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Methyl 7-chloro-6,7,8-trideoxy-6-((hydroxy(1-methyl-4-propylpyrrolidin-2-yl)methylidene)amino)-1-thiooctopyranoside

HCID 29029
NotesReactions
Basic informationOverviewNames & identifiersPropertiesSafety & regulationChemistry & industryRelated reactionsCompound notes
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Basic information

CAS
13441-63-9
Standard SMILES
CCC[C@@H]1C[C@@H](C(=O)NC(C(C)Cl)[C@H]2O[C@H](SC)[C@H](O)[C@@H](O)[C@H]2O)N(C)C1
InChIKey
KDLRVYVGXIQJDK-NOWPCOIGSA-N
Molecular formula
C18H33ClN2O5S
Average molar mass
425 g/mol
Monoisotopic mass
424.179871

Overview

Clindamycin is a carbohydrate-containing antibiotic that is the semisynthetic derivative of lincomycin, a natural antibiotic. It has a role as a xenobiotic and an environmental contaminant. It is a carbohydrate-containing antibiotic, a S-glycosyl compound, an organochlorine compound, a pyrrolidinecarboxamide and a semisynthetic derivative. It is functionally related to a lincomycin.

Names & identifiers

Preferred name
Methyl 7-chloro-6,7,8-trideoxy-6-((hydroxy(1-methyl-4-propylpyrrolidin-2-yl)methylidene)amino)-1-thiooctopyranoside
IUPAC
(2S,4R)-N-[2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methylsulfanyloxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboxamide

Names & synonyms

DTXSID9092860813441-63-9Methyl 7-chloro-6,7,8-trideoxy-6-((hydroxy(1-methyl-4-propylpyrrolidin-2-yl)methylidene)amino)-1-thiooctopyranosideMethyl 7-chloro-6,7,8-trideoxy-6-{[hydroxy(1-methyl-4-propylpyrrolidin-2-yl)methylidene]amino}-1-thiooctopyranosideRefChem:1089518DTXCID801357373Clindamycine [French]Clindamycine [INN-French]Clindamycinum [INN-Latin]Clindamicina [INN-Spanish]Cleocin (TN)Cleocin
Show more names
SCHEMBL537702CHEMBL376185DB01190PD009752NS00008463ST50865923AB01018248-03Q422273

Database identifiers

CAS
13441-63-9、18323-44-9
PubChem CID
29029
DTXSID
DTXSID90928608
ChEMBL
CHEMBL376185
ChEBI
CHEBI:3745

Properties

Computed structural properties

XLogP
2.2
Topological polar surface area
128 Ų
Hydrogen bond donors
4
Hydrogen bond acceptors
7
Rotatable bonds
7
Heavy atoms
27
Formal charge
0
Complexity
502

Experimental & physicochemical properties

LogP1.6
Solubility · 2 items

Water soluble

3.10e+00 g/L

Melting Point · 2 items

141-143C

142 °C (hydrochloride salt)

Physical DescriptionSolid
Dissociation Constants · 2 items

7.72

7.6

Safety & regulation

Safety information is for reference only and does not replace the supplier’s Safety Data Sheet (SDS), applicable regulations, or professional assessment.

Toxicology

Exposure Routes · 1 item

Oral; topical; parenteral (intramuscular, intravenous). Rapidly absorbed after oral administration with peak serum concentrations observed after about 45 minutes. Absorption of an oral dose is virtually complete (90%) and the concomitant intake of food does not appreciably modify the serum concentrations; serum levels have been uniform and predictable from person to person and dose to dose. Clindamycin does not penetrate the blood brain barrier.

Toxicity Summary · 1 item

Systemic/vaginal clindamycin inhibits protein synthesis of bacteria by binding to the 50S ribosomal subunits of the bacteria. Specifically, it binds primarily to the 23s RNA subunit. Topical clindamycin reduces free fatty acid concentrations on the skin and suppresses the growth of Propionibacterium acnes (Corynebacterium acnes) , an anaerobe found in sebaceous glands and follicles.

Signs and Symptoms · 1 item

Orally and parenterally administered clindamycin has been associated with severe colitis (pseudomembranous colitis) which may result in patient death. Use of the topical formulation of clindamycin results in absorption of the antibiotic from the skin surface. Diarrhea, bloody diarrhea, and colitis (including pseudomembranous colitis) have been reported with the use of topical and systemic clindamycin.

Carcinogen ClassificationNo indication of carcinogenicity to humans (not listed by IARC).

