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CX-5461 (Pidnarulex) RNA Polymerase I inhibitor

Name: CX-5461 (Pidnarulex)
SKU: S2684
Availability: InStock
Rating: 5 (83 reviews)

Cat.No.S2684

CX-5461 (Pidnarulex) is an inhibitor of rRNA synthesis that selectively inhibits Pol I-driven transcription of rRNA with an IC50 of 142 nM in HCT-116, A375, and MIA PaCa-2 cells. It has no effect on Pol II and possesses 250- to 300-fold selectivity for inhibition of rRNA transcription versus DNA replication and protein translation.

Chemical Structure

Molecular Weight: 513.61

Jump to Mechanism of Action Cell Culture & Working Concentration Solubility Chemical Information, Storage & Stability Specificity

Quality Control

Batch: Purity: 99.07%

99.07

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Cell Culture, Treatment & Working Concentration

Cell Lines	Assay Type	Concentration	Incubation Time	Activity Description	PMID
MNNG	Cell viability assay		72 h	IC50=0.5-1.5 µM	27729807
U2-OS	Cell viability assay		72 h	IC50=0.5-1.5 µM	27729807
RS4;11	Proliferation assay	250 nM	24 h	time dependent decrease in proliferation relative to their DMSO treated controls	26472108
SEM	Proliferation assay	250 nM	24 h	time dependent decrease in proliferation relative to their DMSO treated controls	26472108
KOPN-8	Proliferation assay	250 nM	24 h	time dependent decrease in proliferation relative to their DMSO treated controls	26472108
NALM-6	Proliferation assay	250 nM	24 h	time dependent decrease in proliferation relative to their DMSO treated controls	26472108
NB-EBc1	qHTS assay			qHTS of pediatric cancer cell lines to identify multiple opportunities for drug repurposing: Primary screen for NB-EBc1 cells	29435139
Click to View More Cell Line Experimental Data

Chemical Information, Storage & Stability

Molecular Weight	513.61	Formula	C₂₇H₂₇N₇O₂S	Storage (From the date of receipt)	3 years-20°Cpowder
CAS No.	1138549-36-6	Download SDF		Storage of Stock Solutions	1 year-80°Cin solvent 1 month-20°Cin solvent
Synonyms	N/A			Smiles	CC1=CN=C(C=N1)CNC(=O)C2=C3N(C4=CC=CC=C4S3)C5=C(C2=O)C=CC(=N5)N6CCCN(CC6)C

Solubility

In vitro
Batch:

DMSO : Insoluble
(Moisture-contaminated DMSO may reduce solubility. Use fresh, anhydrous DMSO.)

Water : Insoluble

Ethanol : Insoluble

Molarity Calculator

Mass	Concentration	Volume	Molecular Weight
=	×	×

Dilution Calculator Molecular Weight Calculator

In vivo Batch:
Homogeneous suspension	CMC-NA	≥5mg/ml	Taking the 1 mL working solution as an example, add 5 mg of this product to 1 ml of CMC-Na solution, mix evenly to obtain a homogeneous suspension with a final concentration of 5 mg/ml.
Clear solution	5%DMSO 1 40%PEG300 2 5%Tween80 3 50%ddH2O Validated by Selleck labs. Should you need adjustments to this formulation, contact our sales team for custom testing.	0.150mg/ml (0.29mM)	Taking the 1 mL working solution as an example, add 50 μL of 3 mg/ml clarified DMSO stock solution to 400 μL PEG300, mix evenly to clarify it; add 50 μL Tween80 to the above system, mix evenly to clarify it; then continue to add 500 μL ddH2O to adjust the volume to 1 mL. The mixed solution should be used immediately for optimal results.
Clear solution	5% DMSO 1 95% corn oil Validated by Selleck labs. Should you need adjustments to this formulation, contact our sales team for custom testing.	0.150mg/ml (0.29mM)	Taking the 1 mL working solution as an example, add 50 μL of 3 mg/ml clear DMSO stock solution to 950 μL of corn oil and mix evenly. The mixed solution should be used immediately for optimal results.
Clear solution	5%DMF 1 40%PEG300 2 5%Tween80 3 50%ddH2O Validated by Selleck labs. Should you need adjustments to this formulation, contact our sales team for custom testing.	2.000mg/ml (3.89mM)	Taking the 1 mL working solution as an example, add 50 μL 40 mg/ml clarified DMF stock solution to 400 μL PEG300, mix evenly to clarify it; add 50 μL Tween80 to the above system, mix evenly to clarify it; then continue to add 500 μL ddH2O to adjust the volume to 1 mL. . The mixed solution should be used immediately for optimal results.
Homogeneous suspension	CMC-NA	≥5mg/ml	Taking the 1 mL working solution as an example, add 5 mg of this product to 1 ml of CMC-Na solution, mix evenly to obtain a homogeneous suspension with a final concentration of 5 mg/ml.
Clear solution	5%DMF 1 95%Corn oil Validated by Selleck labs. Should you need adjustments to this formulation, contact our sales team for custom testing.	2.000mg/ml (3.89mM)	Taking the 1 mL working solution as an example, add 50 μL of 40 mg/ml clarified DMF stock solution to 950 μL of corn oil and mix evenly. The mixed solution should be used immediately for optimal results.
Clear solution	5%DMF 1 95%Corn oil Validated by Selleck labs. Should you need adjustments to this formulation, contact our sales team for custom testing.	2.000mg/ml (3.89mM)	Taking the 1 mL working solution as an example, add 50 μL of 40 mg/ml clarified DMF stock solution to 950 μL of corn oil and mix evenly. The mixed solution should be used immediately for optimal results.

