123318-82-1

Basic information

• Product Name: Clofarabine
• Synonyms: 2-CHLORO-2'-ARABINOFLUORO-2'-DEOXYADENOSINE;5-(6-amino-2-chloro-purin-9-yl)-4-fluoro-2-(hydroxymethyl)oxolan-3-ol;CLOFARABINE;CAFDA;2-chloro-9-(2-deoxy-2-fluoroarabinofuranosyl)adenine;2-chloro-9-(2-deoxy-2-fluoro-beta-d-arabinofuranosyl)-9h-purin-6-amin;2-chloro-9-(2-deoxy-2-fluoro-beta-d-arabinofuranosyl)adenine;Clolar
• CAS NO: 123318-82-1
• Molecular Formula: C₁₀H₁₁ClFN₅O₃
• Molecular Weight: 303.68
• EINECS: 2017-001-1
• Product Categories: Inhibitors;Intermediates & Fine Chemicals;Pharmaceuticals;Bases & Related Reagents;Nucleotides;Pharmaceutical intermediate;CLOLAR;Antineoplastic;Anti-cancer&immunity
• Mol File: 123318-82-1.mol

Chemical Properties

• Melting Point: 228-2310C
• Boiling Point: 550 °C at 760 mmHg
• Flash Point: 286.4 °C
• Appearance: white/Powder
• Density: 1.4804 (estimate)
• Vapor Pressure: 3.19E-15mmHg at 25°C
• Refractive Index: 1.843
• Storage Temp.: Desiccate at +4°C
• Solubility: DMSO: >10mg/mL
• PKA: 12.56±0.70(Predicted)
• Merck: 14,2372
• CAS DataBase Reference: Clofarabine(CAS DataBase Reference)
• NIST Chemistry Reference: Clofarabine(123318-82-1)
• EPA Substance Registry System: Clofarabine(123318-82-1)

Safety Data

• Hazard Codes: T
• Statements: 25
• Safety Statements: 45
• RIDADR: UN 2811 6.1 / PGIII
• WGK Germany: 2
• RTECS: UD7473000
• HazardClass: 6.1
• Hazardous Substances Data: 123318-82-1(Hazardous Substances Data)

Usage

Uses

Used in Oncology:
Clofarabine is used as an antimetabolite antineoplastic agent for the treatment of relapsed or refractory acute lymphoblastic leukemia. Its higher potency compared to other purine nucleoside analogs is attributed to the higher efficiency of its phosphorylation by deoxycytidine kinase and the longer intracellular half-life of the triphosphate metabolite (＞24 h).
Used in Research:
Clofarabine has been used in cell viability assays to analyze the sensitivity of isogenic cell lines towards the drug. Additionally, it is used to study the interaction of the anticancer drug clofarabine with human serum albumin and human α-1 acid glycoprotein, which can provide insights into its pharmacokinetics and potential applications in cancer treatment.

Anti-cancer drugs

Clofarabine is a novel purine nucleoside anticancer drugs is first successfully developed by the Top10 biopharmaceutical company of the United States---Genzyme Corporation, NASDAQ: GENZ) with the trade names being “Clofarabine”. On December 28, 2004 the US food and Drug Administration (FDA) used fast-track for approval of clofarabine for application to children with refractory or relapsed acute lymphocytic leukemia. It is currently the only available drugs for the special treatment of children with acute myelogenous leukemia (ALL); it has an excellent efficacy on the treatment of leukemia with well tolerance and no unpredictable adverse reactions. It can be administrated through either administered intravenously or administered orally. This drug is the first product approved for being dedicated to the treatment of the children's leukemia in more than ten years.

Pharmacological effects

Clofarabine has also combined the advantages of fludarabine and cladribine that can inhibit both DNA polymerase as well as inhibit ribonucleotide reductase with strong anti-cancer activity against different cell lines and tumor models. Early studies have also shown that the product, when having a concentration of micromolar or less, can already effectively inhibit the proliferation of human CNS tumors, lung cancer, kidney cancer, and leukemia and melanoma cell lines. In vivo and in vitro experiments have showed that clofarabine can induce apoptosis of leukemia cells with the mechanism being the down-regulation of de-phosphorylation of BCL-2 family proteins BCL-X and MCL-1 as well as the AKT. Its inhibitory effect on the human leukemia cells K-562 is stronger than cladribine and fluorine with the IC50 being 5 nmol/L while the IC50 for cladribine and fluorine is 16 nmol/L and 460nmol/L, respectively. Preclinical and drug combination experiments have showed that clofarabine, similar as other deoxynucleotide analogs as well as other types of anti-cancer drugs such as Etoposide, can enhance the activity of the deoxycytidine kinase in normal or abnormal human lymphocytes, and therefore increasing the anti-cancer effect.

