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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5886_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

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self-interactions and weak nonspecic interactions [154]. Calculation of the pI on
the basis of the mAb sequences is offered by multiple software tools as MassLynx
[], Vector NTI [155], and EMBOSS [156], and the calculated pIs have been shown
to be within a range of 15% compared to experimentally determined ones [157].
Tools that predict the pI on basis of the protein structure can provide a more accurate result, since the underlying residue pKa values are calculated by taking into
account the residual microenvironments, e.g., shifts in pKa values in case the side
chain forms a salt-bridge. A case study conrmed that structure-based pI calculations (via PROPKA) [158] corresponded to the measured values at least by ±1 pI
unit, whereby the remaining discrepancies result from protein interactions with salt
ions that leave room for improvements [11, 159].
J. Bauer et al.
14.3.6 Viscosity andDiffusion Interaction Parameter (kD)
Predictors of the concentration-dependent viscosity of formulations need to consider the pairwise and higher orderself-association of antibodies [19]. Consequently,
the main driving forces behind viscosity, i.e., electrostatics and hydrophobicity [20]
have been linked to predictable characteristics of the Fv sequence and structure
[159, 160]. While the viscosity of mAb formulations increases with hydrophobicity,
charge dipole distribution, and aggregation propensity, it decreases with net charge
[159, 160]. Considering these principles, the in silico tool SCM (spatial charge
map) offers to detect highly viscous antibodies on the basis of the Fv structure
[161]. The high-throughput approach makes it especially attractive for the lead
identication and optimization performed at discovery. An alternative mathematical
model considers again the hydrophobicity and charges of antibody regions to predict concentration-dependent viscosity curves [162]. Charge-related in silico
descriptors (e.g., pI, net charge, charge on Fv, zeta potential) could be used to calculate the diffusion interaction parameter kD [163] that itself is widely-used in
developability assessments to predict the viscoelastic behavior of mAb solutions
[164–166]. Several case studies conrmed that these computational tools as well as
their underlying principles are powerful to rationally (re-)design antibodies with
decreased viscosity [137, 138, 141, 142, 167–171]. Further studies indicated that
MD simulations can be conducted to additionally estimate the effect of formulation
components on the viscosity [137, 170, 172–176].
14.3.7 Aggregation andSelf-Association
Aggregation in biotherapeutics can nucleate from a wide array of origins ranging
from reversible self-association, conformational change, chemical modication,
hydrophobic and electrostatic complementarity among the interacting partners.
Despite this complexity, aggregation could be directly associated to characteristics

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such as presence of aggregation prone regions, hydrophobicity [177], electrostatics
[178], and dipole moments [179], paving the way for both sequence- and structurebased computational predictions. The in silico tools are particularly powerful in
guiding the design of mAb candidates with high colloidal stability, since the effect
of single and multiple amino acid exchanges on the aggregation propensity can be
predicted. A selection of these predictors is summarized below, and this aspect has
been described in several reviews in more details [147, 151, 180].
A vast majority of aggregation predictors are based on the sequence as they calculate aggregation propensity values for sequence stretches. These methods are
based on the fact that natural amino acids differ in their physicochemical properties,
and individually inuence the aggregation of peptides and proteins [181]. Therefore,
techniques as Zyggregator and Pag use intrinsic properties of the amino acids such
as hydrophobicity, charge and secondary-structure propensity to identify
aggregation- promoting regions and predict the rate of growth [182, 183]. Similarly,
a method called AGGRESCAN identies aggregation-prone segments via the
aggregation propensity of natural amino acids, whereby this method was trained on
empirical data [184]. Alternative tools like TANGO, PASTA, PASTA2, FoldAmyloid,
SALSA; and AggreRATE-Pred detect aggregation-prone regions and impact of
mutations on aggregation kinetics via the physicochemical properties of secondary
structure elements, in particular the ability to form intermolecular cross-β-structures
[133, 150, 185–188]. In accordance, the frequency of β-sheets was amongst others
(e.g., pI and atom-based hydrophobic moment) carved out by a neural network
approach that led to the development of APPNN [189]. Another predictor named
WALTZ consults a database of experimentally determined amyloid-forming hexapeptides to predict amyloid-forming sequences [190, 191]. Following a consensus
prediction algorithm, 5 and later on 11 other methods (AGGRESCAN, Pag, Tango,
Waltz, and other conformational predictors) have been combined to produce
AMYLPRED and AMYLPRED2 [192, 193]. Similarly, a statistical approach combined existing tools (SALSA, PAFIG, FoldAmyloid, and Waltz) to develop a metapredictor for amyloid proteins called MetAmyl [194]. Alternatively, articial
neuronal networks (ANN) were applied to predict the aggregation temperature (T
agg
)
of antibodies based on the amino acid composition, of which charged residues and
Met affected the temperature induced aggregation the most [195]. Machine-learning
techniques were conducted to develop CISI, which predicts the cross-interaction or
self-interaction of mAbs on the basis of tripeptide sequences [196]. Interestingly,
this study indicated that tripeptides comprising Tyr, Ser and Ala residues were
amongst the most prominent antibody-binding sites.
In comparison to these sequence-based methods, the structure-based ones consider the three-dimensional context of the protein fold to predict aggregation.
Therefore, methods as AGGRESCAN3D (A3D) or Solubis combine distinct aggregation propensity scales (AGGRESCAN or TANGO) with the protein structure
[148, 197, 198]. The A3D server further allows to include dynamic uctuations of
the protein structure in solution that might affect the aggregation tendency [197]. It
was further pointed out that atomic level characteristics might be relevant for

