Inhibitors of the kinase IspE: structure-activity relationships and co-crystal structure analysis

Enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are therapeutic targets for the treatment of important infectious diseases. Whereas this pathway is absent in humans, it is used by plants, many eubacteria and apicomplexan protozoa, including major human pathogens such as Plasmodium falciparum and Mycobacterium tuberculosis. Herein, we report on the design, preparation and biological evaluation of a new series of ligands for IspE protein, a kinase from this pathway. These inhibitors were developed for the inhibition of IspE from Escherichia coli, using structure-based design approaches. Structure-activity relationships (SARs) and a co-crystal structure of Aquifex aeolicus IspE bound to a representative inhibitor validate the proposed binding mode. The crystal structure shows that the ligand binds in the substrate-rather than the adenosine 5'-triphosphate (ATP)-binding pocket. As predicted, a cyclopropyl substituent occupies a small cavity not used by the substrate. The optimal volume occupancy of this cavity is explored in detail. In the co-crystal structure, a diphosphate anion binds to the Gly-rich loop, which normally accepts the triphosphate moiety of ATP. This structure provides useful insights for future structure-based developments of inhibitors for the parasite enzymes.     

Replacement of Water Molecules in a Phosphate Binding Site by Furanoside‐Appended lin‐Benzoguanine Ligands of tRNA‐Guanine Transglycosylase (TGT)

The enzyme tRNA‐guanine transglycosylase has been identified as a drug target for the foodborne illness shigellosis. A key challenge in structure‐based design for this enzyme is the filling of the polar ribose‐34 pocket. Herein, we describe a novel series of ligands consisting of furanoside‐appended lin‐benzoguanines. They were designed to replace a conserved water cluster and differ by the functional groups at C(2) and C(3) of the furanosyl moiety being either OH or OMe. The unfavorable desolvation of Asp102 and Asp280, which are located close to the ribose‐34 pocket, had a significant impact on binding affinity. While the enzyme has tRNA as its natural substrate, X‐ray co‐crystal structures revealed that the furanosyl moieties of the ligands are not accommodated in the tRNA ribose‐34 site, but at the location of the adjacent phosphate group. A remarkable similarity of the position of the oxygen atoms in these two structures suggests furanosides as a potential phosphate isoster.     

New99mTc-diiodine substituted IDA derivative (DIIODIDA) for hepatobiliary imaging

A new diiodine substituted IDA derivative, 2,4-diiodine-6-methyl IDA (DIIODIDA) was synthesized and labeled with^99mTc. It was established that^99mTc-DIIODIDA had high radiochemical purity. Biodistribution and influence of bilirubin on^99mTc-DIIODIDA biokinetics has been studied in rats and compared to the corresponding results for^99mTc-SOLCOIODIDA. Related to^99mTc-SOLCOIODIDA,^99mTc-DIIODIDA has much better biliary exretion (55.18 versus 43.63%). No change of^99mTc-DIIODIDA biokinetics, under influence of bilirubin was noticed. Biliary excretion of^99mTc-SOLCOIODIDA has been reduced for about 60%. The protein binding of^99mTc-DIIODIDA and^99mTc-SOLCOIODIDA were also determined, using in vitro method of precipitation. These results showed that^99mTc-DIIODIDA hepatobiliary imaging agent is superior to the presently used^99mTc-monoiodine IDA derivatives.     

一般n阶特征量泛函的Euler-Lagrange方程及与定量因果原理、相对性原理和广义牛顿三定律的统一

本文获得了有各种相互作用的一般n阶特征量泛函,其耦合系数反映了不同特征量泛函之间的耦合强度.依据定量因果原理,导出了一般n阶特征量泛函的变分原理,获得了一般n阶特征量泛函的Euler-Lagrange方程,它的不同系数可拟合不同的物理现实,如从线性到任意n阶非线性物理系统,使复杂难解的任意n阶非线性物理系统变得具体可解.并获得了该对称变换下不变的m个的守恒量,以及它们之间的关系和统一描述.依据定量因果原理导出了相对性原理,证明了绝对加速参考系、牵连参考系和相对参考系的力都有来自加速度和质量变化的贡献.利用定量因果原理自然导出了广义牛顿第一定律和广义牛顿第二定律,而且还导出了一个新定律,即广义牛顿第三定律,亦即平移不变性系统合力为零定理.进而将研究结论应用于对银河系的修正引力势、分子势、夸克禁闭势等,且其结果与物理实验一致.     

On relative stability of linear stationary feedback control systems with time delay

A method is presented whereby the absolute and relative stabilityof linear control systems containing transport lag can be determined.As a result feedback systems with variable time delay and loopgain, may be investigated in straightforward manner.     

Free enthalpies of replacing water molecules in protein binding pockets

Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH₃ group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH₃ at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.     

From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters

The foodborne illness shigellosis is caused by Shigella bacteria that secrete the highly cytotoxic Shiga toxin, which is also formed by the closely related enterohemorrhagic Escherichia coli (EHEC). It has been shown that tRNA-guanine transglycosylase (TGT) is essential for the pathogenicity of Shigella flexneri. Herein, the molecular recognition properties of a guanine binding pocket in Zymomonas mobilis TGT are investigated with a series of lin-benzohypoxanthine- and lin-benzoguanine-based inhibitors that bear substituents to occupy either the ribose-33 or the ribose-34 pocket. The three inhibitor scaffolds differ by the substituent at C(6) being H, NH(2), or NH-alkyl. These differences lead to major changes in the inhibition constants, pK(a) values, and binding modes. Compared to the lin-benzoguanines, with an exocyclic NH(2) at C(6), the lin-benzohypoxanthines without an exocyclic NH(2) group have a weaker affinity as several ionic protein-ligand hydrogen bonds are lost. X-ray cocrystal structure analysis reveals that a new water cluster is imported into the space vacated by the lacking NH(2) group and by a conformational shift of the side chain of catalytic Asp102. In the presence of an N-alkyl group at C(6) in lin-benzoguanine ligands, this water cluster is largely maintained but replacement of one of the water molecules in the cluster leads to a substantial loss in binding affinity. This study provides new insight into the role of water clusters at enzyme active sites and their challenging substitution by ligand parts, a topic of general interest in contemporary structure-based drug design.