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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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Table 11.4 Overview on point mutations to enable heterodimerization of Fc domains
Company Technology Mutations HC1 Mutations HC2 Genentech Knobs-into-
holes Genmab DuoBody F405L K409R Zymeworks Azymetric T350V, L351Y,
Amgen Charge Pair K392D, K409D E356K, D399K Rinat-Pzer Charge Pair D221E, P228E, L368E D221R, P228R, K409R Xencor HA-TF S364H, F405A Y349T, T394F
T366W T366S,L368A, Y407V
T350V, T366L, K392L,
F405A,Y407V
T394W
S. R. Schmidt
11.3.3.3 Trimer
Trimeric formats can be generated by utilizing naturally occurring proteins based on trimers such as collagen. Some years ago, the combination of scFV with the collagen- like peptide scaffold (GPP)10 was evaluated. Fusions at the N-terminus of the peptide resulted in stable homotrimers. Due to the increased avidity, the trimer bound 20 and 1000-fold stronger than the bivalent or monovalent versions of the same scFv, respectively. When expressed in NS0 cells, the murine prolyl 4- hydroxylase converted approximately 61% of the 10 available prolines into hydroxyproline, thus giving a thermo-stability comparable to the naturally occur­ring collagen. The so-called Collabody is currently evaluated as a CD3-specic T-cell engager for therapeutic applications [38].
11.3.3.4 Tetramer
The next oligomeric level are tetramers. A naturally available building block is the self-assembling tetramerization domain from p53 (p53TD) that can surpass the naturally occurring afnity threshold of antibodies through higher avidity. In mul­tiple examples, modules such as dAbs, scFv, Fabs, and extracellular protein domains were fused to p53TD either at its N- or C-terminus. Due to its self-assembling capa­bilities active tetramers could be successfully expressed, secreted, and puried from a single poly-peptide chain. As the p53 domain is deeply embedded in the overall structure, no detrimental immunogenic effects are expected. Involving a dimeriza­tion unit such as the Fc-domain, even an octamer could be obtained. Octameric versions of Humira were approximately 50-fold more potent than the original diva­lent Humira. Due to the higher potency the so-called Quads could either be used at lower doses than the original antibody or allow a switch from intravenous to subcu­taneous application [39].
Tetrameric antibodies have been described since many years. One recent exam­ple is the evaluation of tetrameric formats to ght COVID infections. Here the vari­able domain of heavy chain is either duplicated at the N-terminus or fused to the C-terminus of the Fc-domain, while maintaining the light chain. This antibody with
11 Fusion Proteins: Current Status andFuture Perspectives
301
four binding domains neutralizes the virus with enhanced potency so limiting its ability to achieve resistance though escape mutations [40].
11.3.3.5 Pentamer
Some receptor ligand interaction happens at low afnity and therefore requires mul­tiple ligands to bind simultaneously. For instance, CD200 binds to its corresponding receptor at approximately 1μM.When generating a pentamer by fusing CD200 with an eleven amino acid linker to cartilage oligomeric matrix protein (COMP), the receptor binding was highly improved [41].
11.3.3.6 Hexamer
Larger multimers have also been described in the form of tandem repeats of Fc domains to increase the antibody-dependent cellular cytotoxicity (ADCC) and complement- dependent cytotoxicity (CDC) [42]. Even larger hexameric complexes have been designed by adding small 18-mer peptides to theC-terminus. These tail­pieces connect six Fc-dimers to form a large multi-subunit molecule with the ability to crosslink low afnity FcγR binding. The hexameric format exhibits stronger avidity with 12 potential binding sites or fusion partners [43].
Looking at other fusion partners beyond Fc-domains, a dimerization can be enforced by leucine zippers, naturally occurring peptide sequences. For instance, a noncovalently bound heterodimeric Fab fragment, a so-called “Zipbody” was designed by fusing leucine zipper pairs LZA and LZB or c-Jun and c-Fos to the C-terminus of heavy and light chain thus enhancing correct pairing and resulting in a properly folded active Fab [44]. A similar example was described earlier by creat­ing bispecic homodimers based on two different designed ankyrin repeat proteins (DARPins) and a leucine zipper linker [45].
