The Display of Antibodies track at the PEGS Summit is the cornerstone event that showcases innovative design and engineering of biologics through phage and yeast display. This field has spawned an expanded array of constructs with improved activity and
pharmacokinetic properties to address new and intractable targets and optimize the efficacy of molecules.
Scientific Advisory Board
Andrew M. Bradbury, M.D., Ph.D., Staff Scientist, Biosciences, Los Alamos National Laboratory
Jennifer Cochran, Ph.D., Hitachi America Associate Professor, Bioengineering and Chemical Engineering, Stanford University
David Lowe, Ph.D., Senior Director, R&D, Antibody Discovery and Protein Engineering, MedImmune Ltd
Aaron K. Sato, Ph.D., CSO, LakePharma
Gregory A. Weiss, Ph.D., Professor, Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
K. Dane Wittrup, Ph.D., J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology
Final Agenda
Recommended Short Courses*
SC3: Genomics in the Service of Cancer Immunotherapy - Detailed Agenda
SC9: Target Selection for Biologics - Detailed Agenda
*Separate registration required
MONDAY, MAY 1
7:00 am Registration and Morning Coffee
8:30 Chairperson’s Remarks
Gregory A. Weiss, Ph.D., Professor, Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
8:40 KEYNOTE PRESENTATION: Targeting Dynamic Protein Targets for Structural and Functional Insight
Charles S. Craik, Ph.D., Professor, Pharmaceutical Chemistry, University of California, San Francisco
Fabs that recognize 3D protein conformations against proteins with high conformational entropy and large hetero-oligomeric complexes can enable subnanometer resolution in single particle cryo-electron microscopy. Once engineered, these Fabs can probe
dynamic complex assembly in cells. Examples will be presented where Fabs are accelerating both structural and functional studies of dynamic and complex protein targets to accelerate their understanding and validation as bona fide therapeutic targets.
9:10 Protein Engineering of Phage-Antibody Complexes for Biomarker Detection
Jennifer Cha, Ph.D., Norviel Associate Professor, Chemical & Biological Engineering, University of Colorado, Boulder
This talk will highlight our recent efforts at using protein engineering to build covalent crosslinks between bacteriophage and the Fc portion of monoclonal antibodies. The phage-antibodies are used to target and bind specific analytes while the phage
genome is genetically modified to generate amplified signals in real time with specific primers.
9:40 Bio-Inspired Phage Material Assembly and Applications
Seung-Wuk Lee, Ph.D., Professor, Bioengineering, University of California, Berkeley; Faculty Scientist, Biological
Systems and Engineering, Lawrence Berkeley National Laboratory
I will demonstrate a facile biomimetic process to create functional nanomaterials utilizing M13 phage. A single-step process produces long-range-ordered films showing multiple levels of hierarchical organization. Using the self-assembly processes,
we have created various biomimetic supramolecular nanostructures. The resulting materials show distinctive optical and photonic properties. Through the directed evolution of the phages, I will show how resulting materials can be utilized as functional
nanomaterials for biomedical and biosensor applications.
10:10 Coffee Break
10:45 Chairperson’s Remarks
K. Dane Wittrup, Ph.D., J.R. Mares Professor, Chemical Engineering & Bioengineering, Massachusetts Institute of Technology
10:50 Cytosol-Penetrating IgG Antibody and Its Application for Directly Targeting Disease-Associated Cytosolic Proteins
Yong-Sung Kim, Ph.D., Professor, Molecular Science and Technology, Graduate School; Professor, Applied Chemistry
and Biological Engineering; Director, Pioneer Research Center for iMab, Ajou University
The ability of an IgG-format antibody to reach the cytosol of target mammalian cells from outside of cells is highly desired for diverse purposes. In this talk, I will introduce the cytosol-penetrating antibody, named cytotransmab, and its application
for directly targeting disease-associated cytosolic proteins after systematic administration.
11:20 Precision Delivery of Proteins into the Cytosol of Cells
Bradley L. Pentelute, Ph.D., Pfizer Laubach Career Development Assistant Professor, Chemistry,
Massachusetts Institute of Technology
There are a number of methods to deliver bioactive peptides and proteins into mammalian cells for biotechnological purposes. Most approaches do not allow for routine precision delivery of chemical entities such as mirror image peptides and intrabodies.
Here, we present a macromolecular delivery platform based on an engineered bacterial transport machine that allows for facile delivery of bioactive variants to the cytosol of cells. We show the delivered cargo can disrupt protein-protein interactions
in cancer cells and induce cell death. Further, we show targeted delivery of a RAS/RAP specific protease to pancreatic cells.
