Albicidin sodium

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MedKoo CAT#: 592469

CAS#: Albicidin sodium

Description: Albicidin is a DNA gyrase inhibitor produced by Xanthomonas albilineans which causes leaf scald, a lethal disease of sugarcane. Albicidin blocks chloroplast differentiation, resulting in the characteristic white foliar stripe symptoms of leaf scald. Albicidin has inhibitory effects significantly better than most DNA gyrase inhibitors. Albicidin acts primarily by inhibiting the religation of the cleaved DNA intermediate during the gyrase catalytic sequence similar to quinolones. The clinical realization of albicidin has been hampered by limited production and its unsolved structure.


Chemical Structure

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Albicidin sodium
CAS# Albicidin sodium

Theoretical Analysis

MedKoo Cat#: 592469
Name: Albicidin sodium
CAS#: Albicidin sodium
Chemical Formula: C44H37N6NaO12
Exact Mass: 842.2548
Molecular Weight: 864.8
Elemental Analysis: C, 61.11; H, 4.31; N, 9.72; Na, 2.66; O, 22.20

Price and Availability

This product is not in stock, which may be available by custom synthesis. For cost-effective reason, minimum order is 1g (price is usually high, lead time is 2~3 months, depending on the technical challenge). Quote less than 1g will not be provided. To request quote, please email to sales @medkoo.com or click below button.
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Related CAS #: 1622253-00-2 (S-isomer)   96955-97-4   1669446-71-2 (R-isomer)   Albicidin sodium  

Synonym: Albicidin sodium,

IUPAC/Chemical Name: sodium 4-[[4-[[4-[[(2S)-3-Cyano-2-[[4-[[(2E)-3-(4-hydroxyphenyl)-2-methyl-1-oxo-2-propen-1-yl]amino]benzoyl]amino]-1-oxopropyl]amino]benzoyl]amino]-2-hydroxy-3-methoxybenzoyl]amino]-2-hydroxy-3-methoxybenzoate

InChi Key: YRNQQUYPBZJTRC-MVSXQLBBSA-M

InChi Code: InChI=1S/C44H38N6O12.Na/c1-23(22-24-4-14-29(51)15-5-24)39(54)46-27-10-6-26(7-11-27)41(56)50-34(20-21-45)43(58)47-28-12-8-25(9-13-28)40(55)48-32-18-16-30(35(52)37(32)61-2)42(57)49-33-19-17-31(44(59)60)36(53)38(33)62-3;/h4-19,22,34,51-53H,20H2,1-3H3,(H,46,54)(H,47,58)(H,48,55)(H,49,57)(H,50,56)(H,59,60);/q;+1/p-1/b23-22+;/t34-;/m0./s1

SMILES Code: O=C([O-])C1=CC=C(NC(C2=CC=C(NC(C3=CC=C(NC([C@@H](NC(C4=CC=C(NC(/C(C)=C/C5=CC=C(O)C=C5)=O)C=C4)=O)CC#N)=O)C=C3)=O)C(OC)=C2O)=O)C(OC)=C1O.[Na+]

Appearance: Solid powder

Purity: >98% (or refer to the Certificate of Analysis)

Shipping Condition: Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.

Storage Condition: Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).

Solubility: Soluble in DMSO

Shelf Life: >3 years if stored properly

Drug Formulation: This drug may be formulated in DMSO

Stock Solution Storage: 0 - 4 C for short term (days to weeks), or -20 C for long term (months).

HS Tariff Code: 2934.99.03.00

Preparing Stock Solutions

The following data is based on the product molecular weight 864.8 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.

Recalculate based on batch purity %
Concentration / Solvent Volume / Mass 1 mg 5 mg 10 mg
1 mM 1.15 mL 5.76 mL 11.51 mL
5 mM 0.23 mL 1.15 mL 2.3 mL
10 mM 0.12 mL 0.58 mL 1.15 mL
50 mM 0.02 mL 0.12 mL 0.23 mL

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1: Chen L, Huang H, Bian R, Deng Z, Gao S, Zhang H. [Advances in albicidin]. Sheng Wu Gong Cheng Xue Bao. 2022 Aug 25;38(8):2738-2753. Chinese. doi: 10.13345/j.cjb.210832. PMID: 36002407.

