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MedKoo Cat#: 525748 | Name: Netropsin free base

Description:

WARNING: This product is for research use only, not for human or veterinary use.

Netropsin is a DNA minor groove binder originally isolated from S. netropsis. It binds to A/T rich regions of DNA (Ka = 4.9 x 105 M-1 for poly(dA)poly(dT) DNA). Netropsin inhibits topoisomerase II (IC90 = 200 µM in a cell-free assay) and teniposide-induced crosslinks in nuclei from 935.1 mouse fibrosarcoma cells (IC50 = 65 µM). It is active against several bacteria, including S. aureus, S. typhosa, K. pneumoniae, and A. aerogenes with MIC values of 5, 10, 10, and 5 µg/ml, respectively. Netropsin (75 µg/ml) inhibits viral plaque formation in Shope fibroma virus- or vaccinia virus-infected BS-C-1 host cells.5 It increases survival in a mouse model of endotoxemia induced by LPS when administered at a dose of 25 mg/kg.

Chemical Structure

Netropsin free base
Netropsin free base
CAS#1438-30-8 (free base)

Theoretical Analysis

MedKoo Cat#: 525748

Name: Netropsin free base

CAS#: 1438-30-8 (free base)

Chemical Formula: C18H26N10O3

Exact Mass: 430.2189

Molecular Weight: 430.47

Elemental Analysis: C, 50.22; H, 6.09; N, 32.54; O, 11.15

Price and Availability

This product is currently not in stock but may be available through custom synthesis. To ensure cost efficiency, the minimum order quantity is 1 gram. The estimated lead time is 2 to 4 months, with pricing dependent on the complexity of the synthesis (typically high for intricate chemistries). Quotes for quantities below 1 gram will not be provided. To request a quote, please click the button below. Note: If this product becomes available in stock in the future, pricing will be listed accordingly.
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Related CAS #
1438-30-8 (free base) 18133-22-7 (HCl)
Synonym
Antibiotic 1142; Antibiotic T-1384; Antibiotic T1384; Antibiotic T 1384; Sinanomycin; Congocidin; Congocidine; F 6; F6; F-9; IA-887; IA887; IA 887; K-117; K117; K 117; Netropsin
IUPAC/Chemical Name
N-(3-amino-3-iminopropyl)-4-(4-(2-guanidinoacetamido)-1-methyl-1H-pyrrole-2-carboxamido)-1-methyl-1H-pyrrole-2-carboxamide
InChi Key
IDBIFFKSXLYUOT-UHFFFAOYSA-N
InChi Code
InChI=1S/C18H26N10O3/c1-27-9-11(6-12(27)16(30)23-4-3-14(19)20)26-17(31)13-5-10(8-28(13)2)25-15(29)7-24-18(21)22/h5-6,8-9H,3-4,7H2,1-2H3,(H3,19,20)(H,23,30)(H,25,29)(H,26,31)(H4,21,22,24)
SMILES Code
O=C(C1=CC(NC(C2=CC(NC(CNC(N)=N)=O)=CN2C)=O)=CN1C)NCCC(N)=N
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, not in water
Shelf Life
>2 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
2934.99.9001
More Info
Product Data
Product Data
Instruction
View handling instruction
Biological target:
Netropsin is a DNA minor groove binder originally isolated from S. netropsis.
In vitro activity:
Netropsin suppressed the increase of intracellular proteolytic activity when added to B. megaterium incubated in a sporulation medium. Different concentrations of netropsin affected various aspects of protein catabolism differently. Reference: Folia Microbiol (Praha). 1993;38(1):10-4. https://pubmed.ncbi.nlm.nih.gov/8388845/
In vivo activity:
Netropsin improved survival from endotoxaemia in wild-type mice, yet not in NOS2-deficient mice, supporting an important role for NOS2 in the beneficial effects of MGB administration. Netropsin significantly attenuated NOS2 promoter activity in macrophage transient transfection studies and the AT-rich HMGA1 DNA-binding site was critical for this effect. Reference: Biochem J. 2009 Feb 15;418(1):103-12. https://pubmed.ncbi.nlm.nih.gov/18937643/

