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The emergence of resistance to existing classes of antiretroviral drugs underlines the need to find novel human immunodeficiency virus (HIV)-1 targets for drug discovery. The viral capsid protein (CA) represents one such potential target. Recently, a series of benzodiazepine inhibitors was identified via high-throughput screening using an in vitro capsid assembly assay (CAA). Here, we demonstrate how a combination of NMR and X-ray co-crystallography allowed for the rapid characterization of the early hits from this inhibitor series. Ligand-based (19)F NMR was used to confirm inhibitor binding specificity and reversibility as well as to identify the N-terminal domain of the capsid (CA(NTD)) as its molecular target. Protein-based NMR ((1)H and (15)N chemical shift perturbation analysis) identified key residues within the CA(NTD) involved in inhibitor binding, while X-ray co-crystallography confirmed the inhibitor binding site and its binding mode. Based on these results, two conformationally restricted cyclic inhibitors were designed to further validate the possible binding modes. These studies were crucial to early hit confirmation and subsequent lead optimization.

A novel series of inhibitors of the HPV11 E1E2 proteinprotein interaction was identified. These inhibitors, which were discovered as a result of high-throughput screening, feature an indandione system spiro-fused onto an appropriately substituted tetrahydrofuran ring. Early stability studies indicated, surprisingly, that this particular series of compounds were readily converted, in binding assay buffer, to the corresponding carboxylates. NMR and mass spectrometry techniques were used to elucidate the structures of these products and the mechanism by which they are produced.

The tetrapeptide Boc-Trp-Phg-Asp-(1-Nal)-NH2 is a potent CCK-B agonist. Interestingly, bis-methylation of the C-terminal carboxamide group of this compound leads to Boc-Trp-Phg-Asp-(1-Nal)-N(Me)2 which behaves as a CCK-B antagonist in electrophysiological studies on hippocampal neurones (Corringer et al., 1993). In order to ascertain whether bismethylation of the terminal carboxamide group has an influence on the conformational preferences of the peptide, we have undertaken a comparative conformational analysis of the two tetrapeptides by the combined use of 2D NMR spectroscopy and restrained molecular dynamics. The solution conformation of the two peptides were examined by 1H NMR in a d6-DMSO/H2O (80:20) mixture. 1H-1H distance constraints, derived from 2D NOESY and ROESY experiments, were used as inputs for subsequent restrained molecular dynamics simulations. Comparison of the NMR and molecular modeling data indicates different conformational preferences for these two peptides. Interestingly, the aromatic side chains of the CCK-B antagonist Boc-Trp-Phg-Asp-(1-Nal)-N(Me)2 in its preferential conformation, overlap their corresponding moieties in the two non peptide CCK-B antagonists L-362,260 and LY-288,513. The differences in conformational behaviour of the studied tetrapeptides could, at least in part, account for their opposite agonist/antagonist profile, a findings which could serve for the design of new conformationally restricted CCK-B analogs.

The present paper reports the molecular modeling-based design and synthesis of an optically pure noncarbohydrate mimetic of sialyl Lewis X to inhibit E-selectin. Biological evaluation of the designed substance as well as that of its enantiomer gave, contrary to expectations, comparable IC50 values. Results are discussed in terms of receptor binding specificity and the molecular modeling protocol used.

The virally encoded NS3 protease is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. The design and synthesis of 15-membered ring beta-strand mimics which are capable of inhibiting the interactions between the HCV NS3 protease enzyme and its polyprotein substrate will be described. The binding interactions between a macrocyclic ligand and the enzyme were explored by NMR and molecular dynamics, and a model of the ligand/enzyme complex was developed.