Anti-hepatitis B virus drugs in clinical and preclinical development

Up to date, there are two types of drugs approved to treat hepatitis B: interferons and nucleos (t) ide analogues. However, the therapies are limited in the clinical context because of the negative side effects of interferon-α and the development of substantial viral resistance to nucleos (t) idic inhibitors. Therefore, new drugs with novel structures and mechanisms are needed. In this article, the drugs approved by FDA or the European Commission for treating chronic hepatitis B virus infection, as well as those under clinical trials, and several compounds in preclinical studies are reviewed. Additionally, some potential targets and strategies to combat chronic hepatitis B virus infection are discussed.     

NMR structures of polytopic integral membrane proteins

Abstract

Membrane proteins represent up to 30% of the proteins in all organisms, they are involved in many biological processes and are the molecular targets for around 50% of validated drugs. Despite this, membrane proteins represent less than 1% of all high-resolution protein structures due to various challenges associated with applying the main biophysical techniques used for protein structure determination. Recent years have seen an explosion in the number of high-resolution structures of membrane proteins determined by NMR spectroscopy, especially for those with multiple transmembrane-spanning segments. This is a review of the structures of polytopic integral membrane proteins determined by NMR spectroscopy up to the end of the year 2010, which includes both β-barrel and α-helical proteins from a number of different organisms and with a range in types of function. It also considers the challenges associated with performing structural studies by NMR spectroscopy on membrane proteins and how some of these have been overcome, along with its exciting potential for contributing new knowledge about the molecular mechanisms of membrane proteins, their roles in human disease, and for assisting drug design.     

Systematic crosstalk in plasmalogen and diacyl lipid biosynthesis for their differential yet concerted molecular functions in the cell

Plasmalogen is a major phospholipid of mammalian cell membranes. Recently it is becoming evident that the sn-1 vinyl-ether linkage in plasmalogen, contrasting to the ester linkage in the counterpart diacyl glycerophospholipid, yields differential molecular characteristics for these lipids especially related to hydrocarbon-chain order, so as to concertedly regulate biological membrane processes. A role played by NMR in gaining information in this respect, ranging from molecular to tissue levels, draws particular attention. We note here that a broad range of enzymes in de novo synthesis pathway of plasmalogen commonly constitute that of diacyl glycerophospholipid. This fact forms the basis for systematic crosstalk that not only controls a quantitative balance between these lipids, but also senses a defect causing loss of lipid in either pathway for compensation by increase of the counterpart lipid. However, this inherent counterbalancing mechanism paradoxically amplifies imbalance in differential effects of these lipids in a diseased state on membrane processes. While sharing of enzymes has been recognized, it is now possible to overview the crosstalk with growing information for specific enzymes involved. The overview provides a fundamental clue to consider cell and tissue type-dependent schemes in regulating membrane processes by plasmalogen and diacyl glycerophospholipid in health and disease.     

Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR

In structural genomics centers, nuclear magnetic resonance (NMR) screening is in increasing use as a tool to identify folded proteins that are promising targets for three-dimensional structure determination by X-ray crystallography or NMR spectroscopy. The use of 1D ¹H NMR spectra or 2D [¹H,¹⁵N]-correlation spectroscopy (COSY) typically requires milligram quantities of unlabeled or isotope-labeled protein, respectively. Here, we outline ways towards miniaturization of a structural genomics pipeline with NMR screening for folded globular proteins, using a high-density micro-fermentation device and a microcoil NMR probe. The proteins are micro-expressed in unlabeled or isotope-labeled media, purified, and then subjected to 1D ¹H NMR and/or 2D [¹H,¹⁵N]-COSY screening. To demonstrate that the miniaturization is functioning effectively, we processed nine mouse homologue protein targets and compared the results with those from the “macro-scale” Joint Center of Structural Genomics (JCSG) high-throughput pipeline. The results from the two pipelines were comparable, illustrating that the data were not compromised in the miniaturized approach.     

