Metabolism, Biochemical Actions, and Chemical Synthesis of Anticancer Nucleosides, Nucleotides, and Base Analogs

Abstract

Nucleoside, nucleotide, and base analogs have been in the clinic for decades to treat both viral pathogens and neoplasms. More than 20% of patients on anticancer chemotherapy have been treated with one or more of these analogs. This review focuses on the chemical synthesis and biology of anticancer nucleoside, nucleotide, and base analogs that are FDA-approved and in clinical development since 2000. We highlight the cellular biology and clinical biology of analogs, drug resistance mechanisms, and compound specificity towards different cancer types. Furthermore, we explore analog syntheses as well as improved and scale-up syntheses. We conclude with a discussion on what might lie ahead for medicinal chemists, biologists, and physicians as they try to improve analog efficacy through prodrug strategies and drug combinations.

Figure 1.

FDA-approved anticancer nucleoside analogs.

Figure 2.

Various nucleoside analogs in clinical trials or used outside of the U.S.

Figure 2.

Various nucleoside analogs in clinical trials or used outside of the U.S.

Figure 3.

Various nucleoside analogs that have stalled in clinical trials.

Figure 4.

General biological mechanism of action of anticancer nucleoside analogs.

Figure 5.

General synthetic approaches to anticancer nucleoside analogs.

Figure 6.

Metabolism of 6-MP 1 and 6-TG 3.

Figure 7.

Structures of PMEG, PMEDAP, and PMEA, and proposed cellular metabolism of GS-9219 53.

Figure 8.

Complex of 5,10-methylenetetrahydrofolate and thymidylate synthase with 5-FU-5′-monophosphate.

Figure 9.

Metabolism of 5-FU 2 and derivatives.

Figure 10.

Proposed mechanism for phosphoramidate decomposition of NUC-3373 37.

Figure 11.

Structures of tetrahydrouridine 39 and (4R)-2′-deoxy-2′,2′-difluoro-3,4,5,6-tetrahydrouridine.

Figure 12.

Covalent trapping paradigm: mechanism-based DNMT1 degradation by decitabine 14.

Figure 13.

Chemical structure of CP-4200.

Figure 14.

CNDAC structure and hypothesized mechanism of DNA strand break with incorporated CNDAC.

Figure 15.

Proposed mechanism of catalytic reduction of nucleoside-5′-diphosphates by ribonucleotide reductase (upper), and proposed mechanism of ribonucleotide reductase inhibition by tezacitabine-5′-diphosphate (lower).

Figure 16.

Transition state model for the phosphorolysis of inosine by purine nucleoside phosphorylase and the protonated form of forodesine.

Figure 17.

Proposed biological mechanisms of actions of triciribine 30 as an Akt inhibitor (see Section 7.1, Triciribine Biology); MLN4924 44 as a Cullins inhibitor (see Section 7.3, MLN4924 Biology); and acadesine 41 as an AMPK activator (see Section 8.5, Acadesine Biology).

Figure 18.

Structures of MLN4924 44 and adenosine-5′-monophosphate.

Figure 19.

DOT1L-catalyzed methylation of H3K79.

Scheme 1.. Synthesis of 6-Mercaptopurine 1^a

^aReagents and conditions: (a) Na₂S₂O₄, H₂O, 60–70 °C, 80–85%; (b) Raney Ni, Na₂CO₃, H₂O, reflux, 2 h then H₂SO₄, 88%; (c) HCO₂H, reflux, 2 h then aq NaOH, AcOH, 93%; (d) P₂S₅, tetralin, 190–200 °C, 12 h, 40%; or 58, DMSO₂, 165–170 °C, 85%.

Scheme 2.. Synthesis of 6-Thioguanine 3^a

^aReagents and conditions: (a) P₂S₅, pyr, reflux, 2.5 h, 32%; (b) P₂S₅, pyridine hydrochloride, pyr, 110 °C, 4 h, then HCl, H₂O, pH 4, recrystallization, 75%.

Scheme 3.. Synthesis of GS-9219 53^a

^aReagents and conditions: (a) HO(CH₂)₂OCH₂PO(O-iPr)₂, DIAD, PPh₃, DMF, −15 °C to rt, 4 h, 63%; (b) cyclopropylamine, CH₃CN, 100 °C, 4 h, 90%; (c) TMSBr, CH₃CN, rt, overnight, 90%; (d) d-alanine ethyl ester HCl, 2,2′-dithiodipyridine, PPh₃, Et₃N, pyr, 60 °C, overnight, 50%.

Scheme 4.. Synthesis of GS-9219 53^a

^aReagents and conditions: (a) Cl(CH₂)₂OCH₂P(O)(O-iPr)₂, Cs₂CO₃, DMF, 80 °C, 8 h, 56%; (b) cyclopropylamine, EtOH, reflux, 3 h, 65%; (c) TMSBr, CH₃CN, rt, overnight; (d) d-alanine ethyl ester, aldrithiol-2, PPh₃, Et₃N, pyr, 50 °C, 3 h, 92–98% (over two steps).

Scheme 5.. Synthesis of Fluorouracil 2^a

^aReagents and conditions: (a) CF₃OF/CCl₃F, MeOH, −78 °C, 5 min; (b) Et₃N, MeOH, H₂O, rt, 11 min, 90% (over two steps); (c) F₂ (g), TFA, 0 °C to 10 °C, 3 h, 80%; (d) triethyleneglycol dimethyl ether, 130 °C to 200 °C, 20 min, 90%.

Scheme 6.. Synthesis of Fluorouracil 2^a

^aReagents and conditions: (a) Na, MeOH; (b) POCl₃, PhNMe₂; (c) proton sponge hydrofluoride; (d) NaF, F₂, CFCl₃; (e) HCl (g), 160 °C, 4 h, 38%; (f) Pd/C, H₂, Et₃N, EtOAc, 3.5 h, 82%; (g) aq NaOH, 80 °C, 4 h, 93%.