Dosage

Clofarabine belongs to the anticancer drug which affects tubulin and is mainly used for clinical treatment of the following diseases: 1. treatment of relapsed or refractory acute lymphocytic leukemia; 2. it also has efficacy in treating acute myeloid leukemia and myelodysplastic syndrome (MDS) in older patients and can be used in combination with cytarabine. General adult dose: 1. relapsed or refractory acute lymphoblastic leukemia: suitable for the patient (1 to 21 years) should have previously received at least two kinds of treatment programs; take 52 mg/m2 daily X 5 days, have intravenous injection (more than 2 hours) until the organ get function recovery or return back to the baseline level, repeat 1 time every 2 to 6 weeks. 2. Acute myeloid leukemia and MDS: daily 52 mg/m2 × 5 days, have intravenous infusion for 1 hour; After 4 hours, administer cytarabine with 1 g(daily)/m2 X 5 days, perform intravenous infusion for 2 hours, it has positive effect for the newly diagnosed elderly patients with acute myelogenous leukemia and high-risk MDS. Child: It can be used for treating refractory and relapsed acute lymphocytic leukemia with the same amount for adults. For the treatment of the refractory and relapsed acute non-lymphocytic leukemia, use daily 52mg/m2 × 5 days, perform intravenous infusion (more than 2 hours) and repeat the treatment per 2-6 weeks depending on the reaction and toxicity in patients. The above information is edited by the lookchem of Dai Xiongfeng.

Adverse reactions and precautions

Common adverse reactions about clofarabine are as follows: Blood system: leukocytes and neutropenia, thrombocytopenia, anemia. Digestive system: loss of appetite, nausea, vomiting, abdominal pain, constipation; stomatitis, gingival bleeding, sore throat. Nervous System: fatigue, drowsiness, headache, dizziness; anxiety, depression; irritability, excitability. Cardiovascular System: tachycardia, hypertension, hypotension, transient systolic dysfunction of the left ventricular; the drug should be discontinued upon any causes of hypotension; it was occasionally observed in pediatric patient of capillary leak syndrome and systemic inflammatory response syndrome (SIRS) which can be prevented by administration of hormone during the 1st to 3rd day of treatment. During the medication, once the above syndrome occurs, it should be discontinued immediately and combined with concurrent support treatment. Once the condition is stabilized and the organ gets function recovery, the patients can re-initiate the administration from low dosage. Liver toxicity: reversible liver damage, increased level of aspartate aminotransferase, alanine aminotransferase and bilirubin; hepatomegaly and jaundice. Respiratory system: respiratory distress, coughing, pleural effusions. Urogenital: hematuria, secondary hyperuricemia, elevated level of serum creatinine and creatine. Other: dermatitis, erythema; muscle pain, joint pain; fever and infection. [Note] women of childbearing age should take care of contraception during medication, lactation women should stop breastfeeding. Patients of hypotension, dehydration, liver and kidney dysfunction as well as secondary infection of bone marrow suppression should take with caution. Clofarabine may cause tumor lysis syndrome and should drawn attention.

Flammability and hazard characteristics

It is combustible with fire decomposition releasing toxic nitrogen oxides; fluorides and chlorides fume.

Storage characteristics

warehouse: low-temperature, dry and ventilated.

Extinguishing media

Water, carbon dioxide, dry, sandy soil.

Originator

Southern Research Institute (US)

Biological Activity

Deoxycytidine kinase (dCK) substrate. Phosphorylated to form clofarabine triphosphate, which competes with dATP for DNA polymerase- α and - ε and potently inhibits ribonucleotide reductase (IC 50 = 65 nM). Induces apoptosis by directly altering mitochondrial transmembrane potential. Demonstrates growth inhibition and cytotoxic activity in a variety of leukemias and solid tumors.

Biochem/physiol Actions

Clofarabine is a second-generation nucleoside analog, used in cancer treatments. Clofarabine is metabolized to 5′-triphosphate and is known to block DNA synthesis. The human equilibrative nucleoside transporters (hENT1 and hENT2) and human concentrative nucleoside transporter (hCNT2 and hCNT3) mediates clofarabine transport into the cell. It also serves as a substrate for mitochondrial deoxyguanosine kinase. Clofarabine is an inhibitor of ribonucleotide reductase. It resists the phosphorolytic cleavage catalyzed by purine nucleoside phosphorylase of bacterias. Clofarabine also withstands deamination by adenosine deaminase.

