NAV

Arbekacin

Identification

Generic Name
Arbekacin
DrugBank Accession Number
DB06696
Background

An semisynthetic aminoglycoside antibiotic. Often used for treatment of multi-resistant bacterial infection such as methicillin-resistant Staphylococcus aureus (MRSA).

Type
Small Molecule
Groups
Experimental, Investigational
Structure
3D
Similar Structures
Weight
Average: 552.619
Monoisotopic: 552.311891658
Chemical Formula
C22H44N6O10
Synonyms
  • ABK
  • Arbekacin
  • Arbekacina
  • Arbekacine
  • Arbekacinum
  • Haberacin
External IDs
  • 1665-RB
  • AHB-DBK
  • HABA-Dibekacin
  • HABA-DKB
  • HBK
  • ME-1100
  • ME1100
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Pharmacology

Indication

Arbekacin is used for the short term treatment of multi-resistant bacterial infections, such as methicillin-resistant Staphylococcus aureus (MRSA).

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Contraindications & Blackbox Warnings
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Pharmacodynamics

Arbekacin is an aminoglycoside. Aminoglycosides function by binding to bacterial 30S ribosomal subunits, causing t-RNA misreads, and preventing the production of proteins. Anaerobes are less susceptible to aminoglycosides because they do not spend as much energy as aerobes on taking up chemicals like aminoglycosides. Aminoglycosides are useful primarily in infections involving aerobic, gram-negative bacteria, such as Pseudomonas, Acinetobacter, and Enterobacter.

Mechanism of action

Arbekacin irreversibly binds bacterial 30S and 16S ribosomal subunits inhibiting protein synthesis. Arbekacin binds to 4 nucleotides of the 16S subunit and 1 amino acid of protein S12 to interfere with the decoding site around nucleotide 1400 in the 16S subunit. Interference with the decoding site interferes with its interaction with the wobble base of tRNA. This hindered interaction causes mRNA to be misread and the incorrect amino acids are inserted into protein. These error filled proteins are not able to function or may even be toxic.

TargetActionsOrganism
A30S ribosomal protein S12
inhibitor
Escherichia coli (strain K12)
Absorption

Aminoglycosides are not well absorbed from the gastrointestinal tract. Their absorption is markedly improved by parenteral administration.

Volume of distribution

Not Available

Protein binding

3-12%

Metabolism
Not Available
Route of elimination

Not Available

Half-life

3 hours

Clearance

Not Available

Adverse Effects
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Toxicity

Patients with renal impairment or those taking ototoxic and nephrotoxic drugs are at the highest risk for ototoxicity and nephrotoxicity associated with aminoglycoside use. Normal duration of IM or IV aminoglycoside therapy is 7-10 days. Although a longer duration may be necessary in some cases, toxicity is more likely to occur when aminoglycoside treatment is continued for longer than 10 days.

Pathways
PathwayCategory
Arbekacin Action PathwayDrug action
Pharmacogenomic Effects/ADRs Browse all" title="About SNP Mediated Effects/ADRs" id="snp-actions-info" class="drug-info-popup" href="javascript:void(0);">
Not Available

Interactions

Drug Interactions Learn More" title="About Drug Interactions" id="structured-interactions-info" class="drug-info-popup" href="javascript:void(0);">
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
DrugInteraction
Integrate drug-drug
interactions in your software
AbacavirAbacavir may decrease the excretion rate of Arbekacin which could result in a higher serum level.
AceclofenacAceclofenac may decrease the excretion rate of Arbekacin which could result in a higher serum level.
AcemetacinAcemetacin may decrease the excretion rate of Arbekacin which could result in a higher serum level.
AcenocoumarolThe risk or severity of bleeding can be increased when Arbekacin is combined with Acenocoumarol.
AcetaminophenAcetaminophen may decrease the excretion rate of Arbekacin which could result in a higher serum level.
Food Interactions
Not Available

Products

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Product Ingredients
IngredientUNIICASInChI Key
Arbekacin sulfateG7395HZ992104931-87-5UTUVRPOLEMRKQC-XDJMXTNXSA-N

