2a and 2b, among the most potent 6-substituted pyrrolo[2,3-d]pyrimidine analogs previously reported by us^5,11, albeit without any evidence of PCFT transport. Likewise, there was no indication of RFC membrane transport, as an engineered CHO cell line expressing ample human RFC and established in vitro cytotoxicities to RFC antifolate substrates was completely unaffected by the most potent non-benzoyl analogs.

Our results establish that although the phenyl side chain is not essential for FR binding and cellular uptake, it appears to be absolutely necessary for PCFT transport. Inhibition of cell proliferation was attributable to potent inhibition of GARFTase in de novo purine nucleotide bioynthesis at concentrations approximating those which inhibited cell proliferation. Thus, our results are entirely consistent with previous reports that the absence of a side chain phenyl ring in a series of non-benzoyl analogs of LMTX analogs preserved substantial catalytic activity for FPGS and inhibition of isolated GARFTase.^19,20 The structural simplicity and extraordinary antitumor activities of the 6-substituted straight chain compounds described herein provide an excellent starting point for future rational design efforts to further optimize selective cellular uptake by FRs and GARFTase inhibition as an important step toward discovering additional potent targeted antitumor agents.

EXPERIMENTAL SECTION

All evaporations were carried out in vacuo with a rotary evaporator. Analytical samples were dried in vacuo (0.2 mmHg) in a CHEM-DRY drying apparatus over P₂O₅ at 80 °C. Melting points were determined on a MEL-TEMP II melting point apparatus with a FLUKE 51 K/J electronic thermometer and are uncorrected. Nuclear magnetic resonance spectra for proton (¹H NMR) were recorded on either a Bruker WH-400 (400 MHz) spectrometer or a Bruker WH-500 (500 MHz) spectrometer. The chemical shift values are expressed in ppm (parts per million) relative to tetramethylsilane as an internal standard: s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet; br, broad singlet. Mass spectra were recorded on a VG-7070 double-focusingmass spectrometer or in a LKB-9000 instrument in the electron ionization (EI) mode. Chemical names follow IUPAC nomenclature. Thin-layer chromatography (TLC) was performed on Whatman Sil G/UV254 silica gel plates with a fluorescent indicator, and the spots were visualized under 254 and 365 nm illumination. All analytical samples were homogeneous on TLC in three different solvent systems. Proportions of solvents used for TLC are by volume. Column chromatography was performed on a 230–400 mesh silica gel (Fisher, Somerville, NJ) column. Elemental analyses were performed by Atlantic Microlab, Inc., Norcross, GA. Element compositions are within 0.4% of the calculated values. Fractional moles of water frequently found in the analytical sample of antifolates could not be prevented in spite of 24–48 h of drying in vacuo and were confirmed where possible by the presence in the ¹H NMR spectra. All solvents and chemicals were purchased from Aldrich Chemical Co. or Fisher Scientific and were used as received. For all the compounds submitted for biological evaluation, elemental analysis (C, H, N) was performed to confirm >95% purity.

Ethyl 8-bromo-7-oxooctanoate (5a)

To a solution of 7-methoxy-7-oxoheptanoic acid (4a) (0.32 g, 1.5 mmol) in a 50 mL flask was added oxalyl chloride (1.5 mL) and anhydrous CH₂Cl₂ (10 mL). The resulting solution was refluxed for 1 h and then cooled to room temperature. After evaporation of solvent under reduced pressure, the residue was dissolved in ethyl ether (20 mL). The resulting solution was added dropwise to an ice-cold ether solution of diazomethane (generated in situ from 1.4 g N-nitroso-N-methylurea) over 10 min. To this solution was added 48% HBr (1.5 mL). The resulting mixture was refluxed for 1.5 h. After the mixture was cooled to room temperature, the organic layer was separated and the aqueous layer was extracted with ethyl ether (20 mL x 3). The combined organic layers were washed with two portions of 10% Na₂CO₃ solution and dried over Na₂SO₄. The solvent was evaporated to afford 0.38 g 5a: yield 79% as white crystals, mp 68–69 °C, R_f = 0.50 (Hexane/EtOAc, 5:1 ). ¹H NMR (CDCl₃) δ 1.24–1.27 (t, 3 H, CH_3, J = 7.5 Hz ), 1.32–1.37 (m, 2 H, CH₂), 1.62–1.65 (m, 4 H, 2 CH₂), 2.28–2.31 (t, 2 H, CH_2, J = 7.5 Hz ), 2.65–2.69 (m, 2 H, CH₂), 3.87 (s, 2H, CH₂Br), 4.10–4.14 (q, 2 H, CH_2, J = 7.5 Hz).

