Record Information
Version2.0
Creation Date2009-07-15 20:41:25 UTC
Update Date2014-12-24 20:25:48 UTC
Accession NumberT3D2663
Identification
Common NameClodronate
ClassSmall Molecule
DescriptionClodronate is only found in individuals that have used or taken this drug. It is a diphosphonate which affects calcium metabolism. It inhibits bone resorption and soft tissue calcification. [PubChem]The bisphosphonate group binds strongly to the bone mineral, hydroxyapatite. This explains the specific pharmacological action of these compounds on mineralized tissues, especially bone. The exact mechanism of action of clodronate is not known, however it is known that it does not inhibit protein isoprenylation but can be metabolized intracellularly to a β-γ-methylene (AppCp-type) analog of ATP (AppCCl2p), which is cytotoxic to macrophages in vitro. Inhibition of the ADP/ATP translocase by the metabolite AppCCl2p is a likely route by which clodronate causes osteoclast apoptosis and inhibits bone resorption. Recently, the slime mold Dictyostelium discoideum was shown to take up bisphosphonates by pinocytosis. In these cells, clodronate, but not other pharmacologically active bisphosphonates, was incorporated into adenine nucleotides, which could potentially explain why this bisphosphonate sometimes seems to act differently than the other bisphosphonates. Clodronate, like all biphosphonates, also binds protein-tyrosine-phosphatase.
Compound Type
  • Antihypocalcemic Agent
  • Antineoplastic Agent
  • Bisphosphonate
  • Bone Density Conservation Agent
  • Drug
  • Metabolite
  • Organic Compound
  • Organochloride
  • Osteoporosis Prophylactic
  • Synthetic Compound
Chemical Structure
Thumb
Synonyms
Synonym
(Dichloro-phosphono-methyl)-phosphonic acid
(Dichloromethylene)bisphosphonic acid
(Dichloromethylene)diphosphonic acid
Acide Clodronique
Acido Clodronico
Acidum Clodronicum
Bonefos
Clasteon
Clodronic acid
Clodronsaeure
Clodronsäure
Dichloromethanediphosphonic acid
Dichloromethylene-1,1-bisphosphonic acid
Dichloromethylene-1,1-diphosphonic acid
Dichloromethylidene diphosphonate
Lodronat
Loron
Lytos
Ostac
Sindronat
Chemical FormulaCH4Cl2O6P2
Average Molecular Mass244.892 g/mol
Monoisotopic Mass243.886 g/mol
CAS Registry Number10596-23-3
IUPAC Name[dichloro(phosphono)methyl]phosphonic acid
Traditional Nameclodronate
SMILESOP(O)(=O)C(Cl)(Cl)P(O)(O)=O
InChI IdentifierInChI=1S/CH4Cl2O6P2/c2-1(3,10(4,5)6)11(7,8)9/h(H2,4,5,6)(H2,7,8,9)
InChI KeyInChIKey=ACSIXWWBWUQEHA-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as bisphosphonates. These are organic compounds containing two phosphonate groups linked together through a carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic phosphonic acids and derivatives
Sub ClassBisphosphonates
Direct ParentBisphosphonates
Alternative Parents
Substituents
  • Bisphosphonate
  • Organophosphonic acid
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organophosphorus compound
  • Organochloride
  • Organohalogen compound
  • Alkyl halide
  • Alkyl chloride
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
Applications
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting Point250°C
Boiling PointNot Available
Solubility395 mg/L
LogP-2.4
Predicted Properties
PropertyValueSource
Water Solubility7.47 g/LALOGPS
logP0.16ALOGPS
logP-0.067ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)0.62ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115.06 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity38.21 m³·mol⁻¹ChemAxon
Polarizability15.3 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9040000000-af3c2e18902e147f8d422017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-1190000000-c4ab9891e7e58566d92f2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03ed-3940000000-c29d8ff76855c0aaef6c2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-01a0eea1cf84ed37407a2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03dl-0950000000-1845236a124e15b5c59b2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-006x-1390000000-3ae475737e6b4b8c76642016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-974168c5223d898e9a792016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000x-6090000000-8989f8d7643382de70bc2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-95542c15d3d7df8beff22021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03ea-4900000000-e088c1d2fe760f01f20d2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00dl-0090000000-125baa903034088b47b62021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00fr-6590000000-8d753c1dbb524b991ddf2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-1090000000-29462d306ece6e9df24d2021-10-11View Spectrum
Toxicity Profile
Route of ExposureOral, Intravenous. After oral administration, absorption is estimated at 1–3% of the ingested dose because of the low uptake from the gastrointestinal tract.