Scheme 7.. Synthesis of Capecitabine 10^a

^aReagents and conditions: (a) HCl, MeOH/Me₂CO, 78%; (b) MsCl, pyr; (c) NaI, DMF; (d) Pd/C, H₂, 27%; (e) aq HCl, 100 °C, 97%; (f) Ac₂O, pyr, 64%; (g) 5-fluorocytosine, HMDS, SnCl₄, DCM, 76%; (h) n-pentyl chloroformate, pyr; (i) aq NaOH, MeOH.

Scheme 8.. Synthesis of Doxifluridine 23 and Capecitabine 10^a

^aReagents and conditions: (a) 2,2-dimethoxypropane, TsOH, Me₂CO, rt, 2 h, 95%; (b) methyltriphenoxyphosphonium iodide, DMF, rt, 2.5 h, then MeOH, rt, 1 h, 74%; (c) Et₃N, H₂, Pd/C, MeOH, rt, 1.5 h, 93%; (d) TFA, 40 min, 78%; (e) CH₃(CH₂)₄OCOCl, pyr, DCM, −5 °C to rt, overnight, 92%; (f) NaOH, MeOH, −10 °C, 15 min, then concd HCl, 87%; (g) 87, THF, reflux, 66%.

Scheme 9.

Flow Synthesis of Capecitabine 10

Scheme 10.. Synthesis of NUC-3373 37^a

^aReagents and conditions: (a) l-alanine benzyl ester salt, Et₃N, DCM, −78 °C, 1–3 h, 74%; (b) t-BuMgCl, THF, rt, 18 h, 8%.

Scheme 11.. Synthesis of Floxuridine 5, 5-Fluoro-2′-deoxycytidine 38, and Tetrahydrouridine 39^a

^aReagents and conditions: (a) Ac₂O, DMAP, rt, 24 h, 88% (for 95a); Ac₂O, pyr, rt, 4.5 h, 99% (for 95b); (b) CF₃OF, CCl₃F, CHCl₃, −30 °C, evaporation, then Et₃N, MeOH, H₂O, rt, (55% for 5),(69% for 38); (c) Rh/Al, H₂ (g), H₂O, overnight; (d) H₂O, pH 6, 92% (over two steps); (e) Rh/Al, H₂ (g), NaOH, H₂O, 24 h, 45% of 99, 35% of 39; (f) NaBH₄, H₂O, freezer, overnight.

Scheme 12.. Synthesis of Floxuridine 5^a

^aReagents and conditions: (a) AcCl, MeOH, 25 °C, 45 min, then pyr; (b) pyr, DMAP, 4-ClBzCl, 0 °C, 1 h then 25 °C, 12 h; (c) HOAc, HCl (g), 0 °C, 7–10 min, 82% (α-anomer crystallizes from the solvent); (d) p-nitrophenol, CHCl₃, 30 °C, 12 h, 92%; (e) NH₃/MeOH, 30 °C, 16 h, 81%.

Scheme 13.. Synthesis of Tegafur 19 and Carmofur 24^a

^aReagents and conditions: (a) 130 °C, 4 h, 69%; (b) NaOMe, MeOH, reflux, 10 min, 84%; (c) 2,3-dihydrofuran, pyr, 180 °C; (d) F₂, AcOH, rt; (e) 1 N NaOH, rt, 1 h, 62% (over two steps); (f) aq HCHO, 55 °C, 6 h, 82%; (g) KBrO₃, 80 °C, then H₂N(CH₂)₅CH₃, DCC, MeCN, 0 °C to rt, 6 h, 40%.

Scheme 14.. Synthesis of Flucytosine 31^a

^aReagents and conditions: (a) CF₃OF, CCl₃F, MeOH, −78 °C to rt; (b) Et₃N, MeOH, H₂O, rt, 8 h, 85% (over two steps).

Scheme 15.. Synthesis of Gimeracil 20^a

^aReagents and conditions: (a) CH₃C(OCH₃)₃, MeOH, then (CH₃)₂NHCH(OCH₃)₂, reflux, 92%; (b) aq AcOH, 130 °C, 2 h, 95%; (c) SO₂Cl₂, HOAc, 50 °C, 0.5 h, 91%; (d) 40% H₂SO₄, 130 °C, 4 h, 91%; (e) SO₂Cl₂, HOAc, 50 °C, 45 min, 86%; (f) 75% H₂ SO₄, 140 °C, 3 h, then NaOH, then pH 4–4.5, 89%.

Scheme 16.. Synthesis of Oteracil 21^a

^aReagents and conditions: (a) LiOH, I₂, H₂O, 5 °C, 5 min, then AcOH, 75%; (b) aq KOH, 20 min, rt, 82%.

Scheme 17.. Synthesis of Trifluorothymidine 15^a

^aReagents and conditions: (a) NaCN, H₂SO₄, H₂O, 10 °C, 3 h, 99%; (b) Ac₂O, concd H₂SO₄, reflux, 1 h, 78%; (c) 500 °C, 4 h, 64%; (d) HBr (g), MeOH, 0 °C, 36 h, 82%; (e) (NH₂)₂CO, H₂O, 100 °C, 30 min, 28%; (f) aq HCl, reflux, 1 h, 58%; (g) Br₂/AcOH, reflux, 3 h, 85%; (h) DMF, 140 °C, 75 min, 80%; (i) thymidine, bactotryptone, NaCl, Escherichia coli B, 0.067 M phosphate buffer (pH 6.7), 37 °C, 3.5 h, 14%.

Scheme 18.. Synthesis of Trifluorothymidine 15^a

^aReagents and conditions: (a) AcCl, MeOH, 25 °C then pyr; (b) pyr, DMAP, 4-ClBzCl, 0 °C, 1 h, then 25 °C, 12 h; (c) HOAc, HCl (g), 0 °C, 7–10 min, 82% (over three steps); (d) 127, anisole, 50 °C, 3.5 h, 85% (β/α = 85.7:14.3); (e) NaOMe, MeOH, 4 °C, 3.5 h, then AcOBu, 97% (β/α = 99.92:0.08).

