As the pharmaceutical and biotech industries increasingly shift attention to biologics, much more attention is being paid to the prospect of membrane-bound proteins as drug targets for antibodies and other protein scaffolds. For the large GPCR and ion channel target classes, biologics offer improved selectivity, an alternative for targets with known function that have not been amenable to small molecule drugs and the potential for using antibodies for the targeted delivery of therapeutics. However, for the field to advance, fundamental challenges in optimizing antigen quality and presentation, discovery methodologies, protein engineering and target identification must be resolved.

This two-part meeting provides a forum in which discovery biologists and protein engineers can come together to discuss next-generation strategies and technologies that will allow antibody- and alternate scaffold-based therapeutics directed against these target families to advance into the clinic and beyond.

Part One:
The first meeting in the set, The Discovery Workflow, offers an examination of state of the art approaches for the expression of high quality membrane protein antigens and antibody generation, then explores selection and screening strategies that can be applied to discover binders with functional activity against GPCR and ion channel targets.

Final Agenda

Day 1 | Day 2 | Download Brochure

Tuesday, September 26

7:00 am Registration Open and Morning Coffee

8:00 Welcome Remarks

Kent Simmons, Senior Conference Director, Cambridge Healthtech Institute

8:05 Chairperson’s Opening Remarks

Jonas Lee, Ph.D., Scientist, Membrane Protein Purification, Amgen

8:10 KEYNOTE PRESENTATION: Prospects and Perspectives for Biotherapeutic Discovery against GPCRs, Channels and Transporters

Partha Chowdhury, Ph.D., Senior Director and Head, Antibody Discovery, Sanofi Genzyme

GPCRs, ion channels and transporters are a big part of the human proteome and linked with many diseases. Not counting the anti-infectives, over 35% of approved drugs are targeted to these classes of proteins and are exclusively small molecules. In recent times there has been a precipitous drop in discovery of these drugs. The challenges behind this open an opportunity for biologics development against GPCRs, ion channels, transporters and other MSMs.

GENERATION AND OPTIMIZATION OF MEMBRANE PROTEIN ANTIGENS

8:40 Isolation of Membrane Proteins into SMA Lipid Particles (SMALPs)

Tim Dafforn, Ph.D., Professor, Biotechnology, University of Birmingham, United Kingdom

In 2009, we developed an entirely detergent-free method (SMALPs) that allows the generic extraction and study of membrane proteins without removing them from their native lipid environment. In our current work, we have examined structure and function of SMALP solubilized proteins using techniques that include X-ray crystallography, Cryo-electron microscopy and small angle X-ray and neutron scattering. Together these approaches produce unique insights into the membrane protein function in the presence of the native lipid environment.

9:10 Customized Cell-Free Production of Membrane Proteins

Erik Henrich, Researcher, Institute of Biophysical Chemistry, University of Frankfurt, Germany

Cell-free synthetic biology provides new platforms for the efficient production of pharmaceutically relevant membrane proteins such as enzymes, transporters or GPCRs. Adjusting and refining artificial hydrophobic expression environments is a prerequisite for the functional folding of cell-free synthesized membrane proteins. We demonstrate synergies of nanoparticle technologies and cell-free systems as well as the importance of systematic lipid screening for the generation of high quality samples of even difficult membrane proteins.

9:40 Grand Opening Coffee Break in the Exhibit Hall with Poster Viewing

10:25 Production of Membrane Protein Targets in Yeast Pichia pastoris by Auto-Induction

Jonas Lee, Ph.D., Scientist, Membrane Protein Purification, Amgen

Membrane proteins are important therapeutic targets, but they are challenging to produce in large scale. We produced mg scale of human membrane proteins for drug screening and phage display using yeast Pichia pastoris. To overcome challenges of low expression level and cumbersome expression protocol in Pichia, we invented an auto-induction method by exploiting the properties of an AOX1 promoter to maximize expression level per cell mass to improve protein purity.

10:55 Nanodiscs for Structural and Functional Studies of Membrane Proteins

Stephen G. Sligar, Ph.D., Swanlund Chair and Director, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign

Membrane proteins make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists. The Nanodisc platform provides a self-assembled system that renders typically insoluble yet biologically and pharmacologically significant targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media. I will present the latest discoveries and applications enabled by Nanodiscs.

11:25 Production of Monoclonal Antibodies against GPCRs Using Cell-Free Synthesized GPCR Antigen

Hiroyuki Takeda, Ph.D., Associate Professor and Principal Investigator, Division of Protea-Drug-Discovery Sciences, Proteo-Science Center, Ehime University, Japan

Production of high quality and large amounts of recombinant GPCR antigen is one of the bottlenecks of antibody development against GPCR. Recently we developed a large-scale GPCR expression method using wheat cell-free system and liposome. Using our bilayer-dialysis method, several mg of GPCRs can be synthesized efficiently in a short time with a high success rate. I will report recent antibody development results demonstrating the performance of cell-free synthesized liposomes as antigens.