Mechanism of ToxicityThe bisphosphonate group binds strongly to the bone mineral, hydroxyapatite. This explains the specific pharmacological action of these compounds on mineralized tissues, especially bone. The exact mechanism of action of clodronate is not known, however it is known that it does not inhibit protein isoprenylation but can be metabolized intracellularly to a β-γ-methylene (AppCp-type) analog of ATP (AppCCl2p), which is cytotoxic to macrophages in vitro. Inhibition of the ADP/ATP translocase by the metabolite AppCCl2p is a likely route by which clodronate causes osteoclast apoptosis and inhibits bone resorption. Recently, the slime mold Dictyostelium discoideum was shown to take up bisphosphonates by pinocytosis. In these cells, clodronate, but not other pharmacologically active bisphosphonates, was incorporated into adenine nucleotides, which could potentially explain why this bisphosphonate sometimes seems to act differently than the other bisphosphonates. Clodronate, like all biphosphonates, also binds protein-tyrosine-phosphatase.
MetabolismClodronate is not metabolized in humans. It can be metabolized intracellularly to a beta-gamma-methylene (AppCp-type) analog of ATP (AppCCl2p), which is cytotoxic to macrophages in vitro. Half Life: Approximately 13 hours.
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesA diphosphonate which affects calcium metabolism. It inhibits bone resorption and soft tissue calcification. For the management of hypercalcemia of malignancy and as an adjunct in the management of osteolysis resulting from bone metastases of malignant tumors.
Minimum Risk LevelNot Available
Health EffectsDecreases in serum calcium following substantial overdosage may be expected in some patients.
SymptomsSigns and symptoms of hypocalcemia also may occur in some of these patients.
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB00720
HMDB IDHMDB14858
PubChem Compound ID25419
ChEMBL IDCHEMBL12318
ChemSpider ID23731
KEGG IDNot Available
UniProt IDNot Available
OMIM ID
ChEBI ID110423
BioCyc IDNot Available
CTD IDNot Available
Stitch IDClodronic acid
PDB IDNot Available
ACToR IDNot Available
Wikipedia LinkClodronate
References
Synthesis Reference

Fritz Demmer, Berthold Stemmle, “Clodronate-containing medicaments and a process for the preparation thereof.” U.S. Patent US4859472, issued September, 1980.

MSDSLink
General References
  1. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M: DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6. Epub 2007 Nov 29. [18048412 ]
  2. Cancer Care (2009). Fact Sheet for Clodronate. [Link]
  3. Drugs.com [Link]
  4. Drugs.com [Link]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

General Function:
Adenine transmembrane transporter activity
Specific Function:
Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane.
Gene Name:
SLC25A4
Uniprot ID:
P12235
Molecular Weight:
33064.265 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. [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. [17016423 ]
General Function:
Ubiquitin protein ligase binding
Specific Function:
Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane. As part of the mitotic spindle-associated MMXD complex it may play a role in chromosome segregation.
Gene Name:
SLC25A5
Uniprot ID:
P05141
Molecular Weight:
32851.965 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. [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. [17016423 ]
General Function:
Atp:adp antiporter activity
Specific Function:
Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis.
Gene Name:
SLC25A6
Uniprot ID:
P12236
Molecular Weight:
32866.025 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. [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. [17016423 ]
References
  1. Ganguli A, Steward C, Butler SL, Philips GJ, Meikle ST, Lloyd AW, Grant MH: Bacterial adhesion to bisphosphonate coated hydroxyapatite. J Mater Sci Mater Med. 2005 Apr;16(4):283-7. [15803271 ]
  2. Nancollas GH, Tang R, Phipps RJ, Henneman Z, Gulde S, Wu W, Mangood A, Russell RG, Ebetino FH: Novel insights into actions of bisphosphonates on bone: differences in interactions with hydroxyapatite. Bone. 2006 May;38(5):617-27. Epub 2005 Jul 20. [16046206 ]
General Function:
Zinc ion binding
Specific Function:
Tyrosine-protein phosphatase which acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. May play an important role in CKII- and p60c-src-induced signal transduction cascades. May regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganization and cell-cell repulsion. May also regulate the hepatocyte growth factor receptor signaling pathway through dephosphorylation of MET.
