Ismail Fidan

Carbonic anhydrase inhibitors: Design, synthesis, kinetic, docking and molecular dynamics analysis of novel glycine and phenylalanine sulfonamide derivatives.

The inhibition of two human cytosolic carbonic anhydrase isozymes I and II, with some novel glycine and phenylalanine sulfonamide derivatives were investigated. Newly synthesized compounds G1-4 and P1-4 showed effective inhibition profiles with KI values in the range of 14.66-315μM for hCA I and of 18.31-143.8μM against hCA II, respectively. In order to investigate the binding mechanisms of these inhibitors, in silico docking studies were applied. Atomistic molecular dynamic simulations were performed for docking poses which utilize to illustrate the inhibition mechanism of used inhibitors into active site of CAII. These sulfonamide containing compounds generally were competitive inhibitors with 4-nitrophenylacetate as substrate. Some investigated compounds here showed effective hCA II inhibitory effects, in the same range as the clinically used sulfonamide, sulfanilamide or mafenide and might be used as leads for generating enzyme inhibitors possibly targeting other CA isoforms which have not been yet assayed for their interactions with such agents.

Synthesis of 3,4-dihydroxypyrrolidine-2,5-dione and 3,5-dihydroxybenzoic acid derivatives and evaluation of the carbonic anhydrase I and II inhibition.

Abstract The inhibition of two human cytosolic carbonic anhydrase (hCA, EC 4.2.1.1) isozymes I and II, with some 3,4-dihydroxypyrrolidine-2,5-dione and 3,5-dihydroxybenzoic acid derivatives, were investigated by using the esterase assay, with 4-nitrophenyl acetate (4-NPA) as substrate. Compounds 10–13 showed KI values in the range of 112.7–441.5 μM for hCA I and of 3.5–10.76 μM against hCA II, respectively. These hydroxyl group containing compounds generally were competitive inhibitors. Some hydroxyl group containing compounds investigated here showed effective hCA II inhibitory effects, in the same range as the clinically used sulfonamide acetazolamide, and might be used as leads for generating enzyme inhibitors possibly targeting other CA isoforms which have not been yet assayed for their interactions with such agents.

Kinetic and in silico analysis of thiazolidin-based inhibitors of α-carbonic anhydrase isoenzymes

Carbonic anhydrases (CAs, EC 4.2.1.1) are inhibited by sulfonamides, inorganic anions, phenols, salicylic acid derivatives (acting as drug or prodrugs). A novel class of CA inhibitors (CAIs), interacting with the CA isozymes I and II (cytosolic) in a different manner, is reported here. Kinetic measurements allowed us to identify thiazolidin-based compounds as submicromolar-low micromolar inhibitors of these two CA isozymes. Molecular docking studies of a set of such inhibitors within CA I and II active site allowed us to understand the inhibition mechanism. This new class of inhibitors bind differently compared to other classes of inhibitors known to date: they were found between the phenol-binding site, filling thus the middle of the enzyme cavity.

Effect of substituents on spin density in benzimidazole nitronyl nitroxide radicals studied by electron spin resonance

Several novel benzimidazole‐3‐oxide‐1‐oxyl radicals with substituents at 5 and/or 6 position were synthesized. The ESR analysis of nitrogen hyperfine coupling constants (hfccs) revealed that substituents at 5 and 6‐position affect the spin density to greater extent than substituents on the phenyl ring at 2‐position. Density functional theory calculations of nitrogen hfccs were performed using several different Pople type basis sets, as well as double and triple zeta quality individual gauge for localized orbital (IGLO‐II, IGLO‐III) and electron paramagnetic resonance (EPR‐II, EPR‐II) basis sets. Experimental and theoretical hfccs are compared. Copyright

Structure-Photoproperties Relationship Investigation of the Singlet Oxygen Formation in Porphyrin-Fullerene Dyads

A systematic structure-photoproperties relationship study of the interactions of porphyrin-fullerene dyads with molecular oxygen was conducted on a set of three porphyrin-fullerene dyads, as this approach of related applications - oxygen sensitivity and photo-induced singlet oxygen generation - of such dyads remained to be endeavoured. To promote energy transfers between the porphyrin and fullerene units and limit undesired charge separation, a particular attention was devoted to the choice of the solvents for the photoproperties determination. Toluene, in which in addition the compounds investigated are not aggregated, was selected accordingly. The molecular orbital levels and energy gaps of the dyads were determined by electrochemistry and theoretical calculations. Their ground state absorption, steady-state fluorescence-based oxygen sensitivity and photo-induced singlet oxygen generation were determined. The dyads were designed to benefit from a facilitated synthetic porphyrin-fullerene coupling thanks to an easy access to formyl-functionalized porphyrins. The effect of two structural parameters was investigated: the presence of electron-donating hexyloxy chains at the para position of the meso-phenyl, and the presence of a phenylacetylene spacer. This latest factor appeared to have the most predominant effect on all these properties.