Methyl 9-bromo-8-oxononanoate (5b)

Compound 5b was synthesized as described for 5a: yield 83% as light yellow crystals, mp 70–71 °C, R_f = 0.51 (Hexane/EtOAc, 5:1 ). ¹H NMR (CDCl₃) δ 1.32–1.33 (m, 4 H, 2 CH₂), 1.60–1.63 (m, 4 H, 2 CH₂), 2.28–2.31 (t, 2 H, CH_2, J = 7.5 Hz ), 2.63–2.66 (t, 2 H, CH_2, J = 7.5 Hz ), 3.66 (s, 3H, CH₃), 3.87 (s, 2H, CH₂Br).

Methyl 10-bromo-9-oxodecanoate (5c)

Compound 5c was synthesized as described for 5a: yield 78% as yellow crystals, mp 123–124 °C, R_f = 0.51 (Hexane/EtOAc, 5:1 ). ¹H NMR (CDCl₃) δ 1.31–1.33 (m, 6 H, 3 CH₂), 1.60–1.62 (m, 4 H, 2 CH₂), 2.28–2.31 (t, 2 H, CH_2, J = 7.5 Hz ), 2.63–2.66 (t, 2 H, CH_2, J = 7.5 Hz ), 3.66 (s, 3H, CH₃), 3.87 (s, 2H, CH₂Br).

Methyl 11-bromo-10-oxoundecanoate (5d)

Compound 5d was synthesized as described for 5a: yield 72% as yellow crystals, mp 92–93 °C, R_f = 0.52 (Hexane/EtOAc, 3:1). ¹H NMR (CDCl₃) δ 1.31–1.33 (m, 8 H, 4 CH₂), 1.59–1.62 (m, 4 H, 2 CH₂), 2.28–2.31 (t, 2 H, CH_2, J = 7.5 Hz ), 2.62–2.65 (t, 2 H, CH_2, J = 7.5 Hz ), 3.66 (s, 3H, CH₃), 3.87 (s, 2H, CH₂Br).

Ethyl 6-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)hexanoate (7a)

To a suspension of 2,4-diamino-6-hydroxypyrimidine 6 (1.26 g, 10.0 mmol) in anhydrous DMF (40 mL) was added 5a (2.64 g, 10.0 mmol). The resulting mixture was stirred under N₂ at room temperature for 3 days. TLC showed the disappearance of starting materials and the formation of one major spot. After evaporation of solvent, CH₃OH (20 mL) was added followed by silica gel (5 g). Evaporation of the solvent afforded a plug, which was loaded onto a silica gel column (3.5 cm x 15 cm) and eluted initially with CHCl₃ followed by 10% MeOH in CHCl₃ and then 15% MeOH in CHCl₃. Fractions showing R_f = 0.39 were pooled and evaporated to afford 1.20 g 7a: yield 41% as a yellow solid, mp 189–190 °C, R_f = 0.39 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.15–1.17 (t, 3 H, CH_3, J = 7.5 Hz), 1.26–1.31 (m, 2 H, CH₂), 1.52–1.57 (m, 4 H, 2 CH₂), 2.25–2.28 (t, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 4.01–4.06 (m, 2 H, OCH₂), 5.84 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 10.10 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH).

Methyl 7-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanoate (7b)

Compound 7b was synthesized as described for 7a: yield 39% as a yellow solid, mp 178–179 °C, R_f = 0.39 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.24–1.29 (m, 4 H, 2 CH₂), 1.49–1.56 (m, 4 H, 2 CH₂), 2.27–2.30 (t, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (m, 2 H, CH₂), 3.57 (s, 3 H, OCH₃), 5.83 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 10.11 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH).

