Use of hydrogen/deuterium exchange mass spectrometry and mutagenesis as a tool to identify the binding region of inhibitors targeting the human mitotic kinesin Eg5

An experimental procedure associating both hydrogen/deuterium exchange mass spectrometry (H/D-MS) and mutagenesis was developed to identify the protein-binding region of small inhibitors targeting the motor domain of the human mitotic kinesin Eg5. All the tested inhibitors decrease the deuterium incorporation rate of the same peptides corresponding to the following secondary structure elements: loop L5/helix alpha2 (region Tyr125-Glu145) and strand beta5/helix alpha3 (region Ile202-Leu227). Replacement of these two regions by the equivalent ones from N. crassa conventional kinesin heavy chain completely abolishes the modification of the deuterium incorporation rate by the inhibitors as well as their effects on the basal ATPase activity. The six tested inhibitors thus share a common binding site on Eg5. The strategy reported here allows the regions of a protein involved in ligand binding to be rapidly pinpointed and can be applied to other proteins and used as a general in vitro screening procedure to identify compounds targeting specific binding regions.     

聚乙撑二氧噻吩阳极降解的研究

研究了聚乙撑二氧噻吩(PEDOT)膜在水溶液中的阳极降解过程. 研究发现PEDOT的阳极过程可以分为p掺杂区[电位范围－0.3～0.5 V (相对于饱和甘汞电极; vs. SCE)]、过渡区[电位范围0.6～1 V (vs. SCE)]、过氧化区[电位范围1.2～1.6 V (vs. SCE)]三个电位区域. 用电化学阻抗谱法、循环伏安法、红外光谱技术、膜电阻测量以及电子自旋共振技术分别研究了PEDOT膜在这三个电位区域的行为. 结果表明: PEDOT膜在这三个电位区域的性质有明显不同. 在p掺杂区PEDOT膜的官能团、共轭结构、导电性均保持, 即在这个电位区发生可逆的掺杂/脱掺杂反应, 膜几乎不降解. 在过渡区和过氧化区, PEDOT膜均发生了降解. 与传统的导电聚合物在高电位的阳极降解的过氧化过程不同, 我们认为膜在较高电位(过渡区)发生一个驰豫过程, 该过程使得膜的官能团改变, 但是膜的共轭结构和导电性均保持; 而在更高的电位区(过氧化区)膜的降解和一般意义的过氧化降解相同, 此时膜的官能团、共轭结构、导电性均发生不可逆的破坏.     

Syntheses and characterization of lisinopril-coated gold nanoparticles as highly stable targeted CT contrast agents in cardiovascular diseases

Lisinopril was used as the targeting moiety to prepare gold nanoparticle-based functional CT contrast agents. Pure lisinopril, thioctic acid-lisinopril conjugate, and reduced thioctic acid-lisinopril conjugate were used to obtain GNP-Lis, GNP-TA-Lis, and GNP-RTA-Lis, respectively, via ligand exchange reaction on citrate-coated gold nanoparticles (GNPs). These lisinopril-decorated GNPs were fully characterized, and their chemical stabilities in biological relevant media and in high salt concentration were compared. Their relative stabilities toward lyophilization and against cyanide-induced decomposition were also investigated. Because of their higher stability, GNP-TA-Lis were used to assess the targeting of angiotensin converting enzyme (ACE) using X-ray computed tomography (CT). The images obtained displayed high contrast in the region of the lungs and heart, clearly indicating the targeting of ACE, whose overexpression is associated with development of cardiac and pulmonary fibrosis. Thus, the new nanoprobes prepared here will serve as very useful tools for the monitoring of cardiovascular pathophysiologies using CT imaging.     

Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.     

Strong host-guest interaction enables facile and controllable surface modification of cucurbit[6]uril-based polymer nanocapsules for in vivo cancer targeting

Cucurbit[6]uril-based polymer nanocapsules (CB[6]PNs), covalently conjugated with a near-infrared dye (Cy 7), was exploited as a stable platform (Cy7-CB[6]PNs) for in vivo cancer targeting. The strong host-guest interaction between CB[6] and spermidine (spmd) enabled us to modify the surface of the nanocapsules with spmd-conjugated cancer targeting functional tags in a facile, controllable and non-covalent manner. Thanks to the strong host-guest interaction retained even in the bloodstream of a mouse, enhanced accumulation of Cy7-CB[6]PNs on cancer tissues of mice was successfully detected via NIR imaging when the nanocapsules were treated with more number of the cancer targeting functional tags. This result showed the potential of the CB[6]-based strong host-guest interaction as a controllable and efficient tool for surface modification of in vivo cancer targeting nanomaterials.     