Synthesis

The drug was discovered by Ilex oncology (now Genzyme) and currently marketed by Genzyme [3,6]. Several routes to the synthesis of clofarabine have been published, including a process scale-up chemistry as shown in the Scheme. Treatment of commercially available 2-deoxy-2-β-fluoro-1,3,5-tri- O-benzoyl-1-R-D-arabinofuranose (6) with 33%HBr in acetic acid provided the bromo sugar 7 in 88% yield. The bromide 7 was reacted with 2-chloroadenine (8) in optimized mixed solvent system in the presence of calcium hydride and potassium t-butoxide to give the desired β-anomeric product 9 in 50:1 ratio. Deprotection of the benzoyl groups with sodium methoxide then provided clofarabine (II).

InChI:InChI=1/C10H11ClFN5O3/c11-10-15-7(13)5-8(16-10)17(2-14-5)9-4(12)6(19)3(1-18)20-9/h2-4,6,9,18-19H,1H2,(H2,13,15,16)/t3-,4-,6?,9-/m1/s1

Synthetic route

6-amino-2-chloro-9-(2'-deoxy-2'-fluoro-3',5'-di-O-benzoyl-β-D-arabinofuranosyl)-9H-purine (355138-50-0) → clofarabine (123318-82-1)

Conditions	Yield
With methanol; sodium methylate at 15 - 20℃; for 2h;	95.41%
With methanol; sodium methylate at 20℃; for 2h; pH=9 - 10; Reagent/catalyst; Green chemistry;	95.5%
With methanol; sodium methylate at 0℃; for 2h;	95.5%

6-amino-2-chloro-9-(2-deoxy-2-fluoro-3,5-di-O-(triisopropylsilyl)-β-D-arabinofuranosyl)-9H-purine (1234346-14-5) → clofarabine (123318-82-1)

Conditions	Yield
With tetramethylammonium fluoride; acetic acid In N,N-dimethyl-formamide at 20℃;	90%
With tetramethylammonium fluoride; acetic acid In N,N-dimethyl-formamide at 20℃;	90%

C25H19ClF3N5O8S → clofarabine (123318-82-1)

Conditions	Yield
With ammonia In methanol at 60℃; for 5h;	90%

2-chloro-6-heptanoylamido-9-(2-deoxy-2-fluoro-3,5-di-O-benzoyl-β-D-arabinofuranosyl)-9H-purine → clofarabine (123318-82-1)

Conditions	Yield
	60%

2-deoxy-2-fluoro-α,β-D-arabinofuranose 1-phosphate + 2-chloroadenine (1839-18-5) → clofarabine (123318-82-1)

Conditions	Yield
With recombinant E.coli purine nucleoside phosphorylase In water at 52℃; for 168h; Enzymatic reaction;	42%

2,6-dichloro-9-(3-O-acetyl-5-O-benzoyl-2-deoxy-2-fluoro-β-D-arabinofuranosyl)-9H-purine (103884-99-7) → clofarabine (123318-82-1)

Conditions	Yield
With lithium hydroxide; ammonia 1.) ethanol, RT, 3 d, 2.) acetonitrile, RT, 3 h; Yield given. Multistep reaction;

2-chloro-9-(3',5'-di-O-benzoyl-β-D-ribofuranosyl)adenine (1353040-42-2) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 3 steps 1.1: pyridine / dichloromethane / 0 - 20 °C / Inert atmosphere 2.1: guanidine carbonate / dichloromethane; ethyl acetate / 60 °C 2.2: 80 °C 3.1: sodium methylate; methanol / 30 - 40 °C View Scheme
Multi-step reaction with 3 steps 1: pyridine; dichloromethane / 0 - 20 °C / Inert atmosphere 2: guanidine hydrogen carbonate; triethylamine hydrofluoride / ethyl acetate / 20 - 80 °C 3: sodium methylate / methanol / 30 - 40 °C View Scheme
Multi-step reaction with 3 steps 1: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 2: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 3: sodium methylate / methanol / 0.5 h / 30 °C View Scheme

6-amino-2-chloro-9-(2',3',5'-tri-O-benzoyl-β-D-ribofuranosyl)-9H-purine (1055168-98-3) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 4 steps 1.1: pyridine; hydrazine hydrate; acetic acid / 75 - 80 °C / Inert atmosphere 2.1: pyridine / dichloromethane / 0 - 20 °C / Inert atmosphere 3.1: guanidine carbonate / dichloromethane; ethyl acetate / 60 °C 3.2: 80 °C 4.1: sodium methylate; methanol / 30 - 40 °C View Scheme
Multi-step reaction with 4 steps 1.1: pyridine; hydrazine hydrate; acetic acid / 75 - 80 °C / Inert atmosphere 1.2: 65 °C 2.1: pyridine / dichloromethane / 0 - 20 °C / Inert atmosphere 3.1: guanidine carbonate / dichloromethane; ethyl acetate / 60 °C 3.2: 80 °C 4.1: sodium methylate; methanol / 30 - 40 °C View Scheme
Multi-step reaction with 4 steps 1: hydrazine / pyridine; acetic acid / 20 - 80 °C / Inert atmosphere 2: pyridine; dichloromethane / 0 - 20 °C / Inert atmosphere 3: guanidine hydrogen carbonate; triethylamine hydrofluoride / ethyl acetate / 20 - 80 °C 4: sodium methylate / methanol / 30 - 40 °C View Scheme

