PMC:7128678 / 4626-6517 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7128678","sourcedb":"PMC","sourceid":"7128678","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7128678","text":"2 Materials and methods\nIn-silico analyses were performed using Hyperchem and Molegro Molecular viewer as described [11,13,14]. The initial coordinates of GM1 were obtained from CHARMM-GUI Glycolipid Modeler (http://www.charmmgui.org/?doc=input/glycolipid; [15]), which uses the internal coordinate information of common glycosidic torsion angle values, orients the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, especially the membrane-embedded ceramide part. In the next step, the ganglioside was included in a periodic box solvated with 1128 water molecules. The system was energy-minimized six times, switching between runs using the steepest descent gradients and runs using Polak–Ribière conjugate gradients until convergence to machine precision. The ganglioside was subsequently merged with the NTD domain of SARS-CoV-2 S protein as obtained from pdb file # 6VSB [16]. Initial conditions corresponded to minimized structures obtained with the Polak–Ribière algorithm. Docked complexes were subsequently submitted to iterative cycles of molecular dynamics using the CHARMM36 force field optimized for carbohydrates [17]. Interaction energies were calculated from stable complexes using the Ligand Energy Inspector function of Molegro [13].\nN-acetylneuraminic acid (Neu5Ac) was generated with the Hyperchem database. 9-O-acetyl-N-acetylneuraminic acid (9-O-SIA) was retrieved from pdb file 6Q06 [18]. CLQ is N-(7-chloroquinolin-4-yl)-N,N-diéthyl-pentane-1,4-diamine. Its three-dimensioanl structure was retrieved from pdb file # 4V2O [19]. CLQ-OH is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of CLQ with Hyperchem. Both CLQ and CLQ-OH were energy-minimized and merged with water molecules as described 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