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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5608_Библиотеки_им_академика_М_И_Перельмана.pdf
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- •Foreword
- •Preface
- •Acknowledgements
- •Contents
- •Contributors
- •About the Editors
- •1.2.2.3 Progeria
- •1. Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry: Using Chemistry and Bioengineering to Improve the Performance of Biologics
- •1.1 Introduction
- •1.2.2.2 Cystic Fibrosis
- •1.3.2.1 ADC Drugs
- •1.4 Top 25 Best-Selling Drugs
- •1.5.1 An Overview
- •1.5.2 Synthetic Biology
- •1.5.8 Biopharmaceutical Regulatory CMC
- •1.5.9 Technology Transfer
- •References
- •2.1 What Is Synthetic Biology?
- •2.6 CAR-T Cell Therapies
- •2.7 Conclusion
- •References
- •3.1 Introduction
- •3.2.1 Oligonucleotide Synthesis
- •3.2.1.1 Early Synthetic Chemistries
- •3.2.2 Solid Supports
- •3.2.3 Modern Oligo Synthesis Platforms
- •3.3 Gene Synthesis
- •3.3.1 Early DNA Assembly Methods
- •3.3.2 Array-Based Gene Synthesis
- •3.4 New Discovery Bottleneck
- •3.4.1.1 Hybridoma Technology
- •3.4.1.2 Phage Display Technology
- •3.4.1.3 Synthetic Antibody Library Construction
- •Semi-Synthetic Libraries
- •Fully Synthetic Libraries
- •3.5 Perspectives
- •References
- •4.1 Introduction
- •4.2.1 Batch
- •4.2.2 Fed-Batch
- •4.2.4 Hybrid Processes
- •4.2.7 Dynamic Perfusion Processes
- •4.3.2 Glucose Limitation
- •4.4.1 N-1 Perfusion
- •4.4.3 Linked Bioreactors
- •4.5 Process Analytical Technology
- •4.6 Single-Use Bioreactors (SUBs)
- •4.7 Conclusions
- •References
- •5.1 Introduction
- •5.2.1 Molecular Format Considerations
- •5.2.1.1 The Charge-Based Electrostatic Approach
- •5.2.1.2 The Knob into Hole Approach
- •5.2.2.1 Stable CHO Host Cell Integration System—Random or Targeted?
- •5.2.2.2 Expression Vector Considerations
- •5.2.2.3 Cell Line Screening Strategy Considerations
- •5.3.1 Upstream Process Development
- •5.3.2 Downstream Process Development Considerations
- •5.3.2.1 Unique Impurity Challenges
- •5.3.2.2 Stability Concerns
- •5.5.2.1 H/H Removal
- •5.5.2.2 HMMS Removal
- •References
- •6.1 Introduction
- •6.2.1 N-Linked Glycosylation
- •6.2.2 O-Linked Glycosylation
- •6.2.3 Glycosaminoglycan Synthesis
- •6.3.1 Mannosylation
- •6.3.2 Fucosylation
- •6.3.3 Galactosylation
- •6.3.4 Sialylation
- •6.5 Glycoengineering
- •6.5.1 Manipulating Heterogeneity
- •6.5.2 Manipulating Sialylation
- •6.5.2.1 Increasing α-2,6 Sialylation
- •6.5.3 Manipulating Fucosylation
- •6.5.4 Manipulating Branching
- •6.6.1 Temperature
- •6.6.2 pH
- •6.6.3.2 Amino Acids
- •6.6.3.3 Glycosaminoglycan Production
- •6.6.4 Culture Additives
- •References
- •7.1 Introduction
- •7.1.1 AAV Gene Therapy
- •7.3.1 Humoral Immunity
- •7.3.2 Cell-Mediated Immunity
- •7.4 Conclusion
- •References
- •8.1 Introduction
- •8.2 mRNA Vaccines
- •8.2.1 Background
- •8.2.2 Production Process
- •8.2.2.2 Production
- •8.4.1 Background
- •8.4.2 Production Process
- •8.4.2.2 Production
- •8.4.2.3 Viral Inactivation
- •8.5 Protein-Based Vaccines
- •8.5.1 Background
- •8.5.2 Production Processes
- •8.5.2.1 NVX-CoV2373 (Novavax)
- •8.3 Viral Vectors
- •8.3.1 Background
- •8.3.2 Production Process
- •8.3.2.2 Production
- •8.4 Whole Inactivated Virus Vaccines
- •8.5.2.2 CoVLP (Medicago)
- •8.5.2.3 EpiVacCorona (Vector Institute)
- •8.7 Conclusions
- •References
- •9. CAR-T Bioprocessing
- •9.1 Introduction
- •9.2.1 Introduction
- •9.2.2 Lentiviral Vector Design
- •9.2.5 Upstream Bioprocessing
- •9.2.6 Downstream Bioprocessing
- •9.3 Cell Product Bioprocessing
- •9.3.1 End-to-End Systems
- •9.3.4 Activation
- •9.3.6 Cell Expansion
- •9.3.8 T-Cell Cryopreservation
- •References
- •10.1.1 What Is CRISPR?
