Current Drug Discovery Technologies - Volume 3, Issue 2, 2006

In the past several years nuclear magnetic resonance (NMR) spectroscopy has emerged as a valuable tool in the drug discovery field. In such context, several NMR-based techniques have been developed aimed at the identification and subsequent optimization of novel binders for a given protein target. Among the different NMR approaches, those relying on the transferred Nuclear Overhauser Effect (tr-NOE) appear to be particularly useful as in some instances, in addition to binding, tr-NOE may provide also structural information on the binding mode of a ligand. In the current work we will reiterate the basic principles and applications that are related to measurements of tr-NOEs. The tr-NOE can be applied as a screening tool to recognize ligands for a given target protein in a mixture of compounds or to identify pair of molecules that bind to a protein simultaneously on adjacent sites (interligand NOEs). Moreover, in the case of peptide-ligands, tr- NOEs furnish intra-molecular distance constraints that can be used to determine their bioactive conformation. Starting from the conformation thus obtained, a pharmacophoric model can be derived and later used to search within a 3D database of small molecules to find new potentially active non-peptide compounds that fit the pharmacophore. We will report examples of each of the above mentioned strategies.

A P450 catalyzed N-para-hydroxy metabolite was suggested to be a prerequisite for N-dephenylation occurrence. Although two mechanisms have been proposed to describe this process as a consequence of either a chemical degradation or P450 lead epoxidation of the hydroxy metabolite, direct evidence has not been demonstrated. In this study, we started with a novel technique using a dipeptide, Lys-Phe, to trap the byproduct of N-dephenylation, a quinone-like compound, forming a peptide adduct to facilitate LC/MS characterization. N-dephenylation via chemical degradation was assessed by LC/MS characterization of the resulting (Lys-Phe)2-quinone from 4-hydroxyphenyl-2- naphthylamine following interaction with Lys-Phe in pH 7.4 buffer. N-dephenylation mediated by P450 catalysis proposed was investigated in N-para-hydroxy benzodioxane derivative incubated with mouse liver microsomes in the presence of Lys-Phe in 50/50 H2 16O/H2 18O. LC/MS demonstrated that only one of two hydroxy oxygens in the byproduct was exchanged with water and the MS signal intensity of the 16O labeled peptide adduct was equal to that of 18O labeled. These observations suggested us that the origin of the oxygen in the byproduct was from water only, not from O2. Therefore, it appears that N-dephenylation occurs via a stepwise process, namely the substrate is initially metabolized to a N-para-hydroxy metabolite by P450, which was readily oxidized to a quinone imine/iminium chemically or enzymatically, then hydrolyzed resulting in N-dephenylation. However, in our studies, the proposed P450 mechanism involving epoxidation of a N-para-hydroxy metabolite was disproved.

The quality of the data generated in a high throughput screening (HTS) run is fundamental for selecting bona fide inhibitors and for ensuring the capture of the full richness of inhibitors present in a chemical library. For this purpose a quality control filter based on three one dimensional (1D) proton NMR experiments is proposed. The approach called SPAM (Solubility, Purity and Aggregation of the Molecule) Filter requires the acquisition of a 1D reference spectrum, a WaterLOGSY spectrum and/or a selective longitudinal relaxation filter spectrum for the identified hits dissolved in aqueous solution and in the presence of a water soluble reference molecule. This palette of experiments permits the rapid characterization of the identity, purity, solubility and aggregation state of the active compound. This knowledge is crucial for deriving accurate IC50 and KI values of the inhibitors, for identifying false negatives and for detecting promiscuous inhibitors. Only compounds that pass through the SPAM Filter can be considered as starting points for medicinal chemistry efforts directed toward lead optimization. Examples of this approach in the identification of false positives in a screening run against the enzyme thymidine phosphorylase (TP) and the rescue of a false negative in a screening run against the Ser/Thr kinase AKT1 are presented.

Mucobromic and mucochloric acid were used as building blocks for the construction of a chemical combinatorial library of 3,4,5-trisubstituted 2(5H)-furanones. With these 2 butenolide building blocks, and eight alcohols a sublibrary of 16 dihalogenated 5-alkoxy-2(5H)-furanones was prepared. This sublibrary of 5-alkoxylated furanones was reacted with 16 amines generating a full size focussed combinatorial library of 256 individual compounds. This three dimensional combinatorial library of 3-halogen-4-amino-5-alkoxy-2(5H)-furanones was prepared around the benzimidazolyl furanone lead structure by applying a solution phase combinatorial chemistry concept. Typical representatives of the library were purified and fully characterized and one x-ray structures was recorded, additionally. The 3-bromo-4-benzimizazolyl-5-methoxy-2(5H)furanone, Br-A-l, showed an MIC of 8 μg/ml against the multiresistant Staphylococcus aureus ( MRSA).

Macrophages play an important role in inflammatory processes and are crucially involved in the onset and progression of atherosclerosis and tumorigenesis. Therefore, macrophages are regarded as an excellent target for therapeutic intervention. Since the scavenger receptor class A (SRA) is highly expressed on macrophages, we developed in the present study an SRA-specific particulate drug carrier by providing phosphatidylcholine liposomes with a targeting ligand for SRA. To enable firm association with liposomes, the high-affinity SRA ligand decadeoxyguanine was covalently attached via a linker to lithocholic oleate (LCO-dA2dG10). Incorporation of LCO-dA2dG10 into liposomes resulted in an increased electronegative surface charge and a dramatically enhanced serum clearance (t1/2 < 2 min versus > 5 h). The LCO-dA2dG10-induced liposome clearance was fully dependent on SRA, as the clearance could be efficiently inhibited by the SRA competitor polyinosinic acid. LCO-dA2dG10 enhanced the affinity of liposomes for SRA in vivo selectively, since introduction of overall or clustered negative charges by other modifications (e.g. oxidation, inclusion of phosphatidylserine, or exposure of glutamic acid residues) did not affect their serum clearance substantially, albeit that these modifications resulted in an at least equally high negative surface charge. LCO-dA2dG10 also increased the association of liposomes with RAW264.7 cells, resulting in an enhanced intracellular delivery and bioactivity of encapsulated dexamethasone-phosphate. Therefore, the SRA-specificity of LCOdA2dG10- liposomes may be applied for the specific delivery of drugs to macrophages, which may be of therapeutic benefit in general inflammatory disorders, atherosclerosis, and tumorigenesis.

Amyloidosis comprises a group of diseases characterized by the deposition of insoluble protein fibrils in specific organs and includes several serious medical disorders, such as Alzheimer's disease, prion-associated transmissible spongiform encephalitis, and type II diabetes. Despite the structural dissimilarity between the soluble proteins and peptides, these fibrils exhibit similar morphologies under electron microscopy with a characteristic 'cross β- sheet' pattern examined by x-ray fiber diffraction experiments. Many studies have revealed that each of these diseases is associated to a specific protein that is partially unfolded, misfolded, and aggregated. However, the detailed structures of the causative agents and the toxicity mechanisms are less known. This review summarizes recent studies in the conformational disorders leading to aggregation; including which proteins potentially cause conformational diseases, the aggregation mechanisms of these proteins, and recent researches on the conformational changes using advanced experiments or molecular dynamics simulations. Finally, current drug designs towards these protein conformational diseases are also discussed. It is believed that the advances in basic understanding of the mechanisms of conformational changes as well as biological functions of these proteins will shed light on the development and design of potential interfering compounds against amyloid formation associated with protein conformational diseases.