Scheme 19.. Synthesis of Tipiracil Hydrochloride 16^a

^aReagents and conditions: (a) SO₂Cl₂, AcOH, 50 °C, 2.5 h, 83%; (b) NH₃/MeOH, 120 °C, 10 h, 83%; (c) NaOEt, DMF, rt, 16 h, then aq HCl, 38%.

Scheme 20.. Synthesis of Azacytidine 11^a

^aReagents and conditions: (a) HCl (g), Ac₂O, Et₂O; (b) AgNCO, 60%; (c) 2-methylisourea, 68%; (d) HC(OC₂H₅)₃; (e) NH₃/MeOH, 40%.

Scheme 21.. Synthesis of Azacytidine 11^a

^aReagents and conditions: (a) HCO₂H, 80 °C, 15 min, 85%; (b) (CH₃)₂NCH(OCH₃)₂, NaOMe, MeOH, 40–50 °C, 4 h, 90%; (c) HMDS, (NH₄)₂SO₄, CH₃CN, reflux, 4–8 h; (d) 1,2,3,5-tetra-O-acetyl-β-d-ribofuranose, CF₃SO₃H, EtOAc, 45 °C, 30 min, then HCl, DCM, rt, 45 min; (e) n-BuNH₂, MeOH, 65 °C, 1 h, 49% (over three steps).

Scheme 22.. Early Synthesis of Decitabine 14^a

^aReagents and conditions: (a) AcCl, HCl, Et₂O, 0 °C; (b) bis(trimethylsilyl)-5-azacytosine 142, CH₃CN, 10%; (c) NH₃/EtOH; (d) anomer separation, 7%.

Scheme 23.. Kilogram-Scale Synthesis of Decitabine 14^a

^aReagents and conditions: (a) bis(trimethylsilyl)-5-azacytosine 142, TMSOTf, DCM, cold, 55%; (b) NaOMe/MeOH, 65%.

Scheme 24.. Synthesis of Decitabine 14^a

^aReagents and conditions: (a) AcCl/MeOH, 99%; (b) AcCl/pyr/DCM, 78%; (c) 5-azacytosine, HMDS, NH₄SO₄, TMSOTf, 60% (β/α = 1:1); (d) NH₃/MeOH, 34%.

Scheme 25.. Synthesis of SGI-110 22^a

^aReagents and conditions: (a) DMF, dimethylacetal; (b) vinyl acetate, Lipozyme RM IM, CH₃CN, dioxane; (c) [(iPr)₂N]POCH₂CH₂CN, DCM; (d) DCM; (e) tBuOOH; (f) NH₃/MeOH; (g) NaOAc, H₂O, EtOH.

Scheme 26.. Synthesis of Gemcitabine Hydrochloride 9^a

^aReagents and conditions: (a) BrCF₂CO₂Et, Zn, THF, Et₂O, 87% (3:1 anti/syn); (b) Dowex 50, MeOH, H₂O; (c) TBDMSOTf, lutidine, DCM, 86% (over two steps); (d) DIBAL-H; (e) MsCl, Et₃N, DCM, 71% (over two steps); (f) 2,4-bis(trimethylsilyl)cytosine, TMSOTf, DCE, reflux; (g) AG 50W-X8 resin, MeOH; (h) reverse phase HPLC, 10% (over two steps).

Scheme 27.. Synthesis of Gemcitabine 163^a

^aReagents and conditions: (a) PhBzCl, Et₃N, DCM; (b) K₂CO₃, H₂O, THF, MeOH, 67%; (c) HCl, CH₃CN, reflux; (d) BzCl/Pyr, EtOAc, rt, 72%; (e) LiAl(O-tBu)₃H, THF; (f) ClP(O)(OPh)₂, Et₃N, PhMe, rt, 77%; (g) HBr/HOAc, rt, 82%; (h) 2,4-bis(trimethylsilyl)cytosine, octane/heptane, Ph₂O, 140–150 °C; (i) NH₃/MeOH, H₂O, rt, 65%.

Scheme 28.. Synthesis of Gemcitabine Hydrochloride 9 and LY2334737 52^a

^aReagents and conditions: (a) Dowex 50W-X12 resin, MeOH, H₂O, rt, 4 days, 94%; (b) (E)-cinnamoyl chloride, pyr, EtOAc, 30 °C, 3 h, 43%; (c) LiAl(O-tBu)₃H, THF, −10 °C, 2 h, then TsCl, Et₃N, PhMe, −10 °C, 5 h, 62%; (d) N-acetyl cytosine, (TMS)₂NH, TMSOTf, DCE, reflux, 12 h, then 5% NaHCO₃, 47%; (e) NH₃/MeOH, rt, overnight, then HCl, Me₂CO, rt, 12 h, 80%; (f) 2-propylpentanoic acid, EDC, HOBt, NMM, DMF, DMSO, 55 °C, 17 h, 95%.

Scheme 29.. Synthesis of CP-4126 49 and NUC-1031 32^a

^aReagents and conditions: (a) Et₃N, DCM, −80 °C, 1 h, 98%, (b) NMI, pyr, THF, −80 °C to rt, 2 h, 16%; (c) HCl (g), DMF, elaidic acid chloride, rt, 12 h, 30%.

Scheme 30.. Discovery Synthesis of DFP-10917 26 and Process Synthesis of Sapacitabine 25^a

^aReagents and conditions: (a) 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane, pyr; (b) Ac₂O, EtOH; (c) CrO₃/pyr/Ac₂O, DCM; (d) NaCN, NaHCO₃, Et₂O, H₂O; (e) PhOC(S)Cl, DMAP, CH₃CN; (f) Bu₃SnH, AIBN, PhMe (57% over 3 steps); (g) Bu₄NF, CH₃CO₂H, THF then HCl/MeOH, 49% (over two steps); (h) Et₃N, MeOH, DCM, 30 °C, 10 min, 97%; (i) palmitic anhydride, dioxane, H₂O, 85 °C, 89%.

