The field of protein engineering is at an exciting point in its development, with new generations of therapeutic antibodies now reaching the market, great advances in protein science, and a body of clinical evidence that can be used to inform the development of safe, highly effective therapies for unmet medical needs. The PEGS Engineering Antibodies conference explores case examples of the most significant emerging technologies used by protein engineers working at the discovery and design stages to quickly and efficiently craft biotherapeutics directed at the most elusive targets and biological functions.

Final Agenda

Recommended Short Course(s)*

SC8: Introduction to Biophysical Analysis for Biotherapeutics: Discovery & Development Applications

*Separate registration required.

WEDNESDAY, MAY 2

7:30 am Registration (Commonwealth Hall) and Morning Coffee (Harbor Level)

ANTIBODIES AGAINST DIFFICULT TARGETS
Amphitheater

8:30 Chairperson’s Remarks

Jonas V. Schaefer, PhD, Lab Head/Investigator II, Novartis Institutes for BioMedical Research (NIBR)

8:40 Anti-RAS DARPins as Multipurpose Tools to Investigate Its Versatile Functions and to Design Novel Approaches to Make It a Druggable Target

Jonas V. Schaefer, PhD, Lab Head/Investigator II, Novartis Institutes for BioMedical Research (NIBR)

Even after decades of research, a direct inhibition of the high-priority anticancer drug target KRAS with small molecules has been extremely challenging. Therefore, DARPins – very potent proteinaceous binders with highly beneficial properties – were generated to bind to various sites of oncogenic Ras mutants, thus efficiently interfering with the numerous interactions with their effector proteins. These DARPins might therefore help to investigate various approaches to attack this so far ‘undruggable’ target.

9:10 New Strategies to Identify Functional Antibodies against Complex Membrane Proteins

JT Koerber, PhD, Scientist, Antibody Engineering, Genentech

Integral membrane proteins comprise a large untapped target space for therapeutic antibodies, but the discovery of functional antibodies against this class of proteins remains a challenge. The dynamic nature of these targets coupled with complex functional assays can limit the efficiency of all project stages from initial discovery to ultimately characterization of lead antibodies. I will discuss our efforts towards addressing these challenges.

9:40 Distinct 4-1BB Binding Properties of Therapeutic Utomilumab and Urelumab Antibodies

Andy Yeung, PhD, Associate Research Fellow, Rinat, Oncology R&D, Pfizer, Inc.

Agonistic anti-human 41BB (CD137) antibodies, utomilumab (PF-05082566) and urelumab (BMS-663513) showed distinctive therapeutic efficacy and toxicity profiles in clinical trials. To gain insight into their binding modes, we solved structures of the human 4-1BB receptor-ligand complex and the 4-1BB receptor bound to either utolilumab or urelumab. We also compared their binding epitopes to that of surrogate anti-m41BB antibodies. Our work provide insight into the future development of 4-1BB targeted biologics.

10:10 Coffee Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

DISCOVERY OF UNIQUE ANTIBODIES
Amphitheater

10:55Structure-Function Analysis to Identify Rare Epitopes with Unique Binding Properties

Bruno Correia, PhD, Professor, Protein Design and Immunoengineering, EPFL Zurich, Switzerland

We developed a computational design strategy with the ultimate goal of designing accurate epitope mimics for the development of novel vaccine candidates. Recently, a first proof of principle has shown that a computationally designed protein presenting the Respiratory Syncytial Virus (RSV) Motavizumab epitope elicited potent neutralizing antibodies in nonhuman primates. We have extended this approach to several epitopes in RSV, and I will present biochemical, biophysical and immunological characterization of the computationally designed immunogens.

11:25 Discovery of High-Affinity Human PD-1 and LAG-3 Antibodies Using Novel Microfluidic and Molecular Genomic Methods

David S. Johnson, PhD, CEO, GigaGen

Conventionally, mouse hybridomas or well-plate screening are used to identify therapeutic monoclonal antibody candidates. We have developed a novel alternative to hybridoma-based discovery that combines microfluidics, yeast single chain variable fragment (scFv) display, and deep sequencing. We have used our technology to rapidly discover thousands of checkpoint inhibitor candidates against sixteen targets, in less than six months. In this talk, we will specifically focus on our PD-1 and LAG-3 programs.

11:55 KEYNOTE PRESENTATION: Engineering Antibodies to Modulate Antibody Dynamics

E. Sally Ward, Ph.D., Professor, Molecular and Cellular Medicine, Texas A&M Health Science Center

There have been multiple developments in the engineering of FcRn-IgG interactions to modulate the in vivo dynamics of antibodies and their target antigens. In parallel, analyses of the behavior of FcRn and its ligands at the subcellular level can be used to inform the design of therapeutics. The presentation will cover recent progress in these areas.

