Chlorophyll a π-Cation Radical as Redox Mediator in Superoxide Dismutase (SOD) Mimetics

The extensive speciation of copper(II) chloride in organic solvents varies with concentration, temperature, pressure and oxygen content, providing the ability to switch between different chlorophyll transmetalation pathways. We found that one of them is exceptionally suitable for the formation and stabilisation of the chlorophyll π-cation radical. This is due to unique redox cycling, which is coupled to the generation and transformation of various reactive oxygen species. In the presence of a proton donor, our system shows behavior which resembles that of superoxide dismutase (SOD). Regardless of light, chlorophyll acts as an electron transfer mediator.     

Compounds based on meso-tri(4-pyridyl)-p-acrylamidophenylporphyrin able to interact with DNA

A new type of porphyrinyl-nucleoside was synthesized by the Heck reaction of meso-tri(4-pyndyl)-p-acrylamidophenylporphyrin with (+)5-iodo-2′-deoxyuridine. The porphyrin used in this reaction was also applied in obtaining a water soluble porphyrin polymer and a copolymer with acrylamide. The porphyrinyl-nucleoside and the polymer and copolymer were investigated for their interaction with ds DNA, oligonucleotides and oligonucleotide duplexes. The extend of the red-shift of the Soret band of porphyrins and the slowing of the mobolity of DNA during electrophoresis of the interacting systems suggested that intercalation of cationic porphyrin units into ds DNA cannot be solely responsible for the observed phenomena.     

VoteDock: Consensus docking method for prediction of protein–ligand interactions

Molecular recognition plays a fundamental role in all biological processes, and that is why great efforts have been made to understand and predict protein–ligand interactions. Finding a molecule that can potentially bind to a target protein is particularly essential in drug discovery and still remains an expensive and time‐consuming task. In silico, tools are frequently used to screen molecular libraries to identify new lead compounds, and if protein structure is known, various protein–ligand docking programs can be used. The aim of docking procedure is to predict correct poses of ligand in the binding site of the protein as well as to score them according to the strength of interaction in a reasonable time frame. The purpose of our studies was to present the novel consensus approach to predict both protein–ligand complex structure and its corresponding binding affinity. Our method used as the input the results from seven docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) that are widely used for docking of ligands. We evaluated it on the extensive benchmark dataset of 1300 protein–ligands pairs from refined PDBbind database for which the structural and affinity data was available. We compared independently its ability of proper scoring and posing to the previously proposed methods. In most cases, our method is able to dock properly approximately 20% of pairs more than docking methods on average, and over 10% of pairs more than the best single program. The RMSD value of the predicted complex conformation versus its native one is reduced by a factor of 0.5 Å. Finally, we were able to increase the Pearson correlation of the predicted binding affinity in comparison with the experimental value up to 0.5. © 2010 Wiley Periodicals, Inc. J Comput Chem 32: 568–581, 2011     

Existence results for evolutionary inclusions and variational–hemivariational inequalities

We consider an abstract first-order evolutionary inclusion in a reflexive Banach space. The inclusion contains the sum of L-pseudomonotone operator and a maximal monotone operator. We provide an existence theorem which is a generalization of former results known in the literature. Next, we apply our result to the case of nonlinear variational–hemivariational inequalities considered in the setting of an evolution triple of spaces. We specify the multivalued operators in the problem and obtain existence results for several classes of variational–hemivariational inequality problems. Finally, we illustrate our existence result and treat a class of quasilinear parabolic problems under nonmonotone and multivalued flux boundary conditions.     

A Conjugated Thiophene‐Based Rotaxane: Synthesis,Spectroscopy, and Modeling

A dithiophene rotaxane 1 ?β‐CD and its shape‐persistent corresponding dumbbell 1 were synthesized and fully characterized. 2D NOESY experiments, supported by molecular dynamics calculations, revealed a very mobile macrocycle (β‐CD). Steady‐state and time‐resolved photoluminescence experiments in solution were employed to elucidate the excited‐state dynamics for both systems and to explore the effect of cyclodextrin encapsulation. The photoluminescence (PL) spectrum of 1 ?β‐CD was found to be blueshifted with respect to the dumbbell 1 (2.81 and 2.78 eV, respectively). Additionally, in contrast to previous observations, neither PL spectra nor the decay kinetics of both threaded and unthreaded systems showed changes upon increasing the concentration or changing the polarity of the solutions, thereby providing evidence for a lack of tendency toward aggregation of the unthreaded backbone.     

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.