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understanding aggregation, which is offered by ANuPP [145]. Another method
called AggScore identies aggregation hotspots on the protein surface via calculation of hydrophobic and electrostatic patches [199]. Orthogonal to these technologies, SAP (spatial aggregation propensity) calculates dynamically exposed
hydrophobicity of protein patches [123, 200]. The Developability Index (DI) has
complemented the SAP concept with additional information about the net charge of
the full-length mAb to account for hydrophobicity and electrostatic interactions
[201]. Recently, a machine learning approach combined SAP with other tools
(Spatial negative charge map (SCM neg), Spatial positive charge map (SCM pos))
that extract molecular features from MD simulations to train predictive models for
the aggregation rate at high mAb concentrations [202].
14.3.8 Prediction ofParatope
Once an experimentally determined or accurately modeled structure of the therapeutic candidate is available, the mAb can be further analyzed to identify the paratope comprising the amino acid residues that mediate the binding of its cognate
antigen epitope. Oversimplied approaches assume that the paratope equals the six
CDR regions comprising together 50–60 residues on average, but statistic evaluation of Ab/Ag complexes showed that the actual paratope is only formed by 18–19
residues on average [203]. Therefore, gathering a detailed understanding of the
exact paratope is crucial to guide an individually tailored engineering and development strategy that avoids costly and time-consuming failures. However, especially
at early research stages, the Ab/Ag complex might not have been experimentally
characterized. In case information about the antigen sequence and/or structure are
known, bioinformatic tools offer the prediction of the mAb interaction with the Ag
structure/model that can complement experimental paratope studies and streamline
conventional R&D workows [204]. Similar to homology modelling, great advances
have also been made in the eld of paratope prediction [204, 205]. In the last years,
several paratope predictors that pursue individual approaches were established. The
most common technique considers the docking of Ab/Ag for the prediction of the
paratope [206–208]. Another method identies the paratope via circular patches of
the antibody surface that exhibit certain physicochemical properties [209]. Deep
neural networks are not only suitable for the paratope prediction but outperformed
classical methods [205, 210]. Accurate prediction of paratopes is essential to identify potential physicochemical liabilities motifs that may overlap with antigenbinding regions. Removal of such motifs via mutations in paratope, might lead to
signicant modication of the biologic drug candidate’s afnity toward its cognate
receptor.