- •10.1.4 Mechanism Behind CRISPR Gene Editing
- •10.2.1 Creating Gene Knockouts
- •10.2.2 Creating Gene Knock-Ins
- •10.2.4 CRISPR Screens
- •10.3.1 Derivative Technologies
- •10.4.2 Delivery Methods
- •10.6.2 TCR Engineered T Cell Therapy
- •10.6.3 Chimeric Antigen Receptor T Cell Therapy
- •10.9.2 Safety Considerations
- •References
- •11.1 Introduction
- •11.1.2 Categories
- •11.2 Current Status
- •11.2.1 Approved Products
- •11.2.2 Market
- •11.3 Design
- •11.3.1 Building Blocks
- •11.3.2 Linkers
- •11.3.3 Oligomerization
- •11.3.3.1 Monomer
- •11.3.3.2 Dimer
- •11.3.3.3 Trimer
- •11.3.3.4 Tetramer
- •11.3.3.5 Pentamer
- •11.3.3.6 Hexamer
- •11.3.3.7 Octamer
- •11.3.4 Orientation
- •11.3.5 Protein Engineering
- •11.3.6 Immunogenicity
- •11.4 Manufacturing
- •11.4.1 Upstream
- •11.4.2 Downstream
- •11.4.3 Glycosylation
- •11.4.4 Aggregation
- •11.4.5 Analytics
- •11.5 Therapeutic Concepts
- •11.5.1 Half-Life Extension
- •Albumin Fusions
- •Fc Fusions
- •Transferrin Fusions
- •Repetitive Peptide Fusions
- •Glycosylated Peptides
- •11.5.1.3 Aggregate Forming Peptides
- •11.5.2 Targeting Functions
- •11.5.3.1 Fc Domain Receptor-Mediated Toxicity
- •11.5.3.2 Toxins
- •11.5.3.3 Immunocytokines
- •11.5.3.4 Human Enzymes
- •11.5.3.5 Apoptosis Induction
- •11.6 Summary
- •11.7 Future Perspectives
- •References
- •12.1 Introduction
- •12.2 ADC History
- •12.3 Target Selection
- •12.4 Antibody Selection
- •12.6 ADC Technology
- •12.7 ADC Clinical Development
- •12.8.1 Mylotarg
- •12.8.2 Adcetris
- •12.8.3 Kadcyla
- •12.8.4 Besponsa
- •12.8.5 Polivy
- •12.8.6 Padcev
- •12.8.7 Enhertu
- •12.8.8 Trodelvy
- •12.8.9 Blenrep
- •12.8.10 Zynlonta
- •12.8.11 Tivdak
- •12.9 Concluding Remarks
- •References
- •13.1 Introduction
- •13.2 Gemtuzumab Ozogamicin
- •13.3 Gemtuzumab Antibody
- •13.4 Calicheamicin
- •13.7.3 Isolation of N-Acetyl Calicheamicin
- •13.10 Conclusions
- •References
- •14.1 Introduction
- •14.2.1 Antibody Generation
- •14.3.1 Structure Prediction
- •14.3.2 Biophysical Properties
- •14.3.3 Hydrophobicity
- •14.3.5 Isoelectric Point (pI)
- •References
- •15.1 Introduction
- •15.2 ADA Program Development
- •15.2.3 Project Approach
- •15.2.4 Model Library
- •15.3 Case Study
- •15.3.3 Hypothesis Generation
- •15.3.5 Feature Engineering Example
- •15.3.7 Model Insights
- •References
- •16.1 Introduction
- •16.1.1.1 United States
- •16.1.1.2 European Union
- •16.1.2 Global Markets
- •16.4.1 United States FDA
- •16.4.2 European Medicines Agency (EMA)
- •16.4.3 The World Health Organization
- •References
- •17.1 Introduction
- •17.3.1.2 Clone Selection

290
S. R. Schmidt
