Cambridge Healthtech Institute’s 5th Annual
Biophysical Approaches for Drug Discovery
Lead Generation Methods against PPIs, GPCRs, and Other Difficult Targets
New DATES - AUGUST 28, 2020
This symposium convenes medicinal and biophysical chemists, computational chemists, and structural biologists to discuss advances in biophysical methods in drug discovery. An emphasis will be on case studies that highlight integration of various biophysical
techniques for new drug lead generation. We will also cover applying biosensor-based screens to more ‘difficult’ target classes, such as protein-protein interactions (PPIs) and G protein-coupled receptors (GPCRs) or other complex membrane
proteins, where traditional high-throughput screens are not ideal because of the absence of an enzymatic assay or physiologically relevant parameters.
Friday, April 17
7:30 am Registration Open and Morning Coffee
7:55 Welcome and Opening Remarks
Anjani Shah, PhD, Senior Conference Director, Cambridge Healthtech Institute
Phillip Schwartz, PhD, Principal Scientist, Biophysics, Frontier Medicines
8:00 FEATURED PRESENTATION: Label-Free Biosensing for Meeting the Challenges of Increasingly Diverse Chemical Matter
John Quinn, Biophysical Group, Biochemical and Cellular Pharmacology, Genentech
Increasingly challenging targets have prompted the development of diverse chemical matter supporting many targeting strategies. Typically, routine SAR/SKR provided by biochemical/cell assays requires coupling of complex reporter labels/mechanisms
rendering them time consuming to develop and deploy. We show that label-free biosensing allows characterization of on-target binding with acceptable throughput to drive early SAR/SKR for rigorous compound prioritization/optimization over a diverse
range of chemical matter.
8:30 Enabling Drug Discovery with Crude Reaction Mixture Screening
Ben Davis, PhD, Research Fellow, Vernalis Research
In our experience, gains in potency within a series are largely due to increased residence time. We exploit this feature to assess crude reaction mixtures (CRMs) to identify molecules with slower k-off. We demonstrate that CRMs can be used across
a range of important biophysical techniques, thus improving H2L turn-around times, reducing costs and allowing more hit series to be explored. We will demonstrate this approach with examples from a range of targets.
9:00 Biophysical Techniques to Identify Aggregating Compounds and Select Hits
Samantha Allen, PhD, Principal Scientist, Discovery Sciences, Janssen R&D
Small-molecule drug discovery can be hindered by aggregating compounds that act as non-selective inhibitors of drug targets. These aggregates appear as false positives in high-throughput screening campaigns and can complicate structure-activity relationships
during triage and compound optimization. They can also cause problems in secondary biophysics assays such as SPR. I’ll discuss high-throughput microplate-based approaches to identify compound aggregation.
9:30 Networking Coffee Break
10:00 Determining Affinity from Irreversible Thermal Shifts
Justin Hall, PhD, Principal Scientist, Structural Biology & Biophysics, Pfizer
We describe here methods and equations to fit ligand affinity from irreversible protein denaturation. Irreversible denaturation occurs for most proteins, particularly in the space of human therapeutics, but equations to fit these data have eluded
investigators for many years. These results suggest the kinetic energy barrier for unfolding is similar across proteins; application of these findings should allow investigators to calculate ligand affinity from a single thermal denaturation data
10:30 Dissecting the Role of 5’-triphosphate in RNA-induced Conformational Changes of Full Length RIG-I
Justyna Sikorska, PhD, Associate Principal Scientist, Mass Spectrometry & Biophysics, Merck Research Labs
Retinoic inducible gene (RIG)-I senses differences between endogenous and viral RNA for triggering immune response through induction of type I interferons. We present structural biophysical characterization of conformational signatures of 5’-ppp
versus 5’-OH dsRNA bound forms of full length RIG-I. Our results were analyzed in the context of the recently published SAXS data, and laid foundation for the hypothesis that motif IVa can be involved in RIG-I activation.