Quantitation and characterization of process impurities and extractables in protein‐containing solutions using proton NMR as a general tool

The ability to detect and quantitate a variety of components in solution has become increasingly important in carrying out efficient and rigorous validation studies for biopharmaceutical manufacturing processes. Here, we demonstrate the general applicability of NMR spectroscopy for the identification and quantitation of leachables and other impurities in protein‐based drugs, at low levels previously unattainable in protein‐containing solutions. With improved NMR technology (i.e., CryoProbes) and the application of a Carr‐Purcell‐Meiboom‐Gill pulse sequence (CPMG) to attenuate protein signals, we have been able to use NMR to quantify impurities in a protein‐based biopharmaceutical product at ～1 μg mL^?1. The data indicate that NMR spectra can be used to quantitate a range of impurities, from small molecule components to higher molecular weight leachables, without removing protein from solution. Furthermore, quantitation of impurities by NMR is reliable and accurate enough for biopharmaceutical process validation, even for high molecular weight extractables whose structures are not precisely known. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Observation of slow dynamic exchange processes in Ras protein crystals by 31P solid state NMR spectroscopy

The folding, structure and biological function of many proteins are inherently dynamic properties of the protein molecule. Often, the respective molecular processes are preserved upon protein crystallization, leading, in X-ray diffraction experiments, to a blurring of the electron density map and reducing the resolution of the derived structure. Nuclear magnetic resonance (NMR) is known to be an alternative method to study molecular structure and dynamics. We designed and built a probe for phosphorus solid state NMR that allows for the first time to study static properties as well as dynamic processes in single-crystals of a protein by NMR spectroscopy. The sensitivity achieved is sufficient to detect the NMR signal from individual phosphorus sites in a 0.3mm(3) size single-crystal of GTPase Ras bound to the nucleotide GppNHp, that is, the signal from approximately 10(15) phosphorus nuclei. The NMR spectra obtained are discussed in terms of the conformational variability of the active center of the Ras-nucleotide complex. We conclude that, in the crystal, the protein complex exists in three different conformations. Magic angle spinning (MAS) NMR spectra of a powder sample of Ras-GppNHp show a splitting of one of the phosphate resonances and thus confirm this conclusion. The MAS spectra provide, furthermore, evidence of a slow, temperature-dependent dynamic exchange process in the Ras protein crystal.     

Synthesis and characterization of functionalized thymidine as a potential carrier for cisplatin-like drugs

Pursuing the idea of using a biological nanovector to drive the non-specific cytotoxic activity of Pt(II) complexes toward biological targets, we have singled out thymidine (T) as a potential biological carrier for delivery of cisplatin-like drugs to DNA. Thymidine was functionalized by first reacting it with solid sodium hydride and 1,3-diiodopropane, producing high yields of N3-iodopropylthymidine. Further reaction with ethylenediamine gave the bio-ligand N3-(3-ethylenediamine)propylthymidine which reacts in turn with K₂PtCl₄, resulting in a cisplatin-like nucleoside.This derivative (or more soluble analogues) can be phosphorylated by the cellular enzyme pool and incorporated into the growing DNA chain, thus making them suitable candidates as potential antiproliferative agents, exploiting both alkylating and antimetabolite mechanisms.     

Isolation and detailed 1H and 13C NMR structural assignment for three trachylobanes from Psiadia punctulata (Asteraceae) grown in Africa

The first isolation of a trachylobane from an African specimen of Psiadia punctulata (Asteraceae) is presented in this paper. A complete ¹H and ¹³C NMR spectral analysis of this compound and two other trachylobane diterpenes, previously isolated from the same plant, are also provided. The use of NMR techniques such as gCOSY, gHSQC, gHMBC and 2D-J-resolved, in combination with a software-assisted methodology, led to a complete and unequivocal assignment of ¹H and ¹³C signals. This was achieved together with the measurement of all homonuclear hydrogen coupling constants. The presented detail level of the assignment data has never been published before for trachylobanes. Furthermore, with all determined NMR experimental data from the spectra and to obtain a reliability assessment, signals were simulated in the FOMSC3 and NMR_MultSim software.     

A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents

The cyclic octa-peptide octreotide and its derivatives are used as diagnostics and therapeutics in relation to particular types of cancers. This led to investigations of their conformational properties using spectroscopic, NMR and CD, methods. A CF₃-substituted derivative, that was designed to stabilize the dominant octreotide conformer responsible for receptor binding, turned out to have a lower affinity. The obtained spectroscopic data were interpreted as to show an increased flexibility of the CF₃ derivative compared to the unsubstituted octreotide, which could then explain the lower affinity.In this article, we use MD simulation without and with time-averaged NOE distance and time-averaged local-elevation ³J-coupling restraining representing experimental NMR data to determine the conformational properties of the different peptides in the different solvents for which experimental data are available, that are compatible with the NOE atom–atom distance bounds and the ³J_HNHα-couplings as derived from the NMR measurements. The conformational ensembles show that the CF₃ substitution in combination with the change of solvent from water to methanol leads to a decrease in flexibility and a shift in the populations of the dominant conformers that are compatible with the experimental data.     

