Biophysics

Inhibition of SARS-CoV-2 polymerase by nucleotide analogs: a single molecule perspective

1. Mona Seifert
2. Subhas Chandra Bera
3. Pauline van Nies
4. Robert N. Kirchdoerfer
5. Ashleigh Shannon
6. Thi-Tuyet-Nhung Le
7. Xiangzhi Meng
8. Hongjie Xia
9. James M. Wood
10. Lawrence D. Harris
11. Flávia S. Papini
12. Jamie J. Arnold
13. Steven C. Almo
14. Tyler L. Grove
15. Pei-Yong Shi
16. Yan Xiang
17. Bruno Canard
18. Martin Depken
19. Craig E. Cameron
20. David Dulin

• Curated by eLife

  Evaluation Summary:

  This work presented in this manuscript paper may advance our understanding of an important class of anti-viral drugs (nucleoside analogs) that target polymerase enzymes by being directly incorporated into the product strand. This class of drugs is known to be quite diverse in their precise mechanisms of action, yet many of the particular details have remained elusive, often due to experimental limitations. The current study employs a single-molecule magnetic-tweezers platform to provide a new paradigm for the mechanism of drug remdesivir against the SARS-CoV-2 polymerase target. The authors propose that remdesivir does not prevent the complete viral RNA synthesis but causes an increase of polymerase pausing and back tracking. This paper is of broad interest to readers and scientists working on SARS-CoV-2 and general nucleotide inhibitors. The work includes the single molecule characterization of other NAs.

  (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

A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics

1. Jonas Gossen
2. Simone Albani
3. Anton Hanke
4. Benjamin P. Joseph
5. Cathrine Bergh
6. Maria Kuzikov
7. Elisa Costanzi
8. Candida Manelfi
9. Paola Storici
10. Philip Gribbon
11. Andrea R. Beccari
12. Carmine Talarico
13. Francesca Spyrakis
14. Erik Lindahl
15. Andrea Zaliani
16. Paolo Carloni
17. Rebecca C. Wade
18. Francesco Musiani
19. Daria B. Kokh
20. Giulia Rossetti

Reviewed by ScreenIT

pH Effect on the Dynamics of SARS-CoV-2 Main Protease (M ^pro )

1. Shilpa Sharma
2. Shashank Deep

Reviewed by ScreenIT

On the molecular mechanism of SARS-CoV-2 retention in the upper respiratory tract

1. Kristina A. Paris
2. Ulises Santiago
3. Carlos J. Camacho

Reviewed by ScreenIT

Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M ^pro and cathepsin L

1. Michael Dominic Sacco
2. Chunlong Ma
3. Panagiotis Lagarias
4. Ang Gao
5. Julia Alma Townsend
6. Xiangzhi Meng
7. Peter Dube
8. Xiujun Zhang
9. Yanmei Hu
10. Naoya Kitamura
11. Brett Hurst
12. Bart Tarbet
13. Michael Thomas Marty
14. Antonios Kolocouris
15. Yan Xiang
16. Yu Chen
17. Jun Wang

Reviewed by ScreenIT

Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals

1. Tek Narsingh Malla
2. Suraj Pandey
3. Ishwor Poudyal
4. Denisse Feliz
5. Moraima Noda
6. George Phillips
7. Emina Stojkovic
8. Marius Schmidt

Reviewed by ScreenIT

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

1. Serdar Durdagi
2. Çağdaş Dağ
3. Berna Dogan
4. Merve Yigin
5. Timucin Avsar
6. Cengizhan Buyukdag
7. Ismail Erol
8. Fatma Betul Ertem
9. Seyma Calis
10. Gunseli Yildirim
11. Muge D. Orhan
12. Omur Guven
13. Busecan Aksoydan
14. Ebru Destan
15. Kader Sahin
16. Sabri O. Besler
17. Lalehan Oktay
18. Alaleh Shafiei
19. Ilayda Tolu
20. Esra Ayan
21. Busra Yuksel
22. Ayse B. Peksen
23. Oktay Gocenler
24. Ali D. Yucel
25. Ozgur Can
26. Serena Ozabrahamyan
27. Alpsu Olkan
28. Ece Erdemoglu
29. Fulya Aksit
30. Gokhan Tanisali
31. Oleksandr M. Yefanov
32. Anton Barty
33. Alexandra Tolstikova
34. Gihan K. Ketawala
35. Sabine Botha
36. E. Han Dao
37. Brandon Hayes
38. Mengning Liang
39. Matthew H. Seaberg
40. Mark S. Hunter
41. Alex Batyuk
42. Valerio Mariani
43. Zhen Su
44. Frederic Poitevin
45. Chun Hong Yoon
46. Christopher Kupitz
47. Raymond G. Sierra
48. Edward H. Snell
49. Hasan DeMirci

Reviewed by ScreenIT

Multi-parameter formulation development for an HIV-vaccine protein with direct validation of epitope binding integrity and stoichiometry

1. Corinna Popp
2. Philipp Schramm
3. Ralf Wagner
4. David Peterhoff
5. Christopher Battle
6. Christian Kleusch
7. Maximilian G. Plach

Reviewed by ScreenIT

Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV ‐2 spike protein receptor‐binding domain

1. Jonathan K. Williams
2. Baifan Wang
3. Andrew Sam
4. Cody L. Hoop
5. David A. Case
6. Jean Baum

Reviewed by ScreenIT

Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment

1. Sameer Kumar Malladi
2. Randhir Singh
3. Suman Pandey
4. Savitha Gayathri
5. Kawkab Kanjo
6. Shahbaz Ahmed
7. Mohammad Suhail Khan
8. Parismita Kalita
9. Nidhi Girish
10. Aditya Upadhyaya
11. Poorvi Reddy
12. Ishika Pramanick
13. Munmun Bhasin
14. Shailendra Mani
15. Sankar Bhattacharyya
16. Jeswin Joseph
17. Karthika Thankamani
18. V. Stalin Raj
19. Somnath Dutta
20. Ramandeep Singh
21. Gautham Nadig
22. Raghavan Varadarajan

Reviewed by ScreenIT