Current Topics in Medicinal Chemistry - Volume 14, Issue 23, 2014

Studying the effects of drugs on the metabolome constitutes a huge part of the metabolomics discipline. Whether the approach is associated with drug discovery (altered pathways due to the disease that provide future targets and information into the mechanism of action or resistance, etc.) or pharmacometabolomics (studying the outcome of treatment), there have been many aspiring published articles in this area. With specific experimental design, including fingerprinting analysis with different analytical platforms in a non-targeted way, the approach is advancing towards the discovery of markers for the implication of personalised medicine, while also providing information that could help to improve the efficacy and reduce the side effects associated with a treatment. In this review, the evolution of pharmacometabolomics from other areas of drug efficacy metabolomics studies is explored.

Nanodiscs are disc-like structures formed by two copies of a membrane scaffold protein, engineered from apolipoprotein A-I, surrounding a phospholipid mixture that can incorporate membrane proteins preserving their natural properties. They behave as soluble entities allowing the use of high-resolution structural techniques to determine the structural organization of the embedded membrane protein, and the use of solution biochemical-biophysical tools to measure its activity, assembly and interactions with other proteins in membranelike environments. In addition, nanodiscs are biocompatible which makes them an attractive technology to be used in therapy, drug discovery, and other biotechnological applications.

Peptide nanotubes are novel supramolecular nanobiomaterials that have a tubular structure. The stacking of cyclic components is one of the most promising strategies amongst the methods described in recent years for the preparation of nanotubes. This strategy allows precise control of the nanotube surface properties and the dimensions of the tube diameter. In addition, the incorporation of 3- aminocycloalkanecarboxylic acid residues in the nanotube-forming peptides allows control of the internal properties of the supramolecular tube. The research aimed at the application of membrane-interacting self-assembled cyclic peptide nanotubes (SCPNs) is summarized in this review. The cyclic peptides are designed to interact with phospholipid bilayers to induce nanotube formation. The properties and orientation of the nanotube can be tuned by tailoring the peptide sequence. Hydrophobic peptides form transmembrane pores with a hydrophilic orifice, the nature of which has been exploited to transport ions and small molecules efficiently. These synthetic ion channels are selective for alkali metal ions (Na+, K+ or Cs+) over divalent cations (Ca2+) or anions (Cl-). Unfortunately, selectivity was not achieved within the series of alkali metal ions, for which ion transport rates followed the diffusion rates in water. Amphipathic peptides form nanotubes that lie parallel to the membrane. Interestingly, nanotube formation takes place preferentially on the surface of bacterial membranes, thus making these materials suitable for the development of new antimicrobial agents.

The delivery of drugs can be improved with the use of different carriers, such as those based on nanoparticles. The nanostructures loaded with the therapeutic molecules should be able to reach the target cells and, what is more, release the drugs efficiently. Ideally, the drugs should be delivered only in the target cells, and not along their way to the cells. For these reasons several approaches have been developed to control the release of the drugs at the desired sites. In this review article we have summarized the reports that describe the use of glutathione to trigger the release of the therapeutic molecules from different nanostructures.

Toll-like receptors (TLRs) are a family of proteins with a key role in the innate immune system. They are specialized in the recognition of molecular patterns present in microbial components, through mechanisms not yet unraveled at atomic level. Improvement in the understanding of the molecular mechanisms that drive TLR signaling is of paramount importance to grasp key aspects of immunity, potentially leading to the design of new molecules able to modulate their functions. Toll-like receptor 4 (TLR4), along with its accessory protein myeloid differentiation factor 2 (MD-2), builds a heterodimeric complex that specifically recognizes lipopolysaccharides (LPS), which are present on the cell wall of gramnegative bacteria, activating the immune response. Some TLR4 modulators are undergoing preclinical and clinical evaluation for the treatment of sepsis, inflammatory diseases, cancer, and rheumatoid arthritis. Reported X-ray crystal structures together with molecular modeling studies, not reviewed before in the literature, have recently contributed to the elucidation of key interactions at atomic level of the binding between the TLR4/MD-2 system and different TLR4/MD-2 ligands. The purpose of this review is to summarize these reported studies which may account for the SAR rationalization of natural/ synthetic agonist/antagonist TLR4 binders and may also guide further design of novel TLR4 modulators.

Choline kinase (CK) is a homodimeric enzyme that catalyses the transfer of the ATP γ-phosphate to choline, generating phosphocholine and ADP in the presence of magnesium. Several isoforms of CK are present in humans but only the HsCKα has been associated with cancer and validated as a drug target to treat this disease. As a consequence a large number of compounds based on Hemicholinium (HC-3) have been described. Two compounds, previously reported to inhibit the human enzyme, have recently been shown to inhibit P. falciparum CK (PfCK) and therefore their potential applications might be anticipated to other pathogens. Herein, using molecular dynamic simulations, we have firstly observed that the ATP and the choline binding site of different CK in pathogens and human are conserved, suggesting that previous compounds inhibiting the human enzyme may also interact with CKs from different pathogens. We have substantiated such observation with experimental assays showing that HsCKα1, PfCK and CpCK bind to two compounds with distinct structural features in the low μM range. Collectively, these results uncover similarities among the choline kinase binding site from different pathogenic species and the human enzyme, highlighting the feasibility of designing novel inhibitors based on the choline binding pocket.