Scheme 31.. Synthesis of TAS-106 46^a

^aReagents and conditions: (a) TBDMSCl, pyr, rt, 1.5 h, 100%; (b) CrO₃, Ac₂O, pyr, rt, 1.5 h, 77%; (c) trimethylsilylacetylene, n-BuLi, THF, −78 °C, 99%; (d) n-Bu₄NF, THF, rt; (e) BzCl, pyr, rt, 93% (over two steps); (f) 20% HCl, MeOH, rt; (g) BzCl, DMAP, pyr, 100 °C, 87% (over two steps); (h) concd H₂SO₄, AcOH, Ac₂O, rt, 93%; (i) 2,4-bis(trimethylsilyl)cytosine, SnCl₄, CH₃CN, 0 °C to rt, 18 h, 81%; (j) NH₃/MeOH, rt, 2 days, 90%.

Scheme 32.. Synthesis of TAS-106 46^a

^aReagents and conditions: (a) 4-ClBzCl, Et₃N, DCM, 0 °C, 2 h, 74%; (b) TEMPO, DCM NaClO₄, NaHCO₃, H₂O, 0 °C, 30 min, then 2-propanol, rt, 10 min, 88%; (c) trimethylsilylacetylene, EtMgBr, THF, 4 °C, 30 min, 25%; (d) HCO₂H, H₂O, reflux, 45 min, 97%; (e) i-BuCl, Et₃N, DMAP, rt, 5 h, 87%; (f) 2,4-bis(trimethylsilyl)cytosine, SnCl₄, MeCN, 30 °C, 3 h, 81%; (g) DBU, MeOH, 30 °C, 3 h, 68%.

Scheme 33.. Synthesis of Tezacitabine 45^a

^aReagents and conditions: (a) TIPSiCl, pyr, 34 °C, 18 h; (b) (CH₃)₂NCH(OCH₃)₂, 37 °C, 4 h, 85% (over two steps); (c) (COCl)₂, DMSO, DCM, −75 °C, 0.5 h, then Et₃N, −75 °C to rt, 1 h, 90%; (d) PhSO₂CH₂F, ClP(O)(OEt)₂, 1 M LiHMDS, −60 °C to rt, 3 h; (e) NH₃/MeOH, rt, overnight, 66% (over two steps); (f) Bu₃SnH, AIBN, cyclohexane, reflux, 18 h, 83%; (g) CsF, MeOH, reflux, 24 h, 69%.

Scheme 34.. Synthesis of Troxacitabine 48^a

^aReagents and conditions: (a) PhCH₂OCH₂CH(OMe)₂, TsOH, CH₃CN, 95%; (b) H₂O₂, K₂CO₃, EtOH; (c) RuCl₃ hydrate, NaOCl, DCE/MeCN/H₂O, BnEt₃NCI; (d) H⁺, 51% (over three steps); (e) Pb(OAc)₄, MeCN/DCM, pyr, 80%; (f) silylated N-acetylcytosine, TMSOTf, DCM, rt; (g) deprotection, 30%.

Scheme 35.. Synthesis of Troxacitabine 48^a

^aReagents and conditions: (a) aq HCl, reflux, 20 h, 60%; (b) NaIO₄, MeOH, H₂O, then NaBH₄; (c) TsOH, Me₂CO, 6 h, 62%; (d) BzCl, pyr, DCM, rt, 2 h; (e) TsOH, MeOH, rt, 2 h, 83% (over two steps); (f) NaIO₄, RuO₂·H₂O, CH₃CN:CCl₄:H₂O (1:1:1.5 v/v), rt, 5 h; (g) Pb(OAc)₄, pyr, THF, rt, 45 min, 63% (over two steps); (h) N⁴-Bzcytosine, HMDS, NH₄SO₄, DCE, reflux, 2.5 h, then TMSOTf, DCE, rt, 1.5 h; (i) NH₃/MeOH, 0 °C, rt, 72 h, 38% (over two steps).

Scheme 36.. Synthesis of Thiarabine 47^a

^aReagents and conditions: (a) Na, ether, reflux, 16 h, then BnBr, 70 °C, 16 h; (b) Ac₂O, H₂O, 40 °C, 16 h; (c) AcCl, pyr, 25 °C, 16 h, 78% (over three steps); (d) Na, MeOH, 16 h; (e) BzCl, pyr, −15–25 °C, 20 h; (f) TsCl, pyr, CHCl₃, 40 °C, 36 h, 92% (over three steps); (g) NaOMe, CHCl₃, MeOH, −15 to 0 °C, 2 h, 87%; (h) NaOBn, BnOH, 40 °C; (i) TsCl; (j) KSC(O)CH₃, DMF, 115 °C, 73%; (k) HOAc, H₂O, 70 °C, 36 h, 78%; (l) NaIO₄, EtOH, H₂O, 30 °C, 0.5 h, 97%; (m) aq HCl, MeOH, reflux, 3 h, 41%; (n) Na, NH₃, ~100%; (o) BnCl; (p) HBr/HOAc; (q) bis(trimethylsilyl)-N-acetylcytosine, 130 °C, 3 h, 20%; (r) NH₃/MeOH, 0 °C, 2 days, 89%.

Scheme 37.. Synthesis of Thiarabine 47^a

^aReagents and conditions: (a) HCl, MeOH, rt, 5 h, 95%; (b) BnBr, NaH, TBAI, THF, rt, 3 days, 87%; (c) BnSH, SnCl₄, DCM, rt, overnight, 57%; (d) Ph₃P, imidazole, I₂, PhMe, CH₃CN, 90 °C, 24 h, 83%; (e) uracil, BSA, NBS, MeCN, 50–55 °C, 18 h, column purification (α:β = 1:1.15), 36%; (f) TPSCl, Et₃N, DMAP, 5 °C to rt, overnight; (g) NH₄OH, MeCN, rt, overnight, 50%.

