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Home> Encyclopedia >Immune Function Agents>Pharmaceutical Intermediates>Pharmaceutical
Rapamycin structure
Rapamycin structure


Iupac Name:(1R,9S,12S,15R,16E,18R,19R,21R,23S,24E,26E,28E,30S,32S,35R)-1,18-dihydroxy-12-[(2R)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[,9]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone
CAS No.: 53123-88-9
Molecular Weight:914.17186
Modify Date.: 2023-02-20 06:51
Introduction: Rapamycin (Sirolimus) is a potent and specific mTOR inhibitor with an IC50 of 0.1 nM. View more+
1. Names and Identifiers
1.1 Name
1.2 Synonyms

(1R,9S,12S,15R,16E,18R,19R,21R,23S,24E,26Z,28E,30S,32S,35R)-1,18-Dihydroxy-12-{(2S)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]-2-propanyl}-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4- 23,27-EPOXY-3H-PYRIDO(2,1-C)(1,4)OXAAZACYCLOHENTRIACONTINE 23,27-Epoxy-3H-pyrido[2,1-c][1,4]oxaazacyclohentriacontine 23,27-Epoxy-3H-pyrido[2,1-c][1,4]oxaazacyclohentriacontine-1,5,11,28,29(4H,6H,31H)-pentone, 9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-9,27-dihydroxy-3-[(1S)-2-[(1S,3R,4R)-4-hydroxy -3-methoxycyclohexyl]-1-methylethyl]-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-, (3S,6R,7E,9R,10R,12R,14S,15E,17Z,19E,21S,23S,26R,27R,34aS)- AY 22989 azatricyclo[,9]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone EINECS 262-640-9 MFCD00867594 NSC-226080 RAPA Rapamicin RAPAMUNE RAPAMYCIN, STREPTOMYCES HYGROSCOPICUS RPM sila9268a Sirolimus

1.3 CAS No.
1.4 CID
1.6 Molecular Formula
C51H79NO13 (isomer)
1.7 Inchi
1.8 InChkey
1.9 Canonical Smiles
1.10 Isomers Smiles
2. Properties
2.1 Density
2.1 Melting point
183-185 oC
2.1 Boiling point
973.017 oC at 760 mmHg
2.1 Refractive index
2.1 Flash Point
542.261 oC
2.1 Precise Quality
2.1 PSA
2.1 logP
2.1 Solubility
ethanol: soluble2MM
2.2 Appearance
yellow solid
2.3 Storage
Store at -20°C.
2.4 Chemical Properties
White to Off-White Solid
2.5 Color/Form
Colorless crystalline solid from ether
2.6 pKa
2.7 Water Solubility
Soluble in DMSO and Methanol
2.8 Spectral Properties
UV max (95 percent ethanol): 267, 277, 288 nm (the absorbance of a solution containing one gram per 100 ml contained in a cell having an absorption path of one cm: 417, 541, and 416)
Specific optical rotation at 25 deg C for D (sodium) line = -58.2 deg (methanol)
2.9 Stability
Stable if stored as directed.
2.10 StorageTemp
3. Use and Manufacturing
3.1 Definition
ChEBI: A macrolide isolated from Streptomyces hygroscopicus consisting of a 29-membered ring containing 4 trans double bonds, three of which are conjugated. It is an antibiotic, immunosupressive and antineoplastic agent.
3.2 Usage
Tool for immunochemistry.
4. Safety and Handling
4.1 Symbol
GHS02, GHS07
4.1 Hazard Codes
4.1 Signal Word
4.1 Risk Statements
4.1 Safety Statements
4.1 Exposure Standards and Regulations
The Approved Drug Products with Therapeutic Equivalence Evaluations List identifies currently marketed prescription drug products, incl sirolimus, approved on the basis of safety and effectiveness by FDA under sections 505 of the Federal Food, Drug, and Cosmetic Act.
4.2 Octanol/Water Partition Coefficient
log Kow = 4.81 /Estimated/
4.3 Hazard Declaration
H225-H302 + H312 + H332-H319
4.3 DisposalMethods
SRP: The most favorable course of action is to use an alternative chemical product with less inherent propensity for occupational exposure or environmental contamination. Recycle any unused portion of the material for its approved use or return it to the manufacturer or supplier. Ultimate disposal of the chemical must consider: the material's impact on air quality; potential migration in soil or water; effects on animal, aquatic, and plant life; and conformance with environmental and public health regulations.
UN 1648 3 / PGII
4.4 Caution Statement
P210-P280-P305 + P351 + P338
4.4 Formulations/Preparations
Oral: Solution 1mg/mL Rapamune (Wyeth). Tablets: 1 mg Rapamune (with povidone), (Wyeth); 2 mg Rapamune (with Povidone), (Wyeth).
4.5 WGK Germany
4.5 Safety

