CrystalDock: a novel approach to fragment-based drug design

We present a novel algorithm called CrystalDock that analyzes a molecular pocket of interest and identifies potential binding fragments. The program first identifies groups of pocket-lining receptor residues (i.e., microenvironments) and then searches for geometrically similar microenvironments present in publically available databases of ligand-bound experimental structures. Germane fragments from the crystallographic or NMR ligands are subsequently placed within the novel binding pocket. These positioned fragments can be linked together to produce ligands that are likely to be potent; alternatively, they can be joined to an inhibitor with a known or suspected binding pose to potentially improve binding affinity. To demonstrate the utility of the algorithm, CrystalDock is used to analyze the principal binding pockets of influenza neuraminidase and Trypanosoma brucei RNA editing ligase 1, validated drug targets in the fight against pandemic influenza and African sleeping sickness, respectively. In both cases, CrystalDock suggests modifications to known inhibitors that may improve binding affinity.     

Quinoxaline excision: a novel approach to tri- and diquinoxaline cavitands

[structure: see text] Selective excision of one or two quinoxaline units from tetraquinoxaline cavitand using catechol and base in DMF yields tri- and diquinoxaline cavitands in yields of up to 71%.     

Sulfonamidoglycosylation of methyl ribofuranosides: a novel approach to furanosylsulfonamides

The sulfonamidoglycosylation of benzylated methyl ribofuranosides using boron trifluoride etherate as catalyst, proceeded effectively to give the new sulfonamidofuranosides with good to high yields.     

SURFCOMP: a novel graph-based approach to molecular surface comparison

Analysis of the distributions of physicochemical properties mapped onto molecular surfaces can highlight important similarities or differences between compound classes, contributing to rational drug design efforts. Here we present an approach that uses maximal common subgraph comparison and harmonic shape image matching to detect locally similar regions between two molecular surfaces augmented with properties such as the electrostatic potential or lipophilicity. The complexity of the problem is reduced by a set of filters that implement various geometric and physicochemical heuristics. The approach was tested on dihydrofolate reductase and thermolysin inhibitors and was shown to recover the correct alignments of the compounds bound in the active sites.     

Extended RCM-ROM sequences: a novel approach to polyunsaturated trisaccharides

The first examples of RCM-ROM-RCM-ROM-RCM sequences involving non-strained heterocyclic relays are described. The method can be used for the preparation of polyunsaturated trisaccharides.     

Clicking polymers: a straightforward approach to novel macromolecular architectures

Living/controlled polymerization techniques have enabled the synthesis of a large variety of different well-defined (co)polymer structures. In addition, the use of click chemistry in polymer science is a quickly emerging field of research since it allows the fast and simple creation of well-defined and complex polymeric structures in yields that were previously unattainable. In this critical review, the application of the azide-alkyne 1,3-dipolar cycloaddition for the construction of well-defined polymer architectures will be discussed in detail, providing a comprehensive overview for all disciplines related to polymeric materials.     

69mZn-containing radiopharmaceuticals: a novel approach to molecular design

^69mZn was produced and separated for medical applications. Possibilities and perspectives for production of radiopharmaceuticals based on ^69mZn containing derivatives of thiazine, thiazoline and thiourea are considered. Each one of the latters is a zinc chelator and a nitric oxide synthase (NOS) effector at the same time. Cytotoxic effect of NOS activator and NOS inhibitors are shown in experiments with HL-60, K-562 and MOLT-4 cell lines and in bone marrow cells of the acute B-lymphoblastic leukemia patients. Some of those compounds are worthy to get selected for further application as radiopharmaceuticals including their antitumor speciements.

     

Ligand trans-effect: using an old concept as a novel approach to bis(dipolar) NLO-phores

In plane parallel arrangement and enhancement of NLO-activity are observed upon coordination of heteroditopic dipoles containing a phosphole ring on square-planar d8-palladium centre.     

