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RNPA1000

Alias: RNPA1000 RNPA-1000 RNPA 1000
Cat No.:V5381 Purity: ≥98%
RNPA1000 is a novel and potent inhibitor of growth of Staphylococcus aureus.
RNPA1000
RNPA1000 Chemical Structure CAS No.: 359600-10-5
Product category: New15
This product is for research use only, not for human use. We do not sell to patients.
Size Price Stock Qty
5mg
10mg
Other Sizes
Official Supplier of:
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Purity & Quality Control Documentation

Purity: ≥98%

Product Description

RNPA1000 is a novel and potent inhibitor of growth of Staphylococcus aureus. It is a antimicrobial agent acting as a RNase inhibitor.

Biological Activity I Assay Protocols (From Reference)
ln Vitro
RNPA1000 exhibits minimal toxicity to human cells and antibacterial efficacy against Gram-positive bacteria [2]. Staphylococcus aureus mRNA growth and turnover are restricted by RNPA1000. Along with its antimicrobial activity against biofilm-associated Staphylococcus aureus, RNPA1000 also inhibits the growth of other significant Gram-positive bacterial pathogens and guards against S. aureus pathology in animal infection models [3]. Commercially available E. Coli RNase HI, RNase A, RNase I, and in-house purified S. aureus RNase J1 are not affected by RNPA1000 (IC50= 100-125 µM) at any tested concentration (0-750 µM). However, E. Coli RNase III activity (IC50= 500-750 µM) is modestly inhibited[3].
References
[1]. Eidem TM, et al. Drug-eluting cements for hard tissue repair: a comparative study using vancomycin and RNPA1000 to inhibit growth of Staphylococcus aureus. J Biomater Appl. 2014 Apr;28(8):1235-46.
[2]. Eidem TM, et al. Small-molecule inhibitors of Staphylococcus aureus RnpA-mediated RNA turnover and tRNA processing. Antimicrob Agents Chemother. 2015 Apr;59(4):2016-28.
[3]. Patrick D Olson, et al. Small molecule inhibitors of Staphylococcus aureus RnpA alter cellular mRNA turnover, exhibit antimicrobial activity, and attenuate pathogenesis. PLoS Pathog. 2011 Feb 10;7(2):e1001287.
These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C23H18BRN3O3
Molecular Weight
464.311324596405
Exact Mass
463.053
CAS #
359600-10-5
Related CAS #
359600-10-5;
PubChem CID
1268985
Appearance
Light yellow to khaki solid powder
LogP
5.1
Hydrogen Bond Donor Count
2
Hydrogen Bond Acceptor Count
4
Rotatable Bond Count
5
Heavy Atom Count
30
Complexity
723
Defined Atom Stereocenter Count
0
SMILES
CC1=CC(=C(N1C2=CC=C(C=C2)C(=O)O)C)/C=C(\C#N)/C(=O)NC3=CC(=CC=C3)Br
InChi Key
WQCMDUBFZYCGMI-WOJGMQOQSA-N
InChi Code
InChI=1S/C23H18BrN3O3/c1-14-10-17(15(2)27(14)21-8-6-16(7-9-21)23(29)30)11-18(13-25)22(28)26-20-5-3-4-19(24)12-20/h3-12H,1-2H3,(H,26,28)(H,29,30)/b18-11+ SMILES
Chemical Name
4-[3-[3-[(3-Bromophenyl)amino]-2-cyano-3-oxo-1-propen-1-yl]-2,5-dimethyl-1H-pyrrol-1-yl]-benzoic acid InChi Key
Synonyms
RNPA1000 RNPA-1000 RNPA 1000
HS Tariff Code
2934.99.9001
Storage

Powder      -20°C    3 years

                     4°C     2 years

In solvent   -80°C    6 months

                  -20°C    1 month

Shipping Condition
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
Solubility Data
Solubility (In Vitro)
DMSO : ~50 mg/mL (~107.69 mM)
Solubility (In Vivo)
Solubility in Formulation 1: ≥ 2.5 mg/mL (5.38 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL.
Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution.

Solubility in Formulation 2: ≥ 2.5 mg/mL (5.38 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly.
Preparation of 20% SBE-β-CD in Saline (4°C,1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution.

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Solubility in Formulation 3: ≥ 2.5 mg/mL (5.38 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly.


 (Please use freshly prepared in vivo formulations for optimal results.)
Preparing Stock Solutions 1 mg 5 mg 10 mg
1 mM 2.1537 mL 10.7687 mL 21.5373 mL
5 mM 0.4307 mL 2.1537 mL 4.3075 mL
10 mM 0.2154 mL 1.0769 mL 2.1537 mL

*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.

Calculator

Molarity Calculator allows you to calculate the mass, volume, and/or concentration required for a solution, as detailed below:

  • Calculate the Mass of a compound required to prepare a solution of known volume and concentration
  • Calculate the Volume of solution required to dissolve a compound of known mass to a desired concentration
  • Calculate the Concentration of a solution resulting from a known mass of compound in a specific volume
An example of molarity calculation using the molarity calculator is shown below:
What is the mass of compound required to make a 10 mM stock solution in 5 ml of DMSO given that the molecular weight of the compound is 350.26 g/mol?
  • Enter 350.26 in the Molecular Weight (MW) box
  • Enter 10 in the Concentration box and choose the correct unit (mM)
  • Enter 5 in the Volume box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 17.513 mg appears in the Mass box. In a similar way, you may calculate the volume and concentration.

