Literature DB >> 25179005

HDX-MS guided drug discovery: small molecules and biopharmaceuticals.

David P Marciano1, Venkatasubramanian Dharmarajan1, Patrick R Griffin2.   

Abstract

Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS or DXMS) has emerged as an important tool for the development of small molecule therapeutics and biopharmaceuticals. Central to these advances have been improvements to automated HDX-MS platforms and software that allow for the rapid acquisition and processing of experimental data. Correlating the HDX-MS profile of large numbers of ligands with their functional outputs has enabled the development of structure activity relationships (SAR) and delineation of ligand classes based on functional selectivity. HDX-MS has also been applied to address many of the unique challenges posed by the continued emergence of biopharmaceuticals. Here we review the latest applications of HDX-MS to drug discovery, recent advances in technology and software, and provide perspective on future outlook.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 25179005      PMCID: PMC4253076          DOI: 10.1016/j.sbi.2014.08.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  83 in total

Review 1.  Target validation of G-protein coupled receptors.

Authors:  Alan Wise; Katy Gearing; Stephen Rees
Journal:  Drug Discov Today       Date:  2002-02-15       Impact factor: 7.851

2.  Mapping of discontinuous conformational epitopes by amide hydrogen/deuterium exchange mass spectrometry and computational docking.

Authors:  Deepangi Pandit; Steven J Tuske; Stephen J Coales; Sook Yen E; Anita Liu; Jessica E Lee; Jeffrey A Morrow; Jennifer F Nemeth; Yoshitomo Hamuro
Journal:  J Mol Recognit       Date:  2012-03       Impact factor: 2.137

3.  Time window expansion for HDX analysis of an intrinsically disordered protein.

Authors:  Devrishi Goswami; Srikripa Devarakonda; Michael J Chalmers; Bruce D Pascal; Bruce M Spiegelman; Patrick R Griffin
Journal:  J Am Soc Mass Spectrom       Date:  2013-07-25       Impact factor: 3.109

4.  Antibody-drug conjugates.

Authors:  Rachel S Zolot; Satarupa Basu; Ryan P Million
Journal:  Nat Rev Drug Discov       Date:  2013-04       Impact factor: 84.694

5.  Dynamics of the beta2-adrenergic G-protein coupled receptor revealed by hydrogen-deuterium exchange.

Authors:  Xi Zhang; Ellen Y T Chien; Michael J Chalmers; Bruce D Pascal; Jovylyn Gatchalian; Raymond C Stevens; Patrick R Griffin
Journal:  Anal Chem       Date:  2010-02-01       Impact factor: 6.986

6.  H/D exchange and mass spectrometry in the studies of protein conformation and dynamics: is there a need for a top-down approach?

Authors:  Igor A Kaltashov; Cedric E Bobst; Rinat R Abzalimov
Journal:  Anal Chem       Date:  2009-10-01       Impact factor: 6.986

7.  HDX reveals unique fragment ligands for the vitamin D receptor.

Authors:  Matthew W Carson; Jun Zhang; Michael J Chalmers; Wayne P Bocchinfuso; Karol D Holifield; Thierry Masquelin; Ryan E Stites; Keith R Stayrook; Patrick R Griffin; Jeffery A Dodge
Journal:  Bioorg Med Chem Lett       Date:  2014-05-29       Impact factor: 2.823

8.  Partial agonists activate PPARgamma using a helix 12 independent mechanism.

Authors:  John B Bruning; Michael J Chalmers; Swati Prasad; Scott A Busby; Theodore M Kamenecka; Yuanjun He; Kendall W Nettles; Patrick R Griffin
Journal:  Structure       Date:  2007-10       Impact factor: 5.006

9.  Development of a peptide probe for the occurrence of hydrogen (1H/2H) scrambling upon gas-phase fragmentation.

Authors:  Kasper D Rand; Thomas J D Jørgensen
Journal:  Anal Chem       Date:  2007-10-13       Impact factor: 6.986

10.  A new approach to measuring protein backbone protection with high spatial resolution using H/D exchange and electron capture dissociation.

