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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5366_Библиотеки_им_академика_М_И_Перельмана.pdf
X
- •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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J. Bauer et al.
[27]
Reduced conformational stability,
reduced melting temperature,
increased levels of fragments,
aggregates, and particles,
Light-induced, free
radicals,
metal-catalysis
[28–33]
immunogenicity, reduced biological
activity, and coloration
and anionic properties, antibody
self-association, aggregation,
[29,
34–39]
structural changes, loss of function
biological activity, and
immunogenicity
[43–50]
Increased charge heterogeneity [40–42]
Aggregation, adsorption, increased
viscosity, decreased solubility, and
monosaccharides
Air-water interface,
freeze-thaw, shear,
[51–54]
loss of function
Aggregation, low solubility, high
agitation,
temperature, and
light stresses
[49,
55–59]
viscosity, liquid-liquid and liquid-solid
phase separation, off-target binding,
fast antibody clearance
complementarity
determining regions
(CDRs))
Deamidation Asn, Gln (in theCDRs) Basic pH A decreased pI, altered hydrophobic
Category Mechanism Liability Initiator Effect References
Chemical instability Oxidation Trp, Met (in the
Table 14.2 Most common developability challenges in biologics
Chemical modications,
destabilized domain folds
Isomerization Asp Acidic pH Altered conformational exibility,
Glycation Lys Reducing
Changes in the secondary,
Conformational
tertiary, and quaternary
instability
Nonuniform distributions
of hydrophobic and
charged regions on
molecular surface
destabilized domain folds
structural features of the
native fold
of natively folded mAbs
Colloidal stability Reversible self-association
Non-native aggregation Chemical modications,

14 Biopharmaceutical Informatics: A Strategic Vision for Discovering Developable…
all the stages described in this table. In the next section, we discuss the opportunities
that are beginning to mature.
411
14.2 In Silico Assessments ofBiologics inResearch
andDevelopment
14.2.1 Antibody Generation
Puried antigens can be used to generate antibodies against them either by immunizing animals (typically laboratory mice, humanized/transgenic mice or other animals like chicken, rabbit, or cows), using hybridoma techniques, or screening of
natural and/or synthetic antibody libraries via display technologies such as phage or
yeast. Promising hits are selected and validated via antigen binding assays. Currently
available methods for antibody generation are almost entirely experimental in
nature. Depending on the methods used to generate antibodies against a given antigen, it commonly takes several months before an initial set of antibody-based binders becomes available for further investigations and for lead identication. However,
computational technologies that have been originally developed for small molecule
drug discovery can be also transferred to antibody-based drug discovery. Once fully
developed and deployed, these in silico methods will open another set of means to
generate antibody binders against a target antigen.
A potential computational tool originates from the strategy of pharmacophorebased screening of small molecules. Transferring the idea to biologics, the molecular surface features of a desired antigen epitope must be known to screen a database
of antibody structures, and to identify potential hits based on molecular shape and
electrostatic complementarity. The hits can be prioritized by modelling antigen:
antibody complexes via protein: protein docking. However, protein: protein docking
scoring methods and selection of the “correct” poses remain a topic of debate,
although considerable progress is being made [60]. Further, rst antibody binding
mutational databases have been established that will help to improve computational
afnity predictions [61]. Subsequently, the most promising candidates can be
selected for experimental conrmation of binding, and computational optimization
of the afnity and developability of the antibody. A crucial part of this innovative
approach is the database of antibody structures and molecular models required for
the pharmacophore search. Importantly, the database does not require the structures
of full-length antibodies, but structures and homology-based molecular models of
the variable regions only. As of now, Protein Data Bank (PDB) contains thousands
of high-resolution crystal structures of Fragment variable (Fv) as well as fragment
antigen-binding (Fab) regions. In addition, several homology-based antibody modelling methods have been developed in past few years and, although some issues
remain, the eld has matured enough to provide highly accurate antibody models
capable of supporting pharmacophore like searches. The second potential approach

