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     

Rhenium(IV)–copper(II) heterobimetallic complexes: Synthesis,crystal structure and magnetic properties

Two Re(IV)–Cu(II) heterometallic complexes {(CuL_α)[ReCl₄(ox)]}_n (where L_α = N-meso-5,12-Me₂-7,14-Et₂-[14]-4,11-dieneN₄), 1, and (CuL_β)[ReCl₄(ox)] (L_β = N-rac-5,12-Me₂-7,14-Et₂-[14]-4,11-dieneN₄N-rac-5,12-Me₂-7,14-Et₂-[14]-4,11-dieneN₄), 2, were synthesized. The [CuL²⁺] macrocyclic cation is coordinated from above and below by [ReCl₄(ox)]²⁻ units through the chloro-ligands and creates a chloro-bridged heterometallic Re^IV–Cu^II one-dimensional zig-zag chain. Compound 2 can be viewed as a heterobimetallic dinuclear unit, in which the Re(IV)-Cu(II) centers are linked by an oxalato bridge. The magnetic behavior of 1 and 2 has been investigated over the temperature range 1.8–300 K. Compound 1 behaves like a ferrimagnetic {Re(IV)–Cu(II)} bimetallic, one-dimensional chain with intrachain antiferromagnetic coupling. Compound 2 shows a weak antiferromagnetic interaction within the [Re(IV)–Cu(II)] unit along with a strong single-ion anisotropy, D(Re) = −63 cm⁻¹.     

1H and 13C NMR characteristics of β-blockers

The β-blockers are important drugs and decades of clinical experience proved their high medical status. However, to the best of our knowledge, there is no complete assignment of (1)H and (13)C NMR resonances of popular representatives: acebutolol, alpenolol, pindolol, timolol and propranolol and the published NMR data on carvedilol and atenolol are incorrect. Therefore, (1)H and (13)C NMR spectroscopy was applied for the characterization of a series of β-adrenolytics: carvedilol (1), pindolol (2), alprenolol (3), acebutolol (4), atenolol (5), propranolol (6) and timolol (7). Two-dimensional NMR experiments (COSY, HMQC, HMBC, NOESY) allowed the unequivocal assignment of (1)H and (13)C spectra for solution (DMSO-d(6) ). Salts and bases can be easily distinguished based on (13)C chemical shifts which are within 65.0-65.5 ppm (OC2) and 46.9-47.0 (NC3) for hydrochlorides and larger, ca. 68.4 ppm (OC2) and 50.3-52.6 (NC3) for bases. NMR data of 1-7 should be included in pharmacopoeias.     

Physicochemical characteristics of 2-, 3- and 4-methylpyridinium tetrachloroferrates(III)

The crystal structure of 2-methylpyridinium tetrachloroferrate(III) was determined. The iron cation is tetracoordinated by chloride anions, and it adopts a slightly distorted tetrahedral coordination with three angles smaller, two almost equal and one larger than the tetrahedral. The compound is isostructural with its 3-, and 4-methylpyridinium analogues. The thermal properties of 2-, 3- and 4-methylpyridinium tetrachloroferrates(III) have been studied using TG and DSC techniques. The compounds exhibit a high stability in the melt.      

Synthesis of Phosphorylated Enaminoketones and Their Application in the Preparation of Trifluoromethyl-Functionalized 2-Phosphonopyrroles

Abstract

New trifluoromethyl-functionalized 2-phosphonopyrroles were obtained by 5-exotrig cyclization of trifluoromethyl and phosphonyl functionalized enaminoketones.

GRAPHICAL ABSTRACT      

Synthesis, crystal structures and the preliminary evaluation of the new dibenzotetraaza[14]annulene-based DNA/RNA binding agents

A series of water-soluble dicationic dibenzotetraaza[14]annulenes have been prepared in order to examine their interactions with nucleic acids. Pendant water-solubilizing N-pyridinium, 4,4′-bipyridinium and N-methyl pyridinium moieties have been attached to the central core via linkers generated by direct N-alkylations and ester creating couplings, respectively. The crystal structures of derivatives equipped with 3-(N-pyridinium-1-yl)propyl and 3-(4,4′-bipyridinium-1-yl)propyl substituents have been determined. Interactions with ct-DNA have been studied and evidenced by means of spectrophotometric titrations with Scatchard analysis and thermal denaturation experiments.     

