Synthesis and biological evaluation of a novel β-D-2'-deoxy-2'-α-fluoro-2'-β-C-(fluoromethyl)uridine phosphoramidate prodrug for the treatment of hepatitis C virus infection

Discovery of a 2'-α-Fluoro-2'-β-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent

A novel 2'-α-fluoro-2'-β-C-(fluoromethyl) purine nucleoside phosphoramidate prodrug 15 has been designed and synthesized to treat SARS-CoV-2 infection. The SARS-CoV-2 central replication transcription complex (C-RTC, nsp12-nsp7-nsp82) catalyzed in vitro RNA synthesis was effectively inhibited by the corresponding bioactive nucleoside triphosphate (13-TP). The cryo-electron microscopy structure of the C-RTC:13-TP complex was also determined. Compound 15 exhibited potent in vitro antiviral activity against the SARS-CoV-2 20SF107 strain (EC50 = 0.56 ± 0.06 μM) and the Omicron BA.5 variant (EC50 = 0.96 ± 0.23 μM) with low cytotoxicity. Furthermore, it was well tolerated in rats at doses of up to 2000 mg/kg, and a single oral dose of this prodrug at 40 mg/kg led to high levels of 13-TP in the target organ lungs of rats with a long half-life. These findings support the further development of compound 15 as an orally available antiviral agent for the treatment of SARS-CoV-2 infection.

Construction of quaternary stereocenters at carbon 2' of nucleosides

The non-natural nucleosides with a quaternary stereogenic center at C2' are crucial to drug discovery. They have become a cornerstone for the treatment of cancer and various viral infections as exemplified by gemcitabine and sofosbuvir. Major research effort has been expended to gain synthetic access to these nucleoside analogues with a significant steric bulk at C2' in the furanoside ring. The 2'-ketonucleosides and 2'-deoxy-2'-methylenenucleosides emerged as key intermediates in these synthetic strategies. For example, α-face addition of methyl lithium to the 2'-ketonucleosides followed by fluorination of resulting tertiary arabino alcohol with DAST provided 2'-fluoro-2'-C-methyluridine - a core nucleoside component of sofosbuvir. The α-face addition of HCN or HN₃ to the 2'-deoxy-2'-methylene nucleosides gave access to the synthetically versatile 2'-cyano-2'-C-methyl and 2'-azido-2'-C-methyl nucleosides. Likewise, the addition of diazomethane to the 2'-exomethylene group gave access to the 2'-spirocyclopropyl analogue. This review primarily discusses synthetic strategies which employs natural nucleosides as substrates but selected approaches involving coupling of the preelaborated sugar precursors with nucleobases are also examined.

In silico design of a novel nucleotide antiviral agent by free energy perturbation

Nucleoside analogs are the backbone of antiviral therapies. Drugs from this class undergo processing by host or viral kinases to form the active nucleoside triphosphate species that selectively inhibits the viral polymerase. It is the central hypothesis that the nucleoside triphosphate analog must be a favorable substrate for the viral polymerase and the nucleoside precursor must be a satisfactory substrate for the host kinases to inhibit viral replication. Herein, free energy perturbation (FEP) was used to predict substrate affinity for both host and viral enzymes. Several uridine 5'-monophosphate prodrug analogs known to inhibit hepatitis C virus (HCV) were utilized in this study to validate the use of FEP. Binding free energies to the host monophosphate kinase and viral RNA-dependent RNA polymerase (RdRp) were calculated for methyl-substituted uridine analogs. The 2'-C-methyl-uridine and 4'-C-methyl-uridine scaffolds delivered favorable substrate binding to the host kinase and HCV RdRp that were consistent with results from cellular antiviral activity in support of our new approach. In a prospective evaluation, FEP results suggest that 2'-C-dimethyl-uridine scaffold delivered favorable monophosphate and triphosphate substrates for both host kinase and HCV RdRp, respectively. Novel 2'-C-dimethyl-uridine monophosphate prodrug was synthesized and exhibited sub-micromolar inhibition of HCV replication. Using this novel approach, we demonstrated for the first time that nucleoside analogs can be rationally designed that meet the multi-target requirements for antiviral activity.

Investigation of crystal structures, energetics and isostructurality in halogen-substituted phosphoramidates

A total of 14 compounds, one unsubstituted and 13 halogen-substituted phosphoramidates, have been synthesized from unsubstituted and halogenated (fluoro-, difluoro-, chloro-, bromo-, iodo-substituted) aniline and diphenyl phosphoryl chloride to investigate their molecular assembly in solid-state structures. Amongst them, six groups were formed based on similarities in unit-cell dimensions, space group and molecular assembly of the crystal. The analysis reveals that all the crystal structures contain robust N-H...O hydrogen bonds which are the primary building blocks with ancillary interactions such as C-H...O, C-H...π, C-H...F/Cl/Br/I, F...F, F...π, I...π, Br...π, I...O and Br...O. The role of short and directional C-H...O and C-H...π interactions providing significant stabilization to the densely packed crystalline arrangement is discussed. The contribution of these interactions in stabilizing the crystalline assembly was deduced via computing total interaction energy between dimers and the overall lattice energies using the computer programs Crystal Explorer 17.5 and PIXELC, respectively. Additionally, the occurrence of 3D isostructurality in phosphoradimates and their halogenated analogs was investigated using the XPac program. A comparison of the magnitudes of the torsion angles in the compounds substantiates the role of conformational flexibility in the solid state.

Uridine derivatives from the seeds of Lepidium apetalum Willd. and their estrogenic effects

Ten uridine derivatives (lepidiumuridine B-K) were isolated from the seeds of Lepidium apetalum Willd. Lepidiumuridine B-J were previously undescribed compounds, and were structurally characterized using analysis of their NMR and MS data. Lepidiumuridine C, D, I, and J increased cell proliferation and expression of ERα in the MCF-7 cell line. In addition, blockage of ERα completely abolished cell proliferation and expression of ERα in MCF-7 cells, suggesting that the proliferation effects of lepidiumuridine C, D, I, and J were ERα-mediated. The uridine derivatives might belong to undescribed phytoestrogens.

Lepidiumuridine A: A New Natural Uridine Derivative as a Phytoestrogen Isolated from the Seeds of Lepidium apetalum Willd

There has been great interest in phytoestrogens, which are polyhydric compounds that are derived from plants and have a structure similar to that of the mammalian steroid hormone 17β-estradiol. The present study examined the estrogenic effects of a new natural uridine derivative, lepidiumuridine A (LA), that was isolated from the seeds of Lepidium apetalum. The structure was clarified and determined via analysis of extensive spectroscopic data interpretation. The activity of LA was investigated by measuring the levels of estradiol (E2), luteinizing hormone (LH), follicle stimulating hormone (FSH), and the uterus growth in mice. The proliferation experiment of MCF-7 breast cancer cells was also conducted. Western blot, in-cell western, and antagonist assays with methyl piperidino-pyrazole (MPP) were used for exploring the mechanism of the effects of LA. The results showed that LA elevated the uterine coefficient, the levels of E2, and FSH significantly. In addition, LA significantly elevated ERα expression in the uterus and MCF-7 cells. MPP inhibited the proliferation of LA-stimulated MCF-7 cell and ERα expression in MCF-7 cells. Taken together, LA had an estrogen-like effect, which was mainly mediated by the estrogen receptor ERα.