MCL-1/BCL-2-IN-3

 CAS No.: 2163793-55-1  Cat No.: BP-300083  Purity: ≥97% 4.5  

MCL-1/BCL-2-IN-3 is a dual BCL-family ligand designed to engage anti-apoptotic proteins involved in mitochondrial apoptosis regulation. By targeting the BH3-binding grooves of MCL-1 and BCL-2-related proteins, it provides a recognition scaffold for degrader strategies aimed at protein-protein interaction regulators. In a bifunctional degrader, an MCL-1/BCL-2-IN-3-derived moiety could bind the anti-apoptotic target protein, while a linker connects it to an E3 ligase recruiter to promote ternary complex formation. The intended mechanism is ubiquitination and proteasome-dependent depletion of the bound survival protein, enabling researchers to distinguish direct binding antagonism from protein-level removal. This ligand is useful for apoptosis pathway research, BCL-family degrader design, selectivity engineering between related anti-apoptotic targets, linker optimization, and mechanistic studies of mitochondrial survival signaling.

MCL-1/BCL-2-IN-3

Structure of 2163793-55-1

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Ligand for Target Protein
Molecular Formula
C27H25BrN2O5S
Molecular Weight
569.47

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

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Purity
≥97%
Solubility
Soluble in DMSO (17.86 mg/mL, Need ultrasonic)
Storage
Store at -20°C
IUPACName
methyl 6-[2-[6-(4-bromophenyl)sulfanyl-1,3-dioxobenzo[de]isoquinolin-2-yl]ethylamino]-6-oxohexanoate
Synonyms
Hexanoic acid, 6-[[2-[6-[(4-bromophenyl)thio]-1,3-dioxo-1H-benz[de]isoquinolin-2(3H)-yl]ethyl]amino]-6-oxo-, methyl ester; Methyl 6-((2-(6-((4-bromophenyl)thio)-1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)ethyl)amino)-6-oxohexanoate; Methyl 6-[(2-{6-[(4-bromophenyl)sulfanyl]-1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl}ethyl)amino]-6-oxohexanoate
Boiling Point
769.3±60.0°C (Predicted)
Density
1.51±0.1 g/cm3 (Predicted)
InChI Key
HZZXWFWVQWMGAR-UHFFFAOYSA-N
InChI
InChI=1S/C27H25BrN2O5S/c1-35-24(32)8-3-2-7-23(31)29-15-16-30-26(33)20-6-4-5-19-22(14-13-21(25(19)20)27(30)34)36-18-11-9-17(28)10-12-18/h4-6,9-14H,2-3,7-8,15-16H2,1H3,(H,29,31)
SMILES
COC(=O)CCCCC(=O)NCCN1C(=O)C2=C3C(=C(C=C2)SC4=CC=C(C=C4)Br)C=CC=C3C1=O
Mechanism

Target: This ligand targets anti-apoptotic proteins MCL-1 and BCL-2 in biochemical or cellular target-engagement studies.

Mechanism of Action: Used as the target-protein recognition element, this ligand provides the binding interface for anti-apoptotic proteins MCL-1 and BCL-2. In PROTAC design, a derivatizable position on the ligand can be connected through an optimized linker to an E3 ligase ligand, such as a CRBN, VHL, or IAP recruiter, while preserving productive target engagement. The resulting bifunctional molecule brings anti-apoptotic proteins MCL-1 into proximity with the recruited E3 ligase, enabling ternary-complex formation. If the complex has favorable geometry and residence time, target lysine ubiquitination is promoted, leading to proteasome-dependent degradation in experimental systems.

Applications

• MCL-1/BCL-2 Degradation Targeting: Use MCL-1/BCL-2-IN-3 as a PROTAC ligand to engage anti-apoptotic BCL-2 family proteins and drive ubiquitin-mediated degradation. This enables systematic testing of how selective removal of MCL-1 versus BCL-2 alters mitochondrial priming, caspase activation, and apoptosis sensitivity in cancer-relevant cellular models.

• Apoptosis Sensitization Studies: Incorporate MCL-1/BCL-2-IN-3 into chimeric degraders to evaluate whether targeted protein loss enhances pro-death signaling. By degrading key survival factors, PROTACs can be used to map dose–response relationships, determine degradation-dependent apoptosis thresholds, and compare outcomes against non-degrading binding controls.

• Resistance Mechanism Probing: Apply MCL-1/BCL-2-IN-3-based PROTACs to investigate therapeutic resistance driven by shifts in BCL-2 family dependency. Targeted degradation can help distinguish whether resistance phenotypes arise from altered expression, compensatory pathway rewiring, or changes in ubiquitination and proteasome susceptibility.

