2. MAPK/ERK Pathway Cell Cycle/DNA Damage
  3. JNK Eukaryotic Initiation Factor (eIF) p38 MAPK
  4. IDB-001

IDB-001 is a human ribosomal peptidyl transferase center (PTC) inhibitor that induces conformational changes and blocks translational elongation in specific sequence contexts through complementary interactions with Asp/Glu residues in nascent polypeptides. IDB-001 preferentially stalls ribosomes at positions containing acidic peptide motifs, thereby inhibiting cancer cell proliferation, and activates the integrated stress response via eIF2α phosphorylation at high concentrations. In addition, IDB-001 mildly triggers ribotoxic stress responses through phosphorylation of JNK and p38. IDB-001 has been applied to mechanistic studies of triple-negative breast cancer.

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IDB-001

IDB-001 Chemical Structure

CAS No. : 3079913-81-5

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Solid or liquid + Solvent (Highly Recommended)
10 mM * 1 mL in DMSO
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Based on 1 publication(s) in Google Scholar

IDB-001 Related Antibodies

Top Publications Citing Use of Products

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JNK1 JNK2 JNK3 JNK

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p38 MAPK Akt1 p38α p38β MAPK13 p38δ p38γ

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Description

IDB-001 is a human ribosomal peptidyl transferase center (PTC) inhibitor that induces conformational changes and blocks translational elongation in specific sequence contexts through complementary interactions with Asp/Glu residues in nascent polypeptides. IDB-001 preferentially stalls ribosomes at positions containing acidic peptide motifs, thereby inhibiting cancer cell proliferation, and activates the integrated stress response via eIF2α phosphorylation at high concentrations. In addition, IDB-001 mildly triggers ribotoxic stress responses through phosphorylation of JNK and p38. IDB-001 has been applied to mechanistic studies of triple-negative breast cancer[1].

In Vitro

IDB-001 (10 μM; 60 min) induces translation elongation defects characterized by context-dependent stalling, preferentially targeting nascent polypeptide chains with an acidic residue at the -1 position, and elicits mild ribosome collisions upstream of stalling sites in HCC-1143 triple-negative breast cancer cells[1].
IDB-001 potently and specifically inhibits in vitro translation of reporter gene constructs containing acidic tetrameric sequences, exhibiting a biochemical selectivity window of at least 15-fold across different nascent peptide motifs. Its activity against the FTED motif is 3-fold higher than that of IDB-002 (HY-P991496), and its activity against the DDEY motif is 6-fold higher than that of IDB-002[1].
IDB-001 (50 μM; 30 min) induces a conformational change in the aspartic acid at position -1 of the nascent peptide chain to form a stable salt bridge, and triggers specific structural rearrangement of ribosomal RNA residues, thereby constricting the peptidyl transferase center and regulating the channel volume in human ribosome-nascent chain complexes containing MYC-derived QEDE peptides[1].
IDB-001 inhibits cancer cell proliferation, with an EC50 ranging from 0.663 μM (in HCC-1143 triple-negative breast cancer cells) to 5.440 μM (in MRC-5 fibroblasts). It exhibits the strongest activity against HCC-1143 cells among human cancer cell lines and fibroblast cell lines[1].
IDB-001 (10 μM; 2-8 h) induces a moderate ribotoxic stress response in MCF7 breast cancer cells: weak phosphorylation of JNK and p38 occurs after 2 h of treatment, while the integrated stress response is activated via eIF2α phosphorylation after 8 h of treatment[1].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

IDB-001 Related Antibodies

Cell Viability Assay[1]

Cell Line: 22Rv1, HCC-1143, LS411N, MCF7, MRC-5
Concentration: dose-response curve
Incubation Time: 72 h
Result: Inhibited cell proliferation with EC50 values of 4.983 μM (22Rv1 prostate cancer cells), 0.663 μM (HCC-1143 triple-negative breast cancer cells), 4.233 μM (LS411N colorectal cancer cells), 1.364 μM (MCF7 HR+/HER2- breast cancer cells), and 5.440 μM (MRC-5 fibroblast cells).

Western Blot Analysis[1]

Cell Line: MCF7
Concentration: 10 μM
Incubation Time: 0, 15 min, 2 h, 4 h, 8 h
Result: Did not induce detectable JNK phosphorylation at 15 min.
Caused modest phosphorylation of JNK and p38 after 2 h, though the magnitude was significantly lower than that observed for IDB-002.
Induced phosphorylation of eIF2α after 8 h of treatment.
Molecular Weight

363.45

Formula

C19H29N3O4
CAS No.
Appearance

Solid-Liquid Mixture

Color

White to off-white

SMILES

O=C(NCC[C@@H]1CCCN1)O[C@H]([C@H](CN2)O)[C@H]2CC3=CC=C(C=C3)OC
Shipping

Room temperature in continental US; may vary elsewhere.
Storage

4°C, protect from light, stored under nitrogen

*In solvent : -80°C, 6 months; -20°C, 1 month (protect from light, stored under nitrogen)

Solvent & Solubility
In Vitro: 

DMSO : 50 mg/mL (137.57 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)

Preparing
Stock Solutions
Concentration Solvent Mass 1 mg 5 mg 10 mg
1 mM 2.7514 mL 13.7570 mL 27.5141 mL
5 mM 0.5503 mL 2.7514 mL 5.5028 mL
View the Complete Stock Solution Preparation Table

* Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month (protect from light, stored under nitrogen). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

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Mass (g) = Concentration (mol/L) × Volume (L) × Molecular Weight (g/mol)

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In Vivo:

Select the appropriate dissolution method based on your experimental animal and administration route.