2-chloro-9-(3',5'-di-O-benzoyl-2'-O-trifluoromethylsulfonyl-β-D-ribofuranosyl)adenine (1353040-43-3) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 2 steps 1: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 2: sodium methylate / methanol / 0.5 h / 30 °C View Scheme

2-deoxy-2-fluoro-3,5-di-O-benzoyl-α-D-arabinofuranosyl bromide (97614-44-3) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 2 steps 1: sodium iodide / acetonitrile; tert-Amyl alcohol / 24 h / 20 °C / Inert atmosphere 2: sodium methylate / methanol / 7 h / 33 °C / Inert atmosphere View Scheme
Multi-step reaction with 2 steps 1.1: potassium tert-butylate / acetonitrile; 1,2-dichloro-ethane; tert-Amyl alcohol / 19 h / 50 °C / Inert atmosphere 2.1: sodium methylate / methanol / 5 h / 20 °C / Inert atmosphere 2.2: 20 - 64 °C View Scheme
Multi-step reaction with 3 steps 1: calcium hydride; sodium hydride / dichloromethane; acetonitrile / 20 °C / Inert atmosphere 2: ammonia / acetonitrile / 20 °C 3: sodium methylate / methanol / 0.67 h / 30 - 35 °C View Scheme

2-deoxy-2-fluoro-α,β-D-arabinofuranose 1-phosphate (2Li+ SALT) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 2 steps 1: hydrogenchloride / water / pH 7.5 2: recombinant E.coli purine nucleoside phosphorylase / water / 168 h / 52 °C / Enzymatic reaction View Scheme

2-chloroadenine (1839-18-5) + 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl)uracil (69123-94-0) → clofarabine (123318-82-1)

Conditions	Yield
Stage #1: 2-chloroadenine; 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl)uracil In aq. buffer at 50℃; for 0.5h; pH=6.5; Stage #2: With nucleoside deoxyribosyltransferase enzyme (NDT enzyme) In aq. buffer at 50℃; Concentration; Solvent; Temperature; Enzymatic reaction;

2-Chloroadenosine (146-77-0) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 4 steps 1.1: pyridine / acetonitrile / 0.5 h / -5 - 5 °C 1.2: Reflux 2.1: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 3.1: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 4.1: sodium methylate / methanol / 0.5 h / 30 °C View Scheme
Multi-step reaction with 4 steps 1: pyridine / acetonitrile / 0.5 h / -5 - 5 °C 2: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 3: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 4: sodium methylate / methanol / 0.5 h / 30 °C View Scheme

G (118-00-3) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 5 steps 1.1: hydrogenchloride; potassium dihydrogenphosphate; potassium hydroxide / water; dimethyl sulfoxide / 4 h / 58 - 61 °C / pH 7.1-7.2 / Enzymatic reaction 2.1: pyridine / acetonitrile / 0.5 h / -5 - 5 °C 2.2: Reflux 3.1: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 4.1: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 5.1: sodium methylate / methanol / 0.5 h / 30 °C View Scheme
Multi-step reaction with 5 steps 1: hydrogenchloride; potassium dihydrogenphosphate; potassium hydroxide / water; dimethyl sulfoxide / 4 h / 58 - 61 °C / pH 7.1-7.2 / Enzymatic reaction 2: pyridine / acetonitrile / 0.5 h / -5 - 5 °C 3: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 4: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 5: sodium methylate / methanol / 0.5 h / 30 °C View Scheme

uridine (58-96-8) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 5 steps 1.1: hydrogenchloride; potassium dihydrogenphosphate; potassium hydroxide / water; dimethyl sulfoxide / 4 h / 58 - 61 °C / pH 7.1-7.2 / Enzymatic reaction 2.1: pyridine / acetonitrile / 0.5 h / -5 - 5 °C 2.2: Reflux 3.1: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 4.1: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 5.1: sodium methylate / methanol / 0.5 h / 30 °C View Scheme
Multi-step reaction with 5 steps 1: hydrogenchloride; potassium dihydrogenphosphate; potassium hydroxide / water; dimethyl sulfoxide / 4 h / 58 - 61 °C / pH 7.1-7.2 / Enzymatic reaction 2: pyridine / acetonitrile / 0.5 h / -5 - 5 °C 3: pyridine / dichloromethane / 0.5 h / -10 - 0 °C / Inert atmosphere 4: N-ethyl-N,N-diisopropylamine; triethylamine tris(hydrogen fluoride) / toluene / 48 h / 35 - 40 °C 5: sodium methylate / methanol / 0.5 h / 30 °C View Scheme