Preparing Stock Solutions

The following data is based on the product molecular weight 430.47 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
Formulation protocol:
1. Kucerová H, Chaloupka J. Netropsin inhibits the increase of intracellular Ca(2+)-dependent serine proteinase activity in sporulating Bacillus megaterium. Folia Microbiol (Praha). 1993;38(1):10-4. doi: 10.1007/BF02814541. PMID: 8388845. 2. Ueno A, Baek K, Jeon C, Agarwal K. Netropsin specifically enhances RNA polymerase II termination at terminator sites in vitro. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3676-80. doi: 10.1073/pnas.89.9.3676. PMID: 1315032; PMCID: PMC525553. 3. Grant MA, Baron RM, Macias AA, Layne MD, Perrella MA, Rigby AC. Netropsin improves survival from endotoxaemia by disrupting HMGA1 binding to the NOS2 promoter. Biochem J. 2009 Feb 15;418(1):103-12. doi: 10.1042/BJ20081427. PMID: 18937643; PMCID: PMC2821790.
In vitro protocol:
1. Kucerová H, Chaloupka J. Netropsin inhibits the increase of intracellular Ca(2+)-dependent serine proteinase activity in sporulating Bacillus megaterium. Folia Microbiol (Praha). 1993;38(1):10-4. doi: 10.1007/BF02814541. PMID: 8388845. 2. Ueno A, Baek K, Jeon C, Agarwal K. Netropsin specifically enhances RNA polymerase II termination at terminator sites in vitro. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3676-80. doi: 10.1073/pnas.89.9.3676. PMID: 1315032; PMCID: PMC525553.
In vivo protocol:
1. Grant MA, Baron RM, Macias AA, Layne MD, Perrella MA, Rigby AC. Netropsin improves survival from endotoxaemia by disrupting HMGA1 binding to the NOS2 promoter. Biochem J. 2009 Feb 15;418(1):103-12. doi: 10.1042/BJ20081427. PMID: 18937643; PMCID: PMC2821790.
1: Chung JH, Bhat A, Kim CJ, Yong D, Ryu CM. Combination therapy with polymyxin B and netropsin against clinical isolates of multidrug-resistant Acinetobacter baumannii. Sci Rep. 2016 Jun 16;6:28168. doi: 10.1038/srep28168. PubMed PMID: 27306928; PubMed Central PMCID: PMC4910107. 2: Andronova VL, Grokhovsky SL, Surovaya AN, Gursky GV, Galegov GA. Effect of dimeric netropsin analogue 15Lys-bis-Nt and acyclovir on the reproduction of herpes simplex virus type 1. The search for variants of herpes virus with drug resistance to 15Lys-bis-Nt and acyclovir. Dokl Biochem Biophys. 2015;460:42-6. doi: 10.1134/S1607672915010123. Epub 2015 Mar 13. PubMed PMID: 25772989. 3: Szerszenowicz J, Drozdowska D. Semi-automatic synthesis, antiproliferative activity and DNA-binding properties of new netropsin and bis-netropsin analogues. Molecules. 2014 Jul 31;19(8):11300-15. doi: 10.3390/molecules190811300. PubMed PMID: 25090119. 4: Ramos JP, Le VH, Lewis EA. Role of water in netropsin binding to an A(2)T(2) hairpin DNA site: osmotic stress experiments. J Phys Chem B. 2013 Dec 19;117(50):15958-65. doi: 10.1021/jp408077m. Epub 2013 Dec 5. PubMed PMID: 24274393. 5: andronova VL, Grokhovskiĭ SL, Surovaia AN, Gurskiĭ GV, Deriabin PG, L'vov DK, Galegov GA. [Estimation of activity of bis-netropsin derivatives based on a model of an experimental cutaneous herpes simplex virus disease of guinea pigs]. Vopr Virusol. 2013 Jan-Feb;58(1):32-5. Russian. PubMed PMID: 23785759. 6: Ghosh S, Salsbury FR Jr, Horita DA, Gmeiner WH. Cooperative stabilization of Zn(2+):DNA complexes through netropsin binding in the minor groove of FdU-substituted DNA. J Biomol Struct Dyn. 2013;31(11):1301-10. doi: 10.1080/07391102.2012.732343. Epub 2012 Nov 16. PubMed PMID: 23153072; PubMed Central PMCID: PMC3825453. 7: Andronova VL, Grokhovskiĭ SL, Deriabin PG, Gurskiĭ GV, Galegov GA, L'vov DK. [Antiherpetic activity of netropsin derivatives as tested in experiments in laboratory animals]. Vopr Virusol. 