Computational Protein-Ligand Docking Sample Clauses

Computational Protein-Ligand Docking. The acid dissociation constant (pKa) of the benzene sulfonamide derivatives was predicted by ACD software.[108] Based on the pKa values, the protonation state of the nitrogen sites in these compounds was determined. All prepared benzene sulfonamide derivatives with the appropriate N-site protonated were docked flexibly into the cavity region of the human chemokine receptor CXCR4 crystallographic structure (PDB code: 3ODU) devoid of small-molecule antagonist IT1t using Glide with standard precision (Schrödinger, LLC).[109] This methodology regards the protein structure as a rigid body, but treats the ligand as a conformationally flexible molecule. The resulting CXCR4/benzenesulfonamide complexes were subsequently sorted energetically with the MM-GBSA scoring algorithm, which provides an estimate of relative binding free energies. The volume of the CXCR4 cavity was obtained by the web-based CASTp package.[47]
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