Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Highly sensitive voltammetric biosensor for nitric oxide based on its high affinity with hemoglobin

Although heme protein-based, amperometric nitric oxide (NO) biosensors have been well documented in previous studies, most have been conducted in anaerobic conditions. Herein we report a novel hemoglobin-based NO biosensor that is not only very sensitive but also usable in air. The heme protein was entrapped in a sodium montmorillonite film, which was immobilized at a pyrolytic graphite electrode surface. Film-entrapped hemoglobin can directly exchange electrons with the electrode, and this process has proven to favor the catalytic reduction of oxygen. In addition, NO induced a cathodic potential shift of the catalytic reduction peak of oxygen. This potential shift was proportional to the logarithm of NO concentration ranging from 4.0 × 10⁻¹¹ to 5.0 × 10⁻⁶ mol/L. The detection limit has been estimated to be 20 pM, approximately four orders lower than previously reported amperometric detectors.     

Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3-benzazepines for the D1receptor

We computed the free energy of solvation for a series of ions and neutral molecules using two different continuum approaches. First, we used the AM1–SM1 technique, where the AM1 Fock matrix is modified to include a generalized Born contribution. Second, we applied the DelPhi approach, where the electrostatic component of the free energy of solvation is evaluated by resolving the Poisson–Boltzman equation by a finite difference method. Both methods appear equally reliable for ionic systems. For neutral compounds, AM1–SM1 performs better than DelPhi; however, the differences become less pronounced for compounds with larger free energies of solvation. In parallel, both methods were applied to study the influence of the solvation process in the overall drug receptor interaction for a series of closely related ligands for the D₁ dopamine receptor. An inverse linear relationship was found between the free energy of solvation and the logarithm of the affinity of the ligands; nevertheless, electrostatic properties are likely to modulate affinity as well. © 1993 John Wiley & Sons, Inc.     

Insertion reactions of [M(SR)3(PMe2Ph)2] with CS2 (M = Ru, Os; R = C6F4H-4, C6F5). X-ray structures of [Ru(S2CSC6F4H-4)2(PMe2Ph)2], trans-thiolates [M(SR)2(S2CSR)(PMe2Ph)2] (M = Ru; R = C6F5 and M = Os; R = C6F4H-4), and trans-thiolate-phosphine [Os(SC6F5)2(S2CSC6F5)(PMe2Ph)2

Reactions of [M(SR)(3)(PMe(2)Ph)(2)] (M = Ru, Os; R = C(6)F(4)H-4, C(6)F(5)) with CS(2) in acetone afford [Ru(S(2)CSR)(2)(PMe(2)Ph)(2)] (R = C(6)F(4)H-4, 1; C(6)F(5), 3) and trans-thiolates [Ru(SR)(2)(S(2)CSR)(PMe(2)Ph)(2)] (R = C(6)F(4)H-4, 2; C(6)F(5), 4) or the isomers trans-thiolates [Os(SR)(2)(S(2)CSR)(PMe(2)Ph)(2)] (R = C(6)F(4)H-4, 5; C(6)F(5), 7) and trans-thiolate-phosphine [Os(SR)(2)(S(2)CSR)(PMe(2)Ph)(2)] (R = C(6)F(4)H-4, 6; C(6)F(5), 8) through processes involving CS(2) insertion into M-SR bonds. The ruthenium(III) complexes [Ru(SR)(3)(PMe(2)Ph)(2)] react with CS(2) to give the diamagnetic thiolate-thioxanthato ruthenium(II) and the paramagnetic ruthenium(III) complexes while osmium(III) complexes [Os(SR)(3)(PMe(2)Ph)(2)] react to give the paramagnetic thiolate-thioxanthato osmium(III) isomers. The single-crystal X-ray diffraction studies of 1, 4, 5, and 8 show distorted octahedral structures. (31)P [(1)H] and (19)F NMR studies show that the solution structures of 1 and 3 are consistent with the solid-state structure of 1.     

