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.
Structure of 2163793-55-1
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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.
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.
* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2
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