In vivo Formulation Calculator (Clear solution)

Step 1: Enter information below (Recommended: An additional animal making an allowance for loss during the experiment)

Dosage: mg/kg Average weight of animals: g Dosing volume per animal:μL Number of animals:

Step 2: Enter the in vivo formulation (This is only the calculator, not formulation. Please contact us first if there is no in vivo formulation at the solubility Section.)

% DMSO + % + % Tween 80 + % ddH₂O

%DMSO+ %

Calculation results:

Working concentration: mg/ml;

Method for preparing DMSO master liquid: mg drug pre-dissolved in μL DMSO ( Master liquid 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 master liquid, next addμL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH₂O, mix and clarify.

Method for preparing in vivo formulation: Take μL DMSO master liquid, next add μL Corn oil, mix and clarify.

Note: 1. Please make sure the liquid is clear before adding the next solvent.
2. Be sure to add the solvent(s) in order. You must ensure that the solution obtained, in the previous addition, is a clear solution before proceeding to add the next solvent. Physical methods such
as vortex, ultrasound or hot water bath can be used to aid dissolving.

Mechanism of Action

Targets/IC₅₀/Ki	Pol I-driven transcription of rRNA ^[1] (HCT-116, A375, MIA PaCa-2 cells) 142 nM
In vitro	CX-5461 (Pidnarulex) is found to selectively inhibit rRNA synthesis (Pol I IC50=142 nM; Pol II IC50 > 25 μM; selectivity ~200-fold) in the HCT-116 cells. This selective inhibition is confirmed in two other human solid tumor cell lines; melanoma A375 (Pol I IC50 = 113 nM; Pol II IC50 > 25 μM) and pancreatic carcinoma MIA PaCa-2 (Pol I IC50=54 nM; Pol II IC50 ~25 mM). It possesses 250- to 300-fold selectivity for inhibition of rRNA transcription versus DNA replication and protein translation. The compound exhibits broad antiproliferative potency in a panel of cancer cell lines in human cancer cell lines, but has minimal effect on viability of nontransformed human cells. The median EC50 across all tested cell lines is 147 nM, yet all normal cell lines have EC50 values of approximately 5, 000 nM. Evaluation of the antiproliferative dose response for HCT-116, A375, and MIA PaCa-2 cell lines yield EC50 values of 167, 58, and 74 nM. It induces autophagy and senescence in solid tumor cancer cells, rather than apoptosis, through a p53-independent process. ^[1]
Kinase Assay	Pol I and Pol II Transcription Assay
Kinase Assay	Two short-lived RNA transcripts (half-lives ~20-30 minutes), one produced by Pol I and another by Pol II, are quantitated by qRT-PCR as a measure of CX-5461 (Pidnarulex)-related effects on transcription. The 45S pre-rRNA served as the Pol I transcript and the mRNA for the protooncogene c-myc served as the comparator Pol II transcript. Both Pol I and Pol II transcription are known to be affected by general cellular stress. To minimize the potential effects of such stress, cells are exposed to test agents for only a short period of time (2 hours). This is sufficient time for these transcripts to be reduced by greater than 90% if this compound affects their synthesis.
In vivo	CX-5461 (Pidnarulex) is orally bioavailable and demonstrates in vivo antitumor activity against human solid tumors in murine xenograft models. This compound demonstrates significant MIA PaCa-2 TGI with TGI equal to 69% on day 31. Likewise, it demonstrates significant A375 TGI with TGI equal to 79% on day 32. ^[1]
References	[1] https://pubmed.ncbi.nlm.nih.gov/21159662/

Applications

Methods	Biomarkers	PMID
Western blot	Cyclin D1 / p53 / p16 53BP1 / γ-H2AX / p-ATM Bcl-2 / Bax / Caspase3 cleaved PARP / cleaved Caspase-9 / cleaved caspase-3 p-AMPK / AMPK / p-mTOR / mTOR EG5 / Histone H3 / p-Histone H3 (S10)	29631594
Immunofluorescence	Vimentin / Phalloidin / Snail1 Rictor / Calnexin Fibrillarin LC3 γH2AX / 53BP1 / RPA / RAD51 chromosome / telomere F-actin / Aurora B	31068593
Growth inhibition assay	Cell viability	26061708

Clinical Trial Information

(data from https://clinicaltrials.gov, updated on 2024-05-22)

NCT Number	Recruitment	Conditions	Sponsor/Collaborators	Start Date	Phases
NCT02719977	Completed	Cancer	Canadian Cancer Trials Group\|Senhwa Biosciences Inc.\|Stand Up To Cancer	June 13 2016	Phase 1

Tech Support

Handling Instructions

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Frequently Asked Questions

Question 1:
I want to make it for further in vivo treatment.

Answer:
This compound has poor solubility in common vehicles. It can be dissolved in DMF at 3 mg/ml with warming.

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