2012 Jul-Aug;57(4):24-6. Russian. PubMed PMID: 23012980. 8: Bazhulina NP, Surovaia AN, Gurskiĭ IaG, Andronova VL, Arkhipova VS, Golovkin MV, Nikitin AM, Galegov GA, Gorokhovskiĭ SL, Gurskiĭ GV. [Inhibition of herpes simplex virus helicase UL9 by netropsin derivatives and antiviral activities of bis-netropsins]. Biofizika. 2012 Mar-Apr;57(2):232-42. Russian. PubMed PMID: 22594278. 9: Hansen N, Dolenc J, Knecht M, Riniker S, van Gunsteren WF. Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. J Comput Chem. 2012 Mar 5;33(6):640-51. doi: 10.1002/jcc.22879. Epub 2012 Jan 7. PubMed PMID: 22228455. 10: Lewis EA, Munde M, Wang S, Rettig M, Le V, Machha V, Wilson WD. Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site. Nucleic Acids Res. 2011 Dec;39(22):9649-58. doi: 10.1093/nar/gkr699. Epub 2011 Sep 3. PubMed PMID: 21890907; PubMed Central PMCID: PMC3239193. 11: Andronova VL, Grokhovskiĭ SL, Galegov GA, Deriabin PG, Gurskiĭ GV, L'vov DK. [Antiviral properties of the derivatives of netropsin and distamycin against herpes simplex viruses type 1 and variolovaccine]. Vopr Virusol. 2010 Nov-Dec;55(6):24-7. Russian. PubMed PMID: 21381336. 12: Andac CA, Miandji AM, Hornemann U, Noyanalpan N. Use of the parmbsc0 force field and trajectory analysis to study the binding of netropsin to the DNA fragment (5'CCAATTGG)(2) in the presence of excess NaCl salt in aqueous solution. Int J Biol Macromol. 2011 May 1;48(4):531-9. doi: 10.1016/j.ijbiomac.2011.02.004. Epub 2011 Feb 16. PubMed PMID: 21335028. 13: Fang YY, Morris VR, Lingani GM, Long EC, Southerland WM. Genome-Targeted Drug Design: Understanding the Netropsin-DNA Interaction. Open Conf Proc J. 2010;1:157-163. PubMed PMID: 21297883; PubMed Central PMCID: PMC3032215. 14: Dolenc J, Gerster S, van Gunsteren WF. Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA. J Phys Chem B. 2010 Sep 2;114(34):11164-72. doi: 10.1021/jp100483f. PubMed PMID: 20690690. 15: Zhang R, Wu X, Guziec LJ, Guziec FS, Chee GL, Yalowich JC, Hasinoff BB. Design, synthesis and biological evaluation of a novel series of anthrapyrazoles linked with netropsin-like oligopyrrole carboxamides as anticancer agents. Bioorg Med Chem. 2010 Jun 1;18(11):3974-84. doi: 10.1016/j.bmc.2010.04.028. Epub 2010 Apr 18. PubMed PMID: 20471276; PubMed Central PMCID: PMC2880227. 16: Ameerunisha Begum MS, Saha S, Nethaji M, Chakravarty AR. Iron(III) Schiff base complexes of arginine and lysine as netropsin mimics showing AT-selective DNA binding and photonuclease activity. J Inorg Biochem. 2010 Apr;104(4):477-84. doi: 10.1016/j.jinorgbio.2010.01.001. Epub 2010 Jan 11. PubMed PMID: 20106530. 17: Mishra K, Bhardwaj R, Chaudhury NK. Netropsin, a minor groove binding ligand: a potential radioprotective agent. Radiat Res. 2009 Dec;172(6):698-705. doi: 10.1667/RR1815.1. PubMed PMID: 19929416. 18: Premvardhan L, Maurizot JC. Netropsin binding in five duplex-dimer DNA constructs as a function of size and distance between binding sites: circular dichroism and absorption spectroscopy. Eur Biophys J. 2010 Apr;39(5):781-7. doi: 10.1007/s00249-009-0550-x. Epub 2009 Oct 28. PubMed PMID: 19859703. 19: Wolter FE, Molinari L, Socher ER, Schneider K, Nicholson G, Beil W, Seitz O, Süssmuth RD. Synthesis and evaluation of a netropsin-proximicin-hybrid library for DNA binding and cytotoxicity. Bioorg Med Chem Lett. 2009 Jul 15;19(14):3811-5. doi: 10.1016/j.bmcl.2009.04.042. Epub 2009 Apr 18. PubMed PMID: 19427785. 20: Patra AK, Bhowmick T, Roy S, Ramakumar S, Chakravarty AR. Copper(II) complexes of L-arginine as netropsin mimics showing DNA cleavage activity in red light. Inorg Chem. 2009 Apr 6;48(7):2932-43. doi: 10.1021/ic8017425. PubMed PMID: 19254037.