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Identification
NameVidarabine
Accession NumberDB00194  (APRD00333, EXPT02753)
TypeSmall Molecule
GroupsApproved
DescriptionA nucleoside antibiotic isolated from Streptomyces antibioticus. It has some antineoplastic properties and has broad spectrum activity against DNA viruses in cell cultures and significant antiviral activity against infections caused by a variety of viruses such as the herpes viruses, the vaccinia VIRUS and varicella zoster virus. [PubChem]
Structure
Thumb
Synonyms
2-(6-AMINO-purin-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol
9-beta-D-Arabinofuranosyl-9H-purin-6-amine
9-beta-D-arabinofuranosyl-adenine
9-beta-D-Arabinofuranosyladenine
9-β-D-arabinofuranosyl-9H-purin-6-amine
9-β-D-arabinofuranosyladenine
Spongoadenosine
Vidarabine
External Identifiers Not Available
Approved Prescription ProductsNot Available
Approved Generic Prescription ProductsNot Available
Approved Over the Counter ProductsNot Available
Unapproved/Other Products Not Available
International Brands
NameCompany
Arasena-ANot Available
Vira-ANot Available
Brand mixturesNot Available
SaltsNot Available
Categories
UNIIFA2DM6879K
CAS number24356-66-9
WeightAverage: 267.2413
Monoisotopic: 267.096753929
Chemical FormulaC10H13N5O4
InChI KeyOIRDTQYFTABQOQ-UHTZMRCNSA-N
InChI
InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7+,10-/m1/s1
IUPAC Name
(2R,3S,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol
SMILES
NC1=NC=NC2=C1N=CN2[C@@H]1O[[email protected]](CO)[C@@H](O)[C@@H]1O
Pharmacology
IndicationFor treatment of chickenpox - varicella, herpes zoster and herpes simplex
Structured Indications Not Available
PharmacodynamicsVidarabine is a synthetic purine nucleoside analogue with in vitro and in vivo inhibitory activity against herpes simplex virus types 1 (HSV-1), 2 (HSV-2), and varicella-zoster virus (VZV). The inhibitory activity of Vidarabine is highly selective due to its affinity for the enzyme thymidine kinase (TK) encoded by HSV and VZV. This viral enzyme converts Vidarabine into Vidarabine monophosphate, a nucleotide analogue. The monophosphate is further converted into diphosphate by cellular guanylate kinase and into triphosphate by a number of cellular enzymes. in vitro, Vidarabine triphosphate stops replication of herpes viral DNA. When used as a substrate for viral DNA polymerase, Vidarabine triphosphate competitively inhibits dATP leading to the formation of 'faulty' DNA. This is where Vidarabine triphosphate is incorporated into the DNA strand replacing many of the adenosine bases. This results in the prevention of DNA synthesis, as phosphodiester bridges can longer to be built, destabilizing the strand.
Mechanism of actionVidarabine stops replication of herpes viral DNA in 2 ways: 1) competitive inhibition of viral DNA polymerase, and consequently 2) incorporation into and termination of the growing viral DNA chain. This drug is a nucleoside analog and therefore has to be phosphorylated to be active. Vidarabine is sequentially phosphorylated by kinases to the triphosphate ara-ATP. This is the active form of vidarabine and is both an inhibitor and a substrate of viral DNA polymerase. When used as a substrate for viral DNA polymerase, ara-ATP competitively inhibits dATP leading to the formation of ‘faulty’ DNA. This is where ara-ATP is incorporated into the DNA strand replacing many of the adenosine bases. This results in the prevention of DNA synthesis, as phosphodiester bridges can longer to be built, destabilizing the strand
TargetKindPharmacological actionActionsOrganismUniProt ID
DNA polymerase catalytic subunitProteinyes
inhibitor
HHV-4P03198 details
DNANucleotideyes
incorporation into and destabilization
Humannot applicabledetails
Thymidine kinaseProteinyes
inducer
HHV-3P09250 details
Thymidine kinaseProteinyes
inducer
HHV-1Q9QNF7 details
Related Articles
AbsorptionSystemetic absorption of vidarabine should not be expected to occur following ocular administration and swallowing lacrimal secretions.
Volume of distributionNot Available
Protein binding24-38%
Metabolism

In laboratory animals, vidarabine is rapidly deaminated in the gastrointestinal tract to Ara-Hx.

Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityAcute massive overdosage by oral ingestion of the ophthalmic ointment has not occurred. However, the rapid deamination to arabinosylhypoxanthine should preclude any difficulty. The oral LD50 for vidarabine is greater than 5020 mg/kg in mice and rats. No untoward effects should result from ingestion of the entire contents of the tube. Overdosage by ocular instillation is unlikely because any excess should be quickly expelled from the conjunctival sac.
Affected organisms
  • Human Herpes Virus
PathwaysNot Available
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available
References
Synthesis ReferenceNot Available
General ReferencesNot Available
External Links
ATC CodesJ05AB03S01AD06
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSDownload (73.8 KB)
ADMET
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.9227
Blood Brain Barrier+0.9383
Caco-2 permeable-0.8957
P-glycoprotein substrateNon-substrate0.7026
P-glycoprotein inhibitor INon-inhibitor0.966
P-glycoprotein inhibitor IINon-inhibitor0.9533
Renal organic cation transporterNon-inhibitor0.9444
CYP450 2C9 substrateNon-substrate0.8639
CYP450 2D6 substrateNon-substrate0.8349
CYP450 3A4 substrateNon-substrate0.5866
CYP450 1A2 substrateNon-inhibitor0.9667
CYP450 2C9 inhibitorNon-inhibitor0.9595
CYP450 2D6 inhibitorNon-inhibitor0.977
CYP450 2C19 inhibitorNon-inhibitor0.9514
CYP450 3A4 inhibitorNon-inhibitor0.962
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9701
Ames testNon AMES toxic0.9133
CarcinogenicityNon-carcinogens0.9182
BiodegradationNot ready biodegradable0.9738
Rat acute toxicity1.9715 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.989
hERG inhibition (predictor II)Non-inhibitor0.9102
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397 )
Pharmacoeconomics
Manufacturers
  • Parkedale pharmaceuticals inc
Packagers
Dosage formsNot Available
Prices
Unit descriptionCostUnit
Vidarabine monohydrate powder687.0USD g
Vidarabine powder366.59USD g
DrugBank does not sell nor buy drugs. Pricing information is supplied for informational purposes only.
PatentsNot Available
Properties
StateSolid
Experimental Properties
PropertyValueSource
logP-2.115Not Available
Predicted Properties
PropertyValueSource
Water Solubility14.0 mg/mLALOGPS
logP-1.2ALOGPS
logP-2.1ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)12.45ChemAxon
pKa (Strongest Basic)4.99ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area139.54 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity63.2 m3·mol-1ChemAxon
Polarizability24.49 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as purine nucleosides. These are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassNot Available
Direct ParentPurine nucleosides
Alternative Parents
Substituents
  • Purine ribonucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Aminopyrimidine
  • Imidolactam
  • Pyrimidine
  • Primary aromatic amine
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors

Targets

Kind
Protein
Organism
HHV-4
Pharmacological action
yes
Actions
inhibitor
General Function:
Nucleotide binding
Specific Function:
Replicates viral genomic DNA in the late phase of lytic infection, producing long concatemeric DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein.
Gene Name:
Not Available
Uniprot ID:
P03198
Molecular Weight:
113417.06 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Suzuki M, Okuda T, Shiraki K: Synergistic antiviral activity of acyclovir and vidarabine against herpes simplex virus types 1 and 2 and varicella-zoster virus. Antiviral Res. 2006 Nov;72(2):157-61. Epub 2006 May 30. [PubMed:16797734 ]
2. DNA
Kind
Nucleotide
Organism
Human
Pharmacological action
yes
Actions
incorporation into and destabilization
General Function:
Used for biological information storage.
Specific Function:
DNA contains the instructions needed for an organism to develop, survive and reproduce.
Molecular Weight:
2.15 x 1012 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
HHV-3
Pharmacological action
yes
Actions
inducer
General Function:
Thymidine kinase activity
Specific Function:
In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome.
Gene Name:
Not Available
Uniprot ID:
P09250
Molecular Weight:
37816.49 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Suzuki M, Okuda T, Shiraki K: Synergistic antiviral activity of acyclovir and vidarabine against herpes simplex virus types 1 and 2 and varicella-zoster virus. Antiviral Res. 2006 Nov;72(2):157-61. Epub 2006 May 30. [PubMed:16797734 ]
  4. Henrot A: [Mother-infant and indirect transmission of HSV infection: treatment and prevention]. Ann Dermatol Venereol. 2002 Apr;129(4 Pt 2):533-49. [PubMed:12122323 ]
  5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]
Kind
Protein
Organism
HHV-1
Pharmacological action
yes
Actions
inducer
General Function:
Thymidine kinase activity
Specific Function:
In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome.
Gene Name:
TK
Uniprot ID:
Q9QNF7
Molecular Weight:
40896.475 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Suzuki M, Okuda T, Shiraki K: Synergistic antiviral activity of acyclovir and vidarabine against herpes simplex virus types 1 and 2 and varicella-zoster virus. Antiviral Res. 2006 Nov;72(2):157-61. Epub 2006 May 30. [PubMed:16797734 ]
  4. Henrot A: [Mother-infant and indirect transmission of HSV infection: treatment and prevention]. Ann Dermatol Venereol. 2002 Apr;129(4 Pt 2):533-49. [PubMed:12122323 ]

Enzymes

Kind
Protein
Organism
Human
Pharmacological action
unknown
Actions
substrate
General Function:
Zinc ion binding
Specific Function:
Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion.
Gene Name:
ADA
Uniprot ID:
P00813
Molecular Weight:
40764.13 Da
References
  1. Agarwal RP, Blatt J, Miser J, Sallan S, Lipton JM, Reaman GH, Holcenberg J, Poplack DG: Clinical pharmacology of 9-beta-D-arabinofuranosyladenine in combination with 2'-deoxycoformycin. Cancer Res. 1982 Sep;42(9):3884-6. [PubMed:6980706 ]
  2. Balzarini J, De Clercq E: The antiviral activity of 9-beta-D-arabinofuranosyladenine is enhanced by the 2',3'-dideoxyriboside, the 2',3'-didehydro-2',3'-dideoxyriboside and the 3'-azido-2',3'-dideoxyriboside of 2,6-diaminopurine. Biochem Biophys Res Commun. 1989 Feb 28;159(1):61-7. [PubMed:2538128 ]
  3. Cristalli G, Franchetti P, Grifantini M, Vittori S, Lupidi G, Riva F, Bordoni T, Geroni C, Verini MA: Adenosine deaminase inhibitors. Synthesis and biological activity of deaza analogues of erythro-9-(2-hydroxy-3-nonyl)adenine. J Med Chem. 1988 Feb;31(2):390-3. [PubMed:3339608 ]
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Drug created on June 13, 2005 07:24 / Updated on August 17, 2016 12:23