Authors:  Rinat R Abzalimov; Cedric E Bobst; Igor A Kaltashov
Journal:  Anal Chem       Date:  2013-09-12       Impact factor: 6.986

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  31 in total

1.  Identification and function of conformational dynamics in the multidomain GTPase dynamin.

Authors:  Saipraveen Srinivasan; Venkatasubramanian Dharmarajan; Dana Kim Reed; Patrick R Griffin; Sandra L Schmid
Journal:  EMBO J       Date:  2016-01-18       Impact factor: 11.598

2.  Integration of G protein α (Gα) signaling by the regulator of G protein signaling 14 (RGS14).

Authors:  Nicole E Brown; Devrishi Goswami; Mary Rose Branch; Suneela Ramineni; Eric A Ortlund; Patrick R Griffin; John R Hepler
Journal:  J Biol Chem       Date:  2015-02-09       Impact factor: 5.157

Review 3.  Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes.

Authors:  Stuart L Schreiber; Joanne D Kotz; Min Li; Jeffrey Aubé; Christopher P Austin; John C Reed; Hugh Rosen; E Lucile White; Larry A Sklar; Craig W Lindsley; Benjamin R Alexander; Joshua A Bittker; Paul A Clemons; Andrea de Souza; Michael A Foley; Michelle Palmer; Alykhan F Shamji; Mathias J Wawer; Owen McManus; Meng Wu; Beiyan Zou; Haibo Yu; Jennifer E Golden; Frank J Schoenen; Anton Simeonov; Ajit Jadhav; Michael R Jackson; Anthony B Pinkerton; Thomas D Y Chung; Patrick R Griffin; Benjamin F Cravatt; Peter S Hodder; William R Roush; Edward Roberts; Dong-Hoon Chung; Colleen B Jonsson; James W Noah; William E Severson; Subramaniam Ananthan; Bruce Edwards; Tudor I Oprea; P Jeffrey Conn; Corey R Hopkins; Michael R Wood; Shaun R Stauffer; Kyle A Emmitte
Journal:  Cell       Date:  2015-06-04       Impact factor: 41.582

4.  Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

Authors:  Yiming Xiao; Lars Konermann
Journal:  Protein Sci       Date:  2015-04-02       Impact factor: 6.725

Review 5.  Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.

Authors:  Xiaoran Roger Liu; Mengru Mira Zhang; Michael L Gross
Journal:  Chem Rev       Date:  2020-04-22       Impact factor: 60.622

6.  Hydrogen-Deuterium Exchange and Hydroxyl Radical Footprinting for Mapping Hydrophobic Interactions of Human Bromodomain with a Small Molecule Inhibitor.

Authors:  Ke Sherry Li; Elizabeth T Schaper Bergman; Brett R Beno; Richard Y-C Huang; Ekaterina Deyanova; Guodong Chen; Michael L Gross
Journal:  J Am Soc Mass Spectrom       Date:  2019-11-12       Impact factor: 3.109

7.  AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production.

Authors:  Simon Schäper; Wieland Steinchen; Elizaveta Krol; Florian Altegoer; Dorota Skotnicka; Lotte Søgaard-Andersen; Gert Bange; Anke Becker
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-30       Impact factor: 11.205

8.  ApoE: In Vitro Studies of a Small Molecule Effector.

Authors:  Tridib Mondal; Hanliu Wang; Gregory T DeKoster; Berevan Baban; Michael L Gross; Carl Frieden
Journal:  Biochemistry       Date:  2016-04-27       Impact factor: 3.162

9.  Probing the Time Scale of FPOP (Fast Photochemical Oxidation of Proteins): Radical Reactions Extend Over Tens of Milliseconds.

Authors:  Siavash Vahidi; Lars Konermann
Journal:  J Am Soc Mass Spectrom       Date:  2016-04-11       Impact factor: 3.109

10.  Dimerization interface of osteoprotegerin revealed by hydrogen-deuterium exchange mass spectrometry.

Authors:  Yiming Xiao; Miaomiao Li; Rinzhi Larocque; Fuming Zhang; Anju Malhotra; Jianle Chen; Robert J Linhardt; Lars Konermann; Ding Xu
Journal:  J Biol Chem       Date:  2018-09-25       Impact factor: 5.157

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