11.2 Current Status
11.2.1 Approved Products
In 1998, the rst fusion protein, Etanercept, was approved. It belongs to the class of
(fragment crystallizable) Fc fusions and receptor traps, consisting of the extracellular domain of tumor necrosis factor-alpha (TNF-α) receptor connected to a
sequence encoding the Fc portion and hinge region of an immunoglobulin G1
(IgG1) heavy chain. This drug has been marketed under the name Enbrel® and is
the best-selling fusion protein to date. Since this rst regulatory approval, multiple
other fusion proteins successfully passed clinical trials and became available for
patients.
So far 22 19 fusion proteins received approval by the U.S.Food and Drug
Administration (FDA). The most successful year was 2014, with four new fusion
proteins getting commercial licenses. Twelve proteins contain an Fc-domain that is
not only a typical building block for receptor traps but also serves as module to
extend the plasma half-life to generate biobetters. An alternative approach is the
fusion to human serum albumin (HSA) that binds as well to the neonatal Fc gamma
receptor (FcRn) thus enabling recycling and improved pharmacokinetics. Another
category with a few other examples is immunotoxins. Here a bacterial toxin is fused
to a targeting moiety that allows to selectively kill malignant cells bearing the corresponding target. A summary of the approved fusion protein is displayed in
Table11.2.
11.2.2 Market
The therapeutic success of the rst approved fusion protein, Enbrel®, triggered the
interest of many scientists. For the rst time, a non-naturally existing protein
designed from unrelated building blocks was used for the treatment of severe diseases. Some fusion proteins are real blockbuster drugs with multibillion USD sales
per year. The four most successful therapeutic fusion proteins are Eylea®,
Trulicity®, Enbrel®, and Orencia® with annual revenues of more than 9.2, 6.5, 4.5,
and 3.3 billion USD in 2021, respectively, as described in Fig.11.1.
Due to their unique functionality and the difculty to copy their mode of action,
fusion proteins are interesting for investors and thus became the target of mergers
and acquisitions. Over the last two decades, multiple transactions took place that
included single molecules, platform technologies, and whole pipelines at different
development levels as displayed in Table11.3. Only a minority contained approved
fusion proteins, indicating that most companies were taken over for expectations of
future success for the molecules. Interestingly, 2021 has been the year with the
highest number of deals in that context.