Poison by intraperitoneal route. Moderately toxic by ingestion. Mutation data reported. When heated to decomposition it emits toxic fumes of NOx.
Hazard Codes:?IrritantXi
Risk Statements: 36/38?
R36/38:Irritating to eyes and skin.
Safety Statements: 22-24/25-37/39-26?
S22:Do not breathe dust.?
S24/25:Avoid contact with skin and eyes.?
S37/39:Wear suitable gloves and eye/face protection.?
S26: In case of contact with eyes, rinse immediately with plenty of water and seek medical advice.
RTECS of Rapamycin (CAS NO.53123-88-9): VE6250000

4.6 Sensitive
Moisture Sensitive/Light Sensitive/Hygroscopic
4.7 Specification

? Rapamycin (CAS NO.53123-88-9), its Synonyms are 23,27-Epoxy-3H-pyrido(2,1-c)(1,4)oxaazacyclohentriacontine-1,5,11,28,29(4H,6H,31H)-pentone, 9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-9,27-dihydroxy-3-(3-(4-hydroxy-3-methoxycyclohexyl)-1-methylethyl)-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-, (3S-
(3R*S*1R*,3S*,4S*)),6S*,7E,9S*,10S*,12S*,14R*,15E,17E,19E,21R*,23R*,26S*,27S*,34aR*))- ; Sirolimus ; Rapammune ; Rapamune . It is white to off-white solid.

4.8 Toxicity

Organism Test Type Route Reported Dose (Normalized Dose) Effect Source
mouse LD50 intraperitoneal 597mg/kg (597mg/kg) ? Journal of Antibiotics. Vol. 31, Pg. 539, 1978.
mouse LD50 oral > 2500mg/kg (2500mg/kg) ? Journal of Antibiotics. Vol. 28, Pg. 721, 1975.
rat LD50 intraperitoneal 18220ug/kg (18.22mg/kg) ? National Technical Information Service. Vol. PB83-228577,


2.Hazard identification

2.1 Classification of the substance or mixture

Carcinogenicity, Category 2

Reproductive toxicity, Category 2

2.2 GHS label elements, including precautionary statements

Signal word


Hazard statement(s)

H351 Suspected of causing cancer

H361 Suspected of damaging fertility or the unborn child

H372 Causes damage to organs through prolonged or repeated exposure

Precautionary statement(s)

P201 Obtain special instructions before use.

P202 Do not handle until all safety precautions have been read and understood.

P280 Wear protective gloves/protective clothing/eye protection/face protection.


P308+P313 IF exposed or concerned: Get medical advice/ attention.


P405 Store locked up.


P501 Dispose of contents/container to ...

