A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa

Blood coagulation is an essential physiological process for hemostasis; however, abnormal coagulation can lead to various potentially fatal disorders, generally known as thromboembolic disorders, which are a major cause of mortality in the modern world. Recently, the FDA has approved several anticoagulant drugs for Factor Xa (FXa) which work via the common pathway of the coagulation cascade. A main side effect of these drugs is the potential risk for bleeding in patients. Coagulation Factor IXa (FIXa) has recently emerged as the strategic target to ease these risks as it selectively regulates the intrinsic pathway. These aforementioned coagulation factors are highly similar in structure, functional architecture, and inhibitor binding mode. Therefore, it remains a challenge to design a selective inhibitor which may affect only FIXa. With the availability of a number of X-ray co-crystal structures of these two coagulation factors as protein–ligand complexes, structural alignment, molecular docking, and pharmacophore modeling were employed to derive the relevant criteria for selective inhibition of FIXa over FXa. In this study, six ligands (three potent, two selective, and one inactive) were selected for FIXa inhibition and six potent ligands (four FDA approved drugs) were considered for FXa. The pharmacophore hypotheses provide the distribution patterns for the principal interactions that take place in the binding site. None of the pharmacophoric patterns of the FXa inhibitors matched with any of the patterns of FIXa inhibitors. Based on pharmacophore analysis, a selectivity of a ligand for FIXa over FXa may be defined quantitatively as a docking score of lower than −8.0 kcal/mol in the FIXa-grids and higher than −7.5 kcal/mol in the FXa-grids.     

Development of enzyme technology and enzyme engineering in China

Enzymes have been utilized in China for thousands of years for the production of various foods and alcoholic beverages. Today China manufactures and uses enzymes for not only the traditional areas of application, but is expanding the use of enzymes for a variety of nonfood areas. This report describes the present state of the art of enzyme manufacture and application in China today.     

Proteinase of germinated cotton seeds

A scheme has been developed to isolate and purify proteinase D from 3-day germinated cotton seeds. The physicochemical properties and substrate specificity were studied. It is found that cysteinic proteinase D cleaves auxiliary proteins to low-molecular-weight peptides and free amino acids.S. Yu. Yunusov Institute of the Chemistry of Plant Substances. Academy of Sciences of the Republic of Uzbekistan. Tashkent, fax (99871) 120 64 75. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 249–251, May–June, 2000.     

Role of Water Activity on the Synthesis of Vinyl Thymidine Catalyzed by Protease from Bacillus Subtilis

The transesterification activity of Bioprase, a protease from Bacillus subtilis, in dimethylformamide (DMF) is found to depend strongly on water addition. For the transesterification between thymidine and divinyl adipate by Bioprase in DMF with water (5–40%), the conversion rate of thymidine to the ester is much higher than the rate in DMF without the addition of water. For example, the transesterification reaction of 0.25 M thymidine with 1 M divinyl adipate in DMF in the presence of 10% water was catalyzed by Bioprase (50 mg · ml^?1) at 30 °C for only 10–20 minutes to give 5′‐O‐vinyladipoyl thymidine (conversion ca. 90%), but the reaction did not proceed without the addition of water. Furthermore, the water effect is useful for the transesterification of thymidine with divinyl sebacate, which has a longer alkyl chain than divinyl adipate. This investigation showed that DMF adsorbs on the enzyme surface instead of essential water in the reaction of DMF without addition of water. On the other hand, in the reaction of DMF/water cosolvents, essential water bound to enzyme was not removed by DMF, and a higher transesterification activity occurs thereafter.

Effect of water on the transesterification of thymidine catalyzed by Bioprase in DMF.     

