Cyclomarin A
Cyclomarin A is an antibacterial agent with a Kd of 2.3 nM against Mycobacterium tuberculosis ClpC1, a Kd of 2.2 nM against ClpC2, and an IC50 of 0.004 μM against Plasmodium falciparum PfAp3Aase. Cyclomarin A binds to the N-terminal domain of ClpC1, stimulates ATPase and proteolytic activities, dysregulates proteolysis, and induces proteome imbalance; it also binds to ClpC2 and upregulates its transcription level. Cyclomarin A binds to PfAp3Aase in dimeric form, blocks the substrate-binding pathway, inhibits the growth of Plasmodium falciparum in the erythrocytic stage, and shows no activity against human cells. Cyclomarin A exhibits moderate cytotoxicity against a variety of cancer cell lines. Cyclomarin A can serve as a lead compound for the development of Homo-BacPROTAC. Cyclomarin A is applicable to research related to tuberculosis and malaria.
For research use only. We do not sell to patients.
- CAS No.: 169062-92-4
- Formula: C56H82N8O11
- Molecular Weight:1043.30
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Storage:
Please store the product under the recommended conditions in the Certificate of Analysis.
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Biological Activity
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Chemical Information
- Protocols
- Purity & Documentation
- References
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Help & FAQs
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Biological Activity
Description
IC50 & Target
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ClpC2 2.2 nM (Kd) |
ClpC1 2.3 nM (Kd) |
PfAp3Aase 4 nM (IC50) |
In Vitro
Cyclomarin A binds to a conserved hydrophobic pocket on Mycobacterium tuberculosis ClpC1NTD, which serves as the receptor site for misfolded proteins[1].
Cyclomarin A (0.01-25 μM) potently activates the ATPase activity of the chimeric protein NMtb-ClpC, with a K0.5 of 0.3 μM; it partially activates Sa ClpC-Y80F, but has no effect on wild-type Sa ClpC[4].
Cyclomarin A (0.1-25 μM) enables NMtb-ClpC/Sa ClpP to degrade FITC-casein in an adaptor-independent manner, with a half-maximal activity concentration of 0.13 μM; this agent induces partial degradation of Sa ClpC-Y80F/Sa ClpP, but exerts no effect on wild-type Sa ClpC/Sa ClpP[4].
Cyclomarin A (10 μM) activates NMtb-ClpC/Sa ClpP to degrade unlabeled casein and the native substrate FtsZ, while inhibiting the degradation of MecA by this complex[4].
Cyclomarin A (10 μM) activates NMtb-ClpC/Sa ClpP to degrade the stably folded substrates Casein-YFP and GFP-SsrA, but its unfolding activity is significantly reduced compared with MecA activation[4].
Cyclomarin A (20 μM) induces the formation of a large, homogeneous 24.2-mer assembly composed of multiple hexamers from NMtb-ClpC-DWB, and this assembly interacts with Sa ClpP[4].
Cyclomarin A (20 μM; 10 min) induces conformational changes in NMtb-ClpC, which are highly similar to those induced by MecA, including increased stability of key domains associated with ATP binding and hydrolysis[4].
Cyclomarin A exhibits moderate cytotoxicity against a variety of cancer cell lines, with an IC50 of ~2.5 μM[2].
Cyclomarin A selectively inhibits PfAp3Ase of Plasmodium falciparum in the nanomolar concentration range, without inhibiting the human FHIT enzyme[2].
Cyclomarin A inhibits the growth of the erythrocytic stage of *Plasmodium falciparum* strain NF54, with an IC50 of 40 nM[3].
Cyclomarin A potently inhibits recombinant *Plasmodium falciparum* PfAp3Aase with an IC50 of 4 nM; it does not inhibit recombinant *Plasmodium falciparum* PfAp4Aase or human hFHIT even at concentrations as high as 10 μM[3].
