High-throughput protein crystallography and drug discovery

Single crystal X-ray diffraction is the technique of choice for studying the interactions of small organic molecules with proteins by determining their three-dimensional structures; however the requirement for highly purified protein and lack of process automation have traditionally limited its use in this field. Despite these shortcomings, the use of crystal structures of therapeutically relevant drug targets in pharmaceutical research has increased significantly over the last decade. The application of structure-based drug design has resulted in several marketed drugs and is now an established discipline in most pharmaceutical companies. Furthermore, the recently published full genome sequences of Homo sapiens and a number of micro-organisms have provided a plethora of new potential drug targets that could be utilised in structure-based drug design programs. In order to take maximum advantage of this explosion of information, techniques have been developed to automate and speed up the various procedures required to obtain protein crystals of suitable quality, to collect and process the raw X-ray diffraction data into usable structural information, and to use three-dimensional protein structure as a basis for drug discovery and lead optimisation.This tutorial review covers the various technologies involved in the process pipeline for high-throughput protein crystallography as it is currently being applied to drug discovery. It is aimed at synthetic and computational chemists, as well as structural biologists, in both academia and industry, who are interested in structure-based drug design.     

Copper(I)-catalysed homo-coupling of aryldiazonium salts: synthesis of symmetrical biaryls

Copper(I) triflate acts as an efficient stoichiometric reagent for the homo-coupling of aryldiazonium salts bearing electron-withdrawing group(s), to yield symmetrical biaryls in acetonitrile under mild reaction conditions. Aryldiazonium salts bearing electron-donating groups undergo the reaction by using catalytic amounts of a copper complex prepared in situ from copper(II) triflate and 2,2′-bipyridine with metallic copper as an ultimate reductant.     

The effects of eluent mixing on TLS detection in gradient elution HPLC

The effects of changing solvent composition on the LOD of TLS detection in gradient elution HPLC have been studied from the perspective of thermo-optical properties of the solvent. Hyphenated gradient high-performance liquid chromatography (HPLC)-thermal lens spectrometry (TLS), was used to separate and detect 13 carotenoid compounds and two chlorophylls. Utilization of mixing coils into the system reduces the inhomogeneities during eluent changes and therefore enables the application of thermal lens detection in the gradient HPLC method. For gradient chromatographic conditions in which the thermo-optical properties and related enhancement factor change as much as 50% over 10 min, the LODs for the TLS detector were enhanced by as much as three times in comparison with UV-Vis detection. For the isocratic part of the chromatogram, up to a tenfold improvement of LODs was achieved with TLS detection.     

CO2 dynamic adsorption/desorption on zeolite 5A studied by 13C magnetic resonance imaging

We present the first 13C magnetic resonance imaging study of CO2 transient adsorption/desorption processes in a zeolite 5A column. CO2 transient concentration profiles were measured with a centric scan spin-echo single point imaging technique. The adsorption wave profiles were determined under flow conditions, with the results analyzed by the Bohart-Adams model. The model adequately accounts for the spatial and the temporal behavior of CO2 in the column. CO2 adsorption rate constants were calculated from the fit. Desorption profiles were acquired by blowing a helium stream through a zeolite 5A column saturated with CO2. An asymmetry between the adsorption and desorption profiles is readily apparent. A linear relationship between the CO2 condensed phase concentration and square root of time was observed.     

Mechanistic study of the decomposition reactions of azobenzene

The electron impact-induced fragmentation of azobenzenes and its d₁, d₂, d₅, d₁₀, and ¹⁵N analogues was studied by mass Spectrometry and ion kinetic energy spectroscopy. The main fragment ions found in the mass spectrum of azobenzene are due to two parallel stepwise processes from the molecular ion: the expulsion of N₂ and two hydrogen radicals producing an ion at m/z 152 having possibly a biphenylene radical cation structure and loss of C₆H₅? and N₂. Except in the elimination of two hydrogen atoms from [M ? N₂]^+· ions, hydrogen scrambling between the phenyl rings does not feature in azobenzene upon electron impact.     

