Novel inhibitors of procollagen C-proteinase. Part 2: glutamic acid hydroxamates

Glutamic acid derived hydroxamates were identified as potent and selective inhibitors of procollagen C-proteinase, an essential enzyme for the processing of procollagens to fibrillar collagens. Such compounds have potential therapeutic application in the treatment of fibrosis.

Novel inhibitors of procollagen C-terminal proteinase. Part 1: diamino Acid hydroxamates

The parallel synthesis of novel inhibitors of procollagen C-terminal proteinase is described. The synthetic strategy allowed for the facile synthesis of a large number of side-chain diversified diamino acid hydroxamates, of which the D-diaminopropionic acid derivatives were shown to be single digit nanomolar PCP inhibitors.

Applications of random sampling to virtual screening of combinatorial libraries

We describe statistical techniques for effective evaluation of large virtual combinatorial libraries (> 10(10) potential compounds). The methods described are used for computationally evaluating templates (prioritization of candidate libraries for synthesis and screening) and for the design of individual combinatorial libraries (e.g., for a given diversity site, reagents can be selected based on the estimated frequency with which they appear in products that pass a computational filter). These statistical methods are powerful because they provide a simple way to estimate the properties of the overall library without explicitly enumerating all of the possible products. In addition, they are fast and simple, and the amount of sampling required to achieve a desired precision is calculable. In this article, we discuss the computational methods that allow random product selection from a combinatorial library and the statistics involved in estimating errors from quantities obtained from such samples. We then describe three examples: (1) an estimate of average molecular weight for the several billion possible products in a four-component Ugi reaction, a quantity that can be calculated exactly for comparison; (2) the prioritization of four templates for combinatorial synthesis using a computational filter based on four-point pharmacophores; and (3) selection of reagents for the four-component Ugi reaction based on their frequency of occurrence in products that pass a pharmacophore filter.

A rapid computational method for lead evolution: description and application to alpha(1)-adrenergic antagonists

The high failure rate of drugs in the development phase requires a strategy to reduce risks by generating lead candidates from different chemical classes. We describe a new three-dimensional computational approach for lead evolution, based on multiple pharmacophore hypotheses. Using full conformational models for both active and inactive compounds, a large number of pharmacophore hypotheses are analyzed to select the set or "ensemble" of hypotheses that, when combined, is most able to discriminate between active and inactive molecules. The ensemble hypothesis is then used to search virtual chemical libraries to identify compounds for synthesis. This method is very rapid, allowing very large virtual libraries on the order of a million compounds to be filtered efficiently. In applying this method to alpha(1)-adrenergic receptor ligands, we have demonstrated lead evolution from heterocyclic alpha(1)-adrenergic receptor ligands to highly dissimilar active N-substituted glycine compounds. Our results also show that the active N-substituted glycines are part of our smaller filtered library and thus could have been identified by synthesizing only a portion of the N-substituted glycine library.

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains

Polymers of N-substituted glycines ("peptoids") containing chiral centers at the alpha position of their side chains can form stable structures in solution. We studied a prototypical peptoid, consisting of five para-substituted (S)-N-(1-phenylethyl)glycine residues, by NMR spectroscopy. Multiple configurational isomers were observed, but because of extensive signal overlap, only the major isomer containing all cis-amide bonds was examined in detail. The NMR data for this molecule, in conjunction with previous CD spectroscopic results, indicate that the major species in methanol is a right-handed helix with cis-amide bonds. The periodicity of the helix is three residues per turn, with a pitch of approximately 6 A. This conformation is similar to that anticipated by computational studies of a chiral peptoid octamer. The helical repeat orients the amide bond chromophores in a manner consistent with the intensity of the CD signal exhibited by this molecule. Many other chiral polypeptoids have similar CD spectra, suggesting that a whole family of peptoids containing chiral side chains is capable of adopting this secondary structure motif. Taken together, our experimental and theoretical studies of the structural properties of chiral peptoids lay the groundwork for the rational design of more complex polypeptoid molecules, with a variety of applications, ranging from nanostructures to nonviral gene delivery systems.

Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure

We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide alpha-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the alpha-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions.

NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library

Synthesis and screening of combinatorial libraries for pharmaceutical lead discovery is a rapidly expanding field. Oligo-N-substituted glycines (NSGs) were one of the earliest sources of molecular diversity in combinatorial libraries. In one of the first demonstrations of the power of combinatorial chemistry, two NSG trimers, CHIR-2279 and CHIR-4531, were identified as nM ligands for two 7-transmembrane G-protein-coupled receptors. The NMR characterization of these two lead compounds was undertaken to verify covalent connectivity and to determine solution conformations, if any. The sequential chemical shift assignments were performed using a new strategy for assigning 1H and 13C resonances of NSGs. The conformational preferences were then determined in both an aqueous co-solvent system and an organic solvent to probe the effects of hydrophobic collapse. NSGs are expected to be more flexible than peptides due to the tertiary amide, with both cis and trans amide bond conformations being accessible. Solution NMR studies indicate that although CHIR-2279 and CHIR-4531 have identical backbones and termini, and very similar side chains, they do not display the same solution conformational characteristics.

Synthesis, molecular modelling, and NMR structure determination of four cyclic peptide antagonists of endothelin

A combined distance geometry and molecular mechanics/dynamics (MM/MD) protocol was unable to predict the active conformation of the cyclic pentapeptide inhibitor of endothelin-1 receptor, BQ-123, and two analogues. However, the MM/MD method alone is sufficient to predict the solution conformation of a third analogue. In that one case, the combination of proline at residue 3 and an N alpha-methyl substitution at residue 5 provides enough internal constraints to eliminate conformational flexibility seen in the other three analogues. For this constrained analogue, the 50 lowest energy conformations (out of a set of 500 DGEOM-generated, MM/MD minimized conformations) differ by no more than 3.9 kcal/mol. Thirty three of these 50 conformations have backbone atom RMSDs of less than 0.33 A, relative to the lowest energy conformation. The accuracy of this MM/MD model is verified by determining the solution structure of each of the four analogues with 2D NMR techniques. Each of the cyclic pentapeptides has a well defined solution conformation where a proline residue is clearly in a gamma-turn, leaving the remaining residues in a loose beta-turn. All four experimental NMR conformations agree closely with the MM/MD model.

Solution structure of omega-conotoxin GVIA using 2-D NMR spectroscopy and relaxation matrix analysis

We report here the solution structure of omega-conotoxin GVIA, a peptide antagonist of the N-type neuronal voltage-sensitive calcium channel. The structure was determined using two-dimensional NMR in combination with distance geometry and restrained molecular dynamics. The full relaxation matrix analysis program MARDIGRAS was used to generate maximum and minimum distance restraints from the crosspeak intensities in NOESY spectra. The 187 restraints obtained were used in conjunction with 23 angle restraints from vicinal coupling constants as input for the structure calculations. The backbones of the best 21 structures match with an average pairwise RMSD of 0.58 A. The structures contain a short segment of triple-stranded beta-sheet involving residues 6-8, 18-21, and 24-27, making this the smallest published peptide structure to contain a triple-stranded beta-sheet. Conotoxins have been shown to be effective neuroprotective agents in animal models of brain ischemia. Our results should aid in the design of novel nonpeptide compounds with potential therapeutic utility.

Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance

We have designed a set of 17-residue synthetic peptides to be monomeric helices in aqueous solution. Circular dichrosim experiments indicate the presence of helical structure in aqueous solution at low temperature and low pH. The two-dimensional nuclear magnetic resonance results for one of the peptides show a segment of ten residues which clearly meets all of the criteria for the existence of helical structure at both 5 degrees C and 15 degrees C. The first four residues of the peptide are in a largely extended conformation. Calculations suggest that residues 5 through 14 are significantly helical at 5 degrees C. When the temperature is increased, circular dichroism spectra indicate that the helical content decreases. At 15 degrees C, the 3JN alpha coupling constants increase in the helical region, indicating an increase in motion or conformational averaging in the helical segment. None of the peptides has pH titration behavior consistent with salt bridge stabilization of helical conformation. Our data lend themselves to interpretation with the helix dipole model and specific side-chain interactions. When the N and C termini charges are removed the helical content of the peptides increases. The amount of helicity increases as the pH is lowered, due to the ionization of His16. Much of the helical stabilization appears to be due to a specific side-chain interaction between His16 and Tyr12.