SIM1

 CAS No.: 2719051-84-8  Cat No.: BP-400158  Purity: ≥99% 4.5  

SIM1 is a trivalent VHL-based BET PROTAC built from BET bromodomain inhibitor motifs connected through branched linkers to a von Hippel-Lindau ligand. Public sources describe it as capable of degrading BET family proteins with preference for BRD2, illustrating how multivalent architecture can alter potency, paralog preference, and degradation kinetics relative to classical bivalent degraders. The BET-recognition components engage bromodomain acetyl-lysine reader sites, while the VHL ligand recruits the VHL-associated ubiquitin-ligase complex. Mechanistically, SIM1 promotes formation of degradation-competent BET–PROTAC–VHL assemblies, resulting in ubiquitination and proteasomal removal of BET proteins. It is useful for studying trivalent PROTAC design, avidity effects, BET paralog selectivity, sustained transcriptional suppression, comparison of branched versus linear linkers, and the broader question of how molecular valency influences target engagement and degradation efficiency.

SIM1

Structure of 2719051-84-8

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PROTAC
Molecular Formula
C79H98Cl2N14O13S3
Molecular Weight
1618.81
Related CAS
2769753-29-7 (9R-isomer) 2719051-98-4 (4S-isomer)

* For research and manufacturing use only. Not for human or clinical use.

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Purity
≥99%
Storage
Store at -20°C, protect from light, stored under nitrogen
IUPACName
(2S,4R)-1-[(2S)-2-[[2-[3-[2-[2-[2-[[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.02,6]trideca-2(6),4,7,10,12-pentaen-9-yl]acetyl]amino]ethoxy]ethoxy]ethoxy]-2-[2-[2-[2-[[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.02,6]trideca-2(6),4,7,10,12-pentaen-9-yl]acetyl]amino]ethoxy]ethoxy]ethoxymethyl]-2-methylpropoxy]acetyl]amino]-3,3-dimethylbutanoyl]-4-hydroxy-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]pyrrolidine-2-carboxamide
Synonyms
N,N'-(11-((2-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-2-oxoethoxy)methyl)-11-methyl-3,6,9,13,16,19-hexaoxahenicosane-1,21-diyl)bis(2-((S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetamide)
Density
1.39±0.1 g/cm3
InChI Key
RARNTROXRCXFHV-CMRSQZKGSA-N
InChI
InChI=1S/C79H98Cl2N14O13S3/c1-46-49(4)110-76-66(46)68(54-16-20-57(80)21-17-54)86-60(72-91-89-51(6)94(72)76)37-63(97)82-24-26-102-28-30-104-32-34-106-42-79(11,44-108-41-65(99)88-71(78(8,9)10)75(101)93-40-59(96)36-62(93)74(100)84-39-53-12-14-56(15-13-53)70-48(3)85-45-109-70)43-107-35-33-105-31-29-103-27-25-83-64(98)38-61-73-92-90-52(7)95(73)77-67(47(2)50(5)111-77)69(87-61)55-18-22-58(81)23-19-55/h12-23,45,59-62,71,96H,24-44H2,1-11H3,(H,82,97)(H,83,98)(H,84,100)(H,88,99)/t59-,60+,61+,62+,71-/m1/s1
SMILES
CC1=C(SC2=C1C(=NC(C3=NN=C(N32)C)CC(=O)NCCOCCOCCOCC(C)(COCCOCCOCCNC(=O)CC4C5=NN=C(N5C6=C(C(=C(S6)C)C)C(=N4)C7=CC=C(C=C7)Cl)C)COCC(=O)NC(C(=O)N8CC(CC8C(=O)NCC9=CC=C(C=C9)C1=C(N=CS1)C)O)C(C)(C)C)C1=CC=C(C=C1)Cl)C
Mechanism

Target: SIM1 targets BET family proteins BRD2, BRD3, and BRD4, preferentially degrading BRD2.

Binding site: Its BET ligands bind acetyl-lysine recognition pockets within BET bromodomains.

Mechanism of action: SIM1 is a trivalent VHL-recruiting BET PROTAC constructed from BET bromodomain inhibitors connected to a von Hippel-Lindau ligand through branched linkers. This multivalent architecture enhances target engagement and promotes productive ternary-complex formation between BET proteins and VHL-containing ubiquitin ligase machinery. The resulting proximity enables ubiquitination and proteasome-dependent depletion of BRD2, BRD3, and BRD4, with preferential and rapid BRD2 degradation reported. SIM1 is useful for studying BET paralog dependency, multivalent degrader design, chromatin-reader turnover, and degradation-driven transcriptional suppression.

Applications

• PROTAC-Mediated SIM1 Degradation: This application focuses on the use of SIM1-targeting PROTACs to facilitate the selective degradation of SIM1 protein. By recruiting E3 ligases, these PROTACs enable researchers to study the functional consequences of SIM1 depletion in cellular models, advancing understanding of its role in gene regulation and neuronal differentiation.

• Targeted Degradation in Neurobiology: Utilizing SIM1-specific PROTACs allows for precise protein degradation within neurobiological research. This approach aids in dissecting SIM1's involvement in neural development and function, providing valuable insights into its contribution to neurodevelopmental disorders and potential therapeutic strategies.

• Mechanistic Studies of SIM1 Pathways: PROTAC technology targeting SIM1 enables detailed investigation of its signaling pathways. By degrading SIM1, researchers can elucidate its interactions and downstream effects, facilitating the exploration of novel regulatory mechanisms and potential intervention points in cellular signaling networks.

