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Robotnikinin

Cat No.:V11355 Purity: ≥98%
Robotnikinin is a first-in-class small molecule inhibitor of Shh (Sonic Hedgehog) signaling that acts upstream of Smo, binding directly to Shh with a Kd value of 3.1 μM.
Robotnikinin
Robotnikinin Chemical Structure CAS No.: 1132653-79-2
Product category: New1
This product is for research use only, not for human use. We do not sell to patients.
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1mg
5mg
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Product Description
Robotnikinin is a first-in-class small molecule inhibitor of Shh (Sonic Hedgehog) signaling that acts upstream of Smo, binding directly to Shh with a Kd value of 3.1 μM.
Robotnikinin (CAS# 1132653-79-2) is a first-in-class small molecule inhibitor of the Sonic Hedgehog (Shh) signaling pathway. With a molecular formula of C₂₅H₂₇ClN₂O₄ and a molecular weight of 454.95 g/mol, Robotnikinin acts by directly binding to the Sonic Hedgehog ligand with a Kd value of 3.1 μM. The compound functions upstream of Smoothened (Smo), distinguishing it from other Hedgehog pathway inhibitors that target Smo. Robotnikinin is used in research to study Hedgehog-mediated regulation of cell proliferation, differentiation, and tissue patterning.
Biological Activity I Assay Protocols (From Reference)
Targets
The primary target of Robotnikinin is the Sonic Hedgehog (Shh) ligand. Robotnikinin binds directly to Shh with a Kd value of 3.1 μM. By binding to the Shh ligand, Robotnikinin inhibits Shh signaling upstream of Smo. The Hedgehog signaling pathway plays a critical role in embryonic development, cell proliferation, and tissue patterning. Dysregulation of Hedgehog signaling is associated with various cancers and developmental disorders. Robotnikinin's direct binding to the Shh ligand provides a unique tool for studying the role of Shh in Hedgehog signaling.
ln Vitro
Robotnikinin exhibits ShhN-binding ability at doses ranging from 1.56 μM to 25 μM. Based on kinetic data, a KD of 3.1 μM was determined[2]. Robotnikinin (50 µM) inhibits the rise in LC3-II caused by ShhN[3]. In H929 and U266 cell lines cocultured with HS-5 cells, robotnikinin (5 μM) downregulates classical NF-κB pathway proteins, indicating a connection between Hh signaling and the NF-κB pathway in MM[4].
In vitro, Robotnikinin demonstrates ShhN-binding ability at doses ranging from 1.56 μM to 25 μM. Based on kinetic data, a Kd of 3.1 μM was determined. Robotnikinin (50 µM) inhibits the rise in LC3-II caused by ShhN. In H929 and U266 cell lines cocultured with HS-5 cells, Robotnikinin (5 μM) downregulates classical NF-κB pathway proteins, indicating a connection between Hh signaling and the NF-κB pathway in multiple myeloma. The compound's ability to inhibit Shh signaling can be evaluated in various cell-based assays measuring Hedgehog pathway activity.
ln Vivo
In vivo, Robotnikinin has been evaluated in models of Hedgehog-dependent tumors. The compound's ability to inhibit Shh signaling upstream of Smo makes it a valuable tool for studying the role of Hedgehog signaling in tumor growth and progression. By modulating this pathway, Robotnikinin can be used to study Hedgehog-mediated regulation of cell proliferation, differentiation, and tissue patterning. In skin and cosmetic research, it is used to study Hedgehog-mediated regulation of cell proliferation and differentiation. Further in vivo studies are needed to fully characterize its efficacy and safety in animal models.
Enzyme Assay
In vitro enzyme/receptor binding studies for Robotnikinin focus on its interaction with the Shh ligand. Binding affinity to Shh can be assessed using surface plasmon resonance (SPR) or isothermal titration calorimetry (ITC). A Kd value of 3.1 μM has been determined from kinetic data. The compound's ability to inhibit Shh signaling can be evaluated using Gli-luciferase reporter assays in cells expressing the Hedgehog pathway. Selectivity profiling against other ligands and signaling pathways can be performed to assess specificity. These methods are for research purposes only.
Cell Assay
RT-PCR[4]
Cell Types: NCI -H929 or U266 cells.
Tested Concentrations: 5 μM.
Incubation Duration: 48 h.
Experimental Results: Downregulated classical NF-κB pathway proteins in H929 and U266 cell lines cocultured with HS-5 cells.
In vitro cell-based assays for Robotnikinin evaluate its effects on Hedgehog signaling. Cells expressing the Hedgehog pathway (e.g., H929 and U266 multiple myeloma cell lines) are treated with Robotnikinin at various concentrations (typically 0.1-50 µM). Hedgehog pathway activity is measured using Gli-luciferase reporter assays or by measuring the expression of Hedgehog target genes (e.g., GLI1, PTCH1) by qRT-PCR. NF-κB pathway proteins are measured by Western blot. Cell proliferation is assessed using MTT or CellTiter-Glo assays. RT-PCR can be performed to measure gene expression changes. Standard cell culture conditions are used with appropriate media and supplementation.
Animal Protocol
In vivo animal studies for Robotnikinin would typically involve mouse models of Hedgehog-dependent tumors or developmental disorders. Tumor-bearing mice are treated with Robotnikinin via intraperitoneal or oral administration at various doses. Tumor volumes are measured regularly using calipers, and body weight is monitored for toxicity assessment. Pharmacodynamic studies evaluate Hedgehog pathway inhibition by measuring Gli1 expression in tumor tissues. The compound's ability to inhibit Shh signaling upstream of Smo can be distinguished from Smo inhibitors in these models. All procedures must comply with institutional animal care guidelines.
ADME/Pharmacokinetics
The pharmacokinetic properties of Robotnikinin are not fully characterized in publicly available literature. The compound has a molecular weight of 454.95 g/mol. It is soluble in DMSO and should be stored at -20°C. The compound's half-life, Cmax, AUC, and clearance would need to be determined in preclinical pharmacokinetic studies. Information concerning product stability, particularly in solution, has rarely been reported. The compound is for research use only and is not approved for clinical use.
Toxicity/Toxicokinetics
The toxicity profile of Robotnikinin is not fully characterized in publicly available literature. The compound is classified for research use only and not for human consumption. Standard safety precautions for handling chemical compounds apply, including the use of personal protective equipment and working in a chemical fume hood. Preclinical toxicology studies would be required for clinical development. The compound should be handled with care due to its biological activity.
References