11 Fusion Proteins: Current Status andFuture Perspectives
291
Brand Approval Protein 1N-Term Protein 2 C-Term Indication Host Mode of action
Enbrel® 11/98 TNFαR IgG1 Fc Arthritis CHO Receptor trap
Ontak® 02/99 Diphtheria toxin IL2 Lymphoma Escherichia coli Immunotoxin
Table 11.2 Overview on currently approved fusion proteins
Amevive® 01/03 LFA-3 IgG1 Fc Psoriasis CHO
Orencia® 02/06 CTLA-4 IgG1 Fc Arthritis CHO
Arcalyst® 02/08 IL1R & AP IgG1 Fc Cryopyrin syndrome CHO Receptor trap
Nplate® 08/08 IgG1 Fc Peptide ITP E. coli Peptibody
Elonva® 02/10 FSH CTP Fertility CHO Biobetter
Nulojix® 06/11 CTLA-4 IgG1 Fc Transplant rejection CHO
Eylea®/Zaltrap® 11/11 VEGF R1/2 IgG1 Fc Macular degen./Cancer CHO Receptor trap
Alprolix® 03/14 FIX IgG1 Fc Hemophilia B HEK Biobetter
Tanzeum® 04/14 GLP-1 HSA Diabetes Saccharomyces cerevisiae Biobetter
Eloctate® 06/14 FVIII IgG1 Fc Hemophilia A HEK Biobetter
Trulicity® 09/14 GLP-1 IgG4 Fc Diabetes CHO Biobetter
Strensiq® 10/15 Alkaline phosphatase IgG1 Fc Hypophosphatasia CHO
Idelvion® 03/16 FIX HSA Hemophilia B CHO Biobetter
Lumoxiti® 09/18 aCD22 scFv Pseudomonas toxin Hairy cell leukemia E. coli Immunotoxin
Elzonris® 12/18 Diphtheria toxin IL3 BPDCN E. coli Immunotoxin
Reblozyl® 08/19 Activin receptor IIB IgG1 Fc Beta-thalassemia CHO Receptor trap
Altuviiio® 02/23 IgG1-Fc FVIII-VWF-XTEN Hemophilia A HEK293 Biobetter
Ngenla® 06/23 CTP hGH Growth hormone deciency CHO Biobetter
Ryzneuta® 09/23 G-CSF IgG2 Fc Neutropenia CHO Biobetter
Anktiva® 04/24 IL15/IL15R IgG1 Fc Bladder cancer CHO

292
Fig. 11.1 Global sales of top selling fusion proteins
S. R. Schmidt
The huge revenues generated by some fusion proteins are obviously attractive for
biosimilar developers. For instance, Enbrel® as one of the blockbusters has lost patent protection in Europe and other parts of the world in 2015. As a consequence, a
wave of biosimilar variants appeared in those markets, causing a signicant drop of
sales for the originator drug since then. Since its peak sales in 2015 with close to $b
9, its sales dropped signicantly. However, in the US, Amgen’s Enbrel® patent will
expire only in 2029.
11.3 Design
11.3.1 Building Blocks
The design of fusion proteins relies on the combination of several modules. One
source of these building blocks are antibodies or their derivates such as the constant
Fc domain [4] or the variable domains often used as single chain (scFv). Also all
kinds of protein scaffolds containing some loops that are accessible for mutagenesis
to generate novel afnity binders have frequently been used [5]. Fully synthetic
therapeutic fusion proteins based on de novo design are still rather uncommon.
Interestingly, synthetic fusion proteins generated invitro allow the insertion of
chemical modication not possible with the cellular translational apparatus. This
could comprise non-natural amino acids, chemical conjugation of nonprotein molecules as, for instance, in the case of antibody drug conjugates (ADC) [6]. Chemical
synthesis is only advantageous if it really allows cost efcient manufacturing of
non-natural moieties. The topic of this chapter, however, focuses on fusion proteins

11 Fusion Proteins: Current Status andFuture Perspectives
293
Phase (at
acquis.)
