Use of the tubulin bound paclitaxel conformation for structure-based rational drug design

A new computational docking protocol has been developed and used in combination with conformational information inferred from REDOR-NMR experiments on microtubule bound 2-(p-fluorobenzoyl)paclitaxel to delineate a unique tubulin binding structure of paclitaxel. A conformationally constrained macrocyclic taxoid bearing a linker between the C-14 and C-3'N positions has been designed and synthesized to enforce this "REDOR-taxol" conformation. The novel taxoid SB-T-2053 inhibits the growth of MCF-7 and LCC-6 human breast cancer cells (wild-type and drug resistant) on the same order of magnitude as paclitaxel. Moreover, SB-T-2053 induces in vitro tubulin polymerization at least as well as paclitaxel, which directly validates our drug design process. These results open a new avenue for drug design of next generation taxoids and other microtubule-stabilizing agents based on the refined structural information of drug-tubulin complexes, in accordance with typical enzyme-inhibitor medicinal chemistry precepts.     

Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

The biosynthesis of quadrone and terrecyclic acid

Feedings of [1-¹³C]- and [1,2-¹³C₂]acetate Aspergillus terreus gave quadrone and terrecyclic acid which were analyzed by ¹³C NMR. The pattern of ¹³C-enrichments and couplings is consistent with the formation of 1 and 2 by cyclization of farnesyl pyrophosphate.     

Subsolidus phase relations and crystal structure of compounds in the PrOx-CaO-CuO system

The subsolidus phase relations of the PrO_x-CaO-CuO pseudo-ternary system sintered at 950-1000°C have been investigated by X-ray powder diffraction. In this system, there exist one compound Ca₁₀Pr₄Cu₂₄O₄₁, one Ca₂Pr₂Cu₅O₁₀-based solid solution, seven three-phase regions and two two-phase regions. The crystal structures of Ca₁₀Pr₄Cu₂₄O₄₁ and Ca₂Pr₂Cu₅O₁₀-based solid solution have been determined. Compound Ca₁₀Pr₄Cu₂₄O₄₁ crystallizes in an orthorhombic cell with space group D_2h²⁰−Cccm, Z=4. Its lattice parameters are a=11.278(2) Å, b=12.448(3) Å and c=27.486(8) Å. The crystal structure of Ca₂Pr₂Cu₅O₁₀-based solid solution is an incommensurate phase based on the orthorhombic NaCuO₂ type subcell. The lattice parameters of the subcell of the Ca_2.4Pr_1.6Cu₅O₁₀ are a₀=2.8246(7) Å, b₀=6.3693(5) Å, c₀=10.679(1) Å, and those of the orthorhombic superstructure are with a=5a₀, b=b₀, c=5c₀. The Ca_2.4Pr_1.6Cu₅O₁₀ structure can also be determined by using a monoclinic supercell with space group C_2h⁵−P2₁/c, Z=4, a=5a₀, b=b₀, and β=104.79(1)° or 136.60(1)°, V=5a₀b₀c₀.     

Theoretical formalism and experimental verification of line shapes of NMR intermolecular multiple-quantum coherence spectra

Although the theories and potential applications of intermolecular multiple-quantum coherences (iMQCs) have been under active investigations for over a decade, discussion of iMQC NMR signal formation was mainly confined in the time domain. In this paper, a full line-shape theory was developed to describe iMQC signals in the frequency domain. Relevant features of the line shape, such as peak height, linewidth, and phase, were investigated in detail. Predictions based on the theory agree well with experimental and simulated results. Since radiation-damping effects always couple with iMQCs in highly polarized liquid-state NMR systems, and strongly radiation-damped signals have many spectral characteristics similar to those of iMQCs, a detailed comparison was also made between them from different spectral aspects. With detailed comparison of peak height, linewidth, and phase, this work demonstrates that the iMQC and radiation-damping phenomena result from two completely different physical mechanisms despite that both present similar signal features and coexist in highly polarized liquid-state NMR systems.     

The deformation of103Nb

Tie half-lives of 8 low lying levels of¹⁰³Nb have been determined at the fission-product separator JOSEF. A B-- triple-coincidence method was used which consists in a measurement of the time delay between the feeding of the levels through the B^– decay of¹⁰³Zr and their decay, in coincidence with a tagging ray, with plastic, BaF₂ and Ge detectors, respectively. Most of the investigated levels are members of the three known rotational bands based on the ground state and the 164 and 248 keV levels. The deformation B_q=0.31(3) of¹⁰³Nb could be deduced from the half-life data. The half-lives are well reproduced through calculations in the frame of the Nilsson model.The authors thank Dr. T. Seo for valuable advise in connection with the Nilsson-model calculations.     

