Protein Engineering Paving the Way for Next-Generation Therapies in Cancer
Abstract
1. Introduction
2. Foundations of Protein Engineering
2.1. Directed Evolution: Mimicking Natural Selection in the Lab
2.2. Rational Design: Precision Engineering Based on Structural Insights
2.3. Hybrid Approaches: Combining the Best of Both Worlds
2.4. Tools and Technologies in Protein Engineering
2.4.1. CRISPR-Based Systems for Directed Modifications
2.4.2. Advances in AI and Machine Learning for Protein Design
2.4.3. High-Throughput Screening and Automation
2.4.4. Synthetic Biology and De Novo Protein Design
3. Key Applications of Engineered Proteins in Cancer Therapeutics
3.1. Monoclonal Antibodies
3.2. Bispecific and Multispecific Antibodies
Antibody Name | Engineering Strategy | Target(s) | Mechanism/Engineering Purpose | Cancer Indication(s) | FDA Approval Year | Ref. |
---|---|---|---|---|---|---|
Trastuzumab (Herceptin) | Humanized IgG1 | HER2 | Humanization to reduce immunogenicity | HER2+ breast, gastric cancer | 1998 | [148] |
Atezolizumab (Tecentriq) | Fc-engineered IgG1 | PD-L1 | Fc mutation reduces ADCC to preserve immune cells | NSCLC, urothelial carcinoma, | 2016 | [149] |
Durvalumab (Imfinzi) | Fc-engineered IgG1 | PD-L1 | Reduced Fc effector function | NSCLC, SCLC, bladder cancer | 2017 | [150] |
Blinatumomab (Blincyto) | Bispecific T cell engager | CD3/CD19 | BiTE format links T cells to B cells | B-cell ALL | 2014 | [151] |
Mosunetuzumab | Bispecific antibody | CD20/CD3 | Redirects T cells to B cells | Follicular lymphoma | 2022 | [152] |
Glofitamab | Bispecific antibody | CD20/CD3 | 2:1 binding format for enhanced avidity | DLBCL | 2023 | [153] |
Brentuximab vedotin (Adcetris) | ADC | CD30 | MMAE cytotoxin via cleavable linker | Hodgkin lymphoma | 2011 | [154] |
Trastuzumab emtansine (Kadcyla) | ADC | HER2 | DM1 payload conjugated to trastuzumab | HER2+ breast cancer | 2013 | [155] |
Trastuzumab deruxtecan (Enhertu) | ADC | HER2 | Topoisomerase I inhibitor payload | HER2+ breast, gastric, lung cancers | 2019 | [156] |
Sacituzumab govitecan (Trodelvy) | ADC | Trop-2 | SN-38 (irinotecan active form) conjugated | TNBC, urothelial carcinoma | 2020 | [157] |
Margetuximab | Fc-engineered anti-HER2 | HER2 | Fc domain optimized for better FcγRIIIa binding (enhanced ADCC) | HER2+ breast cancer | 2020 | [158] |
Elranatamab | Bispecific antibody | CD3/BCMA | Engages T cells with BCMA-expressing myeloma cells | Multiple myeloma | 2023 | [159] |
3.3. Engineered Cytokines and Fusion Proteins
3.4. Nanobodies and Single-Domain Antibodies
3.5. Protein-Based Drug Delivery Systems
4. Challenges and Limitations and Future
4.1. Protein Stability and Folding in Therapeutic Contexts
4.2. Immunogenicity and Strategies for Immune Evasion
4.3. Manufacturing and Scalability Issues
Challenge | Underlying Issue | Example Case | Proposed Engineering Strategies |
---|---|---|---|
Protein Stability | Aggregation, misfolding, or degradation during production or storage | Bispecific antibodies prone to aggregation | Stabilizing mutations; computational folding models; optimized expression systems and formulations |
Immunogenicity | Host immune system recognizes engineered protein as foreign | Anti-drug antibodies (ADAs) generated against cytokine fusion proteins | Deimmunization; humanization; epitope masking; computational T-cell epitope mapping |
Manufacturing Scale-Up | Low yield, complex purification, batch variability | CAR T-cell therapies; bispecific antibody production | Automation; closed-system bioreactors; mammalian expression platforms; advanced chromatography |
Regulatory Complexity | Need for extensive safety, efficacy, and stability data | Approval of bispecifics like blinatumomab required extended trials | Early engagement with regulators; adaptive trial design; real-world evidence generation |
Cost and Accessibility | High development and production costs limit patient access | Limited access to ADCs and CAR T-cell therapies in low-resource settings | Biosimilar development; value-based pricing; process optimization for cost reduction |