AMX-818 Oncology 1
TGF-β blocker Approved3
XTEN
Sotatercept
KD033 Solid tumors 1
immunocytokine
Hematological malignancies 1b/2
621TTI- 622
Approved
cell neoplasm
Hemophilia Approved
Alprolix®
(continued)
DEL106 Autoimmune Preclinical
protein
Value
[$M] Technology Fusion protein Indication
14.06.2022 n.a. On demand cytokine Cytokines Oncology Preclinical
Trutino
Biosciences
Buyer Target Date
Boehringer
Ingelheim
Sano Amunix 21.12.2021 1000 Masked T-cell engager,
Table 11.3 Mergers and acquisitions involving companies with fusion protein technology
MSD Acceleron 30.09.2021 11,500 Receptor traps Reblozyl®
23.08.2021 2260 SIRPα-Fc fusion protein TTI-
Therapeutics
Sano Kadmon 08.09.2021 1900 aPD-L1/IL15
Pzer Trillium
09.03.2021 525 T-cell engagers MVC-101 Solid tumors 1b/2
Amgen Teneobio 27.07.2021 900 T-cell engagers TNB-585 Prostate cancer 1
Takeda Maverick
25.02.2021 1850 IL-2 mutein PT-101 Colitis 1a/2b
Therapeutics
Therapeutics
MSD Pandion
AstraZeneca Alexion 12.12.2020 39,000 multiple Strensiq® Rare diseases, immunology Various
05.05.2020 677 Immunotoxin Elzonris® Blastic plasmacytoid dendritic
Therapeutics
MSD OncoImmune 23.11.2020 425 CD24-Fc MK-7110 COVID-19 3
Menarini Stemline
Sotio Cytune 30.08.2018 n.a. IL-2/IL-15Rβγ agonist SO-C101 Oncology Preclinical
Sano Bioverativ 22.01.2018 11,000 monomeric Fc-fusions Eloctate®
Celgene Delinia 26.01.2017 300 IL-2 mutein Fc fusion

294
Phase (at
acquis.)
3
Bladder cancer
2
Squamous cell carcinoma
Proxinium
2
2
Febrile neutropenia
TRU-016
Congestive heart failure
Cardeva
Autoimmune oncology 2
111
Oncology
Oncology
Type 2 diabetes
CVX-045
CVX-060
CVX-096
S. R. Schmidt
IL-6 inhibitor Inammation, autoimmune 1
Value
[$M] Technology Fusion protein Indication
Buyer Target Date
Table 11.3 (continued)
Viventia 21.09.2016 14 Immunotoxin Vicinium
Celgene EngMab 03.10.2013 600 T-cell engagers Oncology Preclinical
Eleven
Opko Health Prolor 24.04.2013 480 Half-life extension hGH-CTP Growth hormone deciency 3
Biotherapeutics
Amgen Micromet 26.01.2012 1160 T-cell engagers Blincyto® Acute lymphoblastic leukemia 2
Alexion Taligen 31.01.2011 111 C3d targeting TT30 Autoimmune Preclinical
Alexion Enobia 07.02.2012 610 Bone targeting ENB-0040 Hypophosphatasia 2
Zymogenetics 07.09.2010 885 Fc-Fusion Atacicept Autoimmune 2
Bristol-Myers
Squibb
Insys Neopharm 29.10.2010 135 Immunotoxins NK-408 Oncology 3
Biomarin Zystor 07.09.2010 22 GILT ZC-701 Pompe’s disease 1
Emergent Trubion 18.08.2010 97 SMIP and Scorpion SBI-087
CovX body (peptide-
Pzer CovX 22.01.2008 n.a.
Teva CoGenesys 12.08.2010 400 Albumin fusion Neugranin
mAb fusion)
Pzer Biorexis 11.04.2007 n.a. Transferrin fusion BRX-0585 Type 2 diabetes Preclinical
Topotarget Apoxis 18.12.2007 19 Mega Ligand APO010 Oncology 1
domains)
Medigene Avidex 31.08.2006 62 TCR technology EsoDex Oncology Preclinical
Amgen Avidia 29.09.2006 290 Avimer (modular binding
Biogen Idec Syntonix 01.02.2007 40 Monomeric Fc fusion FIX-Fc Hemophilia B IND
FIX factor IX, hGH human growth hormone, GILT glycosylation independent lysosomal targeting, IL interleukin, SMIP small modular immunopharmaceuti-
cal, TCR T-cell receptor, TGF transforming growth factor)

11 Fusion Proteins: Current Status andFuture Perspectives
295
generated by recombinant biological processes. Recently a new trend to improve
biological functions such as higher selectivity, stability, half-life, and/or lower toxicity/immunogenicity can be observed. Most of these so-called biobetters belong to
the class of fusion proteins [7]. Building blocks that contribute to the extension of
plasma half-life are discussed in a later paragraph.
