CombiDOCK: Structure-based combinatorial docking and library design

We have developed a strategy for efficiently docking a large combinatorial library into a target receptor. For each scaffold orientation, all potential fragments are attached to the scaffold, their interactions with the receptor are individually scored and factorial combinations of fragments are constructed. To test its effectiveness, this approach is compared to two simple control algorithms. Our method is more efficient than the controls at selecting best scoring molecules and at selecting fragments for the construction of an exhaustive combinatorial library. We also carried out a retrospective analysis of the experimental results of a 10×10×10 exhaustive combinatorial library. An enrichment factor of approximately 4 was found for identifying the compounds in the library that are active at 330 nM.     

Long-range magnetic ordering of quasi-one-dimensional S=1/2 Heisenberg antiferromagnet Sr2Cu(PO4)2

Magnetic properties of quasi-one-dimensional S=1/2 Heisenberg antiferromagnet Sr₂Cu(PO₄)₂ were investigated by temperature and field dependence of AC susceptibility down to 0.03 K. A sharp peak was observed at on the temperature dependence of AC susceptibility indicating long-range magnetic ordering. Taking into account the exchange constant, (Hamiltonian =J∑S_iS_i+1), the ratio k_BT_N/J is 0.06%. Sr₂Cu(PO₄)₂ is, therefore, one of the best one-dimensional Heisenberg antiferromagnet known so far.     

Optimization of the extraction of paclitaxel from Taxus baccata L. by the use of microwave energy

A simple and rapid microwave-assisted extraction (MAE) procedure was developed and optimized for the extraction of paclitaxel (Taxol) from the needles of yew trees Taxus baccata L. grown in Iranian habitats. The samples, immersed in a methanol-water mixture, were irradiated with microwaves in a closed-vessel system. The method was evaluated using a factorial design approach based on parameters such as extraction time, temperature, methanol concentration in water (v/v), and the ratio of grams of sample to 10 mL of solvent. Statistical treatment of the results revealed that the selected parameters were all significant except the extraction time. Optimum conditions would be 1.5 g samples in 10 mL solvent (90% methanol), an extraction temperature of 95 degrees C, and an extraction time of 7 min. The extracts has been analyzed by reverse-phase high-performance liquid chromatography with UV detection (LC/UV) at 227 nm for quantification. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for confirmation. The main advantage of the proposed MAE method versus conventional solvent extraction (CSE) are the considerable reductions in time (7 min versus 16 h) and in solvent consumption (20 mL versus 150 mL). The MAE procedure yielded extracts that could be analyzed directly without any preliminary clean-up or solvent exchange steps. Both extraction methods show RSDs lower than 10% and lead to comparable recoveries of paclitaxel (87-92%).     

Flow system to gas capture from a nebulized solution

The use of aerosol produced in a nebulization chamber is proposed as an alternative to gas sample capture in flow systems. This paper describes the coupling of a sampling interface with a flow system, for in situ gas monitoring. Aspects related with the behavior of aerosol formation and gas solubilization in liquid drops are discussed. The method is applied to the determination of residual lime in acidic soils. Aliquots of 5.0 ml of 1.0 mol l⁻¹ HCl were mixed with soil samples (1 g). The CO₂ released from these samples was captured by a nebulized aerosol and determined conductivity. The analytical curve from 1.0×10⁻² to 5.0×10⁻² mol kg⁻¹ CaCO₃ was ploted applying the matrix matching approach. This proposition, allowed an increase in the sensibility with detection limit of 6.0×10⁻³ mol kg⁻¹. The precision was good (R.S.D. <3%) for an analytical frequency of 22 determinations per hour. A fair agreement, at 95% confidence level, was found between the results from the proposed method and certified values of the investigated samples.     

Methods for research on immune complement activation on modified sensor surfaces

We have developed a methodological system consisting of a new surface sensitive quartz crystal microbalance with dissipation monitoring (QCM-D) sensor surfaces together with different surface modification methods for the investigation of surface associated complement activation in human sera. The QCM-D surface, 10 mm in diameter, was modified by spin-coating of poly(urethane urea) (PUUR) and polystyrene (PS). Some sensor surfaces were also sputtered with titanium (Ti) or modified by hydrophobic self-assembled monolayer (SAM) of an 18-carbon alkane thiol with a ---CH₃ end group. The amount of surface deposited complement protein was investigated by incubation of the modified sensor surfaces in human sera, followed by incubation with antibodies directed against complement factor 3c (C3c). The amounts of bound anti-C3c were then used as an arbitrary measure of surface induced complement activation. The order of complement activation of the different surfaces, as judged by three separate measurements per surface modification, was PUUR>PS=SAM>Ti. The Ti surface had a similar low degree of anti-C3c binding as the negative controls (heat inactivated sera). The novel QCM-D methodology was found to be very simple, accurate, sensitive and well suited as a screening method for complement activation and protein adsorption on different materials. We also compared the sensitivity of QCM-D method with surface plasmon resonance (SPR) for the quantification of protein adsorption and complement activation on gold sensor surfaces. The QCM-D method was equally sensitive as the SPR for the detection of protein adsorption from a solution independently if low flow rate (5 μl/min) was used. A slight increase in sensitivity was found at higher flow rate (30 μl/min). However, we found it difficult to use the SPR method on the Ti, PS and PUUR surfaces due to decreased light penetration of the modified SPR sensor chip.     