[1]. The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study. Front Chem.

[2]. A small molecule that binds Hedgehog and blocks its signaling in human cells. Nat Chem Biol. 2009 Mar;5(3):154-6.

[3]. Sonic hedgehog promotes autophagy in hippocampal neurons. Biol Open. 2013 Apr 8;2(5):499-504.

[4]. Targeting the cross-talk between the hedgehog and NF-κB signaling pathways in multiple myeloma. Leuk Lymphoma. 2019 Mar;60(3):772-781.

Additional Infomation
It binds to the sound hedgehog factor protein, blocking its signaling pathway; the structure is described in the first article.
Additional information: Robotnikinin has the CAS number 1132653-79-2 and the molecular formula C₂₅H₂₇ClN₂O₄. The compound is a first-in-class small molecule inhibitor of Shh signaling that acts upstream of Smo, binding directly to Shh with a Kd value of 3.1 μM. Robotnikinin has a purity of >98% and a molecular weight of 454.95 g/mol. The compound is also known as N-[(4-chlorophenyl)methyl]-2-[(2R,6S,8E)-5,12-dioxo-2-phenyl-1-oxa-4-azacyclododec-8-en-6-yl]acetamide. Robotnikinin is used in research to study Hedgehog-mediated regulation of cell proliferation, differentiation, and tissue patterning. This product is for research use only and is not approved for clinical or therapeutic applications.
These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C25H27CLN2O4
Molecular Weight
454.9459
Exact Mass
454.166
CAS #
1132653-79-2
PubChem CID
25109985
Appearance
White to off-white solid powder
LogP
4.823
Hydrogen Bond Donor Count
2
Hydrogen Bond Acceptor Count
4
Rotatable Bond Count
5
Heavy Atom Count
32
Complexity
654
Defined Atom Stereocenter Count
2
SMILES
C\1CC(=O)O[C@@H](CNC(=O)[C@@H](C/C=C1)CC(=O)NCC2=CC=C(C=C2)Cl)C3=CC=CC=C3
InChi Key
DRDSZZCLAHXSAE-BQIDRLATSA-N
InChi Code
InChI=1S/C25H27ClN2O4/c26-21-13-11-18(12-14-21)16-27-23(29)15-20-9-5-2-6-10-24(30)32-22(17-28-25(20)31)19-7-3-1-4-8-19/h1-5,7-8,11-14,20,22H,6,9-10,15-17H2,(H,27,29)(H,28,31)/b5-2+/t20-,22-/m0/s1
Chemical Name
N-[(4-chlorophenyl)methyl]-2-[(2R,6S,8E)-5,12-dioxo-2-phenyl-1-oxa-4-azacyclododec-8-en-6-yl]acetamide
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)
May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples
Solubility (In Vivo)
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.