2.3 Other hazards which do not result in classification


8. Other Information
8.0 Merck
8.1 description
Rapamycin (also known as Sirolimus) is macrocyclic lactone produced by the bacterium Streptomyces hygroscopicus isolated from soil samples from Easter Island. Rapamycin is an antifungal agent with immunosuppressive properties. Rapamycin has antirejection properties without the side effects associated with other antirejection agents. Rapamycin binds to a specific protein, Target of Rapamycin (TOR). TOR is serine/threonine kinase. TOR (mTOR) forms two major complexes: mTORC1,and mTORC2. The mTORC1 consists of mTOR, Raptor, mLST8, FKBP38, PRAS40, and Deptor, and through specific binding of rapamycin to FKBP12, rapamycin inhibits the activity of mTORC1 leading to a decrease in protein synthesis, increased autophagy and inhibition of cell growth.
8.2 Indications and Usage
Rapamycin (Rapa, or Sirolimus) is a new form of macrolide immunosuppressive agent. It is a white solid crystal. Its melting point is 183-185℃ and it is lipophilic. It is soluble in methanol, ethanol, acetone, chloroform, and other organic solvents, very slightly soluble in water, and almost insoluble in ether. It was first discovered in 1975 on the Chilean Easter Island as a secondary metabolite secreted by soil Streptomyces, and its chemical structure is that of a three-polyene macrolide compound.
Rapamycin is a new form of immunosuppressive agent with good curative effects, low toxicity, and no nephrotoxicity. It can be used to maintain the immunity of transplant organs (especially in kidney transplants) to alleviate immunological rejections after organ transplant surgeries. The latest research has shown that Rapamycin can also be used to treat Alzheimer’s. When used on afflicted lab rats, it had a memory-restoring effect. Rapamycin oral tablets can be taken with grapefruit juice to treat melanoma (a type of benign tumor common among Western populations), dramatically increase other chemotherapy drugs’ anticancer effects, and extend patient survival. Rapamycin is a mammalian target of rapamycin (mTOR) targeting inhibitor, which can treat tumors that are related to this pathway including kidney cancer, lymphoma, lung cancer, liver cancer, breast cancer, neuroendocrine carcinoma, gastric cancer, etc. Its curative effects are especially strong for the rare diseases LAM (lymphangiomyomatosis) and TSC (tuberous sclerosis).
8.3 Mechanisms of Action
Rapamycin is a type of macrolide antibiotic and has a similar structure to Prograf (FK506), but has very different immunosuppressing mechanisms. FK506 suppresses T lymph cells from proliferating from G0 to G1 stage, while RAPA uses different cytokine receptors to block signal transduction, thus preventing T lymph cells and other cells from proliferating from G1 to S stage. Compared to Prograf, Rapamycin can block the signal transduction pathways of the calcium dependency and calcium non-dependency of T lymph cells and B lymph cells.
8.4 Application

As an mTOR inhibitor, sirolimus has a broad spectrum of activity that has demonstrated the ability to inhibit inflammation, proliferation, angiogenesis, fibrosis, and hyperpermeability. Sirolimus currently has multiple uses in the prevention of rejection in organ transplantation and, recently, in the treatment of advanced renal cell carcinoma. Sirolimus-eluting cardiac stents have been shown to limit the rate of overgrowth of tissue and thus prevent coronary restenosis. Early studies suggest that it may be an effective agent for controlling severe uveitis and that it may also have a role in treating agerelated macular degeneration.

