2015 Archived Content


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.

The second conference, Structural Analysis, Characterization and Development, explores structural, biochemical and biophysical studies used to understand the behavior of membrane protein targets in native and inhibited or activated states – and then considers issues related to the preclinical and clinical development of antibodies and other biologics as drug products against these challenging targets.

Final Agenda

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Wednesday, September 23

11:30 am Registration

12:55 pm Plenary Keynote Program

2:40 Refreshment Break in the Exhibit Hall with Poster Viewing

3:25 Chairperson’s Opening Remarks

Christopher Koth, Ph.D., Senior Scientist, Structural Biology, Genentech

3:35 Keynote Presentation: Expanding the Genetic Code to Probe Membrane Protein Drug Targets

Thomas P. Sakmar, M.D., Richard M. & Isabel P. Furlaud Professor, Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University

Novel methods are now available to probe GPCRs, channels and other difficult-to-express membrane proteins. A variety of experimental approaches will be presented, including targeted photocrosslinking to map antibody epitopes, and bioorthogonal labeling reactions to introduce site-specific fluorophores and monoclonal antibody epitopes. These strategies can be used in combination with traditional approaches to enhance drug discovery strategies.


4:05 Sodium Channel Structures in Complex with Drugs

Bonnie Ann Wallace, Ph.D., Professor, Institute of Structural and Molecular Biology, Birkbeck College, United Kingdom

Mutations in human sodium channels represent key targets for pharmaceutical drugs. We have shown that drugs that block human sodium channels also block the NavMs sodium channel from Magnetococcus marinus. Using crystallography and computational methods we have determined the locations of channel blockers within the NavMs channel cavity and validated these sites in designed mutants.

Schrodinger4:35 Computational Approaches to Antibody Design: Improvements to the Predictions of Structure, Stability, and Affinity

David A. Pearlman, Ph.D., Senior Principal Scientist & Product Manager, Schrödinger

We discuss computational advances demonstrating significant promise both for improved prediction of antibody structure from sequence, and for the ability to predict the changes in stability and affinity resulting from residue mutations. The Prime approach to de novo loop prediction is an appreciable improvement over previous methods for CDR loop prediction, while substantive improvements to free energy calculations (FEP) allow us to calculate the effects of residue mutations on stability and affinity with high precision.

5:05 Refreshment Break in the Exhibit Hall with Poster Viewing

5:40 Structure of a Human Ion Channel

Christopher Koth, Ph.D., Senior Scientist, Structural Biology, Genentech

6:10 Use of Antibody Fragments to Solve GPCR Structures

Andrew Kruse, Ph.D., Assistant Professor, Biological Chemistry and Molecular Pharmacology, Harvard Medical School

Antibody fragments including Fabs and nanobodies have served as critical enabling tools in studies of GPCR structure, function, and dynamics. I will present an overview of key results using antibody fragments, as well as recent methodological advances and results using antibody fragments to study drug-like allosteric modulator function in the muscarinic acetylcholine receptor family.

6:40 Close of Day

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Thursday, September 24

7:30 am Registration


8:00 Interactive Breakfast Breakout Discussion Groups

This interactive session provides conference delegates and speakers an opportunity to choose a specific roundtable 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.

Targeting Membrane Proteins with Non-Standard IgG Scaffolds

Matthew Gardener, Ph.D., Senior Scientist, Research, MedImmune, United Kingdom

  • Do novel scaffolds represent an advantage over more classical mAbs?
  • Does an understanding of the molecular mechanism of the target provide clues to the best approach?
  • Which is better monovalent or bivalent?
  • Should we be targeting intracellular epitopes with novel scaffolds / approaches?
  • Antibody – drug conjugates for ion channels and GPCRS?

