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Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5608_Библиотеки_им_академика_М_И_Перельмана.pdf
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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 Table11.2.
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 difculty 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 Table11.3. 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 andFuture Perspectives
291
Brand Approval Protein 1N-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 deciency 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 signicant drop of sales for the originator drug since then. Since its peak sales in 2015 with close to $b 9, its sales dropped signicantly. 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 afnity 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 invitro allow the insertion of chemical modication 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 efcient manufacturing of non-natural moieties. The topic of this chapter, however, focuses on fusion proteins
11 Fusion Proteins: Current Status andFuture 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
[$M] Technology Fusion protein Indication
14.06.2022 n.a. On demand cytokine Cytokines Oncology Preclinical
Trutino
Biosciences
Buyer Target Date
Boehringer
Ingelheim
Sano Amunix 21.12.2021 1000 Masked T-cell engager,
Table 11.3 Mergers and acquisitions involving companies with fusion protein technology
MSD Acceleron 30.09.2021 11,500 Receptor traps Reblozyl®
23.08.2021 2260 SIRPα-Fc fusion protein TTI-
Therapeutics
Sano Kadmon 08.09.2021 1900 aPD-L1/IL15
Pzer Trillium
09.03.2021 525 T-cell engagers MVC-101 Solid tumors 1b/2
Amgen Teneobio 27.07.2021 900 T-cell engagers TNB-585 Prostate cancer 1
Takeda Maverick
25.02.2021 1850 IL-2 mutein PT-101 Colitis 1a/2b
Therapeutics
Therapeutics
MSD Pandion
AstraZeneca Alexion 12.12.2020 39,000 multiple Strensiq® Rare diseases, immunology Various
05.05.2020 677 Immunotoxin Elzonris® Blastic plasmacytoid dendritic
Therapeutics
MSD OncoImmune 23.11.2020 425 CD24-Fc MK-7110 COVID-19 3
Menarini Stemline
Sotio Cytune 30.08.2018 n.a. IL-2/IL-15Rβγ agonist SO-C101 Oncology Preclinical
Sano Bioverativ 22.01.2018 11,000 monomeric Fc-fusions Eloctate®
Celgene Delinia 26.01.2017 300 IL-2 mutein Fc fusion
294
Phase (at
acquis.)
3
Bladder cancer
2
Squamous cell carcinoma
Proxinium
2
2
Febrile neutropenia
TRU-016
Congestive heart failure
Cardeva
Autoimmune oncology 2
111
Oncology
Oncology
Type 2 diabetes
CVX-045
CVX-060
CVX-096
S. R. Schmidt
IL-6 inhibitor Inammation, autoimmune 1
Value
[$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 deciency 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-
Pzer CovX 22.01.2008 n.a.
Teva CoGenesys 12.08.2010 400 Albumin fusion Neugranin
mAb fusion)
Pzer 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 andFuture 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 specic 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 from100% 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 inuence 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 benecial 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 iscleaved leaving the fusion protein just joined through the disulde 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 asactivator 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 specic and therefore would be limited dueto 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 exemplied with IFN-HSA fusions. Versions with a cleavable linker generally showed a lower concentration distribution over time but a signicantly 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 cellproteases 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 signi­cant 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 andFuture 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 sufcient to prevent aggregation, heterogeneity, and instability of the fusion protein and increased purication 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 efciency 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 classied 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 sufcient 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 inuenced [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 afnity 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-dened 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 modications 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 modication 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 disulde-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 andFuture 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 signicantly 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 benetting 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 bispecic antibodies. Therefore, a great body of knowledge can be found there which is applicable for Fc fusion proteins as well [37]. Table11.4 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.