2: Zborovsky L, Kleebauer L, Seidel M, Kostenko A, von Eckardstein L, Gombert FO, Weston J, Süssmuth RD. Improvement of the antimicrobial potency, pharmacokinetic and pharmacodynamic properties of albicidin by incorporation of nitrogen atoms. Chem Sci. 2021 Oct 19;12(43):14606-14617. doi: 10.1039/d1sc04019g. PMID: 34881013; PMCID: PMC8580050.

3: Kleebauer L, Zborovsky L, Hommernick K, Seidel M, Weston JB, Süssmuth RD. Overcoming AlbD Protease Resistance and Improving Potency: Synthesis and Bioactivity of Antibacterial Albicidin Analogues with Amide Bond Isosteres. Org Lett. 2021 Sep 17;23(18):7023-7027. doi: 10.1021/acs.orglett.1c02312. Epub 2021 Aug 16. PMID: 34398605.

4: Wang Z, Kasper A, Mehmood R, Ternei M, Li S, Freundlich JS, Brady SF. Metagenome-Guided Analogue Synthesis Yields Improved Gram-Negative-Active Albicidin- and Cystobactamid-Type Antibiotics. Angew Chem Int Ed Engl. 2021 Oct 4;60(41):22172-22177. doi: 10.1002/anie.202104874. Epub 2021 Sep 7. PMID: 34355488.

5: Kortright KE, Doss-Gollin S, Chan BK, Turner PE. Evolution of Bacterial Cross-Resistance to Lytic Phages and Albicidin Antibiotic. Front Microbiol. 2021 Jun 17;12:658374. doi: 10.3389/fmicb.2021.658374. PMID: 34220747; PMCID: PMC8245764.

6: Behroz I, Kleebauer L, Hommernick K, Seidel M, Grätz S, Mainz A, Weston JB, Süssmuth RD. Acetylenic Replacement of Albicidin's Methacrylamide Residue Circumvents Detrimental E/Z Photoisomerization and Preserves Antibacterial Activity. Chemistry. 2021 Jun 21;27(35):9077-9086. doi: 10.1002/chem.202100523. Epub 2021 May 21. PMID: 33769627; PMCID: PMC8362182.

7: Behroz I, Durkin P, Grätz S, Seidel M, Rostock L, Spinczyk M, Weston JB, Süssmuth RD. Extensive Structure-Activity Relationship Study of Albicidin's C-Terminal Dipeptidic p-Aminobenzoic Acid Moiety. Chemistry. 2019 Dec 20;25(72):16538-16543. doi: 10.1002/chem.201904752. Epub 2019 Dec 11. PMID: 31642561; PMCID: PMC6972991.

8: Hashimi SM. Albicidin, a potent DNA gyrase inhibitor with clinical potential. J Antibiot (Tokyo). 2019 Nov;72(11):785-792. doi: 10.1038/s41429-019-0228-2. Epub 2019 Aug 26. PMID: 31451755.

9: Rostock L, Driller R, Grätz S, Kerwat D, von Eckardstein L, Petras D, Kunert M, Alings C, Schmitt FJ, Friedrich T, Wahl MC, Loll B, Mainz A, Süssmuth RD. Molecular insights into antibiotic resistance - how a binding protein traps albicidin. Nat Commun. 2018 Aug 6;9(1):3095. doi: 10.1038/s41467-018-05551-4. PMID: 30082794; PMCID: PMC6078987.

10: Kerwat D, Grätz S, Kretz J, Seidel M, Kunert M, Weston JB, Süssmuth RD. Synthesis of Albicidin Derivatives: Assessing the Role of N-terminal Acylation on the Antibacterial Activity. ChemMedChem. 2016 Sep 6;11(17):1899-903. doi: 10.1002/cmdc.201600231. Epub 2016 Jul 21. PMID: 27439374.

11: Grätz S, Kerwat D, Kretz J, von Eckardstein L, Semsary S, Seidel M, Kunert M, Weston JB, Süssmuth RD. Synthesis and Antimicrobial Activity of Albicidin Derivatives with Variations of the Central Cyanoalanine Building Block. ChemMedChem. 2016 Jul 19;11(14):1499-502. doi: 10.1002/cmdc.201600163. Epub 2016 Jun 1. PMID: 27245621.

