Synthesis of Novel 3‘-C-Methylene Thymidine and 5-Methyluridine/Cytidine H-Phosphonates and Phosphonamidites for New Backbone Modification of Oligonucleotides

• Published in: Journal of organic chemistry Vol. 66; no. 8; pp. 2789 - 2801
• Main Authors: An, Haoyun, Wang, Tingmin, Maier, Martin A, Manoharan, Muthiah, Ross, Bruce S, Cook, P. Dan
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 20.04.2001; Amer Chemical Soc
• Subjects: Anti-Infective Agents - chemical synthesis; Antineoplastic Agents - chemical synthesis; Chemistry; Chemistry, Organic; Cytidine - analogs & derivatives; Cytidine - chemical synthesis; Oligonucleotides - chemical synthesis; Oligonucleotides, Antisense - chemical synthesis; Organophosphonates; Physical Sciences; Science & Technology; Thymidine - analogs & derivatives; Thymidine - chemical synthesis; Uridine - analogs & derivatives; Uridine - chemical synthesis; REPLACEMENT; PHASE; ANALOGS; DNA; PHOSPHODIESTER LINKAGE; STEREOSELECTIVE-SYNTHESIS; N-GLYCOSYLATION; CONFORMATION; ANTISENSE OLIGONUCLEOTIDES; DERIVATIVES
• DOI: 10.1021/jo001699u
• ISSN: 0022-3263

Novel 5‘-O-DMT- and MMT-protected 3‘-C-methylene-modified thymidine, 5-methyluridine, and 5-methylcytidine H-phosphonates 1−7 with O-methyl, fluoro, hydrogen, and O-(2-methoxyethyl) substituents at the 2‘-position have been synthesized by a new effective strategy from the corresponding key intermediates 3‘-C-iodomethyl nucleosides and intermediate BTSP, prepared in situ through the Arbuzov reaction. The modified reaction conditions for the Arbuzov reaction prevented the loss of DMT- and MMT-protecting groups, and directly provided the desired 5‘-O-DMT- and/or MMT-protected 3‘-C-methylene-modified H-phosphonates 1−6 although some of them were also prepared through the manipulation of protecting groups after the P−C bond formation. The modified Arbuzov reaction of 3‘-C-iodomethyl-5-methylcytidine 53, prepared from its 5-methyluridine derivative 42, with BTSP provided the 5-methylcytidine H-phosphonate 54, which was further transferred to the corresponding 4-N-(N-methylpyrrolidin-2-ylidene)-protected H-phosphonate monomer 7. 5‘-O-MMT-protected 3‘-C-methylene-modified H-phosphonates 5, 3, and 7 were converted to the corresponding cyanoethyl H-phosphonates 50, 51, and 56 using DCC as a coupling reagent. One-pot three-step reactions of 50, 51, and 56 provided the desired 3‘-C-methylene-modified phosphonamidite monomers 8−10. Some of these new 3‘-methylene-modified monomers 1−10 have been successfully utilized for the synthesis of 3‘-methylene-modified oligonucleotides, which have shown superior antisense properties including nuclease resistance and binding affinity to the target RNA.