Protein structure prediction assisted with sparse NMR data in CASP13

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and ¹⁵N-¹H residual dipolar coupling data, typical of that obtained for ¹⁵N,¹³C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.     

Cell cycle target validation: approaches and successes

Evasion of the checks and balances that govern the human cell division cycle lies at the heart of all proliferative diseases. Because of the astonishing variety of ways that cancer cells manage to achieve growth advantages over normally proliferating cells, it can be expected that pharmacological reinstatement of cell cycle progression control should also be achievable in a multitude of ways. Very few cell cycle targets have so far been exploited for the discovery of mechanism-based anticancer drugs; even fewer targets have yielded actual or experimental clinical drugs. Here, we discuss the approaches that have been and are beginning to be used to identify and validate molecular targets whose pharmacological modulation holds the promise of nongenotoxic and inherently selective cancer therapy. We discuss an approach based on using the genetically amenable organism Drosophila melanogaster as a model for the identification of cell cycle targets, particularly those involved in the processes of mitosis.     

A Proline-Tryptophan Turn in the Intrinsically Disordered Domain 2 of NS5A Protein Is Essential for Hepatitis C Virus RNA Replication

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) and its interaction with the human chaperone cyclophilin A are both targets for highly potent and promising antiviral drugs that are in the late stages of clinical development. Despite its high interest in regards to the development of drugs to counteract the worldwide HCV burden, NS5A is still an enigmatic multifunctional protein poorly characterized at the molecular level. NS5A is required for HCV RNA replication and is involved in viral particle formation and regulation of host pathways. Thus far, no enzymatic activity or precise molecular function has been ascribed to NS5A that is composed of a highly structured domain 1 (D1), as well as two intrinsically disordered domains 2 (D2) and 3 (D3), representing half of the protein. Here, we identify a short structural motif in the disordered NS5A-D2 and report its NMR structure. We show that this structural motif, a minimal Pro³¹⁴–Trp³¹⁶ turn, is essential for HCV RNA replication, and its disruption alters the subcellular distribution of NS5A. We demonstrate that this Pro-Trp turn is required for proper interaction with the host cyclophilin A and influences its peptidyl-prolyl cis/trans isomerase activity on residue Pro³¹⁴ of NS5A-D2. This work provides a molecular basis for further understanding of the function of the intrinsically disordered domain 2 of HCV NS5A protein. In addition, our work highlights how very small structural motifs present in intrinsically disordered proteins can exert a specific function.     

Inflammasome regulation by adaptor isoforms,ASC and ASCb,via differential self-assembly

ASC is an essential adaptor of the inflammasome, a micrometer-size multiprotein complex that processes proinflammatory cytokines. Inflammasome formation depends on ASC self-association into large assemblies via homotypic interactions of its two death domains, PYD and CARD. ASCb, an alternative splicing isoform, activates the inflammasome to a lesser extent compared with ASC. Thus, it has been postulated that adaptor isoforms differentially regulate inflammasome function. At the amino acid level, ASC and ASCb differ only in the length of the linker connecting the two death domains. To understand inflammasome regulation at the molecular level, we investigated the self-association properties of ASC and ASCb using real-time NMR, dynamic light scattering (DLS), size-exclusion chromatography, and transmission electron microscopy (TEM). The NMR data indicate that ASC self-association is faster than that of ASCb; a kinetic model for this oligomerization results in differing values for both the reaction order and the rate constants. Furthermore, DLS analysis indicates that ASC self-associates into more compact macrostructures compared with ASCb. Finally, TEM data show that ASCb has a reduced tendency to form densely packed filaments relative to ASC. Overall, these differences can only be explained by an effect of the linker length, as the NMR results show structural equivalence of the PYD and CARD in both proteins. The effect of linker length was corroborated by molecular docking with the procaspase-1 CARD domain. Altogether, our results indicate that ASC’s faster and less polydisperse polymerization is more efficient, plausibly explaining inflammasome activation differences by ASC isoforms at the molecular level.     

bioNMR-based identification of natural anti-Aβ compounds in Peucedanum ostruthium

