Acylphosphonates

10th anniversary of discovering cGAMP: synthesis and beyond

The discovery of cGAMP in 2012 filled an important gap in our understanding of innate immune signaling. It has been known for over a century that DNA can induce immune responses, but the underlying mechanism was not clear. With the identification of STING as a key player in interferon induction, the DNA detector that activates STING was the last missing link in TBK1-IRF3 signaling. Somewhat unexpectedly, it turns out that nature relays the DNA danger signal through a small molecule. cGAMP is a cyclic dinucleotide produced from cyclodimerization of ATP and GTP upon detection of cytosolic DNA by cGAS, a previously uncharacterized protein, to promote the assembly of the STING signalosome. This article covers a personal account of the discovery of cGAMP, a short history of the relevant nucleotide chemistry, and a summary of the latest development in this field of research in chemistry. It is the author's hope that, with a historic perspective, the readers can better appreciate the synergy between chemistry and biology in drug development.

Synthesis of dinucleoside acylphosphonites by phosphonodiamidite chemistry and investigation of phosphorus epimerization

The reaction of the diamidite, (iPr2N)2PH, with acyl chlorides proceeds with the loss of HCl to give the corresponding acyl diamidites, RC(O)P(N(iPr)2)2 (R = Me (7), Ph (9)), without the intervention of sodium to give a phosphorus anion. The structure of 9 was confirmed by single-crystal X-ray diffraction. The coupling of the diamidites 7 and 9 with 5'-O-DMTr-thymidine was carried out with N-methylimidazolium triflate as the activator to give the monoamidites 3'-O-(P(N(iPr)2)C(O)R)-5'-O-DMTr-thymidine, and further coupling with 3'-O-(tert-butyldimethylsilyl)thymidine was carried out with activation by pyridinium trifluoroacetate/N-methylimidazole. The new dinucleoside acylphosphonites could be further oxidized, hydrolyzed to the H-phosphonates, and sulfurized to give the known mixture of diastereomeric phosphorothioates. The goal of this work was the measurement of the barrier to inversion of the acylphosphonites, which was expected to be low by analogy to the low barrier found in acylphosphines. However, the barrier was found to be high as no epimerization was detected up to 150 °C, and consistent with this, density functional theory calculations give an inversion barrier of over 40 kcal/mol.

Sulfurization of dinucleoside phosphite triesters with chiral disulfides

Sixteen chiral analogues of phenylacetyl disulfide (PADS) and 5-methyl-3H-1,2,4-dithiazol-3-one (MEDITH) were used to sulfurize five dithymidine phosphite triesters, each incorporating a β-cyanoethoxy or siloxy group. Each mixture of S(P):R(P) phosphite triester diastereomers was combined with approximately one fourth of an equivalent of each of the sulfurizing reagents, and the R(PS):S(PS) diastereomer ratios of the resulting phosphite sulfides or phosphorothioates were determined by reverse-phase HPLC. Diastereoselectivities and corresponding diastereomeric excess (de) values were calculated by correcting for the starting triester diastereomer ratios. The highest de values for R(PS) and S(PS) phosphorothioates were 14.7% and 7.9%, respectively, both using MEDITH analogues.

Preparation of asymmetric alpha-ketophosphonates by [3,3]-sigmatropic shift of enolphosphonates

Alpha-ketophosphonates are prepared by a [3,3]-sigmatropic shift of enolphosphonates.

Studies on stereospecific formation of P-chiral internucleotide linkage: synthesis of all-Rp and all-Sp methylphosphonate pentanucleotide d(MMTrAPMeTPMeTPMeCPMeTAc) via Grignard activated coupling

Synthesis of stereoregular 3',5'-protected all-Rp and all-Sp methylphosphonate heterooligonucleotides d(MMTrAPMeTPMeTPMeCPMeTAc) (12) complementary to the fragment of HIV-1 splicing acceptor site was achieved via stereo-controlled formation of internucleotide linkage. The coupling was based on the transesterification of P-stereodefined monomer type of 5'-O-monomethoxytrityl-2'-O-deoxynucleoside 3'-O-[O-(4-nitrophenyl)methylphosphonate]. The nucleophile was a t-butylmagnesium chloride activated 5'-terminal hydroxyl function of the growing oligonucleotide chain. This and other P-homochiral oligomers will be used as building blocks for the synthesis of biologically significant, longer stereoregular oligonucleotides.

Preparation of 35S-labeled polyphosphorothioate oligodeoxyribonucleotides by use of hydrogen phosphonate chemistry

The title compounds were chemically synthesized as their 5'-dimethoxytrityl derivatives by base-catalyzed reaction of 35S-enriched elemental sulfur with support-bound hydrogen phosphonate oligomer. This was derived from adamantane carbonyl chloride-activated coupling of nucleotide hydrogen phosphonate monomers, and similarly activated capping with isopropyl phosphite. A convenient, disposable, reversed-phase cartridge was utilized to purify and isolate the 5'-dimethoxytrityl derivative for subsequent in situ detritylation and elution of the final product. The specific activity obtained for the title compounds was ca. 10(7) cpm/mumols-eq P(O)S-. The procedure should be readily adaptable to appropriate syntheses of other P-S containing analogs of DNA and RNA.