Literature DB >> 33381049

A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface.

Charlie Nichols1,2, Joseph Ng1, Annika Keshu1, Franca Fraternali1, Gian F De Nicola1,2.   

Abstract

In-crystal fragment screening is a powerful tool to chemically probe the surfaces used by proteins to interact, and identify the chemical space worth exploring to design protein-protein inhibitors. A crucial prerequisite is the identification of a crystal form where the target area is exposed and accessible to be probed by fragments. Here we report a crystal form of the SARS-CoV-2 Receptor Binding Domain in complex with the CR3022 antibody where the ACE2 binding site on the Receptor Binding Domain is exposed and accessible. This crystal form of the complex is a valuable tool to develop antiviral molecules that could act by blocking the virus entry in cells.
Copyright © 2020 De Nicola, Nichols, Fraternali, Ng and Keshu.

Entities:  

Keywords:  CR3022; PPI inhibitors; SARC-CoV-2-RBD; drug discovery; in-crystal fragment screening

Year:  2020        PMID: 33381049      PMCID: PMC7768231          DOI: 10.3389/fphar.2020.615211

Source DB:  PubMed          Journal:  Front Pharmacol        ISSN: 1663-9812            Impact factor:   5.810


  11 in total

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Authors:  N S Pannu; G N Murshudov; E J Dodson; R J Read
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2.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

3.  Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.

Authors:  Jun Lan; Jiwan Ge; Jinfang Yu; Sisi Shan; Huan Zhou; Shilong Fan; Qi Zhang; Xuanling Shi; Qisheng Wang; Linqi Zhang; Xinquan Wang
Journal:  Nature       Date:  2020-03-30       Impact factor: 49.962

4.  Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes.

Authors:  Charlie Nichols; Joseph Ng; Annika Keshu; Geoff Kelly; Maria R Conte; Michael S Marber; Franca Fraternali; Gian F De Nicola
Journal:  J Med Chem       Date:  2020-07-01       Impact factor: 7.446

5.  Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease.

Authors:  Maria L Agostini; Erica L Andres; Amy C Sims; Rachel L Graham; Timothy P Sheahan; Xiaotao Lu; Everett Clinton Smith; James Brett Case; Joy Y Feng; Robert Jordan; Adrian S Ray; Tomas Cihlar; Dustin Siegel; Richard L Mackman; Michael O Clarke; Ralph S Baric; Mark R Denison
Journal:  mBio       Date:  2018-03-06       Impact factor: 7.867

6.  Remdesivir for the Treatment of Covid-19 - Final Report.

Authors:  John H Beigel; Kay M Tomashek; Lori E Dodd; Aneesh K Mehta; Barry S Zingman; Andre C Kalil; Elizabeth Hohmann; Helen Y Chu; Annie Luetkemeyer; Susan Kline; Diego Lopez de Castilla; Robert W Finberg; Kerry Dierberg; Victor Tapson; Lanny Hsieh; Thomas F Patterson; Roger Paredes; Daniel A Sweeney; William R Short; Giota Touloumi; David Chien Lye; Norio Ohmagari; Myoung-Don Oh; Guillermo M Ruiz-Palacios; Thomas Benfield; Gerd Fätkenheuer; Mark G Kortepeter; Robert L Atmar; C Buddy Creech; Jens Lundgren; Abdel G Babiker; Sarah Pett; James D Neaton; Timothy H Burgess; Tyler Bonnett; Michelle Green; Mat Makowski; Anu Osinusi; Seema Nayak; H Clifford Lane
Journal:  N Engl J Med       Date:  2020-10-08       Impact factor: 91.245

7.  Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys.

Authors:  Travis K Warren; Robert Jordan; Michael K Lo; Adrian S Ray; Richard L Mackman; Veronica Soloveva; Dustin Siegel; Michel Perron; Roy Bannister; Hon C Hui; Nate Larson; Robert Strickley; Jay Wells; Kelly S Stuthman; Sean A Van Tongeren; Nicole L Garza; Ginger Donnelly; Amy C Shurtleff; Cary J Retterer; Dima Gharaibeh; Rouzbeh Zamani; Tara Kenny; Brett P Eaton; Elizabeth Grimes; Lisa S Welch; Laura Gomba; Catherine L Wilhelmsen; Donald K Nichols; Jonathan E Nuss; Elyse R Nagle; Jeffrey R Kugelman; Gustavo Palacios; Edward Doerffler; Sean Neville; Ernest Carra; Michael O Clarke; Lijun Zhang; Willard Lew; Bruce Ross; Queenie Wang; Kwon Chun; Lydia Wolfe; Darius Babusis; Yeojin Park; Kirsten M Stray; Iva Trancheva; Joy Y Feng; Ona Barauskas; Yili Xu; Pamela Wong; Molly R Braun; Mike Flint; Laura K McMullan; Shan-Shan Chen; Rachel Fearns; Swami Swaminathan; Douglas L Mayers; Christina F Spiropoulou; William A Lee; Stuart T Nichol; Tomas Cihlar; Sina Bavari
Journal:  Nature       Date:  2016-03-02       Impact factor: 49.962

8.  A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV.

Authors:  Meng Yuan; Nicholas C Wu; Xueyong Zhu; Chang-Chun D Lee; Ray T Y So; Huibin Lv; Chris K P Mok; Ian A Wilson
Journal:  Science       Date:  2020-04-03       Impact factor: 47.728

9.  Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.

Authors:  Alexandra C Walls; Young-Jun Park; M Alejandra Tortorici; Abigail Wall; Andrew T McGuire; David Veesler
Journal:  Cell       Date:  2020-03-09       Impact factor: 41.582

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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  4 in total

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2.  Vascular Endothelial Growth Factor Receptor, fms-Like Tyrosine Kinase-1 (Flt-1), as a Novel Binding Partner for SARS-CoV-2 Spike Receptor-Binding Domain.

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Authors:  Jasdeep Singh; Jasmine Samal; Vipul Kumar; Jyoti Sharma; Usha Agrawal; Nasreen Z Ehtesham; Durai Sundar; Syed Asad Rahman; Subhash Hira; Seyed E Hasnain
Journal:  Viruses       Date:  2021-03-09       Impact factor: 5.048

4.  Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.

Authors:  Sophie M-C Gobeil; Katarzyna Janowska; Shana McDowell; Katayoun Mansouri; Robert Parks; Victoria Stalls; Megan F Kopp; Kartik Manne; Dapeng Li; Kevin Wiehe; Kevin O Saunders; Robert J Edwards; Bette Korber; Barton F Haynes; Rory Henderson; Priyamvada Acharya
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  4 in total

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