CryoEM in Pharma: Structure-based drug design beyond X-ray crystallography

Conference: 2020: 70th ACA Annual Meeting
08/05/2020: 12:00 PM  - 3:00 PM 
Oral Session 


For long, X-ray crystallography had been the backbone of structure based drug design. However, since the advent of direct electron detectors in 2012 and development in data processing algorithms in the field, single particle cryo-EM has become a widely and routinely used structure solution method for difficult targets including integral membrane proteins. Pharmaceutical companies kept them in par with the development of the technique and readily expanded their drug design portfolios to non-crystallizable proteins. In this session, we are going to learn about efforts and success with cryo-EM which pharmaceutical companies have made in the past few years. The session will also talk about challenges and path forward with this technique.


Industrial CryoEM: reasons why and examples of impact

12:00 PM - 12:20 PM 
This talk will focus on the reasons why Pharmaceutical Companies such as AstraZeneca are investing in building cryoEM capabilities and give some early examples of impact in drug discovery projects, not only through traditional structure based design approaches but also through insights into the molecular basis of disease process. Specifically the talk will describe the complex of phospholipase C gamma with the FGFR1 kinase domain and insights into the mechanism of disease relevant mutations. 

View Abstract 367


Chris Phillips

Astex's journey of fragment-based drug discovery using cryo-EM

12:20 PM - 12:40 PM 
Recent advances in electron cryo-microscopy (cryo-EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. In light of these advances, Astex has decided to heavily invest in this technology and has developed a streamlined pipeline to facilitate fragment-based drug discovery (FBDD) using cryo-EM. This presentation will give an overview of the cryo-EM journey which Astex has embarked upon since 2016. It will also show in-house results to demonstrate that the current reproducibility, quality, and throughput of cryo-EM are compatible with FBDD (see also Saur, Hartshorn et al. (2020) Drug Discovery Today). 

View Abstract 239


Michael Saur

Structural basis for chemokine receptor CCR6 activation by the endogenous protein ligand CCL20

12:40 PM - 1:00 PM 
Chemokines are important protein-signaling molecules that regulate various immune responses by activating chemokine receptors which belong to the G protein-coupled receptor (GPCR) superfamily. Despite the substantial progression of our structural understanding of GPCR activation by small molecule and peptide agonists, the molecular mechanism of GPCR activation by protein agonists remains unclear. Here, we present a 3.3-Å cryo-electron microscopy structure of the human chemokine receptor CCR6 bound to its endogenous ligand CCL20 and an engineered Go. CCL20 binds in a shallow extracellular pocket, making limited contact with the core 7-transmembrane (TM) bundle. The structure suggests that this mode of binding induces allosterically a rearrangement of a noncanonical toggle switch and the opening of the intracellular crevice for G protein coupling. Our results demonstrate that GPCR activation by a protein agonist does not always require substantial interactions between ligand and the 7TM core region. 

View Abstract 348


David Wasilko, Pfizer Groton, CT 

Additional Author

Seungil Han, Pfizer Inc Groton, CT 

Coffee Break

1:00 PM - 1:20 PM 

Maximizing the value of cryoEM in drug discovery

1:20 PM - 1:40 PM 
For decades, protein structures have helped to understand the mechanism of action and facilitate the design of drug candidates. The rapid development of cryo-EM has provided unprecedented opportunities for obtaining structural knowledge for challenging targets, such as membrane proteins and multi-protein complexes. We will describe the approach taken to implement cryo-EM in a pharmaceutical environment. We will then show how cryo-EM structures have been used in drug discovery programs, including modalities such as small molecules, peptides and antibodies. Finally, we will discuss the current challenges and future outlook for increasing the impact of cryoEM in pharmaceutical research and development. 

View Abstract 286


Chuan Hong

Structural characterization of different TRPA1 inhibitors

1:40 PM - 2:00 PM 
Mammalian transient receptor potential (TRP) channels control cell homeostasis by mediating Ca2+ across membranes in response to physical and chemical environmental stimuli. TRPA1 has been a target of interest for the pharmaceutical industry for its implication in pain and neurogenic inflammation. It is mostly expressed by primary afferent nociceptors and detects a variety of compounds through covalent modification of conserved cysteine and lysine residues. Because of its therapeutic value, an internal program was launched to identify specific TRPA1 inhibitors: this campaign led to the discovery of multiple interesting chemotypes. In order to guide optimization of these molecules, an effort to structurally enable TRPA1 for structure based drug design was initiated based on a previously published cryo-EM structure (Paulsen et al., Nature, 2015). A combination of protein engineering, biochemistry and cryo-EM approaches led to the establishment of a robust system (e.g. improved resolution, high reproducibility) which allowed us to identify a novel binding site and optimize molecules with improved properties. 

View Abstract 323


Lionel Rouge

CryoEM at Sanofi

2:00 PM - 2:20 PM 
We present our path to establish cryo-EM project support at Sanofi with examples of project impact and added value in multiple therapeutic areas. 

View Abstract 244



A cryoEM and microED pipeline for the pharmaceutical and biotechnology industry

2:20 PM - 2:40 PM 
Cryo-electron microscopy (cryoEM) has become an established and viable alternative to X-ray analysis for high resolution protein structure determination. The technique is parsimonious in its material requirements and captures the specimens in their fully hydrated state, close to their native environment. Single particle CryoEM is increasingly used as the method of choice for 3D structure determination of targets that are difficult to crystallize, are available in limited quantity, display conformational variability or suffer from instability. There are significant barriers though to adopting cryoEM in the pharmaceutical and biotech industries, including the high costs and maintenance of the electron microscopes, the shortage of experienced personnel and the demanding computational infrastructure required for data collection and image processing. This presentation provides information on how to access cryoEM through outsourcing some or all aspects of the cryoEM workflow, including sample preparation, data collection and structure determination. As a specific example, the unique offerings provided by NanoImaging Services (NIS) will be described. NIS melds traditional CRO service packages with training and instrument access that is typically only accessible through academic and national laboratory facilities. Since 2017, dozens of pharma and biotech clients have successfully completed their cryoEM projects at NIS with over 60 client protein structures solved at 1.8 – 3.5Å resolution. Microcrystal electron diffraction (microED) is another, emerging cryoEM structure determination technique of high interest to the pharmaceutical and biotechnology industries. MicroED can rapidly determine atomic-resolution structures from microcrystals with minimal sample requirements. NIS has developed robust commercial services for small molecule microED studies to support a variety of industrial chemistry workflows. Details of this workflow and determination of over 20 small molecule structures during our initial testing program will be discussed. 

View Abstract 350


Anette Schneemann