Scheme 38.. Synthesis of RX-3117 29^a

^aReagents and conditions: (a) concd H₂SO₄, Me₂CO, then TBDPSCl, imidazole, 99%; (b) Ph₃PCH₃Br, t-BuOK, THF, 93%; (c) (COCl)₂, DMSO, DCM, −78 °C, 1 h, then Et₃N, rt, 96%; (d) CH₂=CHMgBr, THF, −78 °C, 84%; (e) n-Bu₄NF, THF, 97%; (f) Bu₂Sn(O), PhMe, 15 h, then TBAI, BnBr, 50 °C, 16 h, 76%; (g) Grubbs’ catalyst (2^nd generation), PhMe, 80 °C, 90%; (h) PDC, DMF, rt, 18 h, 59%; (i) I₂, pyr, THF, 55%; (j) NaBH₄, CeCl₃, MeOH, 93%; (k) TBDPSCl, imidazole, DMF, 97%; (l) NFSI, n-BuLi, THF, −78 °C; (m) n-Bu₄NF, THF, 63% (over two steps); (n) N³-benzoyluracil, DEAD, Ph₃P, THF, 87%; (o) NH₃/MeOH; (p) BBr₃, DCM, −78 °C, 50%; (q) Ac₂O, pyr, then POCl₃, Et₃N, 1,2,4-triazole; (r) NH₄OH, dioxane; (s) NH₃/MeOH, 40% (over three steps).

Scheme 39.. Synthesis of Cytarabine 4^a

^aReagents and conditions: (a) polyphosphoric acid; (b) prostatic phosphatase; (c) OH^–.

Scheme 40.. Synthesis of Cytarabine 4^a

^aReagents and conditions: (a) (PhCO)₂O, DMF, 100 °C, then K₂CO₃, 137 °C, 1.5 h, 78%; (b) aq HCl, 80 °C, 2 h, 68%; (c) HMDS, high pressure, 150 °C, 80 h; (d) MeOH, 5 °C, 1 h, 87% (over two steps); (e) Ac₂O, pyr, rt, 3 h, 91%; (f) POCl₃, 1H-1,2,4-triazole, Et₃N, CHCl₃, <8 °C then rt, overnight, 84%; (g) NH₄OH, NH₃, dioxane, H₂O, rt, overnight, 70%.

Scheme 41.. Synthesis of Elacytarabine 51 and MB 07133 34^a

^aReagents and conditions: (a) oleic anhydride, DMF, Mucor miehei lipase (MML), 60 °C, 48 h, 88%; (b) TBSCl, imidazole, DMF, rt, overnight, 85%; (c) 50% TFA, THF, −10 °C, 18 h, 65%; (d) DMF-dimethyl acetal, pyr, rt, 16 h, 90%;(e) EDC, DMAP, l-N,N-dimethyl-phenylalanine, DCM, rt, 16 h, 83%; (f) LiAlH₄, ether, −20 °C, 1 h, 66%; (g) 4-nitrophenyl phosphorodichloridate, THF, pyr, 0 °C to rt, 3.5 h, then sodium 4-nitrophenoxide, 40 °C, 4 h, 63%; (h) t-BuMgCl, THF, rt, 16 h, 78%; (i) 70% TFA, 60 °C, 16 h, 83%.

Scheme 42.. Synthesis of Cordycepin 27^a

^aReagents and conditions: (a) 2-acetoxyisobutyryl bromide, CH₃CN, H₂O, rt, 1 h; (b) Amberlite IRA-400 (OH^–) resin, MeOH, 92% (over two steps); (c) 1 M LiEt₃BH, THF, Me₂SO, 0 °C to rt, overnight, then 5% HOAc/H₂O, Et₃B, 98%.

Scheme 43.. Synthesis of Cordycepin 27^a

^aReagents and conditions: (a) 2-acetoxyisobutyryl bromide, CH₃CN, EtOAc, <35 °C, 6 h, 52% for 243b; (b) AcBr, MeOH, concd HCl, 20 °C, rt, 2–4 days, 70%; (c) AcONa, EtOH, H₂O then Pd/C, H₂ (50 psi), rt to 50 °C, 60%.

Scheme 44.. Synthesis of Cladribine 8^a

^aReagents and conditions: (a) 2,6-dichloropurine, melt, then dichloroacetic acid, and fusion under vacuum; (b) NH₃/NaOMe.

Scheme 45.. Synthesis of Cladribine 8^a

^aReagents and conditions: (a) NaH, CH₃CN, rt, 8 h; (b) then 247, 0 °C to rt, 22 h, 100% (over two steps); (c) BnI, CH₃CN, 60 °C, 1.5 h; (d) NH₃/MeOH, 60 °C, 11 h, >90% (over two steps).

Scheme 46.. Synthesis of Cladribine 8^a

^aReagents and conditions: (a) 25% NaOMe/MeOH.

Scheme 47.. Synthesis of Pentostatin 6^a

^aReagents and conditions: (a) PhCHO, piperidine, 95 °C, 21 h, 70%; (b) BnCl, K₂CO₃, DMF, 75 °C, 6 h, 96%; (c) O₃, DCM, −78 °C, 8 h, then HCO₂H, H₂O₂, 0 °C to rt, overnight, 67%; (d) CDI, THF, reflux, 1 h, then t-BuOK, CH₃NO₂, THF, 0 °C, 45 min, 68%; (e) SnCl₂, concd HCl, 60 °C, 2.5 h, then H₂S, rt, 75%; (f) H₂, Pd/C, MeOH, H₂O, rt, 16 h, 96%; (g) HC(OEt)₃, Me₂SO, 65 °C, 15 min, 81%; (h) N,N-bis(trimethylsilyl)trifluoroacetamide, pyr, CH₃CN, rt, overnight; (i) 2-deoxy-3,4-di-O-p-toluoyl-D-pentofuranosyl chloride, SnCl₄, DCE, CH₃CN, −50 °C, 45 min; (j) NaHCO₃, H₂O, rt, 0.5 h, 23% (over three steps); (k) NaOMe, MeOH, rt, 1 h; (l) NaBH₄, H₂O, MeOH, 25 °C, 30 min, 26% (over two steps).

