Protected monomers

A protected monomer having a formula (I)

• wherein,
• B is selected from the consisting of:
• X2 is an ortho ester protecting group, hydrogen, ethers, alkyl ethers, esters, halogens, protected amines, or protected hydroxyl moieties;
• X3 is —O—P(OR27)N(R28)2 or —O-L-R29;
• X5′, X5″, X5′″ include at least one alkoxy or siloxy substituent;
• R1 is hydrogen or C1-C4 alkyl;
• R2 is hydrogen, C1-C4 alkyl, or C2-C6 alkenyl optionally substituted with hydroxy, or C(O)NHRa;
• R3 is hydrogen, halo, C1-C4 alkyl, C1-C4 thioalkoxy, NH2, NHRb, or NRbRc;
• R4 when taken together with R4′ forms oxo, or R4 when taken together with R5 forms a double bond between the carbon and nitrogen atoms to which they are attached;
• R4′ when taken together with R4 forms oxo, or is O−;
• R5 is hydrogen, C1-C4 alkyl, or when taken together with R4 forms a double bond between the carbon and nitrogen atoms to which they are attached;
• R6 is hydrogen, halo, NH2, NHRb, or NRbRc;
• R7 is an unshared electron pair, or C1-C4 alkyl;
• R8 when taken together with R9 forms a double bond between the carbon and nitrogen atoms to which they are attached, or R8 when taken together with R11 forms a double bond between the carbon and nitrogen atoms to which they are attached;
• R9 is hydrogen, C1-C4 alkyl, or when taken together with R8 forms a double bond between the carbon and nitrogen atoms to which they are attached;
• R10 is hydrogen or is absent;
• R11 is hydrogen, C1-C4 alkyl, or when taken together with R8 forms a double bond between the carbon and nitrogen atoms to which they are attached;
• R12 is hydrogen, formyl, or C1-C4 alkyl optionally substituted with hydroxy or protected hydroxy;
• R13 and R14 are each independently hydrogen or C1-C4 alkyl;
• R15 is hydrogen, C1-C4 alkyl, or (CH2)nCH(Rd)CH(NHRe)(COORg);
• R16 is hydrogen or C1-C4 alkyl;
• R17 is halo, NH2, NHRb, or NRbRc;
• R18 is cyano, C(═NH)NH2, or CH2NH(Rh);
• R19 is hydrogen, or C1-C4 alkyl;
• R20 is:
• (i) hydrogen;
• (ii) hydroxy or protected hydroxy;
• (iii) C1-C4 alkoxy optionally substituted with COORf;
• or
• (iv) C1-C4 alkyl optionally substituted with hydroxy and/or COORf, NH2, NHRm, or CONH2;
• R21 is hydrogen, or when taken together with R23 forms a double bond between the carbon atoms to which they are attached;
• R22 is hydrogen;
• R23 is hydrogen, or when taken together with R21 forms a double bond between the carbon atoms to which they are attached;
• R24 and R25 are each, independently, hydrogen or C1-C4 alkyl;
• R26 is (CH2)nCH(Rd)CH(NHRe)(COORg);
• R27 is C1-C6 alkyl optionally substituted with cyano, or C2-C6 alkenyl;
• R28 is C1-C10 alkyl;
• R29 is a liquid or solid phase support reagent;
• Q is N or CR44;
• Q′ is N or CR45;
• Q″ is N or CR47;
• Q′″ is N or CR49;
• Qiv is N or CR50;
• R44 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, a ligand, a tethered ligand, or when taken together with R45 forms —OCH2O—;
• R45 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, a ligand, a tethered ligand, or when taken together with R44 or R46 forms —OCH2O—;
• R46 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, a ligand, a tethered ligand, or when taken together with R45 or R47 forms —OCH2O—;
• R47 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, a ligand, a tethered ligand, or when taken together with R46 or R48 forms —OCH2O—;
• R48 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, a ligand, a tethered ligand, or when taken together with R47 forms —OCH2O—;
• R49 R50, R51, R52, R53 R54, R57, R58 R59, R60, R61, R62, R63, R64, R65, R66, R67 R68, R69R70, R71, and R72 are each independently selected from hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C2-C6 alkynyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, NC(O)R17, or NC(O)Ro;
• R55 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C2-C6 alkynyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, NC(O)R17, or NC(O)Ro, or when taken together with R56 forms a fused aromatic ring which may be optionally substituted;
• R56 is hydrogen, halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C2-C6 alkynyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, NC(O)R17, or NC(O)Ro, or when taken together with R55 forms a fused aromatic ring which may be optionally substituted;
• X is O, S, or Se;
• Y is O or S;
• L is —C(O)(CH2)qC(O)—, or —C(O)(CH2)qS—;
• Provided that R1, R2, and R3 cannot all be hydrogen;
• further provided that when R5 is hydrogen, R6 cannot be NH2, NH(protecting group), or NH(iBu);
• further provided that when R12 is hydrogen and R8 and R11 together form a double bond between the carbon and nitrogen atoms to which they are attached, R9 and R10 cannot both be hydrogen;
• further provided that when X and Y are O, R19 is hydrogen, and R21 and R23 together form a double bond between the carbon atoms to which they are attached, R20 cannot be hydrogen or CH3;
• Ra is glycinyl, threonyl, or norvalyl, each of which may optionally be partially or fully protected;
• Rb is C1-C6 alkyl or a nitrogen protecting group;
• Rc is C1-C6 alkyl;
• Rd is hydrogen, hydroxy, protected hydroxy, or OOH;
• Re is hydrogen, a nitrogen protecting group, or COOR8;
• Rf is hydrogen, or C1-C6 alkyl;
• Rg is C1-C10 alkyl;
• Rh is hydrogen, or
• Ri and Rj when taken together forms a double bond between the carbon atoms to which they are attached, or Ri and Rj when taken together form —O— between the carbon atoms to which they are attached;
• Rk and Rl are each, independently, hydrogen, a hydroxylprotecting group, a sugar, or a fully or partially protected sugar;
• Rm is C1-C4 alkyl optionally substituted with COOH;
• Ro is alkyl optionally substituted with halo, hydroxy, nitro, protected hydroxy, NH2, NHRb, or NRbRc, C1-C6 alkyl, C2-C6 alkynyl, C6-C10 aryl, C6-C10 heteroaryl, C3-C8 heterocyclyl, NC(O)R17, or NC(O)Ro;
• n is 1-4;
• and
• q is 0-4.