412
J. Bauer et al.
focuses on the design of computational libraries for phage or yeast display experiments. The availability and growth of large and heterogeneous databases of antibody sequences and structures provide an ideal starting point for the design of
computational libraries [62–67].
From the perspective of experimental approaches, fully synthetic human antibody libraries comprising Fabs that have been selected for biophysical characteristics favorable to development have already been created [68]. Thereby, a special
focus was placed on the selection of molecules with increased chemical, conformational, and colloidal stability [68]. The idea of optimized antibody libraries for the
generation of developable antibodies could be hybridized with de novo computational databases of an extremely large number of diverse combinations of humanoid
light and heavy chains [69]. Mutations targeted at specic sequence positions (e.g.,
CDRs) in the antibody sequences could further expand the library either to make it
recognize different antigens, or to optimize its binding afnity toward a given antigen. Recently, a generative adversarial network was successfully applied to create a
diverse library of novel antibodies that mimic somatically hypermutated human repertoire response [70]. This in silico approach further unraveled the residue diversity
throughout the variable region [70] that might be helpful for further computational
tools such as CDR redesign. This approach uses a highly developable antibody
framework that is altered in the original CDRs, i.e., paratope to recognize a novel
antigen. In the last years, signicant advances were made in the design of not only
thermodynamically stable but also biologically functional antibodies [71].
Remarkably, rst computational methods offer the possibility to design humanized antibody variable regions against targeted antigen epitopes de novo [72, 73].
Alternatively, it was shown that the design can also start with a structural model of
an antigen: antibody (Ag: Ab) complex generated using molecular docking of the
structures of the Ag and Ab [73]. In the next step, the afnity of the antigen toward
the antibody could be either varied by randomly introducing sequence variations
[73] or selectively re-designed via structure-based approaches. Subsequently, interfacial residues in the Ab and Ag structures which contribute signicantly toward
instability of the Ag: Ab complex could be identied via computational alanine
(Ala) scanning. In the next step, the identied residue positions could be scanned
for mutations that can increase/decrease the stability of Ag: Ab complex and
improve or lower afnity of the Ab toward the Ag [74], as per project requirements.
Another attractive alternative for the rational antibody design refers to hotspot grafting with CDR loop swapping, which only requires information about the interactions with the antigen [75].
14.2.2 Hit Selection andLead Identication
After production of antigen-binding antibodies by immunized animals, hybridoma
cells, or phage and yeast display techniques, the variable regions of the antibodies
are sequenced, and the binders are validated. The wide variety of hits must then be

14 Biopharmaceutical Informatics: A Strategic Vision for Discovering Developable…
413
prioritized, and the most promising lead candidates identied (LI, lead identication). Consequently, extensive resources are required to experimentally test each hit
and conrm antigen binding.
Several bioinformatic techniques can support the prioritization and selection of
hits for invitro conrmation of antigen binding as well as lead identication. A
commonly used strategy is to cluster the hits into bins of high, medium, and low
binding afnity, based on the initial estimates, analyze each bin for the diversity of
heavy and light chain germlines followed by diversity of the CDRs, and select multiple but few representatives from each germline pair in each bin for experimental
testing. Alternatively, one could directly bin the hits based on the germline pairings
and CDR diversity and select multiple but few of them based on their estimated
antigen binding. In addition to the antigen binding, the aspect of developability can
already be considered early at this point of hit selection by employing computational tools. In a simple application, one can score heavy (HC) and light chain (LC)
sequences of hits based on presence of potential chemical degradation motifs,
aggregation prone regions (APRs), and T-cell immune epitopes present or overlapping with the CDRs of the heavy and light chains. Such scoring schemes can be
further optimized by adding different weights based on which CDRs contain these
motifs and whether they are present in the at the beginning/end or in the middle of
the CDRs. In a more structure-based approach, three-dimensional homology models of all or a subset of hits can be analyzed regarding physicochemical descriptors
such as pI, charge, dipole moment, and solvent exposed hydrophobic and ionic
patches [22, 24]. In subsequent studies, one or few of the best hits are experimentally tested thoroughly for biological function, cross-reactivity across species, nonspecic binding, and pharmacology indicators such as serum stability. This process
culminates into identication of one or more lead candidates.
14.2.3 Lead Humanization andOptimization
Lead optimization (LO) is conducted once one or more lead candidates have been
identied and revalidated for function. During LO, the Fv regions may need to be
humanized, if necessary, corrected for post-translational modication (PTM) sites,
optimized for afnity, and in the best case, for developability (Fig.14.2). Below it
is described, how the LO process of therapeutic antibodies can be supported in
every aspect by computational biophysics [76].
Humanization aims for an optimal amino acid sequence in the Fv by converting
as many nonhuman residues to human germline residues to decrease the likelihood
of immunogenicity and antidrug antibodies (ADAs) which can impact drug efcacy
and safety [77, 78]. If necessary, mouse residues essential for binding are identied
by back mutations to retain Ag binding similar to the mouse/human chimeric candidate [79]. A better understanding of the structure-function relationship helps to
identify tting templates and back-mutations critical to preserve CDR conformations [80]. Consequently, computational protein design methods have been

