Revolutionizing Small Molecule Drug Discovery Pipelines with Cryo-EM: A Workflow for High-Throughput Screening and High-Resolution Data Collection

TL;DR

This paper introduces a cryo-EM workflow that enables high-throughput screening and high-resolution imaging for drug discovery, particularly for the CDK-Activating Kinase complex.

Contribution

The study presents a novel workflow using 200 kV and 300 kV cryo-TEMs to accelerate drug discovery with high productivity and resolution.

Findings

Structures at 4 Å resolution were obtained in one hour, identifying lead compound binding pockets.

Four hours of data collection achieved 3 Å resolution, revealing lead compound conformation.

2 Å resolution structures from 300 kV cryo-TEMs enabled modeling of ordered waters for compound optimization.

Abstract

Cryo-electron microscopy (cryo-EM) has revolutionized structure-based drug discovery by allowing accurate and rapid visualization of drug-target interactions at high resolutions1. In this study, we demonstrate a workflow using a 200 kV Thermo Scientific Glacios cryo-transmission electron microscope (cryo-TEM) equipped with a Thermo Scientific Selectris X imaging filter and Thermo Scientific Falcon 4i detector for high-throughput screening of drug binding on CDK-Activating Kinase (CAK) complex. With just one hour of data collection, we obtained structures at 4 Å, sufficient to identify lead compound binding pocket and density. With four hours of data collection, the structures approached 3 Å, enabling visualization of lead compound conformation. Best grids imaged using the 300 kV Thermo Scientific Krios cryo-TEM resolved the structure to 2 Å, allowing the modelling of ordered waters to inform lead compound optimization. Our study demonstrates that 200 kV cryo-TEMs can deliver the high productivity needed for structure-based drug discovery and design, while targeted imaging on 300 kV cryo-TEMs can provide even higher resolutions.