Methyl 8-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanoate (7c)

Compound 7c was synthesized as described for 7a: yield 43% as a yellow solid, mp 162–163 °C, R_f = 0.41 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.21–1.30 (m, 6 H, 3 CH₂), 1.49–1.56 (m, 4 H, 2 CH₂), 2.27–2.29 (t, 2 H, CH_2, J = 7.5 Hz), 2.43–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 3.57 (s, 3 H, OCH₃), 5.84 (s, 1 H, CH), 6.00 (s, 2 H, 2-NH₂), 10.16 (s, 1 H, 3-NH), 10.79 (s, 1H, 7-NH).

Methyl 9-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)nonanoate (7d)

Compound 7d was synthesized as described for 7a: yield 42% as a yellow solid, mp 165–166 °C, R_f = 0.41 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.21–1.30 (m, 8 H, 4 CH₂), 1.49–1.56 (m, 4 H, 2 CH₂), 2.26–2.29 (t, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 3.57 (s, 3 H, OCH₃), 5.85 (s, 1 H, CH), 6.03 (s, 2 H, 2-NH₂), 10.20 (s, 1 H, 3-NH), 10.81 (s, 1H, 7-NH).

6-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)hexanoic acid (7e)

To a solution of the ester 7a (100 mg, 0.26 mmol) was added 1N NaOH (5 mL), and the mixture was stirred under N₂ at room temperature for 1 h. TLC showed the disappearance of the starting material and formation of one major spot at the origin (CHCl₃/MeOH, 5:1). The resulting solution was cooled in an ice bath, and the pH was adjusted to 3–4 with dropwise addition of 1N HCl or acetic acid. The resulting suspension was frozen in a dry ice/acetone bath, thawed in a refrigerator to 4–5 °C, and filtered. The residue was washed with a small amount of cold water, dichloromethane and ethyl acetate and dried in vacuo using P₂O₅ to afford 81 mg 7e: yield 93% as a yellow powder, mp 188–189 °C decomposed, R_f = 0.06 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.20–1.30 (m, 2 H, CH₂), 1.47–1.56 (m, 4 H, 2 CH₂), 2.17–2.20 (t, 2 H, CH_2, J = 7.5 Hz), 2.43–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 5.83 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 10.11 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH), 11.95 (s, 1H, COOH). Anal. (C₁₂H₁₆N₄O₃ · 0.2 CH₃COOC₂H₅· 0.2 CH₃COOH) C, H, N.

7-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanoic acid (7f)

Compound 7f was synthesized as described for 7e: yield 91% as a brown powder, mp 200–201 °C decomposed, R_f = 0.08 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.20–1.30 (m, 4 H, 2 CH₂), 1.47–1.56 (m, 4 H, 2 CH₂), 2.17–2.20 (t, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (t, 2 H, CH₂, J = 7.5 Hz), 5.83 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 10.11 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH), 11.95 (s, 1H, COOH). Anal. (C₁₃H₁₈N₄O₃· 0.6 CH₃OH) C, H, N.

8-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanoic acid (7g)

Compound 7g was synthesized as described for 7e: yield 89% as a brown powder, mp 211–212 °C decomposed, R_f = 0.06 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.20–1.30 (m, 6 H, 3 CH₂), 1.47–1.56 (m, 4 H, 2 CH₂), 2.17–2.20 (t, 2 H, CH_2, J = 7.5 Hz), 2.43–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 5.83 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 10.10 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH), 11.94 (s, 1H, COOH). Anal. (C₁₄H₂₀N₄O₃ · 0.4 H₂O) C, H, N.

