Pradimicin A
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| Category | Antibiotics |
| Catalog number | BBF-02052 |
| CAS | 117704-65-1 |
| Molecular Weight | 840.78 |
| Molecular Formula | C40H44N2O18 |
| Purity | ≥98% (HPLC) |
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Description
Pradimicin A is an antibiotic produced by Actinomadura hibisca. It has strong antifungal and yeast activity.
Specification
| Synonyms | Pradimicin A|117704-65-1|CHEBI:8349|(R)-2-((5S,6S)-1,6,9,14-Tetrahydroxy-5-(((2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-(((2S,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl)oxy)tetrahydro-2H-pyran-2-yl)oxy)-11-methoxy-3-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracene-2-carboxamido)propanoic acid|Pradimicin-A|BMY 28567|BMY-28567|(2R)-2-[[(5S,6S)-1,6,9,14-tetrahydroxy-5-[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-11-methoxy-3-methyl-8,13-dioxo-5,6-dihydrobenzo[a]tetracene-2-carbonyl]amino]propanoic acid|(2R)-2-[[(5S,6S)-1,6,9,14-tetrahydroxy-5-[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-[(2S,3R,4S,5R)-3,4,5-trihydroxytetrahydropyran-2-yl]oxy-tetrahydropyran-2-yl]oxy-11-methoxy-3-methyl-8,13-dioxo-5,6-dihydrobenzo[a]tetracene-2-carbonyl]amino]propanoic acid|Pradimicin A & Pectin|Pradimicin A & Glycogen|SCHEMBL499208|CHEMBL1673205|GLXC-25326|HY-132191|CS-0169773|Q27108053|(2R)-2-({[(5S,6S)-1,6,9,14-tetrahydroxy-5-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl]oxy}tetrahydro-2H-pyran-2-yl]oxy}-11-methoxy-3-methyl-8,13-dioxo-5,6,8,13-tetrahydrobenzo[a]tetracen-2-yl]carbonyl}amino)propanoic acid|D-Alanine, N-[[(5S,6S)-5-[[4,6-dideoxy-4-(methylamino)-3-O-.beta.-D-xylopyranosyl-.beta.-D-galactopyranosyl]oxy]-5,6,8,13-tetrahydro-1,6,9,14-tetrahydroxy-11-methoxy-3-methyl-8,13-dioxobenzo[a]naphthacen-2-yl]carbonyl]- |
| Storage | Store at -20°C |
| IUPAC Name | (2R)-2-[[(5S,6S)-1,6,9,14-tetrahydroxy-5-[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-11-methoxy-3-methyl-8,13-dioxo-5,6-dihydrobenzo[a]tetracene-2-carbonyl]amino]propanoic acid |
| Canonical SMILES | CC1C(C(C(C(O1)OC2C(C3=CC4=C(C(=C3C5=C2C=C(C(=C5O)C(=O)NC(C)C(=O)O)C)O)C(=O)C6=C(C4=O)C(=CC(=C6)OC)O)O)O)OC7C(C(C(CO7)O)O)O)NC |
| InChI | InChI=1S/C40H44N2O18/c1-11-6-18-24(31(49)21(11)37(53)42-12(2)38(54)55)23-16(9-17-25(32(23)50)28(46)15-7-14(56-5)8-19(43)22(15)27(17)45)29(47)35(18)59-40-34(52)36(26(41-4)13(3)58-40)60-39-33(51)30(48)20(44)10-57-39/h6-9,12-13,20,26,29-30,33-36,39-41,43-44,47-52H,10H2,1-5H3,(H,42,53)(H,54,55)/t12-,13-,20-,26+,29+,30+,33-,34-,35+,36+,39+,40+/m1/s1 |
| InChI Key | WPICPWIIIBCXCV-NJGWPHBESA-N |
Properties
| Appearance | Red Amorphous Powder |
| Antibiotic Activity Spectrum | fungi; yeast |
| Boiling Point | 1120.3±65.0°C at 760 mmHg |
| Melting Point | 193-195°C (dec.) |
| Flash Point | 631.316°C |
| Density | 1.7±0.1 g/cm3 |
| Solubility | In vitro: 10 mM in DMSO |
Reference Reading
1. d-Mannose binding, aggregation property, and antifungal activity of amide derivatives of pradimicin A
Wataru Miyanishi, Makoto Ojika, Dai Akase, Misako Aida, Yasuhiro Igarashi, Yukishige Ito, Yu Nakagawa Bioorg Med Chem. 2021 Dec 27;55:116590. doi: 10.1016/j.bmc.2021.116590. Online ahead of print.