Categories

ATC Codes
J01GB12 — Arbekacin
Drug Categories
Chemical TaxonomyProvided by Classyfire
Description
This compound belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.
Kingdom
Organic compounds
Super Class
Organic oxygen compounds
Class
Organooxygen compounds
Sub Class
Carbohydrates and carbohydrate conjugates
Direct Parent
4,6-disubstituted 2-deoxystreptamines
Alternative Parents
O-glycosyl compounds / Aminocyclitols and derivatives / Cyclohexanols / Cyclohexylamines / Oxanes / Monosaccharides / 1,3-aminoalcohols / 1,2-aminoalcohols / Propargyl-type 1,3-dipolar organic compounds / Acetals
show 6 more
Substituents
1,2-aminoalcohol / 1,3-aminoalcohol / 4,6-disubstituted 2-deoxystreptamine / Acetal / Alcohol / Aliphatic heteromonocyclic compound / Amine / Aminocyclitol or derivatives / Carboximidic acid / Carboximidic acid derivative
show 20 more
Molecular Framework
Aliphatic heteromonocyclic compounds
External Descriptors
aminoglycoside, kanamycins (CHEBI:37922)
Affected organisms
  • Enteric bacteria and other eubacteria
  • Escherichia coli
  • Staphylococcus aureus
  • Acinetobacter

Chemical Identifiers

UNII
G7V6SLI20L
CAS number
51025-85-5
InChI Key
MKKYBZZTJQGVCD-XTCKQBCOSA-N
InChI
InChI=1S/C22H44N6O10/c23-4-3-12(30)20(34)28-11-5-10(26)18(37-21-9(25)2-1-8(6-24)35-21)17(33)19(11)38-22-16(32)14(27)15(31)13(7-29)36-22/h8-19,21-22,29-33H,1-7,23-27H2,(H,28,34)/t8-,9+,10-,11+,12-,13+,14-,15+,16+,17-,18+,19-,21+,22+/m0/s1
IUPAC Name
(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide
SMILES
NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C@H]2N)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O

References

Synthesis Reference

Shinichi Kondo, Seiji Shibahara, Takayuki Usui, Toshiaki Kudo, Shuichi Gomi, Atsushi Tamura, Yoko Ikeda, Daishiro Ikeda, Tomio Takeuchi, "Dibekacin derivatives and arbekacin derivatives active against resistant bacteria, and the production thereof." U.S. Patent US5618795, issued October, 1989.

US5618795
General References
  1. Inoue M, Nonoyama M, Okamoto R, Ida T: Antimicrobial activity of arbekacin, a new aminoglycoside antibiotic, against methicillin-resistant Staphylococcus aureus. Drugs Exp Clin Res. 1994;20(6):233-9. [Article]
  2. Morikawa K, Nonaka M, Yoshikawa Y, Torii I: Synergistic effect of fosfomycin and arbekacin on a methicillin-resistant Staphylococcus aureus-induced biofilm in a rat model. Int J Antimicrob Agents. 2005 Jan;25(1):44-50. [Article]
  3. Doi Y, Yokoyama K, Yamane K, Wachino J, Shibata N, Yagi T, Shibayama K, Kato H, Arakawa Y: Plasmid-mediated 16S rRNA methylase in Serratia marcescens conferring high-level resistance to aminoglycosides. Antimicrob Agents Chemother. 2004 Feb;48(2):491-6. [Article]
  4. Antimicrobial agents and Chemotherapy [Link]
Human Metabolome Database
HMDB0015642
KEGG Drug
D07462
PubChem Compound
68682
PubChem Substance
99443250
ChemSpider
61936
RxNav
26397
ChEBI
37922
ChEMBL
CHEMBL426926
ZINC
ZINC000009575047
PharmGKB
PA165958370
PDBe Ligand
84G
Drugs.com
Drugs.com Drug Page
Wikipedia
Arbekacin
PDB Entries
6cgg