More complicated trivalent molecules based on tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) utilized leucine zippers forming trimers. One case incorporated the yeast GCN4-pII leucine zipper in fusion to the N-terminus of TRAIL.The Ile substitutions in the “a” and “d’ positions stabilizes the trimer for­mation. Replacing the yeast protein GCN4-pII by the human ATF7-pII greatly reduced the immunogenicity while maintaining high antitumor potency [46]. To enable an even more oligomeric molecule, the building blocks human IgG4 Fc-domain, the TNF receptor-associated factor 2 (TRAF2) coiled coil domain, and the extracellular receptor binding domain (RBD) of human OX40 ligand (OX40L) were fused together to obtain a 300kDa large hexameric fusion protein [47]. A functional OX40L multimer can also be obtained by using similar building blocks, but using trimerizing isoleucine zipper domain GCN4 instead of TRAF2 and IgG1 Fc instead of IgG4 Fc. The nal hexameric molecule consists of three Fc-induced disulde linked dimers that forming two connected trimers [48]. A more elegant and less complicated solution to generating trimeric fusion proteins was described in the
302
S. R. Schmidt
hexavalent receptor agonist (HERA) Technology. These hexameric fusion proteins comprise three receptor binding domains in a single chain arrangement, connected to an Fc-silenced human IgG1 not requiring FcγR-mediated crosslinking for tumor killing activity [49]. Other approaches with the class of homo-multimeric proteins focused on nding the most active version of CD40L as adjuvant for DNA vaccines. Three different self-assembling versions were compared. The starting point was a leucine zipper-based trimer. The next variant contained two trimers connected through fusion to the N-terminal part of adiponectin (Acrp30). The third molecule was a tetra-trimer containing 12 individual CD40L arranged through fusion to sur­factant protein D.Their immunostimulatory activity increased in direct proportion to the valency of the trimers [50]. Naturally occurring trimeric proteins such as the noncollagenous domain (NC1) of human collagen XVIII NC1 can be utilized as well in fusion protein applications. NC1 is composed of a trimerization domain (TD), a hinge region, and the endostatin domain. Proteolytic cleavage on the hinge region releases the endostatin domains to establish a fully functional TRAIL-TD trimer [51].
11.3.3.7 Octamer
So far, the highest described order of fusion proteins are octamers. Here the natu­rally occurring afnity threshold can be surpassed by higher avidity. The base ele­ment in that context is the self-assembling tetramerization domain from p53.
11.3.4 Orientation
On the rst glance, the orientation of both fusion partners seems to be irrelevant as long as a single polypeptide chain can be obtained. However, as soon as a free N- or C- terminus is required for activity this parameter needs to be considered in the design. An overview with current examples for an orientation preference can be seen in Table11.5.
Sometimes simply following the natural conguration is giving the best results. For instance, this is true for all receptor traps consisting of the extracellular domain of membrane bound receptors fused at their C-terminus to an IgG Fc domain. Peptibodies are another class of Fc fusions but with opposite orientation. Here small peptides or concatemers are fused to the C-terminus of Fc domains. One underlying reason for this conguration is the protection from peptidases that attack free N-termini. Furthermore, for so far unknown reasons, a C-terminally fused NGF peptibody was 1500 times more potent than its N-terminal counterpart [52].
A wide range of other examples can be found in the literature about human serum albumin (HSA) fusions. Interestingly in few cases N-terminal fusion of HSA was preferable. Although the real reason for that has rarely been properly identied, but in the here mentioned examples the N-terminal fusion typically resulted in better
11 Fusion Proteins: Current Status andFuture Perspectives
Table 11.5 Examples of fusion proteins with a clear preference of the orientation of their fusion partners
N-Term C-Term Effect (better) Reason TNF-R Fc Functionality Natural conguration Fc FGF21 Activity Unknown Fc EPO Half-life and activity Endosomal stability X ELP Activity, expression Mis-folding in N-Term fusion scFv ANG Functionality Free C-Term required ANG END Potency Unknown IFN-a2b HSA Reduced aggregation Improved S-S formation TNF-RI HSA Activity Improved S-S formation HSA IL28B Activity and expression Unknown HSA BNP HM3 HSA Half-life, stability, activity Unknown hLF HSA Stability, low proteolysis Steric hindrance HSA TMP SS28
2
2
2
HSA Activity and expression Lower degradation
Activity and expression Lower degradation
Expression Unknown
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expression levels and higher activity. For instance, only IL28B fused to HSA at its N-terminus was active and exhibited better stability than its C-terminal counter­part [53].
