Bio-Chemoinformatics-Driven Analysis of nsp7 and nsp8 Mutations and Their Effects on Viral Replication Protein Complex Stability
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript "Bio-chemoinformatics-driven analysis of nsp7 and nsp8 mutations and their effects on viral replication protein complex stability" analyzes mutations in the nsp7 and nsp8 proteins of SARS-CoV-2 and predicting their effects on the stability of the viral replication complex. The authors performed bioinformatics analyses on large global datasets of nsp7 and nsp8 sequences from 2022-2023. They identified frequent mutations, critical interaction residues, and potential mutational hotspots that could destabilize the replication complex. I have some suggestions to further strengthen the manuscript:
1. Clearly summarize key results/conclusions in abstract - which mutations destabilize or stabilize?
2. The introduction could benefit from more background on the specific roles and interactions of nsp7 and nsp8 in viral replication. This would help readers better understand the significance of mutating these proteins.
3. In the results, it would be helpful to visualize some of the mutated structures and important residue interactions identified in the computational analyses. For example, show structures of critical nsp7/8 residues before and after mutation.
4. For interpretations of the results, relate back more specifically to potential effects on viral replication and infectivity. Do certain mutations suggest increased/decreased replication or transmission?
5. Discussion could be expanded with limitations of computational approach, future directions, and implications for drug targeting or vaccine development.
6. In the discussion, when assessing the role of Thr to Ile mutations, some mechanisms by which those mutations affect viral protein stability have already been describe, the authors may cite some of this articles, e.g.: 10.3390/biom11040566
7. Carefully proofread to fix minor typos, grammar issues, formatting inconsistencies.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript sounds interesting and worthy of publication, after some minor revisions.
Introduction
- please, add the proper reference and PDB code for the experimental data shown in Figure 1.
- please, add a workflow of the whole study
Materials
Please, add more details of the protein modeling analysis
Results
Destabilizing or stabilizing effects played by mutations involving charged aminoacids with hydrophobic or still charged ones are quite obvious. Please, refer to other case studies in the literature to support the reliability of your methods and consider to compare your results with those obtained for similar studies of other analogue proteins, as shown in the literature.
A section including the spread rate of these protein mutants should be added, based on experimental data. This could support your models.
Figure 5 is very difficult to read, please revise or include in upporting materials.
Captions to figures are too long.
Figures 6-7, please clearly add in proximity of each diagram the mutated aminoacid of the wild-type protein.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors have successfully addressed the reviewers' comments and suggestions, enhancing the clarity and depth of the manuscript.