4.4. Future Perspectives and Research Directions
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Strategy | Key Features | Advantages | Limitations | Applications for Cancer Therapeutics |
---|---|---|---|---|
Directed Evolution | Iterative rounds of random mutagenesis and selection | Does not require structural knowledge; explores large sequence space | Time- and resource-intensive screening; less predictable outcomes | Optimizing antibody affinity; improving enzyme stability |
Rational Design | Structure-guided site-directed mutagenesis | High precision; targeted functional improvements | Requires high-resolution structural data; limited by model accuracy | Reducing immunogenicity; improving thermal stability of therapeutic proteins |
Hybrid Approaches | Combines rational design to guide focused libraries for directed evolution | Balances precision and diversity; more efficient than fully random libraries | Dependent on computational tools and effective screening strategies | Bispecific antibody design; fusion protein stability optimization |
AI-Driven Design | Uses machine learning and deep learning to predict structure-function relations | Rapid in silico screening; enables de novo design; expands design possibilities | Requires large, high-quality datasets; experimental validation still needed | De novo protein design; optimizing stability, solubility, and immune evasion properties of therapeutics |
Therapeutic Modality | Mechanism of Action | Representative Example(s) | Clinical/Application Highlights | Ref. |
---|---|---|---|---|
Monoclonal Antibodies | Bind specific tumor-associated antigens to mediate immune responses (ADCC, CDC) | Trastuzumab, Rituximab | HER2+ breast cancer, B-cell malignancies; immune checkpoint blockade (e.g., anti-PD-1/PD-L1) | [11,117] |
Bispecific Antibodies | Engage two different targets (CD3 on T cells and CD19 on tumor cell) | Blinatumomab, BiA9*2_HF | Redirects T cells to tumor anddual signaling modulation in B-cell acute lymphoblastic leukemia and multiple myeloma | [118,119] |
Engineered Cytokines | Modulate immune response; enhance effector cell activity | Bempegaldesleukin (NKTR-214), L19-IL-2 | Biased receptor targeting to reduce toxicity, synergy with checkpoint inhibitors and tumor-specific immune activation in renal cell carcinoma and melanoma | [120,121] |
Fusion Proteins | Combine targeting and effector domains into one protein | VEGF-HNc, NHS-IL-12 | Tumor-specific delivery of toxins or cytokines, improved specificity and reduced systemic effects in solid malignancies | [9,122] |
Nanobodies (Single-domain Abs) | Small antibody fragments target specific epitopes | 68Ga-labeled anti-HER2, EGFR nanobody-drug conjugates | Enhanced tumor penetration and clearance; suitable for imaging and ADCs in HER2+ breast cancer, EGFR-expressing solid tumors and glioblastoma | [123,124] |
Protein-Based Delivery Systems | Targeted delivery of drugs or nucleic acids using protein carriers | Trastuzumab emtansine (T-DM1), Ferritin-based nanocages | Improved stability and bioavailability; siRNA and chemotherapy delivery with tumor selectivity in HER2+ breast cancer and | [10,125] |
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Naderiyan, Z.; Shoari, A. Protein Engineering Paving the Way for Next-Generation Therapies in Cancer. Int. J. Transl. Med. 2025, 5, 28. https://doi.org/10.3390/ijtm5030028
Naderiyan Z, Shoari A. Protein Engineering Paving the Way for Next-Generation Therapies in Cancer. International Journal of Translational Medicine. 2025; 5(3):28. https://doi.org/10.3390/ijtm5030028
Chicago/Turabian StyleNaderiyan, Zahra, and Alireza Shoari. 2025. "Protein Engineering Paving the Way for Next-Generation Therapies in Cancer" International Journal of Translational Medicine 5, no. 3: 28. https://doi.org/10.3390/ijtm5030028
APA StyleNaderiyan, Z., & Shoari, A. (2025). Protein Engineering Paving the Way for Next-Generation Therapies in Cancer. International Journal of Translational Medicine, 5(3), 28. https://doi.org/10.3390/ijtm5030028