Complex molecular assemblies at hand via interactive simulations

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low‐resolution coarse‐grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well‐balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all‐atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N‐ethylmaleimide‐sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid–protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle‐based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

7-(2-Anilinopyrimidin-4-yl)-1-benzazepin-2-ones Designed by a “Cut and Glue” Strategy Are Dual Aurora A/VEGF-R Kinase Inhibitors

Although overexpression and hyperactivity of protein kinases are causative for a wide range of human cancers, protein kinase inhibitors currently approved as cancer drugs address only a limited number of these enzymes. To identify new chemotypes addressing alternative protein kinases, the basic structure of a known PLK1/VEGF-R2 inhibitor class was formally dissected and reassembled. The resulting 7-(2-anilinopyrimidin-4-yl)-1-benzazepin-2-ones were synthesized and proved to be dual inhibitors of Aurora A kinase and VEGF receptor kinases. Crystal structures of two representatives of the new chemotype in complex with Aurora A showed the ligand orientation in the ATP binding pocket and provided the basis for rational structural modifications. Congeners with attached sulfamide substituents retained Aurora A inhibitory activity. In vitro screening of two members of the new kinase inhibitor family against the cancer cell line panel of the National Cancer Institute (NCI) showed antiproliferative activity in the single-digit micromolar concentration range in the majority of the cell lines.     

Advances in the studies of bisphosphorylated dihydric phenols

The data on the synthesis, structure, and chemical properties of bisphosphorylated dihydric phenols are summarized. All the currently known methods for the synthesis of the systems in question are shown. Specific features of their structure, chemical and complexation properties, as well as areas of application of these compounds were analyzed.     

二咪唑-Ag(I)配位聚合物发光凝胶的设计与制备

本文设计合成了新型的氟硼荧（氟硼二吡咯,BODIPY）功能化的间苯二咪唑配体5。利用刚性二咪唑配体的配位作用及氟硼二吡咯的荧光特性,配体5与Ag(I) 络合后成功地获得了具有优良发光特性的配位聚合物凝胶,并通过TEM、SEM、荧光光谱等检测手段对该凝胶的结构和性能进行了表征。研究显示,银离子的加入并未影响荧光团的发射波长及荧光强度,使得配体的荧光特性在凝胶状态下得以保持。这一研究结果是本课题组刚性二咪唑-Ag(I)配合物凝胶的又一成功范例,使得采用类似方法构筑其它不同类型的配位聚合物发光凝胶成为可能。     

Effects of Specific Inhibitors for CaMK1D on a Primary Neuron Model for Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common cause of dementia worldwide. Despite extensive research and targeting of the main molecular components of the disease, beta-amyloid (Aβ) and tau, there are currently no treatments that alter the progression of the disease. Here, we examine the effects of two specific kinase inhibitors for calcium/calmodulin-dependent protein kinase type 1D (CaMK1D) on Aβ-mediated toxicity, using mouse primary cortical neurons. Tau hyperphosphorylation and cell death were used as AD indicators. These specific inhibitors were found to prevent Aβ induced tau hyperphosphorylation in culture, but were not able to protect cells from Aβ induced toxicity. While inhibitors were able to alter AD pathology in cell culture, they were insufficient to prevent cell death. With further research and development, these inhibitors could contribute to a multi-drug strategy to combat AD.     

Large-Scale Production of the Immunomodulator c-di-GMP from GMP and ATP by an Enzymatic Cascade