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14.3.9 Post-Translational Modications (PTM)
Many different approaches have been pursued to develop predictive tools for sites
of post-translational modications of which oxidation, deamidation, isomerization,
and glycation are the most prominent ones.
Oxidation occurs most frequently at the side chains of Trp and Met that differ in
their atomistic nature (aromatic ring; sulfur), sensitivity toward different oxidative
stress (light exposure, metal-catalyzation and free radicals), and oxidized products
[211]. Therefore, different in silico tools have been developed for the prediction of
Trp and Met oxidation sites. For the prediction of Met oxidation, correlations
between the experimental oxidation data of stressed mAbs and the solvent accessible surface area (SASA) of the Met side chain have been seen [212]. Recently,
several different machine learning approaches have been conducted to train and t
different classication models such as MetODeep for the prediction of oxidationsensitive Met sites [213–217]. Some of the resulting models used random forest
algorithm and consider characteristics about sequence, secondary andtertiary structures, and dynamics to predict Met oxidation. Interestingly, again the SASA of the
Met side chain was amongst the most important discriminators. Furthermore, the
number of residues between the analyzed Met and the next Met toward the
N-terminus and the spatial distance between the sulfur atom and the closest aromatic residue affected the oxidation propensity [215]. Typically, MD simulations
are conducted to capture the dynamics of the structure and improve the prediction
of critical oxidation sites [218, 219].
Like the Met oxidation sites, high solvent accessibility of the Trp residue is a
prerequisite for oxidation [159, 220, 221]. However, it is hypothesized that in case
of Met residues the solvent exposure of the sulfur atom is more important than that
of the entire side chain [27, 215, 219]. In contrast, the entire side chain is considered
for the prediction of Trp sites sensitive to oxidation. The oxidation susceptibility
does not linearly correlate to the SASA of the Trp residue, indicating that other
structural characteristics as side chain orientation and/or surrounding structural elements might play a role [221]. The predictive power of such tools remains to be
veried for molecules that underwent different types of stress (light, reactive oxygen, metal).
Sites sensitive to deamidation and isomerization have been historically identied
via sequence motifs (e.g., NG), but this approach was shown to be less accurate and
prone to overprediction [222]. Therefore, the risk predictions could be improved for
mAbs by not only considering the motif but also the CDR region [223]. Later algorithms as NGOME were developed under consideration of simple predictions of
secondary structure elements [224]. Finally, the complex conformational environment of the reactive groups, particularly the local structure, structure exibility and
solvent accessibility, has been considered in several other studies [159, 225–228].
Furthermore, a predictor for Asn deamidation was recently trained on structural
features via machine learning algorithms [229]. Thereby, Asn torsion, exibility,

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solvent exposure, structural elements, and the distance between C-N for the nucleophilic attack were identied as the most relevant descriptors [229].
14.4 Conclusion andFuture Directions
Computational approaches are nding increasing applications toward discovery and
development of biotherapeutics in recent years. This chapter has attempted to provide an overview of this emerging eld, we call as biopharmaceutical informatics.
However, several major challenges remain toward increasing the contribution of
biopharmaceutical informatics andthereby increasingthe probability ofsuccessful
translation of biologic drug candidates into medicines available in the clinic. One of
the most signicant hurdles for greater acceptance for biopharmaceutical informatics is the predictability and validation of the computational tools. Validation via
self-consistent experimental data is important for the development of these emerging computational tools, but self-consistent experimental data sets on biologic macromolecules are rarely available in public domain. A second hurdle is that the use of
antibody-based biologics as medicines is more recent when compared to the small
molecule drugs. Therefore, the number of biologic drug products currently available
in the market is small and our overall pharmaceutical development experience with
these macromolecules is not as extensive as in thecase of the small molecule drug
products. This situation is further complicated by the pervasive nature of empiricism inherent to both experimental and computational tools used to study biologic
drug candidates, and with the arrival of novel biotherapeutic formats such as bispecic and multi-specic antibodies. A third hurdle for the progress of biopharmaceutical informatics is created if the computational tools are not available easily to
everyone, and the underlying core programming codes are not published. A fourth
hurdle is the general unavailability of the data in digital format in central repositories within and outside the biopharmaceutical companies. The need for digital transformation of biopharmaceutical industry cannot be understated. However, digital
transformation of biopharmaceutical industry is hampered by the lack of digitization of the experimental data. Overcoming the digitization hurdle that makes the
experimental data available to computational biophysicists, data scientists, and
machine learners is the foundational step toward digital transformation. Once this is
accomplished, the scientists shall then be able to use the data and connect them with
sequence and structural characteristics of biologic drug candidates. Discovery of
correlations among “microscopic” (properties/descriptors derived from amino acid
sequence, protein structure and molecular simulations) and “macroscopic” (experimental biochemical and biophysical experiments) attributes of biologic drug candidates will prove crucial for navigating developability of biologic drugs and will
truly enable biopharmaceutical informatics. As summarized in this article, these are
still early days for this eld as computational as well as hybrid studies containing
computational and experimental data are beginning to emerge. Overall, this eld is
expected to grow exponentially in the coming years.

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