On the contrary for IFNα2b, lower heterogeneity and instability were observed for this orientation but could be signicantly enhanced by changing to a C-terminal fusion [54]. The underlying reason for that effect seems to be the improved ability to form di-sulde bridges. The same cause was identied for the better TNF-α neu­tralizing activity of a receptor trap consisting of TNF-RI fused to HSA on its C-terminus [55].
Sometimes the benet of one version is different in the other version. For instance, evaluating the ideal orientation for a HSA lactoferrin fusion, it was found out that placing HSA at the N-terminus of the construct results in sixfold increased half-life, but for the cost of reduced thermal and proteolytic stability [56]. Peptides typically suffer from a short half-life that can be extended by HSA-fusion. On the one hand, there are examples such as the integrin antagonistic peptide HM-3, where the best result in terms of higher stability and activity was achieved with connecting HSA to the C-terminus of the peptide [57]. On the other hand, cases such as the human brain natriuretic peptide (BNP) obtained best biological potency when two copies are fused to the C-terminus of HSA [58]. Similarly TPO mimetic peptide (TMP) in tandem could signicantly better expressed having HSA at its N-terminus [59]. Interestingly another example utilizing tandem peptides showed lower degra­dation and higher activity for the variant with somastatin at the N-terminus [60].
The orientation of bifunctional molecules not relying on the classical building blocks Fc domain or albumin is even more difcult to predict. When connecting angiostatin (ANG) and endostatin (ENG) to inhibit vascularization a clear prefer­ence of the arrangement is not obvious. However, in biological assays the
304
S. R. Schmidt
ANG-ENG version was signicantly more potent than its ENG-ANG counterpart [61]. Another special case is the fusion to elastin like peptides (ELP). When testing the position of ELP in fusion to four different proteins, it was found out that the ELP at the C-terminus resulted in higher expression and better activity than the N-terminal fusion of ELP.The underlying reason for that effect is most probably an increase in misfolded protein when the translation starts with ELP [62]. The class of immuno­toxins consisting of a targeting ligand such as scFv and a toxin was also evaluated for the optimal orientation of both elements. Chimeric toxins containing the scFv at the C-terminus of restrictocin were shown to be more active than those havinga ligand at the N-terminus of the toxin, most probably due to folding differences [12].
The multitude of examples here clearly demonstrates the fact that it is very dif­cult to predict the ideal orientation upfront, but rather requires empirical results testing both variations. Typical parameters to differentiate between the options are expression levels, activity, stability, and improved pharmacokinetics.
11.3.5 Protein Engineering
The paragraph above highlighted design details on linker sequences. But protein engineering can also help in solving other issues such as efcacy, production yield that impact the therapeutic effect of fusion proteins.
11.3.5.1 Modications ofFc asBuilding Block
When designing Fc-fusion proteins, it is worthwhile to have a closer look on the inbuilt features of the constant region. The Fc domain has multiple functions such as dening half-life through recycling via the FcRn receptor, triggering effects such as ADCC or CDC via FcyR, and enabling oligomerization from asymmetrical monomer and homo- or heteromeric dimer. Over the last decade, the underlying amino acid interactions were revealed. In some cases, when bivalency is not possi­ble due to steric hindrance of too large fusion partners or not desirable to avoid receptor crosslinking, the availability of a truly monomeric Fc would be benecial. Unfortunately, most attempts were unsuccessful and resulted in instable molecules or suffered from decreased half-life. The rst stable Fc monomer was obtained by introducing two additional N-glycosylation sites at the CH3-CH3 interface with the double replacement Ser364Asn and Phe405Asn [63]. The contemporary approaches on Fc optimizations to address receptor binding have been summarized in a compre­hensive review [64]. Details can be found in Table11.6.