Gene Name:
PTPN1
Uniprot ID:
P18031
Molecular Weight:
49966.44 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. [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. [17016423 ]
General Function:
Zinc ion binding
Specific Function:
Ubiquitinous metalloproteinase that is involved in diverse functions such as remodeling of the vasculature, angiogenesis, tissue repair, tumor invasion, inflammation, and atherosclerotic plaque rupture. As well as degrading extracellular matrix proteins, can also act on several nonmatrix proteins such as big endothelial 1 and beta-type CGRP promoting vasoconstriction. Also cleaves KISS at a Gly-|-Leu bond. Appears to have a role in myocardial cell death pathways. Contributes to myocardial oxidative stress by regulating the activity of GSK3beta. Cleaves GSK3beta in vitro. Involved in the formation of the fibrovascular tissues in association with MMP14.PEX, the C-terminal non-catalytic fragment of MMP2, posseses anti-angiogenic and anti-tumor properties and inhibits cell migration and cell adhesion to FGF2 and vitronectin. Ligand for integrinv/beta3 on the surface of blood vessels.Isoform 2: Mediates the proteolysis of CHUK/IKKA and initiates a primary innate immune response by inducing mitochondrial-nuclear stress signaling with activation of the pro-inflammatory NF-kappaB, NFAT and IRF transcriptional pathways.
Gene Name:
MMP2
Uniprot ID:
P08253
Molecular Weight:
73881.695 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
IC50145 uMNot AvailableBindingDB 50216172
References
  1. Sasanelli R, Boccarelli A, Giordano D, Laforgia M, Arnesano F, Natile G, Cardellicchio C, Capozzi MA, Coluccia M: Platinum complexes can inhibit matrix metalloproteinase activity: platinum-diethyl[(methylsulfinyl)methyl]phosphonate complexes as inhibitors of matrix metalloproteinases 2, 3, 9, and 12. J Med Chem. 2007 Jul 26;50(15):3434-41. Epub 2007 Jun 21. [17583333 ]
General Function:
Zinc ion binding
Specific Function:
May be involved in tissue injury and remodeling. Has significant elastolytic activity. Can accept large and small amino acids at the P1' site, but has a preference for leucine. Aromatic or hydrophobic residues are preferred at the P1 site, with small hydrophobic residues (preferably alanine) occupying P3.
Gene Name:
MMP12
Uniprot ID:
P39900
Molecular Weight:
54001.175 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
IC50121 uMNot AvailableBindingDB 50216172
References
  1. Sasanelli R, Boccarelli A, Giordano D, Laforgia M, Arnesano F, Natile G, Cardellicchio C, Capozzi MA, Coluccia M: Platinum complexes can inhibit matrix metalloproteinase activity: platinum-diethyl[(methylsulfinyl)methyl]phosphonate complexes as inhibitors of matrix metalloproteinases 2, 3, 9, and 12. J Med Chem. 2007 Jul 26;50(15):3434-41. Epub 2007 Jun 21. [17583333 ]
General Function:
Zinc ion binding
Specific Function:
Can degrade fibronectin, laminin, gelatins of type I, III, IV, and V; collagens III, IV, X, and IX, and cartilage proteoglycans. Activates procollagenase.
Gene Name:
MMP3
Uniprot ID:
P08254
Molecular Weight:
53976.84 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
IC50300 uMNot AvailableBindingDB 50216172
References
  1. Sasanelli R, Boccarelli A, Giordano D, Laforgia M, Arnesano F, Natile G, Cardellicchio C, Capozzi MA, Coluccia M: Platinum complexes can inhibit matrix metalloproteinase activity: platinum-diethyl[(methylsulfinyl)methyl]phosphonate complexes as inhibitors of matrix metalloproteinases 2, 3, 9, and 12. J Med Chem. 2007 Jul 26;50(15):3434-41. Epub 2007 Jun 21. [17583333 ]