11:50 Rapid Screening of Cyclotide-Based Libraries against Intracellular Protein-Protein Interactions
Julio A. Camarero, Ph.D., Associate Professor, Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California
The cyclotide scaffold has a tremendous potential for the development of therapeutic leads based on their extraordinary stability and potential for grafting and molecular evolution applications. We will show an example, where a large cyclotide-based
genetically encoded library was used to screen for low nanomolar inhibitors of the Hdm2-HdmX complex. We will also present different strategies to improve the cellular uptake and pharmacokinetic profiles of bioactive cyclotides.
12:20 pm Further Advancements for Human Antibody Discovery
Vera Molkenthin, Ph.D., Chief Scientist, AbCheck s.r.o.
AbCheck has developed Mass Humanization to generate humanized libraries. This approach utilizes batch cloning of CDR3 immune repertoires from immunized rabbits into selected human frameworks containing specifically diversified CDR1 and CDR2 regions.
For selecting high affinity binders from the resulting, highly diverse library, AbCheck routinely applies Phage or Yeast Display under various conditions. In this talk, AbCheck will present new technological developments regarding its human antibody
discovery and optimization platform.
12:50 Luncheon Presentation I: Antibody Library Display on a Mammalian Virus: Application to both Soluble and Complex Membrane Antigens
Ernest S. Smith, Ph.D., Senior Vice President, Research & Chief Scientific Officer, Vaccinex, Inc.
We have developed an antibody discovery platform that enables efficient expression of a library of antibodies in IgG format on the surface of both a mammalian virus and the cell surface, enabling rapid selection of high quality antibodies. We have
also modified this technology to enable the direct incorporation of multipass membrane proteins into the viral membrane. Antigen expressing virus can be readily purified and used for antibody selection.
1:20 Luncheon Presentation II: The Use of Biosensor Display
Libraries in Antibody Discovery
Paul Kang, CSO, Discovery Research, Innovative Targeting Solutions
Cell-based biosensors are extremely sensitive and can be used to detect a diverse range of biological targets. The presentation will describe the use of V(D)J recombination mediated de novo antibody sequence diversification,
mammalian display and antigen dependent signaling based biosensors to generate a powerful new antibody discovery platform, Biosensor Display. Antibody based cell biosensor libraries will provide unparalleled access to traditionally challenging
multi-pass membrane targets, such as GPCRs and ion channels, in their native environments.
1:50 Session Break
These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout discussion group to join. Each group has a moderator to ensure focused discussions around key issues within
the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not
meant to be a corporate or specific product discussion. Pre-registration to sign up for one of the topics will occur a week or two prior to the Event via the App.
Deep Sequencing in Biological/Ligand Discovery
Ratmir Derda, Ph.D., Assistant Professor, Chemistry, University of Alberta
Table 2: Upstream Bottlenecks - What do we need to improve to turn more hits into leads
Moderator: Johan Rockberg, Ph.D., Assistant Professor, Proteomics and Nanobiotechnology, KTH - Royal Institute of Technology
- Targets
- Libraries adn selection methods
- Novel formats
- Functional screening
- Expression yields, Stability
3:20 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 Chairperson’s Remarks
Gregory A. Weiss, Ph.D., Professor, Chemistry, Molecular Biology & Biochemistry, University of California, Irvine
4:10 Bicycles and Bicycle Drug Conjugates: Next Generation Therapeutics
Sir Gregory Winter, Ph.D., FRS, Master, Trinity College and Co-Founder and Director, Bicycle Therapeutics
Bicycles® are a novel therapeutic class of constrained bicyclic peptides that combine antibody-like affinity and selectivity with small molecule-like tissue penetration, tunable exposure and chemical synthesis. They have potential in many indications,
including oncology, where Bicycles’ unique properties have been used to develop Bicycle Drug Conjugates™ (BDCs); a novel toxin delivery platform which greatly improves toxin loading into tumour tissues. This presentation will describe
both the Bicycle® and BDC platforms.
4:55 Young Scientist Keynote: Programming Proteins by Deep Sequencing and Design
Tim Whitehead, Ph.D., Assistant Professor, Chemical Engineering and Materials Science, Michigan State
University
Next-generation sequencing has presented protein scientists with the ability to observe entire populations of molecules before, during, and after a high-throughput screen or selection for function. My group leverages this unprecedented wealth
of sequence-function information to design and engineer protein affinity, specificity, and function and to infer structural complexes of proteins. My talk will present an overview of the above and detail methodological improvements that
enable the engineering work.
