Ribocil | CAS#1381289-58-2 | riboswitch modulator

MedKoo Cat#: 563486 | Name: Ribocil

Description:

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

Ribocil is a selective modulator of bacterial riboflavin riboswitches. Ribocil depletes cellular levels of riboflavin with an IC50 value of 0.3 µM and inhibits E. coli growth with an MIC value of 2 µg/ml.

Chemical Structure

Ribocil

CAS#1381289-58-2

Theoretical Analysis

MedKoo Cat#: 563486

Name: Ribocil

CAS#: 1381289-58-2

Chemical Formula: C19H22N6OS

Exact Mass: 382.1576

Molecular Weight: 382.48

Elemental Analysis: C, 59.66; H, 5.80; N, 21.97; O, 4.18; S, 8.38

Price and Availability

Size	Price	Availability
25mg	USD 450.00	2 Weeks
50mg	USD 750.00	2 Weeks
100mg	USD 1,250.00	2 Weeks
200mg	USD 1,850.00	2 Weeks
500mg	USD 2,850.00	2 Weeks
1g	USD 4,250.00	2 Weeks
2g	USD 7,250.00	2 Weeks

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Synonym

Ribocil;

IUPAC/Chemical Name

2-(1-((2-(methylamino)pyrimidin-5-yl)methyl)piperidin-3-yl)-6-(thiophen-2-yl)pyrimidin-4(3H)-one

InChi Key

ZSXCVAIJFUEGJR-UHFFFAOYSA-N

InChi Code

InChI=1S/C19H22N6OS/c1-20-19-21-9-13(10-22-19)11-25-6-2-4-14(12-25)18-23-15(8-17(26)24-18)16-5-3-7-27-16/h3,5,7-10,14H,2,4,6,11-12H2,1H3,(H,20,21,22)(H,23,24,26)

SMILES Code

O=C1NC(C2CN(CC3=CN=C(NC)N=C3)CCC2)=NC(C4=CC=CS4)=C1

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

More Info

Product Data

Product Data

Instruction

View handling instruction

Biological target:

Ribocil competes with the natural ligand to inhibit FMN riboswitch-mediated expression of rib. Ribocil depletes cellular levels of riboflavin with an IC50 value of 0.3 µM and inhibits E. coli growth with an MIC value of 2 µg/ml.

In vitro activity:

Ribocil binds to the riboswitch of E. coli, which results in ribB expression repression and the inhibition of riboflavin biosynthesis (IC50 = 0.3 μM) and bacterial growth. Reference: Methods Mol Biol. 2018;1787:19-40. https://pubmed.ncbi.nlm.nih.gov/29736707/

In vivo activity:

To be determined

	Solvent	mg/mL	mM
Solubility
	DMF	10.0	26.15
	DMSO	12.0	31.37

Note: There can be variations in solubility for the same chemical from different vendors or different batches from the same vendor. The following factors can affect the solubility of the same chemical: solvent used for crystallization, residual solvent content, polymorphism, salt versus free form, degree of hydration, solvent temperature. Please use the solubility data as a reference only. Warming and sonication will facilitate dissolving. Still have questions? Please contact our Technical Support scientists.

Preparing Stock Solutions

The following data is based on the product molecular weight 382.48 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.

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. Balibar CJ, Villafania A, Barbieri CM, Murgolo N, Roemer T, Wang H, Howe JA. Validation and Development of an Escherichia coli Riboflavin Pathway Phenotypic Screen Hit as a Small-Molecule Ligand of the Flavin Mononucleotide Riboswitch. Methods Mol Biol. 2018;1787:19-40. doi: 10.1007/978-1-4939-7847-2_2. PMID: 29736707. 2. Howe JA, Xiao L, Fischmann TO, Wang H, Tang H, Villafania A, Zhang R, Barbieri CM, Roemer T. Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch. RNA Biol. 2016 Oct 2;13(10):946-954. doi: 10.1080/15476286.2016.1216304. Epub 2016 Aug 2. PMID: 27485612; PMCID: PMC5056776.

In vitro protocol:

In vivo protocol:

To be determined

1: Balibar CJ, Villafania A, Barbieri CM, Murgolo N, Roemer T, Wang H, Howe JA. Validation and Development of an Escherichia coli Riboflavin Pathway Phenotypic Screen Hit as a Small-Molecule Ligand of the Flavin Mononucleotide Riboswitch. Methods Mol Biol. 2018;1787:19-40. doi: 10.1007/978-1-4939-7847-2_2. PubMed PMID: 29736707. 2: Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim HY, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker PJ, Smith GF, Nickbarg EB. Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry. ACS Chem Biol. 2018 Mar 16;13(3):820-831. doi: 10.1021/acschembio.7b01013. Epub 2018 Feb 14. PubMed PMID: 29412640. 3: Krajewski SS, Ignatov D, Johansson J. Two Are Better Than One: Dual Targeting of Riboswitches by Metabolite Analogs. Cell Chem Biol. 2017 May 18;24(5):535-537. doi: 10.1016/j.chembiol.2017.05.004. PubMed PMID: 28525764. 4: Wang H, Mann PA, Xiao L, Gill C, Galgoci AM, Howe JA, Villafania A, Barbieri CM, Malinverni JC, Sher X, Mayhood T, McCurry MD, Murgolo N, Flattery A, Mack M, Roemer T. Dual-Targeting Small-Molecule Inhibitors of the Staphylococcus aureus FMN Riboswitch Disrupt Riboflavin Homeostasis in an Infectious Setting. Cell Chem Biol. 2017 May 18;24(5):576-588.e6. doi: 10.1016/j.chembiol.2017.03.014. Epub 2017 Apr 20. PubMed PMID: 28434876. 5: Howe JA, Xiao L, Fischmann TO, Wang H, Tang H, Villafania A, Zhang R, Barbieri CM, Roemer T. Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch. RNA Biol. 2016 Oct 2;13(10):946-954. Epub 2016 Aug 2. PubMed PMID: 27485612; PubMed Central PMCID: PMC5056776. 6: Dissecting How Mtb Makes Its Wall, Buffering Endosomal pH, and Discovery of Ribocil. Chem Biol. 2015 Nov 19;22(11):1415-1416. doi: 10.1016/j.chembiol.2015.11.003. PubMed PMID: 26590635. 7: Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, Malinverni JC, Mayhood T, Villafania A, Nahvi A, Murgolo N, Barbieri CM, Mann PA, Carr D, Xia E, Zuck P, Riley D, Painter RE, Walker SS, Sherborne B, de Jesus R, Pan W, Plotkin MA, Wu J, Rindgen D, Cummings J, Garlisi CG, Zhang R, Sheth PR, Gill CJ, Tang H, Roemer T. Selective small-molecule inhibition of an RNA structural element. Nature. 2015 Oct 29;526(7575):672-7. doi: 10.1038/nature15542. Epub 2015 Sep 30. PubMed PMID: 26416753. 8: Hermann T. Non-coding RNA: Antibiotic tricks a switch. Nature. 2015 Oct 29;526(7575):650-1. doi: 10.1038/nature15635. Epub 2015 Sep 30. PubMed PMID: 26416738.