Cambridge Healthtech Institute’s Inaugural

Targeting Complex Membrane Proteins

Biophysical Techniques, Structure-Based Drug Design and Other Advances

April 4-5, 2018 | Hilton Bayfront | San Diego, California

Proteins that span the cellular membrane several times such as ion channels, transporters and G-protein coupled receptors, play important physiological roles and are therefore often the target for potential therapeutics. Many antidepressants, pain medications, and diabetes drugs for example, achieve their effect via complex membrane proteins. These therapeutics, however, were generally discovered without detailed structural knowledge of the membrane proteins on which they act. Membrane-embedded proteins are notoriously difficult to purify for structural studies which, in turn, impedes rational drug design. However, advances in membrane protein purification, an increase in the number of x-ray crystal structures for various complex membrane proteins, and the advent of better biophysical tools that facilitate the study of proteins while in the membrane, are enabling progress in the area of rational drug design against this target class. This meeting gathers leading researchers in the field to discuss advances in studying complex membrane proteins and explore the impact of the new findings on drug discovery.

Final Agenda

Wednesday, April 4

12:30 pm Registration

12:45 Dessert Break in the Exhibit Hall with Poster Viewing

STRUCTURE-BASED DESIGN FOR COMPLEX MEMBRANE PROTEINS

1:30 Welcome Remarks

Anjani Shah, PhD, Conference Director, Cambridge Healthtech Institute

1:35 Chairperson’s Opening Remarks

Sid Topiol, PhD, CSO, 3D-2drug, LLC; New Jersey Institute of Technology

1:40 FEATURED PRESENTATION: Structure, Activation and Inhibition of Chemokine Receptors

Tracy M. Handel, PhD, Professor and Chair, Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, School of Medicine, University of California, San Diego

Chemokine receptors and their endogenous protein ligands are key to the etiology of many inflammatory diseases. Preclinical studies have demonstrated the therapeutic potential of many chemokine receptors, yet successful drug discovery has been slow with only two FDA-approved small molecule drugs. Fortunately, recent structural information should reverse this trend. In this presentation, our current understanding of the structure and activation mechanisms of chemokine receptors by chemokines, and strategies for receptor inhibition with small molecules, will be summarized.

2:10 The Shifting Landscape of Structure-Based Drug Design through Developments in Cryo Electron Microscopy

Stephen Muench, PhD, Assistant Professor, Department of Membrane Biology, School of Biomedical Sciences, University of Leeds

Membrane proteins represent over 30% of the genome and make up ~60% of therapeutic targets. However, despite their importance, our structural and biochemical understanding is still lacking. This talk will detail how new developments in electron microscopy and extraction methodologies have opened up new opportunities for studying membrane proteins and driving therapeutic design. In particular, it will discuss how we are now driving drug design through electron microscopy on a range of membrane protein targets.

2:40 Solute Carrier Transporters: An Emerging Drug Target Class

Alan Wickenden, PhD, Scientific Director, Discovery Sciences, Janssen Research & Development, LLC

3:10 Late Breaking Presentation:A Pocketome-Based Approach to Unlock Therapeutic Targets of the Future
Gerard Rosse, PhD, formerly Associate Director, Structure-Guided Chemistry, Dart Neuroscience LLC

3:40 Refreshment Break in the Exhibit Hall with Poster Viewing

ALLOSTERIC MODULATION AND BIASED SIGNALING: NOT JUST FOR GPCRs?

4:30 Allosteric Modulation in and by Transporters of GPCR Ligands

Sid Topiol, PhD, CSO, 3D-2drug, LLC; New Jersey Institute of Technology

Allosteric modulation of protein action has become increasingly more sought after as a means to achieve advantageous features such as ligand selectivity and tone. For endogenous amine GPCRs, these attributes are effectively achieved via independent proteins such as the SERT transporter. Recent X-ray structural reports for dDAT and hSERT elucidate the structural basis for drug binding at these targets. Further, the transporters themselves offer allosteric sites which are shown to enrich drug discovery opportunities.

5:00 Signaling Bias across Receptor Classes

Brian J. Arey, PhD, Director, Mechanistic Pharmacology, Leads Discovery and Optimization, Bristol-Myers Squibb Co.