11:55 Generation of Antibodies to Difficult Membrane Protein Targets

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

Multi-pass trans-membrane and multimeric membrane proteins are challenging targets for antibody generation. Results for a multi-pass heteromeric amino acid transporter and other difficult membrane protein targets will be presented to show the key elements of an antibody discovery platform.

 12:10 pm AptaAnalyzer™ - A New NGS Analysis Tool for Improved Identification of Peptide and Antibody Ligands

Michael Blank, Ph.D., CSO, AptaIT GmbH

AptaAnalyzer™ is an intuitive software tool enabling the improved identification of ligands from biopanning experiments or of B-cell receptors derived from defined stages of the immune system. AptaAnalyzer™ enables archiving of experiments as well as improved identification and optimization of rare but relevant peptide or antibody ligands.

12:25 Session Break

12:35 Luncheon Presentation: Optimization of Membrane Protein Antigens for Antibody Discovery

Benjamin Doranz, Ph.D., President and CEO, Integral Molecular

Membrane proteins often represent challenging antigens for antibody discovery due to their low expression, structural complexity, and toxicity. We have developed a multi-tiered strategy to improve cell-surface protein expression and conformational stability. In addition to conventional optimization methods to improve protein trafficking, we employ a proprietary high-throughput mutagenesis strategy, using arrays of point mutations, engineered disulfide bonds and chimeras. Case studies will be presented for successfully engineered antigens that yielded high-affinity antibodies against native targets.

1:15 Refreshment Break in the Exhibit Hall with Poster Viewing

Antibody Generation

1:50 Chairperson’s Remarks

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

1:55 Generating Functional Antibodies against GPCRs and Ion Channels

Trevor Wilkinson, Ph.D., Associate Director, Antibody Discovery and Protein Engineering, MedImmune, United Kingdom

Structurally complex membrane proteins such as GPCRs and ion channels are acknowledged as challenging targets for monoclonal antibody discovery. Strategies for the discovery of functional antibodies to these target classes are emerging. In this presentation, we will provide an overview of these emerging strategies and provide a number of case studies highlighting the discovery and optimization of antibodies against GPCRs and ion channels.

2:25 Strategies and Technologies for Antibody Discovery without Purified Protein

Jane Seagal, Ph.D., Senior Scientist, Biologics Generation Group, AbbVie Bioresearch Center

Lack of purified antigens is a limiting factor for antibody discovery against multi-spanning proteins. In this talk, enabling approaches (cell lines, membrane extracts, or peptides mimicking extracellular loops and cDNA immunizations) and orthogonal screening assays for the discovery of functional antibodies against challenging targets are discussed.

2:55 HuMab Chickens: The Next Generation Antibody Discovery Platform

Bill Harriman, Ph.D., CSO, Crystal Bioscience

Transgenic rodents producing human sequence antibodies are widely accepted as a reliable source of therapeutic candidates. However, their repertoires are limited by their evolutionary similarity to humans. Crystal Bioscience has expanded the repertoire of transgenic animals by engineering HuMab chickens producing fully human sequence, high affinity mAbs. In addition to revealing novel epitopes and, therefore novel IP, the Crystal Platform yields mAbs recognizing murine orthologs of human antigens that facilitate pre-clinical studies.

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing and Poster Competition Winner Announced

4:05 Generating Ion Channel Blocking Antibodies by Fusing Cysteine-Knot Miniproteins into Peripheral CDR Loops

John McCafferty, Ph.D., CEO, IONTAS, United Kingdom

Cysteine-knot miniproteins (knottins) have potential as therapeutic agents to block proteases and ion channels but suffer from manufacturing difficulties, short half-lives and a lack of specificity. We demonstrated that functional knottins can be inserted into peripheral antibody CDRs via short linkers while allowing additional contribution of binding from the remaining CDRs. The resulting “knotbody” retains the advantage of blocking activity from the knottin while enjoying extended half-life and additional specificity conferred by the antibody molecule.

4:35 Selection and Design of Agonist Antibodies to Receptor Tyrosine Kinases

Peter S. DiStefano, Ph.D., CSO, Zebra Biologics, Inc.

Recent technologies have allowed the selection of both agonist and antagonist antibodies to a variety of cell surface receptor types using large combinatorial antibody libraries infected into sensitive reporter cells bearing the receptor of interest. We have utilized this strategy to identify agonists to specific members of the receptor tyrosine kinase (RTK) family of cell surface receptors. Agonist antibodies can be identified with potent activity and selectivity.

5:05 Interactive Breakout Discussion Groups

Join a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic. Details on the topics and moderators are below. Please click here for full details on all breakouts.

