Crystal structure and Hirshfeld surface analysis of a salt of antineoplastic kinase inhibitor vandetanib

A salt of vandetanib, namely, 4-({4-[(4-bromo-2-fluorophenyl)amino]-6-methoxyquinazolin-7-yl}methoxy)-1-methylpiperazin-1-ium 2-(butylamino)-4-phenoxy-6-sulfamoylbenzoate acetonitrile monosolvate, C₂₂H₂₅BrFN₄O₂⁺·C₁₇H₁₉N₂O₅S⁻·C₂H₃N, composed of kinase inhibitor vandetanib and sulfamyl diuretic bumetanide in a 1:1 molar ratio, is reported. There is proton transfer between the piperidine ring of vandetanib and the carboxyl group of bumetanide to form the salt. In the vandetanib cation, the arene and pyrimidine rings are not coplanar, their planes subtending a dihedral angle of 60.47 (14)°. The roles of the intermolecular interactions in the crystal packing were clarified using Hirshfeld surface analysis, and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H…H (40.5%), O…H/H…C (20.7%), C…H/ H…C (18.8%) and N…C/C…N (9.0%) contacts.     

Optical probes for detection and quantification of neutrophils’ oxidative burst. A review

Neutrophils, also known as polymorphonuclear leukocytes (PMN), are the most common type of white blood cells, comprising about 50-70% of all white blood cells. In the event of inflammatory processes, neutrophils display increased mobility, tissue influx ability, prolonged life span, and an increased phagocytic capacity, constituting the initial participants in the cellular defense of the organism. One of the most important defense systems of neutrophils corresponds to their ability to mediate a strong oxidative burst through the formation of reactive oxygen species (ROS) and reactive nitrogen species (RNS). While oxidative burst is important for the elimination of invading microorganisms, the overproduction of ROS and RNS or the impairment of endogenous antioxidant defenses may result to detrimental effects to the host. The nature and the extent of ROS and RNS production by neutrophils in response to different stimuli is, consequently, a matter of extensive research, with scientific reports showing an enormous variability on the detection methodologies employed. This review attempts to provide a critical assessment of the most common approaches to identify and quantify reactive species formed during the neutrophils’ oxidative burst. The detection mechanisms and performance, as well as advantages and limitations of the different methodologies, are scrutinized, focusing on the use of fluorimetric, chemiluminometric and colorimetric probes.     

Enantioseparation of chiral benzimidazole derivatives by electrokinetic chromatography using sulfated cyclodextrins

Baseline separation of 18 new substituted benzimidazole derivatives, potent AMP‐activated protein kinase (AMPK) activators, with one chiral center, was achieved by CD‐EKC using sulfated and highly sulfated CDs (SCDs and HS‐CDs) as chiral selectors. The influence of the type and concentration of the chiral selectors on the enantioseparations was investigated. The SCDs exhibit a very high enantioselectivity power since they allow excellent enantiomeric resolutions compared to those obtained with the neutral CDs. The enantiomers were resolved with analysis times around 6 min using 25 mM phosphate buffer at pH 2.5 containing either β‐S‐CD, HS‐β‐CD, HS‐γ‐CD (3 or 4% w/v) at 25°C, with a voltage of 20 kV. The apparent association constants of the inclusion complexes were calculated. The study of the solute structure‐enantioseparation relationships seems to show the high contribution of the interactions between the solutes phenyl ring and the CDs to the enantiorecognition process. The optimized method was briefly validated (LOD less than 1%) and the purity of enantiomers of compound 3 was determined. The enantiomer migration shows reversal order depending on the kind of CD.     

细管电泳-激光诱导荧光检测用于多个胞内蛋白激酶的抑制剂筛选和选择性评价

发展了一种基于毛细管电泳(CE)-激光诱导荧光(LIF)检测的多个细胞内源激酶的抑制剂平行筛选及选择性评价方法。CE高效的分离能力和LIF检测器的高选择性,使得同时测试多个胞内激酶的活性成为可能。共4种细胞系、3种特异性蛋白激酶底物肽、2种选择性蛋白激酶抑制剂和1种非选择性蛋白激酶抑制剂用于方法的建立。特异性底物肽与细胞裂解液混合后孵育,被其相应的激酶选择性地磷酸化,利用CE-LIF分离检测磷酸化产物和底物肽。同时测定一个抑制剂对几种蛋白激酶的抑制活性,用于评价抑制剂的选择性。与传统的单靶标筛选模式相比,这种基于细胞裂解液的多靶标筛选方法能提供更多的信息,更加高效,且细胞裂解液作为一种廉价的激酶来源大大降低了筛选成本。     

腺苷酸激酶催化循环后期Mg2+转移的分子动力学模拟

腺苷酸激酶是一个包含三个结构域(LID结构域、NMP结构域和CORE结构域)的蛋白质分子,其主要作用是催化化学反应Mg²⁺ + ATP + AMP ⇌ 2ADP + Mg²⁺,进而将细胞内ATP分子的浓度维持在合适的范围内。在腺苷酸激酶催化上述化学反应的过程中,需要有Mg²⁺的参与。最近的实验发现Mg²⁺不仅参与上述反应的化学步骤,而且对化学反应发生后底物的释放过程至关重要。已有晶体结构数据显示,在催化循环过程的化学反应步骤完成后,一个Mg²⁺可同时和分别位于LID结构域及NMP结构域的两个ADP分子配位。然而,在底物的释放与分离过程中, Mg²⁺可能只与其中一个ADP分子结合。由于Mg²⁺与ADP分子的结合情况会在很大程度上影响作为催化循环限速步骤的底物释放过程,因此人们有必要研究清楚在底物释放前Mg²⁺与催化产物ADP分子的配位情况,即Mg²⁺更倾向于与LID结构域的ADP分子结合还是与NMP结构域的ADP分子结合。本文中,我们对催化反应后底物释放前的酶-底物复合物(包含酶、两个ADP分子以及Mg²⁺)做了分子动力学模拟研究。我们基于metadynamics方法得到了Mg²⁺在两个ADP分子间转移的自由能面,发现在底物分离与释放过程中, Mg²⁺更倾向于与LID结构域的ADP分子结合。只有当LID结构域的ADP分子被质子化,同时NMP结构域的ADP分子处于去质子化状态时, Mg²⁺才会倾向于与NMP结构域的ADP分子结合。另外,我们也刻画了Mg²⁺转移过程中配体交换与脱水过程。本工作的研究结果有助于理解腺苷酸激酶催化循环后期的分子过程。     

