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- •Contents
- •Foreword
- •Preface
- •About the Editors
- •Contributors
- •References
- •2.3.4 Barriers to Automation Adoption
- •2.4 Core Ingredients for Successful Digital Transformation
- •2.1 Introduction
- •2.3.1 Operational Challenges
- •2.3.2 Cultural Challenges
- •2.4.2 Cloud Computing
- •2.5 Case Studies of Successful Digital Transformation
- •2.6 Conclusion
- •References
- •3. Computational Protein Design Strategies for Optimization of Antigen Generation to Drive Antibody Discovery
- •3.1 Introduction
- •3.3 Antigen Generation Strategies
- •3.4 Computational Methods
- •3.4.2 Computational Protein Structure Prediction
- •References
- •4. Bioinformatic Analyses of Antibody Repertoires and Their Roles in Modern Antibody Drug Discovery
- •4.1 Introduction
- •4.6 Summary and Future Directions
- •Acknowledgments
- •References
- •5.1 Introduction
- •5.2 Databases
- •5.2.1 Databases in Machine Learning Approaches
- •5.2.2 Database Types
- •5.3 Applications of Machine Learning in Antibody Discovery and Development
- •5.3.1 Structure Prediction with Deep Learning
- •5.3.3 Developability
- •5.4 Antibody Generation and Design by Language Models
- •5.4.1 Antibody Representations
- •5.4.2 Representation Learning
- •5.4.3 Language Models
- •References
- •6.1 Introduction
- •6.2 Antibody Generation through Deep Generative Models
- •6.3.1 Sampling and Scoring
- •6.5 Conclusions and Perspectives
- •Acknowledgments
- •References
- •7.1 Introduction
- •7.2.3 Computational Approaches to Predict Antibody–Antigen Interaction
- •7.3 Conclusion
- •Competing Interests
- •Acknowledgments
- •References
- •8.2 Common Types of Molecular Simulations for Biomolecules
- •8.2.1 Molecular Dynamics (MD) Simulations
- •8.2.2 Monte Carlo (MC) Simulations
- •8.2.3 Challenges of Molecular Simulations
- •8.3.1 Periodic Boundary Conditions
- •8.4 Uses of Molecular Simulation in Antibody Drug Development
- •8.5 Conclusion
- •References
- •9. Considerations of Developability During the Early Stages of Antibody Drug Discovery and Design
- •9.1 Introduction
- •9.2 Historical Perspective
- •9.3 Clinical Antibody Data Set
- •9.5 Control Antibodies
- •9.7 Assessment of Chemical Liabilities
- •9.8 Conclusions and Future Perspectives
- •Acknowledgments
- •References
- •Abbreviations
- •10.1 Introduction
- •10.4.1 Conclusions and Outlook
- •Acknowledgments
- •References
- •11.8 Conclusions and Future Directions
- •References
- •12.1 Introduction to PK/PD and QSP Modeling
- •12.1.1 PK/PD Modeling
- •12.1.2 QSP Modeling
- •12.2.1 Monoclonal Antibodies (mAbs)
- •12.2.3 Cell Therapies
- •12.2.4 Gene Therapies
- •12.2.5 Vaccines
- •12.2.6 mRNA/siRNA/Oligonucleotide Therapeutics
- •12.4 Case Studies
- •12.5 Conclusions and Future Perspectives
- •References
- •13.1 Introduction
- •13.2 AI/ML: A Game Changer for Antibody Design
- •13.3 Multispecific Antibody Design
- •13.4 Adapting AI to the Design of Multispecific Antibodies
- •13.4.1 Structure Prediction and Modeling
- •13.4.2 Developability Prediction and Optimization
- •13.4.4 In Silico Modeling and Simulation
- •13.5 The Future: Beyond Optimization
- •13.5.1 Market Trends and Commercialization
- •13.5.2 Logic Gates, Biosensors, and De Novo Design
- •13.5.3 Challenges and Opportunities
- •13.6 Conclusion
- •Acknowledgments
- •References
- •Index

12 • Recent Advances in PK/PD 341
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The Articial
Intelligence
13
Revolution
Transforming the Design
and Optimization of
Multispecic Antibodies
Per Jr.Greisen, Ziwei Pang, and
Fernando Garces
13.1 INTRODUCTION
Multispecic antibodies (MsAbs) have emerged as a new class of biologics with added
therapeutic benets over the classical monoclonal antibodies (mAbs) [1]. This engi‑
neered mechanism recognizing two or more epitopes located on the same or distinct
targets expands the functionality of conventional mAbs, allowing for diverse applica‑
tions, such as recruiting immune cells to destroy tumor cells or crosslinking distinct
cell surface proteins [2–4]. Moreover, MsAbs are new molecular entities (NMEs) that
display signicant variation in size, conguration, valencies, exibility, and angle of
approach of their binding modules, biodistribution, and pharmacokinetic attributes
[2,3]. However, the development of MsAbs quickly exposed the limitations of current
workows, including the computational tools available and the overall approach to a
344 DO I: 10.1201/ 9781003300311-13

