Building the Phytochemical Library
Various servers were searched (PubMed, Carrot2 and DLAD4U) to commence studies in different research papers, and about 41 compounds from the plant Urtica dioica were collected. Urtica was undertaken in this study due to its various therapeutic role against viral infections 
Protein selection and preparation
ACE-2 the Protein which has formed the major target for this virus in humans was retrieved from the database PDB (URL: https://www.rcsb.org) with PDB ID: 1R4L. Also, the selection of target protein for docking study is based on their X-Ray diffraction. The selected protein should not have protein break in entire 3D conformation and to meet requirements of docking analysis, protein should be in the form of PDB formats. X-ray crystallographic structure of 1R4L (Angiotensin Converting Enzyme-2 (ACE2) was prepared for molecular docking in such a way that all hetero atoms (water, ions, etc.) were removed. By using the chimera tool, protein binding sites of the chain are selected and others are removed.
Pubchem (URL: https://pubchem.ncbi.nlm.nih.gov) was used to retrieve 2D structures of the phytochemicals in SDF format and further using open babel (software) these compounds were converted to PDB format. The reference molecule used in the entire docking analysis is Remdesivir with Pubchem CID-121304016 were retrieved from Pubchem.
Phylogeny and homology modeling
MSA was done to check the similarities between the molecules present in the branch of the RAS system occurring in the lungs. Amino acid sequence of the target ACE2 (PDB ID:1R4L) along with the active site of ACE (AAH36375.1), the mature chain of DPP4 (sp|P27487.2), ADAM17 (sp|P78536.1) and MasR (sp|P35410.1), and also amino acid sequence of the protein AT1R(NP_114038.4), AT2R (NP_000677.2) and Collectrin (AAG09466) were retrieved from the database NCBI (URL: www.ncbi.nlm.nih.gov) in FASTA format and later these sequences were scanned for their similarities using Clustal W. Furthermore, a phylogenetic tree was developed using the aligned sequences.
An In silico approach for ligand and receptor docking analysis was employed to examine structural complexes of the 1R4L (target protein) with Urtica dioica compounds (ligand molecule) in order to emphasize structural conformation of this protein target specificity. In the present investigation, we use PyRx virtual screening tool which uses both Vina and Auto Dock 4.2 with Lamarckian genetic algorithm as scoring function and contributes higher docking accuracy [15,16].
The target protein was defined as the total number of atoms of 5218; the number of residues is 655 with unique five chains. The chemical structure of macromolecule was determined by X-Ray Crystallography with a resolution of 3.00 Å. We continue to the preparation of target by eliminating the bound ligands and water molecules through UCSF Chimera tool. Also, we remove all chains except Chain A as it shows only ligand binding site chain. Then we introduced it into the PyRx tool by remarked as macromolecule in PyRx workflow. In this method, the protein and ligand molecules were converted to their proper readable file format (pdbqt) using auto dock tools. All docking studies were performed as blind docking which was set in the grid box and encompasses all possible ligand-receptor complex and dimensions were X= 39.021, Y= 4.078 and Z= 22.898 to dock all the ligands where 8 maximum exhaustiveness was calculated for each ligand. All other parameters of software were kept as default and all bonds contained in ligand were allowed to rotate freely, considering receptor as rigid. The final visualization of the docked structure was performed using Discovery Studio Visualizer 3.0. Before testing potentiality of the Urtica dioica compounds against 1R4L, a broad-spectrum anti-viral drug i.e. remdesivir was also used .