414
Fig. 14.2 Process of lead optimization (LO)
J. Bauer et al.
successfully applied to efciently increase the humanness of antibodies while maintaining their structural stability [81]. In line with that, a retrospective analysis of a
humanization campaign suggested that hotspots in both, the FW regions and Vernier
Zones, can affect the antigen binding and thermodynamic stability [82]. State-ofthe-art software such as MOE from Chemical Computing Group [83] can facilitate
CDR grafting via identication of appropriate human FWs and back-mutations by
considering large databases of human sequences [63, 84]. Furthermore, the rating
and optimization of humanness can be done via in silico calculations [19, 84–89].
Besides that, statistical interference approaches have been created to characterize
the statistical distribution of human Fv sequences [90]. Furthermore, bioinformatic
studies have shed light on subtle structural differences between the lambda (VL)
and kappa (VK) isotypes that need to be considered during (re-)engineering [91].
Structure-guided approaches can help improve the biophysical properties of a therapeutic mAb by switching from a problematic lambda framework (FW) region to a
more stable kappa FW [92].
The humanized sequence(s) are then proceeded with liability engineering campaigns. The cumulative recommendations based on pre-formulation assessment,
forced degradation studies analyzing PTMs and stability, and in silico assessments
can be considered along with CDR germline residues in the engineering design
plan. At this time, the power of phage display or other screening technologies can
be used to screen a large panel of variants (typically 103–109 Escherichia coli
expressed Fabs). A panel of nal lead optimized variants (~50–100) might be formatted as immunoglobulin Gs (IgGs), expressed, and puried at small scales, and
characterized by binding and pre-formulation assessments. Complementary, in
silico assessments help to investigate intrinsic differences between the candidates.
Various predictive in silico tools are available that help to monitor and guide the
redesign of the candidate’s individual weak points that mediate chemical,

14 Biopharmaceutical Informatics: A Strategic Vision for Discovering Developable…
conformational, colloidal, and physical instability (see Sect. 14.3). In addition,
comparison of the molecular characteristics of the lead candidate against marketed
antibodies allows us to estimate the medicine-likeness, which can be further
improved by modication of relevant properties such as the extent and magnitude of
surface hydrophobicity and charged patches[24].
The resulting recommendations of single or combinations of distinct amino acid
exchanges help to design a highly individual engineering strategy of humanization
and optimization that is specically tailored to the mAb candidate. Based on the
criteria of the research target prole (RTP), the best LO candidates (~3–6) are then
selected for large-scale production to supply material for the next phase. These processes are mostly applied for the optimization of conventional mAbs but can also be
extended for multi-specics along with the additional engineering required to optimize the second and/or third Fv or scFv domains. In addition, identifying an optimal
multi-specic format that combines the individually optimized variable domains is
required to nalize the LO candidate(s).
415
14.2.4 Formatting ofConventional
andNext-Generation Antibodies
After optimizing the Fv portions, the engineering of conventional mAbs continues
with the formatting of the Fvs in the desired antibody format. In this step, the Fv is
combined with the Fc of a desired IgG isotype. In this phase, engineering of the Fc
might be required to adapt the receptor-mediated functions of the mAb such as
ADCC, ADCP, CDC, and endosomal recycling [93]. Depending upon the therapeutic concept, the design of next-generation biotherapeutics as bi- and multi-specic
antibodies might require another intermediate formatting step to assess physicochemical compatibility of individual specicities with one another, assuring that the
multi-specic modalities have desirable developability properties. Individual case
studies already reported how structure-based engineering can support antibody formatting. One case study showed that after converting from scFv to IgG, the afnity
of a TGFβ1 (Transforming growth factor β1) binder could be successfully restored
by structure-guided reengineering of elbow region [94]. Analogous computationalguided approaches have the power to support formatting of more complex nextgeneration antibodies such as multi-specic biotherapeutics.
In the last step of the discovery process, a few of the top performing lead variants
are assessed in pre-formulation studies prior totransfer to development for cell line
generation and early developability assessments to test the t of the nale molecule(s)
to the platforms of upstream, downstream and formulation development [4]. The
research phase is completed by the selection of the nal candidate for the start of
development.