Quantitation of unbound sunitinib and its metabolite N-desethyl sunitinib (SU12662) in human plasma by equilibrium dialysis and liquid chromatography-tandem mass spectrometry: application to a pharmacokinetic study

A rapid, selective, and sensitive liquid chromatography–tandem mass spectrometry method was developed and validated for the simultaneous determination of unbound sunitinib and its active metabolite N‐desethyl sunitinib in plasma. Plasma and post‐dialysis buffer samples were extracted using a liquid–liquid extraction procedure with acetonitrile–n‐butylchloride (1:4, v/v). Chromatographic separation was achieved on a Waters X‐Terra® MS RP₁₈ column with a mobile phase consisting of acetonitrile and water (60:40, v/v) containing formic acid (0.1%, v/v) using an isocratic run, at a flow‐rate of 0.2 mL/min. Analytes were detected by electrospray tandem mass spectrometry in the selective reaction monitoring mode. Linear calibration curves were generated over the ranges 0.1–100 and 0.02–5 ng/mL for sunitinib and 0.2–200 and 0.04–10 ng/mL for N‐desethyl sunitinib in plasma and in phosphate‐buffered solution, respectively. The values for both within‐day and between‐day precision and accuracy were well within the generally accepted criteria for analytical methods. The analytical range was sufficient to determine the unbound and total concentrations of both analytes. The method was applied for measurement unbound concentrations in addition to total concentrations of sunitinib and its metabolite in plasma of a cancer patient receiving 50 mg daily dose. Copyright © 2012 John Wiley & Sons, Ltd.     

Modeling loop backbone flexibility in receptor‐ligand docking simulations

The relevance of receptor conformational change during ligand binding is well documented for many pharmaceutically relevant receptors, but is still not fully accounted for in in silico docking methods. While there has been significant progress in treatment of receptor side chain flexibility sampling of backbone flexibility remains challenging because the conformational space expands dramatically and the scoring function must balance protein–protein and protein–ligand contributions. Here, we investigate an efficient multistage backbone reconstruction algorithm for large loop regions in the receptor and demonstrate that treatment of backbone receptor flexibility significantly improves binding mode prediction starting from apo structures and in cross docking simulations. For three different kinase receptors in which large flexible loops reconstruct upon ligand binding, we demonstrate that treatment of backbone flexibility results in accurate models of the complexes in simulations starting from the apo structure. At the example of the DFG‐motif in the p38 kinase, we also show how loop reconstruction can be used to model allosteric binding. Our approach thus paves the way to treat the complex process of receptor reconstruction upon ligand binding in docking simulations and may help to design new ligands with high specificity by exploitation of allosteric mechanisms. © 2012 Wiley Periodicals, Inc.     

A Point-of-Care Immunotest for Bedside Determination of Heart-Type Fatty Acid-Binding Protein

Heart-type fatty acid-binding protein (H-FABP) is a small cytosolic protein abundant in heart muscle cells. It offers great potential as a sensitive biomarker for early diagnosis of acute myocardial infarction (AMI).

Ninety-one patients presented to the Emergency Department suspected of AMI with a median symptom onset of 6 h (IQR 3–20 h), of which 75 (82.4%) had AMI. The diagnostic performance of a point-of-care immunotest for H-FABP was compared with those of cardiac troponin T (cTnT), creatinine kinase MB (CK-MB), and myoglobin. The H-FABP immunotest was found to have a significant better sensitivity than the other markers and a better specificity than myoglobin and CK-MB. The H-FABP Immunotest gave the greatest area under the receiver operating characteristic (ROC) curve (0.864) for those admitted within 6 h after the onset of symptoms; whereas, cTnT gave the greatest area under the ROC curve (0.936) for those admitted 6–24 h. The H-FABP was also found to be the most efficient marker to diagnose patients suspected of AMI without ST-elevation and with a negative cTnT.

Early detection of H-FABP using the point-of-care immunotest in patients suspected of AMI may allow more accurate targeting of appropriate therapy and considerable cost savings than the current diagnostic tests.     

PKA酶及其抑制剂balanol的计算化学*

蛋白激酶通过磷酸化蛋白底物来调节细胞内的信号转导途径,是重要的药物设计靶标。蛋白激酶A（PKA）是最早获得催化结构域X衍射晶体结构的激酶,是蛋白激酶家族中代表性结构。本文综述了PKA在计算化学领域的研究进展,包括PKA全酶以及它的催化（C）亚基和调节(R)亚基在水溶液中的分子动力学模拟研究,磷酰基转移机理和C亚基与其抑制剂balanol的结合自由能预测、柔性对接。分子动力学、分子对接、同源模建、QM/MM等计算机辅助设计方法在该体系中得到运用。