Literature DB >> 25117499

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

Disha Patel1, Joseph D Bauman1, Eddy Arnold2.   

Abstract

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility.
Copyright © 2014. Published by Elsevier Ltd.

Entities:  

Keywords:  Fragment screening; HIV; Influenza; X-ray crystallography

Mesh:

Substances:

Year:  2014        PMID: 25117499      PMCID: PMC4501029          DOI: 10.1016/j.pbiomolbio.2014.08.004

Source DB:  PubMed          Journal:  Prog Biophys Mol Biol        ISSN: 0079-6107            Impact factor:   3.667


  38 in total

1.  Discovering novel ligands for macromolecules using X-ray crystallographic screening.

Authors:  V L Nienaber; P L Richardson; V Klighofer; J J Bouska; V L Giranda; J Greer
Journal:  Nat Biotechnol       Date:  2000-10       Impact factor: 54.908

2.  Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.

Authors:  A C English; S H Done; L S Caves; C R Groom; R E Hubbard
Journal:  Proteins       Date:  1999-12-01

3.  Experimental and computational active site mapping as a starting point to fragment-based lead discovery.

Authors:  Jürgen Behnen; Helene Köster; Gerd Neudert; Tobias Craan; Andreas Heine; Gerhard Klebe
Journal:  ChemMedChem       Date:  2011-12-23       Impact factor: 3.466

4.  Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

Authors:  Theresa Tiefenbrunn; Stefano Forli; Meaghan Happer; Ana Gonzalez; Yingssu Tsai; Michael Soltis; John H Elder; Arthur J Olson; Charles D Stout
Journal:  Chem Biol Drug Des       Date:  2013-10-30       Impact factor: 2.817

5.  The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea.

Authors:  Qin Zou; Brian J Bennion; Valerie Daggett; Kenneth P Murphy
Journal:  J Am Chem Soc       Date:  2002-02-20       Impact factor: 15.419

6.  Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening.

Authors:  Joseph D Bauman; Disha Patel; Chhaya Dharia; Marc W Fromer; Sameer Ahmed; Yulia Frenkel; R S K Vijayan; J Thomas Eck; William C Ho; Kalyan Das; Aaron J Shatkin; Eddy Arnold
Journal:  J Med Chem       Date:  2013-02-20       Impact factor: 7.446

7.  Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors.

Authors:  Joseph D Bauman; Disha Patel; Steven F Baker; R S K Vijayan; Amy Xiang; Ajit K Parhi; Luis Martínez-Sobrido; Edmond J LaVoie; Kalyan Das; Eddy Arnold
Journal:  ACS Chem Biol       Date:  2013-09-13       Impact factor: 5.100

8.  Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function.

Authors:  Susanne M Saalau-Bethell; Andrew J Woodhead; Gianni Chessari; Maria G Carr; Joseph Coyle; Brent Graham; Steven D Hiscock; Christopher W Murray; Puja Pathuri; Sharna J Rich; Caroline J Richardson; Pamela A Williams; Harren Jhoti
Journal:  Nat Chem Biol       Date:  2012-09-30       Impact factor: 15.040

9.  Halogen-enriched fragment libraries as leads for drug rescue of mutant p53.

Authors:  Rainer Wilcken; Xiangrui Liu; Markus O Zimmermann; Trevor J Rutherford; Alan R Fersht; Andreas C Joerger; Frank M Boeckler
Journal:  J Am Chem Soc       Date:  2012-04-05       Impact factor: 15.419

10.  Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.

Authors:  Daniel G Kuroda; Joseph D Bauman; J Reddy Challa; Disha Patel; Thomas Troxler; Kalyan Das; Eddy Arnold; Robin M Hochstrasser
Journal:  Nat Chem       Date:  2013-01-27       Impact factor: 24.427

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  30 in total

1.  Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.