Raman spectroscopy in combination with background near-infrared autofluorescence enhances the in vivo assessment of malignant tissues

The diagnostic ability of optical spectroscopy techniques, including near-infrared (NIR) Raman spectroscopy, NIR autofluorescence spectroscopy and the composite Raman and NIR autofluorescence spectroscopy, for in vivo detection of malignant tumors was evaluated in this study. A murine tumor model, in which BALB/c mice were implanted with Meth-A fibrosarcoma cells into the subcutaneous region of the lower back, was used for this purpose. A rapid-acquisition dispersive-type NIR Raman system was employed for tissue Raman and NIR autofluorescence spectroscopic measurements at 785-nm laser excitation. High-quality in vivo NIR Raman spectra associated with an autofluorescence background from mouse skin and tumor tissue were acquired in 5 s. Multivariate statistical techniques, including principal component analysis (PCA) and linear discriminant analysis (LDA), were used to develop diagnostic algorithms for differentiating tumors from normal tissue based on their spectral features. Spectral classification of tumor tissue was tested using a leave-one-out, cross-validation method, and the receiver operating characteristic (ROC) curves were used to further evaluate the performance of diagnostic algorithms derived. Thirty-two in vivo Raman, NIR fluorescence and composite Raman and NIR fluorescence spectra were analyzed (16 normal, 16 tumors). Classification results obtained from cross-validation of the LDA model based on the three spectral data sets showed diagnostic sensitivities of 81.3%, 93.8% and 93.8%; specificities of 100%, 87.5% and 100%; and overall diagnostic accuracies of 90.6%, 90.6% and 96.9% respectively, for tumor identification. ROC curves showed that the most effective diagnostic algorithms were from the composite Raman and NIR autofluorescence techniques.     

Gels with exceptional thermal stability formed by bis(amino acid) oxalamide gelators and solvents of low polarity

Some bis (amino acid) oxalamide gelators form common thermo-reversible gels with various organic solvents but also gels of exceptional thermal stability with some solvents of medium and low polarity; the latter gels can be heated up to 50 degrees C higher temperatures than the bp of the solvent without apparent gel-to-sol transition.     

CELLULAR DELIVERY AND RETENTION OF PHOTOFRIN: II. THE EFFECTS OF HUMAN versus MOUSE AND BOVINE SERUM

The effects of human serum (HS), mouse serum (MS) and fetal bovine serum (FBS) on cellular delivery and retention of Photofrin were examined using human lung tumor cells (A549) cultured in vitro. The results show that these three kinds of sera exhibit substantial differences in: (i) degree of inhibition of Photofrin cellular uptake, (ii) retention capacity of Photofrin delivered to the cells in their presence and (iii) efficacy of promoting the clearance of Photofrin from the cells. It is suggested that these differences originate from unequal interaction of each of the sera with Photofrin material, which in turn is the consequence of variability in composition and in the levels of serum proteins in HS, MS and FBS. The highest degree of Photofrin disaggregation and and competitive binding of its constituents was attributed to HS. The lowest degree of Photofrin disaggregation, and the competitive binding limited mostly to monomeric porphyrin forms was implicated for FBS. For MS, the spectroscopic and cellular data indicated a lesser degree of Photofrin disaggregation than with HS, with little if any consequence in Photofrin retention characteristics. The implication of this comparative analysis is that in vitro studies using FBS may underestimate the extent of interaction of Photofrin with serum proteins in humans, and overestimate the retention capacity of the photosensitizer in human tissues. Studies in vivo using a mouse model may also underestimate the degree of disaggregation of Photofrin in human circulation, and give different photosensitizer tissue retention levels than in humans.     

Algorithms for Greechie Diagrams

We give a new algorithm for generating Greechie diagrams with arbitrary chosennumber of atoms or blocks (with 2, 3, 4, . . . atoms) and provide a computerprogram for generating the diagrams. The results show that the previous algorithmdoes not produce every diagram and that it is atleast 10⁵ times slower. We alsoprovide an algorithm and programs for checking Greechie diagram passage byequations defining varieties of orthomodular lattices and give examples fromHilbert lattices. We also discuss some additional characteristics of Greechiediagrams.