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J. Bauer et al.
14.2.5 In Silico Assessments inDevelopment
The preliminary stages of drug substance and drug product development are known
to be resource intense. Consequently, the full development program comprising of
cell line development, upstream and downstream manufacturing process, and formulation development can in most cases only be conducted for the nal lead candidate. However, at the time of selection of the nal lead candidate, experimental data
is only sparsely available due to limitations on quantity as well as quality of material
available. At the same time, the sequence of the nal lead candidate gets locked at
the start of development and not even single point mutations are allowed. This decision inherently puts product development in a disadvantaged situation since realtime data of the candidates’ stability are typically not available at the start of
development but are essential to meet the regulatory requirements for shelf-life,
CQAs, and product heterogeneity. Therefore, there is a particularly strong demand
for an early, fast, and reliable prediction of various stability aspects that can be covered by hybrid approaches of invitro and in silico techniques.
14.3 In Silico Tools forDevelopability Assessments
Over the last decade, the scientic community has developed a diverse set of computational tools that can be applied in R&D to assess many different developability
aspects of biotherapeutics. In discovery, the result obtained from in silico developability assessments can be considered during the selection of hits as well as identication/optimization and engineering of the lead molecule to produce more easily
developable antibody drug candidates for drug product development. In the development phase, the in silico tools can help to estimate the nal t of the candidate to
standardized platforms, identify potential developability issues, guide adjustments
from the platforms that might be required, and nally interpret the complex results
of experimental studies [95]. The following section provides an overview of in
silico tools that computationally characterize therapeutic candidates and predict
important developability properties.
14.3.1 Structure Prediction
Some risk factors such as chemical modication sites can be even identied at the
level of the amino acid sequence, but many other developability factors such as
biophysical properties depend on the three-dimensional structure of the biotherapeutic. Therefore, most biopharmaceutical companies conduct experimental studies
as X-ray crystallography or nuclear magnetic resonance spectroscopy to solve the
molecular structures of the lead candidates alone or in complex with the respective

14 Biopharmaceutical Informatics: A Strategic Vision for Discovering Developable…
417
target. In case no experimental structures are available at the required time in the
project, homology modelling is often used to predict the three-dimensional structure of biologic drug candidates using their amino acid sequence. The modelling
abilities have been signicantly improved over the last decade by advances in computational power, modelling techniques, and databases of sequences (NGS, nextgeneration sequencing) and structures [96–101]. Since the modelling of the variable
regions of the antibodies can be performed automatically in a high-throughput manner, it is particularly useful toward discovery stages to analyze large sets of candidates [102–105]. Homology modelling is especially suited for the prediction of
mAb structures since the framework regions are highly conserved [106]. Despite
technological advances in template-based, fragment-based, and template-free modelling, the greatest challenge remains the prediction of diverse CDR canonical
classes. Particularly, modelling of the conformations of HCDR3 loops with signicantly varying lengths is challenging due to the sequence variability and structure
exibility [103, 107–111]. Currently, the most accurate loop models seem to be
achieved via hybrid strategies that combine the benets of knowledge- and physicsbased approaches [107, 112]. For a further improved understanding of the structural
characteristics of the dynamic structure of a mAb in solution, additional molecular
dynamics (MD) techniques that can capture antibody uctuations can be applied
[69, 113, 114]. Currently, modelling the full-length structures for IgG mAbs, and,
for next- generation multi-specicantibodies is challenging because the PDB contains only a handful of such crystal structures.
DeepMind’s AlphaFold demonstrated the great potential of deep learning for
protein structure prediction [100, 101]. Furthermore, the prediction of exible systems suchas interfaces is still complicated due to the complex balancing of polar
and nonpolar interactions as well as solvation effects [97]. At the same time, ML
techniques have a great potential to revolutionize the eld of template-free prediction of protein structures [97]. Particular attention was attracted by a protein-specic fragment library that has been recently generated via deep neural networks
[100, 101]. The analysis identied patterns in protein sequence and co-evolutionary
couplings, which have been converted in contact maps [100]. Novel algorithms have
further been able to engineer de novo high-order assemblies with therapeutic potential using bioinformatics, even so the design from scratch remains a massive undertaking [98, 115, 116].
14.3.2 Biophysical Properties
The developability of drugs is mostly specied by its biophysical properties.
Lipinski’s “rule-of-ve” represented a substantial leap for the discovery and development campaigns of small molecules since it related calculable physicochemical
properties with drug characteristics as solubility and permeability [117]. The complexity of biological entities hampered the denition of similar guidelines for NBEs
(New Biological Entities) for decades, but a biophysical screening of clinical stage