Metal phosphonates applied to biotechnologies: a novel approach to oligonucleotide microarrays

A new process for preparing oligonucleotide arrays is described that uses surface grafting chemistry which is fundamentally different from the electrostatic adsorption and organic covalent binding methods normally employed. Solid supports are modified with a mixed organic/inorganic zirconium phosphonate monolayer film providing a stable, well-defined interface. Oligonucleotide probes terminated with phosphate are spotted directly on to the zirconated surface forming a covalent linkage. Specific binding of terminal phosphate groups with minimal binding of the internal phosphate diesters has been demonstrated. The mixed organic/inorganic thin films have also been extended for use arraying DNA duplex probes, and therefore represent a viable general approach to DNA-based bioarrays. Ideas for interfacing mixed organic/inorganic interfaces to other bioapplications are also discussed.     

A systematic SAR study of C10 modified paclitaxel analogues using a combinatorial approach

A library with 63 paclitaxel analogues modified at the C10 position of paclitaxel has been prepared using parallel solution phase synthesis. Most of the C10 analogues were slightly less active than paclitaxel in the tubulin assembly assay and had reduced potency in the B16 melanoma and MCF-7 cell line cytotoxicity assays. These modifications at C10, however, did not lead to the total loss of activity, indicating that the C10 moiety of paclitaxel may not be directly involved in the drug-microtubule interactions, but could influence its binding affinity to P-glycoprotein. Approximately 50% of the analogues demonstrated better activity against the drug resistant cell line MCF7-ADR. However, the increase in activity was 10-fold at most. This result demonstrates that the cytotoxicity against this drug resistant cancer cell line is sensitive to structural changes at the C10 position of paclitaxel. It was also found that the presence of a nitrogen atom in the C10 substituent might play a role in the interaction of analogues with microtubules.     

Tandem modular protein-based hydrogels constructed using a novel two-component approach

Leucine zipper sequences have been widely used to engineer protein-based hydrogels for biomedical applications. Previously, we have used this method to engineer tandem modular protein-based hydrogels as a step toward developing extracellular matrix-mimetic hydrogels. However, the spontaneous self-association of leucine zipper sequences in solution has made it challenging to express and purify tandem modular proteins carrying leucine zipper under native conditions. To obviate this problem, here we report a novel two-component approach to engineer tandem modular protein-based hydrogels. This methodology makes use of two complementary leucine zipper sequences (CCE and CCK), which do not self-associate but self-assemble into heterodimeric coiled-coils at neutral pH, as functional groups to drive the self-assembly of protein hydrogels. The two protein components are bifunctional and trifunctional tandem modular proteins carrying the leucine zipper functional groups. We found that the two proteins carrying CCE or CCK can be expressed and purified under native conditions with high yield. Upon mixing, the aqueous solution of the two proteins readily forms a transparent hydrogel. The resultant hydrogel can undergo reversible sol-gel transitions as a function of temperature, and shows much improved erosion properties. This method provides a new approach to tune the topology and physical properties of the protein hydrogels via genetic engineering, and opens the possibility to systematically explore the use of large native extracellular proteins to engineer extracellular matrix-mimetic hydrogels.     

SAR by ILOEs: an NMR-based approach to reverse chemical genetics

Reverse chemical genetics is an emerging technique that makes use of small molecule inhibitors to characterize how a protein functions. In this regard, we have developed an NMR-based approach (SAR by ILOEs) that enables the identification of high affinity ligands for a given protein target without the need of a specific assay. Our approach is of general applicability and could result very powerful in reverse chemical-genetics studies, target validation, and lead discovery. We report a recent application on the design and synthesis of compounds that inhibit protein-membrane interactions.     

Tandem hydroformylation-hydrazone formation-Fischer indole synthesis: a novel approach to tryptamides

A novel one-pot synthesis of indole systems via tandem hydroformylation-hydrazone formation-Fischer indolization starting from allylic amides and aryl hydrazines is described. This tandem procedure directly leads to biologically interesting tryptamides and analogues.     

Pd-catalyzed carbonylative lactamization: a novel synthetic approach to FR900482

An asymmetric synthesis of the benzazocine core of FR900482 has been achieved in 15 steps from 3,5-dinitro-p-toluic acid. Key features of the synthesis include an enantioselective N-methylephedrine-mediated zinc acetylide addition to a highly enolizable arylacetaldehyde and a novel Pd-catalyzed carbonylative lactamization to form an eight-membered ring. [reaction--see text]     

Au-catalyzed isomerization of cyclopropenes: a novel approach to indene derivatives

AuPPh₃Cl/AgOTf-catalyzed reaction of cyclopropenes is found to be highly efficient, giving indene derivatives in high yields. The reaction is suggested to proceed through gold vinyl carbenoid intermediate.     

