Aguilar-Pineda et al. Structural and functional analysis of female sex hormones against SARS-Cov-2 cell entry
This dataset contains all the raw data and codes used for th adquision of the data presented in the manuscript: "Structural and functional analysis of female sex hormones against SARS-Cov-2 cell entry " by Aguilar-Pineda et al. Here we report new insights into the molecular basis of the interactions between the SARS-CoV-2 spike (S) protein and the human ACE2 receptor. We further report that glycosylation of the ACE2 receptor enhances SARS-CoV-2 infectivity. Importantly estrogens can disrupt glycan-glycan interactions and glycan-protein interactions between the human ACE2 and the SARS-CoV2 thereby blocking its entry into cells.
Steps to reproduce
I. For the Docking interaction analysis , we used the PatchDock server using default parameters were used. The ACE2 protein was used as a receptor molecule, and Spike protein as a ligand molecule. II. For FEL maps, and generation of 3D figures, we carried out the following steps: - Obtain the structural coordinates (RMSD and radius of gyration) of the 3D structures protein. and we used the following commands: - perl sham.pl -i1 RG-file.xvg -i2 rmsd-file.xvg -data1 1 -data2 1 -o gsham-file.xvg - gmx sham -f gsham-file.xvg -ls free-energy-landscape.xpm - python xpm2txt.py -f FEL.xpm -o FEL.txt The FEL.txt file it's visualized on the Mathematica 12.1 software. III. For molecular dynamics simulations, all input files and the force fields used are provided. The simulations were performed using Gromacs v2019.4 package. To carry out the MD simulations by using the following commands: - gmx grompp -f file.mdp -c file.gro -p topol.top -o MD.tpr - gmx mdrun -deffnm MD IV. For the quantum calculations, we provide the Gaussian input files (.gjf) in order to run it on Gaussian 16 package. V. Finally, we provide the statistical files used to obtain the RMSD, RMSF, radius of gyrations, and H bonds plots.