9-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)nonanoic acid (7h)

Compound 7h was synthesized as described for 7e: yield 95% as a brown powder, mp 186 °C decomposed, R_f = 0.09 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.20–1.30 (m, 8 H, 4 CH₂), 1.45–1.56 (m, 4 H, 2 CH₂), 2.17–2.20 (t, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 5.83 (s, 1 H, CH), 5.97 (s, 2 H, 2-NH₂), 10.13 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH), 11.95 (s, 1H, COOH). Anal. (C₁₅H₂₂N₄O₃ · 0.46 CH₂Cl₂) C, H, N.

(S)-Diethyl 2-(6-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)hexanamido)pentanedioate (8a)

To a suspension of 7e (81 mg, 0.34 mmol) in anhydrous DMF (5 mL) was added 6-chloro-2,4-dimethoxy-1,3,5-triazine (72 mg, 0.42 mmol) and N-methylmorpholine (43 mg, 0.42 mmol). After the mixture was stirred at r.t. for 2 h, N-methylmorpholine (43 mg, 0.42 mmol) and diethyl L-glutamate hydrochloride (120 mg, 0.51 mmol) were added all at once. The mixture was stirred at r.t. for 4 h. TLC showed the formation of one major spot at R_f = 0.62 (CHCl₃/MeOH, 5:1). The reaction mixture was evaporated to dryness under reduced pressure. The residue was dissolved in a minimum amount of CHCl₃/MeOH, 5:1, and chromatographed on a silica gel column (2 cm x 15 cm) with 4% MeOH in CHCl₃ as the eluent. Fractions that showed the desired single spot at R_f = 0.62 were pooled and evaporated to dryness to afford 8a 102 mg: yield 67% as a yellow syrup, R_f = 0.62 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.15–1.18 (t, 6 H, 2 CH_3, J = 7.0 Hz), 1.23–1.29 (m, 2 H, CH₂), 1.48–1.58 (m, 4 H, 2 CH₂), 1.76–1.82 (m, 1 H, CH), 1.92–1.98 (m, 1 H, CH), 2.09–2.12 (t, 2 H, CH_2, J = 7.0 Hz), 2.33–2.37 (m, 2 H, CH₂), 2.44–2.47 (m, 2 H, CH₂), 4.02–4.07 (m, 4 H, 2 CH₂), 4.19–4.24 (m, 1 H, CH), 5.84 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 8.16 (d, 1 H, CONH, J = 3.8 Hz), 10.10 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH).

(S)-Diethyl 2-(7-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanamido)pentanedioate (8b)

Compound 8b was synthesized as described for 8a: yield 70% as a yellow syrup, R_f = 0.62 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.15–1.18 (m, 6 H, 2 CH₃), 1.23–1.30 (m, 4 H, 2 CH₂), 1.48–1.58 (m, 4 H, 2 CH₂), 1.76–1.82 (m, 1 H, CH), 1.92–1.99 (m, 1 H, CH), 2.09–2.12 (t, 2 H, CH_2, J = 7.0 Hz), 2.33–2.37 (m, 2 H, CH₂), 2.44–2.47 (m, 2 H, CH₂), 4.02–4.08 (m, 4 H, 2 CH₂), 4.20–4.24 (m, 1 H, CH), 5.83 (s, 1 H, CH), 5.93 (s, 2 H, 2-NH₂), 8.15 (d, 1 H, CONH, J = 3.8 Hz), 10.10 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH).

(S)-Diethyl 2-(8-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanamido)pentanedioate (8c)

Compound 8c was synthesized as described for 8a: yield 68% as a yellow syrup, R_f = 0.64 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.16–1.19 (t, 6 H, 2 CH_3, J = 7.0 Hz), 1.22–1.32 (m, 6 H, 3 CH₂), 1.47–1.57 (m, 4 H, 2 CH₂), 1.76–1.82 (m, 1 H, CH), 1.92–1.99 (m, 1 H, CH), 2.09–2.12 (t, 2 H, CH_2, J = 7.0 Hz), 2.34–2.37 (m, 2 H, CH₂), 2.45–2.48 (m, 2 H, CH₂), 4.02–4.08 (m, 4 H, 2 CH₂), 4.20–4.24 (m, 1 H, CH), 5.84 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 8.15 (d, 1 H, CONH, J = 3.8 Hz), 10.10 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH).

