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Updated: Sep 6, 2025
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently
Seonghoon Kim1, Hee-Sung Park2, Byung-Ha Oh1
1Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
Abstract:
One of the hallmarks of cancer cells is their ability to evade apoptosis, which confers survival advantages and resistance to anti-cancer drugs. Cancers often exhibit overexpression of anti-apoptotic BCL-2 proteins, the loss of which triggers apoptosis. In particular, the inhibition of both BCL-xL and MCL-1, but neither one individually, synergistically enhances apoptotic cell death. Here, we report computational design to produce a protein that inhibits both BCL-xL and MCL-1 simultaneously. To a reported artificial three-helix bundle whose second helix was designed to bind MCL-1, we added a fourth helix and designed it to bind BCL-xL. After structural validation of the design and further structure-based sequence design, we produced a dual-binding protein that interacts with both BCL-xL and MCL-1 with apparent dissociation constants of 820 pM and 196 pM, respectively. Expression of this dual binder in a subset of cancer cells induced apoptotic cell death at levels significantly higher than those induced by the pro-apoptotic BIM protein. With a genetic fusion of a mitochondria-targeting sequence or the BH3 sequence of BIM, the activity of the dual binder was enhanced even further. These data suggest that targeted delivery of this dual binder alone or as a part of a modular protein to cancers in the form of protein, mRNA, or DNA may be an effective way to induce cancer cell apoptosis.
Insights
Scientists computationally designed a novel protein to simultaneously inhibit anti-apoptotic BCL-xL and MCL-1 proteins, enhancing cancer cell apoptosis. This dual-binder shows promise for cancer therapy delivery via protein, mRNA, or DNA.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Cancer cells evade apoptosis, a programmed cell death, conferring survival and drug resistance.
- Overexpression of anti-apoptotic BCL-2 proteins like BCL-xL and MCL-1 is common in cancers.
- Simultaneous inhibition of BCL-xL and MCL-1 synergistically induces cancer cell apoptosis.
Purpose of the Study:
- To computationally design a novel protein capable of simultaneously inhibiting both BCL-xL and MCL-1.
- To validate the structure and binding affinity of the designed dual-inhibitor protein.
- To assess the efficacy of the dual-binder in inducing apoptotic cell death in cancer cells.
Main Methods:
- Computational protein design incorporating a fourth helix to bind BCL-xL.
- Structural validation and structure-based sequence optimization.
- Binding affinity assessment using apparent dissociation constants (Kd).
- Expression of the dual-binder in cancer cells and comparison with BIM protein.
Main Results:
- A dual-binding protein targeting both BCL-xL and MCL-1 was successfully designed and produced.
- The protein exhibited high binding affinities with Kd values of 820 pM for BCL-xL and 196 pM for MCL-1.
- Expression of the dual-binder significantly increased apoptotic cell death in cancer cells compared to BIM.
- Enhanced activity was observed with mitochondria-targeting or BIM BH3 sequence fusions.
Conclusions:
- The designed dual-binder effectively inhibits BCL-xL and MCL-1, inducing significant cancer cell apoptosis.
- Targeted delivery of this dual-binder, as protein, mRNA, or DNA, represents a promising strategy for cancer therapy.
- Further development could involve modular protein designs for enhanced therapeutic potential.
Related Concept Videos
01:31The Intrinsic Apoptotic Pathway
01:17The Extrinsic Apoptotic Pathway