5:40 Welcome Reception in the Exhibit Hall with Poster Viewing
6:55 End of Day
TUESDAY, MAY 2
8:00 am Registration and Morning Coffee
8:25 Chairperson’s Remarks
Jennifer Cochran, Ph.D., Hitachi America Associate Professor, Bioengineering and Chemical Engineering, Stanford University
8:30 Genetically-Encoded Libraries of Chemically-Modified Peptides
Ratmir Derda, Ph.D., Assistant Professor, Chemistry, University of Alberta
Genetically-encoded (GE) libraries of polypeptides are one of the major sources of discovery of biological drugs. They are often limited to handling of structures made of 20 natural amino acids. We use GE-libraries of peptides as a starting
material for multi-step organic synthesis to produce GE-molecules that combine peptide scaffolds with variable, genetically-encoded “unnatural” modifications. These libraries allow attacking unsolved problems in molecular recognition
and discovery of ligands for “undruggable targets” such as carbohydrate binding proteins.
9:00 Reprogramming Immunity with Engineered Interleukin-2 Antibodies
Jamie Spangler, Ph.D., Postdoctoral Fellow, Garcia Lab, Molecular & Cellular Physiology and Structural
Biology, Stanford University School of Medicine
Interleukin-2 (IL-2) is a multi-functional cytokine that regulates immune homeostasis, but its concurrent promotion of both immune effector cells and regulatory T cells has limited its efficacy as an immunotherapeutic. Certain anti-IL-2 antibodies
selectively direct cytokine activity toward particular cell subsets, presenting an exciting opportunity for targeted therapy. We elucidated the molecular mechanisms through which antibodies bias cytokine function and built on our insights
to engineer promising cytokine-targeted antibody therapeutics.
9:30 Synthetic Human Antibody Fragment Libraries for CAR T Cell Therapy
Thomas J. Van Blarcom, Ph.D., Associate Research Fellow, Rinat Laboratories, Bio-Therapeutics
Division, Pfizer Inc.
Unlike most therapeutic antibodies, CAR T cells are typically generated with single chain variable fragment (scFv) antibodies. In this study, we present a human synthetic scFv antibody library that we use to simplify the generation and testing
of large panels of antibodies for use as CAR T cells. The CAR T cells generated from these antibodies had desirable phenotypes and demonstrated robust and specific cytotoxic activity in vitro.
10:00 Coffee Break in the Exhibit Hall with Poster Viewing
10:45 Chairperson’s Remarks
David Lowe, Ph.D., Senior Director, R&D, Antibody Discovery and Protein Engineering, MedImmune Ltd
10:50 Transpo-mAb: Transposon-Mediated B Cell Display and Functional Screening of Full-Length IgG Libraries
Roger R. Beerli, Ph.D., CSO, NBE-Therapeutics AG
Transpo-mAb is a novel and highly efficient non-viral antibody discovery and engineering platform, allowing for the efficient display of full-length antibodies on the surface of B lymphocytes. Due to a built-in switch between surface and secreted
expression, functional screening can be seamlessly integrated into the antibody discovery workflow. Several examples, including the direct identification of mAbs suitable as backbones of antibody drug conjugates, will be presented.
11:20 Chairperson’s Remarks
Andrew M. Bradbury, M.D., Ph.D., Staff Scientist, Biosciences, Los Alamos National Laboratory
11:25 Computational Design and Experimental Validation of Antibodies with Increased Affinity
Roland L. Dunbrack, Jr., Ph.D., Professor, Institute for Cancer Research, Program in Developmental Therapeutics, Fox Chase Cancer Center
We have developed an antibody design computational protocol, implemented in Rosetta, that is based on our clustering of CDR structures (doi:10.1016/j.jmb.2010.10.030). The program replaces CDRs with loops of different lengths and conformations
and performs sequence design on the inserted CDR to improve binding. In benchmarking, we are able recapitulate native antibodies. We have designed new CDRs for two antibodies and were able to increase the experimental binding affinity
2-50 fold.
11:55 Antibody Discovery Using Natural and Nature-Emulating Diversity Libraries
Eunice Zhou, Ph.D., Associate Adjunct Professor, Anesthesia, University of California, San Francisco
Naïve human antibody CDR sequences were collated and used to design non-redundant synthetic CDRs matching the naturally occurring diversities. These synthetic non-redundant CDRs were inserted into the well expressing V-gene frameworks,
and displayed to construct phage Ab library. Such phage Ab library was used to isolate high quality renewable antibodies (rAbs), which are essential reagents for determining how proteins function under normal and pathophysiological
conditions.
