Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins.

Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.

Pharmacophore optimization of imidazole chalcones to modulate microtubule dynamics.

We recently reported a new class of imidazole-based chalcones as potential antimitotic agents. In view of their promising cytotoxic activity, a comprehensive structure-activity relationship (SAR) of these compounds was undertaken focusing on four major structural variations: the length of the molecule, the Michael acceptor character, the nature and substitution pattern of ring B, and the nature of the amide functionality tethering ring B. These second-generation analogs (IBCs) demonstrated a superior bioactivity profile than the previously reported imidazole chalcones (referred to as IPEs). The analog IBC-2 with one less methylene group (nor series) and para-fluoro substituted ring B demonstrated the best cytotoxicity profile among the library of compounds. A computational analysis of the NCI-60 data associated both IBCs and the previously reported IPEs with the privileged pharmacological pharmacophore of chalcones. Interestingly, biological studies suggest that the imidazole ring is essential for cytotoxic activity of the elongated chalcone analogues. Immunofluorescence studies revealed that IBC-2, unlike IPEs, has the ability to induce microtubule catastrophe independently of Aurora-B inhibition. The effects of IBC-2 on microtubule dynamics are similar to those of Nocodazole, but the cell cycle effects appear to be different. In-silico studies demonstrate that the members of the new series have the ability to bind to the colchicine binding site of ß-tubulin with binding scores similar to those of IPEs, corresponding chalcones and Nocodazole. Although tubulin binding can partially explain the biological effects of IBC-2, on-going target identification studies are aimed at further investigation of its biological targets.

Synthesis and characterization of luminescent cadmium selenide/zinc selenide/zinc sulfide cholinomimetic quantum dots.

Luminescent quantum dots conjugated with highly selective molecular recognition ligands are widely used for targeting and imaging biological structures. In this paper, water soluble cholinomimetic cadmium selenide (core), zinc selenide/zinc sulfide (shell) quantum dots were synthesized for targeting cholinergic sites. Cholinomimetic specificity was incorporated by conjugation of the quantum dots to an aminated analogue of hemicholinium-15, a well known competitive inhibitor of the high affinity choline uptake transporter. Detailed evaluation of the nanocrystal synthesis and characterization of the final product was conducted by (1)H and (31)P NMR, absorption and emission spectroscopy, as well as transmission electron microscopy.

Electrochemical detection of acetylcholine and choline: application to the quantitative nonradiochemical evaluation of choline transport.

The development of analytical methods for determining the cholinergic biomarkers acetylcholine (ACh) and choline (Ch) is important for assessing their role in neurological and cognitive functions. In this review, electrochemical (EC) strategies to detect ACh and Ch are summarized and compared to other analysis methods. Recent research focusing on the development of a versatile nonradiochemical in vitro assay to evaluate Ch transport is also described. The assay coupled to analysis by capillary electrophoresis (CE) with indirect EC detection at an enzyme-modified microelectrode affords exceptional selectivity and sensitivity. Femtomole or lower mass detection limits for ACh (1 fmol) and Ch (100 amol) have been readily achieved, opening up a new range of possible experiments for investigating transport or turnover of Ch and ACh in neurobiological systems. The value of this method is illustrated through the evaluation of the pharmacological efficacy and mode of inhibition of a new class of quaternary ammonium alkyl-substituted catechol-based inhibitors of high-affinity choline transport (CHT). This microanalytical approach is particularly useful when knowledge of endogenous concentrations of Ch or ACh is desired or when the amount of available compounds or the sample size is limited. A brief description of the principles of CE is also provided.

Design, total synthesis, and evaluation of novel open-chain epothilone analogues.

[structure: see text] The design, total synthesis, and biological evaluation of two open-chain analogues of epothilone incorporating the critical C1-C8 fragment and the aromatic side chain held together by a small molecular scaffold have been achieved. Biological evaluation revealed that further restraint between the flexible C1-C8 region and the molecular scaffold may be necessary for potent inhibition of cell proliferation.

Evaluation of chiral discrimination of highly negatively charged enantiomers by quaternary ammonium beta-cyclodextrin using 1H NMR.

The positively charged quaternary ammonium cyclodextrin, QA-beta-CD, was previously used as a chiral selector to achieve baseline resolution of two of the dianionic enantiomers of disodium 3-(p-isothiocyanatophenoxy)-3-(p-isothiocyanatophenyl)propane-1,2-disulfate by capillary electrophoresis. The basis of the chiral discrimination between QA-beta-CD and the enantiomers was investigated by (1)H NMR spectroscopy. COSY and NOESY spectra were used to infer the role that molecular interactions and the stereocenters have upon association of QA-beta-CD with the enantiomers. A parallel two-step complexation model is used to rationalize the NMR and the chiral discrimination observed during separation of the enantiomers.