title: Synthesis of novel 3'-C-methylene thymidine and 5-methyluridine/cytidine H-phosphonates and phosphonamidites for new backbone modification of oligonucleotides.
abstract: 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.
authors: Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA. han@isisph.com
authors: H
authors: H
authors: An
authors: T
authors: T
authors: Wang
authors: M A
authors: MA
authors: Maier
authors: M
authors: M
authors: Manoharan
authors: B S
authors: BS
authors: Ross
authors: P D
authors: PD
authors: Cook
mesh_terms: D000890:Anti-Infective Agents / Q000138:chemical synthesis*; D000970:Antineoplastic Agents / Q000138:chemical synthesis; D003562:Cytidine / Q000031:analogs & derivatives* / Q000138:chemical synthesis*; D009841:Oligonucleotides / Q000138:chemical synthesis*; D016376:Oligonucleotides, Antisense / Q000138:chemical synthesis; D063065:Organophosphonates; D013936:Thymidine / Q000031:analogs & derivatives / Q000138:chemical synthesis*; D014529:Uridine / Q000031:analogs & derivatives* / Q000138:chemical synthesis
chemical_list: C438461:3'-C-methylene thymidine; D000890:Anti-Infective Agents; D000970:Antineoplastic Agents; D009841:Oligonucleotides; D016376:Oligonucleotides, Antisense; D063065:Organophosphonates; C009182:ribothymidine; D003562:Cytidine; C016568:5-methylcytidine; D013936:Thymidine; D014529:Uridine