Biophysics

Novel inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives

1. Kangsa Amporndanai
2. Xiaoli Meng
3. Weijuan Shang
4. Zhenmig Jin
5. Yao Zhao
6. Zihe Rao
7. Zhi-Jie Liu
8. Haitao Yang
9. Leike Zhang
10. Paul M. O’Neill
11. S. Samar Hasnain

Reviewed by ScreenIT

Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement

1. Lim Heo
2. Michael Feig

Reviewed by ScreenIT

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

1. Fang Tian
2. Bei Tong
3. Liang Sun
4. Shengchao Shi
5. Bin Zheng
6. Zibin Wang
7. Xianchi Dong
8. Peng Zheng

• Curated by eLife

  Evaluation Summary:

  Tian et al. used a battery of biophysical techniques to compare wild-type SARS-CoV-2 with two variants (B.1.1.7 and B.1.351). The authors obtained evidence consistent with the receptor-binding domain (RBD) of the variants exhibiting higher affinity ACE2, providing a possible explanation for their higher transmission. However, the effects are modest, and further work will be needed to confirm that this difference explains the increased transmission of the variants. Despite the need for follow-up studies, the paper is among the first to show definitively that the N501Y mutation confers enhanced binding to ACE2.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife, ScreenIT

Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2

1. Vivek Govind Kumar
2. Dylan S Ogden
3. Ugochi H Isu
4. Adithya Polasa
5. James Losey
6. Mahmoud Moradi

Reviewed by ScreenIT

Perturbation of ACE2 structural ensembles by SARS-CoV-2 spike protein binding

1. Arzu Uyar
2. Alex Dickson

Reviewed by ScreenIT

High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Non-Covalent Inhibitor

1. Austin Clyde
2. Stephanie Galanie
3. Daniel W. Kneller
4. Heng Ma
5. Yadu Babuji
6. Ben Blaiszik
7. Alexander Brace
8. Thomas Brettin
9. Kyle Chard
10. Ryan Chard
11. Leighton Coates
12. Ian Foster
13. Darin Hauner
14. Vilmos Kertesz
15. Neeraj Kumar
16. Hyungro Lee
17. Zhuozhao Li
18. Andre Merzky
19. Jurgen G. Schmidt
20. Li Tan
21. Mikhail Titov
22. Anda Trifan
23. Matteo Turilli
24. Hubertus Van Dam
25. Srinivas C. Chennubhotla
26. Shantenu Jha
27. Andrey Kovalevsky
28. Arvind Ramanathan
29. Martha S. Head
30. Rick Stevens

Reviewed by ScreenIT

Structural Analysis of Spike Protein Mutations in the SARS-CoV-2 P.3 Variant

1. Neil Andrew D. Bascos
2. Denise Mirano-Bascos
3. Cynthia P. Saloma

Reviewed by ScreenIT

Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility

1. Ryan R. Cheng
2. Esteban Dodero-Rojas
3. Michele Di Pierro
4. José N. Onuchic

Reviewed by ScreenIT

Computational Analysis of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike and Their Effects on Antibody Binding

1. Marine E. Bozdaganyan
2. Konstantin V. Shaitan
3. Mikhail P. Kirpichnikov
4. Olga S. Sokolova
5. Philipp S. Orekhov

Reviewed by ScreenIT

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

1. Maxwell I. Zimmerman
2. Justin R. Porter
3. Michael D. Ward
4. Sukrit Singh
5. Neha Vithani
6. Artur Meller
7. Upasana L. Mallimadugula
8. Catherine E. Kuhn
9. Jonathan H. Borowsky
10. Rafal P. Wiewiora
11. Matthew F. D. Hurley
12. Aoife M Harbison
13. Carl A Fogarty
14. Joseph E. Coffland
15. Elisa Fadda
16. Vincent A. Voelz
17. John D. Chodera
18. Gregory R. Bowman

Reviewed by ScreenIT