Multiplexed identification of different fish species by detection of parvalbumin, a common fish allergen gene: a DNA application of multi-analyte profiling (xMAP™) technology

Fish are a common cause of allergic reactions associated with food consumption, with parvalbumin being the major allergenic protein. Some fish-hypersensitive patients tolerate some fish species while being allergic to others. Reliable detection methods for allergenic fish species in foods are necessary to ensure compliance with food allergen labeling guidelines to protect fish-allergic consumers. The objective of this project was to develop a multi-analyte detection method for the presence of fish in food. Therefore, conserved parvalbumin exon sequences were utilized for the design of universal PCR primers amplifying intron DNA and small regions of exons flanking the enclosed intron from even very distantly related fish species. An assay for the identification of eight fish species was developed using xMAP™ technology with probes targeting species-specific parvalbumin intron regions. Additionally, a universal fish probe was designed targeting a highly conserved exon region located between the intron and the reverse primer region. The universal fish assay showed no cross-reactivity with other species, such as beef, pork, lamb, chicken, turkey, and shrimp. Importantly, with the exception of one notable case with fish in the same subfamily, species-specific detection showed no cross-reactivity with other fish species. Limits of detection for these eight species were experimentally estimated to range from 0.01% to 0.04%, with potential to increase the detection sensitivity. This report introduces a newly developed method for the multiplex identification of at least eight allergenic fish species in food, which could conceivably be extended to detect up to 100 species simultaneously in one sample.     

An analysis of nonlocal density functionals in chemical bonding

In this work, we carry out an analysis of the gradient-corrected density functionals in molecules that are used in the Kohn–Sham density functional approach. We concentrate on the special features of the exchange and correlation energy densities and exchange and correlation potentials in the bond region. By comparing to the exact Kohn–Sham potential, it is shown that the gradient-corrected potentials build in the required peak in the bond midplane, but not completely correctly. The gradient-corrected potentials also exhibit wrong asymptotic behavior. Contributions from different regions of space (notably bond and outer regions) to nonlocal bonding energy contributions are investigated by integrating the exchange and correlation energy densities in various spatial regions. This provides an explanation of why the gradient corrections reduce the local density approximation (LDA ) overbinding of molecules. It explains the success of the presently used nonlocal corrections, although it is possible that there is a cancellation of errors, too much repulsion being derived from the bond region and too little from the outer region. © John Wiley & Sons, Inc.     

Fenchone, camphor, 2-methylenefenchone and 2-methylenecamphor: a vibrational circular dichroism study

We report and discuss the infrared (IR) vibrational circular dichroism (VCD) spectra of the enantiomeric pairs of the olefin derivatives of fenchone (1,3,3-trimethyl-2-methylenebicyclo[2.2.1]heptane) and camphor (1,7,7-trimethyl-2-methylenebicyclo[2.2.1]heptane), respectively, together with those of the parent molecules. The VCD spectra were taken in three spectral regions: the mid-IR region, encompassing the fundamental deformation modes, the region of CH-stretching fundamental modes and the NIR-region between 1100 and 1300 nm, which corresponds to the second CH-stretching overtone. The VCD and absorption spectra in the first two regions are analyzed by use of current density functional theory (DFT) calculations. The NIR region is analyzed by a protocol that consists of the use of DFT-based calculations and in assuming local mode behavior: the local mode approach is found appropriate for interpreting the absorption spectra and, for the moment, acceptable for calculating NIR-VCD spectra. The analysis of the first region allows us to track the contribution of the C=O group in the vibrational optical activity of C-C stretching modes; notable differences are indeed found in olefins and ketones. On the contrary, in the other two regions the VCD spectra of olefins and ketones are more similar: in the normal mode region of CH stretching fundamentals the spectra are determined by the mutual orientation of the CH bonds; in the second overtone local mode region olefins and ketones signals show some differences.     

Targeting structural features of viral genomes with a nano-sized supramolecular drug

RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.     