11:00 Application of Biophysical and Structure-Based Methods in Membrane Protein Drug Discovery
Michael Hennig, PhD, CEO, leadXpro AG
Based on excellence in membrane protein science, leadXpro has established a platform that combines most advanced biophysical assay technologies with high-resolution X-ray and cryo-EM to enable drug design. Expect to see examples of membrane
protein targets highlighting the applicability of leadXpro’s approach, including binding characterization by grating-coupled interferometry (GCI).
11:15 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
12:00 pm Session Break
1:00 Chairperson’s Remarks
Gottfried Schroeder, PhD, Senior Scientist, Department of Quantitative Biosciences,
Merck Research Labs Boston
1:05 Novel Thermo-FRET and BRET-Based Thermostability Assays Applied to GPCRs
Dmitry Veprintsev, PhD, Professor, Molecular and Cellular Pharmacology, University of Nottingham
Sensitive protein stability assays are crucial to structural and biophysical studies. Here, we describe novel high-throughput 384-well FRET and BRET-based thermostability assay allowing for the ultrasensitive determination of GPCR stability. These
assays are functional in crude lysates, without any requirement for protein purification enabling the profiling of molecules at orphan GPCRs for which tracers do not currently exist.
1:35 Biophysical Studies of Human GPCR Allosteric Modulators
Matthew Eddy, PhD, Assistant Professor, Chemistry, University of Florida
We leverage nuclear magnetic resonance in solution to provide fresh insights into the structural mechanisms of partial agonism in human GPCRs. We also describe NMR studies of endogenous GPCR allosteric modulators (e.g. lipids) and their impact
on function-related dynamics.
2:05 Expanding the Domain of Applicability of Structure-Based Drug Design with IFD-MD
Cesar de Oliveira, PhD, Principal Scientist II, Applications Science, Schrödinger
Schrödinger’s IFD-MD application uses a combination of docking algorithms, water thermodynamics, empirical scoring functions, implicit solvent force field energies and explicit solvent metadynamics trajectories to reliably identify
protein-ligand binding poses when the sequence identity between the target protein and template is as low as 40%. In this presentation we’ll show some examples of the impact IFD-MD can have on real-world drug discovery programs limited
by the availability of high-resolution crystal structures.
2:35 Networking Refreshment Break
3:05 Applying Biophysical Tools for Lead Identification, Validation and Optimization – Case Studies and Lessons Learned
Anup Upadhyay, PhD, Senior Scientist III, Drug Discovery Science & Technology, AbbVie
I will discuss how and when we use different biophysical tools (NMR, SPR, ITC, TSA and MST) to validate HTS hits, understand their binding modes and enable lead optimizations. I will present 2 to 3 different case studies from the papers that
we have published recently.
3:35 Targeting the Kringle Domains of Apolipoprotein(a)
Jenny Sandmark, PhD, Associate Principal Scientist, Drug Discovery, AstraZeneca
There is a strong link between lipoprotein(a) levels in plasma and cardiovascular disease. Several of the pathological effects associated with lipoprotein(a) are expected to be mediated via kringle domains on apolipoprotein(a). Therefore,
we set out to identify inhibitors targeting the small polar lysine binding sites on the kringles. The hit identification campaign followed by structure-based drug design resulted in a compound that specifically bound to kringle IV-10.
4:05 Successes and Challenges in Targeting RNA with Small Molecules
Nathan Baird, PhD, Interim Chair, Department of Chemistry & Biochemistry, Associate Professor
of Biochemistry, University of the Sciences
Efforts targeting RNA with small molecules have been deterred by the inherent propensity of structured RNA molecules to adopt multiple conformations. The Baird Lab works to take direct advantage of RNA structural flexibility to discover
small molecule inhibitors of RNA by simultaneously evaluating RNA structures and chemical screens. Our results demonstrate that targeting non-functional RNA structures is a challenging yet effective approach for therapeutic development.
4:35 Close of Symposium