11.3.2 Linkers
Connecting two nonrelated protein domains is usually done by inserting a linker
between both partners to generate a continuous uninterrupted poly-peptide chain.
Besides bridging the gap between the two modules, these spacers can not only contribute to improve expression by enabling independent folding of the two domains
but can also add specic functions as summarized in Fig.11.2.
For instance, exibility between the different domains could be required. A high
degree of exibility can be obtained by multiple glycine-serine (G4S)n repeats,
whereas higher rigidity is observed for helical linkers containing (EA3K)n sequences.
By alternating between both elements, the degree of exibility and distance can be
ne-tuned. Combining ve of these modules in different ratios resulted in a variability of helical content from100% for (EA3K)n only motifs to 0% for pure (G4S)n
structures [8]. The same set of rigid (R) (EA3K)n and exible (F) (G4S)n linker was
applied to evaluate the impact of the linker on the enzymatic activity of alkaline
phosphatase (PhoA) when fused to green uorescent protein (GFP). PhoA can catalyze hydrolysis or exert the reverse activity on the substrate inosine. The rate of
phosphatase and phosphotransferase varies under the inuence of the linker exibility. The best ratio between both activities could be obtained by a FRRRR linker with
just one exible module [9].
Fig. 11.2 Linker variants connecting fusion protein partners. The orientation of linkers has an
impact on folding by allowing access of the domains, which is even more pronounced by exible
linkers that help avoiding steric hindrance. The same is true for longer linkers that furthermore
enable the execution of separate functions. Cleavable linkers allow the activation of domains in
proximity to certain proteases as, for instance, in tumors

296
S. R. Schmidt
In some cases, it can be benecial to enable cleaving the linker to release both
subunits. One version is dithiocyclopeptide, connecting transferrin and granulocyte
colony-stimulating factor (G-CSF). As this linker contains as well a thrombin cleavage site, G-CSF is released in a two-step mode in the liver. This linker can be applied
for other fusion partners as well [10]. A variation in that theme is the use of a different dithiocyclopeptide including a target sequence for secretion signal proteases.
This means during secretion the peptide iscleaved leaving the fusion protein just
joined through the disulde bridge [11]. The furin recognition motifs is a quite useful sequence to release anticancer domains in proximity to malignant cells with high
extracellular concentration of this protease. This furin sensitive spacer was successfully tested with an immunotoxin [12]. Another motif that was applied in the context of tumor targeting is the recognition sequence of matrix metalloproteinase-2
(MMP2). In combination with a brin clot binding peptide interferon-y could thus
be delivered and released to tumors [13]. The protease-rich tumor microenvironment can act asactivator for masked antibodies which cover their binding sites by a
peptide that can be released after cleavage and thus allow binding of the antibody to
its target. This prodrug concept is particularly useful for antibodies against epitopes
that are not fully cancer specic and therefore would be limited dueto unwanted
toxicity on normal tissue [14]. Further examples can be found with fusion proteins
acting in the blood coagulation cascade that anyhow contain protease activities. The
long half-life of FXIII-B subunit can be transferred to FIX by fusing both molecules
together. Using a short linker sequence cleavable by activated FX (FXa), FIX can be
released in the presence of trace amounts of FXa to exert its coagulating function
when needed and remains in the inactive long half-life variant until then [15]. The
release of a bioactive compound from a carrier or a half-life extension module such
as HSA through a cleavable linker was exemplied with IFN-HSA fusions. Versions
with a cleavable linker generally showed a lower concentration distribution over
time but a signicantly higher bioactivity [11]. Besides extracellular proteases,
intracellular ones such as furin have been exploited to split fusion proteins like
immunotoxins at the linker region after their internalization to allow their endosomal escape [12]. As unwanted protease degradation can destroy fusion proteins, it
is preferable to screen for cryptic protease sites already during the design phase.