(3'-5')-Cyclic diguanylate (c-di-GMP) is a bacterial second messenger with immunomodulatory activities in mice suggesting potential applications as a vaccine adjuvant and as a therapeutic agent. Clinical studies in larger animals or humans will require larger doses that are difficult and expensive to generate by currently available chemical or enzymatic synthesis and purification methods. Here we report the production of c-di-GMP at the multi-gram scale from the economical precursors guanosine monophosphate (GMP) and adenosine triphosphate by a "one-pot" three enzyme cascade consisting of GMP kinase, nucleoside diphosphate kinase, and a mutated form of diguanylate cyclase engineered to lack product inhibition. The c-di-GMP was purified to apparent homogeneity by a combination of anion exchange chromatography and solvent precipitation and was characterized by reversed phase high performance liquid chormatography and mass spectrometry, nuclear magnetic resonance spectroscopy, and further compositional analyses. The immunomodulatory activity of the c-di-GMP preparation was confirmed by its potentiating effect on the lipopolysaccharide-induced interleukin 1β, tumor necrosis factor α, and interleukin 6 messenger RNA expression in J774A.1 mouse macrophages.     

Polar Thin Films Produced by Phosphonium Liquid Crystals: Two-Dimensional Self-Assembled Ionic Layers with Spontaneous Polarization

Nonlinear optical properties are shown by the smectic phase formed by simple dialkyl phosphonium salts. The molecules form into layers, featuring ion pairs separated by insulating glassy alkyl coating to produce a spontaneous polarization (P(s)) in the sheets (see picture). Applications of this material are currently leading to the development of novel electrical and electrooptical devices.     

Cytoprotective Role of Mitogen-activated Protein Kinase Phosphatase-1 in Light-damaged Human Retinal Pigment Epithelial Cells

The role of the mitogen-activated protein (MAP) kinase phosphatases (MKPs) in light-damaged cells is unclear. Therefore we investigated the involvement of MKP-1 in the regulation of apoptosis and cell survival mediated by MAP kinase pathways in light-damaged human retinal pigment epithelial cells (ARPE-19). Light dose-dependent changes in the expression of MKP-1 and in the phosphorylation status of the MAP kinases, c-Jun-N-terminal kinase (JNK) and p38 were demonstrated. Low light doses up to 2 J cm⁻² led to an upregulation of MKP-1 which resulted in the prevention of cell death by inactivating JNK kinase. However, higher light doses (≥3 J cm⁻²) significantly reduced MKP-1 protein expression and subsequently led to an increased JNK kinase activity followed by a significant increase in cell death. JNK kinase inactivation by the JNK inhibitor SP600125 significantly reduced light-induced cell death, suggesting that the cytoprotective properties of MKP-1 are mediated mainly by the JNK MAP kinase pathway. Physiological concentrations of ascorbic acid or taurine were seen to prevent apoptosis and cell death in light-damaged ARPE-19 cells by reducing oxidative stress within cells, thus maintaining MKP-1 at high levels, leading to an inactivation of the JNK kinase pathway which resulted in an increased cell viability.     

Characterization of calcium and phospholipid dependent protein kinase in isolated rat adipocytes

Calcium and phospholipid-dependent protein kinase (protein kinase C) from isolated rat adipocytes has been partially purified using DEAE-Sepharose CL-6B and characterized. The enzyme was shown to have similar properties as the kinase isolated from brain or spleen. When histone was used as substrate, an equal amount of cAMP-dependent and calcium and phospholipid-dependent kinase activity was detected from the DEAE Sepharose CL-6B fractions. The major part of protein kinase C (72%) was isolated from the soluble adipocyte fraction. Of the membranous fractions, the plasma membrane exhibited the highest specific activity. The protein kinase preparations bound [3H]-phorbol-12,13-dibutyrate (PDBU) with high affinity (Kd = 2 nM) and the number of PDBU binding sites per cell was calculated to 63 000.     

Rewiring kinase specificity with a synthetic adaptor protein

Signaling cascades are managed in time and space by interactions between and among proteins. These interactions are often aided by adaptor proteins, which guide enzyme-substrate pairs into proximity. Miniature proteins are a class of small, well-folded protein domains possessing engineered binding properties. Here we made use of two miniature proteins with complementary binding properties to create a synthetic adaptor protein that effectively redirects a ubiquitous signaling event: tyrosine phosphorylation. We report that miniature-protein-based adaptor 3 uses templated catalysis to redirect the Src family kinase Hck to phosphorylate hDM2, a negative regulator of the p53 tumor suppressor and a poor Hck substrate. Phosphorylation occurs with multiple turnover and at a single site targeted by c-Abl kinase in the cell.     

