Synthesis of Classical, Three-Carbon-Bridged 5-Substituted Furo[2,3-d]pyrimidine and 6-Substituted Pyrrolo[2,3-d]pyrimidine Analogues as Antifolates

Biology and therapeutic applications of the proton-coupled folate transporter

INTRODUCTION

The proton-coupled folate transporter (PCFT; SLC46A1) was discovered in 2006 as the principal mechanism by which folates are absorbed in the intestine and the causal basis for hereditary folate malabsorption (HFM). In 2011, it was found that PCFT is highly expressed in many tumors. This stimulated interest in using PCFT for cytotoxic drug targeting, taking advantage of the substantial levels of PCFT transport and acidic pH conditions commonly associated with tumors.

AREAS COVERED

We summarize the literature from 2006 to 2022 that explores the role of PCFT in the intestinal absorption of dietary folates and its role in HFM and as a transporter of folates and antifolates such as pemetrexed (Alimta) in relation to cancer. We provide the rationale for the discovery of a new generation of targeted pyrrolo[2,3-d]pyrimidine antifolates with selective PCFT transport and inhibitory activity toward de novo purine biosynthesis in solid tumors. We summarize the benefits of this approach to cancer therapy and exciting new developments in the structural biology of PCFT and its potential to foster refinement of active structures of PCFT-targeted anti-cancer drugs.

EXPERT OPINION

We summarize the promising future and potential challenges of implementing PCFT-targeted therapeutics for HFM and a variety of cancers.

Exploration of 4-aminopyrrolo[2,3-d]pyrimidine as antitubercular agents

Tuberculosis (TB) is one of the leading causes of death worldwide. Developing new anti-TB compounds using cost-effective processes is critical to reduce TB incidence and accomplish the End TB Strategy milestone. Herein, we describe the synthesis and structure–activity relationships of a library of thirty 7H-Pyrrolo[2,3-d]pyrimidine derivatives providing insights into the contributions of different aromatic, aryl and alkyl substitution at the C-4 position of the 7-deazapurine ring. The minimum inhibitory concentration (MIC) of the compounds against the green fluorescent protein (GFP) reporter strain of Mycobacterium tuberculosis was assayed using the standard broth microdilution method, and cell toxicity was determined using the MTT assay. Sixteen compounds displayed in vitro activity against the GFP reporter strain of Mycobacterium tuberculosis with MIC₉₀ values of 0.488–62.5 µM. This study highlights the most potent derivative, N-(4-phenoxy phenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine with a MIC₉₀ value of 0.488 µM and was non-cytotoxic to the Vero cell line. Moreover, all the potent compounds from this series have a ClogP value less than 4 and molecular weight < 400; thus, likely to maintain drug-likeness during lead optimisation.

Recent Developments in the Synthesis of Bicyclic Condensed Pyrimidinones

Abstract:

Functionalized bicyclic pyrimidinones and their derivatives are significant heterocyclic scaffolds being their all-around prevalence in biologically potent compounds. In several attempts to explore the different synthetic methodologies for the construction of bicyclic condensed pyrimidinones, different researchers from all across the globe have reported numerous substantial methods. In the present review, considerable work has been critically compiled on the synthesis of substituted and functionalized bicyclic pyrimidinones from 2000 onwards.

One-pot synthesis of highly substituted poly(furopyrimidine)s via catalyst-free multicomponent polymerizations of diisocyanides, N,N′-dimethylbarbituric acid, and dialdehyde

In this work, the catalyst-free multicomponent polymerizations of diisocyanides, N,N′-dimethylbarbituric acid, and dialdehyde for highly substituted poly(furopyrimidine)s has been achieved. All the experimental conditions such as polymerization solvents, temperature and time were investigated in detail. Through the systematic optimization of the polymerization conditions, the obtained polymers could have molecular weights of up to 16 400 g mol⁻¹, and excellent yields (up to 84%) can be achieved. All the polymers were well characterized by gel permeation chromatography (GPC), nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy. The thermal properties of the polymers were investigated and the decomposition temperature (T_d, 5%) was 277 °C.