Different chemoenzymatic strategies for the preparation of carbohydrates and analogues possessing antidiabetic or anticancer activity are summarized. In this sense, some examples illustrating the use of enzymes such as aldolases, lipases or glycosidases (in some cases improved by genetic engineering techniques) are presented, showing the advantages of the implementation of chemoenzymatic protocols, which combine the flexibility of chemical synthesis with the efficiency, selectivity and sustainability of biotransformations to obtain diverse complex carbohydrates, glycoconjugates and glycomimetics.

Cys-Xxx-Ser-Xxx-Pro-Cys (Xxx= any amino acid but Pro) is the most common sequence present in naturally occurring peptides and proteins glycosylated with β-O-glucose (β-O-Glc). Taking into account the lack of studies concerning the spatial disposition of this sequence, we have synthesized and analyzed, in aqueous solution, the conformational behavior of peptides and a glycopeptide derived from the particular fragment Cys-Ala-Ser-Ser-Pro-Cys. This sequence is found in the crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Our studies, based on the use of NOESY experiments in combination with molecular dynamics (MD) simulations, indicate that for this particular fragment, initially characterized by a type I β-turn motif, the glycosylation with β-O-Glc forces the peptide backbone into an extended conformation. This conformation is stabilized by the presence of both hydrogen bonds and water pockets between the peptide and the sugar moieties.

The synthesis of a variety of phenyl- and indeno-1,5-naphthyridine derivatives as new substrates with anticancer activity is described. Several of the prepared products were addressed to in vitro anticancer screening which indicated that some of them exhibited inhibitory effect of Top1 and antiproliferative activity against human colon cancer cells (COLO 205).

Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes joint inflammation and extra-articular manifestations. To prevent progressive and irreversible structural damage, early diagnosis of RA is of paramount importance. Antibodies directed against citrullinated proteins and peptides (ACPAs) are the most specific serological markers available for diagnosing RA. ACPAs may be detected several years before symptoms appear, and their presence at disease onset is a good predictor of the development of erosive joint lesions. Synthetic peptides can replace cognate proteins in solid-phase assays for specific autoantibody recognition in RA patients. The use of synthetic peptides instead of proteins represents an advantage in terms of the reproducibility of such immunoassays. They give absolute control over the exact epitopes presented. Furthermore, it is difficult to prepare sufficient amounts of high-quality antigenic proteins with a well-defined degree of citrullination. Synthetic citrullinated peptides, in contrast, are easily obtained in a pure form with a well-defined chemical structure and the epitopes can be precisely oriented in the plate by covalent binding of the peptides. We have recently obtained and highlighted the application of chimeric peptides bearing different citrullinated protein domains for the design of RA diagnosis systems. Our results indicate that more than one serological test is required to classify RA patients based on the presence or absence of ACPAs. Each of the target molecules reported (fibrin, vimentin and filaggrin) helps to identify a particular subset of RA patients.

The properties of triplet excited states are markedly medium-dependent, which turns this species into valuable tools for investigating the microenvironments existing in protein binding pockets. Monitoring of the triplet excited state behavior of drugs within transport proteins (serum albumins and α1-acid glycoproteins) by laser flash photolysis constitutes a valuable source of information on the strength of interaction, conformational freedom and protection from oxygen or other external quenchers. With proteins, formation of spatially confined triplet excited states is favored over competitive processes affording ionic species. Remarkably, under aerobic atmosphere, the triplet decay of drug@protein complexes is dramatically longer than in bulk solution. This offers a convenient dynamic range for assignment of different triplet populations or for stereochemical discrimination. In this review, selected examples of the application of the laser flash photolysis technique are described, including drug distribution between the bulk solution and the protein cavities, or between two types of proteins, detection of drug-drug interactions inside proteins, and enzyme-like activity processes mediated by proteins. Finally, protein encapsulation can also modify the photoreactivity of the guest. This is illustrated by presenting an example of retarded photooxidation.

The regeneration of brain tissue is one of the major challenges in regenerative medicine due to the lack of viable grafts to support the re-growth of functional tissue after a traumatic injury. The development of biocompatible and biodegradable structures with appropriate morphology for the interaction with neural tissue is required. The objective pursued in this work is to develop a biodegradable 2D scaffold structure for neural tissue engineering. Poly(ε-caprolactone) (PCL) was the selected material due to its biocompatibility and biodegradability in the long term. PCL (15%w/w) was dissolved in N-methylpyrrolidone and the film was fabricated by phase inversion casting technique employing ethanol and isopropanol as coagulation baths. The physical structure, morphology and topography of the flat scaffolds were characterized using different techniques. The two different scaffolds presented homogeneous structure with high porosity (higher than 85%), contact angles higher than 90°, high roughness (Ra 0.6 μm) and superficial pore sizes of 0.7 and 1.7 μm, respectively. Permeance tests showed high water permeabilities (~350-590 mL m-1 bar-1 h-1) indicative of promising nutrients supply to the cells. Finally, in vitro human glioblastoma cells cultures after 48 hours showed good cell attachment, proliferation and penetration in the scaffolds. Detailed evaluation of the interaction between the surface morphology and the properties of the scaffolds with the cell response has been done. Thus, the PCL films herein fabricated show promising results as scaffolds for neural tissue regeneration.