2017 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. 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 Two:
The second conference, Structural Analysis, Characterization and Biopharmaceutical Development, explores new developments in structural biology and characterization assays used to support research against these challenging targets. This segment then examines progress in biotherapeutic development for GPCR, ion channel and transporter targets, with emphasis on overcoming challenges that have impacted the progress of past programs from development into the clinic.
Final Agenda
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Wednesday, September 27
11:50 am Conference Registration Open
12:35 pm Plenary Keynote Program
(click here for details)
2:00 Refreshment Break in the Exhibit Hall with Poster Viewing
2:45 Welcome Remarks
Kent Simmons, Senior Conference Director, Cambridge Healthtech Institute
2:50 Chairperson’s Opening Remarks
Dana Lord, Ph.D., Scientist, Sanofi-Genzyme
2:55 KEYNOTE PRESENTATION: State of the Science: Tools for Structural Studies of Membrane Protein Targets
Thomas P. Sakmar, M.D., Richard M. & Isabel P. Furlaud Professor, Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University; Guest Professor, Karolinska Institute, Sweden
Novel methods, including time-resolved X-ray crystallography and high-resolution molecular microscopy, often in combination with computational molecular dynamics simulations, are providing new insights about how membrane proteins really work. Developing biotherapeutics or small molecule drugs increasingly requires a multidisciplinary team effort to apply both new and traditional approaches to enhance pre-clinical drug discovery efforts. My goal is to provide an up-to-date critical summary of some new single-molecule drug discovery tools.
3:25 Large Scale Determination of Previously Unsolved Protein Structures Using Evolutionary Information from Metagenomic Sequence Data
Sergey Ovchinnikov, Biologist, Baker Lab, Institute for Protein Design, University of Washington
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We generate models for 614 protein families, of which 206 are membrane proteins.
3:55 Computational Approaches to Antibody Engineering: Advances in Modeling Liabilities
Christopher Negron, Ph.D., 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. Thus we describe computational workflows for identifying and removing liabilities such as aggregation propensity. Beyond this, we will discuss tools such as FEP, that can be used to maintain affinity and stability during the optimization of other "drug-like" properties.
4:25 Refreshment Break in the Exhibit Hall with Poster Viewing
5:00 Structure and Function of Chemokine Receptors
Martin Gustavsson, Ph.D., Post-Doctoral Scholar, Handel Lab, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
Chemokines are small, secreted proteins that interact with G protein coupled chemokine receptors in the cell membrane to drive cell migration and regulate a number of physiological processes. I will present our recent advances in understanding the structure, dynamics and function of chemokine receptors using x-ray crystallography in combination with other biophysical and biochemical methods.
5:30 Implementation and Application of Internal Cryo-EM Lab for Support of Membrane Protein Research
Claudio Ciferri, Ph.D., Senior Scientist, Structural Biology, Genentech
Recent breakthroughs in cryo-EM enabled atomic resolution structure determinations of several proteins including integral membrane proteins. At Genentech, we are establishing a state-of-the-art cryo-EM group to support small and large molecule drug discovery as well as basic research projects, with a particular focus on membrane proteins. In my talk, I will present the workflow we established to enable structure determination of our membrane protein targets in lipid bi-layer environment.
6:00 The Peptidisc for Trapping Membrane Proteins in Water-Soluble Nanoparticles
Franck Duong, Ph.D., Professor, Biochemistry, University of British Columbia, Canada
Purified membrane proteins are insoluble without detergents, adding difficulty to antibody production and protein crystallisation. We present the Peptidisc for their facile capture into water-soluble nanoparticles. Unlike the Nanodisc, which requires scaffold proteins of different lengths and precise amounts of exogenous lipids, the peptidisc just requires a short bi-helical peptide and no lipids. We show the effective reconstitition of 5 different membrane protein systems using ‘on-column’, ‘on-gel’, and ‘on-beads’ methods.
6:30 Close of Day
6:30 Dinner Short Course Registration
Click here for details on short courses offered.
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Thursday, September 28
7:30 am Registration Open
8:00 Interactive Breakout Discussion Groups with Continental Breakfast
Grab a cup of coffee and 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.
Emerging Methods for Expression and Reconstitution of GPCRs
Moderator: Scott R. Prosser, Ph.D., Professor, Chemistry and Biochemistry, University of Toronto, Canada
- E. coli - challenges with GPCRs
- Yeast - opportunities and developments
- Purification, extraction, reconstitution
- Micelles versus HDLs versus liposomes
- Biosynthetic labeling and the use of isotopes
- Insect cells & HEK cells - efficiencies and opportunities
Characterization of Antibodies Against Membrane Proteins
Moderator: Joseph Rucker, Ph.D., Vice President, Research and Development, Integral Molecular, Inc.
- Affinity and Kinetics: Useful approaches for characterizing antibody binding; interpreting complex binding.
- Epitopes: Different techniques for epitope mapping; binning versus mapping; does epitope matter?
- Cell Function: Integrating functional assays into antibody discovery and development; ion channel assays beyond electrophysiology.
- Endocytosis: What are the best approaches for measuring antibody endocytosis? Recycling versus degradation.
9:00 Chairperson’s Remarks
Joseph Rucker, Ph.D., Vice President, Research and Development, Integral Molecular, Inc.
