Single-Particle cryo-EM as a Pipeline for Obtaining Atomic Resolution Structures of Druggable Targets in Preclinical Structure-Based Drug Design

  • Ramanathan NateshEmail author
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 27)


Single-particle cryo-electron microscopy (cryo-EM) and three-dimensional (3D) image processing have gained importance in the last few years to obtain atomic structures of drug targets. Obtaining atomic-resolution 3D structure better than ~2.5 Å is a standard approach in pharma companies to design and optimize therapeutic compounds against drug targets like proteins. Protein crystallography is the main technique in solving the structures of drug targets at atomic resolution. However, this technique requires protein crystals which in turn is a major bottleneck. It was not possible to obtain the structure of proteins better than 2.5 Å resolution by any other methods apart from protein crystallography until 2015. Recent advances in single-particle cryo-EM and 3D image processing have led to a resolution revolution in the field of structural biology that has led to high-resolution protein structures, thus breaking the cryo-EM resolution barriers to facilitate drug discovery. There are 24 structures solved by single-particle cryo-EM with resolution 2.5 Å or better in the EMDataBank (EMDB) till date. Among these, five cryo-EM 3D reconstructions of proteins in the EMDB have their associated coordinates deposited in Protein Data Bank (PDB), with bound inhibitor/ligand. Thus, for the first time, single-particle cryo-EM was included in the structure-based drug design (SBDD) pipeline for solving protein structures independently or where crystallography has failed to crystallize the protein. Further, this technique can be complementary and supplementary to protein crystallography field in solving 3D structures. Thus, single-particle cryo-EM can become a standard approach in pharmaceutical industry in the design, validation, and optimization of therapeutic compounds targeting therapeutically important protein molecules during preclinical drug discovery research. The present chapter will describe briefly the history and the principles of single-particle cryo-EM and 3D image processing to obtain atomic-resolution structure of proteins and their complex with their drug targets/ligands.


Single-particle cryo-EM Drug development Pharmacological targets Structural biology High resolution 



Three Dimension


Contrast Transfer Function


Cryo-electron microscopy




Direct Detection Device or Direct Electron Detector


Electron Tomography


Electron Microscopy Data Bank


Electron Microscopy


Field Emission Gun


Fourier Shell Correlation


Multivariate Statistical Analysis


Protein Data Bank


Principle Component Analysis


Structure-Based Drug Design


Signal-to-Noise Ratio


Spectral SNR


Transmission Electron Microscopy



RN was supported by Ramalingaswamy Fellowship from DBT. RN would like to thank his laboratory members and colleagues for their constant support, valuable scientific and technical discussion. Last but not least, RN would like to thank IISER-TVM past Director Prof. ED Jemmis and present Director Prof. V. Ramakrishnan for their unstinted support.


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Authors and Affiliations

  1. 1.School of BiologyIndian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM)TrivandrumIndia

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