Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid

Abstract

It is difficult to overestimate the importance of nucleoside triphosphates in cellular chemistry: They are the building blocks for DNA and RNA and important sources of energy. Modifications of biologically important organic molecules with fluorine are of great interest to chemists and biologists because the size and electronegativity of the fluorine atom can be used to make defined structural alterations to biologically important molecules. Although the concept of nonhydrolyzable nucleotides has been around for some time, the progress in the area of modified triphosphates was limited by the lack of synthetic methods allowing to access bisCF 2 -substituted nucleotide analogs-one of the most interesting classes of nonhydrolyzable nucleotides. These compounds have "correct" polarity and the smallest possible steric perturbation compared to natural nucleotides. No other known nucleotides have these advantages, making bisCF 2 -substituted analogs unique. Herein, we report a concise route for the preparation of hitherto unknown highly acidic and polybasic bis(difluoromethylene)triphosphoric acid 1 using a phosphorous(III)/phosphorous(V) interconversion approach. The analog 1 compared to triphosphoric acid is enzymatically nonhydrolyzable due to substitution of two bridging oxygen atoms with CF 2 groups, maintaining minimal perturbations in steric bulkiness and overall polarity of the triphosphate polyanion. The fluorinated triphosphoric acid 1 was used for the preparation of the corresponding fluorinated deoxynucleotides (dNTPs). One of these dNTP analogs (dT) was demonstrated to fit into DNA polymerase beta (DNA pol β) binding pocket by obtaining a 2.5 Å resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate∕Mg 2þ interaction over Watson-Crick hydrogen bonding was found and discussed.DNA polymerase beta | nonhydrolyzable nucleotides | fluorinated triphosphate | pentabasic acid | isopolarity and bioisotericity

Polyfluorinated Groups in Medicinal Chemistry

“…DNA analogs 74a-d can be used as probes to evaluate the mechanism of polymerase action, to explore stereoelectronic effect on active site interactions and to illustrate small differences in the catalytic activity of different enzymes [60].…”

Synthesis and Biological Applications of Phosphinates and Derivatives

“…Tetrafluorophosphinobisphosphonates 266a-d were prepared starting from difluoromethylphosphonate 260 (Scheme 52) [194]. Once deprotonated by LTMPA and treated with diethylaminodichlorophosphine, the resulting aminophosphine intermediate was oxidized by m-CPBA, affording phosphinamide 261 in 75% yield.…”

Synthesis of gem‐Difluorinated Cyclopropanes and Cyclopropenes: Trifluoromethyltrimethylsilane as a Difluorocarbene Source

“…Recently, Hu and co-workers reported that TMSCF 2 Cl can act as an efficient difluorocarbene precursor under chloride-ion catalysis at 110 8C. [12] However, TMSCF 2 Cl is not commercially available and its preparation requires the use of ozone-depleting CBrClF 2 . [13] For substrates that are thermally unstable, the abovementioned methods and reagents could be a serious limitation, and development of better difluorocarbene precursors that can generate difluorocarbenes at lower temperatures is required.…”

“…[1] The difluoromethylene group is also considered as a bioisostere for an oxygen atom in biological studies. [2] Recently, a unique application of difluorocyclopropanes to trap the 1,3-diradical formed during the mechanochemical activation of the polybutadiene backbone was reported. [3] Besides biological and polymeric applications, difluorocyclopropanes are synthetically useful substrates for a variety of reactions such as thermal rearrangements, bimolecular reactions, carbocation, carbanion, and radical chemistry.…”