Chemistry & industry

Pharmacology

Protein BindingClindamycin protein binding is concentration-dependent and ranges from 60-94%. It is bound primarily to alpha-1-acid glycoprotein in the serum.
Pharmacodynamics · 1 item

Clindamycin exerts its bacteriostatic effect via inhibition of microbial protein synthesis. Clindamycin has a relatively short T<sub>max</sub> and half-life necessitating administration every six hours to ensure adequate antibiotic concentrations. _Clostridium difficile_ associated diarrhea (CDAD) has been observed in patients using clindamycin, ranging in severity from mild diarrhea to fatal colitis and occasionally occurring over two months following cessation of antibiotic therapy. Overgrowth of _C. difficile_ resulting from antibiotic use, along with its production of A and B toxins, contributes to morbidity and mortality in these patients. Because of the associated risks, clindamycin should be reserved for serious infections for which the use of less toxic antimicrobial agents are inappropriate. Clindamycin is active against a number of gram-positive aerobic bacteria, as well as both gram-positive and gram-negative anaerobes. Resistance to clindamycin may develop, and is generally the result of base modification within the 23S ribosomal RNA. Cross-resistance between clindamycin and lincomycin is complete, and may also occur between clindamycin and macrolide antibiotics (e.g. [erythromycin]) due to similarities in their binding sites. As antimicrobial susceptibility patterns are geographically distinct, local antibiograms should be consulted to ensure adequate coverage of relevant pathogens prior to use.

Mechanism of Action · 1 item

Clindamycin inhibits bacterial protein synthesis by binding to 23S RNA of the 50S subunit of the bacterial ribosome. It impedes both the assembly of the ribosome and the translation process. The molecular mechanism through which this occurs is thought to be due to clindamycin's three-dimensional structure, which closely resembles the 3'-ends of L-Pro-Met-tRNA and deacylated-tRNA during the peptide elongation cycle - in acting as a structural analog of these tRNA molecules, clindamycin impairs peptide chain initiation and may stimulate dissociation of peptidyl-tRNA from bacterial ribosomes. The mechanism through which topical clindamycin treats acne vulgaris is unclear, but may be related to its activity against _Propionibacterium acnes_, a bacteria that has been associated with acne.

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Compound notes

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On this pageBasic informationOverviewNames & identifiersPropertiesSafety & regulationChemistry & industryRelated reactionsCompound notes
Biological Half-LifeThe elimination half-life of clindamycin is about 3 hours in adults and 2.5 hours in children. Half-life is increased to approximately 4 hours in the elderly.
Metabolism/Metabolites · 2 items

Clindamycin undergoes hepatic metabolism mediated primarily by CYP3A4 and, to a lesser extent, CYP3A5. Two inactive metabolites have been identified - an oxidative metabolite, clindamycin sulfoxide, and an N-demethylated metabolite, N-desmethylclindamycin.

Hepatic Route of Elimination: Approximately 10% of the bioactivity is excreted in the urine and 3.6% in the feces; the remainder is excreted as bioinactive metabolites. Half Life: 2.4 hours

Absorption, Distribution and Excretion · 4 items

Oral bioavailability is nearly complete, at approximately 90%, and peak serum concentrations (Cmax) of, on average, 2.50 µg/mL are reached at 0.75 hours (Tmax). The AUC following an orally administered dose of 300mg was found to be approximately 11 µg•hr/mL. Systemic exposure from the administration of vaginal suppository formulations is 40-fold to 50-fold lower than that observed following parenteral administration and the Cmax observed following administration of vaginal cream formulations was 0.1% of that observed following parenteral administration.

Approximately 10% of clindamycin bioactivity is excreted in the urine and 3.6% in the feces, with the remainder excreted as inactive metabolites.

Clindamycin is widely distributed in the body, including into bone, but does not distribute into cerebrospinal fluid. The volume of distribution has been variably estimated between 43-74 L.

The plasma clearance of clindamycin is estimated to be 12.3-17.4 L/h, and is reduced in patients with cirrhosis and altered in those with anemia.

Cellular LocationsCytoplasm
Metabolite PathwaysClindamycin Action Pathway

Uses & manufacturing

Uses · 1 item

Used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria. It is a common topical treatment for acne and can be useful against some methicillin-resistant Staphylococcus aureus (MRSA) infections. [Wikipedia] For the treatment of serious infections caused by susceptible anaerobic bacteria, including Bacteroides spp., Peptostreptococcus, anaerobic streptococci, Clostridium spp., and microaerophilic streptococci. May be useful in polymicrobic infections such as intra-abdominal or pelvic infections, osteomyelitis, diabetic foot ulcers, aspiration pneumonia and dental infections. May also be used to treat MSSA and respiratory infections caused by S. pneumoniae and S. pyogenes in patients who are intolerant to other indicated antibiotics or who are infected with resistant organism. May be used vaginally to treat vaginosis caused by Gardnerella vaginosa. Clindamycin reduces the toxin producing effects of S. aureus and S. pyogenes and as such, may be particularly useful for treating necrotizing fasciitis. May be used topically to treat acne.