Molecular Recognition of FDA-Approved Small Molecule Protein Kinase Drugs in Protein Kinases

Protein kinases are key enzymes that catalyze the covalent phosphorylation of substrates via the transfer of the γ-phosphate of ATP, playing a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. Due to their pivotal cellular role, the aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Decades of intense development of protein kinase inhibitors (PKIs) resulted in 71 FDA-approved PKI drugs that target dozens of protein kinases for the treatment of various diseases. How do FDA-approved protein kinase inhibitor PKI drugs compete with ATP in their own binding pocket? This is the central question we attempt to address in this work. Based on modes of non-bonded interactions and their calculated interaction strengths by means of the advanced double hybrid DFT method B2PLYP, the molecular recognition of PKI drugs in the ATP-binding pockets was systematically analyzed. It was found that (1) all the FDA-approved PKI drugs studied here form one or more hydrogen bond(s) with the backbone amide N, O atoms in the hinge region of the ATP binding site, mimicking the adenine base; (2) all the FDA-approved PKI drugs feature two or more aromatic rings. The latter reach far and deep into the hydrophobic regions I and II, forming multiple CH-π interactions with aliphatic residues L(3), V(11), A(15), V(36), G(51), L(77) and π-π stacking interactions with aromatic residues F(47) and F(82), but ATP itself does not utilize these regions extensively; (3) all FDA-approved PKI drugs studied here have one thing in common, i.e., they frequently formed non-bonded interactions with a total of 12 residues L(3),V(11), A(15), K(17), E(24),V(36),T(45), F(47), G(51), L(77), D(81) and F(82) in the ATP binding. Many of those 12 commonly involved residues are highly conserved residues with important structural and catalytic functional roles. K(17) and E(24) are the two highly conserved residues crucial for the catalytic function of kinases. D(81) and F(82) belong to the DFG motif; T(45) was dubbed the gate keeper residue. F(47) is located on the hinge region and G(51) sits on the linker that connects the hinge to the αD-helix. It is this targeting of highly conserved residues in protein kinases that led to promiscuous PKI drugs that lack selectivity. Although the formation of hydrogen bond(s) with the backbone of the hinge gives PKI drugs the added binding affinity and the much-needed directionality, selectivity is sacrificed. That is why so many FDA-approved PKI drugs are known to have multiple targets. Moreover, off-target-mediated toxicity caused by a lack of selectivity was one of the major challenges facing the PKI drug discovery community. This work suggests a road map for future PKI drug design, i.e., targeting non-conserved residues in the ATP binding pocket to gain better selectivity so as to avoid off-target-mediated toxicity.     

Isolation and Functional Characterization of a Novel Seed-Specific Promoter Region from Peanut

The importance of using tissue-specific promoters in the genetic transformation of plants has been emphasized increasingly. Here, we report the isolation of a novel seed-specific promoter region from peanut and its validation in Arabidopsis and tobacco seeds. The reported promoter region referred to as groundnut seed promoter (GSP) confers seed-specific expression in heterologous systems, which include putative promoter regions of the peanut (Arachis hypogaea L.) gene 8A4R19G1. This region was isolated, sequenced, and characterized using gel shift assays. Tobacco transgenics obtained using binary vectors carrying uidA reporter gene driven by GSP and/or cauliflower mosaic virus 35S promoters were confirmed through polymerase chain reaction (PCR), RT-PCR, and computational analysis of motifs which revealed the presence of TATA, CAAT boxes, and ATG signals. This seed-specific promoter region successfully targeted the reporter uidA gene to seed tissues in both Arabidopsis and tobacco model systems, where its expression was confirmed by histochemical analysis of the transgenic seeds. This promoter region is routinely being used in the genetic engineering studies in legumes aimed at targeting novel transgenes to the seeds, especially those involved in micronutrient enhancement, fungal resistance, and molecular pharming.     

Architectural and structural optimization of the protective polymer layer for enhanced targeting

Using Monte Carlo simulations we study the influence of ligand architecture (valence, branching length) and structure (polydispersity) of a flat protective polymer layer on the accessibility of its functional groups and efficiency of receptor targeting. Two types of receptor surfaces were considered: the surface homogeneously covered with receptors and the surface containing a finite number of receptor sites. We found that multivalent ligands provide a larger density of targeting groups on the periphery of the layer compared to monovalent ligands for the same overall number of targeting groups per polymer layer. Because of their cooperativity in binding, multivalent ligands were also considerably more efficient in binding to both types of receptor surfaces. With an increase of ligand valence the number of functional groups attached to receptors noticeably increases. Short-branched divalent ligands show an especially high cooperativity in binding to closely packed receptors. However, in the case of immobile receptors separated by a finite distance from each other, the average distance between the functional groups belonging to the same short divalent ligand is too small to reach different receptors simultaneously and the receptor binding is less efficient than in the monovalent ligand case. Using a bidisperse protective polymer layer formed by short nonfunctional polymers and long functionalized polymers considerably increases the fraction of functional groups on the periphery of the layer. Simulations of receptor binding confirm the high efficiency of receptor targeting by bidisperse polymer layers, which is achieved by means of larger compressibility and higher capability of the ligands to reach out compared to the corresponding monodisperse layers. The concepts of multivalent ligands and a bidisperse protective polymer layer each have their own advantages which can be combined for an enhanced targeting effect.     