Fc receptor functions have often been used to optimize therapeutic effects [65]. For instance, an improved version of Enbrel® had higher ADCC and CDC activity than the original fusion protein that could extend its use to other chronic disease such as ulcerative colitis or Morbus Crohn. Additionally, higher afnity to the target TNF-α was observed. Taken together, these modications can lead to a better
11 Fusion Proteins: Current Status andFuture Perspectives
Table 11.6 Point mutations in the Fc domain modulating FcyR-mediated functions
Company ADCC ADCP CDC IgG Mutation Genentech + + 1 S298A, E333A, K334A Xencor + + 1 S239D, I332E Xencor + + 1 S239D, A330L, I332E Applied Molecular
Evolution Applied Molecular
Evolution Macrogenics + + 1 F243L, R292P, Y300L +/ P396L or
Xencor + 1 G236A, S239D, I332E Abgenix/Genentech = + 1 K326A, E333A Abgenix/Genentech 0 + 1 K326W, E333S GlaxoSmithKline/Tolerx 1 N297A Ortho Biotech 1 L234A, L235A Protein Design labs 2 V234A, G237A Welcome Labs 4 L235A, G237A, E318A Merck 2 H268Q, V309L, A330S, A331S Bristol-Myers Squibb 1 C220S, C226S, C229S, Seattle Genetics 1 C226S, C229S, E233P, L234V,
Medimmune 1 L234F, L235E, P331S
+ + 1 P247I, A339D/Q
+ + 1 D280H, K290S +/ S298D/V
V305I
L235A
305
efcacy and a wider applications [66]. A different approach to improve Enbrel® against its primary indication rheumatoid arthritis was taken with a hybrid Fc domain that consists of a immunological silent IgG4 domain connected to the highly exible hinge region of IgD, hiding the junction site inside the structure to avoid unwanted immunogenicity. The molecule showed a 1.5-fold higher neutralizing activity than Enbrel® [67]. The three-dimensional structure of the Fc domain is governed by S-S bridges [68].
11.3.5.2 Modications ofHuman Serum Albumin asBuilding Block
Protein engineering has been applied to HSA fusion proteins as well. An obvious target is the free Cys in HSA that causes aggregation and reduces stability. Cys34 was replaced by Ser by site directed mutagenesis in a IFNα2b-HSA fusion protein. After incubation at 60 °C or prolonged agitation still 90% of the fusion protein was in a monomeric state [69]. Interestingly additional free Cys residues could be useful for chemical conjugation of drugs. Therefore, two more thiol groups were intro­duced at position 93 and 294 resulting in the replacements Lys93Cys and Glu294Cys [70].
As the primary reason for HSA fusion is the extension of half-life, several attempts were undertaken to optimize its binding to FcRn which is the main
306
S. R. Schmidt
contributor. Typically, albumin has a serum half-life of 3weeks. The rst described site directed exchange of Lys573Pro at the C-terminus in domain DIIIb improved afnity to FcRn by a factor of 12, leading to a 1.5-fold prolonged half-life [71]. As the binding to FcRn happens at the C-terminus of HSA, it is obvious that fusions to the N-terminus of HSA will have less impact on recycling through FcRn and are therefore preferable.
Combining yeast display and co-crystallization of FcRn with HSA variants, a double-mutant Glu505Gly and Val547Ala was identied that exhibited a ten-fold higher afnity to FcRn leading to a 1.3-fold improved half-life in cynomolgus mon­keys [72].
Although the DIII domain is the main contributor for FcRn binding, it was found out that two loops in DI at the N-terminus modulate the interaction [73]. It will be worthwhile to utilize that region as well to optimize FcRn afnity at different pH values together with further mutations in DIII to ne tune new designer HSA mol­ecules as fusion partners.
Another group selected different amino acid residues to not only improve half­life but also enabling transcellular delivery. The new albumin variant QMP contains three substitutions: Glu505Gln, Thr527Met and the known mutation Lys573Pro. Compared to the wild-type, QMP was translocated twofold more efcient over mucosal barriers at intranasal application. Fusing the triple mutant HSA to coagula­tion factor VII, the half-life improved 3.6-fold [74]. Table 11.7 summarizes the mutagenesis approaches based on albumin.
