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Literature DB >> 30100349

Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application.

Giovanna Scapin¹, Clinton S Potter², Bridget Carragher³.

Abstract

We present a perspective of our view of the application of cryoelectron microscopy (cryo-EM) to structure-based drug design (SBDD). We discuss the basic needs and requirements for SBDD, the current state of cryo-EM, and the challenges that need to be overcome for this technique to reach its full potential in facilitating the process of drug discovery.

Entities: Chemical Disease Gene Mutation Species

Keywords: automation; cryo-EM; structure-based drug discovery

Mesh：

Substances：

Year: 2018 PMID： 30100349 PMCID： PMC6239957 DOI： 10.1016/j.chembiol.2018.07.006

Source DB: PubMed Journal: Cell Chem Biol ISSN： 2451-9448 Impact factor: 8.116

75 in total

Review 1. Macromolecular modeling with rosetta.

Authors: Rhiju Das; David Baker
Journal: Annu Rev Biochem Date: 2008 Impact factor: 23.643

2. Discovery of an Orally Available, Brain Penetrant BACE1 Inhibitor that Affords Robust CNS Aβ Reduction.

Authors: Andrew W Stamford; Jack D Scott; Sarah W Li; Suresh Babu; Dawit Tadesse; Rachael Hunter; Yusheng Wu; Jeffrey Misiaszek; Jared N Cumming; Eric J Gilbert; Chunli Huang; Brian A McKittrick; Liwu Hong; Tao Guo; Zhaoning Zhu; Corey Strickland; Peter Orth; Johannes H Voigt; Matthew E Kennedy; Xia Chen; Reshma Kuvelkar; Robert Hodgson; Lynn A Hyde; Kathleen Cox; Leonard Favreau; Eric M Parker; William J Greenlee
Journal: ACS Med Chem Lett Date: 2012-07-12 Impact factor: 4.345

3. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

Authors: J M de la Rosa-Trevín; A Quintana; L Del Cano; A Zaldívar; I Foche; J Gutiérrez; J Gómez-Blanco; J Burguet-Castell; J Cuenca-Alba; V Abrishami; J Vargas; J Otón; G Sharov; J L Vilas; J Navas; P Conesa; M Kazemi; R Marabini; C O S Sorzano; J M Carazo
Journal: J Struct Biol Date: 2016-04-20 Impact factor: 2.867

4. Rational design of peptide-based HIV proteinase inhibitors.

Authors: N A Roberts; J A Martin; D Kinchington; A V Broadhurst; J C Craig; I B Duncan; S A Galpin; B K Handa; J Kay; A Kröhn
Journal: Science Date: 1990-04-20 Impact factor: 47.728

5. L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor.

Authors: B D Dorsey; R B Levin; S L McDaniel; J P Vacca; J P Guare; P L Darke; J A Zugay; E A Emini; W A Schleif; J C Quintero
Journal: J Med Chem Date: 1994-10-14 Impact factor: 7.446

6. Identification of Conserved Water Sites in Protein Structures for Drug Design.

Authors: Marko Jukič; Janez Konc; Stanislav Gobec; Dušanka Janežič
Journal: J Chem Inf Model Date: 2017-12-04 Impact factor: 4.956

7. Towards automated crystallographic structure refinement with phenix.refine.

Authors: Pavel V Afonine; Ralf W Grosse-Kunstleve; Nathaniel Echols; Jeffrey J Headd; Nigel W Moriarty; Marat Mustyakimov; Thomas C Terwilliger; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal: Acta Crystallogr D Biol Crystallogr Date: 2012-03-16

8. Outcome of the first electron microscopy validation task force meeting.

Authors: Richard Henderson; Andrej Sali; Matthew L Baker; Bridget Carragher; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Wen Jiang; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal: Structure Date: 2012-02-08 Impact factor: 5.006

9. Structure of the insulin receptor-insulin complex by single-particle cryo-EM analysis.

Authors: Giovanna Scapin; Venkata P Dandey; Zhening Zhang; Winifred Prosise; Alan Hruza; Theresa Kelly; Todd Mayhood; Corey Strickland; Clinton S Potter; Bridget Carragher
Journal: Nature Date: 2018-02-28 Impact factor: 49.962

10. TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.

Authors: Yuan Gao; Erhu Cao; David Julius; Yifan Cheng
Journal: Nature Date: 2016-05-18 Impact factor: 49.962

17 in total

Review 1. Challenges and opportunities in cryo-EM single-particle analysis.

Authors: Dmitry Lyumkis
Journal: J Biol Chem Date: 2019-02-25 Impact factor: 5.157

2. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Authors: Carlos Oscar S Sorzano; Amaya Jiménez-Moreno; David Maluenda; Erney Ramírez-Aportela; Marta Martínez; Ana Cuervo; Robert Melero; Jose Javier Conesa; Ruben Sánchez-García; David Strelak; Jiri Filipovic; Estrella Fernández-Giménez; Federico de Isidro-Gómez; David Herreros; Pablo Conesa; Laura Del Caño; Yunior Fonseca; Jorge Jiménez de la Morena; Jose Ramon Macías; Patricia Losana; Roberto Marabini; Jose-Maria Carazo
Journal: Methods Mol Biol Date: 2021

Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application.

Review 1. Macromolecular modeling with rosetta.

2. Discovery of an Orally Available, Brain Penetrant BACE1 Inhibitor that Affords Robust CNS Aβ Reduction.

3. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

4. Rational design of peptide-based HIV proteinase inhibitors.

5. L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor.

6. Identification of Conserved Water Sites in Protein Structures for Drug Design.

7. Towards automated crystallographic structure refinement with phenix.refine.

8. Outcome of the first electron microscopy validation task force meeting.

9. Structure of the insulin receptor-insulin complex by single-particle cryo-EM analysis.

10. TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.

Review 1. Challenges and opportunities in cryo-EM single-particle analysis.

2. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Review 3. Structural Variability in the RLR-MAVS Pathway and Sensitive Detection of Viral RNAs.

Review 4. Broadening access to cryoEM through centralized facilities.

Review 5. Protein Design: From the Aspect of Water Solubility and Stability.

Review 6. Electron microscopy of cardiac 3D nanodynamics: form, function, future.

Review 7. Mechanics and pharmacology of substrate selection and transport by eukaryotic ABC exporters.

Review 8. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters.

Review 9. Assays and technologies for developing proteolysis targeting chimera degraders.

10. A comparative study of single-particle cryo-EM with liquid-nitrogen and liquid-helium cooling.