Discussion of the catalytic pathway of cysteine proteases based on AM1 calculations

The deacylation reaction of the cysteine protease papain was examined by AM1 reaction-coordinate calculations. The transition-state (TS) structure was extracted from the reaction pathway as corresponding to the maximum point along this minimum-energy pathway. Consistent with experimental kinetic data revealing that deacylation is about 60 times faster for thioester (---C(O)---S---) than dithioester (---C(S)---S---) intermediates, calculated E_a values are about 10 kcal mol⁻¹ lower for the former than the latter. The calculated partial atomic charges indicate that the C=O carbon in the thioester is a good site for nucleophilic attack whereas the corresponding C=S carbon in the dithioester is a poor site. The present calculations reveal that the enzyme's oxyanion hole contributes about 9 kcal mol⁻¹ toward reducing E_a for the anionic tetrahedral intermediate and TS structure. On the other hand, the presence of Asn in the putative Asn-His-Cys catalytic triad contributes only about l kcal mol⁻¹ toward reducing their E_a value. The presence of this Asn, however, did appear to stabilize His in its protonated form (ImH⁺) over its unprotonated form (Im). Two novel mechanisms are introduced to explain the unusual effect of a remote X substituent on the deacylation kinetics of the substrate family under consideration. The first mechanism invokes a “field effect” while the second mechanism embodies the concepts of induction and homoconjugation. The unique feature of these two mechanisms is that, unlike other proposed models, they circumvent the requirement for a close N…S interaction which has stimulated controversy.     

Reaction mechanism of HSH and CH3SH with NH2CH2COCH2X (X = F and Cl) molecules

The reaction mechanism of model compounds H₂S and CH₃SH for cysteine proteases with NH₂CH₂COCH₂X (X = F and Cl) molecules has been investigated using DFT methods with B3LYP and B3PW91 hybrid density functionals at 6‐31+G* basis sets. The single point energy has been calculated for the above reactions with B3LYP and B3PW91 functionals using aug‐cc‐PVDZ infinite basis set in both gas and solution phases. The intrinsic reaction coordinates calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The geometries and relative energies for various stationary points have been determined and discussed. The zero point vibrational energy corrections have been made to predict the reliable energy. The negative value of reaction energy indicates that the overall reaction profile is found to be exothermic. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

人类丝氨酸消旋酶的同源模建及其与多肽类抑制剂的分子对接

利用同源模建和分子动力学模拟方法构建了人类丝氨酸消旋酶(hSR)的三维结构, 并利用profile-3D和procheck方法评估了模型的可靠性. 在此基础上用分子对接程序(affinity)将多肽类抑制剂A和B分别与hSR进行对接, 获得了其复合物结构的理论模型. 通过配体与受体之间相互作用能和结构分析给出了此类抑制剂与hSR的具体结合方式, 明确了hSR与此类抑制剂结合时起重要作用的氨基酸残基, 为基于人类丝氨酸消旋酶三维结构的药物设计提供重要的参考信息.     

Reaction mechanism of cysteine proteases model compound HSH with diketone inhibitor PhCOCOCH3−nXn, (X = F,Cl, n = 0, 1, 2)

Caspases are a family of cysteine proteases, which play a crucial role in apoptosis and inflammation. The reaction mechanisms involving the cysteine proteases model compound HSH with diketone (PhCOCOCH_3‐nX_n, (X = F, Cl, n = 0, 1, 2) substrate have been studied using B3LYP/6‐311+G* level of density functional theory method. The harmonic vibrational frequencies were calculated at the same level of theory used for the characterization of stationary points and zero‐point vibrational energy corrections. The condensed Fukui functions have been calculated to find the favorable reactive site for the electrophilic (f), nucleophilic (f), and radical (f) attacks in the reactants. The transition states were connected with reactants, intermediate, and products, and the minimum energy paths have been confirmed through intrinsic reaction coordinate calculation. The potential energy barrier between each step of the reactions has been calculated to find the most favorable reaction path. The binding nature of cysteine model compound with diketone substrate has been studied through the interaction energies, bond lengths, electron density, natural bond orbital, and atoms in molecules theory analysis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010