1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose (14215-97-5) → clofarabine (123318-82-1)

Conditions	Yield
Multi-step reaction with 3 steps 1.1: hydrogen bromide; tetrabutyl ammonium fluoride / tetrahydrofuran / 3 h / Cooling with ice 1.2: 2 h 2.1: potassium tert-butylate; calcium hydride / acetonitrile; tert-butyl alcohol / 1 h / 60 °C 2.2: 10 h / 60 °C 3.1: sodium methylate; methanol / 2 h / 0 °C View Scheme

clofarabine (123318-82-1) + tert-butyldimethylsilyl chloride (18162-48-6) → 6-amino-2-chloro-9-(2'-deoxy-2'-fluoro-3',5'-di-O-tert-butyldimethylsilyl-β-D-arabinofuranosyl)-9H-purine

Conditions	Yield
With 1H-imidazole In N,N-dimethyl-formamide at 20℃;	93%

clofarabine (123318-82-1) + tert-butylchlorodiphenylsilane (58479-61-1) → (2R,3R,4S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)-2-(((tert-butyldiphenylsilyl)oxy)methyl)-4-fluorotetrahydrofuran-3-ol

Conditions	Yield
With 1H-imidazole In N,N-dimethyl-formamide at 0 - 20℃; Inert atmosphere;	91%
With 1H-imidazole In N,N-dimethyl-formamide at 0 - 20℃; for 8h;	4.1 g
With 1H-imidazole In N,N-dimethyl-formamide at 0 - 20℃; for 8h;	4.1 g

1,3-Dichloro-1,1,3,3-tetraisopropyldisiloxane (69304-37-6) + clofarabine (123318-82-1) → 2-chloro-9-[2-deoxy-2-fluoro-3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-β-D-arabinofuranosyl]adenine (1450815-72-1) + 2-chloro-9-[2-deoxy-2-fluoro-5-O-(1-hydroxy-1,1,3,3-tetraisopropyldisiloxane-3-yl)-β-D-arabinofuranosyl]adenine (1450815-73-2) + C32H48Cl2F2N10O7Si2 (1450815-74-3)

Conditions	Yield
With pyridine at 20℃; for 24h;	A 87% B 9% C 2%

clofarabine (123318-82-1) → 9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)adenine (20187-82-0, 20227-41-2, 64183-27-3, 123334-75-8)

Conditions	Yield
With ammonia; hydrogen; palladium on activated charcoal In ethanol; water at 20℃; for 18h;	82%
With palladium 10% on activated carbon; hydrogen In methanol at 20℃; for 48h;	57%

phosphoric acid-(2R-decyloxy-3-dodecyoxo)propyl ester + clofarabine (123318-82-1) → [2-chloro-9-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl)adenine]-5'-phosphoric acid-(2R-decyloxy-3-dodecyloxy)propyl ester

Conditions	Yield
Stage #1: phosphoric acid-(2R-decyloxy-3-dodecyoxo)propyl ester With pyridine; 2,4,6-triisopropylphenylsulfonyl chloride at 20 - 25℃; for 1h; Inert atmosphere; Stage #2: clofarabine for 20h; Inert atmosphere; Stage #3: With sodium methylate In methanol pH=7; Inert atmosphere;	76%

benzoyl chloride (98-88-4) + clofarabine (123318-82-1) → 2-chloro-N6-benzoyl-9-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl)adenine

Conditions	Yield
Stage #1: clofarabine With pyridine; chloro-trimethyl-silane at 0℃; for 0.5h; Stage #2: benzoyl chloride at 20℃; for 24h;	76%

clofarabine (123318-82-1) + p-toluenesulfonyl chloride (98-59-9) → ((2R,3R,4S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)-4-fluoro-3-hydroxytetrahydrofuran-2-yl)methyl 4-methylbenzenesulfonate

Conditions	Yield
With pyridine at 0 - 20℃; for 24h;	76%

clofarabine (123318-82-1) + phenyl(benzyloxy-L-alaninyl)phosphorochloridate (183370-70-9) → CPF448

Conditions	Yield
With pyridine; 1-methyl-1H-imidazole In tetrahydrofuran at -80 - 20℃; for 12.2667h;	66%

P,P'-methanediyl-bis-phosphonic acid tetrachloride (1499-29-2) + clofarabine (123318-82-1) → C11H12ClFN5O8P2(3-)*3Na(1+)