Pradimicin A (PRM-A) and its derivatives comprise a unique family of antibiotics that show antifungal, antiviral, and antiparasitic activities through binding to d-mannose (Man)-containing glycans of pathogenic species. Despite their great potential as drug leads with an exceptional antipathogenic action, therapeutic application of PRMs has been severely limited by their tendency to form water-insoluble aggregates. Recently, we found that attachment of 2-aminoethanol to the carboxy group of PRM-A via amide linkage significantly suppressed the aggregation. Here, we prepared additional amide derivatives (2-8) of PRM-A to examine the possibility that the amide formation of PRM-A could suppress its aggregation propensity. Sedimentation assay and isothermal titration calorimetry experiment confirmed that all amide derivatives can bind Man without significant aggregation. Among them, hydroxamic acid derivative (4) showed the most potent Man-binding activity, which was suggested to be derived from the anion formation of the hydroxamic acid moiety by molecular modeling. Derivative 4 also exhibited significant antifungal activity comparable to that of PRM-A. These results collectively indicate that amide formation of PRM-A is the promising strategy to develop less aggregative derivatives, and 4 could serve as a lead compound for exploring the therapeutic application of PRM-A.
2. A Pradimicin-Based Staining Dye for Glycoprotein Detection
Yu Nakagawa, Shintaro Kakihara, Kazue Tsuzuki, Makoto Ojika, Yasuhiro Igarashi, Yukishige Ito J Nat Prod. 2021 Sep 24;84(9):2496-2501. doi: 10.1021/acs.jnatprod.1c00506. Epub 2021 Sep 15.
Pradimicin A (PRM-A) and related compounds constitute an exceptional family of natural pigments that show Ca2+-dependent recognition of d-mannose (Man). Although these compounds hold great promise as research tools in glycobiology, their practical application has been severely limited by their inherent tendency to form water-insoluble aggregates. Here, we demonstrate that the 2-hydroxyethylamide derivative (PRM-EA) of PRM-A shows little aggregation in neutral aqueous media and retains binding specificity for Man. We also show that PRM-EA stains glycoproteins in dot blot assays, whereas PRM-A fails to do so, owing to severe aggregation. Significantly, PRM-EA is sensitive to glycoproteins carrying high mannose-type and hybrid-type N-linked glycans, but not to those carrying complex-type N-linked glycans. Such staining selectivity has never been observed in conventional dyes, suggesting that PRM-EA could serve as a unique staining agent for the selective detection of glycoproteins with terminal Man residues.
3. Pradimicin A, a D-mannose-binding antibiotic, binds pyranosides of L-fucose and L-galactose in a calcium-sensitive manner
Yu Nakagawa, Yasunori Watanabe, Yasuhiro Igarashi, Yukishige Ito, Makoto Ojika Bioorg Med Chem Lett. 2015 Aug 1;25(15):2963-6. doi: 10.1016/j.bmcl.2015.05.021. Epub 2015 May 16.
Pradimicin A (PRM-A) is a unique antibiotic with a lectin-like ability to bind D-mannose (D-Man) in the presence of Ca(2+) ion. Although accumulated evidences suggest that PRM-A recognizes the 2-, 3-, and 4-hydroxyl groups of D-Man, BMY-28864, an artificial PRM-A derivative, was shown not to bind L-fucose (L-Fuc) and L-galactose (lLGal), both of which share the characteristic array of the three hydroxyl groups with D-Man. To obtain a plausible explanation for this inconsistency, we performed co-precipitation experiments of PRM-A with L-Fuc, L-Gal, and their methyl pyranosides (L-Fuc-OMe, L-Gal-OMe) by taking advantage of aggregate-forming propensity of the binary [PRM-A/Ca(2+)] complex. While L-Fuc and L-Gal were hardly incorporated into the aggregate, L-Fuc-OMe and L-Gal-OMe were found to exhibit significant binding to PRM-A. However, increased Ca(2+) concentration abolished this binding, raising the possibility that poor binding of L-Fuc and L-Gal to PRM-A is attributed to their chelation with Ca(2+) ion. This possibility was partly supported by (1)H NMR analysis that detected interaction of L-Fuc and L-Gal with Ca(2+) ion in aqueous solution. These results collectively indicate that PRM-A binds pyranosides of L-Fuc and L-Gal when Ca(2+) concentration is not excessive to trap these sugars by chelation but sufficient to form the [PRM-A/Ca(2+)] complex.
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Bio Calculators
* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2
* Total Molecular Weight:
g/mol
Tip: Chemical formula is case sensitive. C22H30N4O √ c22h30n40 ╳
