Dale F. Mierke

Coupling constants again: Experimental restraints in structure refinement

SummaryUtilization of coupling constants as restraints in computational structure refinement is reviewed. In addition, we address the effect of conformational averaging and examine different approaches to apply the restraints when the experimental observable is obviously a result of averaging. Here, two different computational methods are compared. The simulation of a single structure with time-dependent restraints produces results very similar to those obtained with the calculation of numerous copies of the molecule (an ensemble of structures) and ensemble averaging. The advantages and disadvantages of the two methods are illustrated with simulations of cyclosporin A, for which 117 NOEs and 62 homo- and heteronuclear coupling constants have been measured.

1,2,5-Trisubstituted 1,4-diazepine-3-one: A novel dipeptidomimetic molecular scaffold

The continuing effort to transform bioactive peptides into non-peptide peptidomimetics of therapeutic potential requires a diversity of tools such as molecular scaffolds, pseudopeptide modifications, and conformation mimetics. To this end, a novel polyfunctional monoheterocyclic system, 1,2,5-trisubstituted hexahydro-3-oxo-1H-1,4-diazepine ring (DAP), was designed. The linear precursor for the DAP was generated through a reductive alkylation step including a modified side chain and an α-amino function of two amino acid derivatives. Structural analysis of model diastereomeric DAPs, employing1H and13C NMR and computer simulation, revealed the conformational preferences of this system. The structural similarities to the 1,4-benzodiazepine, a common molecular scaffold for many non-peptidic peptidomimetic agents, and the pronounced dipeptidomimetic character of the DAP system offer a new powerful tool to medicinal chemists engaged in rational peptide-based drug design.

Models for understanding and predicting protein structure

Publisher Summary In this chapter, some methods currently employed in the prediction of tertiary structure from the protein sequence are presented. There are many different methods to attack the problem of predicting protein structure. If the protein is a member of a family of closely related proteins, the structure can be postulated through homology analysis. If this is not the case, a sequential approach can be envisioned in which the secondary elements are predicted from the primary sequence and then the different topological orientations of these elements are examined and judged using some energy-function description of the protein. Other methods are based on the observation that protein structures are tightly packed with almost no vacant space in the interior or core of the protein. Such a tight packing of the amino acids then suggests that the arrangements of the polypeptide chain can be restricted to the points of a lattice, greatly reducing the number of possible orientations. These methods do not differentiate between secondary and tertiary structure nor depend on previously determined protein structures.

Conformational investigation of a novel dipeptide based molecular scaffold

The conformational features of a novel, dipeptide-based molecular scaffold are described. Four model systems of a trisubstituted 1,4-diazepine-3-one system, varying in the chirality and amino acid within the ring system, have been investigated by high-resolution NMR and metric-matrix distance geometry calculations. Because of the small number of protons within the scaffold, nuclear Overhauser effects provide only limited conformational information. Instead, extensive use of scalar1H−H1 and1H−13C coupling constants was utilized in the refinement. The resulting conformations of the model systems provide insigh into the expected topological orientation of the amino acids or chemical functionalities and attached to the seven-membered ring system, the first step of the utilization of this scaffold in the rational design of peptidomimetics.