In this work, the catalyst-free multicomponent polymerizations of diisocyanides, N,N′-dimethylbarbituric acid, and dialdehyde for highly substituted poly(furopyrimidine)s has been achieved.

An efficient diastereoselective synthesis of novel fused 5H-furo[2,3-d]thiazolo[3,2-a]pyrimidin-5-ones via one-pot three-component reaction

Herein, a convenient and efficient synthesis of 7-benzoyl-6-(aryl)-6,7-dihydro-5H-furo[2,3-d]thiazolo[3,2-a]pyrimidin-5-one derivatives was achieved from the reaction of isoquinolinium N-ylides, aromatic aldehydes, and heterocyclic 1,3-dicarbonyl compounds via one-pot three-component diastereoselective domino reaction in good-to-excellent yields. The advantages of this protocol are easily available starting materials, operational simplicity, and avoidance of hazardous organic solvents and catalyst. The synthesized products were characterized by IR, ¹H NMR, ¹³C NMR and mass spectra. Additionally, the conclusive structure of target compounds was confirmed by X-Ray diffraction analysis.

A green route for the synthesis of pyrrolo[2,3-d]pyrimidine derivatives catalyzed by β-cyclodextrin

The disclosed synthetic method for pyrrolo[2,3-d]pyrimidine derivatives offers several advantages such as non-toxic catalyst and aqueous reaction medium.

The promise and challenges of exploiting the proton-coupled folate transporter for selective therapeutic targeting of cancer

This review considers the "promise" of exploiting the proton-coupled folate transporter (PCFT) for selective therapeutic targeting of cancer. PCFT was discovered in 2006 and was identified as the principal folate transporter involved in the intestinal absorption of dietary folates. The recognition that PCFT was highly expressed in many tumors stimulated substantial interest in using PCFT for cytotoxic drug targeting, taking advantage of its high level transport activity under the acidic pH conditions that characterize many tumors. For pemetrexed, among the best PCFT substrates, transport by PCFT establishes its importance as a clinically important transporter in malignant pleural mesothelioma and non-small cell lung cancer. In recent years, the notion of PCFT-targeting has been extended to a new generation of tumor-targeted 6-substituted pyrrolo[2,3-d]pyrimidine compounds that are structurally and functionally distinct from pemetrexed, and that exhibit near exclusive transport by PCFT and potent inhibition of de novo purine nucleotide biosynthesis. Based on compelling preclinical evidence in a wide range of human tumor models, it is now time to advance the most optimized PCFT-targeted agents with the best balance of PCFT transport specificity and potent antitumor efficacy to the clinic to validate this novel paradigm of highly selective tumor targeting.

Synthesis of Trans-6-(4-Chlorobenzoyl)-7-(Aryl)-1,3-Dimethyl-6,7-Dihydrofuro[3,2-d]Pyrimidine-2,4-Diones Using Choline Hydroxide as an Efficient Catalyst in an Aqueous Medium

A green and efficient synthesis of the trans-6-(4-chlorobenzoyl)-7-(aryl)-1,3-dimethyl-6,7-dihydrofuro[3,2-d]pyrimidine-2,4-diones has been achieved via a three-component, one-pot condensation of 2-[2-(4-chlorophenyl)-2-oxoethyl)]isoquinolinium bromide with 1,3-dimethylbarbituric acid and an aromatic aldehyde in the presence of catalytic amounts of choline hydroxide in water under reflux conditions. This gives trans-6-(4-chlorobenzoyl)-7-(aryl)-1,3-dimethyl-6,7-dihydrofuro[3,2-d]pyrimidine-2,4-diones in excellent yield and in short reaction times.

Synthesis of Novel 5,6-Disubstituted Pyrrolo [2,3-d]Pyrimidine-2,4-Diones Via One-Pot Three-Component Reactions

A simple and novel method for the synthesis of 5,6-disubstituted pyrrolo[2,3-d]pyrimidine-2,4-diones has been reported using arylglyoxal-based three-component reactions. Under microwave heating conditions, arylglyoxal, 6-amino uracil, or its derivatives reacts with various thiols in acetic acid medium to provide a series of pyrrolo[2,3-d]pyrimidine-2,4-diones (4) having a thioether and an aryl ring in 5 and 6 positions, respectively. On the other hand reaction of arylglyoxal, amino uracil and malononitrile in place of thiols, provided corresponding 5,6-disubstituted pyrrolo[2,3-d]pyrimidine-2,4-diones (5) with selectively converting one of the -CN to -CONH₂ group both in conventional (method A) and microwave heating conditions (method B). This methodology is a simple and efficient protocol for the synthesis of diverse 5,6-disubstituted pyrrolo[2,3-d]pyrimidine-2,4-diones from the readily available starting materials in good yields.

Stereoselective synthesis of medicinally relevant furo[2,3-d]pyrimidine framework by thermal rearrangement of spirocyclic barbiturates

The thermally initiated transformation of substituted spirocyclic barbiturates in DMSO at 100 °C results in the stereoselective formation of medicinally relevant furo[2,3-d]pyrimidines in 50–75% yields.

The human proton-coupled folate transporter: Biology and therapeutic applications to cancer

This review summarizes the biology of the proton-coupled folate transporter (PCFT). PCFT was identified in 2006 as the primary transporter for intestinal absorption of dietary folates, as mutations in PCFT are causal in hereditary folate malabsorption (HFM) syndrome. Since 2006, there have been major advances in understanding the mechanistic roles of critical amino acids and/or domains in the PCFT protein, many of which were identified as mutated in HFM patients, and in characterizing transcriptional control of the human PCFT gene. With the recognition that PCFT is abundantly expressed in human tumors and is active at pHs characterizing the tumor microenvironment, attention turned to exploiting PCFT for delivering novel cytotoxic antifolates for solid tumors. The finding that pemetrexed is an excellent PCFT substrate explains its demonstrated clinical efficacy for mesothelioma and non-small cell lung cancer, and prompted development of more PCFT-selective tumor-targeted 6-substituted pyrrolo[2,3-d]pyrimidine antifolates that derive their cytotoxic effects by targeting de novo purine nucleotide biosynthesis.

Targeting the proton-coupled folate transporter for selective delivery of 6-substituted pyrrolo[2,3-d]pyrimidine antifolate inhibitors of de novo purine biosynthesis in the chemotherapy of solid tumors

The proton-coupled folate transporter (PCFT) is a folate-proton symporter with an acidic pH optimum, approximating the microenvironments of solid tumors. We tested 6-substituted pyrrolo[2,3-d]pyrimidine antifolates with one to six carbons in the bridge region for inhibition of proliferation in isogenic Chinese hamster ovary (CHO) and HeLa cells expressing PCFT or reduced folate carrier (RFC). Only analogs with three and four bridge carbons (N-{4-[3-2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]-pyrimidin-6-yl)propyl]benzoyl}-L-glutamic acid (compound 2) and N-{4-[4-2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]-pyrimidin-6-yl)butyl]benzoyl}*-L-glutamic acid (compound 3), respectively) were inhibitory, with 2 ≫ 3. Activity toward RFC-expressing cells was negligible. Compound 2 and pemetrexed (Pmx) competed with [(3)H]methotrexate for PCFT transport in PCFT-expressing CHO (R2/hPCFT4) cells from pH 5.5 to 7.2; inhibition increased with decreasing pH. In Xenopus laevis oocytes microinjected with PCFT cRNA, uptake of 2, like that of Pmx, was electrogenic. Cytotoxicity of 2 toward R2/hPCFT4 cells was abolished in the presence of adenosine or 5-amino-4-imidazolecarboxamide, suggesting that glycinamide ribonucleotide formyltransferase (GARFTase) in de novo purine biosynthesis was the primary target. Compound 2 decreased GTP and ATP pools by ∼50 and 75%, respectively. By an in situ GARFTase assay, 2 was ∼20-fold more inhibitory toward intracellular GARFTase than toward cell growth or colony formation. Compound 2 irreversibly inhibited clonogenicity, although this required at least 4 h of exposure. Our results document the potent antiproliferative activity of compound 2, attributable to its efficient cellular uptake by PCFT, resulting in inhibition of GARFTase and de novo purine biosynthesis. Furthermore, they establish the feasibility of selective chemotherapy drug delivery via PCFT over RFC, a process that takes advantage of a unique biological feature of solid tumors.

2-Amino-4-(piperidin-1-yl)-11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride monohydrate and 2-amino-4-[methyl(2-methylphenyl)amino]-11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride-benzene-1,2-diamine (1/1): complex sheets generated by multiple hydrogen bonds

In each of 2-amino-4-(piperidin-1-yl)-11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride monohydrate, C(16)H(19)N(6)(+).Cl(-).H(2)O, (I), and 2-amino-4-[methyl(2-methylphenyl)amino]-11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride-benzene-1,2-diamine (1/1), C(19)H(19)N(6)(+).Cl(-).C(6)H(8)N(2), (II), the seven-membered ring in the cation adopts a boat conformation. The pyrimidine ring in (II) adopts a twist-boat conformation, but the corresponding ring in (I) is essentially planar. The amino groups of the benzene-1,2-diamine component of (II) are both pyramidal. The independent components of (I) are linked into complex sheets by a combination of N-H...O, N-H...N, N-H...Cl and O-H...Cl hydrogen bonds. In the crystal structure of (II), one N-H...N hydrogen bond and six independent N-H...Cl hydrogen bonds combine to link the components into complex sheets.

CoMFA analysis of tgDHFR and rlDHFR based on antifolates with 6-5 fused ring system using the all-orientation search (AOS) routine and a modified cross-validated r(2)-guided region selection (q(2)-GRS) routine and its initial application

We report the development of CoMFA analysis models that correlate the 3D chemical structures of 80 compounds with 6-5 fused ring system synthesized in our laboratory and their inhibitory potencies against tgDHFR and rlDHFR. In addition to conventional CoMFA analysis, we used two routines available in the literature aimed at the optimization of CoMFA: all-orientation search (AOS) and cross-validated r(2)-guided region selection (q(2)-GRS) to further optimize the models. During this process, we identified a problem associated with q(2)-GRS routine and modified using two strategies. Thus, for the inhibitory activity against each enzyme (tgDHFR and rlDHFR), five CoMFA models were developed using the conventional CoMFA, AOS optimized CoMFA, the original q(2)-GRS optimized CoMFA and the modified q(2)-GRS optimized CoMFA using the first and the second strategy. In this study, we demonstrate that the modified q(2)-GRS routines are superior to the original routine. On the basis of the steric contour maps of the models, we designed four new compounds in the 2,4-diamino-5-methyl-6-phenylsulfanyl-substituted pyrrolo[2,3-d]pyrimidine series. As predicted, the new compounds were potent and selective inhibitors of tgDHFR. One of them, 2,4-diamino-5-methyl-6-(2',6'-dimethylphenylthio)pyrrolo[2,3-d]pyrimidine, is the first 6-5 fused ring system compound with nanomolar tgDHFR inhibitory activity. The HCl salt of this compound was also prepared to increase solubility. Both forms of the drug were tested in vivo in a Toxoplasma gondii infection mouse model. The results indicate that both forms were active with the HCl salt significantly more potent than the free base.

Synthesis and discovery of high affinity folate receptor-specific glycinamide ribonucleotide formyltransferase inhibitors with antitumor activity

6-Substituted classical pyrrolo[2,3-d]pyrimidine antifolates with a three- to six-carbon bridge between the heterocycle and the benzoyl-L-glutamate (compounds 2-5, respectively) were synthesized starting from methyl 4-formylbenzoate and a Wittig reaction with the appropriate triphenylphosphonium bromide, followed by reduction and conversion to the alpha-bromomethylketones. Cyclocondensation of 2,4-diamino-4-oxopyrimidine with the alpha-bromoketones, coupling with diethyl-L-glutamate, and saponification afforded 2-5. Compounds 2-5 had negligible substrate activity for RFC but showed variably potent (nanomolar) and selective inhibitory activities toward Chinese hamster ovary cells that expressed FRalpha or FRbeta and toward FRalpha-expressing KB and IGROV1 human tumor cells. Inhibition of KB cell colony formation was also observed. Glycinamide ribonucleotide formyl transferase (GARFTase) was identified as the primary intracellular target of the pyrrolo[2,3-d]pyrimidines. The combined properties of selective FR targeting, lack of RFC transport, and GARFTase inhibition resulting in potent antitumor activity are unprecedented and warrant development of these analogues as antitumor agents.

Shaken not stirred: A facile synthesis of 1,4-bis(furo[2,3-d]-pyrimidine-2,4(1H,3H)-dione-5-yl)benzenes by one-pot reaction of isocyanides, N,N′-dimethylbarbituric acid, and terephthaldialdehyde

A simple and efficient synthesis of 1,4-bis(furo[2,3-d]pyrimidine-2,4(1H,3H)-dione-5-yl)benzene derivatives was achieved via a one-pot three-component reaction of isocyanides, N,N'-dimethylbarbituric acid, and terephthaldialdehyde in DMF at room temperature for 30 min. These improved reaction conditions allow the preparation of highly substituted furopyrimidinones in high yields and purity under mild reaction conditions.

Design and Synthesis of a Tetracyclic Pyrimidine-Fused Benzodiazepine Library

Method development for a heterocyclic library which entails novel scaffolds of benzodiazepines fused with various heterocycles, such as pyrimidines, indolines, and tetrahydroquinolines, was accomplished. The new synthetic strategy is based on an electrophilic cyclization reaction involving an iminium intermediate formed by the corresponding aminopyrimidine with a carbonyl compound to give the desired heterocycles in high yields. Subsequent replacement of the chloro group in the resulted structures with a nucleophile, such as boronic acids, amines, alcohols and thiols, led to a library of privileged compounds with up to eight accessible diversity points.

Synthesis of Novel Tricyclic Pyrimido[4,5-b][1,4]benzothiazepines via Bischler−Napieralski-Type Reactions

[reaction: see text] Novel tricyclic pyrimido[4,5-b][1,4]benzothiazepines were readily prepared from 5-amino-4,6-bis(arylthio)pyrimidines and carboxylic acids via Bischler-Napieralski-type reactions. The 6-aryl sulfide group of the resulting pyrimido[4,5-b][1,4]benzothiazepines could be selectively oxidized to its corresponding sulfoxide, which underwent facile substitution reactions when treated with nucleophiles such as an amine. This synthetic strategy provides an efficient way to access a library of novel heterocyclic compounds that are of interest in drug discovery.

Synthesis of classical, four-carbon bridged 5-substituted furo[2,3-d]pyrimidine and 6-substituted pyrrolo[2,3-d]pyrimidine analogues as antifolates

We report, for the first time, the biological activities of four-carbon-atom bridged classical antifolates on dihydrofolate reductase (DHFR), thymidylate synthase (TS), and folylpolyglutamate synthetase (FPGS) as well as antitumor activity. Extension of the bridge homologation studies of classical two-carbon bridged antifolates, a 5-substituted 2,4-diaminofuro[2,3-d]pyrimidine (1) and a 6-subsituted 2-amino-4-oxopyrrolo[2,3-d]pyrimidine (2), afforded two four-carbon bridged antifolates, analogues 5 and 6, with enhanced FPGS substrate activity and inhibitory activity against tumor cells in culture (EC(50) < or = 10(-7) M) compared with the two-carbon bridged analogues. These results support our original hypothesis that the distance and orientation of the side chain p-aminobenzoyl-L-glutamate moiety with respect to the pyrimidine ring are a crucial determinant of biological activity. In addition, this study demonstrates that, for classical antifolates that are substrates for FPGS, poor inhibitory activity against isolated target enzymes is not necessarily a predictor of a lack of antitumor activity.