Dilution Calculator allows you to calculate how to dilute a stock solution of known concentrations. For example, you may Enter C1, C2 & V2 to calculate V1, as detailed below:

What volume of a given 10 mM stock solution is required to make 25 ml of a 25 μM solution?
Using the equation C1V1 = C2V2, where C1=10 mM, C2=25 μM, V2=25 ml and V1 is the unknown:
  • Enter 10 into the Concentration (Start) box and choose the correct unit (mM)
  • Enter 25 into the Concentration (End) box and select the correct unit (mM)
  • Enter 25 into the Volume (End) box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 62.5 μL (0.1 ml) appears in the Volume (Start) box
g/mol

Molecular Weight Calculator allows you to calculate the molar mass and elemental composition of a compound, as detailed below:

Note: Chemical formula is case sensitive: C12H18N3O4  c12h18n3o4
Instructions to calculate molar mass (molecular weight) of a chemical compound:
  • To calculate molar mass of a chemical compound, please enter the chemical/molecular formula and click the “Calculate’ button.
Definitions of molecular mass, molecular weight, molar mass and molar weight:
  • Molecular mass (or molecular weight) is the mass of one molecule of a substance and is expressed in the unified atomic mass units (u). (1 u is equal to 1/12 the mass of one atom of carbon-12)
  • Molar mass (molar weight) is the mass of one mole of a substance and is expressed in g/mol.
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Reconstitution Calculator allows you to calculate the volume of solvent required to reconstitute your vial.

  • Enter the mass of the reagent and the desired reconstitution concentration as well as the correct units
  • Click the “Calculate” button
  • The answer appears in the Volume (to add to vial) box
In vivo Formulation Calculator (Clear solution)
Step 1: Enter information below (Recommended: An additional animal to make allowance for loss during the experiment)
Step 2: Enter in vivo formulation (This is only a calculator, not the exact formulation for a specific product. Please contact us first if there is no in vivo formulation in the solubility section.)
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Calculation results

Working concentration mg/mL;

Method for preparing DMSO stock solution mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.

Method for preparing in vivo formulation:Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O,mix and clarify.

(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
             (2) Be sure to add the solvent(s) in order.

Biological Data
  • RNPA1000 and RNPA2000 inhibit RNase P-mediated ptRNATyr processing in vitro. RNase P activity assays measuring the ability of the enzyme to catalyze conversion of ptRNATyr to tRNATyr in the absence or presence of increasing concentrations (0, 31.25, 62.5, 125, 250, and 500 μM) of RNPA1000 (A) and RNPA2000 (B).[2]. Eidem TM, et al. Small-molecule inhibitors of Staphylococcus aureus RnpA-mediated RNA turnover and tRNA processing. Antimicrob Agents Chemother. 2015 Apr;59(4):2016-28.
  • Antisense rnpA RNA levels influence S. aureus viability and susceptibility to RnpA inhibitors. (A) Serially diluted S. aureus vector (pML100) or isogenic RnpA depletion (pML100::A.S.-rnpA; rnpA mRNA-directed antisense molecule) cells plated on tryptic soy agar (TSA) containing high induction of the antisense transcript (10 ng ml−1 anhydrotetracycline [aTC], left) or under low-induction conditions (5 ng ml−1 ATc, right). (B) As in panel A, except strains were plated under low-induction conditions (5 ng ml−1 ATc) supplemented with 0.25× the MIC RNPA1000 (left) or RNPA2000 (right).[2]. Eidem TM, et al. Small-molecule inhibitors of Staphylococcus aureus RnpA-mediated RNA turnover and tRNA processing. Antimicrob Agents Chemother. 2015 Apr;59(4):2016-28.
  • RNPA2000 treatment leads to ptRNATyr and polycistronic tRNATyr accumulation within S. aureus cells. (A) Northern blotting results for S. aureus tRNATyr following treatment with increasing concentrations of RNPA2000 (0×, 0.5×, 1×, and 2× the MIC). (B) Northern blotting results probing for tRNATyr species within S. aureus treated with the putative RnpA inhibitors RNPA1000, RNPA2000, and RNPA3000, as well as antibiotics affecting other cellular targets. (C) qRT-PCR-based quantification of polycistronic tRNAPhe, Thr, Tyr levels within S. aureus cells treated with 2× the MIC of RNPA1000, RNPA2000, RNPA3000, or the indicated RnpA-independent antibiotic. Levels of tRNAPhe, Thr, Tyr within RnpA depletion cells (pML100:: A.S.-rnpA; rnpA mRNA-directed antisense molecule) cultured for the indicated time under low-induction conditions (5 ng ml−1 ATc, inset) relative to vector-containing cells; RNPA2000-treated cells are also shown (160-fold increase relative to mock-treated S. aureus cells).[2]. Eidem TM, et al. Small-molecule inhibitors of Staphylococcus aureus RnpA-mediated RNA turnover and tRNA processing. Antimicrob Agents Chemother. 2015 Apr;59(4):2016-28.
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