Scheme 48.. Synthesis of Pentostatin 6^a

^aReagents and conditions: (a) (Me₃Si)₂NC(O)CF₃, pyr, MeCN, 12 h; (b) BF₃·Et₂O, DCM, 0 °C, 30 min; (c) TBAF, THF, 0 °C, 2 h; (d) NaBH₄, MeOH, H₂O, rt, 1 h.

Scheme 49.. Synthesis of Clofarabine 12^a

^aReagents and conditions: (a) KF, acetamide, 210 °C, 62%; (b) MeOH–0.7% H₂SO₄ (1:1 v/v); (c) BzCl in DCM, pyr, −15 °C, 80% (over two steps); (d) Amberlite IR-120 (H⁺), H₂O/dioxane, 80 °C, 78%; (e) KIO₄, H₂O; (f) NaOMe, MeOH; (g) Ac₂O, pyr, 80% (over three steps); (h) HBr/HOAc, DCM; (i) 2,6-dichloropurine, DCE, 100 °C, 32% (β-anomer); then NH₃/EtOH, steel bomb, 3 days, solvent switch to MeCN/H₂O, LiOH, 42%.

Scheme 50.. Synthesis of Clofarabine 12^a

^aReagents and conditions: (a) 0.5 M HBr, DCM, 0 °C; (b) H₂O, 81% (over two steps); (c) NaH, DMF, 0 °C, 0.5 h, then N,N′-sulfuryldiimidazole, −40 °C to rt, 2 h, 85%; (d) KHF₂, 2,3-butanediol, HF (50% in H₂O), 160 °C, 1 h, 63%; (e) HBr/HOAc, DCM, rt, 16 h, 98%; (f) 2-chloroadenine, CH₃CN, t-amyl alcohol, tert-BuOK, CaH₂, 50 °C, 40 min, then 279, DCE, 50 °C, 19 h, 50% (β/α = 80:1); (g) NaOMe, MeOH, 33 °C, 7 h, 64%.

Scheme 51.. Synthesis of Nelarabine 13^a

^aReagents and conditions: (a) 10 mM K₃PO₄, n-PrOH, H₂O, pH 6.75, uridine phosphorylase, purine nucleoside phosphorylase, 37 °C, 26 days, 17%.

Scheme 52.. Synthesis of Nelarabine 13^a

^aReagents and conditions: (a) NaH, MeCN; (b) MeONa, MeOH; (c) Pd/C, HCOONH₄, MeOH, reflux, 90 min, 91%.

Scheme 53.. Synthesis of Fludarabine 291 and Fludarabine-5′-monophosphate 7^a

^aReagents and conditions: (a) Hg(CN)₂, CaSO₄, MeNO₂, reflux, 3 h, 11%; (b) NaN₃, EtOH, H₂O, 1 h, 98%; (c) Pd/C, H₂, EtOH, rt, 6 h, 75%; (d) HBF₄, NaNO₂, CHCl₃, −10 °C, 40 min, 36%; (e) Na, NH₃, 34%; (f) POCl₃, PO(OEt)₃, 0 °C, 3.5 h, 96%.

Scheme 54.. Synthesis of Fludarabine 291 and Fludarabine-5′-monophosphate 7^a

^aReagents and conditions: (a) methoxyacetic anhydride, pyr, 88 °C, 1 h, then methyl ethyl ketone, overnight, 90%; (b) HCl (g), DCM, 4–6 °C, 2 h, quantitative; (c) DIPEA, DCE, reflux, overnight, quantitative; (d) NaOMe, MeOH, 68%; (e) POCl₃, TMP, 0 °C, 18 h, 56%.

Scheme 55.. Synthesis of Fludarabine 291 and Fludarabine-5′-monophosphate 7^a

^aReagents and conditions: (a) Enterobacter aerogenes, K₂HPO₄, H₂O, 60 °C, 24 h, 35%; (b) Ac₂O, 95 °C, 9 h, 87%; (c) NH₄OH, H₂O, MeOH, rt, 19 h, 74%.

Scheme 56.. Synthesis of 8-Chloroadenosine 28 and Tocladesine 50^a

^aReagents and conditions: (a) AcCl, m-CPBA, DMF, rt, 20 min, 40%; (b) POCl₃, PO(OEt)₃, 0 °C, 6 h, then aq NaOH, 2 h, 23%.

Scheme 57.. Synthesis of Forodesine Hydrochloride 36^a

^aReagents and conditions: (a) Br₂, K₂CO₃, H₂O, 5 °C to rt, overnight; (b) concd H₂SO₄, Me₂CO, reflux, 4 h, then 30 °C, 8 h, 55% (over two steps); (c) MsCl, Et₃N, DCM, −20 °C, 1 h, then rt, 8 h; (d) aq KOH, <30 °C, 4 h, 59% (over two steps); (e) TBDMSCl, imidazole, DMF, 20 °C, 4 h, 91%; (f) LiBH₄, THF, −30 °C to rt, 24 h, 75%; (g) (MeSO₂)₂O, pyr, 0 °C to rt, 18 h, 88%; (h) NaN₃, DMF, 100 °C, 2 h, 42%; (i) H₂, Pd, NaOAc, dioxane, 20 °C, 72 h, 94%; (j) NCS, pentane, rt, 1 h, then lithium tetramethylpiperidide (LiTMP), THF, −78 °C, 85%; (k) H₂NCH(CO₂C₂H₅)₂, NaOMe, MeOH, reflux, 4 h, 68%; (l) formamidine acetate, C₂H₅OH, reflux, 27 h, 61%; (m) aq KOH, reflux, 40 h, 74%; (n) POCl₃, reflux, 2 h; (o) BOMCl, NaH, THF, 0 °C to rt, 1 h, then NaH, MeOH, 1 h; (p) NBS, DCM, 52% (over three steps); (q) n-BuLi, −78 °C; (r) 307, −78 °C to 0 °C; (s) (Boc)₂O, DCM, rt, 1 h, 76% (over three steps); (t) H₂, Pd/C, 18 h, then NH₄OH, H₂O, 1 h; (u) concd HCl, MeOH, reflux, 1.5 h, 85% (over two steps).

