Synthesis of Nucleobase‐Functionalized Morpholino‐Modified Nucleoside Monomers Through Palladium‐Catalyzed Cross‐Coupling Reactions

Abstract

Morpholino‐modified nucleoside analogues have widespread applications in developmental biology. To achieve nucleobase‐functionalized forms of morpholino nucleosides, syntheses of 5‐substituted cytidine, 8‐substituted adenosine, and 8‐substituted guanosine morpholino nucleoside monomers are described for the first time. The syntheses are based on the use of 5‐iodocytidine, 8‐bromoadenosine, and 8‐bromoguanosine morpholino nucleosides as the key starting materials. These iodo or bromo derivatives have also been synthesized for the first time. Palladium‐mediated cross‐coupling reactions (Sonogashira, Suzuki, and Heck) were then employed with the halo derivatives to accomplish the substitutions. Different reaction conditions for C, A, and G were standardized to achieve the conversions. The strategy was devised in such a way that the useful N‐trityl protecting groups remain at the end. The catalyst combinations used for Sonogashira, Suzuki, and Heck reactions were Pd(PPh3)2Cl2·CuI, Pd(dppf)Cl2·CH2Cl2, and Pd(OAc)2, respectively. Heck coupling between 5‐iodocytidine monomer and methyl acrylate worked well, whereas with acrylonitrile the exocyclic amine of cytidine was found to form the aza‐Michael adduct. In this context, treatment of iodocytidine with methyl acrylate under two different sets of conditions was found to produce either the Michael addition product or the Heck coupling product. Four of the functionalized morpholino monomers have been further confirmed by single‐crystal X‐ray structural analysis. All of these functionalized monomers were obtained in good to excellent overall yields.

C5-pyrimidine-functionalized morpholino oligonucleotides exhibit differential binding affinity, target specificity and lipophilicity

“…As standardized by Nandi et al 31,32 in the case of the morpholino cytidine 2, the functionalizations were done by Pd-catalyzed cross-coupling reactions (Suzuki, Sonogashira and Heck coupling) to obtain products 3a-j. For the synthesis of the m5C morpholino (5-methyl morpholino cytosine) subunit, we started from compound 2a.…”

“…29 In this direction, we initially disclosed the synthesis of 5-alkynylated uracil-morpholino monomers, 5-substituted morpholino cytidine nucleosides including 8-substituted morpholino purine nucleosides using Pd-catalyzed cross-coupling reactions. [30][31][32][33] However, in these reports, none of the nucleosides were converted to chlorophosphoramidates that were suitable for PMO synthesis. Hence, as part of our research towards the development of functionalized PMOs ( F-PMOs), we report herein the synthesis of functionalized morpholino chlorophosphoramidates of cytidine, uridine (Fig.…”

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

“…Halogenation with bromine was achieved in good yields, however, the following Sonogashira reaction reproducibly proceeded with very low yields (data not shown). Therefore, we changed the used halide to iodine, taking into account that direct iodination of purines has been claimed being troublesome [ 26 ], although not impossible [ 27 ]. For C8-iodination of adenosine, first the hydroxy groups at the sugar moiety were protected with tert -butyldimethylsilyl (TBDMS) groups.…”

Changed reactivity of secondary hydroxyl groups in C8-modified adenosine – lessons learned from silylation

“…Halogenation with bromine was achieved in good yields, however the following Sonogashira reaction reproducibly proceeded with very low yields (data not shown). Therefore, we changed the used halide to iodine, taking into account that direct iodination of purines has been claimed being troublesome, 24 although not impossible. 25 For C8-iodination of adenosine, first the hydroxyl groups at the sugar moiety were protected with tert-butyldimethylsilyl (tBDMS) groups.…”