(S)-Diethyl 2-(9-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)nonanamido)pentanedioate (8d)

Compound 8d was synthesized as described for 8a: yield 66% as a yellow syrup, R_f = 0.64 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.15–1.18 (t, 6 H, 2 CH_3, J = 7.0 Hz), 1.22–1.32 (m, 8 H, 4 CH₂), 1.47–1.57 (m, 4 H, 2 CH₂), 1.76–1.82 (m, 1 H, CH), 1.92–1.99 (m, 1 H, CH), 2.09–2.12 (t, 2 H, CH_2, J = 7.0 Hz), 2.34–2.37 (m, 2 H, CH₂), 2.45–2.48 (m, 2 H, CH₂), 4.02–4.08 (m, 4 H, 2 CH₂), 4.20–4.24 (m, 1 H, CH), 5.83 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 8.15 (d, 1 H, CONH, , J = 3.8 Hz), 10.10 (s, 1 H, 3-NH), 10.77 (s, 1H, 7-NH).

(S)-2-(6-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)hexanamido)pentanedioic acid (3a)

To a solution of the diester 8a (100 mg, 0.22 mmol) was added 1N NaOH (5 mL), and the mixture was stirred under N₂ at room temperature for 1 h. TLC showed the disappearance of the starting material and formation of one major spot at the origin (CHCl₃/MeOH, 5:1). The resulting solution was cooled in an ice bath, and the pH was adjusted to 3–4 with dropwise addition of 1N HCl. The resulting suspension was frozen in a dry ice/acetone bath, thawed in a refrigerator to 4–5 °C, and filtered. The residue was washed with a small amount of cold water and ethyl acetate and dried in vacuo using P₂O₅ to afford 78 mg 3a: yield 90% as a white powder, mp 145–146 °C decomposed, R_f = 0.08 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.24–1.30 (m, 2 H, CH₂), 1.48–1.58 (m, 4 H, 2 CH₂), 1.71–1.79 (m, 1 H, CH), 1.88–1.95 (m, 1 H, CH), 2.09–2.12 (t, 2 H, CH_2, J = 7.5 Hz), 2.24–2.27 (m, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (m, 2 H, CH₂), 4.16–4.21 (m, 1 H, CH), 5.84 (s, 1 H, CH), 5.95 (s, 2 H, 2-NH₂), 7.99 (d, 1 H, CONH, J = 4.0 Hz), 10.10 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH), 12.50 (br, 2 H, 2 COOH). Anal. (C₁₇H₂₃N₅O₆ · 2.0 H₂O) C, H, N.

(S)-2-(7-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanamido)pentanedioic acid (3b)

Compound 3b was synthesized as described for 3a: yield 91% as a pale yellow powder, mp 116–117 °C decomposed, R_f = 0.08 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.22–1.32 (m, 4 H, 2 CH₂), 1.45–1.58 (m, 4 H, 2 CH₂), 1.71–1.79 (m, 1 H, CH), 1.91–1.98 (m, 1 H, CH), 2.09–2.12 (t, 2 H, CH₂, J = 7.5 Hz), 2.24–2.28 (m, 2 H, CH₂, J = 7.5 Hz), 2.44–2.47 (m, 2 H, CH₂), 4.16–4.21 (m, 1 H, CH), 5.84 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 8.02 (d, 1 H, CONH, J = 4.0 Hz), 10.10 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH), 12.12 (br, 1 H, 1 COOH), 12.52 (br, 1 H, 1 COOH). Anal. (C₁₈H₂₅N₅O₆ · 0.5 H₂O) C, H, N.

(S)-2-(8-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanamido)pentanedioic acid (3c)

Compound 3c was synthesized as described for 3a: yield 95% as a yellow powder, mp 135–136 °C decomposed, R_f = 0.08 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.20–1.32 (m, 6 H, 3 CH₂), 1.45–1.58 (m, 4 H, 2 CH₂), 1.71–1.79 (m, 1 H, CH), 1.90–1.98 (m, 1 H, CH), 2.08–2.12 (t, 2 H, CH_2, J = 7.5 Hz), 2.24–2.28 (m, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 4.16–4.21 (m, 1 H, CH), 5.84 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 8.02 (d, 1 H, CONH, J = 3.8 Hz), 10.11 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH). Anal. (C₁₉H₂₇N₅O₆ · 0.5 H₂O) C, H, N.