418
antibodies guided the empirical denition of analogous boundaries [22, 24].
Subsequently, the heterogeneous biophysical measures have been successfully correlated with sequence features, indicating signicant relationships between the
sequence of Fv domains and physicochemical properties that dene the developability of antibodies [21, 23]. For instance, general correlates have been established
between mAb polyreactivity and the presence of basic amino acids in the CDRs as
well as Gln in HCDR2 and 3 [23]. Furthermore, mAb aggregation and selfassociation have been correlated with CDR length and content of aromatic residues
[23]. However, since the particular relationship between specic amino acids and
other physicochemical properties of the mAb such as conformational stability
strongly depends on the structural microenvironment, key residues and their modications must be individually evaluated under consideration of the structural context [118]. Therefore, another study considered Fv models to establish developability
guidelines and develop a Therapeutic Antibody Proler (TAP) [24]. This tool
assesses the developability of candidates via ve easily calculablemetricsfor the
total length of CDRs, positively and negatively charged patchesas well as hydrophobic patches in the CDRs, and the asymmetry in the surface charges of heavy and
light chains [24]. Similar guidelines remain to be developed for multi-specic antibodies that often display suboptimal physical properties impeding the development
into therapeutics [119].
J. Bauer et al.
14.3.3 Hydrophobicity
The pharmaceutical industry widely recognizes the relevance of hydrophobicity of
mAbs for its developability into therapeutics, for which reason Hydrophobic
Interaction Chromatography (HIC) is often conducted to compare the apparent
hydrophobicity of mAb candidates toassess downstream risks [6, 11, 22]. Even
though an accurate prediction of HIC retention times is challenging since it is inuenced by the solvent (e.g., salt gradients) and other protein characteristics (e.g.,
charge) [21], HIC retention times could successfully be correlated with sequence
and structure features by using diverse methods asQuantitative Structure Property
Relationship (QSPR) modeling or machine learning [120–122]. To rectify homology modeling errors and capture the dynamics of the rather exible formation and
breakage of hydrophobic patches, it is recommended to consider conformational
sampling or MD simulations [121–125].
14.3.4 Solution- andColloidal-State Properties
The solution- and colloidal-state properties are amongst the most important aspects
to be considered during discovery and development of a Novel Biologic Entity
(NBE) drug candidate, but also amongst the hardest to predict due to multiple

14 Biopharmaceutical Informatics: A Strategic Vision for Discovering Developable…
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inuencing factors as the individual patterning of hydrophobic and charged residues. However, recent advances in understanding the complex principles of protein
solubility enabled the development of predictive tools. First computational tools
such as SOLpro and PROSO II were trained on tens of thousands of proteins and
successfully demonstrated their ability to predict solubility upon expression with an
accuracy of ~75% [126, 127]. Later, web-based tools (e.g., Protein-Sol) have been
developed that offer an easy access to the prediction of protein solubility from
sequence [128]. Complementary to sequence-based approaches, CamSol calculates
a residue-specic intrinsic solubility prole under consideration of structural inuences, and offers to optimize the solubility of a candidate by screening for suitable
mutations [129]. This feature makes it particularly interesting for the design of antibody libraries and the selection of lead candidates [130]. CamSol was recently
extended to predict the aggregation potential of partially unfolded proteins in temperature ramps of molecular dynamics (MD) simulations [131]. For early development activities, such a tool enables us to assess the candidate’s solubility relative to
previous molecules without the need for material and laborious experimentalactivities [132]. An alternative software called SODA estimates changes in the protein
solubility via the propensity of the sequence to aggregate (via PASTA) [133] and
disorder (via ESpritz) [134], and takes further properties as hydrophobicity and
secondary structure (via FELLS) [135] into account [136]. Several computational
approaches have already successfully guided the rational design of mAbs with
increased solution- and colloidal-state properties [137–142].
A currently evolving eld focuses on the prediction of mAb specicity, which
refers not only to nonspecic binding but also self-interaction. Recently, a method
has been described that predicts the overall specicity of antibodies [26]. Individual
and combined sets of chemical rules have been dened that recommend limits of
certain amino acids exposed to the surface of the variable region.
While mechanistic tools are most valuable for the screening and minimization of
APRs in the hits and leadcandidates during discovery [137–139, 143–149], the
kinetic predictors are helpful to estimate the rate of aggregation which is key during
the development of liquid formulations that must meet the regulatory requirements
for the shelf life of the drug product [150–153]. The kinetic models can be trained
by ML on large data sets of combined experimental and sequence/structure information [150, 152]. Desirable predictors could thereby screen different formulations
to identify the optimal composition (pH, salt and excipients) for minimal kinetics.
14.3.5 Isoelectric Point (pI)
The isoelectric point (pI) is an important physicochemical property for mAbs, and
it has been shown to correlate with specic developability aspects as thermostability, viscosity and resistance to HMW formation at low pH [4, 154]. Typically, IgG1s
with weakly basic isoelectric points between 8 and 8.5 and Fv isoelectric points
between 7.5 and 9 typically display the best combinations of strong repulsive
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