title: S···O and S···N Sulfur Bonding Interactions in Protein-Ligand Complexes: Empirical Considerations and Scoring Function.
abstract: Sulfur bonding interactions between organosulfur compounds and proteins were examined using crystal structures deposited to-date in the PDB. The data was analyzed as a function of sulfur-σ-hole-bonding (i.e., sulfur bonds) to main chain Lewis bases, viz. oxygen and nitrogen atoms of the backbone amide linkages. The analyses also included an examination of sulfur bonding to side chain Lewis bases (O, N, and S) and to the "non-classical" Lewis bases present in electron-rich aromatic amino acids as-well-as to donor-acceptor bond angle distributions. The interactions analyzed included those restricted to the sum of van der Waals radii of the respective atoms or to a distance of 4 Å. The surveyed data revealed that sulfur bonding tendencies (C-S-C bond angles) were impacted not only by steric effects but perhaps also by enthalpic features present in both the donor and acceptor participants. This knowledge is not only of fundamental interest but is also important in terms of materials and drug-design involving moieties incorporating the sulfur atom. Additionally, a new empirical scoring function was developed to address the anisotropy of sulfur in protein-ligand interactions. This newly developed scoring function is incorporated into AutoDock Vina molecular docking program and is valuable for modeling and drug design.
authors.affiliation: Department of Basic Sciences, St. Louis College of Pharmacy , St. Louis, Missouri 63110, United States.
authors.forename: Mathew R
authors.initials: MR
authors.lastname: Koebel
authors.affiliation: Department of Basic Sciences, St. Louis College of Pharmacy , St. Louis, Missouri 63110, United States.
authors.forename: Aaron
authors.initials: A
authors.lastname: Cooper
authors.forename: Grant
authors.initials: G
authors.lastname: Schmadeke
authors.forename: Soyoung
authors.initials: S
authors.lastname: Jeon
authors.forename: Mahesh
authors.initials: M
authors.lastname: Narayan
authors.affiliation: Department of Basic Sciences, St. Louis College of Pharmacy , St. Louis, Missouri 63110, United States.
authors.forename: Suman
authors.identifier: 0000-0003-4665-6665
authors.initials: S
authors.lastname: Sirimulla
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000201:enzymology; D001426:Bacterial Proteins / Q000378:metabolism; D030562:Databases, Protein; D015195:Drug Design; D006801:Humans; D006841:Hydrocarbons, Aromatic / Q000737:chemistry / Q000494:pharmacology; D008024:Ligands; D062105:Molecular Docking Simulation; D010963:Plasmodium falciparum / Q000201:enzymology; D011506:Proteins / Q000378:metabolism*; D055672:Static Electricity; D013455:Sulfur / Q000737:chemistry / Q000494:pharmacology; D013457:Sulfur Compounds / Q000737:chemistry* / Q000494:pharmacology*; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D006841:Hydrocarbons, Aromatic; D008024:Ligands; D011506:Proteins; D013457:Sulfur Compounds; D013455:Sulfur