Preparation of functional hybrid palladium nanoparticles using supercritical fluids: a novel approach to detach the growth and functionalization steps

We report a novel and versatile approach to control separately the growth and functionalization steps in preparing functional nanomaterials. The applicability of this method was demonstrated with the preparation of palladium nanoparticles capped with thiol or stabilized with ionic liquid.     

A novel approach to oligonucleotide synthesis using an imidazolium ion tag as a soluble support

The synthesis of oligonucleotides in solution using a soluble, ionic liquid based support is described. Short oligomers of varying base composition were synthesized using this method in high yields and high purity, requiring no chromatography for purification prior to cleavage from the support. The solution-phase-synthesized oligomers were compared to the same sequences prepared using standard gene machine techniques by LCMS. This methodology may provide a cheaper route for the large-scale synthesis of oligonucleotides.     

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model

The theoretical concept of folding probability, p(fold), has proven to be a useful means to characterize the kinetics of protein folding. Here, we illustrate the practical importance of p(fold) and demonstrate how it can be determined theoretically. We derive a general analytical expression for p(fold) and show how it can be estimated from simulations for systems where the transition rates between the relevant microstates are not known. By analyzing the Ising model we are able to determine the scaling behavior of the numerical error in the p(fold) estimate as function of the number of analyzed Monte Carlo runs. We apply our method to a simple, newly developed protein folding model for the formation of alpha helices. It is demonstrated that our technique highly parallelizes the calculation of p(fold) and that it is orders of magnitude more efficient than conventional approaches.     

Molecular basis of protein structure in proanthocyanidin and anthocyanin-enhanced Lc-transgenic alfalfa in relation to nutritive value using synchrotron-radiation FTIR microspectroscopy: A novel approach

To date there has been very little application of synchrotron radiation-based Fourier transform infrared microspectroscopy (SRFTIRM) to the study of molecular structures in plant forage in relation to livestock digestive behavior and nutrient availability. Protein inherent structure, among other factors such as protein matrix, affects nutritive quality, fermentation and degradation behavior in both humans and animals. The relative percentage of protein secondary structure influences protein value. A high percentage of β-sheets usually reduce the access of gastrointestinal digestive enzymes to the protein. Reduced accessibility results in poor digestibility and as a result, low protein value. The objective of this study was to use SRFTIRM to compare protein molecular structure of alfalfa plant tissues transformed with the maize Lc regulatory gene with non-transgenic alfalfa protein within cellular and subcellular dimensions and to quantify protein inherent structure profiles using Gaussian and Lorentzian methods of multi-component peak modeling. Protein molecular structure revealed by this method included α-helices, β-sheets and other structures such as β-turns and random coils. Hierarchical cluster analysis and principal component analysis of the synchrotron data, as well as accurate spectral analysis based on curve fitting, showed that transgenic alfalfa contained a relatively lower (P < 0.05) percentage of the model-fitted α-helices (29 vs. 34) and model-fitted β-sheets (22 vs. 27) and a higher (P < 0.05) percentage of other model-fitted structures (49 vs. 39). Transgenic alfalfa protein displayed no difference (P > 0.05) in the ratio of α-helices to β-sheets (average: 1.4) and higher (P < 0.05) ratios of α-helices to others (0.7 vs. 0.9) and β-sheets to others (0.5 vs. 0.8) than the non-transgenic alfalfa protein. The transgenic protein structures also exhibited no difference (P > 0.05) in the vibrational intensity of protein amide I (average of 24) and amide II areas (average of 10) and their ratio (average of 2.4) compared with non-transgenic alfalfa. Cluster analysis and principal component analysis showed no significant differences between the two genotypes in the broad molecular fingerprint region, amides I and II regions, and the carbohydrate molecular region, indicating they are highly related to each other. The results suggest that transgenic Lc-alfalfa leaves contain similar proteins to non-transgenic alfalfa (because amide I and II intensities were identical), but a subtle difference in protein molecular structure after freeze drying. Further study is needed to understand the relationship between these structural profiles and biological features such as protein nutrient availability, protein bypass and digestive behavior of livestock fed with this type of forage.