(S)-2-(9-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)nonanamido)pentanedioic acid (3d)

Compound 3d was synthesized as described for 3a: yield 90% as a pale yellow powder, mp 123–124 °C decomposed, R_f = 0.08 (CHCl₃/MeOH, 5:1). ¹H NMR (DMSO-d₆) δ 1.20–1.32 (m, 8 H, 4 CH₂), 1.42–1.58 (m, 4 H, 2 CH₂), 1.71–1.79 (m, 1 H, CH), 1.90–1.98 (m, 1 H, CH), 2.08–2.11 (t, 2 H, CH_2, J = 7.5 Hz), 2.24–2.28 (m, 2 H, CH_2, J = 7.5 Hz), 2.44–2.47 (t, 2 H, CH_2, J = 7.5 Hz), 4.16–4.21 (m, 1 H, CH), 5.84 (s, 1 H, CH), 5.94 (s, 2 H, 2-NH₂), 8.01 (d, 1 H, CONH, J = 3.8 Hz), 10.11 (s, 1 H, 3-NH), 10.76 (s, 1H, 7-NH). Anal. (C₂₀H₂₉N₅O₆ · 0.5 H₂O) C, H, N.

Molecular modeling and computational studies

The X-ray crystal structure of human GARFTase at 1.98Å resolution (PDB ID: 1NJS)²² was obtained from the protein database. The human GARFTase crystal structure contains GARFTase complexed with the hydrolyzed form of 10-trifluoroacetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid (10-CF₃CO-DDACTHF). Molecular modeling studies with FRα were carried out using the 2.80 Å crystal structure of human FRα co-crystallized with folic acid (PDB: 4LRH).²³

Docking studies were performed using LeadIT 2.1.3.²⁵ The protonation state of the proteins and the ligands were calculated using the default settings. Water molecules in the active site were permitted to rotate freely. The active site was defined by a sphere of 6.5 Å from the native ligand in the crystal structure. Ligands for docking were built using the molecule builder function in MOE 2010.10²⁶ and energy minimized using the MMF94X forcefield to a constant of 0.05 kcal/mol. Triangle matching was used as the placement method and the docked poses were scored using default settings. The docked poses were exported and visualized in MOE.

In order to validate the docking software for docking the proposed compounds, the native ligand for GARFTase (10-CF₃CO-DDACTHF) and FRα (folic acid) were built using the molecule builder function in MOE, energy minimized and docked using LeadIT 2.1.3 as described above. RMSDs of the docked poses were calculated using an SVL code obtained from the MOE website (www.chemcomp.com) and compared to the conformation of the crystal structure ligands. The best docked pose for 10-CF₃CO-DDACTHF in the human GARFTase crystal structure had an RMSD of 1.0437 Å (Docking score: −40.0853) while the best docked pose for FRα had an RMSD of 0.633 Å (Docking score: −55.5940). Thus, LeadIT 2.1.3 was validated for our docking purposes in GARFTase and FRα.

Reagents for biological studies

[3′, 5′, 7, 9-³H]Folic acid (25 Ci/mmol) and [¹⁴C(U)]glycine (87mCi/mmol) were purchased from Moravek Biochemicals (Brea, CA). Unlabeled folic acid was purchased from Sigma Chemical Co. (St. Louis, MO). LCV [(6R,S) 5-formyl tetrahydrofolate] was provided by the Drug Development Branch, National Cancer Institute, Bethesda, MD. The sources of the classical antifolate drugs were as follows: MTX, Drug Development Branch, National Cancer Institute (Bethesda, MD); RTX [N-(5-[N-(3,4-dihydro-2-methyl-4-oxyquinazolin-6-ylmethyl)-N-methyl-amino]-2-thienoyl)-L-glutamic acid], AstraZeneca Pharmaceuticals (Maccesfield, Cheshire, England); PDX ((2S)-2-[[4-[(1RS)-1-[(2, 4-diaminopteridin-6-yl)methyl]but-3-ynyl]benzoyl]amino]pentanedioic acid), Allos Therapeutics (Henderson, NV); and LMTX (5,10-dideaza-5,6,7,8-tetrahydrofolate) and PMX [N-{4-[2-(2-amino-3,4-dihydro-4-oxo-7H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}-L-glutamic acid] (Alimta), Eli Lilly and Co. (Indianapolis, IN). Other chemicals were obtained from commercial sources in the highest available purity.