Rapid chiral analysis based on liquid-phase cyclic chemiluminescence

Rapid chiral analysis has become one of the important aspects of academic and industrial research. Here we describe a new strategy based on liquid-phase cyclic chemiluminescence (CCL) for rapid resolution of enantiomers and determination of enantiomeric excess (ee). A single CCL measurement can acquire multistage signals that provide a unique way to examine the intermolecular interactions between chiral hosts and chiral guests, because the lifetime (τ) of the multistage signals is a concentration-independent and distinguishable constant for a given chiral host–guest system. According to the τ values, CCL allows discrimination between a wide range of enantiomeric pairs including chiral alcohols, amines and acids by using only one chiral host. Even the chiral systems hardly distinguished by nuclear magnetic resonance and fluorescence methods can be distinguished easily by CCL. Additionally, the τ value of a mixture of two enantiomers is equal to the weighted average of each enantiomer, which can be used for the direct determination of ee without the need to separate the chiral mixture and create calibration curves. This is extremely crucial for the cases without readily available enantiomerically pure samples. This strategy was successfully applied to monitoring of the Walden inversion reaction and analysis of chiral drugs. The results were in good agreement with those obtained by high-performance liquid chromatography, indicating the utility of CCL for routine quick ee analysis. Mechanism study revealed that the τ value is possibly related to the activity of the chiral substance to catalyze a luminol–H₂O₂ reaction. Our research provides an unprecedented and general protocol for chirality differentiation and ee determination, which is anticipated to be a useful technology that will find wide application in chirality-related fields, particularly in asymmetric synthesis and the pharmaceutical industry.

Rapid chiral analysis has become one of the important aspects of academic and industrial research.     

Adiabatic cooling of ions in the penning trap

An ion cloud in a Penning trap can be cooled by adiabatic expansion by reducing the trap's magnetic and electric fields. We treat the ion cloud as a classical gas and obtain the relations between the temperature and the trapping fields. This cooling method may be useful in trapping and cooling of antiprotons with the aim of measuring the gravitational accleration of anti-protons and other experiments on heavy ions.     

Characterization of polyethylene glycol-modified proteins by semi-aqueous capillary electrophoresis

A new program to characterize polyethylene glycol-modified (PEGylated) proteins is outlined using capillary zone electrophoresis (CZE). PEGylated ribonuclease A and lysozyme were selected as examples. Five separation procedures were compared to select out the mixed buffer of acetonitrile-water (1:1, v/v) at pH 2.5 as the best to characterize the PEGylated proteins without sample pretreatment. Polyethylene oxide (PEO) with a high molecular mass of 8 x 10(6) was applied to rinse the capillary to form a dynamic coating which would decrease the undesirable proteins adsorbed to the inner wall of the silica. The electroosmotic flow (EOF) mobility of the five procedures was determined, respectively. It is found that acetonitrile is mainly responsible for the good resolution of PEGylated proteins with the help of PEO coating in the semi-aqueous system. The low EOF mobility and current in the semi-aqueous system might also have some responsibility for the high resolution. The semi-aqueous procedure described in this paper also demonstrates higher resolution of natural proteins than aqueous ones.     

Formation of hydroxyl radical from the photolysis of frozen hydrogen peroxide

Hydrogen peroxide (HOOH) in ice and snow is an important chemical tracer for the oxidative capacities of past atmospheres. However, photolysis in ice and snow will destroy HOOH and form the hydroxyl radical (*OH), which can react with snowpack trace species. Reactions of *OH in snow and ice will affect the composition of both the overlying atmosphere (e.g., by the release of volatile species such as formaldehyde to the boundary layer) and the snow and ice (e.g., by the *OH-mediated destruction of trace organics). To help understand these impacts, we have measured the quantum yield of *OH from the photolysis of HOOH on ice. Our measured quantum yields (Phi(HOOH --> *OH)) are independent of ionic strength, pH, and wavelength, but are dependent upon temperature. This temperature dependence for both solution and ice data is best described by the relationship ln(Phi(HOOH --> *OH)) = -(684 +/- 17)(1/T) + (2.27 +/- 0.064) (where errors represent 1 standard error). The corresponding activation energy (Ea) for HOOH (5.7 kJ mol(-1)) is much smaller than that for nitrate photolysis, indicating that the photochemistry of HOOH is less affected by changes in temperature. Using our measured quantum yields, we calculate that the photolytic lifetimes of HOOH in surface snow grains under midday, summer solstice sunlight are approximately 140 h at representative sites on the Greenland and Antarctic ice sheets. In addition, our calculations reveal that the majority of *OH radicals formed on polar snow grains are from HOOH photolysis, while nitrate photolysis is only a minor contributor. Similarly, HOOH appears to be much more important than nitrate as a photochemical source of *OH on cirrus ice clouds, where reactions of the photochemically formed hydroxyl radical could lead to the release of oxygenated volatile organic compounds to the upper troposphere.