12:25 pm Engineering SURE CHO-M Cell Lines for Optimized and Customized Solutions to Therapeutics Production

Valerie Le Fourn, PhD, Research & Development Cell Culture Director, Selexis SA

New complex biotherapeutics molecules are increasingly being developed resulting in new manufacturing challenges for CHO cell lines. To address these challenges, we developed the SUREtechnology platform. Using our CHO-M cell line genomics/transcriptomics data, we have improved our understanding of endogenous pathways regulating the expression of recombinant proteins. I will describe case studies with customized solutions for Difficult-to-Express Proteins to generate CHO cell lines with high productivities while maintaining product quality.

12:55 Luncheon Presentation I: Rapid Purification, Concentration, and Characterization of Antibodies and Proteins: Capturem High-Capacity Membranes

Tim Larson, PhD, Marketing Specialist II, Marketing, Takara Bio USA

We have developed Capturem technology, a novel, nylon membrane-based system with an extremely fast workflow that can be completed in 5–20 minutes, with the added benefit of resulting in an exceptionally pure and concentrated eluate in single column and high-throughput formats. We have also demonstrated trypsin and pepsin-functionalized membranes for rapid protein digestion for downstream analysis. Capturem membranes can dramatically speed up product development by eliminating the long incubation times required with traditional workflows.

1:25 Luncheon Presentation II: Computationally Optimized SuperHuman Library Generates 100,000 Unique Antibodies Against 24 Immune Targets in Weeks

Jacob Glanville, PhD, Co-Founder & CSO, Distributed Bio

Here we describe a computational antibody library design that was optimized for both sequence diversity, engineering fitness and speed through the analysis of 1000’s of human antibody repertoires. This diversity has resulted in a uniquely engineered library that generates over 5000 unique antibodies saturating all epitopes in all 24 tested antigens. This library can be panned under aggressive conditions, recovering picomolar binders, and isolating multi-species cross-reactive members against target homologs without additional engineering.

1:55 Session Break

ENGINEERING FOR SELECTIVE BINDING
Amphitheater

2:10 Chairperson’s Remarks

Danlin Yang, PhD, Scientist, Biotherapeutics Discovery, Boehringer Ingelheim

2:15 Receptor Engineering and Strategies for Selective Binding

Joel Cohen-Solal, PhD, Senior Research Scientist, Global Protein Sciences, AbbVie Bioresearch Center

Binding studies of IgG-based biologics to Fc Receptors carried out by cell-based assays are valuable to better characterize the interactions in physiologic-like settings and to identify parameters for selective binding.

2:45 Maximizing in vivo Target Clearance by Design of pH-Dependent Target Binding Antibodies with Altered Affinity to FcRn

Danlin Yang, PhD, Scientist, Biotherapeutics Discovery, Boehringer Ingelheim

In the past five years, the concept of recycling and sweeping antibodies has emerged in the literature. These antibodies have demonstrated potential success in reducing target levels compared to conventional antibodies. Here we present the groundwork on how to maximize target reduction through the optimal design of binding kinetics and pH-dependence to both antigen and FcRn in the therapeutic candidate, potentially providing a path to greater patient dosing convenience.

3:15 Advances in Computational Approaches to Antibody Engineering

Christopher Negron, PhD, Senior Scientist, Schrödinger

Experimental techniques for discovering and optimizing antibodies with high affinity for a target have matured significantly. However, the discovery and optimization of other "drug-like" properties for antibodies remain challenging. We describe a computational workflow for identifying and removing those liabilities. Beyond this, we will describe computational approaches for predicting changes in protein stability and binding affinity using a rigorous physics-based approach, free energy perturbation (FEP).

3:45 Refreshment Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

4:45 Problem-Solving Breakout Discussions (Commonwealth Hall)

Structure-based Antibody Engineering: The Good, the Not-so-bad and the Ugly

Christopher Corbeil, Ph.D., Research Officer, Human Health Therapeutics, National Research Council Canada

Traian Sulea, Ph.D., Research Officer, Human Health Therapeutics, National Research Council Canada

• Developability screening tools: good for re-engineering?
• Affinity and specificity optimization: broadly applicable with proven performance?
• De novo design of antibodies: useful and feasible?
• Computational predictions in real-life projects: better integration needed?

Unconventional Antibody Discovery Technology

David S. Johnson, Ph.D., Chief Executive Officer and Co-Founder, GigaGen

• Problems with conventional methods of antibody discovery, i.e., developability problems for Abs from yeast display or phage display libraries, low yield o
f Abs from hybridomas derived from mouse repertoires.
• Pros and cons of various microfluidic and genomic approaches, i.e., single cell barcoding in droplets, deep sequencing, high-density microwells, etc.
• New literature and developments on Ab discovery using microfluidics and genomics and remaining challenges in the field
• Possible next steps for applying similar technologies to Ab development, engineering, epitope mapping, target discovery, etc.