Comprehensive analysis of microRNA-mRNA co-expression in circadian rhythm

To investigate the potential role of microRNA (miRNA) in the regulation of circadian rhythm, we performed microarray-based expression profiling study of both miRNA and mRNA in mouse liver for 48 h at 4-hour intervals. Circadian miRNA-mRNA target pair is defined as the pair both elements of which show circadian expression patterns and the sequence-based target relationship of which can be predicted. Circadian initiators, Clock and Bmal1, showed inversely correlated circadian expression patterns against their corresponding miRNAs, miR-181d and miR-191, targeting them. In contrast, circadian suppressors, Per, Cry, CKIe and Rev-erba, exhibited positively correlated circadian expression patterns to their corresponding miRNAs. Genomic location analysis revealed that intronic region showed higher abundance of cyclic than non-cyclic miRNAs targeting circadian genes while other (i.e., 3''-UTR, exon and intergenic) regions showed no difference. It is suggested that miRNAs are involved in the regulation of peripheral circadian rhythm in mouse liver by modulating Clock:Bmal1 complex. Identifying specific miRNAs and their targets that are critically involved in circadian rhythm will provide a better understanding of the regulation of circadian-clock system.     

Like a bolt from the blue: phthalocyanines in biomedical optics

The purpose of this review is to compile preclinical and clinical results on phthalocyanines (Pcs) as photosensitizers (PS) for Photodynamic Therapy (PDT) and contrast agents for fluorescence imaging. Indeed, Pcs are excellent candidates in these fields due to their strong absorbance in the NIR region and high chemical and photo-stability. In particular, this is mostly relevant for their in vivo activation in deeper tissular regions. However, most Pcs present two major limitations, i.e., a strong tendency to aggregate and a low water-solubility. In order to overcome these issues, both chemical tuning and pharmaceutical formulation combined with tumor targeting strategies were applied. These aspects will be developed in this review for the most extensively studied Pcs during the last 25 years, i.e., aluminium-, zinc- and silicon-based Pcs.     

Vibrational absorption and circular dichroism studies of trans-(3S,4S)-d6-cyclopentene in the gas phase

Vibrational absorption (IR) and circular dichroism (VCD) measurements of trans-(3S,4S)-d6-cyclopentene in the gas phase were performed in the C-H, C-D, and mid-infrared regions. In this study, we report the first VCD spectra recorded at high spectral resolution (up to 0.5 cm(-1)) with a very good signal-to-noise ratio (differential absorbance lower than 5 x 10(-6)). The quality of the experimental spectra allows us the observation of the vibration-rotation structure of the bands in both absorption and VCD spectra. Experimental spectra have been compared with the density functional theory (DFT) absorption and VCD spectra, calculated using B3LYP functional and cc-pVTZ basis set for the axial, equatorial, and planar conformers. Lorentzian and PQR band profiles have been used to convert the calculated dipolar and rotational strengths. In the mid-infrared (<2000 cm(-1)) region, predicted (population-weighted) spectra were in excellent agreement with experiment, allowing the determination of the absolute configuration of this molecule. Above 2000 cm(-1), a reasonable agreement was obtained even if anharmonicity was not considered and if Fermi resonance occurs in the C-D stretching region. Finally, a more precise analysis of the absorption spectrum has been achieved by taking into account anharmonicity of the C-H stretching and its coupling with the ring-puckering motion.     

Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration

The Blueline Rasbora (Rasbora sarawakensis) is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome sequence of R. sarawakensis was sequenced using four primers targeting overlapping regions. The mitogenome is 16,709 bp in size, accommodating 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other genus counterparts. The heavy strand houses 28 genes while the light strand stores the other nine genes. Most protein-coding genes employ ATG as start codon, excluding COI gene, which utilizes GTG instead. The central conserved sequence blocks (CSB-F, CSB-E and CSB-D), variable sequence blocks (CSB-3, CSB-2 and CSB-1) as well as the terminal associated sequence (TAS) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of R. sarawakensis from the basal region of the Rasbora clade, where its evolutionary relationships with R. maculatus and R. pauciperforata are poorly resolved as indicated by the low bootstrap values. This work acts as steppingstone towards further molecular evolution and population genetics studies of Rasbora genus in future.