Emerging Technologies for Developing Antibodies Against Multispan Membrane Targets

Matt Holsti, Ph.D., Principal Scientist, Global BioTX Technologies, Pfizer

  • What has been their experience of generating antibodies against these targets to date?
  • What has been the most challenging part of the process?
  • What technologies could increase the probability of success?
  • Recommendations of new approaches to pursue

Membrane Protein Engineering Strategies for Antibody Discovery

Christopher Koth, Ph.D., Senior Scientist, Structural Biology, Genentech

  • Is this worth the effort?  If so, what are some successful strategies to engineer suitable antigens for difficult-to-produce membrane proteins?
  • Engineering tricks to bias towards functional antibodies
  • Strategies and experience using various matrices to stabilize membrane proteins for antibody discovery, i.e. nanodiscs, amphipols, liposomes, etc.
  • Screening strategies that employ engineered membrane proteins

8:45 Chairperson’s Remarks

Benjamin Doranz, Ph.D., President & CSO, Integral Molecular Inc.

8:55 A Back Scattering Interferometry for Characterization of Membrane Protein Targets

Denise M. O’Hara, Ph.D., Associate Research Fellow, Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc.

Molecular interactions govern biology, human health, disease and pharmacological efficacy of therapeutics.  Clinically relevant binding measurements are especially problematic since target proteins reside in complex physiological environments, such as biological fluids or tissue microenvironments as soluble and/or membrane-bound forms.  This talk will describe how Back-scattering Interferometry (BSI), a label-free, low volume, mix-and-read technology has been used to solve measuring physiologically-relevant affinity used to predict clinical dose and efficacy.

9:25 Characterization Studies for ShK Toxin Peptide against Kv1.3

Christine Beeton, Ph.D., Associate Professor, Molecular Physiology and Biophysics, Baylor College of Medicine

CCR7- effector memory T lymphocytes are involved in chronic inflammatory diseases and upregulate Kv1.3 channels upon activation. We have used ShK, a peptide isolated from a sea anemone venom, to design dalazatide (formerly ShK-186) as a selective and potent Kv1.3 blocker.

9:55 Binding Analysis of Membrane Protein Targets with Label-Free Analytical Biosensor

Wei Wang, Ph.D., Senior Scientist, Therapeutic Discovery, Amgen

Using the emerging label-free analytical biosensor system MASS-1, we have been developing binding assays to characterize the binding activity of membrane protein targets. We aim to establish methods that can utilize membrane proteins prepared in various ways and maintain the protein activity. These assays will be applied to validate membrane protein targets and identify therapeutics for drug discovery.

10:25 Coffee Break in the Exhibit Hall with Poster Viewing and Poster Winner Announced

11:10 Strategies for Optimizing and Characterizing MAbs against Multi-Spanning Membrane Protein Targets

Benjamin Doranz, Ph.D., President & CSO, Integral Molecular Inc.

Integral Molecular has developed specialized strategies to systematically optimize and characterize MAbs against structurally complex membrane proteins, addressing the specific challenges posed by this class of targets. These strategies encompass antibody engineering, antibody characterization, and shotgun mutagenesis. MAb optimization and characterization case studies will be discussed.

11:40 Potent and Efficacious Inhibition of CXCR2 Signaling by Biparatopic Nanobodies Combining Two Distinct Modes of Action

Michelle Bradley, Ph.D., former Investigator, Molecular Pharmacology, Respiratory Disease Area, Novartis Institutes for Biomedical Research (NIBR), United Kingdom

Chemokine receptors are key modulators in inflammatory diseases. We describe the identification and pharmacological characterization of nanobodies selectively blocking CXCR2. Two classes of selective monovalent nanobodies were identified, and detailed epitope mapping showed that these bind to distinct, non-overlapping epitopes on the CXCR2 receptor. Biparatopic nanobodies were generated by combining nanobodies from these two classes.

Crystal Bioscience12:10 pm Diverse Antibody Panels to GPCRs and Ion Channels Generated through Single B Cell Cloning from Avian Immune Repertoires

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

Chickens are known to generate antibodies to epitopes on therapeutic targets that are highly conserved amongst mammals. These antibodies often demonstrate reactivity across multiple species, and are preferred when rodent or primate models of disease are anticipated. Using alternative immunization strategies we can enhance the prevalence of such clones, and by evaluating antibody profiles through a multi-parameter GEM screen of primary B cells, we can efficiently recover antibodies with desired biological activity and/or multispecies cross-reactivity.