Cyclomarin A binds to the central channel of the homodimeric *Plasmodium falciparum* PfAp3Aase, and inhibits enzymatic activity by blocking substrate access to the two binding sites via steric hindrance[3].
Cyclomarin A (100 μM) specifically binds to *Plasmodium falciparum* PfAp3Aase, which is demonstrated by a binding competition rate of >75% in affinity chromatography experiments[3].
Cyclomarin A exhibits antibacterial activity against *Mycobacterium tuberculosis* (MTB)[2].
Cyclomarin A inhibits the growth of *Mycobacterium tuberculosis* with a MIC50 of 0.1 μM by binding to ClpC1 and regulating proteolytic processes[3].
Cyclomarin A (0.1-10 μM; 24 h) is toxic to *E. coli* cells co-expressing NMtb-ClpC and Sa ClpP, reducing cell viability by 1000-fold at a concentration of 10 μM and exerting maximal toxicity at 1 μM, with its mechanism of action being uncontrolled proteolysis of intracellular proteins[4].
Cyclomarin A (5 μM) binds to purified *Mycobacterium tuberculosis* ClpC2 with a dissociation constant of 2.2 nM, exhibiting a tight 1:1 binding mode, and its affinity is comparable to that for ClpC1 NTD[5].
Cyclomarin A (at a 1.1-fold molar excess relative to ClpC294-252) binds to the C-terminal domain (residues 94-252) of Mycobacterium tuberculosis ClpC2 in an almost identical manner to its binding to ClpC1 NTD, as confirmed by a co-crystal structure with a resolution of 1.43 Å[5].
Cyclomarin A (150 nM; up to 100 hours) inhibits the growth of Mycobacterium smegmatis ΔclpC2 strain, while wild-type strains and clpC2-complemented strains remain unaffected, indicating that ClpC2 mediates resistance to CymA-induced toxicity through direct binding[5].
Cyclomarin A (150 nM; 1-8 h) significantly upregulates the expression of ClpC2 protein in *Mycobacterium smegmatis*, and its expression level reaches 84 times that of stably expressed ClpC1 at 8 h post-treatment[5].
Cyclomarin A (150 nM; 1 h) upregulates the transcription level of clpC2 in *Mycobacterium smegmatis* by 263-fold[5].
The proteolytic activity of Cyclomarin A (2-20 μM)-stimulated ClpC1P against FITC-casein is dose-dependently inhibited by purified *Mycobacterium tuberculosis* ClpC2, with nearly complete inhibition observed at a ClpC2 concentration of 20 μM[5].
Cyclomarin A (1 μM; 20 min) inhibits the binding of purified *Mycobacterium tuberculosis* ClpC2 to its own operon DNA[5].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only. Further protocols information, click here.
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Cell Line:Mycobacterium smegmatis wild-type cultures
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Concentration:150 nM
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Incubation Time:1, 2, 4, and 8 h
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Result:Induced a faint ClpC2 band after 1 hour of treatment.
Increased ClpC2 levels by several orders of magnitude by 8 hours.
Resulted in ClpC2 levels rising to 84-fold in excess of constant ClpC1 levels by 8 hours post-treatment.
ClpC2 was undetectable in untreated cultures.
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Cell Line:Mycobacterium smegmatis wild-type cultures
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Concentration:150 nM
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Incubation Time:1 h
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Result:Induced a 263-fold increase in clpC2 mRNA levels compared to untreated cultures.
Chemical Information
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CAS No. 169062-92-4
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Molecular Weight 1043.30
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Formula C56H82N8O11
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SMILES
CC(N1C2=CC=CC=C2C([C@H]([C@@]3([H])C(N([C@H](C(N[C@H](C(N[C@@](C(N[C@H](C(N([C@H](C(N[C@@](C(N3)=O)([H])[C@H](C)/C=C(C)\C)=O)CC(C)C)C)=O)C(C)C)=O)([H])[C@@H](C4=CC=CC=C4)OC)=O)C)=O)C[C@@H](C)CO)C)=O)O)=C1)([C@@H]5CO5)C
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
Please store the product under the recommended conditions in the Certificate of Analysis.
