CRDOCK: An Ultrafast Multipurpose Protein-Ligand Docking Tool

An ultrafast docking and virtual screening program, CRDOCK, is presented that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy minimization algorithms for fine tuning the binding poses, and (3) different scoring functions. This modularity ensures the easy configuration of custom-made protocols that can be optimized depending on the problem in hand. CRDOCK employs a precomputed library of ligand conformations that are initially generated from one-dimensional SMILES strings. Testing CRDOCK on two widely used benchmarks, the ASTEX diverse set and the Directory of Useful Decoys, yielded a success rate of ～75% in pose prediction and an average AUC of 0.66. A typical ligand can be docked, on average, in just ～13 s. Extension to a representative group of pharmacologically relevant G protein-coupled receptors that have been recently cocrystallized with some selective ligands allowed us to demonstrate the utility of this tool and also highlight some current limitations. CRDOCK is now included within VSDMIP, our integrated platform for drug discovery.     

l- and d-Proline Thiosemicarbazone Conjugates: Coordination Behavior in Solution and the Effect of Copper(II) Coordination on Their Antiproliferative Activity

Two enantiomerically pure thiosemicarbazone-proline conjugates with enhanced aqueous solubility, namely, 2-hydroxy-3-methyl-(S)-pyrrolidine-2-carboxylate-5-methylbenzaldehyde thiosemicarbazone [l-Pro-STSC or (S)-H(2)L] and 2-hydroxy-3-methyl-(R)-pyrrolidine-2-carboxylate-5-methylbenzaldehyde thiosemicarbazone [d-Pro-STSC or (R)-H(2)L] have been synthesized and characterized by elemental analysis, spectroscopic methods (UV-vis and (1)H and (13)C NMR), and electrospray ionization mass spectrometry. The metal complexation behavior of l-Pro-STSC, stoichiometry, and thermodynamic stability of iron(II), iron(III), copper(II), and zinc(II) complexes in 30% (w/w) dimethyl sulfoxide/H(2)O solvent mixture have been studied by pH-potentiometric, UV-vis-spectrophotometric, circular dichroism, electron paramagnetic resonance, (1)H NMR spectroscopic, and spectrofluorimetric measurements. By the reaction of CuCl(2)·2H(2)O with (S)-H(2)L and (R)-H(2)L, respectively, the complexes [Cu[(S)-H(2)L]Cl]Cl and [Cu[(R)-H(2)L]Cl]Cl have been prepared and comprehensively characterized. An X-ray diffraction study of [Cu[(R)-H(2)L]Cl]Cl showed the formation of a square-planar copper(II) complex, which builds up stacks with interplanar separation of 3.3 ?. The antiproliferative activity of two chiral ligands and their corresponding copper(II) complexes has been tested in two human cancer cell lines, namely, SW480 (colon carcinoma) and CH1 (ovarian carcinoma). The thiosemicarbazone-proline conjugates l- and d-Pro-STSC show only moderate cytotoxic potency with IC(50) values of 62 and 75 μM, respectively, in CH1 cells and >100 μM in SW480 cells. However, the corresponding copper(II) complexes are 13 and 5 times more potent in CH1 cells, based on a comparison of IC(50) values, and in SW480 cells the increase in the antiproliferative activity is even higher. In both tested cell lines, l-Pro-STSC as well as its copper(II) complex show slightly stronger antiproliferative activity than the compounds with a d-Pro moiety, yielding IC(50) values of 4.6 and 5.5 μM for [Cu(l-Pro-STSC)Cl]Cl in CH1 and SW480 cells, respectively.     

Inhibitors for the immuno- and constitutive proteasome: current and future trends in drug development

Proteolytic degradation is an essential cellular process which is primarily carried out by the 20S proteasome core particle (CP), a protease of 720 kDa and 28 individual subunits. As a result of its central functional role, the proteasome represents an attractive drug target that has been extensively investigated during the last decade and validated by the approval of bortezomib by the US Food and Drug Administration (FDA). Currently, several optimized second‐generation proteasome inhibitors are being explored as anticancer drugs in clinical trials, and most of them target both constitutive proteasomes (cCPs) and immunoproteasomes (iCPs). However, selective inhibition of the iCPs, a distinct class of proteasomes predominantly expressed in immune cells, appears to be a promising therapeutic rationale for the treatment of autoimmune disorders. Although a few selective agents have already been identified, the recently determined crystal structure of the iCP will further promote the development and optimization of iCP‐selective compounds.     