• Selectivity and Mechanism Mapping: Use this ligand to construct PROTACs that interrogate selectivity across BCL-2 family members and define degradation mechanisms. Quantify target turnover kinetics, ubiquitination engagement, and downstream transcriptional or mitochondrial readouts to establish structure–activity relationships governing productive ternary complex formation.

1. Heterogeneous modulation of Bcl-2 family members and drug efflux mediate MCL-1 inhibitor resistance in multiple myeloma
Caroline A Heckman, Juho J Miettinen, Lenka Besse, Jing Tang, Niklas Zojer, Christoph Driessen, Julia Huber, Kristaps Klavins, Andrej Besse, Wolfgang Hübl, J Thomas Hannich, Helene Breid, Arnold Bolomsky, Jo Caers, Alun Parsons, Martin Schreder, Stefanie Fellinger, Heinz Ludwig, Alina Malyutina, Stefan Kubicek Blood Adv . 2021 Oct 26;5(20):4125-4139. doi: 10.1182/bloodadvances.2020003826.
Antiapoptotic Bcl-2 family members have recently (re)emerged as key drug targets in cancer, with a tissue- and tumor-specific activity profile of available BH3 mimetics. In multiple myeloma, MCL-1 has been described as a major gatekeeper of apoptosis. This discovery has led to the rapid establishment of clinical trials evaluating the impact of various MCL-1 inhibitors. However, our understanding about the clinical impact and optimal use of MCL-1 inhibitors is still limited. We therefore explored mechanisms of acquired MCL-1 inhibitor resistance and optimization strategies in myeloma. Our findings indicated heterogeneous paths to resistance involving baseline Bcl-2 family alterations of proapoptotic (BAK, BAX, and BIM) and antiapoptotic (Bcl-2 and MCL-1) proteins. These manifestations depend on the BH3 profile of parental cells that guide the enhanced formation of Bcl-2:BIM and/or the dynamic (ie, treatment-induced) formation of Bcl-xL:BIM and Bcl-xL:BAK complexes. Accordingly, an unbiased high-throughput drug-screening approach (n = 528) indicated alternative BH3 mimetics as top combination partners for MCL-1 inhibitors in sensitive and resistant cells (Bcl-xL>Bcl-2 inhibition), whereas established drug classes were mainly antagonistic (eg, antimitotic agents). We also revealed reduced activity of MCL-1 inhibitors in the presence of stromal support as a drug-class effect that was overcome by concurrent Bcl-xL or Bcl-2 inhibition. Finally, we demonstrated heterogeneous Bcl-2 family deregulation and MCL-1 inhibitor cross-resistance in carfilzomib-resistant cells, a phenomenon linked to the MDR1-driven drug efflux of MCL-1 inhibitors. The implications of our findings for clinical practice emphasize the need for patient-adapted treatment protocols, with the tracking of tumor- and/or clone-specific adaptations in response to MCL-1 inhibition.
2. Pharmacologic Targeting of Mcl-1 Induces Mitochondrial Dysfunction and Apoptosis in B-Cell Lymphoma Cells in a TP53- and BAX- Dependent Manner
Olga V Danilova, Fei Xu, Zheng Xia, Jeffrey W Tyner, Stephen E Kurtz, Xiaoguang Wang, Elana Thieme, Vi Lam, Lili Wang, Tingting Liu, Duanchen Sun, Alexey V Danilov Clin Cancer Res . 2021 Sep 1;27(17):4910-4922. doi: 10.1158/1078-0432.CCR-21-0464.
Purpose:Bcl-2 has been effectively targeted in lymphoid malignancies. However, resistance is inevitable, and novel approaches to target mitochondrial apoptosis are necessary. AZD5991, a selective BH3-mimetic in clinical trials, inhibits Mcl-1 with high potency.Experimental design:We explored the preclinical activity of AZD5991 in diffuse large B-cell lymphoma (DLBCL) and ibrutinib-resistant mantle cell lymphoma (MCL) cell lines, MCL patient samples, and mice bearing DLBCL and MCL xenografts using flow cytometry, immunoblotting, and Seahorse respirometry assay. Cas9 gene editing andex vivofunctional drug screen assays helped identify mechanisms of resistance to Mcl-1 inhibition.Results:Mcl-1 was expressed in DLBCL and MCL cell lines and primary tumors. Treatment with AZD5991 restricted growth of DLBCL cells independent of cell of origin and overcame ibrutinib resistance in MCL cells. Mcl-1 inhibition led to mitochondrial dysfunction as manifested by mitochondrial membrane depolarization, decreased mitochondrial mass, and induction of mitophagy. This was accompanied by impairment of oxidative phosphorylation.TP53andBAXwere essential for sensitivity to Mcl-1, and oxidative phosphorylation was implicated in resistance to Mcl-1 inhibition. Induction of prosurvival proteins (e.g., Bcl-xL) in stromal conditions that mimic the tumor microenvironment rendered protection of primary MCL cells from Mcl-1 inhibition, while BH3-mimetics targeting Bcl-2/xL sensitized lymphoid cells to AZD5991. Treatment with AZD5991 reduced tumor growth in murine lymphoma models and prolonged survival of MCL PDX mice.Conclusions:Selective targeting Mcl-1 is a promising therapeutic approach in lymphoid malignancies.TP53apoptotic network and metabolic reprogramming underlie susceptibility to Mcl-1 inhibition.
3. Combined reduction in the expression of MCL-1 and BCL-2 reduces organismal size in mice
Francine Ke, Stephanie Grabow, Graeme I Lancaster, Andrew J Murphy, Andreas Strasser Cell Death Dis . 2020 Mar 13;11(3):185. doi: 10.1038/s41419-020-2376-5.
The intrinsic apoptotic pathway is controlled by the BCL-2 family of proteins, which exhibit either a pro-death or pro-survival function. Gene knockout studies revealed that different pro-survival BCL-2 proteins are critical for the survival of distinct cell types, although overlapping functions amongst such proteins have also been identified. In the process of studying mice lacking single alleles of Mcl-1 (Mcl-1+/-), Bcl-2 (Bcl-2+/-), or both in combination (Mcl-1+/-Bcl-2+/-), we observed that Mcl-1+/-Bcl-2+/-mice weighed less when compared with their wild-type littermates as they aged. Body composition analysis demonstrated that while fat mass was similar to wild-type controls, lean mass was significantly reduced in Mcl-1+/-, Bcl-2+/-, and, most strikingly in Mcl-1+/-Bcl-2+/-mice. The weights of several tissues including the heart, tibialis anterior, and kidney were likewise reduced in Mcl-1+/-Bcl-2+/-mice. When lean mass and specific tissue weights were expressed relative to body weight, these differences were no longer significant, indicating that that Mcl-1+/-Bcl-2+/-mice, and to a lesser extent Mcl-1+/-and Bcl-2+/-mice, are smaller than their wild-type counterparts. Consistently, the anal-naso length was reduced in Mcl-1+/-Bcl-2+/-mice. While minor reductions in size were observed in female Mcl-1+/-Bcl-2+/-mice, these effects were most prominent in males. Notably, Mcl-1+/-Bcl-2+/-males had markedly smaller testes even after accounting for differences in body weight. Collectively, these data reveal that combined loss of a single allele of Mcl-1 and Bcl-2, while not overtly impairing organismal development, leads to a reduction in animal size.