11.3.5.3 Modication ofOther Functions
Serum half-life is typically inuenced either by the diameter of the molecule that prevents kidney ltration, charge density that would cause repulsion or the ability of recycling through FcRn or transferrin receptors. On the example of immunocyto­kines (fusions between antibodies and cytokines), it was demonstrated that the faster than expected clearance from the bloodstream can be inuenced by altering the afnity to other FcRn either by changing the Fc isotype or mutagenesis of the FcRn binding site on the Fc domain [75]. In a second study, the half-life was further improved by optimizing the junction between IL-2 and the antibody to prevent intracellular degradation during the FcRn-mediated recycling [76].
Stability issues cannot only be attributed to aggregation but can also be the result of degradation. Peptidbodies with N-terminal fusion of short amino acid sequences
Table 11.7 Point mutations in human serum albumin to optimize certain functionalities
Additional functions Half-life extension Translocation Cys34Ser
Improved stability
Lys93Cys, Glu294Cys Additional conjugation sites
Lys573Pro
1.5-fold longer half-life
Glu505Gly, Val547Ala
1.3-fold longer half-life
Glu505Gln, Thr527Met, Lys573Pro Twofold better translocation
3.6-fold longer half-life
11 Fusion Proteins: Current Status andFuture Perspectives
307
can suffer from enzymatic proteolysis. This can be avoided if a glutamate residue is introduced at the rst position of the polypeptide which forms pyroglutamate after cyclization, protecting against protease attacks. Studying the functionality of this peptidbody, an unexpected O-glycosylation site was removed by exchanging Thr to Ala, thus signicantly increasing potency [77]. Similarly, the negative impact of proteolysis and aggregation on an FGF21-Fc fusion protein could be successfully abolished through the replacements Pro171Gly and Leu98Ar, respectively [78].
The next level of engineering targets three-dimensional alterations. One example in that context is the introduction of four point-mutations into the EPO domain within an Fc-EPO fusion protein to improve multiple features. Overall, the amino acid exchanges were His32Gly, Cys33Pro, Trp88Cys and Pro90Ala that resulted in a disulde bridge rearrangement from Cys29-Cys33 to Cys29-Cys88. The modied fusion protein was secreted as monomer with better pharmacokinetic and stability after the removal of N-linked glycosylation [79].
11.3.6 Immunogenicity
Some unwanted effects like glycosylation at novel positions introduced through linker sequences, nonhuman glycosylation or degradation at cryptic protease recog­nition motifs have been described in the paragraphs above. However, another even more deleterious biologic consequence of a novel, non-natural protein design is the eliciting immunogenicity, particularly at novel epitopes created at the junction between both fusion partners, even if only proteins of human origin are being used. Furthermore, fusion proteins might be taken up or processed differently than their native counterparts which could lead to an increased immune response. Therefore, it is benecial to apply rational design of fusion proteins to minimize immunogenic­ity of the new construct. The current approach to identify amino acid positions for targeted mutagenesis is in silico analysis to predict T- and B-cell epitopes [80].
Particularly Fc-fusion proteins could show increased immunogenicity as they bind via Fcy receptors (FcyR) to antigen presenting cells (APC) thus targeting anti­gens to these cells. If that results in enhanced uptake to APCs, or if the fusion pro­tein stimulates these cells, then a stronger immune response could be triggered. Current deimmunization strategies based on prediction of particularly immunogenic epitopes focus on modifying epitope sequences to disrupt HLA binding to eliminate T-cell recognition [81].
The effect of the Fc domain in fusion proteins has also been studied as means to modulate immunogenicity. Primarily CD4 T-cells and B-cells are involved with an important participation of APCs. In case of crosslinking activating FcyR on APCs the antigen presentation to T-cells increases, strengthening the immune response. The other case of signaling through inhibitory FcyR can also occur and will down­regulate immune responses. Interestingly the nature of the fusion partner can inu­ence the afnity of the corresponding Fc- domain to the FcyR [82]. The hypothesis of lowered immunogenicity of Fc-fusion proteins by binding to inhibitory Fc
308
receptors on B lymphocytes, the FcyRIIb was experimentally proven with the injec­tion of DNA coding for a Exendin-4 Fc-fusion protein that did not result in the generation of neutralizing antibodies, which was the case for Exendin-4 alone [83]. Just recently a Fc receptor trap fusion protein consisting of fully human sequences only was risk assessed for immunogenicity. Although fully human sequences reduce the risk of antidrug antibodies (ADA), the effects of ADA might be higher if they occur, as they target the corresponding component on cells with all potential nega­tive consequences [84].