Scheme 58.. Synthesis of Forodesine Hydrochloride 36^a

^aReagents and conditions: (a) PhCHO, TsOH; (b) PhSO₂Me, 59%; (c) OsO₄, Me CO; (d) DMP/H⁺ 2, 63%; (e) lithiated 9-deazahypoxanthine, anisole, Et₂O, −20 °C, 55%; (f) BBr₃, DCM; (g) BH₃·Me₂S, DMF; (h) MeOH/H⁺, 90%.

Scheme 59.. Early Synthesis of Triciribine 30 and Triciribine-5′-monophosphate 33^a

^aReagents and conditions: (a) CH₃NHNH₂, EtOH, rt, 3 min; (b) H₂O, reflux, 16 h; (c) POCl₃, PO(OMe)₃, 0 °C, 16 h, 21%;

Scheme 60.. Synthesis of Triciribine 30^a

^aReagents and conditions: (a) BSA, 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose, TMSOTf, CH₃CN, 80 °C, 80%; (b) Bu₃SnCN, Pd(PPh₃)₄, DMF, 95 °C, 6 h, 72%; (c) H₂NNHCH₃, C₂H₅OH, CHCl₃, rt, 3.5 h, 92%; (d) NaOMe, MeOH, rt, 1 h, then reflux, 18 h, 74%.

Scheme 61.. Synthesis of MLN4924 44^a

^aReagents and conditions: (a) Grubbs’ catalyst (2^nd generation), DCM, rt, 2 days, 95%; (b) PDC, DMF, rt, 2 days, 84%; (c) H₂, Pd/C, MeOH, rt, overnight, 100%; (d) NaBH₄, CeCl₃·H₂O, MeOH, 0 °C to rt, 0.5 h, 98%; (e) Me₃Al, DCM, 0 °C to rt, 2 days, 62%; (f) SOCl₂, Et₃N, 0 °C, 10 min, then RuCl₃·3H₂O, NaIO₄, CCl₄, CH₃CN, H₂O, 87%; (g) N⁶-indanyl-7-deazaadenine, NaH, 18-crown-6, THF, 80 °C, overnight, then concd HCl, 80 °C, 2 h, 65%; (h) PhOC(S)Cl, DMAP, DCM, rt, overnight, then Bu₃SnH, AIBN, PhMe, 110 °C, 1 h, 82%; (i) HF-pyridine, THF, pyr, rt, 1 h, 99%; (j) NH₂SO₂Cl, Et₃N, CH₃CN, 0 °C to rt, 1 h, 92%; (k) TFA, rt, 2 h, 90%.

Scheme 62.. Synthesis of MLN4924 44^a

^aReagents and conditions: (a) m-CPBA, DCM, 4 h, 76%; (b) 1-(dimethoxymethyl)-4-methoxybenzene, PPTS, rt, overnight, 78%; (c) (S)-(+)-1-aminoindan, DIPEA, 1-butanol, reflux, 60 h, 80%; (d) NaH, DMF, 110 °C, 2 h, 69%; (e) DMAP, PhOC(S)Cl, DCM, rt, 1 h, 99%; (f) AIBN, Bu₃SnH, PhMe, reflux, 30 min, 79%; (g) AcOH, THF, H₂O, rt, 60 h, 98%; (h) 1H-imidazole, DMAP, TBDMSCl, DMF, rt, 2 h, then DMAP, Ac₂O, pyr, rt, overnight, 86%; (i) HF-pyridine, THF, pyr, rt, 1 h, 80%; (j) chlorosulfonamide, Et₃N, MeCN, rt, 1 h, 94%; (k) NH₃/MeOH, rt, 5 days, 90%.

Scheme 63.. Synthesis of MLN4924 Hydrochloride 350^a

^aReagents and conditions: (a) Br₂, py, DME, H₂O, 0 °C, 68%; (b) LiBH₄, THF, H₂O, −5 °C; (c) 8.84 M HBr, i-PrOH, 55 °C; (d) H₂, Pd/C, DIPEA, MeOH, 25 °C, 80% (over three steps); (e) 2-(4,6-dichloropyrimidin-5-yl)acetaldehyde, Et₃N, i-PrOH, 75 °C, 78%; (f) (S)-(+)-1-aminoindane hydrochloride, DIPEA, 2-butanol, 130 °C, 81%; (g) 349, MeCN, 53 °C, 5 h, then HCl, 59%; (h) 1.25 M HCl, EtOH, crystallization, 93%.

Scheme 64.. Synthesis of EPZ-5676 43^a

^aReagents and conditions: (a) methyl 3-oxocyclobutanecarboxylate, Ti(O-iPr)₄, MeOH, 45 °C, 2 h, then NaCNBH₄, rt, overnight, 41%; (b) 2-iodopropane, K₂CO₃, CH₃CN, 95 °C, overnight, 86%; (c) DIBAL-H, DCM, −78 °C to rt, then ethyl 2-(diethoxyphosphoryl)acetate, DBU, LiCl, rt, 1 h, 83%; (d) Pd/C, MeOH, rt, overnight, 78%; (e) LiOH·H₂O, THF, MeOH, rt, overnight, 28%; (f) 4-(tert-butyl)benzene-1,2-diamine, EDC, HOBt, Et₃N, rt, overnight, 50%; (g) AcOH, 65 °C, overnight, 98%; (h) HCl/MeOH, rt, 2 h, then HPLC, 51%.

