An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.

The Src-homology-3 (SH3) domain of the Caenorhabditis elegans protein Sem-5 binds proline-rich sequences. It is reported that the SH3 domains broadly accept amide N-substituted residues instead of only recognizing prolines on the basis of side chain shape or rigidity. We have studied the interactions between Sem-5 and its ligands using molecular dynamics (MD), free energy calculations, and sequence analysis. Relative binding free energies, estimated by a method called MM/PBSA, between different substitutions at sites -1, 0, and +2 of the peptide are consistent with the experimental data. A new method to calculate atomic partial charges, AM1-BCC method, is also used in the binding free energy calculations for different N-substitutions at site -1. The results are very similar to those obtained from widely used RESP charges in the AMBER force field. AM1-BCC charges can be calculated more rapidly for any organic molecule than can the RESP charges. Therefore, their use can enable a broader and more efficient application of the MM/PBSA method in drug design. Examination of each component of the free energy leads to the construction of van der Waals interaction energy profiles for each ligand as well as for wild-type and mutant Sem-5 proteins. The profiles and free energy calculations indicate that the van der Waals interactions between the ligands and the receptor determine whether an N- or a Calpha-substituted residue is favored at each site. A VC value (defined as a product of the conservation percentage of each residue and its van der Waals interaction energy with the ligand) is used to identify several residues on the receptor that are critical for specificity and binding affinity. This VC value may have a potential use in identifying crucial residues for any ligand-protein or protein-protein system. Mutations at two of those crucial residues, N190 and N206, are examined. One mutation, N190I, is predicted to reduce the selectivity of the N-substituted residue at site -1 of the ligand and is shown to bind similarly with N- and Calpha-substituted residues at that site.

Maintenance of caspase-3 proenzyme dormancy by an intrinsic "safety catch" regulatory tripeptide.

Caspase-3 is synthesized as a dormant proenzyme and is maintained in an inactive conformation by an Asp-Asp-Asp "safety-catch" regulatory tripeptide contained within a flexible loop near the large-subunit/small-subunit junction. Removal of this "safety catch" results in substantially enhanced autocatalytic maturation as well as increased vulnerability to proteolytic activation by upstream proteases in the apoptotic pathway such as caspase-9 and granzyme B. The safety catch functions through multiple ionic interactions that are disrupted by acidification, which occurs in the cytosol of cells during the early stages of apoptosis. We propose that the caspase-3 safety catch is a key regulatory checkpoint in the apoptotic cascade that regulates terminal events in the caspase cascade by modulating the triggering of caspase-3 activation.

Structure-based design of COX-2 selectivity into flurbiprofen.

Comparative computer modeling of the X-ray crystal structures of cyclooxygenase isoforms COX-1 and COX-2 has led to the design of COX-2 selectivity into the nonselective inhibitor flurbiprofen. The COX-2 modeling was based on a postulated binding mode for flurbiprofen and took advantage of a small alcove in the COX-2 active site created by different positions of the Leu384 sidechain between COX-1 and COX-2. The design hypothesis was tested by synthesis and biological assay of a series of flurbiprofen analogs, culminating in the discovery of several inhibitors having up to 78-fold selectivity for COX-2 over COX-1.

Topological similarities between a cyclic enkephalin analogue and a potent opiate alkaloid: a computer-modeling approach.

The cyclic enkephalin analogue H-Tyr-cyclo[-D-N delta-Orn-Gly-Phe-Leu-] (1-c) and the rigid narcotic alkaloid 7 alpha-[(1R)-1-hydroxy-1-methyl-3-phenylpropyl]-6,14- endo-ethenotetrahydrooripavine (PEO) were studied by using computer graphics methods to investigate potential geometrical congruencies of their respective pharmacophoric elements. Particular emphasis was placed on the relative spatial disposition of the tyramine moiety and the additional aromatic ring that occurs in both molecules. A three-dimensional vector map was generated defining the locus of the C21 aromatic ring for all those conformers of PEO having up to 10 kcal above the minimum energy conformer. A systematic conformational search on the cyclic peptide afforded four allowable sets of conformers whose side chain of the phenylalanine residue coincided with the vector map of PEO. Local energy minima for the peptide within the revised mutual vector space were found and subjected to bimolecular energy refinement with correspondingly local energy minima for the opiate alkaloid. Several low-energy conformers of the cyclic peptide were identified that permitted a good fit with the alkaloid provided that the tyramine moiety of the respective molecules does not coincide. In the designated conformations the basic nitrogen of the former occupies a distinct geometrical locus, and the side chain of the leucine residue has no structural correlate in the alkaloid.