Darwin and mass-velocity relativistic corrections in the non-Born-Oppenheimer calculations of pure vibrational states of H2

The Darwin and mass-velocity relativistic corrections have been calculated for all pure vibrational states of the H2 using the perturbation theory and very accurate variational wave functions obtained without assuming the Born-Oppenheimer (BO) approximation. Expansions in terms of explicitly correlated Gaussians with premultipliers in the form of even powers of the internuclear distance were used for the wave functions. With the inclusion of the two relativistic corrections to the non-BO energies the transition energies for the highest states agree more with the experimental results.     

Water-Soluble Polymeric Carbon Nitride Colloidal Nanoparticles for Highly Selective Quasi-Homogeneous Photocatalysis

Heptazine-based polymeric carbon nitrides (PCN) are promising photocatalysts for light-driven redox transformations. However, their activity is hampered by low surface area resulting in low concentration of accessible active sites. Herein, we report a bottom-up preparation of PCN nanoparticles with a narrow size distribution (ca. 10±3 nm), which are fully soluble in water showing no gelation or precipitation over several months. They allow photocatalysis to be carried out under quasi-homogeneous conditions. The superior performance of water-soluble PCN, compared to conventional solid PCN, is shown in photocatalytic H₂O₂ production via reduction of oxygen accompanied by highly selective photooxidation of 4-methoxybenzyl alcohol and benzyl alcohol or lignocellulose-derived feedstock (ethanol, glycerol, glucose). The dissolved photocatalyst can be easily recovered and re-dissolved by simple modulation of the ionic strength of the medium, without any loss of activity and selectivity.     

Clinical Trials and Basic Research in Photodynamic Diagnostics and Therapies from the Center for Laser Diagnostics and Therapy in Poland

The purpose of this review is to present an overview of the development of photodiagnostic and photodynamic therapy (PDD and PDT) techniques in Poland. The paper discusses the principles of PDD, including fluorescent techniques in determining precancerous conditions and cancers of the skin, digestive tract, bladder and respiratory tract. Methods of PDT of cancer will be discussed and the current state of knowledge as well as future trends in the development of photodynamic techniques will be presented, including the possibility of using photodynamic antimicrobial therapy. Research pioneers in photodynamic medicine such as Thomas Dougherty are an inspiration for the development of methods of PDD and PDT in our Clinic. The Center for Laser Diagnostics and Therapy in Bytom, Poland, promotes the propagation of PDD and PDT through the training of clinicians and raising awareness among students in training and the general public. Physicians at the Center are engaged in photomedical research aimed at clinical implementation and exploration of new avenues in photomedicine while optimizing existing modalities. The Center promotes dissemination of clinical results from a wide range of topics in PDD and PDT and serving as representative authorities of photodynamic medicine in Poland and Europe.     

Flavonoid Preparations from Taraxacum officinale L. Fruits—A Phytochemical,Antioxidant and Hemostasis Studies

Dandelion (Taraxacum officinale L.) roots, leaves, and flowers have a long history of use in traditional medicine. Compared to the above organs, dandelion fruits are the least known and used. Hence, the present paper was aimed at the phytochemical analysis of T. officinale fruit extract and estimating its antiradical, antiplatelet, and antioxidant properties related to hemostasis. Methanolic extract of fruits (E1), enriched with polyphenols (188 mg gallic acid equivalents (GAE)/g), was successfully separated into cinnamic acids (E2; 448 mg GAE/g) and flavonoids (E3; 377 mg GAE/g) extracts. Flavonoid extract was further divided into four fractions characterized by individual content: A (luteolin fraction; 880 mg GAE/g), B (philonotisflavone fraction; 516 mg GAE/g), C (flavonolignans fraction; 384 mg GAE/g), and D (flavone aglycones fraction; 632 mg GAE/g). High DPPH radical scavenging activity was evaluated for fractions A and B (A > B > Trolox), medium for extracts (Trolox > E3 > E2 > E1), and low for fractions C and D. No simple correlation between polyphenol content and antiradical activity was observed, indicating a significant influence of qualitative factor, including higher anti-oxidative effect of flavonoids with B-ring catechol system compared to hydroxycinnamic acids. No cytotoxic effect on platelets was observed for any dandelion preparation tested. In experiments on plasma and platelets, using several different parameters (lipid peroxidation, protein carbonylation, oxidation of thiols, and platelet adhesion), the highest antioxidant and antiplatelet potential was demonstrated by three fruit preparations–hydroxycinnamic acids extract (E2), flavonoid extract (E3), and luteolin fraction (A). The results of this paper provide new information on dandelion metabolites, as well as their biological potential and possible use concerning cardiovascular diseases.