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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvationExpand
Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin.
In an in vitro study, we compared the cytochrome P450 (CYP)-dependent metabolism and drug interactions of the acid and lactone forms of the 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase inhibitorExpand
A Medicinal Chemist’s Guide to Molecular Interactions
Molecular recognition in biological systems relies on the existence of specific attractive interactions between two partner molecules. Structure-based drug design seeks to identify and optimize suchExpand
Disease–Drug–Drug Interaction Involving Tocilizumab and Simvastatin in Patients With Rheumatoid Arthritis
In rheumatoid arthritis (RA), interleukin‐6 (IL‐6) concentration is elevated, which may cause reduced cytochrome P450 (CYP) activity and increased exposure (peak plasma concentration and area underExpand
Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models.
We report calculations of free energies of binding, DeltaG(bind), between a diverse set of nine ligands and avidin as well as between a peptide and streptavidin using the recently developed MM/PBSAExpand
The structure of human α-2,6-sialyltransferase reveals the binding mode of complex glycans.
Human β-galactoside α-2,6-sialyltransferase I (ST6Gal-I) establishes the final glycosylation pattern of many glycoproteins by transferring a sialyl moiety to a terminal galactose. CompleteExpand
Validation and use of the MM-PBSA approach for drug discovery.
The MM-PBSA approach has become a popular method for calculating binding affinities of biomolecular complexes. Published application examples focus on small test sets and few proteins and, hence, areExpand
Systematic investigation of halogen bonding in protein-ligand interactions.
Halogen bonding (XB) refers to the noncovalent interaction of general structure DX···A between halogen-bearing compounds (DX: XB donor, where X=Cl, Br, I) and nucleophiles (A: XB acceptor). Since theExpand
Fluorine in Medicinal Chemistry
Fluorinated compounds are synthesized in pharmaceutical research on a routine basis and many marketed compounds contain fluorine. The present review summarizes some of the most frequently employedExpand
A Novel Partial Agonist of Peroxisome Proliferator-Activated Receptor-γ (PPARγ) Recruits PPARγ-Coactivator-1α, Prevents Triglyceride Accumulation, and Potentiates Insulin Signaling in Vitro
Partial agonists of peroxisome proliferator-activated receptor-γ (PPARγ), also termed selective PPARγ modulators, are expected to uncouple insulin sensitization from triglyceride (TG) storage inExpand