12:20 pm Facilitating Novel Antibody Discovery and Engineering with a Membrane-Based Antibody Purification Workflow
Keren Drori, Ph.D., Product Manager II, Protein Science, Takara Bio USA
There is a constant need for faster, more efficient antibody and protein purification processes at any scale. High-capacity membrane technologies allow for purification directly from complex matrices, such as cell supernatants,
in minutes. This new approach also provides highly purified and concentrated antibodies and his-tagged proteins, even from samples containing additives not compatible with other purification technologies. This talk will review
several applications including purification of a GPCR, hybridoma screening, and purifying secreted protein.
12:50
pm Luncheon Presentation: A New Next-Generation Sequencing Analysis Tool for Improved Identification of Peptide and Antibody Ligands
Michael Blank, Ph.D., CSO, Research & Development, AptaIT GmbH
AptaIT’s new desktop software is an intuitive and user-friendly tool enabling the improved identification of B-cell receptors or ligands from biopanning experiments. Individual selection rounds or defined stages of the immune
response, which are digitalized by NGS, can be analyzed at very high resolution. The software provides results in form of comprehensible, interactive graphs and tables and allows a systematic reduction of big data down to a
number of relevant sequences for subsequent experimental testing.
1:20 Ice Cream Break in the Exhibit Hall with Poster Viewing
2:00 Chairperson’s Remarks
David Lowe, Ph.D., Senior Director, R&D, Antibody Discovery and Protein Engineering, MedImmune Ltd
2:05 Mapping the Targets of Antibody Repertoires for Diagnostic and Therapeutic Development
Patrick S. Daugherty, Ph.D., President & CSO, Serimmune Inc.; Adjunct Professor, University of California, Santa Barbara
The functional composition of antibody repertoires, as defined by the collection of unique antigen-epitope binding specificities, remains obscure. The convergence of display library technologies, robust NGS technology, and computational
advances has provided an opportunity to characterize the diversity of antigen epitope binding specificities present within antibody repertoires in health and disease. This digital serology approach provides a new tool to support
diagnostics, vaccine and therapeutic development.
2:35 Bacterial Surface Display for Antibody Engineering and Stratification of Patients
Johan Rockberg, Ph.D., Assistant Professor, Proteomics and Nanobiotechnology, KTH - Royal
Institute of Technology
There is a need for precise classification of responsive patients for their safe and cost-effective treatment. We use bacterial display for structural epitope mapping of the approved drug eculizumab to C5 identifying six residues
essential for binding, some which were present as germlines of non-responding patients. Instead we show potential of another drug (OmCI) for these groups. Personal medicine and antibody engineering using gram-positive display
will be covered.
3:05 High-Throughput Screening for Antibody Discovery Using Mirrorball
Christyne Kane, Ph.D., Senior Scientist, AbbVie Bioresearch Center, Inc.
3:20 High-Fidelity Next-Generation Sequencing of Full Variable Region of Antibody Libraries
Hyoki Kim, Ph.D., President and CEO, Celemics Inc.
NGS-based antibody library analysis faces key issues of sequencing error rate, short read length and need of gene synthesis for binding assay. In this talk, we will discuss our newly developed technology that enables to obtain
accurate read of antibody libraries and provides the corresponding scFv gene for binding assay.
3:35 Refreshment Break in the Exhibit Hall with Poster Viewing
4:25 Next-Generation Sequencing of mRNA Display Selections
Martin Wright, Ph.D., Associate Director, Selection Technologies, Bristol-Myers Squibb
Applications of NGS with mRNA display selection will be discussed. This will include methods to recover low-abundance sequences from a diverse population and additional methods for rapid optimization of antibodies and other polypeptides.
4:55 Hierarchy and Extremes in Selections from Antibody Libraries
Clément Nizak, Ph.D., Research Scientist, Laboratory of Biochemistry, CNRS-ESPCI
Efficient selection requires sufficiently diverse libraries, but merely counting the number of different clones does not fully characterize a library’s selective potential. We analyzed phage display selection outcome
by high-throughput sequencing to quantitatively characterize selective potentials. They follow simple statistical laws, which can be interpreted with extreme value theory, and show a marked hierarchy between libraries.
We provide a quantitative approach to measure the selective potential of a library.
5:25 End of Display of Antibodies
5:30 Registration for Dinner Short Courses
Recommended Dinner Short Course*
SC13: Phenotypic Screening Applications and Technologies - Detailed Agenda
*Separate registration required