9:05 Biophysical Characterization of Conformational States Accompanying GPCR Activation
Scott R. Prosser, Ph.D., Professor, Chemistry and Biochemistry, University of Toronto, Canada
The spectroscopic characterization of GPCRs reveals a complex conformational landscape, which responds to ligands, allosteric agents, and environmental factors. This ensemble description allows us to consider mechanistic concepts in light of well-known pharmacological phenomena including basal activation, inverse agonism, efficacy, biased signaling, and pre-coupling. Recent studies of the adenosine A2A receptor, a prototypical class A GPCR, will be presented and discussed in terms of consequences to drug discovery in GPCRs.
9:35 Mass Spectrometric Analysis of Membrane Proteins and Complexes in Biopharma
Iain Campuzano, Ph.D., Principal Scientist, Amgen
Membrane proteins make up approximately 50% of possible “druggable” targets, making them very attractive molecules for many research groups. Herein we will demonstrate how native mass spectrometric techniques are currently being used to determine membrane protein molecular weight and subunit stoichiometry. We will also demonstrate how the phospholipid number can be accurately derived for empty nanodisc particles. Finally, a UPLC-MS based method for accurate molecular weight determination will also be discussed.
10:05 Biophysical and Functional Characterization of GPCR Antagonistic Antibodies Raised in Chicken
Jennifer Könitzer, Ph.D., Research Investigator, Immuno-Oncology Large Molecule Discovery, Bristol-Myers Squibb
Antagonizing the glucose-dependent insulinotropic polypeptide receptor GPCR (GIPR) may open up new therapeutic modalities in the treatment of diabetes and obesity. The receptor is highly conserved between rodents and humans, which has contributed to previous rodent immunization campaigns generating very few usable antibodies. Switching the immunization host to chicken enabled the generation of a large and diverse panel of monoclonal antibodies containing 172 unique sequences.
10:35 Coffee Break in the Exhibit Hall with Poster Viewing and Poster Competition Winner Announced
11:20 Structure-Based Engineering to Restore High Affinity Binding of an Isoform-Selective Anti-TGFβ1 Antibody
Dana Lord, Ph.D., Scientist, Sanofi-Genzyme
One problem during antibody generation is the loss of antigen binding affinity during the scFv to IgG conversion. We use binding, potency, and structural biology experiments to show that this can be attributed to decreased conformational flexibility of the IgG elbow region. This study demonstrates the necessity of structural and functional re-examination when converting scFv to IgG molecules and highlights the potential of structure-based engineering to produce fully functional antibodies.
11:50 Joining Forces: Epitope Mapping and Structural Characterization of a Bispecific Antibody
Linda Kaldenberg-Hendriks, Scientist, Merus, The Netherlands
MCLA-128 is a human bispecific IgG targeting HER2 and HER3 that potently inhibits HRG-driven proliferation of HER2-amplified cancer cells. We have performed epitope mapping studies and generated high-resolution crystal structures for both arms of this bispecific antibody and their targets, as well as solution-state small-angle X-ray scattering data for the MCLA-128:HER2:HER3 complex. The resulting data were used to create a model for the unique mode of action of MCLA-128.
12:20 pm Sponsored Presentation (Opportunity Available)
12:50 Session Break
1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:50 Refreshment Break in the Exhibit Hall with Poster Viewing
2:35 Chairperson’s Remarks
Catherine Hutchings, Ph.D., Independent Consultant, United Kingdom
2:40 Erenumab, an Anti-CGRP Receptor Antibody for Migraine Prevention
Cen Xu, Ph.D., Scientific Director, Neuroscience Drug Discovery, Amgen
Generation of antagonist antibodies against the heterodimeric GPCR CGRP receptor is challenging due to the complex structure of the target. Erenumab (AMG 334) was created using a novel antigen that was designed based on the knowledge of how CGRP interacts with its receptor. This highly potent and selective antagonist antibody has now demonstrated efficacy in clinical studies for the prevention of episodic and chronic migraine.
3:10 Progress on the Development of Antibody Therapeutics against GPCR Targets
Catherine Hutchings, Ph.D., Independent Consultant, United Kingdom
G protein-coupled receptors (GPCRs) represent one of the most important target classes for therapeutic drug discovery across a wide range of diseases. The progress made by targeting GPCRs with antibody-based therapeutics will be reviewed outlining the breadth and diversity of antibody molecules and target opportunities in R&D and the clinical pipeline, including recent development to the expansion of opportunities afforded by next-generation modalities.
3:40 Session Break
3:55 Engineered Peptides Targeting Ion Channels in Pain and Immunology
Ronald Swanson, Ph.D., Senior Director, Janssen
Animal venoms are a rich source of pharmacologically active peptides including ion channel blockers. However, properties such as the affinity, specificity, extended half-life, and manufacturability often must be engineered into the molecules. We have engineered scorpion peptides active against Kv1.3 to address the role of this channel in models of immune disease as well as spider toxin peptides active against Nav1.7, a target of high interest for pain.
4:25 Structure-Based Strategy to Develop Therapeutic Antibodies against Nav 1.7 for Pain
Luke Robinson, Ph.D., Principal Scientist, Research, Visterra, Inc.
Ion channels remain a challenging class of targets to generate functional antibodies. Using our HeirotopeTM platform, an atomic network-based approach, we have incorporated a structure-guided approach to the discovery of antibodies targeting Nav1.7. We have engineered proteins to represent conformational and functionally relevant target epitopes of this channel. Application of these engineered proteins coupled with high-gain experimental methods, including droplet microfluidics, toward the discovery of therapeutic antibodies will be discussed.
4:55 Close of Conference
Please click here to visit the agenda for Antibodies Against Membrane Protein Targets Part One
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The quick brown fox jumps over the lazy dog.