For the following dissolution methods, please ensure to first prepare a clear stock solution using an In Vitro approach and then sequentially add co-solvents:
To ensure reliable experimental results, the clarified stock solution can be appropriately stored based on storage conditions. As for the working solution for in vivo experiments, it is recommended to prepare freshly and use it on the same day.
The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.

  • Protocol 1

    Add each solvent one by one:  10% DMSO    40% PEG300    5% Tween-80    45% Saline

    Solubility: ≥ 2.5 mg/mL (6.88 mM); Clear solution

    This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).

    Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 400 μL PEG300, and mix evenly; then add 50 μL Tween-80 and mix evenly; then add 450 μL Saline to adjust the volume to 1 mL.

    Preparation of Saline: Dissolve 0.9 g sodium chloride in ddH₂O and dilute to 100 mL to obtain a clear Saline solution.
  • Protocol 2

    Add each solvent one by one:  10% DMSO    90% (20% SBE-β-CD in Saline)

    Solubility: ≥ 2.5 mg/mL (6.88 mM); Clear solution

    This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).

    Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 900 μL 20% SBE-β-CD in Saline, and mix evenly.

    Preparation of 20% SBE-β-CD in Saline (4°C, storage for one week): 2 g SBE-β-CD powder is dissolved in 10 mL Saline, completely dissolve until clear.
In Vivo Dissolution Calculator
Please enter the basic information of animal experiments:

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Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
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Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
The co-solvents required include: DMSO, . All of co-solvents are available by MedChemExpress (MCE). , Tween 80. All of co-solvents are available by MedChemExpress (MCE).
Calculation results:
Working solution concentration: mg/mL
Method for preparing stock solution: mg drug dissolved in μL  DMSO (Stock solution concentration: mg/mL).

*In solvent : -80°C, 6 months; -20°C, 1 month (protect from light, stored under nitrogen)

The concentration of the stock solution you require exceeds the measured solubility. The following solution is for reference only. If necessary, please contact MedChemExpress (MCE).
Method for preparing in vivo working solution for animal experiments: Take μL DMSO stock solution, add μL . μL , mix evenly, next add μL Tween 80, mix evenly, then add μL Saline.
 If the continuous dosing period exceeds half a month, please choose this protocol carefully.
Please ensure that the stock solution in the first step is dissolved to a clear state, and add co-solvents in sequence. You can use ultrasonic heating (ultrasonic cleaner, recommended frequency 20-40 kHz), vortexing, etc. to assist dissolution.
Purity & Documentation
References

Complete Stock Solution Preparation Table

* Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month (protect from light, stored under nitrogen). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

Optional Solvent Concentration Solvent Mass 1 mg 5 mg 10 mg 25 mg
DMSO 1 mM 2.7514 mL 13.7571 mL 27.5141 mL 68.7853 mL
5 mM 0.5503 mL 2.7514 mL 5.5028 mL 13.7571 mL
10 mM 0.2751 mL 1.3757 mL 2.7514 mL 6.8785 mL
15 mM 0.1834 mL 0.9171 mL 1.8343 mL 4.5857 mL
20 mM 0.1376 mL 0.6879 mL 1.3757 mL 3.4393 mL
25 mM 0.1101 mL 0.5503 mL 1.1006 mL 2.7514 mL
30 mM 0.0917 mL 0.4586 mL 0.9171 mL 2.2928 mL
40 mM 0.0688 mL 0.3439 mL 0.6879 mL 1.7196 mL
50 mM 0.0550 mL 0.2751 mL 0.5503 mL 1.3757 mL
60 mM 0.0459 mL 0.2293 mL 0.4586 mL 1.1464 mL
80 mM 0.0344 mL 0.1720 mL 0.3439 mL 0.8598 mL
100 mM 0.0275 mL 0.1376 mL 0.2751 mL 0.6879 mL
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IDB-001 Related Classifications

Help & FAQs
  • Do most proteins show cross-species activity?

    Species cross-reactivity must be investigated individually for each product. Many human cytokines will produce a nice response in mouse cell lines, and many mouse proteins will show activity on human cells. Other proteins may have a lower specific activity when used in the opposite species.

Keywords:

IDB-0013079913-81-5IDB001IDB 001JNKEukaryotic Initiation Factor (eIF)p38 MAPKc-Jun N-terminal kinaseintegrated stress responsehuman ribosome peptidyl transferase centertriple-negative breast cancerribosomal RNAHCC-1143 triple-negative breast cancer cellscancer cell proliferationnascent polypeptidetranslation elongationMRC-5 fibroblastsribotoxic stress responseInhibitorinhibitorinhibit

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