Besides the elimination of protease recognition motifs, these sequences can be
masked instead to make them inaccessible for the enzyme. A typical building block
supporting that approach is the utilization of glycosylation sites. In the case of a
peptibody containing the GLP-1 peptide, clipping at the transition to the hinge
region of the Fc fusion partner was observed. Interestingly the degree of clipping
varied in different cell lines. The underlying reason for that was not only the expression level of host cellproteases but rather the degree of N-glcosylation in that
region. In addition, highly glycosylated versions had a longer serum half-life [16].
A further parameter to take into account is the linker length. This can be signicant to spatially separate subunits of a fusion protein but might also contribute to the
expression yield. For instance, an onconase albumin fusion protein exhibited higher
activity and expression with longer linkers [17]. Positive effects of long linkers on

11 Fusion Proteins: Current Status andFuture Perspectives
297
bioactivity were also reported for Fynomer Fc fusions [18]. The impact of linker
length and type of linkers on biological functions was systematically evaluated on
the example human serum albumin (HSA) fused to interferon a2b (IFN-a2b).
Independent of their structural features (exible: (G4S)n, rigid: (PA)n, helical:
(AEA3K)n) linkers with at least ve amino acids inserted between both fusion partners were sufcient to prevent aggregation, heterogeneity, and instability of the
fusion protein and increased purication yield twofold. Interestingly rigid linkers
showed the best resistance to hydrolysis, whereas helical linkers improved antiviral
activity [19]. Often the linker length contributes to multiple effects. For instance, a
complex fusion protein consisting of the BH3 domain of BH3 interacting-domain
death agonist (BID) fused to the N-terminus of Tumor Necrosis Factor Related
Apoptosis Inducing Ligand (TRAIL) via multiple protease recognition sites showed
better bioactivity if a cysteine containing linker was added. However, the shorter
version without that cysteine containing module was easier to express [20]. TRAIL
was also part of an experiment as bifunctional protein connected to VAS by either a
rigid, a exible, or a helical linker. Surprisingly, the rigid linker allowed the detection of activity already in inclusion bodies, indicating that this construct contains
some properly folded structures. Consequently, this variant resulted in best bioactivity after refolding [21]. The impact of linker design on enzymatic efciency was
also demonstrated in a glucanase-xylanase fusion. Here the bifunctional catalytic
activity was enhanced to more than 300% when using a (G4S)2 linker. Interestingly
helical linkers improved thermal stability [22].
An early study based on three-dimensional (3D) structures evaluated the amino
acid content of naturally occurring spacers between different protein domains.
Frequently Ser, Thr, Gly, Ala were constituents of linkers. The native sequences
were often composed of short peptides that on the one hand had enough conformational stability, while on the other hand offered enough exibility. Incorporation of
polar residues such as Ser or Thr supports solubility in water by enabling hydrogen
bonding. The average length of linkers of that study was 6.5 amino acids [23]. Too
long linkers could elicit an immune response to the novel epitope. A threshold for
that seems to be around 15 amino acids. An investigation with an even larger sample
group classied linkers into helical and nonhelical types. It was concluded that the
primary function of natural linkers is the spatial separation of domains to prevent
unfavorable interactions during folding. This structural rigidity will isolate the
attached protein modules from each other [24].
Besides the initial purpose of joining protein domains, linkers can also add a
wide range of functionalities to the fusion proteins. They can, for instance, improve
folding, stability, expression by maintaining sufcient distance between domains to
minimize interference and to allow proper folding. But also pharmacokinetics, bioactivity, and targeting tissues or certain cell types can be positively inuenced [25].
Functional parameters like bioavailability were assessed with the examples of
either human growth hormone (hGH) or granulocyte colony stimulating factor
(GCSF) fused to transferrin (Tf). Linker length affected the afnity of both fusion

298
S. R. Schmidt
partners to their respective receptors which also contributed to pharmacokinetic
differences as only the Tf receptor mediates recycling that contributes to extended
half-life [26].