Conditions	Yield
Stage #1: P,P'-methanediyl-bis-phosphonic acid tetrachloride; clofarabine With triethyl phosphate at 0℃; Inert atmosphere; Stage #2:	63%

di-tert-butyl dicarbonate (24424-99-5) + clofarabine (123318-82-1) → (2R,3R,4S,5R)-5-(6-amino-2-chloropurin-9-yl)-3-tert-butyloxycarbonyloxy-4-fluoro-2-(hydroxymethyl)oxolane

Conditions	Yield
With sodium hydroxide In tetrahydrofuran; water at 20℃; for 18h;	58%
With sodium hydroxide In tetrahydrofuran; water at 20℃; for 18h;	58%

clofarabine (123318-82-1) → 6-Amino-9-((2R,3S,4R,5R)-3-fluoro-4-hydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-3,9-dihydro-purin-2-one

Conditions	Yield
With lithium hydroxide; dihydrogen peroxide In water at 60℃; for 24h;	48%

sodium methylate (124-41-4) + clofarabine (123318-82-1) → C11H14FN5O4

Conditions	Yield
In methanol at 60℃; for 168h; Inert atmosphere;	48%

clofarabine (123318-82-1) → C10H12FN5O4

Conditions	Yield
With dihydrogen peroxide; lithium hydroxide In water at 60℃; for 24h; Inert atmosphere;	48%

phosphoric acid-(2S-decyloxy-3-dodecyloxoy)propyl ester + clofarabine (123318-82-1) → [2-chloro-9-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl)adenine]-5'-phosphoric acid-(2S-decyloxy-3-dodecyloxy)propyl ester

Conditions	Yield
Stage #1: phosphoric acid-(2S-decyloxy-3-dodecyloxoy)propyl ester With pyridine; 2,4,6-triisopropylphenylsulfonyl chloride at 20 - 25℃; Inert atmosphere; Stage #2: clofarabine Inert atmosphere; Stage #3: With sodium methylate In methanol pH=7; Inert atmosphere;	28%

clofarabine (123318-82-1) → C10H10ClN5O3

Conditions	Yield
With sodium hydroxide In dimethyl sulfoxide at 54℃; for 3.5h; Inert atmosphere;	25%

C13H19ClNO4P*ClH + clofarabine (123318-82-1) → C23H29ClFN6O7P

Conditions	Yield
With copper(II) bis(trifluoromethanesulfonate); triethylamine In tetrahydrofuran at 20℃; for 12h;	15%

2-fluoro-9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)-9H-purin-6-amine (134217-15-5) + clofarabine (123318-82-1) → C20H21ClF2N10O6

Conditions	Yield
With sodium hydroxide In water at 80℃; for 1.9h; Inert atmosphere;	0.8%

clofarabine (123318-82-1) → 2-chloroadenine (1839-18-5) + 2-deoxy-2-fluoro-α-D-arabinofuranose 1-phosphate (850883-62-4)

Conditions	Yield
With E. coli purine nucleoside phosphorylase Enzyme kinetics; Substitution;

clofarabine (123318-82-1) → (2R,3R,4S,5R)-5-(6-benzamido-9H-purin-9-yl)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)-4-fluorotetrahydrofuran-3-yl (2-cyanoethyl) diisopropylphosphoramidite

Conditions	Yield
Multi-step reaction with 2 steps 1.1: 82 percent / H2; NH3 / Pd/C / ethanol; H2O / 18 h / 20 °C 2.1: pyridine / 18 h / 20 °C 2.2: 72 percent / pyridine / 18 h / 20 °C View Scheme

Upstream product

• 103884-99-7 2,6-dichloro-9-(3-O-acetyl-5-O-benzoyl-2-deoxy-2-fluoro-β-D-arabinofuranosyl)-9H-purine 
• 355138-50-0 6-amino-2-chloro-9-(2'-deoxy-2'-fluoro-3',5'-di-O-benzoyl-β-D-arabinofuranosyl)-9H-purine 
• 97614-43-2 1,3,5-tri-O-benzoyl-2-deoxy-2-fluoro-α-D-arabinofuranose 
• 75788-35-1 9-Trimethylsilyl-2,6-dichlorpurin 
• 5451-40-1 2,6 dichloropurine 
• 329187-80-6 ((2R,3R,4S,5R)-3-(benzoyloxy)-5-(2,6-dichloro-9H-purin-9-yl)-4-fluorotetrahydrofuran-2-yl)methyl benzoate 
• 1234346-14-5 6-amino-2-chloro-9-(2-deoxy-2-fluoro-3,5-di-O-(triisopropylsilyl)-β-D-arabinofuranosyl)-9H-purine 
• 6974-32-9 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose 
• 1839-18-5 2-chloroadenine 
• 1353040-42-2 2-chloro-9-(3',5'-di-O-benzoyl-β-D-ribofuranosyl)adenine 
• 1055168-98-3 6-amino-2-chloro-9-(2',3',5'-tri-O-benzoyl-β-D-ribofuranosyl)-9H-purine 
• 1353040-43-3 2-chloro-9-(3',5'-di-O-benzoyl-2'-O-trifluoromethylsulfonyl-β-D-ribofuranosyl)adenine 
• 97614-44-3 2-deoxy-2-fluoro-3,5-di-O-benzoyl-α-D-arabinofuranosyl bromide 
• 69123-94-0 1-(2'-deoxy-2'-fluoro-β-D-arabinofuranosyl)uracil 