Signaling bias, or functional selectivity, of GPCRs is now a well-accepted phenomenon. With growing access to crystal structures of GPCRs in liganded and un-liganded states, we have begun to get a clearer picture of the conformational rearrangements that give rise to activation/selectivity in receptor signaling. However, understanding of signaling bias as it relates to other receptor classes has not been thoroughly addressed. This presentation will discuss commonalities that occur in activation of receptors across receptor classes that suggest this phenomenon is not restricted to GPCRs.

6:15 End of Day

6:30 Dinner Short Courses*

*Separate registration required

Thursday, April 5

8:00 am Breakfast Presentation: Improvements in NMR Approaches to Fragment Based Screening

Donna Baldisseri, Senior Applications Scientist, Bruker BioSpin

FBDD is a powerful search engine for identification of fragments that bind to disease relevant target proteins ultimately leading to drug candidates. NMR-based FBDD screening requires compound library validation, preparation of hundreds of samples per campaign, automated acquisition, processing of thousands of spectra, and their analysis for binding assessment. Here is described the streamlined solutions offered by Bruker, automating this pipeline to improve the speed and productiveness of FBDD screening for the pharmaceutical industry.

8:45 Plenary Session Welcome Remarks from Event Director

Anjani Shah, PhD, Conference Director, Cambridge Healthtech Institute

8:50 Plenary Keynote Introduction

Chris Petersen, CTO, Scientist.com

8:55 PLENARY KEYNOTE: Targeting Ras and MYC for the Treatment of Cancer

Stephen Fesik, PhD, Professor of Biochemistry, Pharmacology, and Chemistry, Orrin H. Ingram II Chair in Cancer Research, Vanderbilt University School of Medicine
Two of the most important targets in cancer are Ras and MYC. However, both of these highly validated cancer targets are thought to be undruggable. In this presentation, I will discuss our approaches for targeting both of these proteins directly and indirectly using fragment-based methods and structure-based design.

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

NEW DRUG DISCOVERY APPROACHES FOR ION CHANNEL AND TRANSPORTERS

10:40 Chairperson’s Remarks

Alan Wickenden, PhD, Scientific Director, Discovery Sciences, Janssen Research & Development, LLC

10:45 Structural Insights from the Co-Crystal of the Glycine Receptor Ion Channel Bound to Its Modulator

Xin Huang, PhD, Principal Scientist, Department of Molecular Engineering, Amgen
Glycine receptors (GlyRs) mediate inhibitory neurotransmission in the central nervous system. Selective activation of GlyRs has been hypothesized as an alternative approach to treat neuropathic pain. Here we present crystal structures of GlyRa3 with both positive and negative modulators. Our structures provide new insights into molecular recognition of these modulators and their modulation mechanisms. These results also offer promise of rational structure-based design of new classes of GlyR modulators.

11:15 Positive Allosteric Modulators of AMPA Receptors: A Model for PPI Stabilization Studies

Christopher Ptak, PhD, Postdoctoral Research Associate, Laboratory of Robert Oswald, Department of Molecular Medicine, Cornell University, College of Veterinary Medicine

AMPA receptor positive allosteric modulators represent a potential class of nootropic drugs. These modulators act by stabilizing a weak domain-domain dimer that participates in the receptor’s activated state conformation. X-ray crystal structures illuminate the additional bridging contacts formed by the modulator across the dimer interface and have been exploited to develop new modulators with nanomolar affinity. Further, the use of small angle X-ray scattering and NMR spectroscopy provide insight into PPI-stabilizer binding models and the effect of allostery and stoichiometry.

11:45 Selected Poster Presentation(s)

12:00 pm Developing Novel Pain Drugs by Selectively Targeting Nav1.7

David Hackos, PhD, Senior Scientist, Neuroscience, Genentech

Nav1.7 is a sodium ion channel that plays a role in pain sensing. We and others have identified small molecule compounds that bind to a novel site within the 4th voltage-sensing domain that lock the channel into an inactivated state. We solved the structure of the binding site for this class of compounds (Ahuja et al., Science 2015) which led to key insights into the mechanism and the pharmacology of these selective sodium channel inhibitors.