8.5 Adverse reactions
Rapamycin has similar side effects to those of Prograf. Many clinical trials have found that its side effects are dose dependent and reversible. A treatment dosage of Rapamycin has not been found to lead to any significant nephrotoxicity or gingival hyperplasia. Its main toxic side effects include: headache, nausea, dizziness, nosebleed, and join pain. Laboratory inspections for anomalies found: thrombocytopenia, decreased white blood cells, decreased hemoglobin, hypertriglyceridemia, hypercholesterolemia, hyperglycemia, increased liver enzymes (SGOT, SGPT), increased lactate dehydrogenase, hypokalemia, hypokalemia, etc. Rapamycin may lead to puffiness of eyelids and lead to lowered plasma phosphate levels. Similar to other immunosuppressants, Rapamycin may also increase the chance of infection, with reports of increased tendency towards pneumonia.
8.6 Chemical Properties
White to Off-White Solid
8.7 Originator
Rapamune,Wyeth Laboratories,UK
8.8 Occurrence
Rapamycin was first discovered in 1972 in the soil of Easter Island produced by a bacterium called Streptomyces hygroscopicus. It takes its name from Rapa Nui, the indigenous name for the island. It is known clinically as sirolimus or Rapamune.
8.9 Uses
Rapamycin is a triene macrolide discovered in 1995 as a metabolite of Streptomyces hygroscopicus found in a soil obtained on Rapi Nui (Easter Island). Rapamycin displayed potent and selective antifungal activity, notably against Candida albicans. Interest in the metabolite waned until the structural relationship to the potent immunosuppressant fujimycin (Antibiotic FK506) was recognised in the mid-1980s. This recognition led to the re-discovery of rapamycin as a highly selective antitumour and immunosuppressant. Rapamycin inhibits the activity of the protein, mTOR (mammalian target of rapamycin) which functions in a signalling pathway to promote tumour growth. Rapamycin binds to a receptor protein (FKBP12). The rapamycin/FKB12 complex then binds to mTOR and prevents interaction of mTOR with target proteins in this signalling pathway.
8.10 Uses
Rapamycin is a triene macrolide discovered in 1974 as a metabolite of Streptomyces hygroscopicus found in a soil obtained on Rapa Nui (Easter Island). Rapamycin displayed potent and selective antifungal activity, notably against Candida albicans. Interest in the metabolite waned until the structural relationship to the potent immunosuppressant fujimycin (Antibiotic FK506) was recognised in the mid-1980s. This recognition led to the re-discovery of rapamycin as a highly selective antitumor and immunosuppressant. Rapamycin inhibits the activity of the protein, mTOR (mammalian target of rapamycin) which functions in a signalling pathway to promote tumor growth. Rapamycin binds to a receptor protein (FKBP12). The rapamycin/FKB12 complex then binds to mTOR and prevents interaction of mTOR with target proteins in this signalling pathway.
8.11 Uses
Labelled Rapamycin. A triene macrolide antibiotic isolated from Streptomyces hygroscopicus. Name derived from the native word for Easter Island, Rapa?Nui. Used as an immunosuppressant; antirestenotic. This compound contains aproximately 2% d0.;Labeled Sir
8.12 Uses
Rapamycin is an immunosuppressant that is used primarily to prevent the rejection of organ and bone marrow transplant. It was first described as a potent inhibitor of IL-2 activation of lymphocytes (IC50 = 5 pM). It is now known that rapamycin specifically interacts with the cytosolic FK-binding protein 12 (FKBP12) to form a complex which inhibits the mammalian target of rapamycin (mTOR) pathway by directly binding to mTOR Complex 1 (mTORC1). Rapamycin and other inhibitors of mTORC1 signaling show potential in treating cancer, adipogenesis, diabetes, tuberous sclerosis, and cardiovascular disease.[Cayman Chemical]
8.13 Definition
ChEBI: A macrolide isolated from Streptomyces hygroscopicus consisting of a 29-membered ring containing 4 trans double bonds, three of which are conjugated. It is an antibiotic, immunosupressive and antineoplastic agent.
8.14 Usage
Blocks cytokine-mediated signal transduction pathwaysRapamycin is used to inhibit tumor growth by halting tumor cell proliferation and suppressing tumor angiogenesis. It forms a complex with FKBP12 that binds and inhibits the molecular target of rapamycin (mTOR) as well as suppresses the immune system, preventing transplant rejection.
8.15 Indications
Mechanistic target of rapamycin (mTOR) is a serine/threonine-specific protein kinase in the PI3/PI4-kinase family. mTOR was named after the natural macrolide rapamycin, also known as sirolimus, which was isolated from a soil sample from Easter Island in the 1970s and later evaluated as an immunosuppressive agent. The anticancer activity of rapamycin was discovered in the 1980s, although the mechanismof action and the identification of the rapamycin target, mTOR, were not elucidated until the 1990s. Rapamycin and its macrocyclic analogues, such as temsirolimus (Torisel(R), Wyeth/Pfizer) and everolimus (Afinitor(R), Novartis), are grouped as “rapalogs” that constitute the first-generation mTOR inhibitors.