AbCellera12:40 High-Throughput Antibody Discovery against Challenging Targets from Immune Repertoires Using a Microfluidic Platform

Kevin Heyries, Ph.D., Co-Founder & Senior Scientist, AbCellera Biologics Inc.

AbCellera has developed a microfluidic-based platform for the selection of monoclonal antibodies from single antibody secreting cells. This technology enables the selection of panels of antibodies against challenging targets from different natural immune repertoires at a throughput of 1,000,000 cells per run using binding, specificity and functional cellular assays.

12:55 Session Break

Antibody Solutions1:00 Luncheon Presentation: Strategies for Discovery of Therapeutic Antibodies to Difficult Membrane Proteins

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

Some membrane protein targets, including proteins with high homology, G-protein-coupled-receptors (GPCRs), Ion Channels, and Multicomponent Receptor complexes present unique challenges in the generation of specific, high-affinity, and functional antibodies. Each target requires a tailored approach based upon the nature of the target and the desired characteristics of the antibody. Strategies for antigen design, antibody generation, and screening of antibodies to difficult membrane proteins, and results obtained will be presented.

1:40 Refreshment Break in the Exhibit Hall with Poster Viewing


2:15 Chairperson’s Remarks

Michelle Bradley, Ph.D., former Investigator, Molecular Pharmacology, Respiratory Disease Area, Novartis Institutes for Biomedical Research (NIBR), United Kingdom

2:20 Development of Antibody Therapeutics to TrpA1

Ki-Jeong Lee, Ph.D., Principal Scientist, Genome Analysis Unit, Amgen

To generate therapeutic antibodies to TRPA1, we immunized mice with a variety of antigens, cells, plasmid and recombinant adenoviral vector, expressing TRPA1 channels. Antibodies that bind TRPA1 channels were screened by a flow cytometry assay utilizing U2OS or CHO cells stably expressing TRPA1. The purified IgGs were evaluated for antagonism in agonist-induced 45Ca2+ uptake assays using CHO-TRPA1 cells. Antibodies to TRPA1 act as antagonists of multiple modes of TRPA1 activation.

2:50 Antibody Discovery against Multipass Membrane Proteins Directly on the Cell Surface

Vaughn V. Smider, M.D., Ph.D., Assistant Professor, Cell and Molecular Biology, The Scripps Research Institute

Multipass membrane proteins like GPCRs and ion channels are challenging targets for antibody discovery. We use a spatially addressed germline IgG library to screen GPCR targets directly on the cell surface. Pharmacologically active hits can then be functionally matured using small-directed libraries.

3:20 Session Break

3:30 Ligand-Directed Targeting and Molecular Imaging Based on in vivo Phage Display

Renata Pasqualini, Ph.D., Professor, Internal Medicine, Maralyn S. Budke Endowed Chair in Cancer Experimental Therapeutics, Associate Director, Translational Research; Chief, Division of Molecular Medicine, University of New Mexico

Systematic implementation of in vivo phage display enables subsequent identification of tissue-specific receptors to generate a comprehensive map of molecular markers in each organ or tissue, and reveals mechanistic insights related to disease-specific protein biomarkers. Recent updates on ligand-directed targeting of multiple payloads such as cytotoxics, gene therapy vectors, nanoparticles, and imaging agents are discussed.

4:00 GPCR Antibody Discovery Using Whole Cell Selection and Informatics

Cory Ahonen, Scientist, Antibody Discovery, Adimab LLC

Discovery and optimization of antibodies against membrane protein targets, such as GPCR, is a well-known challenge. Use of whole mammalian cells as a source of antigen for human antibody discovery will be described as a case study. Next generation sequencing enables a comprehensive assessment of the enriched binding population and provides complementary information to mAb characterization.

4:30 Identification of Epitopes for the Development of Selective, Functional Antibodies Targeting Sodium Ion Channels

Gregory Babcock, Ph.D., Executive Director, Research, Visterra, Inc.

We have modeled and interrogated the structure of a specific ion channel and applied molecular dynamics and network analysis. By supplementing this with empirical data we attempt to identify novel epitopes for selectively targeting ion channels for inhibition of activity. We apply these methods to design antibodies that target the identified epitopes on specific ion channels and validate antibody function using in vitro models.

5:00 Close of Conference

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