TBK1 PROTAC 1 is a novel, potent and selective TBK1 PROTAC with DC50 of 12nM that selectively degrades TBK1 with excellent selectivity against a related kinase IKKε; It is a chemical tool to assess TBK1 as a target in mutant K-Ras cancer cells. Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that recruit an E3 ligase to a target protein to facilitate ubiquitination and subsequent degradation of that protein. While the field of targeted degraders is still relatively young, the potential for this modality to become a differentiated and therapeutic reality is strong, such that both academic and pharmaceutical institutions are now entering this interesting area of research. In this article, we describe a broadly applicable process for identifying degrader hits based on the serine/threonine kinase TANK-binding kinase 1 (TBK1) and have generalized the key structural elements associated with degradation activities. TBK1 PROTAC 1 is a potent hit (TBK1 DC50 = 12 nM, Dmax = 96%) with excellent selectivity against a related kinase IKKε, which was further used as a chemical tool to assess TBK1 as a target in mutant K-Ras cancer cells.
Physicochemical Properties
| Molecular Formula | C53H74BRN9O9S |
| Molecular Weight | 1093.17857122421 |
| Exact Mass | 1091.451 |
| CAS # | 2052306-13-3 |
| PubChem CID | 124108661 |
| Appearance | White to off-white solid powder |
| Density | 1.3±0.1 g/cm3 |
| Index of Refraction | 1.604 |
| LogP | 4.09 |
| Hydrogen Bond Donor Count | 5 |
| Hydrogen Bond Acceptor Count | 15 |
| Rotatable Bond Count | 31 |
| Heavy Atom Count | 73 |
| Complexity | 1650 |
| Defined Atom Stereocenter Count | 3 |
| SMILES | CC1=C(SC=N1)C2=CC=C(C=C2)CNC(=O)[C@@H]3C[C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)COCCCOCCCCOCCCOC4=CC=C(C=C4)NC5=NC=C(C(=N5)NCCCN(C)C(=O)C6CCC6)Br)O |
| InChi Key | QMGHHBHPDDAGGO-IIWOMYBWSA-N |
| InChi Code | InChI=1S/C53H74BrN9O9S/c1-36-46(73-35-58-36)38-16-14-37(15-17-38)31-56-49(66)44-30-41(64)33-63(44)51(68)47(53(2,3)4)60-45(65)34-71-28-10-26-69-24-6-7-25-70-27-11-29-72-42-20-18-40(19-21-42)59-52-57-32-43(54)48(61-52)55-22-9-23-62(5)50(67)39-12-8-13-39/h14-21,32,35,39,41,44,47,64H,6-13,22-31,33-34H2,1-5H3,(H,56,66)(H,60,65)(H2,55,57,59,61)/t41-,44+,47-/m1/s1 |
| Chemical Name | (2S,4R)-1-((S)-18-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)propyl)amino)pyrimidin-2-yl)amino)phenoxy)-2-(tert-butyl)-4-oxo-6,10,15-trioxa-3-azaoctadecanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide |
| Synonyms | TBK1 PROTAC-1; TBK1 PROTAC1; TBK1 PROTAC 1 |
| 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) |
Biological Activity
| ln Vitro | VHL ligand 2 (10 μM) or the proteasome inhibitor Carfilzomib (100 nM) can both block TBK1 degradation mediated by PROTAC TBK1 degrader-2 (compound 3i) [1]. With an IC50 of 1.3 nM and 8.7 nM, respectively, PROTAC TBK1 degrader-2 (0-3 μM) shows poor selectivity between TBK1 and IKKε; nevertheless, at concentrations more than 50 times higher than the DC50 for TBK1, IKKε levels show no effect[1]. In K-Ras mutant and wild-type cells, PROTAC TBK1 degrader-2 (100 nM; 300 M; 72 h) is not synthetically lethal [1]. |
| Cell Assay |
Cell Viability Assay[1] Cell Types: K-Ras mutant cell lines (H23, A549, and H1792) and K-Rras wild type cell lines (H2110 and HCC827) Tested Concentrations: 100 nM, 300 nM Incubation Duration: 72 hrs (hours) Experimental Results: Lacked synthetically lethality in K-Ras mutant versus wild type cells. |
| References |
[1]. Identification and Characterization of Von Hippel-Lindau-Recruiting Proteolysis Targeting Chimeras (PROTACs) of TANK-Binding Kinase 1. J Med Chem. 2018 Jan 25;61(2):583-598. |
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 : PEG300 ：Tween 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). 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 : PEG300：Tween 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). 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 | 0.9148 mL | 4.5738 mL | 9.1476 mL | |
| 5 mM | 0.1830 mL | 0.9148 mL | 1.8295 mL | |
| 10 mM | 0.0915 mL | 0.4574 mL | 0.9148 mL |