13 • The Articial Intelligence Revolution 345
high complexity in protein engineering. The limited success rate with only nine MsAbs
approved thus far in more than two decades of research highlights the need to consider
new approaches [5]. While much of the low MsAb approval rate can be attributed to sub‑
optimal prediction of the biology, this is likely due to the complexity of these new and
non‑native quaternary structures and challenges in target identication. Furthermore,
the developability of these NMEs largely remains a signicant challenge [6]. Since the
advent of AlphaFold2 in the 14th Critical Assessment of Protein Structure Prediction
(CASP14) [7], machine learning (ML)‑based methods have emerged as the next‑gen‑
eration of technologies with the potential to increase the success rate in developing
MsAbs. Currently, an increasing number of new startups specializing in developing
articial intelligence (AI)/ML models to address the discovery and engineering of bio‑
logics are emerging, attracting strong interest from the pharmaceutical industry. The
main difference between AI and physics‑based approaches lies in their methodology.
Physics‑based models rely on fundamental principles of physics like Newton’s equa‑
tions of motion, while knowledge‑based AI/ML models learn from patterns in data and
incorporate expert insights. Large language models (LLMs) initially gained traction in
protein modeling with the use of long short‑term memory (LSTM) architectures, includ‑
ing specialized variations like the multiplicative LSTM (mLSTM) [8,9] (Figure13.1). A
key advance was the development of the UniRep representation, which allowed LSTMs
to learn complex protein sequence patterns more effectively. Models built on top of
UniRep achieved several breakthroughs, including predicting the stability of natural
and designed proteins, the function of diverse mutants, and even accelerating protein
engineering tasks with vastly improved efciency [10]. One intriguing nding was the
mLSTM’s ability to enhance protein characteristics using zero‑shot or few‑shot learning
techniques, even with limited data (low N) [11]. The advent of transformers revolution‑
ized natural language processing by introducing parallelizable self‑attention mecha‑
nisms, enabling them to process entire sequences simultaneously and capture long‑range
dependencies within text, vastly outperforming the sequential limitations of recurrent
neural networks (RNNs) and LSTMs [12]. Building upon this, Meta’s Evolutionary
Scale Modeling (ESM) model, utilizing transformer‑based models, further advanced
LLM capabilities in this domain [13]. Further advancements led to the development
of larger LLMs, such as ESM‑1b with 650million parameters and ESM‑2 with a sig‑
nicant increase to 15 billion parameters. These larger models demonstrated improved
FIGURE 13.1 Protein design with large language models (LLMs). The LLM, trained on
extensive protein data, generates a new protein sequence that meets design goals such as
afnity, thermostability, among others.

346 Biopharmaceutical Informatics
performance compared to their smaller predecessors. Moreover, researchers found
strong correlations between the language model’s understanding of protein sequences
(measured by perplexity) and the accuracy of structure prediction. The close link
between language modeling and protein structure highlights the potential of LLMs with
even greater scale in parameters, data, and computation for further breakthroughs [14].
Companies like BioMap are pioneering this eld using large‑scale AI models to trans‑
form protein design. Their xTrimoPGLM model, with over 100 billion parameters,
exemplies this potential with its ability to process and generate protein sequences
tailored to specic inputs. These breakthroughs and the eld’s rapid advancement dem‑
onstrate the immense potential of LLMs to transform our understanding of proteins
[15]. A signicant development in LLMs for protein design is the use of labels (e.g.,
function, stability, enzyme activity, among others) to guide the generation of sequences
with desired properties [16]. Expanding these models up to 6.5 billion protein sequences
has demonstrated that larger models have an improved ability to predict and control
these properties [17].
Here, we will describe the AI/ML technologies currently being applied to the
development of mAbs and also offer insights about how the same or improved versions
can be utilized to facilitate the design and engineering of MsAbs.
13.2 AI/ML: A GAME CHANGER FOR ANTIBODY DESIGN
The use of AI techniques is accelerating the pace and quality of mAb discovery and
optimization, and for biologics, in general. These techniques are ushering in a new era
of precision and efciency, and they are changing the way that mAbs are designed and
developed. AI methodologies have been pivotal in enhancing various aspects of mAb
design, including afnity, developability, pharmacokinetics (PK), pharmacodynamics
(PD), immunogenicity, and more, demonstrating a profound impact on the therapeutic
efcacy and safety of these critical biologics [1].
Computational design of libraries has enabled the optimization of protein func‑
tion, laying the groundwork for more targeted and effective generation of libraries for
protein optimization compared with rational or random library generation [18]. One
of the parameters important for therapeutic mAbs is getting the right afnity, which
is often not present in the initial parental mAb coming from discovery platforms. AI
techniques optimize afnity and simplify approaches by inserting benecial mutations
in the mAb’s complementarity‑determining regions (CDRs), while preserving and even
improving specicity [19].
For this, computational methods, including structural modeling tools like Rosetta
[20] or MOE [21], have been instrumental in enabling researchers to netune afn‑
ity through precise modications. For instances where no structural information is
available, homology models can now be generated using advanced ML‑based tools
like AlphaFold 2 [7], AbBuilder [22], or xTrimoABFold [23], offering unprecedented