Making Cell-Free Accessible – Expanding Protein Production Opportunities

Moderator: Erik Henrich, Researcher, Institute of Biophysical Chemistry, University of Frankfurt, Germany 

• Setting up cell-free expression systems
• Hydrophobic expression environments
• Tailored expression conditions
• Toolbox of additive libraries: ligands, co-factors, inhibitors, etc.

In Vitro Binder Selections vs. Immunization Strategies for Membrane Protein Targets

Moderator: Pascal Egloff, Ph.D., Postdoctoral Researcher, Markus Seeger Group, Institute of Medical Microbiology, University of Zurich, Switzerland 

• Synthetic libraries and natural scaffolds
• Target quality and selection biases
• Importance of NGS for selections
• State-specific binders

Selection of Target-Specific Antibodies

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

• Antibody discovery using B cell selection
• Integration of NGS into antibody discovery
• Functional screening methodologies
• Selecting for epitope diversity vs. affinity

6:05 Welcome Reception in the Exhibit Hall (Sponsorship Opportunity Available)

7:10 Close of Day

Day 1 | Day 2 | Download Brochure

Wednesday, September 27

7:30 am Registration Open and Morning Coffee

Selection of Target Specific Antibodies

8:00 Chairperson’s Remarks

Andrew Bradbury, M.D., Ph.D., Chief Scientific Officer, Specifica Inc.

8:05 Strategies to Identify Rare Functional Antibodies against Membrane Proteins

JT Koerber, Ph.D., 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. Numerous factors including antigen format, immunization or phage panning methods, and complex high-throughput functional screening methods limit the success of antibody discovery. I will discuss a new platform to enable efficient mining of antibodies that bind a membrane protein to identify rare functional clones.

8:35 Antibodies to Challenging Receptor Targets through NGS and Cell-Based Antibody Phage Panning

John Wheeler, Principal Research Scientist, Janssen BioTherapeutics

Several receptor targets cannot be made as soluble proteins and others are problematic for discovery of antibodies that bind to native protein conformations. Cell-based phage panning can identify antibodies to such targets, but is inefficient, often producing low antibody diversity. We utilized next generation sequencing to improve the robustness of cell-based selections. We have thus identified large panels of diverse antibody sequences to several difficult receptor targets.

9:05 Functional Therapeutic Antibody Discovery for Challenging Targets by Single-B-Cell Screening in Nano-Droplets

Roshan Kumar, Cambridge Site Head, HiFiBiO, Inc.

We present CelliGO, an integrated process for rapidly identifying functional therapeutic antibodies from immune repertoires, combining phenotypic screening of single B-cells by droplet-based microfluidic cell sorting with genotypic recovery of barcoded antibody sequences. This technology opens up new possibilities for the discovery of functional antibodies modulating challenging targets.

9:20 Antibody Protein de novo Sequencing with LC-MS/MS

Mingjie Xie, MSc, MBA, Co-Founder and CEO, Rapid Novor, Inc.

Many applications in antibody engineering require the direct sequencing of antibody proteins. At Rapid Novor (rapidnovor.com) we have developed a robust workflow and routinely sequenced antibody proteins. Here we share the success experiences, examine common mistakes novices make, and present our practices to ensure the correctness of every amino acid.

9:35 Coffee Break in the Exhibit Hall with Poster Viewing

10:20 A Novel Approach to Overcome Common Binder Selection Biases for Challenging Targets

Pascal Egloff, Ph.D., Postdoctoral Researcher, Markus Seeger Group, Institute of Medical Microbiology, University of Zurich, Switzerland

NestLink is a novel selection technology that enables protein characterization within large pools of candidate molecules in the absence of genetic information. It allows for novel selection pressures beyond binding and for unbiased characterization of thousands of individual pool members in one single experiment. The technology is particularly beneficial for binder development against challenging membrane proteins and it paves the way for a paradigm shift in biopharmaceutical drug delivery testing.

10:50 How Big are Antibody Libraries Really? And Are We Accessing the Full Diversity?

Andrew Bradbury, M.D., Ph.D., Chief Scientific Officer, Specifica Inc.

In vitro antibody libraries have been used to generate antibodies against many different therapeutic lead targets. Theoretical and experimental analyses indicate that for a library with a diversity of 1e7, one would expect to select 1-3 antibodies. While this tends to be true for small libraries, or library subsets, this estimate does not appear to scale to larger libraries with diversities estimated to be >1 billion, suggesting that libraries are not as diverse as thought, or selection methods do not tap the full diversity.

11:20 Enjoy Lunch on Your Own

12:35 pm Plenary Keynote Program

(click here for details)

2:00 Refreshment Break in the Exhibit Hall with Poster Viewing

2:45 Close of Conference

Please click here to continue to the agenda for Antibodies Against Membrane Protein Targets Part Two

Day 1 | Day 2 | Download Brochure