Expedited Cryo-EM Structure-Based Drug Design: From Gene to Novel Chemistry

Structure-based drug design involves uncovering the three-dimensional structure of therapeutically relevant targets for drug discovery and development.

Compared to ligand-based methods, this type of drug design can accelerate the development process and make it possible to precisely design small molecules that either bring out or suppress a response in the human body.

Historically, X-ray crystallography was a critical part of structure-based drug design and resulted in the development of potent inhibitors for the treatment of a wide variety of diseases from AIDS to cancer.

Yet, due to the limits of this technique, many important drug targets—including macromolecular assemblies and membrane proteins—were left out of structure-based drug design efforts.

The good news is that recent advances in protein production, coupled with the increasingly popular cryo-electron microscopy (cryo-EM) technique, are expanding the role of structure-based drug design for these critical targets.

Modern structure-based drug design: a case study

Using cryo-EM in combination with computational chemistry methods, researchers are poised to revolutionize structure-based drug design, which could lead to highly precise drugs that target a wider range of debilitating diseases. In other words, better drugs in less time.

Using Thermo Fisher Scientific’s gene-to-protein and cryo-EM solutions, in combination with the Schrödinger platform, it is possible to get from gene to novel, computationally designed small molecules in just three months.

To demonstrate the potential of cryo-EM in the structure-based drug design process, Thermo Fisher Scientific collaborated with Schrödinger to create a white paper showcasing the expedited gene-to-drug approach, finding hits in only three months. To do so, they utilized Thermo Fisher’s high-powered cryo-EM solutions and Invitrogen GeneArt Gene-to-Protein Services in combination with the Schrödinger Drug Discovery platform.

An expedited gene-to-drug approach

Selection of targets for initiation of drug discovery depends on understanding the unmet medical need of focus, and evidence from clinical, genetic and preclinical studies inform therapeutic potential.

According to the collaborators in this study, “All targets must be modeling enabled for structure-based drug design…The Schrödinger platform is used to analyze protein structure quality and binding site druggability, followed by an assessment of the amenability of the structures for use with the technology. Due to the lack of high-quality structures…[many] interesting targets that meet the criteria for biological rationale and therapeutic momentum need to be discarded. This is often because such targets are…often challenging for X-ray crystallography. Fortunately, these types of targets are often well suited for structural determination by cryo-EM and allow for modelling of previously unreachable targets.”

After a target was selected for the purpose of this study, Thermo Fisher’s GeneArt Gene-to-Protein services team produced a purified protein starting with a digital sequence in just six weeks. This was made possible by harnessing the power of gene optimization, our synthetic gene expertize and advanced Gibco expression systems to produce maximum yields of correctly folded protein. The protein was obtained with a concentration sufficient for creating dense micrographs and with the quantity needed to supply a cryo-EM-based structure determination pipeline for months.
Using the Thermo Scientific iSPA Workflow, including the Thermo Scientific Vitrobot System, Krios Rx Cryo-TEM, and EPU software, it was possible to complete the entire process from vitrifying the protein sample to collecting the required data. Using this workflow, it took just three days to go from sample preparation to the high-resolution reconstruction of the first complex structure—with the ability to solve additional ligand structures within a similar timeframe.
Once protein-ligand complex structures were obtained, atomic models were prepared with the Schrödinger platform, which integrates predictive physics-based methods with machine learning techniques to accelerate drug discovery. Using this platform, it was possible to virtually screen massive numbers of diverse compounds to exploit opportunities and remove known liabilities. The atomic models were refined to be of sufficiently high quality to be used in a structure-based drug design program within just three weeks.

Using Thermo Fisher solutions in combination with the Schrödinger platform, it took just three months to get from gene to novel, computationally designed small molecules. As the white paper demonstrates, this method can play a critical role in structure-based drug design—accelerating drug discovery and the path to the high-efficacy drugs needed to combat a wide range of today’s debilitating diseases.

To learn more, read our white paper, An Expedited Gene-to-Drug Approach Using Thermo Scientific Cryo-EM and the Schrödinger Platform.