May 16, 2022
I’m a somewhat flawed 50-year-old antibiotic that is being used to develop a better one.
What molecule am I?
Image of Clindamycin 3D Image of Clindamycin

Clindamycin is an older antibiotic that is used to treat bacterial infections including pneumonia, strep throat, osteomyelitis, and endocarditis. It was first synthesized in 1966 by Barney J. Magerlein*, Robert D. Birkenmeyer, and Fred Kagan* at Upjohn (Kalamazoo, MI) by chemically modifying lincomycin1, a natural antibiotic. In the next few years, the same authors published additional articles and patents on clindamycin.

Clindamycin works by inhibiting ribosomal translocation in bacteria, reducing their ability to make proteins. It is most effective against aerobic Gram-positive and some anaerobic Gram-negative bacteria. It was approved by the US Food and Drug Administration in 1970.

Over the years, clindamycin has been a useful, versatile drug; but it is not without side effects such as nausea, diarrhea, and rashes. Significantly, it increases the risk of hospital-acquired colitis caused by Clostridium difficile. Although it has some ability to combat methicillin-resistant Staphylococcus aureus (MRSA), many bacteria have developed resistance to it.

Currently, clindamycin is taking on a new use: the development of more effective antibiotics. For an example, see this month’s Molecule of the Future, below.

1. CAS Reg. No. 154-21-2.

Clindamycin hazard information*

Hazard class**GHS code and hazard statement
Acute toxicity, oral, category 4H302—May be harmful if swallowedChemical Safety Warning
Skin corrosion/irritation, category 2H315—Causes skin irritationChemical Safety Warning
Skin sensitizationH317—May cause an allergic skin reactionChemical Safety Warning
Serious eye damage/eye irritation, category 2AH319—Causes serious eye irritationChemical Safety Warning
Reproductive toxicity, effects on or via lactation***H362—May cause harm to breast-fed children
Short-term (acute) aquatic hazard, category 1H400—Very toxic to aquatic lifeChemical Safety Warning
Long-term (chronic) aquatic hazard, category 1H410—Very toxic to aquatic life with long-lasting effectsChemical Safety Warning

*Compilation of multiple safety data sheets.
**Globally Harmonized System (GHS) of Classification and Labeling of Chemicals. 
Explanation of pictograms.
***No category or pictogram assigned.

Molecule of the Future

Iboxamycin1, a member of the oxepanoprolinamide class of antibiotics, is under development as a next-generation successor to clindamycin, described above. In July 2021, Andrew G. Myers and colleagues at Harvard University (Cambridge, MA) reported a practical synthesis of iboxamycin in which they replaced the n-propyl group in clindamycin with an oxepane ring fused to the pyrrolidine ring.

Molecule of  the Future

Later that year, Myers and his group, along with Yury. S. Polikanov and co-workers at the University of Illinois at Chicago, expanded on the original work. They reported that iboxamycin overcomes bacteria that are resistant to clindamycin, including strains of Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii. It also expands the range of Gram-positive and Gram-negative bacteria controlled by clindamycin.

Iboxamycin binds to the same place on the bacterial ribosome as does clindamycin, but it defeats the mechanism that many bacteria developed to become resistant to clindamycin.

1. As of this writing, no CAS Reg. No. has been assigned to iboxamycin.

Molecule of the Future

Once a month we bring you a newly discovered or developed molecule that has important implications for the future of chemistry or society in general. Look for it the third week of each month. Learn more about this month's Molecule of the Future below.

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Clindamycin fast facts

CAS Reg. No.18323-44-9

methyl 7-chloro-6,7,8-trideoxy-6-({[(2S,4R)-1-methyl-4-propyl-2-pyrrolidinyl

Empirical formulaC18H33ClN2O5S
Molar mass424.98 g/mol
AppearanceYellow amorphous solid
Melting point141–143 °Ca
Water solubility31 mg/L (est.)

a. Value for clindamycin hydrochloride, CAS Reg. No. 21462-39-5.

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