Ideally B- and T-cell epitopes are removed, as both contribute to immunogenic­ity. It is easier to remove B-cell epitopes, as they are not restricted to major histo­compatibility complex (MHC). In contrast to that T-cell epitopes rely on the high polymorphism of MHC [85].
S. R. Schmidt

11.4 Manufacturing

On the rst glance, the production of fusion proteins cannot be distinguished from that of regular therapeutic proteins. Manufacturing typically comprises the steps of upstream processing including all aspects of cell culture, downstream processing covering steps to capture and purify the protein of interest from impurities and nally formulation steps that convert the protein into a storable and administrable form. One of the many advantages of fusion proteins is the uninterrupted manufac­turing process of a single but multifunctional molecule. However, fusion proteins suffer from a lot of issues that can complicate the production. The combination of two different proteins with different properties might not always be compatible with respect to their pH preferences, hydrophobicity, native cellular localization, and glycol-isoforms. Furthermore, they are sometimes sensitive to low pH which then does not allow conventional virus inactivation. Fusion proteins are often larger than well-studied molecules like antibodies and therefore might have lower expression levels. Figure 11.4 gives a comprehensive overview on current manufacturing practices.
11.4.1 Upstream
Due to their size and complexity, most modern fusion proteins are expressed in eukaryotic cells. This allows the proper formation of post-translational modica­tions such as glycosylation or disulde bridges. The major host cell is derived from Chinese hamster ovaries (CHO) which is frequently used for Fc-fusions. Yeast cells are applied primarily for albumin fusions. Prokaryotic expression is favored either for relatively small proteins with a molecular mass below 30kDa or proteins that form inclusion bodies to enable the production of toxic proteins like immunotoxins.
11 Fusion Proteins: Current Status andFuture Perspectives
Fig. 11.4 Comparison of mammalian and microbial bioprocesses for the manufacturing of fusion proteins. (a) The upstream part of cultivation and expanding the cells takes typically several weeks in a mammalian bioprocess. Here the protein of interest is secreted to the medium; therefore, cells are separated from the supernatant by either depth ltration or centrifugation. Protein from the cell free harvest is then captured on the rst column and potential virus impurities are inactivated by typical low pH exposure. The protein is further puried in several polishing steps to remove impu­rities before any remaining viruses are removed by virus ltration. In the last step, the pure protein is formulated by the addition of excipients and lled as bulk drug substance. (b) Microbial cultiva­tion processes are usually nished in days. Here the protein of interest often accumulates in the form of inclusion bodies in the host cell. Therefore, these cells are collected by centrifugation, disrupted, and the inclusion bodies are washed and solubilized by denaturing agents. Then the unfolded protein has to be refolded before the regular purication process is started. With the exception of the absence of virus removal steps, the downstream procedure is quite similar. (WCB working cell bank, DF depth ltration, BDS bulk drug substance, IB inclusion body)
309
In principle, the upstream process contains three elements: the DNA construct coding for the gene of interest plus regulating sequences, the host cell, and the cul­tivation conditions. All three elements contribute to the expression level, or titer that can be achieved during upstream processing. Prokaryotic expression can directly work by introducing a plasmid that codes for the fusion protein, accompanied by at least a promoter sequence, a replication origin, and typically a selection marker such as an antibiotic resistance gene into the microbial cell. However, in mamma­lian cells the expression construct is integrated into the cell genome. Often this integration happens at multiple sites simultaneously increasing the expression level. To generate the producer cell line, a selection process is frontloaded that identies the best cell clone based on expression yield, growth characteristics, and genomic stability.
Temperature inuences cell growth and product titer. It was observed that in the case of Etanercept growth at 30 °C resulted in a threefold higher titer than at 37°C.However, increasing the viable cell density at 30°C decreased the productiv­ity. So, essentially both effects have to be systematically assessed to nd optimal expression conditions [86]. A more detailed analysis of cultivation parameters pH, temperature (T), and dissolved oxygen (DO) has been undertaken for EPO-Fc expressed in CHO.Lowering T and pH reduce cell growth and metabolism but increase the viable cell integral and consequently enhance the specic productivity