Halogen bonding triggers activity: Increasing binding affinity was observed for a series of covalent human Cathepsin L inhibitors by exchanging an aryl ring H atom with Cl, Br, and I, which undergo halogen bonding with the CO group of Gly61 in the S3 pocket of the enzyme. Fluorine, in contrast, strongly avoids halogen bonding (see scheme). The strong distance and angle dependence of halogen bonding was confirmed for biological systems.

The retinoid-binding site in CRABPs differs significantly from that observed in CRBP. Structural changes in three juxtaposed areas of the protein create a new, displaced binding site for RA. The carboxylate of the ligand interacts with the expected trio of residues (Arg132, Tyr134 and Arg111; CRABP II numbering). The RA ligand is almost flat with the beta-ionone ring showing a significant deviation (-33 degrees) from a cis conformation relative to the isoprene tail. The edge atoms of the beta-ionone ring are accessible to solvent in a suitable orientation for presentation to metabolizing enzymes. The bulkier synthetic retinoid causes small conformational changes in the protein structure.

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A system was devised which allows the efficient substitution of cysteine residues in a protein by selenocysteine. It involves overexpression of the respective gene with the aid of the T7 promotor/polymerase system in a cysteine auxotrophic strain. The induction of the T7 polymerase formation was performed in cysteine-supplemented medium followed by wash-out of the cysteine and production of the desired gene product in the presence of selenocysteine. The system was applied to substitute the two cysteine residues in Escherichia coli thioredoxin. Analysis of the purified gene product by electrospray mass spectrometry and HPLC revealed that both cysteine residues were replaced in approximately 75-80% of the protein, only one cysteine residue was substituted in about 5-10%, and no substitution had taken place in 12-17% of the protein. The occurrence of diselenide, seleno-sulfur, and disulfide bridges in the purified gene product was revealed by ES/MS and chemical modification studies. The diselenide bridge represents an entity in protein structures which has hitherto not been described. The redox property of the selenocysteine variant of thioredoxin [(Se)2-thioredoxin] was found to be substantially different from that of thioredoxin. Only the latter could be reduced under native conditions in the presence of an excess of beta-mercaptoethanol. The oxidized (Se)2-thioredoxin was then separated from the selectively reduced and carboxymethylated protein by anion-exchange chromatography. The purity of the isolated (Se)2-thioredoxin was at least 92%.

In two series of small-molecule ligands, one inhibiting human cathepsin L (hcatL) and the other MEK1 kinase, biological affinities were found to strongly increase when an aryl ring of the inhibitors is substituted with the larger halogens Cl, Br, and I, but to decrease upon F substitution. X-ray co-crystal structure analyses revealed that the higher halides engage in halogen bonding (XB) with a backbone C=O in the S3 pocket of hcatL and in a back pocket of MEK1. While the S3 pocket is located at the surface of the enzyme, which provides a polar environment, the back pocket in MEK1 is deeply buried in the protein and is of pronounced apolar character. This study analyzes environmental effects on XB in protein-ligand complexes. It is hypothesized that energetic gains by XB are predominantly not due to water replacements but originate from direct interactions between the XB donor (Caryl-X) and the XB acceptor (C=O) in the correct geometry. New X-ray co-crystal structures in the same crystal form (space group P2(1)2(1)2(1)) were obtained for aryl chloride, bromide, and iodide ligands bound to hcatL. These high-resolution structures reveal that the backbone C=O group of Gly61 in most hcatL co-crystal structures maintains water solvation while engaging in XB. An aryl-CF3-substituted ligand of hcatL with an unexpectedly high affinity was found to adopt the same binding geometry as the aryl halides, with the CF3 group pointing to the C=O group of Gly61 in the S3 pocket. In this case, a repulsive F2C-F⋅⋅⋅O=C contact apparently is energetically overcompensated by other favorable protein-ligand contacts established by the CF3 group.