Recently the application of short peptides as switches and sensors was systematically evaluated. Based on well-dened motifs, a molecular toolbox was generated
that contains linkers to mediate conformational coupling or linkers to act as tethers
facilitating domain movements. However, none of these functions has yet been
inserted into therapeutic fusion proteins [27].
Besides the many advantages linker sequences can introduce into fusion proteins, some unexpected post-translational modications were observed with the
linkers. The Ser position in the standard linker (G4S)n was spontaneously
O-xylosylated to 30% when the construct was expressed in HEK293 cells. Changing
the host cells to Chinese hamster ovaries (CHO) reduced the level ten-fold. The
basis for that event is the presence of a cryptic xylosyltransferase motif (GSG) in the
(G4S)n sequence. Replacing the Ser residue by Gly completely abolished this aberrant glycosylation [28]. The same effect was detected in an antibody fusion protein
containing either (G4S)3 or (G4S)4 linkers. Interestingly the intensity of xylosylation
is directly correlated to the accessibility of the sequence to xylosyltransferase and
not the number of (G4S) motifs. Inserting a Pro either before or after the Ser eliminated the glycosylation [29]. Replacement of Gly by Pro, however, can lead to
another variation if Pro is followed by Ala, as this creates a recognition site for
prolyl hydroxylase and introduces hydroxyproline [30]. The unwanted effect is further complicated by the heterogeneity of the additional glycan structures ranging up
to penta-saccharides attached to the Ser. Rarely even phosphorylation of xylose
could be found [31]. Ser in (G4S) motifs can be directly phosphorylated as well. As
in the case of xylosylation the level of modication was higher in HEK cells than in
CHO cells [32]. Undesired O-glycosylation was also detected in Fc-fusion proteins
containing the hinge region of IgG1. The insertion of the bulky glycan structure at
this position has a negative impact on aggregation levels as it disturbs the formation
of disulde-bridges below the hinge region. The problem was solved by eliminating
potential O-glycosylation sites via mutagenesis, hereby improving protein stability
and homogeneity [33].
11.3.3 Oligomerization
Oligomerization or the generation of multimers is one of the advantages that are
introduced by the de novo design of fusion proteins. A graphical overview can be
found in Fig.11.3.

11 Fusion Proteins: Current Status andFuture Perspectives
Fig. 11.3 Examples of fusion protein oligomers. One important element of fusion proteins is the
possibility to generate oligomers containing more than one copy of the fusion partners to increase
avidity, activity or trigger responses by receptor crosslinking. (HSA human serum albumin, TD
tetramerization domain, COMP cartilage oligomeric matrix protein, TRAIL tumor necrosis factor–related apoptosis-inducing ligand)
299
11.3.3.1 Monomer
A downside to that approach is the potential steric hindrance of the fusion partners
that might prevent proper binding to the corresponding receptor or exert stress on
the hinge region of the Fc domain. This is particularly true for naturally occurring
monomeric proteins as, for instance, the large blood coagulation factors [34].
Interestingly, monomeric Fc-fusion proteins have been used to enable pulmonary
uptake of proteins [35]. Furthermore, monomeric Fc-fusions of EPO or IFN exhibited signicantly better bioactivity when compared to their homodimer format. On
the other hand, heterodimers as fusion proteins can be advantageous when they
resemble naturally occurring heterodimers. For instance, proteins like FSH consisting of two subunits can be displayed either as tandem homodimer or heterodimer.
Another protein class benetting from an asymmetric conformation are cytokines.
Here therapeutic effects such as biodistribution and tumor localization of single
cytokines per fusion protein are improved. Overall there are many applications that
favor heterodimers [36]. Heterodimerization has become an important prerequisite
for the generation of bispecic antibodies. Therefore, a great body of knowledge
can be found there which is applicable for Fc fusion proteins as well [37]. Table11.4
summarizes these ndings.
11.3.3.2 Dimer
The simplest version of fusion proteins consists of two connected subunits. As soon
as a Fc domain is utilized, multimerization comes into play. The normal case is a
homodimer pairing two identical polypeptide chains.
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