Protocols
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Research Protocol for Infectious Diseases
Infectious-disease experiments test how pathogens interact with host barriers, innate immune receptors, inflammatory signaling, pathogen replication, and tissue injury; pattern-recognition receptors such as TLRs, RIG-I-like receptors, NOD-like receptors, and inflammasomes detect microbial molecules and activate NF-κB, interferon, and cytokine responses. The central hypothesis is that infection severity reflects the balance between pathogen burden and host response: protective inflammation restricts pathogen growth, whereas excessive or mislocalized inflammation contributes to tissue damage and disease phenotype. Unresolved questions include which host pathways are protective versus pathogenic, why some infection models fail to translate to human disease, and which combined readouts best predict clinically relevant infection outcomes.
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Cell Cytotoxicity Assay
Cytotoxicity assays are usually based on the assessment of cell membrane damage, which can also be indirectly detected by measuring cell viability. Detection methods include MTT assay, CKK-8 assay, LDH assay and ATP assay, etc.
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Mammalian live/dead viability and cytotoxicity staining
Live/dead viability and cytotoxicity staining assays are based on the simultaneous detection of intracellular esterase activity in metabolically active (viable) cells and membrane integrity loss in non-viable cells. In commonly used dual-staining approaches, membrane-permeant fluorogenic substrates are converted by intracellular esterases into fluorescent products in live cells, while impermeant DNA-binding dyes selectively enter cells with compromised plasma membranes and label nucleic acids in dead or dying cells, enabling discrimination between viable and non-viable populations by fluorescence microscopy or flow cytometry.
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Real Time qPCR (Q-PCR)
Real-time quantitative PCR (qPCR) quantifies an amplifiable nucleic-acid target by monitoring fluorescence during PCR cycling rather than measuring product only after amplification. The increase in fluorescence tracks accumulation of PCR product, and the quantification cycle (Cq; historically also Ct/CP) is related to the initial amount of target: samples containing more starting target generally reach the defined fluorescence threshold in fewer cycles.
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Cell Viability Determination by MTT Colorimetric Assay
The following protocol uses the MTT colorimetric assay as a classic literature-established method for assessing cell viability/metabolic activity in cultured mammalian cells. MTT[3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] is reduced by metabolically active cells to a colored formazan product; the amount of formazan is quantified spectrophotometrically and provides an indirect measure of metabolically active viable cells. Importantly, MTT reduction reflects cellular oxidoreductase/metabolic activity rather than an absolute direct count of living cells, so changes in cellular metabolism can alter the signal independently of cell number.
Purity & Documentation
References
[1]. Hoi DM, et al. Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival. Cell. 2023 May 11;186(10):2176-2192.e22. [Content Brief]
[2]. Barbie P, et al. Total Synthesis of Cyclomarin A, a Marine Cycloheptapeptide with Anti-Tuberculosis and Anti-Malaria Activity. Organic letters. 2016 Jan 15;18(2):204-7. [Content Brief]
[3]. Bürstner N, et al. Gift from Nature: Cyclomarin A Kills Mycobacteria and Malaria Parasites by Distinct Modes of Action. Chembiochem : a European journal of chemical biology. 2015 Nov;16(17):2433-6. [Content Brief]
[4]. Maurer M, et al. Toxic Activation of an AAA+ Protease by the Antibacterial Drug Cyclomarin A. Cell Chem Biol. 2019 Aug 15;26(8):1169-1179.e4. [Content Brief]
[5]. Taylor G, et al. ClpC2 protects mycobacteria against a natural antibiotic targeting ClpC1-dependent protein degradation. Communications biology. 2023 Mar 21;6(1):301. [Content Brief]
Calculators
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
Cyclomarin A Related Classifications
HY-P6300 Related Classifications
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