Page 68 - GPD-3-1

Gene & Protein in Disease In silico application of the CoM method

with protein-protein docking, and affinity testing using the doi: 10.7554/eLife.69091
proposed method. 6. Godschalk F, Genheden S, Söderhjelm P, Ryde U.
Comparison of MM/GBSA calculations based on explicit
Acknowledgments and implicit solvent simulations. Phys Chem Chem Phys.
None. 2013;15(20):7731-7739.
doi: 10.1039/C3CP00116D
Funding
7. Stojanov D. Phylogenicity of B.1.1.7 surface glycoprotein,
None. novel distance function and first report of V90T missense
mutation in SARS-CoV-2 surface glycoprotein. Meta Gene.
Conflict of interest 2021;30:100967.

The author declares no competing interest. doi: 10.1016/j.mgene.2021.100967
Author contributions 8. Stojanov D. Data on multiple SARS-CoV-2 surface
glycoprotein alignments. Data Brief. 2021;38:107414.
This is single-authored article. doi: 10.1016/j.dib.2021.107414

Ethics approval and consent to participate 9. Deng JH, Luo J, Mao YL, et al. π-π stacking interactions:
Non-negligible forces for stabilizing porous supramolecular
Not applicable. frameworks. Sci Adv. 2020;6(2):eaax9976.

Consent for publication doi: 10.1126/sciadv.aax9976
10. Ahamad S, Ali H, Secco I, Giacca M, Gupta D. Anti-fungal
Not applicable.
drug anidulafungin inhibits SARS-CoV-2 spike-induced
Availability of data syncytia formation by targeting ACE2-spike protein
interaction. Front Genet. 2022;13:866474.
Data used in this work are available from the corresponding doi: 10.3389/fgene.2022.866474
author on reasonable request.
11. Ahamad S, Gupta D, Kumar V. Targeting SARS-CoV-2
References nucleocapsid oligomerization: Insights from molecular
docking and molecular dynamics simulations. J Biomol
1. Stojanov D. Structural implications of SARS-CoV-2 surface Struct Dyn. 2022;40(6):2430-2443.
glycoprotein N501Y mutation within receptor-binding
domain [499-505]-computational analysis of the most doi: 10.1080/07391102.2020.1839563
frequent Asn501 polar uncharged amino acid mutations. 12. Ahamad S, Hema K, Ahmad S, Kumar V, Gupta D. Insights
Biotechnol Biotechnol Equip. 2023;37(1):2206492. into the structure and dynamics of SARS-CoV-2 spike
doi: 10.1080/13102818.2023.2206492 glycoprotein double mutant L452R-E484Q. 3 Biotech.
2022;12(4):87.
2. Ibrahim MA, Abdelrahman AH, Mohamed TA, et al. In silico
mining of terpenes from red-sea invertebrates for SARS-CoV-2 doi: 10.1007/s13205-022-03151-0
main protease (M ) inhibitors. Molecules. 2021;26(7):2082. 13. Ahamad S, Hema K, Gupta D. Structural stability predictions
pro
doi: 10.3390/molecules26072082 and molecular dynamics simulations of RBD and HR1
mutations associated with SARS-CoV-2 spike glycoprotein.
3. Kumar R, Murugan NA, Srivastava V. Improved binding J Biomol Struct Dyn. 2022;40(15):6697-6709.
affinity of omicron’s spike protein for the human angiotensin-
converting enzyme 2 receptor is the key behind its increased doi: 10.1080/07391102.2021.1889671
virulence. Int J Mol Sci. 2022;23(6):3409. 14. Ahamad S, Kanipakam H, Gupta D. Insights into the
doi: 10.3390/ijms23063409 structural and dynamical changes of spike glycoprotein
mutations associated with SARS-CoV-2 host receptor
4. Carter C, Airas J, Parish CA. Atomistic insights into the binding. J Biomol Struct Dyn. 2022;40(1):263-275.
binding of SARS-CoV-2 spike receptor binding domain
with the human ACE2 receptor: The importance of residue doi: 10.1080/07391102.2020.1811774
493. J Mol Graph Model. 2023;118:108360. 15. Lan J, Ge J, Yu J, et al. Structure of the SARS-CoV-2 spike
receptor-binding domain bound to the ACE2 receptor.
doi: 10.1016/j.jmgm.2022.108360
Nature. 2020;581(7807):215-220.
5. Tian F, Tong B, Sun L, et al. N501Y mutation of spike protein
in SARS-CoV-2 strengthens its binding to receptor ACE2. doi: 10.1038/s41586-020-2180-5
Elife. 2021;10:e69091. 16. Brooks BR, Bruccoleri RE, Olafson BD, States DJ,

Volume 3 Issue 1 (2024) 7 https://doi.org/10.36922/gpd.2657