Rapamycin was approved by the US FDA in 1999 as an immunosuppressive agent to prevent organ rejection in patients receiving kidney transplants. Although a large number of clinical studies have been performed to evaluate the anticancer activities of sirolimus in different types of cancers, such as invasive bladder cancer, breast cancer, and leukemia, most studies show limited efficacy. Outside oncological indications, sirolimus was approved by FDA for the treatment of a rare progressive lung disease lymphangioleiomyomatosis in 2015. Temsirolimus was approved for the treatment of advanced RCC. Everolimus was approved in the EU for the prevention of organ rejection in heart and kidney transplant recipients before FDA approved it in 2009 for the treatment of advanced RCC resistant to sunitinib or sorafenib and for the treatment of advanced or metastatic gastrointestinal and lung tumors in 2016. Additionally, rapamycin and rapalogs are being investigated as antiaging therapeutics or for the treatment of age-related diseases. Studies have revealed that mTOR activity can be retained under hypoxic conditions via mutations in the PI3K pathway, leading to increased translation and hypoxic gene expression and tumor progression.
8.16 Indications
Sirolimus (Rapamune) is structurally related to tacrolimus. It is approved for use as an adjunctive agent in combination with cyclosporine for prevention of acute renal allograft rejection. It blocks IL-2-dependent T-cell proliferation by inhibiting a cytoplasmic serine– threonine kinase. This mechanism of action is different from those of tacrolimus and cyclosporine. This allows sirolimus to augment the immunosuppressive effects of these drugs.
8.17 Manufacturing Process
Streptomyces hygroscopicus NRRL 5491 was grown and maintained on oatmeal-tomato paste agar slants (T. G. Pridham et al.; Antibiotic Annual 1956-1957, Medical Encyclopedia Inc., New York, p. 947) and in Roux bottles containing the same medium. Good growth was obtained after 7 days of incubation at 28°C. Spores from one Roux bottle were washed off and suspended into 50 ml of sterile distilled water. This suspension was used to inoculate the first stage inoculum.The first-stage inoculum medium consisted of Emerson broth [R. L. Emerson et al., J. Bacteriol, 52, 357 (1946)] 0.4% peptone, 0.4% sodium chloride, 0.25% yeast extract and 1% glucose; pH 7.0; flasks containing the above medium were inoculated with 1 % of the spore suspension described above. The inoculated flasks were incubated for 30 hours at 28°C on a reciprocating shaker set at 65 r.p.m. (4 inch stroke).
Production stage
The production stage was run in 250-liter New Brunswick fermenters Model F- 250, equipped with automatic antifoam addition system and pH recordercontroller. The fermenters were charged with 160 L of an aqueous production medium consisting of the following constituents: 1.0% soluble starch; 0.5% (NH4)2SO4; 0.5% K2HPO4; 1.5% glucose (Cerelose); 0.025% MgSO4; 0.005% ZnSO4; 0.001% MnSO4; 0.002% FeSO47H2O; 0.2% CaCO3; 0.5% "Blackstrap" molasses; 0.5% hydrolyzed casein; 0.2% lard oil; pH 7.1 to 7.3 of first stage inoculum. Incubation temperature: 28°C; aeration: 0.5 vol/vol/min; agitation: 250 r.p.m. The fermenters were sterilized at 121°C for 45 min, cooled and inoculated with one flask inoculum).
A titre of ca. 20 μg/ml, determined by microbiological assay on agar plates seeded with Candida albicans, was reached in 5 days. The fermentation was stopped. The fermentation mixture was extracted twice with 1 v/v of nbutanol. The combined butanol extracts were washed with 1 v/v of water, dried with anhydrous sodium sulfate and evaporated to dryness under reduced pressure to yield a residue. The oily residue was extracted 3 times with 2 L of methanol. The combined methanol extracts were passed through diatomaceous earth (Celite) and evaporated to dryness to yield an oily residue containing crude Rapamycin.
8.18 Brand name
Rapamune (Wyeth).
8.19 Therapeutic Function
Immunosuppressive, Antifungal
8.20 General Description
Rapamycin is an anti-fungal antibiotic isolated from Streptomyces hygroscopicus. This antibiotic is active against all strains of Candida albicans. It blocks the signal transduction pathways required for the activation of T-helper cells.
9. Computational chemical data
  • Molecular Weight: 914.17186g/mol
  • Molecular Formula: C51H79NO13
  • Compound Is Canonicalized: True
  • XLogP3-AA: 6
  • Exact Mass: 913.55514157
  • Monoisotopic Mass: 913.55514157
  • Complexity: 1760
  • Rotatable Bond Count: 6
  • Hydrogen Bond Donor Count: 3
  • Hydrogen Bond Acceptor Count: 13
  • Topological Polar Surface Area: 195
  • Heavy Atom Count: 65
  • Defined Atom Stereocenter Count: 15
  • Undefined Atom Stereocenter Count: 0
  • Defined Bond Stereocenter Count: 4
  • Undefined Bond Stereocenter Count: 0
  • Isotope Atom Count: 0
  • Covalently-Bonded Unit Count: 1
10. Question & Answer
  • What is Rapamycin? Jul 01 2020
    Sirolimus, also known as rapamycin, is a macrolide derived from Streptomyces hygroscopicus. Sirolimus and its analog molecules, the so called ‘rapalogs’, belong to the inhibitors of the mammalian target of rapamycin (mTOR). mTOR is a serine-threonine kinase involved in cellular prolifer...
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