Scheme 65.. Synthesis of EPZ-5676 43^a

^aReagents and conditions: (a) BnBr, K₂CO₃, TBAI, Me₂CO, rt, 2 d, 92%; (b) Zn(Cu), ClCOCCl₃, CH₃OCH₂CH₂OCH₃, Et₂O, 50 °C, 3 days, 96%; (c) Zn, AcOH, 50 °C, 2 h, 93%; (d) H₂, Pd/C, (CH₃)₂CHCOOCH₃, PhMe, rt, 20 h, then DCHA, 20 °C, 18 h, 85%; (e) dioxane, DMF, (COCl)₂, 20 °C, 18 h, then 4-tert-butyl-2-nitroaniline, dioxane, 20–40 °C, 5 h, then 20 °C, 18 h, 89%; (f) Fe, AcOH, 75 °C then rt, overnight, 95%; (g) STAB, Me₂CO, MeOH, AcOH, 20 °C, 2 h, 95%; (h) STAB, MeCN, 55 °C, 16 h, 83%; (i) HCl, MeOH, 45 °C, 9 h then rt, overnight, 93%; (i) MeCN/H₂O, crystallization, 65%.

Scheme 66.. Synthesis of CF102 42^a

^aReagents and conditions: (a) TBDPSCl, DMAP, DMF, rt, 18 h, 55%;(b) BzCl, py-DCM, 0 °C to rt, 17 h, 99%; (c) n-Bu₄NF, THF, rt, 2 h, 89%; (d) RuO₂, NaIO₄, CHCl₃, CH₃CN, H₂O, rt, 2.5 h, 90%; (e) EDC, DMAP, MeOH rt, 3 h, 72%; (f) MeNH₂, THF, 50 °C, 15 h; (g) BzCl, py-DCM, rt, 3 h, 72% (over two steps); (h) Ac₂O, H₂SO₄, AcOH, rt, 15 h, 34%; (i) 3-iodobenzylamine·HCl, Et₃N, EtOH, rt, 5 d, 60%; (j) HMDS, (NH₄)₂SO₄, reflux, 4 h; (k) TMSOTf, DCE, reflux, 62 h, 33%; (l) NH₃/MeOH, rt, 16 h, 69%.

Scheme 67.. Synthesis of CF102 42^a

^aReagents and conditions: (a) BSA, TMSOTf, CH₃CN, 2,6-dichloropurine, 50 °C, 18 h, 88%; (b) 3-iodobenzyl amine, Et₃N, EtOH, rt, 2 d, 85%; (c) NaOMe, MeOH, DCM, rt, 1 h, 92%; (d) 2,2-dimethoxypropane, TsOH, DMF, rt, 12 h, 95%; (e) PDC, DMF, rt, 18 h, 70%; (f) MeNH₂·HCl, HOBt, EDAC, DIEA, DCM, DMF, rt, 12 h, 71%; (g) 80% HCO₂H, rt, 12 h, 83%.

Scheme 68.. Synthesis of Ganciclovir 387^a

^aReagents and conditions: (a) BnOH, aq NaOH, rt, 16 h, 63%; (b) HCl (g), (CH₂O)_n, DCM, 0 °C, 16 h; (c) KOAc, Me₂CO, rt, 16 h, ~100%; (d) Diacetylguanine, TsOH, sulfolane, 95 °C, 5 days, 31% (N₉-isomer); (e) 20% Pd(OH)₂/C, cyclohexene–EtOH, reflux, 32 h; (f) NH₄OH–MeOH (1:1 v/v), rt, 16 h, 86% (2 steps).

Scheme 69.. Synthesis of 389^a

^aReagents and conditions: (a) TsOH, DMF, 95–100 °C, 40 h; (b) Crystallization, 70% (N₉-isomer).

Scheme 70.. Synthesis of Valganciclovir Hydrochloride 35^a

^aReagents and conditions: (a) TrCl, DMAP, Et₃N, DMF, 50 °C, overnight; (b) Boc-l-valine, DCC, DMAP, Et₃N, DCM, rt, 16.5 h; (c) TFA, TFE, 20 °C, 5 h; (d) H₂, Pd/C, then HCl/MeOH, 34% (over four steps).

Scheme 71.

Preparation of Valganciclovir Hydrochloride 35

Scheme 72.. Synthesis of Valacyclovir Hydrochloride 17^a

^aReagents and conditions: (a) Cbz-L-val-OH, DCC, DMAP, DMF, 60 °C to rt, 12 h; (b) Pd/C, H₂, MeOH, THF, aq HCl, 55% (over two steps); (c) SO₂Cl₂, imidazole, MeCN; (d) l-valine, CuSO₄, K₂CO₃, MeCN; (e) Acyclovir, DCC, DMAP, DMF, 10–15 °C, 45 min, 82%; (f) Raney Ni, EtOH, 50–60 °C then aq HCl, 82%.

Scheme 73.. Synthesis of Ribavirin 40^a

^aReagents and conditions: (a) SnCl₄, DCM, 15–20 ° C, then reflux, 2 h, 70%; (b) NaOMe/MeOH, 10 °C, 3 h then NH₃/MeOH, 20 °C, 4 h, 79%.

Scheme 74.. Large-Scale Synthesis of Ribavirin 40^a

^aReagents and conditions: (a) TfOH, 135 °C, 2 h, vacuum, 92%; (b) NH₃/MeOH, 20 °C, 40 h, 83%.

Scheme 75.. Synthesis of Ribavirin 40^a

^aReagents and conditions: (a) Phosphopentomutase, purine nucleoside phosphorylase, tris-buffer, 100%.

Scheme 76.. Synthesis of Acadesine 41^a

^aReagents and conditions: (a) cat. HCl, MeOH; (b) BzCl, pyr, DCM; (c) HBr/HOAc; (d) Ac₂O, pyr, 48 h, 57% (from D-ribose); (e) HCl/ether, rt, 7 days; (f) AgCl, xylene, reflux, 1 h; (g) NH₃/MeOH, 90 h, 19% (406a:406b = 1:1); (h) H₂ (1 atm), PtO₂, H₂O, 1 h, 12%.

Scheme 77.. Synthesis of Acadesine 41^a

^aReagents and conditions: (a) MEMCl, DIPEA, DCM, 0 °C, 65 min, 86%; (b) NH₄OH, MeOH, rt, 1 h; (c) aq NaOH, reflux, 1 h, 73%.