Injection Formulations
(e.g. IP/IV/IM/SC)
Injection Formulation 1: DMSO : Tween 80: Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution 50 μL Tween 80 850 μL Saline)
*Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution.
Injection Formulation 2: DMSO : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO 400 μLPEG300 50 μL Tween 80 450 μL Saline)
Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO 900 μL Corn oil)
Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals).
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Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO 900 μL (20% SBE-β-CD in saline)]
*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.
Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin 500 μL Saline)
Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO 100 μLPEG300 200 μL castor oil 650 μL Saline)
Injection Formulation 7: Ethanol : Cremophor : Saline = 10: 10 : 80 (i.e. 100 μL Ethanol 100 μL Cremophor 800 μL Saline)
Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline
Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH 900 μL Corn oil)
Injection Formulation 10: EtOH : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH 400 μLPEG300 50 μL Tween 80 450 μL Saline)


Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium)
Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose
Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals).
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Oral Formulation 3: Dissolved in PEG400
Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose
Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose
Oral Formulation 6: Mixing with food powders


Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.

 (Please use freshly prepared in vivo formulations for optimal results.)
Preparing Stock Solutions 1 mg 5 mg 10 mg
1 mM 2.1980 mL 10.9902 mL 21.9804 mL
5 mM 0.4396 mL 2.1980 mL 4.3961 mL
10 mM 0.2198 mL 1.0990 mL 2.1980 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.

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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
  • (A) A snapshot from an MM MD simulation started from a docking pose with the chlorine atom of the ligand pointing toward the Ca(II) ions (depicted in orange). The snapshot shows a configuration in which the chlorophenyl ring left the binding groove and is oriented toward the ligand's second aromatic ring instead of the Ca(II) ions. This is caused by a lack of stabilizing hydrophobic interactions with the protein as well as steric clashes and indicates that the chosen starting structure is not a stable binding mode. (B) A snapshot from an MM simulation started from the preferred docking pose. (C) Heavy atom RMSD of robotnikinin, calculated from the trajectory of the simulation shown in (A). (D) Heavy atom RMSD of robotnikinin, derived from the trajectory of the simulation shown in (B). Each frame in the RMSD plots represents 100 ps.[1].The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study. Front Chem.
  • Plots of the distances between H134 and robotnikinin's macrocyclic amide group (black), ester (red), as well as the separation of H135 and the macrocyclic amide function (blue) of robotnikinin. Each frame represents a time span of 0.02 ps. (A) Core simulation. (B) Extended simulation (TZ). (C) Extended simulation (DZ).[1].The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study. Front Chem.
  • (A) The most common geometry of the hydrophobic interactions between T126, H181, and robotnikinin. (B) A configuration displaying T-shaped π–π stacking of the aromatics belonging to robotnikinin and Y175, respectively. (C) The more frequent parallel-displaced stacking geometry between the chlorophenyl ring of robotnikinin and Y175 as witnessed during the QM/MM simulations.[1].The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study. Front Chem.
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