13 • The Articial Intelligence Revolution 347
insights into mAb structure in the absence of experimentally determined structures
(crystallographic, CryoEM, and nuclear magnetic resonance (NMR) data). However,
despite these advances, predicting the impact of sequence manipulation on afnity
remains a signicant challenge, plagued with large efforts of trial and error, underscor‑
ing the complexity of mAb optimization.
In addition, the use of AI has already proven benecial to improve several attributes
related to the mAb developability ranging from removing chemical liabilities to improv‑
ing protein expression levels. Chemical liabilities like deamidation, isomerization, tryp‑
tophan/methionine oxidations, but not limited to, are not always possible to remediate
nor are always predicted accurately, leading to unnecessary and expensive engineering
efforts to generate sequence variants that retain the initial properties, including binding
afnity. AI‑based models combining the prediction of attributes like protein folding,
thermostability, expression levels, and protein aggregation have already proven to be
helpful in guiding protein engineers to rst, prioritize which chemical liabilities present
on the therapeutics candidates (e.g., mAbs) must be removed from those ones that not,
and second, when required, generating sequences with high success rate once tested in
the laboratory [24]. AI has also been applied to address other development concerns
like mAb viscosity and aggregation propensity. Traditional methods often struggle to
reliably predict these properties, highlighting the value of AI‑based approaches [25,26].
Therefore, incorporating this approach into the optimization process saves time and
resources, building a workow that can be controlled and whose success can also be
predicted. Another parameter that should be taken into the optimization process early
is deimmunization. Here, the goal is to mitigate immunogenic concerns that could arise
during clinical trials [27]. Deimmunization of CDRs (particularly the foreign H3) and
potentially framework regions (FWRs) is crucial for optimization. Neural networks can
predict potential T‑cell epitopes (e.g., using NetMHC‑II [28]), helping reduce the risk
of immunogenic responses through protein engineering [29]. AI has also transformed
the speed with which one can humanize murine mAbs through LLMs like BioPhi [30],
which previously required data‑driven approaches with feedback from experiments. AI
tools not only speed up mAb optimization but also inform the decision‑making, leading
to faster workows with higher success rate in identifying mAbs with the best overall
drug‑like properties.
Altogether, data‑driven strategies have been applied to multiobjective optimiza‑
tion to generate mAbs with suitable properties as efciently as possible. However, the
continued evolution of AI/ML tools and methodologies promises to further rene our
understanding and capabilities in this space, paving the way for the development of
more effective and safer therapeutic mAbs.
13.3 MULTISPECIFIC ANTIBODY DESIGN
The transition from mAbs to the more complex arena of MsAbs (Figure13.2) calls for
a signicant evolution in the application of AI/ML strategies. While AI/ML has proven
revolutionary in optimizing mAb design across various facets: afnity, developability,

348 Biopharmaceutical Informatics
FIGURE13.2 Schematic representation highlighting the binding specicity (shown in different colors) of monoclonal (mAb) and multispecic antibodies (MsAb), specically bispecic antibodies (BsAbs) and trispecic antibodies (TsAb). Moreover, the number of repeats in
building blocks (e.g., Fabs and ScFvs) directly correlates with the binding valency that these
molecules can exhibit.
pharmacokinetics, and pharmacodynamics, to name a few, the leap to MsAbs intro‑
duces a new layer of complexity that challenges existing computational frameworks.
MsAbs, designed to engage multiple targets simultaneously (Figure 13.2), demand a
rened approach to address not only the challenges inherent in mAb optimization but
also those unique to their multifaceted often new quaternary structure.
One of the primary challenges in MsAb design is managing the intricate relation‑
ship between the angle of approach that the warheads are required to adapt and the
location of those same corresponding epitopes in the case of membrane‑bound targets
(Figure13.3a). Moreover, prior understanding of the target copy number and its distri‑
bution on the surface of the cell will inform the design of molecules with the suitable
valency that matches the surfaceoma (all extracellular domains of proteins anchored to
the cell membrane) of the targeting cell (Figure 13.3a). This complexity signicantly
affects how these NMEs are assembled into a suitable quaternary structure with the
right balance of steric hindrance, valency, and degrees of freedom. Important consider‑
ations that will predetermine developability and their therapeutic efcacy. Companies
like Chugai [31], Amgen [32], and Genentech [33] have been at the forefront, exploring
the nuances of epitope compatibility to ensure that the designed MsAbs can achieve the
desired clinical outcomes without unintended cross‑reactivity [31].