Cell lines and assays of antitumor drug activities

The origin of the engineered CHO cell lines, including the RFC-, PCFT-, and FRα-null MTXRIIOua^R2–4 (R2), and RFC- (pC43-10), PCFT- (R2/PCFT4), or FRα- (RT16) expressing sublines, were previously described.^11,12,21 Likewise, pDNA3.1 vector control CHO cells (R2/VC) were reported.^11,12 The CHO cells were cultured in α-minimal essential medium (MEM) supplemented with 10% bovine calf serum (Invitrogen, Carlsbad, CA), 100 units/ml penicillin/100 μg/ml streptomycin, and 2 mM L-glutamine at 37°C with 5% CO₂. All the R2 transfected cells [PC43-10, RT16, R2/hPCFT4, R2(VC)] were routinely cultured in α-MEM plus 1.5 mg/ml G418. Prior to the cell proliferation assays (see below), RT16 cells were cultured in complete folate-free RPMI 1640 (without added folate) for three days. R2/hPCFT4 and R2(VC) cells were cultured in complete folate-free RPMI 1640 including dFBS (Invitrogen) and 25 nM LCV with 1.5 mg/ml G418. KB human nasopharyngeal carcinoma cells were purchased from the American Type Culture Collection (Manassas, VA). KB cells were routinely cultured in folate-free RPMI 1640 medium, supplemented with 10% fetal bovine serum, penicillin-streptomycin solution, and 2 mM L-glutamine at 37°C with 5% CO₂.

For growth inhibition assays, cells (CHO and KB) were plated in 96 well dishes (~2500–5000 cells/well, total volume of 200 μl medium) with a range of antifolate concentrations.^11–16 The medium was RPMI 1640 (contains 2.3 μM folic acid) with 10% dFBS and antibiotics for experiments with R2 and PC43-10 cells. For RT16 and KB cells, cells were cultured in folate-free RPMI media with 10% dFBS and antibiotics supplemented with 2 nM LCV and 2 mM L-glutamine. The requirement for FR-mediated drug uptake in these assays was established in parallel incubations including 200 nM folic acid. For R2/hPCFT4 cells, the medium was folate-free RPMI 1640 (pH 7.2) containing 25 nM LCV, supplemented with 10% dFBS, antibiotics, and L-glutamine. Cells were routinely incubated for up to 96 h and metabolically active cells (a measure of cell viability) were assayed with CellTiter-blue Cell Viability Assay (Promega, Madison, WI), with fluorescence measured (590 nm emission, 560 nm excitation) using a fluorescence plate reader.^11–16 Raw data were exported from Softmax Pro software to an Excel spreadsheet for analysis and determinations of IC₅₀s, corresponding to the drug concentrations that result in 50% loss of cell growth.^11–16

For some of the in vitro growth inhibition studies, the inhibitory effects of the antifolate inhibitors on de novo thymidylate biosynthesis (i.e., thymidylate synthase) and de novo purine nucleotide biosynthesis (GARFTase and AICARFTase) were tested by co-incubations with thymidine (10 μM) and adenosine (60 μM), respectively.^11–17 For de novo purine nucleotide biosynthesis, additional protection experiments used AICA (320 μM) to distinguish inhibitory effects at GARFTase from those at AICARFTase.^11–17

