Structure-based design of a new series of N -(piperidin-3-yl)pyrimidine-5-carboxamides as renin inhibitors

Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed. Copyright 1999 Academic Press.

A purified preparation of a polypeptide renin substrate prepared by tryptic degradation of the protein renin substrate has been analyzed by the fluorodinitrobenzene method and after degradation with renin, carboxypeptidase, and phenylisothiocyanate, has been found to possess the amino acid sequence; asp-arg-val-tyr-ileu-his-pro-phe-his-leu-leu-val-tyr-ser. The first 10 of these amino acids constitutes hypertensin I which is released by cleavage of the leucyl-leucine bond by renin. The remaining 4 amino acids, leu, val, tyr, ser, apparently link hypertensin I to the protein renin substrate.

Ligand efficiency is a simple metric for assessing whether a ligand derives its potency from optimal fit with the protein target or simply by virtue of making many contacts. Comparison of protein-ligand binding affinities for over 8000 ligands with 28 protein targets shows conclusively that the average ligand binding affinities are not linear with molecular size. It is therefore important to scale ligand efficiencies by the size of the ligand, particularly where small ligands (e.g., fragments) are involved. We propose a simple 'fit quality' metric that removes this dependence.