MCL-1/BCL-2-IN-3 is a BCL-family protein ligand intended for use as the target-engaging component or reference ligand in PROTAC discovery workflows. Its known small-molecule recognition profile enables rational linker-vector evaluation and comparative degrader design. This molecule is described in detail below.

Structure: The structure of MCL-1/BCL-2-IN-3 is characterized by primary or secondary amine/basic nitrogen centers; halogenated aryl/heteroaryl ring system. These features provide defined hydrogen-bonding, hydrophobic, and steric elements that can support affinity retention while enabling analogue-based linker-vector selection.

Reactivity: The amine/basic nitrogen-containing motif can be evaluated for acylation, sulfonylation, alkylation, or carbamate/urea linker installation when that vector is solvent exposed. For PROTAC construction, the POI ligand can be paired with CRBN ligands such as thalidomide, pomalidomide, or lenalidomide analogues, VHL ligands such as VH032 derivatives, or less common IAP/MDM2/cIAP-recruiting ligands, with alkyl, PEG, piperazine, triazole, or amide linkers screened for ternary-complex formation. In practice, incorporation into PROTACs should begin from derivatives that preserve the reported binding pharmacophore, followed by systematic variation of linker length, polarity, rigidity, and exit-vector geometry to optimize target engagement, E3 recruitment, and cellular degradation readouts.

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Tip: Chemical formula is case sensitive. C22H30N4O c22h30n40
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