Protein molecular modeling of spike protein fragment and NRP-1 protein:
Swiss Model web server was utilized to build the 3D structural model for Egyptian sequences for NRP-1 and the spike protein (4). The two solved structures with PDB ID: 7QQm and 6XR8 were chosen to be the homolog solved structures for NRP-1 and the spike protein since they share a sequence identity of 100% and 99.84%, respectively (5,6). After model building, the models were validated through the Structural Analysis and Verification Server (SAVES) webserver of the UCLA and Molprobity from Duke University (7).
Molecular docking between S protein fragment and NRP-1.
Molecular docking studies between S protein fragment and human NRP-1 receptor are performed using ClusPro (8). Following equation has been used to compute cluster scores as well as to predict the lowest binding energy (using ClusPro 2.2 online server (8)
E = 0.40Erep+ −0.40Eatt + 600Eelec + 1.00EDARS.
The repulsive (rep), attractive (att), electrostatic (elec) forces and interactions extracted from the decoys as the reference state (DARS), are measured using molecular docking study (9).
Molecular docking study of some natural compounds and FDA approved drugs
The tested compounds are retrieved from the PubChem database and prepared using PyMOL software (10, 11). Docking experiments were performed using AutoDock Vina software (12). Model built for NRP-1 was used in this study, and its binding affinities against, Carvacrol, Thymol, Amantadine, Daclatasvir, Ravidasvir, Remdesivir, Sofosbuvir, Hesperidine, and Thymoquinone were tested using the Vina scoring function. Chimera software was used to represent and analyze the docking complexes.