12: Petras D, Kerwat D, Pesic A, Hempel BF, von Eckardstein L, Semsary S, Arasté J, Marguerettaz M, Royer M, Cociancich S, Süssmuth RD. The O-Carbamoyl- Transferase Alb15 Is Responsible for the Modification of Albicidin. ACS Chem Biol. 2016 May 20;11(5):1198-204. doi: 10.1021/acschembio.5b01001. Epub 2016 Feb 23. PMID: 26886160.

13: Vieweg L, Kretz J, Pesic A, Kerwat D, Grätz S, Royer M, Cociancich S, Mainz A, Süssmuth RD. The Albicidin Resistance Factor AlbD Is a Serine Endopeptidase That Hydrolyzes Unusual Oligoaromatic-Type Peptides. J Am Chem Soc. 2015 Jun 24;137(24):7608-11. doi: 10.1021/jacs.5b04099. Epub 2015 Jun 15. PMID: 26057615.

14: Cociancich S, Pesic A, Petras D, Uhlmann S, Kretz J, Schubert V, Vieweg L, Duplan S, Marguerettaz M, Noëll J, Pieretti I, Hügelland M, Kemper S, Mainz A, Rott P, Royer M, Süssmuth RD. The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine. Nat Chem Biol. 2015 Mar;11(3):195-7. doi: 10.1038/nchembio.1734. Epub 2015 Jan 19. PMID: 25599532.

15: Kretz J, Kerwat D, Schubert V, Grätz S, Pesic A, Semsary S, Cociancich S, Royer M, Süssmuth RD. Total synthesis of albicidin: a lead structure from Xanthomonas albilineans for potent antibacterial gyrase inhibitors. Angew Chem Int Ed Engl. 2015 Feb 2;54(6):1969-73. doi: 10.1002/anie.201409584. Epub 2014 Dec 12. PMID: 25504839.

16: Hashimi SM, Birch RG. Functional analysis of genes for benzoate metabolism in the albicidin biosynthetic region of Xanthomonas albilineans. Appl Microbiol Biotechnol. 2010 Jul;87(4):1475-85. doi: 10.1007/s00253-010-2620-5. Epub 2010 May 2. PMID: 20437231.

17: Champoiseau P, Daugrois JH, Girard JC, Royer M, Rott PC. Variation in Albicidin Biosynthesis Genes and in Pathogenicity of Xanthomonas albilineans, the Sugarcane Leaf Scald Pathogen. Phytopathology. 2006 Jan;96(1):33-45. doi: 10.1094/PHYTO-96-0033. PMID: 18944203.

18: Hashimi SM, Huang G, Maxwell A, Birch RG. DNA gyrase from the albicidin producer Xanthomonas albilineans has multiple-antibiotic-resistance and unusual enzymatic properties. Antimicrob Agents Chemother. 2008 Apr;52(4):1382-90. doi: 10.1128/AAC.01551-07. Epub 2008 Feb 11. PMID: 18268084; PMCID: PMC2292561.

19: Renier A, Vivien E, Cociancich S, Letourmy P, Perrier X, Rott PC, Royer M. Substrate specificity-conferring regions of the nonribosomal peptide synthetase adenylation domains involved in albicidin pathotoxin biosynthesis are highly conserved within the species Xanthomonas albilineans. Appl Environ Microbiol. 2007 Sep;73(17):5523-30. doi: 10.1128/AEM.00577-07. Epub 2007 Jul 13. PMID: 17630307; PMCID: PMC2042071.

20: Vivien E, Pitorre D, Cociancich S, Pieretti I, Gabriel DW, Rott PC, Royer M. Heterologous production of albicidin: a promising approach to overproducing and characterizing this potent inhibitor of DNA gyrase. Antimicrob Agents Chemother. 2007 Apr;51(4):1549-52. doi: 10.1128/AAC.01450-06. Epub 2007 Jan 12. PMID: 17220426; PMCID: PMC1855474.