FR binding assay

Competitive inhibition of [³H]folic acid binding to FRα and FRβ using RT16 and D4 CHO cells, respectively, was used was used to assess relative binding affinities for assorted (anti)folate ligands.^{11,12,14–16} For these experiments, cells (~1.6x10⁶) were rinsed twice with DPBS, followed by two washes an acidic buffer (10 mM sodium acetate, 150 mM NaCl, pH 3.5) to remove FR-bound folates. Cells were washed twice with ice-cold HEPES-buffered saline (20 mM HEPES, 140 mM NaCl, 5 mM KCl, 2 mM MgCl₂, 5 mM glucose, pH7.4) (HBS), then incubated in HBS with [³H]folic acid (50 nM, specific activity 0.5 Ci/mmol) in the presence and absence of unlabeled folic acid or antifolates (over a range of concentrations) for 15 min at 0°C. The dishes were rinsed three times with ice-cold HBS, after which the cells were solubilized (0.5 N NaOH) and aliquots measured for radioactivity and protein contents. Protein concentrations were measured with Folin phenol reagent.²⁷ [³H]Folic acid bound to FRα and FRβ was calculated as pmol/mg protein and relative binding affinities were calculated in each individual experiment as the inverse molar ratios of unlabeled ligands required to inhibit [³H]folic acid binding by 50%.^{11,12,14–16} By definition, the relative affinity of folic acid is 1. Experiments were performed in triplicate.

In situ GARFT enzyme inhibition assay

Incorporation of [¹⁴C]glycine into [¹⁴C]formyl GAR, as an in situ measure of endogenous GARFTase activity, was measured.^6,11–17 For these experiments, KB cells were seeded in 4 ml complete folate-free RPMI 1640 plus 2 nM LCV in 60 mm dishes at a density of 2x10⁶ cells per dish. On the next day, the medium was replaced with 2 ml fresh complete folate-free RPMI 1640 plus 2 nM LCV. Azaserine (4 μM final concentration) was added in the presence and absence of the antifolate inhibitors. After 30 min, L-glutamine (final concentration, 2 mM) and [¹⁴C]glycine (tracer amounts; final specific activity 0.1 mCi/L) were added. Incubations were at 37°C for 15 h, at which time cells were washed (one-time) with ice-cold folate-free RPMI 1640 plus serum. Cell pellets were dissolved in 2 ml 5% trichloroacetic acid at 0°C. The trichloracetic acid insoluble fraction was removed by centrifugation, solubilized in 0.5N NaOH, and the cell protein contents were measured with Folin phenol reagent.²⁷ The supernatants were extracted twice with 2 ml of ice-cold ether. The aqueous layer was passed through a 1 cm column of AG1x8 (chloride form), 100–200 mesh (Bio-Rad), washed with 10 ml of 0.5N formic acid and then 10 ml of 4N formic acid, and finally eluted with 8 ml 1N HCl. The eluates were collected and determined for radioactivity. The accumulation of [¹⁴C]formyl GAR was calculated as pmol per mg protein over a range of inhibitor concentrations. IC₅₀s were calculated as the concentrations of inhibitors that resulted in a 50% decrease in [¹⁴C]formyl GAR synthesis. Experiments were performed in triplicate.

ABBREVIATIONS USED

AICA

5-aminoimidazole-4-carboxamide

AICARFTase

5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase

CHO

Chinese hamster ovary

dFBS

dialyzed fetal bovine serum

DPBS

Dulbecco’s phosphate-buffered saline

FR

folate receptor

FPGS

folylpolyglutamate synthetase

GAR

glycinamide ribonucleotide

GARFTase

glycinamide ribonucleotide formyltransferase

HBSS

Hank’s balanced salts solution

HBS

HEPES-buffered saline

LCV

leucovorin

LMTX

Lometrexol

MTX

methotrexate

MEM

minimal essential media

PMX

Pemetrexed

PDX

Pralatrexate

PCFT

proton-coupled folate transporter

RTX

Raltitrexed

RFC

reduced folate carrier

SAR

structure-activity relationship

10-CF₃CO-DDACTHF

10-trifluoroacetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid