Acyclic nucleoside phosphonates containing the amide bond

Abstract To study the influence of a linker rigidity and donor–acceptor properties, the P–CH2–O–CHR– fragment in acyclic nucleoside phosphonates (e.g., acyclovir, tenofovir) was replaced by the P–CH2–HN–C(O)– residue. The respective phosphonates were synthesized in good yields by coupling the straight chain of ω-aminophosphonates and nucleobase-derived acetic acids with EDC. Based on the 1H and 13C NMR data, the unrestricted rotation within the methylene and 1,2-ethylidene linkers in phosphonates from series a and b was confirmed. For phosphonates containing 1,3-propylidene (series c) fragments, antiperiplanar disposition of the bulky O,O-diethylphosphonate and substituted amidomethyl groups was established. The synthesized ANPs P–X–HNC(O)–CH2B (X = CH2, CH2CH2, CH2CH2CH2, CH2OCH2CH2) appeared inactive in antiviral assays against a wide variety of DNA and RNA viruses at concentrations up to 100 μM while marginal antiproliferative activity (L1210 cells, IC50 = 89 ± 16 μM and HeLa cells, IC50 = 194 ± 19 μM) was noticed for the analog derived from (5-fluorouracyl-1-yl)acetic acid and O,O-diethyl (2-aminoethoxy)methylphosphonate. Graphical abstract


Introduction
The search for new compounds endowed with antiviral activity has been underway for decades. Several research groups have been active in this field, both in academia and pharmaceutical industry. Despite these efforts, for many viruses efficient drugs have not been yet discovered. In addition, anticancer drugs available so far exhibit limited applicability. The high mutation rate observed for some viruses makes the issue highly complex. Within medications applied to treat viral infections, acyclic nucleoside phosphonates (ANPs) play an important role [1][2][3]. The prototype of the acyclic nucleoside phosphonates (ANPs), (S)-HPMPA (3), was never commercialized but it gave rise to three marketed products [cidofovir (4), adefovir (1), and tenofovir (2)] that are often prescribed by physicians. So far known structural modifications of compounds 1-4 accomplished within a chain connecting nucleobase and phosphonic acid moieties did not lead to discovery of analogs having higher antiviral activity (Fig. 1).
Analysis of the mechanism of action of ANPs [3,4] allows to conclude that within structures of newly designed & Andrzej E. Wróblewski andrzej.wroblewski@umed.lodz.pl analogs of ANPs, the following fragments have to be installed: (1) a phosphonate unit (P-CH 2 ) which prevents enzymatic hydrolysis of the P-O bond present in natural phosphates, while being capable of further phosphorylation; (2) canonical nucleobases or their very close structurally heterocyclic systems to assure efficient interactions with the complementary nucleobases of the other polynucleotide chain; (3) a linker to adjust a distance between a nucleobase and a phosphorus atom which should contain four atoms considered optimal at this moment. Taking into account high antiviral activity of compounds 1-4, one may be interested in specific interactions of oxygen lone pairs and also of the entire phosphonomethoxy (P-CH 2 -O) fragment. The oxygen atom located within a P-CH 2 -O-CHR-fragment can serve as a lone pair donor in intermolecular interactions, and single bonds connecting atoms in the linker ensure free rotation. To modify interactions of atoms located in the linker it is reasonable to consider replacing selected fragments of the linker for another moiety.
During studies on biological activity of peptides, replacements of the amide [-C(O)-NH-] residue for several isosteric fragments (including a methylene ether [-CH 2 -O-] moiety) are commonly applied [5][6][7]. This particular replacement allows to preserve steric conformity of both bonding systems but essentially influences donoracceptor interactions and possibilities of a rotation around the specific bonds within the linker [completely free around the CH 2 -O bond (11.3 kJ/mol-barrier to rotation) as compared to the hindered around the C(O)-NH bond (88 kJ/mol-barrier to rotation)]. In general, this isosteric replacement diminishes affinity of modified peptides in comparison with the natural ones.
The proposed structural modification of ANPs 1-4 relies on the incorporation of a specific fragment which will be able to increase donor-acceptor interactions within the linker. In our first approach, the [P-CH 2 -O-CHR-] fragment will be replaced with the amide [P-CH 2 -HN-C(O)-] residue to provide amides 5 (Scheme 1). In addition, a part of the linker containing the amide bond becomes rigid and thus may influence the activity of modified ANPs.
Several decades ago, a concept of phosphonate peptide nucleic acids (PPNA) was introduced [8][9][10][11] and a variety of related monomers 6 were synthesized, however, limited to aminomethyl-and aminoethylphosphonate derivatives. Our interest in the synthesis of phosphonates of general formula 5 significantly extends structural diversity of potential new monomers 6 primarily in the aminoalkylphosphonate fragment.
Herein, we wish to describe our studies on the synthesis and the biological activity of the amides 5. The synthetic strategy involves the formation of the amide bond from the respective acetic acid derivatives 8 and x-aminophosphonates 7 (Scheme 1).

Results and discussion
To synthesize the first series of the amides 5, xaminophosphonates 7a-7d containing straight chain linkers were selected (Scheme 2). The x-aminophosphonates 7a-7d were prepared according to the described procedures [12][13][14]. Among them, aminomethylphosphonate 7a was considered as the most important since it was later transformed into the analogs 17a-24a in which nitrogen atoms (N1 or N9) in nucleobases and the phosphorus atom are separated by four bonds, thus providing compounds structurally closest to the drugs 1-4.
A large number of coupling reagents have been developed for the efficient formation of the amide bond [23,24] but only some of them proved useful in the peptide chemistry [25]. In search for the coupling system to be applied to our tasks, we were directed by studies of acylation of model secondary amines with (thymine-1yl)acetic acid (12) [26].
The same coupling was next performed with propylphosphonic anhydride (T3P Ò ) [30] and N-(3dimethylaminopropyl)-N 0 -ethylcarbodiimide hydrochloride (EDC) [31,32] to produce pure amide 20a [33] in acceptable yields (Table 1). As expected, microwave irradiation significantly accelerated the amide bond formation. In most cases, couplings of the aminophosphonates 7a-7d with nucleobase-substituted acetic acids 9-16 in the presence of EDC proceeded almost quantitatively. However, the final products 17a-24d were isolated in moderate yields since several crystallizations were necessary to remove the last traces of triethylamine hydrochloride.

Conformational analysis
We also aimed to study the conformational behavior of an acyclic linker connecting a phosphorus atom and the amide nitrogen for future structure-activity considerations. Free rotation around P-CH 2 and H 2 C-NH bonds in phosphonates 17a-25a, as depicted by 26a in Fig. 2, is evidenced from the vicinal HNCH couplings of 5.9 Hz observed in the spectra of 21a and 25a taken in chloroform-d and DMSO-d 6 , respectively. In solutions in these solvents as well as in methanol-d 4 H 2 CP are equivalent since they always appeared as a one doublet from two-bond HP coupling of 11.8 Hz.
Structure 26b (Fig. 2) summarizes conformational flexibility of phosphonates 17b-25b which is proved by the observation of the vicinal H 2 C-CH 2 couplings of 7.6 Hz.
Since 13 C NMR spectra of phosphonates 17c-25c showed large values (18.1-19.6 Hz) of vicinal PCCC couplings, the antiperiplanar disposition of the P-CC-CH 2 groups is proposed and represented by the Newman projection 26c.
Although significant values (11.0-12.1 Hz) were observed in the 13 C NMR spectra of phosphonates 17d-25d for vicinal PCOC couplings, they cannot be applied with confidence to discuss conformational behavior of the -CH 2 OCH 2 CH 2 -linkage since the angular dependence within a P-C-O-C framework has not yet been established.

Antiviral activity
All phosphonates 17-25 were evaluated for inhibitory activity against a wide variety of DNA and RNA viruses, using the following cell-based assays: (e) MDCK cell cultures: influenza A virus (H1N1 and H3N2 subtypes) and influenza B virus. Ganciclovir, cidofovir, acyclovir, brivudine, zalcitabine, zanamivir, alovudine, amantadine, rimantadine, ribavirin, dextran sulfate (molecular weight 10,000, DS-10000), mycophenolic acid, Hippeastrum hybrid agglutinin (HHA) and Urtica dioica agglutinin (UDA) were used as the reference compounds. The antiviral activity was expressed as the EC 50 : the compound concentration required to reduce virus plaque formation (VZV) by 50% or to reduce virus-induced cytopathogenicity by 50% (other viruses). None of the tested compounds showed appreciable antiviral activity toward any of the tested DNA and RNA viruses at concentrations up to 100 lM, nor affected cell morphology of HEL, HeLa, Vero, MDCL, and CrFK cells.

Cytostatic activity
The 50% cytostatic inhibitory concentration (IC 50 ) causing a 50% decrease in cell proliferation was determined against and HeLa cells (IC 50 = 194 ± 19 lM) and thus enlarges a collection of 5-fluorouracil derivatives which together with the parent compound have been widely clinically applied in therapies of various cancers [35]. Furthermore, the closest structural analog of 18d (compound 18e) was found active in vitro against L1210 cells at concentration of 15 lM [36] (Fig. 3).

Conclusion
Replacement of the P-CH 2 -O-CHR-fragment in ANPs (e.g., acyclovir, tenofovir) by the P-CH 2 -HN-C(O)residue was introduced to study the influence of a linker rigidity and changes in donor-acceptor properties. To elaborate an appropriate synthetic methodology, a series of the 36 respective phosphonates as O,O-diethyl esters was prepared in good yields by the EDC-induced coupling of the straight chain x-aminophosphonates and nucleobasederived acetic acids. Besides the rigidity of the amide bond based on the 1 H and 13 C NMR data, it was concluded that the unrestricted rotation within the methylene (series a) and 1,2-ethylidene (series b) linkers takes place while for phosphonates containing 1,3-propylidene (series c) fragments antiperiplanar disposition of the bulky O,Odiethylphosphonate and substituted amidomethyl groups was observed. The phosphonates 17a-25d appeared inactive in antiviral assays against a wide variety of DNA and RNA viruses at concentrations up to 100 lM. Marginal antiproliferative activity (L1210, IC 50 = 89 ± 16 lM and HeLa, IC 50 = 194 ± 19 lM) was noticed for the phosphonate 18d derived from (5-fluorouracyl-1-yl)acetic acid and O,O-diethyl (2-aminoethoxy)methylphosphonate. Studies on the analogous phosphonates containing functionalized linkages are currently ongoing in our laboratory and the most active diethyl esters will be transformed into the free ANP and further derivatized to selected prodrug phosphonates [37].
Experimental 1 H NMR spectra were recorded in CD 3 OD, CDCl 3 , or DMSO-d 6 on the following spectrometers: Varian Gemini 2000BB (200 MHz) and Bruker Avance III (600 MHz) with TMS as internal standard. 13 C NMR spectra were recorder for CD 3 OD, CDCl 3 , or DMSO-d 6 solution on the Bruker Avance III at 151.0 MHz. 31 P NMR spectra were performed on the Varian Gemini 2000BB at 81.0 MHz or on Bruker Avance III at 243.0 MHz. IR spectral data were measured on a Bruker Alpha-T FT-IR spectrometer. Melting points were determined on a Boetius apparatus. Elemental analyses were performed by Microanalytical Laboratory of this Faculty on Perkin Elmer PE 2400 CHNS analyzer and their results were found to be in good agreement (±0.3%) with the calculated values.
The following absorbents were used: column chromatography, Merck silica gel 60 (70-230 mesh); analytical TLC, Merck TLC plastic sheets silica gel 60 F 254 . TLC plates were developed in chloroform-methanol solvent systems. Visualization of spots was effected with iodine vapors. All solvents were purified by methods described in the literature.

Synthesis of amides 17-24
General procedure A A solution of 0.100 g aminophosphonate 7a (0.598 mmol) in 2 cm 3 DMF containing 0.100 g (thymine-1-yl)acetic acid (12, 0.544 mmol) was cooled to 0°C and 0.152 cm 3 TEA (1.09 mmol) followed by a 0.481 cm 3 of a 50% solution of T3P Ò in DMF (0.816 mmol) were added. The reaction mixture was stirred at room temperature for 24 h, concentrated in vacuo and treated with 5 cm 3 water. A solid was filtered off, air dried, and subjected to chromatography on a silica gel column with chloroformmethanol mixtures (20:1, 10:1 v/v) to give pure compound 20a (0.072 g, 40% yield) as a white powder.
General procedure B To a solution of aminophosphonates 7a-7d (1.00 mmol) in 2 cm 3 DMF or chloroform the respective acetic acids 9-16 (1.00 mmol), EDC 9 HCl (1.00 mmol), and TEA (1.00 mmol) were added. The reaction mixture was stirred at room temperature for 48-72 h and then concentrated in vacuo. The residue was chromatographed on a silica gel column with chloroform-methanol mixtures and crystallized from the appropriate solvents. General procedure C To a solution of aminophosphonates 7a-7d (1.00 mmol) in 2 cm 3 chloroform the respective acetic acids 9-16 (1.00 mmol), EDC 9 HCl (1.00 mmol), and TEA (1.00 mmol) were added. The reaction mixture was irradiated (100 W) at 35°C for the specified time (15 min-3 h) and then concentrated in vacuo. The residue was chromatographed on a silica gel column with chloroformmethanol mixtures and crystallized from the appropriate solvents.