Crystal habit modifications of imatinib mesylate under various precipitation conditions

Abstract  

Crystals of the α-form of imatinib mesylate with various habits (e.g., polyhedral-like and plate-like) were prepared from various organic solvents (e.g., butyl lactate, 4-methyl-2-pentanone, 2-methyl-2-butanol, 2-isopropoxyethanol, propyl ether) by several precipitation methods. The methods provide imatinib mesylate in a non-needle-shaped crystalline α-form. The crystal modification was identified by hot-stage microscopy, scanning electron microscopy, differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRPD). The analyses by DSC, IR, and XRPD indicate that imatinib mesylate crystals with various habits have the same crystal structure. The plate-like habit has been also observed in the system where the organic solvent acts as a precipitant.     

Protein and nanoparticle adsorption on orthogonal, charge-density-versus-net-charge surface-chemical gradients

An orthogonal, charge-density-versus-net-charge, surface-chemical gradient, composed of ternary mixed self-assembled monolayers, has been prepared from three hydrophilic components: positively chargeable amine-terminated, negatively chargeable carboxylic-acid-terminated, and hydroxyl-terminated alkanethiols, with the latter bearing a slight negative charge in electrolytes. The chemical composition and its distribution have been monitored by X-ray photoelectron spectroscopy. The adsorption behavior of negatively charged SiO(2) nanoparticles and positively charged amine-modified SiO(2) nanoparticles has been studied. Additionally, negatively charged proteins (bovine serum albumin and fibrinogen) and positively charged proteins (lysozyme) were adsorbed on the gradients. Negatively charged nanoparticles and proteins adsorb mainly in the positively charged region and vice versa, illustrating that the adsorption behavior is mainly influenced by electrostatic interactions, and showing the potential of the gradient for sorting applications. Despite literature reports to the contrary, no area was found that was completely resistant to protein adsorption.     

Chloro- and phenoxy-phosphines in frustrated Lewis pair additions to alkynes

The reaction of tBu(C(6)H(4)O(2))P, with the borane B(C(6)F(5))(3) gives rise to NMR data consistent with the formation of the classical Lewis acid-base adduct tBu(C(6)H(4)O(2))P(B(C(6)F(5))(3)) (1). In contrast, the NMR data for the corresponding reactions of tBu(C(20)H(12)O(2))P and Cl(C(20)H(12)O(2))P with B(C(6)F(5))(3) were consistent with the presence of equilibria between free phosphine and borane and the corresponding adducts. Nonetheless, in each case, the adducts tBu(C(20)H(12)O(2))P(B(C(6)F(5))(3)) (2) and Cl(C(20)H(12)O(2))P(B(C(6)F(5))(3)) (3) were isolable. The species 1 reacts with PhCCH to give the new species tBu(C(6)H(4)O(2))P(Ph)C=CHB(C(6)F(5))(3) (4) in near quantitative yield. In an analogous fashion, the addition of PhCCH to solutions of the phosphines tBu(C(20)H(12)O(2))P, tBuPCl(2) and (C(6)H(3)(2,4-tBu(2))O)(3)P each with an equivalent of B(C(6)F(5))(3) gave rise to L(Ph)C=CHB(C(6)F(5))(3) (L = tBu(C(20)H(12)O(2))P 5, tBuPCl(2)6 and (C(6)H(3)(2,4-tBu(2))O)(3)P 7). X-Ray data for 1, 2, 6 and 7 are presented. The implications of these findings are considered.     

Temperature-sensitive swelling of poly(N-isopropylacrylamide) brushes with low molecular weight and grafting density

Temperature-sensitive poly(N-isopropylacrylamide) (PNIPAAm) brushes with different molecular weights M(n) and grafting densities σ were prepared by the "grafting-to" method. Changes in their physicochemical properties according to temperature were investigated with the help of in situ spectroscopic ellipsometry and in situ attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Brush criteria indicate a transition between a brush conformation below the lower critical solution temperature (LCST) and an intermediate to mushroom conformation above the LCST. By in situ ellipsometry distinct changes in the brush layer parameters (wet thickness, refractive index, buffer content) were observed. A broadening of the temperature region with maximum deswelling occurred with decreasing grafting density. The brush layer properties were independent of the grafting density below the LCST, but showed a virtually monotonic behavior above the LCST. The midtemperature ?(half) of the deswelling process increased with increasing grafting density. Thus grafting density-dependent design parameters for such functional films were presented. For the first time, ATR-FTIR spectroscopy was used to monitor segment density and hydrogen bonding changes of these very thin PNIPAAm brushes as a function of temperature based on significant variations of the methyl stretching, Amide I, as well as Amide II bands with respect to intensity and wavenumber position. No dependence on M(n) and σ in the wavenumber shift of these bands above the LCST was found. The temperature profile of these band intensities and thus segment density was found to be rather step-like, exceeding temperatures around the LCST, while the respective profile of their wavenumber positions suggested continuous structural and hydration processes. Remaining buffer amounts and residual intermolecular segment/water interaction in the collapsed brushes above the LCST could be confirmed by both in situ methods.