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:30 Dessert Break in the Exhibit Hall with Poster Awards

BIOPHYSICAL TOOLS FOR MEMBRANE PROTEINS

2:15 Chairperson’s Remarks

Aaron Thompson, PhD, Scientist II, Department of Structural Biology, Dart Neuroscience; former Postdoctoral Fellow of Ray Stevens Laboratory

2:20 Biophysical Characterization of GPCRs with Crystallization-Enhancing Modifications

Matthew Eddy, PhD, Postdoctoral Fellow, Laboratory of Raymond Stevens, University of Southern California and The Scripps Research Institute

We present two studies where biophysical techniques provide new insight into structure-function relationships of human GPCRs and their implications for drug discovery. First, NMR studies of a GPCR fusion protein used for X-ray crystallography document how the fusion protein affects the signaling-related conformational equilibrium, highlighting potential instances where drug-ligand interactions can be affected. Second, NMR, X-ray diffraction, and other biophysical methods are applied to GPCR variants with mutations in a known allosteric center, and we explore the potential utility of these variants to accelerate GPCR drug discovery.

2:50 Nanodiscs for Biophysical Characterization of Membrane Proteins

Ilia Denisov, PhD, Laboratory of Stephen Sligar, Department of Biochemistry, University of Illinois at Urbana-Champaign

The Nanodisc platform has enjoyed wide applicability as it provides a self-assembled system that renders typically insoluble yet biologically and pharmacologically relevant membrane protein targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media. It has also provided a means for understanding the mechanism of cancer signaling complexes, such as KRas4b and its effectors, which all form on a membrane surface. I will present our latest discoveries enabled by Nanodiscs.

3:20 Using Label-Free Impedimetric Monitoring to Profile the Pharmacology of Cell-Surface Receptors in Vitro

Joachim Wegener, PhD, Professor, Division Cell-Based Sensors, Fraunhofer Research Institution for Microsystems and Solid-State Technologies (EMFT), University of Regensburg

This presentation will highlight several different approaches how non-invasive impedance measurements can be used to characterize the pharmacology of GPCRs and other cell-surface receptors that can be switched from OFF to ON states or changed in their activity by ligand binding. Impedance approaches are especially suited for difficult-to-purify proteins because they can be analyzed label-free in their native state in the membrane of living cells at endogenous expression levels. The non-invasive nature of the measurement allows following the cell response to receptor activation and the intracellular signal amplification in real time.

3:50 Refreshment Break

CANCER-RELATED MEMBRANE TARGETS

4:20 Structure-Based Drug Design for Cancer-Related Membrane Proteins

Avner Schlessinger, PhD, Assistant Professor, Pharmalogical Sciences, Mount Sinai School of Medicine

Solute carrier (SLC) transporters play a major role in mediating nutrient delivery in reprogrammed cancer metabolism networks. We use computational methods including homology modeling and virtual screening, which are followed by experimental testing, to discover novel small molecule ligands for cancer-related transporters. Our results provide useful tool compounds to characterize the role of SLC transporters in cancer, as well as a framework for developing efficacious lead compounds against emerging drug targets.

4:50 Applying Mammalian Membrane Two-Hybrid (MaMTH) Assay Identifies Novel Cancer Targets & Therapeutics

Igor Stagljar, PhD, Professor, Department of Molecular Genetics, Department of Biochemistry, University of Toronto

I will demonstrate how the Mammalian Membrane Two-Hybrid (MaMTH) assay can efficiently be used as a drug discovery assay for identification of inhibitory compounds that change the phosphorylation status of the human Epidermal Growth Factor Receptor (EGFR) in the context of living cells and in the low nanomolar range, an advance which may open up a whole new approach to drug development and lead to more effective treatments for lung cancer patients.

5:20 Thyroid Hormone Analogues as Angiogenic Agents via the Integrin Receptor

Paul Davis, MD, Professor, Department of Medicine, Pharmaceutical Research Institute, Albany Medical College

Acting via a specific integrin receptor on tumor cells, thyroid hormone (T4) and its antagonist (tetrac), modulate transcription of genes for cytokines and chemokines. T4 and tetrac also regulate expression of the PD-L1 gene--thus modifying the inflammatory process and angiogenesis.

5:50 End of Conference