Downstream Products

• 1839-18-5 2-chloroadenine 
• 850883-62-4 2-deoxy-2-fluoro-α-D-arabinofuranose 1-phosphate 
• 20187-82-0 9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)adenine 
• 1450815-87-8 C₄₅H₇₇ClFN₅O₁₀P^(1-)*Na⁽¹⁺⁾ 

Relevant articles and documents

A new process for antineoplastic agent clofarabine

Clofarabine is a promising DNA polymerase inhibitor currently in clinical trials for a variety of liquid and solid tumor indications. The efforts for development of a new manufacturing process for clofarabine are presented. This new process allows for the reliable and efficient production of drug substance in high anomeric excess and high overall purity, without using chromatography. The high anomeric selectivity is achieved by reacting 2-chloroadenine with 1-bromo-2-deoxy-2-fluoro-3,5-di-O-benzoyl-α-D-ribofuranose (4) and potassium tert-butoxide in a mixture of three solvents. Following crystallization, anomeric ratios exceeding 50 (β/α) are achieved. Deprotection and additional crystallization afford a clofarabine drug substance containing less than 0.1% of the α-anomer.

A green synthetic clofarabine pharmaceutical intermediates (by machine translation)

The invention relates to a green synthetic clofarabine medical intermediates, in particular comprises the following steps: The formula II compound is dissolved in the organic solvent, under ice bath by adding 40% of the hydrobromic, tetrabutyl ammonium fluoride, stirring for 3 hours, adding triethylamine three [...], continuing to stir 2 - 3 hours, [...] I compound. (by machine translation)

Green synthesizing technology of clofarabine

The invention relates to a green synthesizing technology of clofarabine which comprises the following steps: (the structural formula is shown in the description), dissolving a compound which is shownin formula II into an organic solvent, adding 40% of hydrobromic acid and tetrabutylammonium fluoride in an ice bath, performing stirring reaction for 3 hours, adding triethylamine trihydrofluoride and continuing the stirring reaction for 2 to 3 hours to obtain a compound which is shown in formula I; (2) dissolving a compound which is shown in formula III into acetonitrile, adding potassium tert-butoxide, calcium hydride and tert-butyl alcohol, heating to 60 DEG C, reacting for 1 hour, adding the compound which is shown in the formula I, keeping at 60 DEG C and continuing reacting for 10 hoursto obtain a compound which is shown in formula IV; (3) removing Bz in the compound which is shown in the formula IV under an alkaline condition to obtain a compound which is shown in a formula V, namely the clofarabine.

Method for synthesizing clofarabine

The invention discloses a method for synthesizing clofarabine; the method comprises the following synthetic routes described in the specification, wherein in the formula III and the formula IV, R1 and R2 are the same or different acyl groups. The method comprises the following steps: 1) ammoniation: dissolving a compound represented by the formula III in an organic solvent, introducing ammonia gas, and carrying out a closed reaction, to obtain a compound represented by the formula IV after the reaction is completed, wherein the organic solvent is any combination of one or two or more of acetonitrile, ethyl acetate, dichloromethane and tetrahydrofuran, the concentration of ammonia gas dissolved in the organic solvent is 0.1-20 wt%, the closed reaction is carried out for 10-40 hours, and the reaction temperature is 0-100 DEG C; and 2) protecting group removal: dissolving the compound represented by the formula IV and prepared in the step 1) in alcohol, adding an alcohol solution of sodium alkoxide, carrying out a reaction, then adjusting the pH value to 6-7, cooling and crystallizing, and thus obtaining a clofarabine crude product.

METHOD FOR THE SYNTHESIS OF CLOFARABINE

The present invention relates to a method for the high yield production of the anticancer nucleoside clofarabine, the method comprising the preparation of 2-chloroadenosine by enzymatic transglycosylation between 2-chloroadenine and nucleosides, benzoylation, isomerization, sulfonate ester formation, fluorination, and deprotection.

