Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase

The SARS coronavirus 3C-like proteinase is considered as a potential drug design target for the treatment of severe acute respiratory syndrome (SARS). Owing to the lack of available drugs for the treatment of SARS, the discovery of inhibitors for SARS coronavirus 3C-like proteinase that can potentially be optimized as drugs appears to be highly desirable. We have built a "flexible" three-dimensional model for SARS 3C-like proteinase by homology modeling and multicanonical molecular dynamics method and used the model for virtual screening of chemical databases. After Dock procedures, strategies including pharmocophore model, consensus scoring, and "drug-like" filters were applied in order to accelerate the process and improve the success rate of virtual docking screening hit lists. Forty compounds were purchased and tested by HPLC and colorimetric assay against SARS 3C-like proteinase. Three of them including calmidazolium, a well-known antagonist of calmodulin, were found to inhibit the enzyme with an apparent K(i) from 61 to 178 microM. These active compounds and their binding modes provide useful information for understanding the binding sites and for further selective drug design against SARS and other coronavirus.     

Two New Pyrrolizidines from Ligularia lankongensis

Two new pyrrolizidines named lankongensisine A (1), B (2) were isolated from the roots of Ligularia lankongensis collected in Lijiang, Yunnan, and their structures were established by spectroscopic analysis.     

κ-卡拉胶热可逆凝胶化行为研究

用固体小角激光散射方法研究κ 卡拉胶 (KC)的热可逆凝胶化行为 .以散色斑点的突停点温度为体系的凝胶化点Tgel,考察了溶液中加入Na+ ,K+ ,NH+4,Ca2 + ,Cu2 + ,Zn2 + 等抗衡离子对Tgel的影响 .结果是随抗衡离子浓度增大Tgel上升 ;Tgel与Na+ 的浓度呈线性关系 ,与K+ ,NH+4,Ca2 + ,Cu2 + ,Zn2 + 等离子浓度的平方根成线性关系 ;另外 ,还得到 30℃时KC在KCl盐溶液中的溶胶 凝胶相图 ,并对比了KC在NaCl溶液中透析前后Tgel的变化 .     

旋转填充床的流体力学特性与传递过程的理论研究进展

旋转填充床(RPB)是一种高效的强化传递过程设备，亦是一种高效的混合与多相反应设备，在化工、材料、冶金、能源、环保等领域有着广泛的应用前景。本文概要地介绍了近年来对该类装置的流体力学特性和传递过程的理论研究进展。     

Intramolecular proton transfer induced by divalent alkali earth metal cation in the gas state

Interactions between divalent alkali earth metal (DAEM) ions M (M?Be, Mg, Ca, Sr, Ba) and the second stable glycine conformer in the gas phase, which can transfer into the ground‐state glycine‐M²⁺ (except the glycine–Be²⁺) among each corresponding isomers when these divalent metal ions are bound, are studied at the hybrid three‐parameter B3LYP level with three different basis sets. Proton transfers from the hydroxyl to the amino nitrogen of the glycine without energy barriers have been first observed in the gas phase in these glycine–M²⁺ systems. The interaction between the glycine and these DAEM ions except beryllium and magnesium ion only create an amino hydrogen pointing to the original hydroxyl due to their weaker interaction relative to those divalent transition metal (DTM) ion‐bound glycine derivatives, being obviously different from that between the glycine and DTM ions, in which two amino hydrogens point to the original hydroxyl oxygen when these metal‐chelated glycine derivatives are produced. The interaction energy between the glycine and divalent magnesium would be the boundary of one or two amino hydrogens pointing to the hydrogyl oxygen, i.e., the ?170.3 kcal/mol of binding energy is a critical point. Similar intramolecular proton transfer has also been predicted for those DTM ion‐chelated glycine systems; however, that in the gas state has not been observed in the monovalent metal ion‐coordinated glycine systems. The binding energy between some monovalent TM ion and the glycine is similar to that of the glycine–Ba²⁺, which has the lowest binding strength among these DAEM–ion chelated glycine complexes. The difference among them only lies in the larger electrostatic and polarized effects in the latter, which favor the stability of the zwitterionic glycine form in the gas phase. According to these observations, we predict that the zwitterionic glycine would exist in the field of two positive charges in the gas phase. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 205–214, 2003     

Dawson结构钨钒磷杂多化合物催化苯酚过氧化氢的羟化作用及其羟化机理

合成了系列Ｄａｗｓｏｎ结构钨钒磷杂多化合物（Ｃｐｙｒ）７＋ｎＰ２Ｗ１８－ｎＶｎＯ６２（ｎ＝１～３），并用ＩＲ，ＮＭＲ等手段对其结构进行了表征．考察了这类杂多化合物对苯酚过氧化氢的羟化活性，探讨了反应机理．     

化合物库的组合技巧和组合合成

从化合物库的组合技巧和组合合成方法两个方面探讨了组合化学及其在药物开发中的应用。     

Two Novel Myrinsol Diterpenes from Euphorbia prolifera

Two novel diterpenes,Euphorprolitherin A(1) and Euphorprolitherin B(2), were isolated from the roots of Euphorbia prolifera. Their structures were elucidated on the basis of spectroscopic methods.     

Improving the quality of 3D-QSAR by using flexible-ligand receptor models

To address the problems associated with molecular conformations and alignments in the 3D-QSAR studies, we have developed the Flexible Ligand - Atomic Receptor Model (FLARM) 2.0 method. The FLARM 2.0 method has three unique features as compared to other pseudoreceptor model methods: (1) the training ligands are flexibly optimized inside the receptors to achieve minimal docking energies; (2) the receptor atoms are spatially moveable in the process of genetic evolving in order to avoid improper initial receptor shapes; and (3) void receptor sites are specially favored in order to obtain open receptor models that allow large gaps. Advantages of an open model include less noise information, a smaller risk of overfitting, and ease of locating the key interaction sites. The latter two features, inherited from the previous FLARM 1.0 method, can improve the predictive ability of the 3D-QSAR models, while the first feature is newly implemented to relieve the uncertainty caused by improper conformation and alignment. Three FLARM 2.0 case studies were performed, and the results show that FLARM 2.0 models are highly predictive and robust. FLARM 2.0 pseudoreceptor models can correspond well with the pharmacophore models and/or the binding sites of the real protein receptors.     

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

The decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005