水／AOT／正庚烷微乳体系中磺酸根水化作用的FT—IR研究

运用傅立叶变换红外光谱（FT－IR）对水／琥珀酸（乙基已基）磺酸钠（AOT）／正庚烷微乳体系中磺酸根的水化作用进行了研究．由于微乳体系中水分子与表面活性剂分子的相互作用，S＝O对称伸缩振动的红外吸收峰向低频方向移动．体系中的加水量W0（水与AOT的摩尔比）由0.5增大至25时，磺酸根对称伸缩振动的红外吸收峰由1051．39cm－1向低频移动至1046．15cm－1．同时，由于Na 的不对称作用，AOT分子中磺酸根反对称伸缩振动分裂成两个吸收峰，分别位于正215cm-1及1245cm－1附近，两个劈裂峰的距离及各自的峰面积均随体系中加水量的变化而变化，应用二阶导数、傅立叶退卷积及曲线拟会等分辨率增强技术可更清楚地反映出这个二重峰的变化情况．固体AOT分子中碳酸根反对称伸缩振动分裂的两个峰之间频率的差值约为42cm－1，形成微乳液以后，这两个峰的差值变小，W0为20时，这两个峰频率的差值逐渐减小到29cm-1，这些变化与磺酸根的水化程度直接相关     

Dithiol proteins as guardians of the intracellular redox milieu in parasites: old and new drug targets in trypanosomes and malaria-causing plasmodia

Parasitic diseases such as sleeping sickness, Chagas' heart disease, and malaria are major health problems in poverty-stricken areas. Antiparasitic drugs that are not only active but also affordable and readily available are urgently required. One approach to finding new drugs and rediscovering old ones is based on enzyme inhibitors that paralyze antioxidant systems in the pathogens. These antioxidant ensembles are essential to the parasites as they are attacked in the human host by strong oxidants such as peroxynitrite, hypochlorite, and H2O2. The pathogen-protecting system consists of some 20 thiol and dithiol proteins, which buffer the intraparasitic redox milieu at a potential of -250 mV. In trypanosomes and leishmania the network is centered around the unique dithiol trypanothione (N1,N8-bis(glutathionyl)spermidine). In contrast, malaria parasites have a more conservative dual antioxidative system based on glutathione and thioredoxin. Inhibitors of antioxidant enzymes such as trypanothione reductase are, indeed, parasiticidal but they can also delay or prevent resistance against a number of other antiparasitic drugs.     

超临界萃取装置的研制及其应用

超临界流体萃取是近的上来兴起的一种新的分离技术，报道了将超临界萃取原理与回流技术相结合研制的二氧化碳回流中低压超临界流体萃取设备，解决了关键实验手段，通过应用证明设备可靠，费用低廉，有实用价值。     

氨基酸在乙醇/磷酸氢二钾双水相体系中分配行为

研究了5种结构和性质各异的氨基酸(谷氨酸,半胱氨酸,苯丙氨酸,赖氨酸,精氨酸)在亲水性有机溶剂乙醇和磷酸盐溶液形成的乙醇/K2HPO4双水相体系中的分配行为及其影响因素。当双水相体系中乙醇的质量分数从22%增加到30%时,半胱氨酸和苯丙氨酸的分配系数明显增大,其它三种氨基酸的分配系数变化幅度不大;当磷酸盐的质量分数从14%增加到22%时,氨基酸的分配系数的变化均不明显;双水相体系的pH值对氨基酸的分配系数影响较大,当pH增加时,5种氨基酸的分配系数均增加,但是当pH约为9.5时,苯丙氨酸、半胱氨酸的分配系数接近相等但与其它3种氨基酸的分配系数相差较多,当pH为6.0~8.0时,苯丙氨酸的分配系数远远大于另外4种氨基酸。氨基酸的支链结构中含有非极性基团将导致其分配系数的增加。     

Design criteria for molecular mimics of fragments of the β-turn. 1. Cα atom analysis

Peptides represent an extensive class of biologically active molecules. They may be used as leads in the development of novel therapeutic agents provided the pharmacophoric information present within them can be translated into non-peptide analogs that lack the peptide backbone and are stable to proteolysis. This is the rationale for peptidomimetic drug design. Frequently, the -turn has been implicated as a conformation important for biological recognition of peptides. Empirical evidence from known peptidomimetics, coupled with a theoretical model of peptide binding and the observation that glycine and proline residues are common within the -turn, has suggested the design of molecules to mimic placement of between two and four of the side-chains. The moderate number of different -turn conformations, combined with the combinatoric nature of side-chain selection complicates the procedure. In this paper, cluster analysis has been used to classify the arrangement of C_{_} atoms about the various fragments of the -turn. Recombination of the observed patterns provides a general model for the -turn which may be used as an effective screen for potential peptidomimetic scaffolds in chemical databases.