Stereoselective synthesis of 2′-modified nucleosides by using ortho-alkynyl benzoate as a gold(i)-catalyzed removable neighboring participation group

In the present paper, we report a novel strategy for highly efficient stereoselective synthesis of 2′-modified nucleosides by using ortho-alkynyl benzoate as neighboring participation group. Subsequently, ortho-alkynyl benzoate can be removed smoothly in the presence of 5 mol% Ph3PAuCl-AgOTf in dichloromethane with H2O (1 eq.) and ethanol (6 eq.) to afford 2′-OH nucleosides in high yields and selectivity.

Preparation methods for clofarabine intermediate and clofarabine

The invention provides preparation methods for a clofarabine intermediate and clofarabine. The preparation method for the clofarabine intermediate, provided by the invention, comprises the steps of firstly mixing tertiary butanol, acetonitrile and calcium hydride; secondly mixing a to-be-reacted liquid obtained after stirring at the room temperature until no bubbles are generated, and 2-chloroadenine and reacting for 2-4 hours; and finally reacting with a 1-bromo-3,5-di-O-benzoyl-2-deoxy-2-fluoro-alpha-D-Arabic ribofuranose solution to obtain clofarabine. Therefore, the time of reaction with the 1-bromo-3,5-di-O-benzoyl-2-deoxy-2-fluoro-alpha-D-Arabic ribofuranose solution is greatly shortened; and the method is simple in post-treatment and relatively high in yield.

BIOCATALYTIC PRODUCTION OF NUCLEOSIDE ANALOGUES AS ACTIVE PHARMACEUTICAL INGREDIENTS

A biocatalytic process for producing active pharmaceutical ingredients (APIs) or intermediates thereof, wherein those APIs or their intermediates are nucleoside analogues (NAs) of formula I and wherein said NAs are active as pharmaceutically relevant antivirals and anticancer medicaments, intermediates or prodrugs thereof.

The chemoenzymatic synthesis of clofarabine and related 2′-deoxyfluoroarabinosyl nucleosides: The electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases

Two approaches to the synthesis of 2-chloro-9-(2-deoxy-2-fluoro-β-D- arabinofuranosyl)adenine (1, clofarabine) were studied. The first approach consists in the chemical synthesis of 2-deoxy-2-fluoro-α-D- arabinofuranose-1-phosphate (12a, 2FAra-1P) via three step conversion of 1,3,5-tri-O-benzoyl-2-deoxy-2-fluoro-α-D-arabinofuranose (9) into the phosphate 12a without isolation of intermediary products. Condensation of 12a with 2-chloroadenine catalyzed by the recombinant E. coli purine nucleoside phosphorylase (PNP) resulted in the formation of clofarabine in 67% yield. The reaction was also studied with a number of purine bases (2-aminoadenine and hypoxanthine), their analogues (5-aza-7-deazaguanine and 8-aza-7- deazahypoxanthine) and thymine. The results were compared with those of a similar reaction with α-D-arabinofuranose-1-phosphate (13a, Ara-1P). Differences of the reactivity of various substrates were analyzed by ab initio calculations in terms of the electronic structure (natural purines vs analogues) and stereochemical features (2FAra-1P vs Ara-1P) of the studied compounds to determine the substrate recognition by E. coli nucleoside phosphorylases. The second approach starts with the cascade one-pot enzymatic transformation of 2-deoxy-2-fluoro-D-arabinose into the phosphate 12a, followed by its condensation with 2-chloroadenine thereby affording clofarabine in ca. 48% yield in 24 h. The following recombinant E. coli enzymes catalyze the sequential conversion of 2-deoxy-2-fluoro-D-arabinose into the phosphate 12a: ribokinase (2-deoxy-2-fluoro-D-arabinofuranose-5-phosphate), phosphopentomutase (PPN; no 1,6-diphosphates of D-hexoses as co-factors required) (12a), and finally PNP. The substrate activities of D-arabinose, D-ribose and D-xylose in the similar cascade syntheses of the relevant 2-chloroadenine nucleosides were studied and compared with the activities of 2-deoxy-2-fluoro-D-arabinose. As expected, D-ribose exhibited the best substrate activity [90% yield of 2-chloroadenosine (8) in 30 min], D-arabinose reached an equilibrium at a concentration of ca. 1:1 of a starting base and the formed 2-chloro-9-(β-D- arabinofuranosyl) adenine (6) in 45 min, the formation of 2-chloro-9-(β-D- xylofuranosyl)adenine (7) proceeded very slowly attaining ca. 8% yield in 48 h.

Preparation of 2-chloro-9-(2'-deoxy-2'-fluoro-Beta-D-arabinofuranosyl)-adenine

A process for making clofarabine comprising: fluorinating a compound of formula VII wherein each R4 is independently a hydroxy protecting group, OR6 is a leaving group, with a fluorinating agent in the presence of guanidine carbonate to give a compound of formula VIII: wherein R4 is as defined above; and deprotecting the compound of formula VIII to give the clofarabine.