13 • The Articial Intelligence Revolution 349
FIGURE13. 3 Schematic representation of the molecule assembly for MsAbs. (a) The combinatorial design approach for bispecic antibodies targeting antigens A and B. Multiple
format variations (e.g., IgG-like, Fab, and scFv-based) are explored to optimize binding
interactions and potential biological effects based on the location of target epitopes. (b)
Assembly of MsAbs often requires engineering approaches to drive effective cognate
pairing of the heavy (HC) and light (LC) chains when multiple chains are expressed in a
single-cell host. Techniques like knob-in-hole (KiH) and charged pairing mutations (CPMs)
(black wheel) have been developed to minimize the chain mispairing.
Moreover, the kinetics of binding presents another layer of complexity. The ef‑
cacy of an MsAb is not just a function of its ability to bind to multiple targets but also
how these binding interactions inuence each other in the context of their kinetics. The
effects of binding kinetics (kON and k
) can dramatically affect the clinical efcacy of
OFF
the therapeutic molecule [34], necessitating sophisticated AI/ML models to predict and
optimize these kinetic proles. While this complexity has previously been addressed
using a combination of surface plasmon resonance (SPR) measurements and ordinary

350 Biopharmaceutical Informatics
differential equations (ODE) to understand bivalent interactions [35], coarse‑grained
simulations [36], or sophisticated analytic solutions [37], accurately estimating muta‑
tional effects on kinetics has remained challenging. Nonetheless, the critical importance
of faster or slower binding rates on clinical efcacy cannot be overstated. Therefore,
there is an urgent need for sophisticated AI/ML models to precisely predict and opti‑
mize these kinetic proles, ensuring the development of MsAbs with the desired thera‑
peutic properties.
The combinatorial explosion in screening potential building blocks (BB) combi‑
nations for MsAbs further underscores the need for AI/ML adaptation (Figure13.3a).
Indeed, in addition to the large number of BBs often generated for each target, we also
need to consider the type of BBs (which can include fragment antigen‑binding (Fab),
single‑chain variable fragments (scFvs), VHH, cytokines, and de novo binders) and
its dening physicochemical properties [1]. Traditional approaches to mAb develop‑
ment, which already involve screening vast libraries of candidates, are exponentially
complicated when each candidate can comprise multiple, distinct binding entities
(Figure13.4a). Indeed, the assembly of MsAbs comprising multiple polypeptide chains
requires sophisticated engineering solutions to drive correct chain pairing, including
the heavy chain‑heavy chain and/or heavy chain‑light chain (Figure13.3b). Although
several solutions have been reported, the chain pairing results in a more native‑like
quaternary arrangement, which translates into a better stability prole. Examples of
such technologies are Genentech’s knob‑into‑hole (KiH) [33] and Amgen’s chain‑pair‑
ing mutations (CPMs), already clinically validated and that are broadly applied in the
MsAbs’ design [38,39]. Moreover, the deployment of a common light chain [40] is also
an elegant approach to the generation of MsAbs molecules in a single‑cell expression
system. Highly dependent on the success of the cognate chain pairing is the purica‑
tion, where the appearance of sub‑products (mispairing) often adds complexity while
decreasing the total recovery of the targeted product. Nevertheless, it is paramount
before functional characterization (Figure13.4b) [41,42].
AI/ML can manage this complexity by efciently navigating the combinatorial
space, predicting optimal combinations that would be infeasible to identify through
empirical methods alone.
Additionally, modeling interactions between the different entities within an MsAb
molecule extends beyond the capabilities of many current computational tools designed
for mAb. The ability to accurately predict how different parts within an MsAb will
interact with each other and with multiple targets requires the development of new algo‑
rithms and models that can handle this increased complexity. For example, two given
BBs, each with acceptable charge and hydrophobic patch distribution on their surface,
could form super patches (e.g., hydrophobic areas exceeding 300 Å2) once plugged in
together, generating unexpected liabilities like aggregation [43]. In summary, the adap‑
tation and renement of AI/ML tools for MsAb design is a new frontier in therapeutic
development. Addressing the unique challenges of MsAbs—ranging from epitope com‑
patibility and kinetic proling to the combinatorial explosion in screening and modeling
inter‑entity interactions—requires innovative computational strategies. As the eld pro‑
gresses, the evolution of these computational tools will undoubtedly play a pivotal role
in unlocking the potential of MsAb, paving the way for next‑generation therapeutics.
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