• Functional Genomics via PROTACs: Employing SIM1-targeted PROTACs in functional genomic studies allows for the dynamic modulation of protein levels. This application supports the identification of SIM1's genetic interactions and regulatory networks, enhancing the understanding of its biological significance and potential as a therapeutic target.

1. BRS3 in both MC4R- and SIM1-expressing neurons regulates energy homeostasis in mice
Ramón A Piñol, Marc L Reitman, Haley Province, Naili Liu, Oksana Gavrilova, Cuiying Xiao Mol Metab . 2020 Jun;36:100969. doi: 10.1016/j.molmet.2020.02.012.
Objective:Bombesin-like receptor 3 (BRS3) is an orphan receptor and Brs3 knockout mice develop obesity with increased food intake and reduced resting metabolic rate and body temperature. The neuronal populations contributing to these effects were examined.Methods:We studied energy metabolism in mice with Cre-mediated recombination causing 1) loss of BRS3 selectively in SIM1- or MC4R-expressing neurons or 2) selective re-expression of BRS3 from a null background in these neurons.Results:The deletion of BRS3 in MC4R neurons increased body weight/adiposity, metabolic efficiency, and food intake, and reduced insulin sensitivity. BRS3 re-expression in these neurons caused partial or no reversal of these traits. However, these observations were confounded by an obesity phenotype caused by the Mc4r-Cre allele, independent of its recombinase activity. The deletion of BRS3 in SIM1 neurons increased body weight/adiposity and food intake, but not to the levels of the global null. The re-expression of BRS3 in SIM1 neurons reduced body weight/adiposity and food intake, but not to wild type levels. The deletion of BRS3 in either MC4R- or SIM1-expressing neurons affected body temperature, with re-expression in either population reversing the null phenotype. MK-5046, a BRS3 agonist, increases light phase body temperature in wild type, but not Brs3 null, mice and BRS3 re-expression in either population restored response to MK-5046.Conclusions:BRS3 in both MC4R- and SIM1-expressing neurons contributes to regulation of body weight/adiposity, insulin sensitivity, food intake, and body temperature.
2. Ectopic expression of Irx3 and Irx5 in the paraventricular nucleus of the hypothalamus contributes to defects in Sim1 haploinsufficiency
Jade Chan, Joe Eun Son, Xi Huang, Xuejun Li, Jacques L Michaud, Zhengchao Dou, Kyoung-Han Kim, Chi-Chung Hui, Siyi Wanggou, Rong Mo Sci Adv . 2021 Oct 29;7(44):eabh4503. doi: 10.1126/sciadv.abh4503.
The paraventricular nucleus of the hypothalamus (PVH) contains a heterogeneous cluster ofSim1-expressing neurons critical for feeding regulation.Sim1haploinsufficiency results in hyperphagic obesity with disruption of PVH neurons, yet the molecular profiles of PVH neurons and the mechanism underlying the defects ofSim1haploinsufficiency are not well understood. By single-cell RNA sequencing, we identified two major populations ofSim1+PVH neurons, which are differentially affected bySim1haploinsufficiency. TheIroquoishomeobox genesIrx3andIrx5have been implicated in the hypothalamic control of energy homeostasis. We found thatIrx3andIrx5are ectopically expressed in theSim1+PVH cells ofSim1+/-mice. By reducing their dosage and PVH-specific deletion ofIrx3, we demonstrate that misexpression ofIrx3andIrx5contributes to the defects ofSim1+/-mice. Our results illustrate abnormal hypothalamic activities ofIrx3andIrx5as a central mechanism disrupting PVH development and feeding regulation inSim1haploinsufficiency.
3. Functional Analysis of the SIM1 Variant p.G715V in 2 Patients With Obesity
Mieke M van Haelst, Owen A Ross, Jay A van Gerpen, Patrick R Blackburn, Alexis G Gerassimou, Mellody Cooiman, Klaas J Wierenga, Paldeep S Atwal, Thomas R Caulfield, Eric W Klee, Murray L Whitelaw, Kimberly G Harris, Adrienne E Sullivan, David C Bersten, Lotte Kleinendorst J Clin Endocrinol Metab . 2020 Jan 1;105(1):dgz192. doi: 10.1210/clinem/dgz192.
Context:Single-minded homologue 1 (SIM1) is a transcription factor with several physiological and developmental functions. Haploinsufficiency of SIM1 is associated with early-onset obesity with or without Prader-Willi-like (PWL) features and may exhibit incomplete penetrance.Case description:Next-generation sequencing was performed for 2 male patients with obesity, including 1 man presenting with intellectual disability (ID), body mass index (BMI) of 47.4, and impulse-control disorder, and the other man with early obesity (BMI of 36); sequencing revealed a missense variant in SIM1 (c.2144G>T; p.G715V) in both individuals. Previous studies have identified several disease-associated variants that fall near the p.G715V variant within the C-terminal domain of SIM1. We examined p.G715V variant stability and activity in a doxycycline-inducible stable cell line transfected with an artificial reporter construct and either ARNT or ARNT2 as a partner protein.Conclusions:Functional testing of the p.G715V variant revealed a significant reduction in SIM1-mediated transcriptional activity. We also generated the first ab initio hybrid protein model for full-length SIM1 to show the predicted spatial relationship between p.G715V and other previously described variants in this region and identified a putative mutation hotspot within the C-terminus. Significant clinical heterogeneity has been observed in patients with SIM1 variants, particularly with regards to the PWL phenotype. In the patient with ID, a second variant of uncertain significance in CHD2 was identified that may contribute to his ID and behavioral disturbances, emphasizing the role of additional genetic modifiers.

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