QUANTUM and albumin binding calculations: the role of protein flexibility

Drug distribution within the body is determined mainly by free (unbound) concentration of drug in circulating plasma. The unbound fraction, in turn, depends on drug absorption by plasma proteins. Human Serum Albumin (HSA) is the most abundant blood plasma protein and is produced in the liver.

Binding of a compound to HSA results in an increased solubility in plasma, decreased toxicity, and /or protection against oxydation of the bound ligand. Binding can also have a significant impact on the pharmacokinetics of drugs, e.g. prolonging in vivo half life of the therapeutic agent. However too strong binding prevents drug release in tissues. That is why HSA binding information is one of the key characteristics of a compound determining its ADME properties. Successful in silico calculation of HSA binding could provide a structural basis of drug derivatives with altered HSA-binding properties.

HSA has at least two main drug binding sites characterized as Sudlow site I and Sudlow site II, which bind a number of drugs selectively. Site I, also known as the warfarin binding site, is formed by a pocket in subdomain IIA of HSA. Site II is located in subdomain IIIA and is known as the benzodiazepine binding site. Ibuprofen and diazepam are selectively bind to site II. Multiple active sites make HSA a complicated target for structure-based modeling.

The ligands with known HSA binding affinities were taken from and prepared with a set of built in QUANTUM molecular preparation and processing tools. Acenocoumarol, Acetylsalicilic_acid, Azapropazone, Benzylpenicillin, Benzylthiouracil, Bilirubin, Canrenoate, Carbamazepine, Carbenicillin, Chlorpropamide, Diphenylhydantoin, Furosemide, Indomethacin, Methyl_p-hydroxybenzoate, N-acetyl-L-tryptophan, Oxyphenbutazone, Phenobarbital, phenyl_salicylate, Phenylbutazone, Piretanide, Propyl_p-hydroxybenzoate, Quercetin, Salicylate, Sodium_benzoate, Spironolactone, Sulfadimethoxine, Sulfamethizole, Sulfathiazole, sulfisoxazole, Tenoxicam, Tolbutamide, Warfarin, Carprofen, Chlofibrate, Iopanoate, L-tryptophan were docked on to both of the sites. Three different structures – 2BXH, 2BXF and 2BXG were taken for docking. 2BXH was used for docking to the first binding site, 2BXF and 2BXG have different structures of the binding site II and we decided to use both structures for docking. Docking grid 20x20x20A were centered around a central ligand atom in appropriate binding site.

The results of the docking runs are summarized on the Figure. Both binding sites show considerable flexibility, molecular dynamics and the binding free energy calculations with flexible protein (large red points) lead to remarkable improvement of the predicted values of HSA binding affinities with respect to experiment (smaller blue points represent the results of docking on a rigid protein model). Since QUANTUM model does not have training parameters the presented correlation proves QUANTUM abilities to predict HSA binding constants of druglike compounds to both of the active sites.