EVENTS SURROUNDING THE EARLY DEVELOPMENT OF EUGLENA CHLOROPLASTS. 12. SPECTROSCOPIC EXAMINATION OF THE PROTOCHLOROPHYLL(IDE) PHOTOTRANSFORMATION IN INTACT CELLS*

Abstract— Absorption measurements in the 600–720 nm region of dark-grown cells of Euglena gracilis Klebs var. bacillaris Cori were made in vivo at room temperature using computer-assisted spectrophotometry. Dark-grown wild-type cells have a prominent absorption maximum at 634 nm due to protochlorophyll(ide) absorption. Upon illumination, the absorption at 634nm decreases and a peak appears at 674nm, representing the phototransformation of protochlorophyll(ide) to chlorophyll(ide). Using difference spectroscopy, the resynthesis in the dark of protochlorophyll(ide) by previously-illuminated wild-type dark-grown cells was found to begin at about 10min after illumination and reached completion by about 25 min, the amount of protochlorophyll(ide) resynthesized being equivalent to that of dark-grown cells. Resynthesis of protochlorophyll(ide) following a second illumination follows the same kinetics, indicating that protochlorophyll(ide) resynthesis is under tight regulation, possibly via feedback control. Cells of dark-grown wild-type and W₃BUL, a mutant lacking protochlorophyll(ide) contain a component absorbing at 658 nm which does not undergo phototransformation when examined by difference spectroscopy at room and liquid N₂ temperatures. Following the phototransformation of protochlorophyll(ide) 634 to chlorophyll(ide) 674, the chlorophyll(ide) 674 shifts to shorter wavelengths, ultimately to 671 nm. Possible relationships among the various spectroscopic forms of protochlorophyll(ide) and chlorophyll(ide) at room temperature and liquid N₂ temperature in Euglena and higher plants are presented. It is concluded that Euglena, unlike older, etiolated higher plants, contains only protochlorophyll(ide) 634, making it an excellent system in which to examine the phototransformation of this pigment species in the absence of other forms.     

A study of the Immune Epitope Database for some fungi species using network topological indices

In the last years, the encryption of system structure information with different network topological indices has been a very active field of research. In the present study, we assembled for the first time a complex network using data obtained from the Immune Epitope Database for fungi species, and we then considered the general topology, the node degree distribution, and the local structure of this network. We also calculated eight node centrality measures for the observed network and compared it with three theoretical models. In view of the results obtained, we may expect that the present approach can become a valuable tool to explore the complexity of this database, as well as for the storage, manipulation, comparison, and retrieval of information contained therein.     

Growth of poly(3,4‐ethylenedioxythiophene) films prepared by base‐inhibited vapor phase polymerization

Transparent [90% transmittance at 550 nm at a sheet resistance (R_s) of 279 Ω sq^?1] poly(3,4‐ethylenedioxythiophene) (PEDOT) films with electrical conductivities up to 1354 S cm^?1 are prepared using base‐inhibited vapor phase polymerization at atmospheric pressure. The influence of reaction conditions, such as temperature and growth time, on the film formation is investigated. A simple and convenient two‐electrode method is used for the in situ measurement of resistance, enabling to investigate the growth mechanism of polymer films and the influence of different parameters (relative humidity and the amount of oxidant) on the film growth. Low humidity exerts a detrimental effect on film growth and conductivity. In situ R_s measurements suggest that a large structural change occurs upon washing the PEDOT‐oxidant film. © 2014 Wiley Periodicals, Inc. J Polym Sci Part B: Polym. Phys. 2014 , 52, 561–571     

Copper(II) complexes with pyridoxal dithiocarbazate and thiosemicarbazone ligands: crystal structure,spectroscopic analysis and cytotoxic activity

Transition Metal Chemistry - The present study reports the synthesis and crystal structures of Cu(II) complexes with pyridoxal S-allyldithiocarbazate (H2L1) and pyridoxal thiosemicarbazones...