Pros and Cons of Human Ab Transgenic vs. Conventional Animals for Ab Discovery

John S. Kenney, Ph.D., President, Antibody Solutions

• Role of species, strain/MHC, Ig structure, and mechanisms of Ab diversity in the immune response to an Antigen
• Perceived advantages and disadvantages of transgenic vs. conventional animals?
• Differences in Ab format, serum response, B-cell populations, and amenability to Ab discovery platforms
• What improvements in animals might give better antibodies?

Integration of Developability Screening into Antibody Discovery

Andrew Nixon, Ph.D., Vice President, Biotherapeutics Molecule Discovery, Boehringer Ingelheim

• Predictive value of developability screening
• Emerging tools for developability screening
• Placement of developability analysis in the discovery workflow

5:45 Networking Reception in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

7:00 End of Day

THURSDAY, MAY 3

8:00 am Registration (Commonwealth Hall) Morning Coffee (Harbor Level)

ENGINEERING ANTIBODIES FOR IMPROVED PROPERTIES
Amphitheater 

8:30 Chairperson’s Remarks

Caroline Colley, PhD, Associate Director, Antibody Discovery and Protein Engineering, MedImmune, United Kingdom

8:35 Agonizing the TNFR Superfamily for Cancer Immunotherapy

Greg Lazar, PhD, Director, Antibody Engineering, Genentech

Multiple technology platforms have been explored to enable antibodies to mediate receptor agonist activity without relying on Fc receptor-mediated crosslinking. This talk will describe engineering approaches and considerations, present data demonstrating in vitro and in vivo proof-of-concept, and discuss biological and clinical context as they relate to cancer immunotherapy.

9:05 Strategies for Identifying Biologics with Specific Mechanisms of Action

Caroline Colley, PhD, Associate Director, Antibody Discovery and Protein Engineering, MedImmune, United Kingdom

In biologics discovery, assay cascades can be designed from the outset to triage thousands of antibodies for the desired function, specificity and affinity. While early functional screening is paramount, it is also important to understand the mechanism of action through which an antibody mediates its effects (e.g. competitive, allosteric), to ensure appropriate target suppression. Using case studies, strategies and learnings for identifying antibodies with the desired mechanism will be highlighted.

9:35 Overcoming Tolerance by Deep Mining of Natural Immune Repertoires

Carl Hansen, PhD, CEO, AbCellera

AbCellera has developed an end-to-end antibody discovery platform for deep screening of natural immune responses. Our microfluidic platform supports a broad array of assay formats, enabling discovery against any target class at a throughput of millions of single cells per run. Here we show that ultra-deep screening of multiple immune tissues can be used to overcome challenges of immune tolerance, generating diverse panels of hundreds of lead candidates against targets with 100% homology.

10:05 Coffee Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

11:05 Fc Engineering for Complement-Mediated Effector Function and FcRn-Mediated Pharmacokinetics

Chang-Han Lee, PhD, Postdoctoral Researcher, Georgiou Lab, The University of Texas at Austin

Engineered Fc domains, which have an asymmetric structure and completely selective binding to C1q without any concomitant FcγR engagement, were used to demonstrate that CDCC and CDCP of therapeutic antibodies mediate removal of target cells with equivalent kinetics and potency as FcγR-dependent ADCC and ADCP mechanisms in vitro and in mouse models. In another engineered Fc domain, it showed enhanced serum half-life in several hFcRn mouse models and is applicable for IgG subclasses.

11:35 Engineering Antibodies for Tissue Specific Inhibition

Abhishek Datta, Ph.D., Director, Antibody Discovery and Engineering, Scholar Rock

Traditional therapeutic approaches directly target a growth factor or its receptor everywhere in the body, not only shutting down its harmful function in disease, but also potentially causing undesirable side effects arising from the inherent biology of growth factors. Individual growth factors occur as members of larger families of structurally related proteins, and a single growth factor can lead to a different biological effect in different tissues. By intervening in supracellular activation, our medicines target growth factors in their latent, inactive forms to selectively and locally modulate growth factor activity.

12:05 pm Designer Proteins: Targeting Protein-Pathogen Interactions

Eva-Maria Strauch, PhD, Research Assistant Professor, Biochemistry, University of Washington

Many viral surface glycoproteins and cell surface receptors are homo-oligomers, and hence can potentially be targeted by geometrically matched homo-oligomers. I will describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites. I will conclude with how we can take the design of binding proteins to the next level using completely customized, de novo designed proteins against pathogens.

12:35 End of Engineering Antibodies