Effect of the Substitution Pattern (Peripheral vs Non-Peripheral) on the Spectroscopic, Electrochemical, and Magnetic Properties of Octahexylsulfanyl Copper Phthalocyanines

In order to investigate the substitution position effect on the spectroscopic, electrochemical, and magnetic properties of copper phthalocyanines, a detailed structure-property analysis has been performed by examining two copper phthalocyanines that are octasubstituted by hexylsulfanyl chains respectively in the peripheral (Cu-P) and non-peripheral (Cu-NP) positions. Cu-NP showed a marked near-IR maximum absorption compared to Cu-P and, accordingly, a smaller HOMO-LUMO energy gap, calculated via the electrochemical results and simulations in the gas phase, as well as for Cu-NP from its crystallographic data. An electron-spin resonance (ESR) technique is used to extract the g values from the powder spectra that are taken at room temperature. The g values were determined to be g∥ = 2.160 and g⊥ = 2.045 for Cu-P and g∥ = 2.150 and g⊥ = 2.050 for Cu-NP. These values indicate that the paramagnetic copper center in both phthalocyanines has axial symmetry with a planar anisotropy ( g∥ > g⊥). The ESR spectra in solution could be obtained only for Cu-P. Curie law is used to fit the experimental data of the magnetic susceptibility versus temperature graphs, and the Curie constant ( C) and diamagnetic/temperature-independent paramagnetic (α) contributions are deduced as 0.37598 (0.39576) cm3·K/mol and -23 × 10-5 (25 × 10-5) cm3/mol respectively for Cu-P and Cu-NP. The room temperature magnetic moment value (1.70 μB) is close to the spin-only value (1.73 μB) for the peripheral complex, showing that there is no orbital contribution to μeff. In contrast, at room temperature, the value of the magnetic moment (1.77 μB) is above the spin-only value, showing an orbital contribution to the magnetic moment. Cu-NPs room temperature magnetic moment value is larger than the value for Cu-P, demonstrating that the orbital contribution to the magnetic moment depends upon the substituent position. The magnitudes of the effective magnetic moment values also support that both Cu-P and Cu-NP complexes have square-planar coordination. This result is consistent with the determined g values. The spin densities were determined experimentally, and the results suggest that the positions of the substituents affect these values (0.469 for Cu-P and 0.490 for Cu-NP).

Revisiting the Ullman's Radical Chemistry for Phthalocyanine Derivatives

Phthalocyanine derivatives do not cease to gain attention due to their numerous properties and applications (e.g., sensor, PDT). This makes them a unique scaffold for the design of new material. In this context, we were interested to develop the synthesis of an imino nitroxide-substituted phthalocyanine by Ullmans procedure; a challenge due to the intrinsic low solubility of most phthalocyanine derivative in much solvents. To overcome this solubility problem, we designed a phthalocyanine with bulky neopentyl substituents in peripheral positions as counterpart to the imino nitroxide moieties. The imino nitroxide-substituted phthalocyanine was obtained by condensation of a monoformyl-substituted phthalocyanine with 2,3-bis(hydroxylamino)-2,3-dimethylbutane in refluxing THF-MeOH (2:1) mixture in the presence of p-toluenesulfonic acid monohydrate, follow by oxidation with PbO2 . Characterization was performed by electrochemistry, UV/Vis and EPR spectroscopy in solution as well as SQUID in solid state.

Modeling and performance analysis of an SMD assembly station using stochastic Petri nets and artificial neural networks

The present paper provides Petri net (PN) modeling and performance analysis of a surface mount device (SMD) assembly station for automated manufacturing of printed circuit boards. Concentrating on the operational aspects, the authors construct PN models for an automated assembly station. These models enable designers to have a better understanding of the system control and analysis from the graphical representations of PNs. Further, the selection of the particular buffer size and its effects on the production rate of the transferline are explored. The analysis mainly uses the PN model to analyze two different transferlines and to examine when local gains propagate to the end of the transferline. Furthermore, artificial neural networks (ANN) are also proposed as a fast function approximation tool for a rapid reanalysis of the system. ANN can predict the output of the transferline for unknown input patterns when the input and output relation is monotonically increasing or decreasing. This capability of the ANN proves to be useful to analyze the transferline when there is no further information available. The approaches as presented in this paper can be generalized and applied to many other applications of multi-robot assembly systems.