The growing interest in medicinal plants for the identification of new bioactive compounds and the formulation of new nutraceuticals and drugs prompted us to develop a powerful experimental approach allowing the detailed metabolic profiling of complex plant extracts, the identification of ligands of macromolecular targets of biomedical relevance and a preliminary characterization of their biological activity. To this end, we selected Peucedanum ostruthium, a plant traditionally employed in Austria and Italy for its several potential therapeutic applications, as case study. We combined the use of NMR and UPLC-HR-MS for the identification of the metabolites present in its leaves and rhizome extracts. Due to the significant content of polyphenols, particularly chlorogenic acids, recently identified as anti-amyloidogenic compounds, polyphenols-enriched fractions were prepared and tested for their ability to prevent Aβ1-42 peptide aggregation and neurotoxicity in a neuronal human cell line. STD-NMR experiments allowed the detailed identification of Aβ oligomers’ ligands responsible for the anti-amyloidogenic activity. These data provide experimental protocols and structural information suitable for the development of innovative molecular tools for prevention, therapy and diagnosis of Alzheimer’s disease.     

Design,synthesis, in vivo and in silico evaluation of phenacyl triazole hydrazones as new anticonvulsant agents

A series of phenacyl triazole hydrazones 3 have been designed based on the hybridization of (arylalkly)triazole and aroyl hydrazone scaffolds as new anticonvulsant agents. The target compounds 3 were easily synthesized from appropriate phenacyl triazoles and aryl acid hydrazides and characterized by IR, NMR and Mass spectroscopy. The in vivo anticonvulsant evaluation of synthesized compounds by using MES and PTZ tests revealed that they are more effective in MES model respect to PTZ test. All compounds showed 33–100% protection against MES-induced seizures at the dose of 100 mg/kg. However, the isonicotinic acid hydrazide derivative 3h showed the best profile of activity in both models. Molecular docking studies of compound 3h with different targets (NMDA, AMPA, GABA_A and sodium channel), postulated that the compound acts mainly via GABA_A receptors. In silico molecular properties predictions indicated that all compounds have favourable oral bioavailability and BBB permeability.     

The flexibility of nonconsciously deployed cognitive processes: evidence from masked congruence priming

Background

It is well accepted in the subliminal priming literature that task-level properties modulate nonconscious processes. For example, in tasks with a limited number of targets, subliminal priming effects are limited to primes that are physically similar to the targets. In contrast, when a large number of targets are used, subliminal priming effects are observed for primes that share a semantic (but not necessarily physical) relationship with the target. Findings such as these have led researchers to conclude that task-level properties can direct nonconscious processes to be deployed exclusively over central (semantic) or peripheral (physically specified) representations.

Principal Findings

We find distinct patterns of masked priming for “novel” and “repeated” primes within a single task context. Novel primes never appear as targets and thus are not seen consciously in the experiment. Repeated primes do appear as targets, thereby lending themselves to the establishment of peripheral stimulus-response mappings. If the source of the masked priming effect were exclusively central or peripheral, then both novel and repeated primes should yield similar patterns of priming. In contrast, we find that both novel and repeated primes produce robust, yet distinct, patterns of priming.

Conclusions

Our findings indicate that nonconsciously elicited cognitive processes can be flexibly deployed over both central and peripheral representations within a single task context. While we agree that task-level properties can influence nonconscious processes, our findings sharply constrain the extent of this influence. Specifically, our findings are inconsistent with extant accounts which hold that the influence of task-level properties is strong enough to restrict the deployment of nonconsciously elicited cognitive processes to a single type of representation (i.e. central or peripheral).     

Effect of incorporation of drugs,vitamins and peptides on the structure and dynamics of lipid assemblies

The characteristics of vesicles formed from Dipalmitoyl Phosphatidyl Choline (DPPC) are sensitive to the presence of perturbing molecules such as drugs, peptides, hormones and vitamins. We have used ESR spin labeling and NMR techniques for studying interaction of such molecules with lipid bilayers. ESR spin labeling has been used to monitor thermotropic behaviour of model membranes. Different NMR probes such as¹H,³¹P,¹³C have been used to gather information regarding the mode of interaction. It has been observed that the model membrane systems respond differently depending upon the localization of the perturbing molecules in the lipid bilayer. Small molecules such as neurotransmitters epinephrine and norepinephrine decrease gel to liquid crystalline phase transition temperature significantly even when present in small amounts. Vitamine E acetate having a hydrophobic hydrocarbon tail orients parallel to the lipid molecule and thereby exhibits dynamics similar to palmitate chain. When the acetate group is replaced by hydroxyl group (-tocopherol), the phase transition becomes broad and the lipid molecules loose freedom of lateral diffusion. This can be attributed to formation of hydrogen bond between the hydroxyl group of -tocopherol and phosphate moiety of lipid. The conformation of antidepressants nitroxazepine and imipramine is significantly altered when embedded in lipid bilayer. Anaesthetic etomidate not only modifies thermotropic characteristics but also induces polymorphism. The normal bilayer arrangement of lipids gets transformed into hexagonal packing. Amino acid tryptophan induces cubic phases in the normal bilayer arrangement of DPPC dispersions. Peptide gonadoliberin shows a reduced internal motion due to the lipid peptide interaction.The major consequences of binding of lipids with externally added molecules are changes in the fluidity and permeability properties of membranes. It has been shown that permeability is effected by the presence of molecules such as propranolol, -tocopherol and its analogue, neurotransmitters, etc. The magnetic resonance methods have thus evolved as power techniques in the study of membrane structure and function.     