Authors:  George T Lountos; Xue Zhi Zhao; Evgeny Kiselev; Joseph E Tropea; Danielle Needle; Yves Pommier; Terrence R Burke; David S Waugh
Journal:  Nucleic Acids Res       Date:  2019-11-04       Impact factor: 16.971

Review 2.  The role of small-angle scattering in structure-based screening applications.

Authors:  Po-Chia Chen; Janosch Hennig
Journal:  Biophys Rev       Date:  2018-10-10

3.  A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.

Authors:  Cho Yeow Koh; Latha Kallur Siddaramaiah; Ranae M Ranade; Jasmine Nguyen; Tengyue Jian; Zhongsheng Zhang; J Robert Gillespie; Frederick S Buckner; Christophe L M J Verlinde; Erkang Fan; Wim G J Hol
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-07-31

4.  A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain.

Authors:  Disha Patel; Janet Antwi; Pratibha C Koneru; Erik Serrao; Stefano Forli; Jacques J Kessl; Lei Feng; Nanjie Deng; Ronald M Levy; James R Fuchs; Arthur J Olson; Alan N Engelman; Joseph D Bauman; Mamuka Kvaratskhelia; Eddy Arnold
Journal:  J Biol Chem       Date:  2016-09-19       Impact factor: 5.157

5.  Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments.

Authors:  Francesca Fata; Ilaria Silvestri; Matteo Ardini; Rodolfo Ippoliti; Luana Di Leandro; Nicola Demitri; Maurizio Polentarutti; Adele Di Matteo; Haining Lyu; Gregory R J Thatcher; Pavel A Petukhov; David L Williams; Francesco Angelucci
Journal:  ACS Infect Dis       Date:  2021-05-05       Impact factor: 5.084

Review 6.  Avoiding Drug Resistance in HIV Reverse Transcriptase.

Authors:  Maria E Cilento; Karen A Kirby; Stefan G Sarafianos
Journal:  Chem Rev       Date:  2021-01-28       Impact factor: 60.622

Review 7.  In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery.

Authors:  Lauro Ribeiro de Souza Neto; José Teófilo Moreira-Filho; Bruno Junior Neves; Rocío Lucía Beatriz Riveros Maidana; Ana Carolina Ramos Guimarães; Nicholas Furnham; Carolina Horta Andrade; Floriano Paes Silva
Journal:  Front Chem       Date:  2020-02-18       Impact factor: 5.221

8.  Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion.

Authors:  Sarah L Kidd; Elaine Fowler; Till Reinhardt; Thomas Compton; Natalia Mateu; Hector Newman; Dom Bellini; Romain Talon; Joseph McLoughlin; Tobias Krojer; Anthony Aimon; Anthony Bradley; Michael Fairhead; Paul Brear; Laura Díaz-Sáez; Katherine McAuley; Hannah F Sore; Andrew Madin; Daniel H O'Donovan; Kilian V M Huber; Marko Hyvönen; Frank von Delft; Christopher G Dowson; David R Spring
Journal:  Chem Sci       Date:  2020-05-14       Impact factor: 9.825

Review 9.  Fragment-based drug discovery: opportunities for organic synthesis.

Authors:  Jeffrey D St Denis; Richard J Hall; Christopher W Murray; Tom D Heightman; David C Rees
Journal:  RSC Med Chem       Date:  2020-12-24

10.  Exploring protein hotspots by optimized fragment pharmacophores.

Authors:  Dávid Bajusz; Warren S Wade; Grzegorz Satała; Andrzej J Bojarski; Janez Ilaš; Jessica Ebner; Florian Grebien; Henrietta Papp; Ferenc Jakab; Alice Douangamath; Daren Fearon; Frank von Delft; Marion Schuller; Ivan Ahel; Amanda Wakefield; Sándor Vajda; János Gerencsér; Péter Pallai; György M Keserű
Journal:  Nat Commun       Date:  2021-05-27       Impact factor: 14.919

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