With over 200 biosimilars approved globally (1) and many top-selling biologics losing exclusivity in the next five years, the demand for cost-efficient, large-scale production of recombinant antibody therapeutics is growing.

New protein engineering methods are helping to overcome fundamental commercial viability and manufacturing challenges in protein-based therapeutics, particularly biosimilars, which are critical for improving access to life-saving biologics.

Increasing yield, controlling costs

The biopharmaceutical industry is constantly looking for ways to improve protein expression and yield in manufacturing.

However, the preclinical development phase of biosimilars presents scientific, technical, regulatory, and logistical hurdles which impact how quickly and broadly affordable biologics can be made available.

Advances in manufacturing, bioprocessing, and facility design have already had a significant impact on lowering costs for monoclonal antibodies (mAbs) over the last 30 years. However, the costs have now stagnated at around $50-100 per gram due to manufacturing complexity.

To make mAbs available in lower-income countries, the manufacturing price should fall to around $10 per gram, the Gates foundation evaluated in their initiative (2).

The many roles of protein engineering

Protein engineering is not only an important cost-reduction strategy but also a vehicle for improving safety, flexibility in development, and capacity planning (3-5).

Protein and cell engineering methods, from UTR and vector optimization, CRISPR-based techniques, signal peptide engineering, and transposon integration to epitranscriptomics, directly increase mAb yield per cell and per volume. This allows pharmaceutical companies to meet production demands without constantly scaling up bioreactor capacity, saving time, cost, and facility footprint (5-6).

Furthermore, drug candidates can be engineered and selected to reduce the dose and/or dosing frequency, reducing both adverse effects andtreatment costs.

The needle in the haystack that can increase yield 5x

The translocation of secretory proteins into the endoplasmic reticulum (ER) remains a bottleneck in cost-efficient and high-quality mAb production.

Signal peptides, short amino acid sequences located at the N-terminus of nascent proteins, play a critical role in guiding these proteins into the ER. Swapping a native signal peptide with a high-performing alternative can boost expression manyfold.

Already in 2015, a study by Haryadi et al. (7) evaluated eight heavy chain signal peptides and two light chain signal peptides to assess their impact on antibody production in five blockbuster antibody drugs: Herceptin, Avastin, Remicade, Rituxan, and Humira. Even a small-scale screen yielded a twofold increase in expression, demonstrating the untapped potential of engineering signal peptides.

Today, high-throughput screening technologies make it possible to analyze thousands of signal peptides simultaneously. Such high-volume analysis is vital, because signal peptides have dramatically different effects on a specific protein. This is especially important in the case of monoclonal antibodies that have a heavy chain and a light chain, requiring the optimal pair of signal peptides to be identified to boost expression.

Engineering without losing biosimilarity

Ensuring equivalence in biological properties between a biosimilar and its reference product is the cornerstone of biosimilar development. This includes critical quality attributes such as protein structure, post-translational modifications (e.g. glycosylation profiles), purity/impurity profiles, and biological function.

Regulatory agencies such as the FDA and EMA emphasize that even minor changes to upstream processes must not affect the clinical performance of the molecule.

Signal peptide engineering offers a unique advantage in this context: Because they do not appear in the final product, their optimization can enhance protein expression, secretion, and process yield without altering the structure or function of the mature antibody.

This makes signal peptide engineering an attractive strategy for biosimilar and biobetter programs: it improves upstream productivity while preserving biosimilarity.

Gaining an advantage in the race for market entry

When reference biologics lose exclusivity, multiple manufacturers often race to launch their biosimilars. Signal peptide engineering can shorten development timelines by identifying optimal expression conditions rapidly and improving manufacturability.

By boosting expression early in development, manufacturers can move more quickly through scale-up and validation. This speed not only supports stronger commercial positioning but also brings lower-cost biologics to patients sooner.

Did you know?

• The biosimilar market size is expected to exceed $200B by 2033.
• Biosimilar development is accelerating quickly: In the USA, the FDA has approved 75 biosimilars as of May 2025 (8)
• Signal peptides can drive 5–7-fold increases in recombinant protein expression, simply by optimizing a sequence that is naturally discarded during protein processing.

Sources:

1. Nupur et al. Analytical Similarity Assessment of Biosimilars: Global Regulatory Landscape, Recent Studies and Major Advancements in Orthogonal Platforms (2022), Frontiers in Bioengineering and Biotechnology.
2. Innovations for Exceptionally Low-Cost Monoclonal Antibody (mAb) Manufacturing (accessed July 10, 2025). https://gcgh.grandchallenges.org/challenge/innovations-exceptionally-low-cost-monoclonal-antibody-mab-manufacturing
3. Chen, C. et al. (2025). Cost and supply considerations for antibody therapeutics. mAbs, 17(1). https://doi.org/10.1080/19420862.2025.2451789
4. Naderiyan, Z.; Shoari, A. Protein EngineeringPaving the Way for Next-Generation Therapies in Cancer. Int. J. Transl. Med.2025, 5, 28. https://doi/full/10.1080/19420862.2025.2451789‍
5. Yang CH, Li HC, Lo SY. Enhancing recombinant antibody yield in Chinese hamster ovary cells. Tzu Chi Med J. 2024 May24;36(3):240-250. 10.4103/tcmj.tcmj_315_23. PMID: 38993821; PMCID: PMC11236083.
6. Papadaki, S., Tournaviti, S., Borth, N. et al.Large-scale transcriptomics analysis reveals a novel stress biomarker in CHO cells producing difficult to express mAbs. Sci Rep 15, 5643 (2025).https://doi.org/10.1038/s41598-025-89667-w
7. Haryadi R, et al. (2015) Optimization of Heavy Chain and Light Chain Signal Peptides for High Level Expression of Therapeutic Antibodies in CHO Cells. PLoS ONE 10(2): e0116878. https://doi.org/10.1371/journal.pone.0116878
8. Generics and Biosimilars Initiative, May 2025. https://www.gabionline.net/biosimilars/general/biosimilars-approved-in-the-us (accessed July 8, 2025)

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Image credit: Alex Shuper