A Fluorescent Kinase Inhibitor that Exhibits Diagnostic Changes in Emission upon Binding

The development of a fluorescent LCK inhibitor that exhibits favourable solvatochromic properties upon binding the kinase is described. Fluorescent properties were realised through the inclusion of a prodan‐derived fluorophore into the pharmacophore of an ATP‐competitive kinase inhibitor. Fluorescence titration experiments demonstrate the solvatochromic properties of the inhibitor, in which dramatic increase in emission intensity and hypsochromic shift in emission maxima are clearly observed upon binding LCK. Microscopy experiments in cellular contexts together with flow cytometry show that the fluorescence intensity of the inhibitor correlates with the LCK concentration. Furthermore, multiphoton microscopy experiments demonstrate both the rapid cellular uptake of the inhibitor and that the two‐photon cross section of the inhibitor is amenable for excitation at 700 nm.     

Ruthenium half-sandwich complexes as protein kinase inhibitors: derivatization of the pyridocarbazole pharmacophore ligand

A general route to ruthenium pyridocarbazole half-sandwich complexes is presented and applied to the synthesis of sixteen new compounds, many of which have modulated protein kinase inhibition properties. For example, the incorporation of a fluorine into the pyridine moiety increases the binding affinity for glycogen synthase kinase 3 by almost one order of magnitude. These data are supplemented with cyclic voltammetry experiments and a protein co-crystallographic study.     

Aqueous two-phase systems in biochemical recovery

The design and application of aqueous two-phase systems for recovery of proteins is reviewed. Reference is made to the properties of polymers and salt forming the systems and their influence on phase separation and partition. The properties of systems important for the design of purification strategies are discussed in relation to the surface properties of proteins. Strategies for the modification of systems for bioaffinity partition are considered including the choice of carrier in terms of molecular type and properties, or by particulate addition. Finally, the scaleup of partition is considered, and the reasons for currently limited adoption at larger scales are elucidated.     

Two-Dimensional Nanomaterials for Photothermal Therapy

Two-dimensional (2D) nanomaterials are currently explored as novel photothermal agents because of their ultrathin structure, high specific surface area, and unique optoelectronic properties. In addition to single photothermal therapy (PTT), 2D nanomaterials have demonstrated significant potential in PTT-based synergistic therapies. In this Minireview, we summarize the recent progress in 2D nanomaterials for enhanced photothermal cancer therapy over the last five years. Their unique optical properties, typical synthesis methods, and surface modification are also covered. Emphasis is placed on their PTT and PTT-synergized chemotherapy, photodynamic therapy, and immunotherapy. The major challenges of 2D photothermal agents are addressed and the promising prospects are also presented.     

dihydroquercetin in the reactions with phosphorous acid hexaethyltriamide

The possibility was demonstrated and conditions were developed of a directional phosphorylation of dihydroquercetin flavonoid with phosphorous hexaethyltriamide. The chemical properties of the obtained compounds of trivalent phosphorus are currently under investigation.     

On Some Structural Properties of Fullerene Graphs

We show how some important structural properties of general fullerene graphs follow from the recently proved fact that all fullerene graphs are cyclically 4-edge connected. These properties, in turn, give us upper and lower bounds for various graph invariants. In particular, we establish the best currently known lower bound for the number of perfect matchings in fullerene graphs.     

A first-principle study of the stability and electronic properties of halide inorganic double perovskite Cs2PbX6 (X = Cl,I) for solar cell application

The problem of lead toxicity in perovskites materials that are currently performing with the most efficiency can be partially solved by choosing double perovskites compounds Cs₂PbX₆ (X = Cl,I), which have considerably reduced lead contents. These materials are slightly more stable, and substituting Cl and I with Br in small percentages further improves their mechanical stability and electronic properties. In this study, the properties of these promising materials were investigated in their pure and mixed forms.