新的抗真菌药物靶点研究进展

近30年来,侵袭性真菌感染发病率持续上升,病死率居高不下,而治疗药物十分有限是造成其高致死率的重要因素之一。因此,发现新的抗真菌靶点和药物,已成为迫切需要。正在研究的新的抗真菌靶点如下：一是信号通路介导的抗真菌靶点,包括钙调神经磷酸酶及其分子伴侣Hsp90、3-磷酸肌醇依赖性蛋白激酶（PKH）以及参与Ras蛋白修饰的相关酶等,其拮抗剂包括传统免疫抑制剂的类似物以及Hsp90抗体、KP-372-1和PS77以及手霉素A等;二是GPI锚定蛋白合成通路的催化酶,其抑制剂有E1210和M720等化合物;三是分泌型天冬氨酸蛋白酶,肽类、逆转录病毒抑制剂,以及砜类的衍生物等均可以抑制这一靶点;四是海藻糖的合成的两个关键酶Tps1和Tps2。鉴于侵袭性真菌感染严重影响人类公共健康安全,而新型抗真菌药物的研发又依赖于新靶点的探索,因此,本文靶向这一核心真菌临床问题,系统介绍了当前新的抗真菌药物靶点发展概况,并在靶点选择可行性以及针对靶点的药物研发策略上提出见解。     

Ruthenium polypyridyl complexes containing the bischelating ligand 2,2′-azobispyridine. Synthesis, characterization and crystal structures

Three ruthenium polypyridyl compounds of structural formula [Ru(apy)(tpy)Lⁿ⁻](ClO₄)_(2−n) (apy = 2,2′-azobispyridine; tpy = 2,2′:6′,2″-terpyridine; L = Cl, H₂O, CH₃CN) (1a-c) were synthesized and crystallized. These complexes were fully characterized by means of 1D and 2D ¹H NMR spectroscopy, as well as mass spectrometry and elemental analysis. Although in theory two isomers are possible, i.e. the one in which the central N atom in tpy is trans to the azo N in apy and the one in which the former is trans to the pyridine N in apy, in all cases only the latter was observed. The molecular structures of the compounds were elucidated by single-crystal X-ray diffraction.     

Cross-linking properties of alginate gels determined by using advanced NMR imaging and Cu<Superscript>2+</Superscript> as contrast agent

The entrapment of enzymes, drugs, cells or tissue fragments in alginates cross-linked with Ca²⁺ or Ba²⁺ has great potential in basic research, biotechnology and medicine. The swelling properties and, in turn, the mechanical stability are key factors in designing an optimally cross-linked hydrogel matrix. These parameters depend critically on the cross-linking process and seemingly minor modifications in manufacture have a large impact. Thus, sensitive and non-invasive tools are required to determine the spatial homogeneity and efficacy of the cross-linking process. Here, we show for alginate microcapsules (between 400 µm and 600 µm in diameter) that advanced ¹H NMR imaging, along with paramagnetic Cu²⁺ as contrast agent, can be used to validate the cross-linking process. Two- and three-dimensional images and maps of the spin-lattice relaxation time T₁ of Ba²⁺ cross-linked microcapsules exposed to external Cu²⁺ yielded qualitative as well as quantitative information about the accumulation of Cu²⁺ within and removal from microcapsules upon washing with Cu²⁺ free saline solution. The use of Cu²⁺ (having a slightly higher affinity constant to alginate than Ba²⁺) for gelling gave a complementary insight into the spatial homogeneity of the cross-linking process together with information about the mechanical stability of the microcapsules. The potential of this technique was demonstrated for alginates extracted from two different algal sources and cross-linked either externally by the conventional air-jet dropping method or internally by the "crystal gun" method.