Literature DB >> 30455147

Discovery of covalent enzyme inhibitors using virtual docking of covalent fragments.

Sandipan Roy Chowdhury1, Steven Kennedy1, Kai Zhu2, Rama Mishra3, Patrick Chuong1, Alyssa-Uyen Nguyen1, Stefan G Kathman4, Alexander V Statsyuk5.   

Abstract

Here we present a virtual docking screen of 1648 commercially available covalent fragments, and identified covalent inhibitors of cysteine protease cathepsin L. These inhibitors did not inhibit closely related protease cathepsin B. Thus, we have established virtual docking of covalent fragments as an approach to discover covalent enzyme inhibitors.
Copyright © 2018 Elsevier Ltd. All rights reserved.

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Year:  2018        PMID： 30455147      PMCID： PMC6319256          DOI： 10.1016/j.bmcl.2018.11.019

Source DB:  PubMed          Journal:  Bioorg Med Chem Lett        ISSN： 0960-894X            Impact factor:   2.823


  16 in total

1.  Selective Inhibition of Oncogenic KRAS Output with Small Molecules Targeting the Inactive State.

Authors:  Matthew P Patricelli; Matthew R Janes; Lian-Sheng Li; Rasmus Hansen; Ulf Peters; Linda V Kessler; Yuching Chen; Jeff M Kucharski; Jun Feng; Tess Ely; Jeffrey H Chen; Sarah J Firdaus; Anjali Babbar; Pingda Ren; Yi Liu
Journal:  Cancer Discov       Date:  2016-01-06       Impact factor: 39.397

2.  Accurate Binding Free Energy Predictions in Fragment Optimization.

Authors:  Thomas B Steinbrecher; Markus Dahlgren; Daniel Cappel; Teng Lin; Lingle Wang; Goran Krilov; Robert Abel; Richard Friesner; Woody Sherman
Journal:  J Chem Inf Model       Date:  2015-10-21       Impact factor: 4.956

3.  Covalent Tethering of Fragments For Covalent Probe Discovery.

Authors:  Stefan G Kathman; Alexander V Statsyuk
Journal:  Medchemcomm       Date:  2016-01-28       Impact factor: 3.597

4.  A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a Distributive Enzymatic Mechanism.

Authors:  Stefan G Kathman; Ingrid Span; Aaron T Smith; Ziyang Xu; Jennifer Zhan; Amy C Rosenzweig; Alexander V Statsyuk
Journal:  J Am Chem Soc       Date:  2015-09-22       Impact factor: 15.419

Review 5.  Cathepsin B and L inhibitors: a patent review (2010 - present).

Authors:  Yu-Yao Li; Jing Fang; Gui-Zhen Ao
Journal:  Expert Opin Ther Pat       Date:  2016-12-23       Impact factor: 6.674

6.  Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor.

Authors:  Matthew R Janes; Jingchuan Zhang; Lian-Sheng Li; Rasmus Hansen; Ulf Peters; Xin Guo; Yuching Chen; Anjali Babbar; Sarah J Firdaus; Levan Darjania; Jun Feng; Jeffrey H Chen; Shuangwei Li; Shisheng Li; Yun O Long; Carol Thach; Yuan Liu; Ata Zarieh; Tess Ely; Jeff M Kucharski; Linda V Kessler; Tao Wu; Ke Yu; Yi Wang; Yvonne Yao; Xiaohu Deng; Patrick P Zarrinkar; Dirk Brehmer; Dashyant Dhanak; Matthew V Lorenzi; Dana Hu-Lowe; Matthew P Patricelli; Pingda Ren; Yi Liu
Journal:  Cell       Date:  2018-01-25       Impact factor: 41.582

7.  Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor.

Authors:  R Janowski; M Kozak; E Jankowska; Z Grzonka; M Jaskólski
Journal:  J Pept Res       Date:  2004-10

8.  Covalent docking of large libraries for the discovery of chemical probes.

Authors:  Nir London; Rand M Miller; Shyam Krishnan; Kenji Uchida; John J Irwin; Oliv Eidam; Lucie Gibold; Peter Cimermančič; Richard Bonnet; Brian K Shoichet; Jack Taunton
Journal:  Nat Chem Biol       Date:  2014-10-26       Impact factor: 15.040

9.  Proteome-wide covalent ligand discovery in native biological systems.

Authors:  Keriann M Backus; Bruno E Correia; Kenneth M Lum; Stefano Forli; Benjamin D Horning; Gonzalo E González-Páez; Sandip Chatterjee; Bryan R Lanning; John R Teijaro; Arthur J Olson; Dennis W Wolan; Benjamin F Cravatt
Journal:  Nature       Date:  2016-06-15       Impact factor: 49.962

10.  A fragment-based method to discover irreversible covalent inhibitors of cysteine proteases.

Authors:  Stefan G Kathman; Ziyang Xu; Alexander V Statsyuk
Journal:  J Med Chem       Date:  2014-05-28       Impact factor: 7.446
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  3 in total

1.  Structure-Based Design and Biological Evaluation of Novel Caspase-2 Inhibitors Based on the Peptide AcVDVAD-CHO and the Caspase-2-Mediated Tau Cleavage Sequence YKPVD314.

Authors:  Merlin Bresinsky; Jessica M Strasser; Bernadette Vallaster; Peng Liu; William M McCue; Jessica Fuller; Alexander Hubmann; Gurpreet Singh; Kathryn M Nelson; Matthew E Cuellar; Carrie M Wilmot; Barry C Finzel; Karen H Ashe; Michael A Walters; Steffen Pockes
Journal:  ACS Pharmacol Transl Sci       Date:  2022-01-05

Review 2.  Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices.

Authors:  Abdul-Quddus Kehinde Oyedele; Abdeen Tunde Ogunlana; Ibrahim Damilare Boyenle; Ayodeji Oluwadamilare Adeyemi; Temionu Oluwakemi Rita; Temitope Isaac Adelusi; Misbaudeen Abdul-Hammed; Oluwabamise Emmanuel Elegbeleye; Tope Tunji Odunitan
Journal:  Mol Divers       Date:  2022-09-04       Impact factor: 3.364

3.  An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor.

Authors:  Daniel Zaidman; Paul Gehrtz; Mihajlo Filep; Daren Fearon; Ronen Gabizon; Alice Douangamath; Jaime Prilusky; Shirly Duberstein; Galit Cohen; C David Owen; Efrat Resnick; Claire Strain-Damerell; Petra Lukacik; Haim Barr; Martin A Walsh; Frank von Delft; Nir London
Journal:  Cell Chem Biol       Date:  2021-06-25       Impact factor: 8.116
  3 in total

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