Clinical Trials

Clinical Trials Learn More" title="About Clinical Trials" id="clinical-trials-info" class="drug-info-popup" href="javascript:void(0);">
PhaseStatusPurposeConditionsCount
2Unknown StatusTreatmentDuchenne Muscular Dystrophy (DMD)1
1CompletedTreatmentBacterial Pneumonia1
1CompletedTreatmentHealthy Subjects (HS)2
Not AvailableNo Longer AvailableNot AvailableInfection Due to Resistant Organism1

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage Forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
PropertyValueSource
melting point (°C)178Not Available
Predicted Properties
PropertyValueSource
Water Solubility41.0 mg/mLALOGPS
logP-2.9ALOGPS
logP-6.9Chemaxon
logS-1.1ALOGPS
pKa (Strongest Acidic)12.49Chemaxon
pKa (Strongest Basic)9.99Chemaxon
Physiological Charge5Chemaxon
Hydrogen Acceptor Count15Chemaxon
Hydrogen Donor Count11Chemaxon
Polar Surface Area297.27 Å2Chemaxon
Rotatable Bond Count10Chemaxon
Refractivity129.08 m3·mol-1Chemaxon
Polarizability56.58 Å3Chemaxon
Number of Rings3Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleYesChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9365
Blood Brain Barrier-0.9659
Caco-2 permeable-0.7588
P-glycoprotein substrateSubstrate0.5786
P-glycoprotein inhibitor INon-inhibitor0.7254
P-glycoprotein inhibitor IINon-inhibitor0.8424
Renal organic cation transporterNon-inhibitor0.8676
CYP450 2C9 substrateNon-substrate0.8204
CYP450 2D6 substrateNon-substrate0.8289
CYP450 3A4 substrateNon-substrate0.559
CYP450 1A2 substrateNon-inhibitor0.933
CYP450 2C9 inhibitorNon-inhibitor0.9392
CYP450 2D6 inhibitorNon-inhibitor0.909
CYP450 2C19 inhibitorNon-inhibitor0.9122
CYP450 3A4 inhibitorNon-inhibitor0.9564
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9002
Ames testNon AMES toxic0.7048
CarcinogenicityNon-carcinogens0.9617
BiodegradationNot ready biodegradable0.6627
Rat acute toxicity1.8593 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9902
hERG inhibition (predictor II)Non-inhibitor0.5444
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSsplash10-0fai-9703350000-a39b12324064de97bb1b
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0fbi-0800090000-0f7cac028272f6813836
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0kai-0001490000-1cea5f641b17b59fef71
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-004i-0905270000-335360774100333d2bee
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-0udj-2301970000-fd993d72f50a7b1ca0bf
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0udi-4910210000-a447f343d33c7fb350b1
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-0f80-9133130000-104f54f5ce7c9c831e4e
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-248.0974632
predicted
DarkChem Lite v0.1.0
[M-H]-215.209
predicted
DeepCCS 1.0 (2019)
[M+H]+248.1856632
predicted
DarkChem Lite v0.1.0
[M+H]+216.93271
predicted
DeepCCS 1.0 (2019)
[M+Na]+247.2710632
predicted
DarkChem Lite v0.1.0
[M+Na]+223.26167
predicted
DeepCCS 1.0 (2019)

Targets

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insights and accelerate drug research.
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Details1. 30S ribosomal protein S12
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Yes
Actions
Inhibitor
General Function
Trna binding
Specific Function
With S4 and S5 plays an important role in translational accuracy.Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Lo...
Gene Name
rpsL
Uniprot ID
P0A7S3
Uniprot Name
30S ribosomal protein S12
Molecular Weight
13736.995 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. [Article]
  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. [Article]
  3. Funatsu G, Yaguchi M, Wittmann-Liebold B: Primary stucture of protein S12 from the small Escherichia coli ribosomal subunit. FEBS Lett. 1977 Jan 15;73(1):12-7. [Article]
  4. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V: Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000 Sep 21;407(6802):340-8. [Article]

Drug created at May 05, 2010 16:31 / Updated at December 02, 2023 07:01