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.     

Preparation and Properties of a Micro Enzyme Sensor for Creatine

Abstract

A micro enzyme sensor using creatine amidinohydrolase (EC 3. 5. 3. 3) and sarcosine oxidase (EC 1. 5. 3. 1) was developed for measuring creatine. The sensor consisted of platinum and silver wires fixed in a glass tubing with epoxy resin adhesive, and creatine amidinohydrolase and sarcosine oxidase immobilized on their tip by cross-linking method. The calibration curve for measurement of creatine, the effects of pH, temperature, the amount of flavin adenine dinucleotide and compounds on the sensitivity, and the life-time of the sensor were examined. Under optimal conditions, the response of the sensor was linear in the concontration range of 10 μ M ～ 0.65 mM creatine.     

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。     

Synthesis of Benzofuran Analogue of Go6976, an Isoform‐Selective Protein Kinase C Inhibitor

Based on the structure of Go6976, a known isoform‐selective protein kinase C inhibitor, a benzofuran analogue (1) was designed. This analogue was synthesized by coupling of benzofuran 3‐acetic acid and 8‐oxo‐tryptamine and subsequent intramolecular Dieckmann condensation, alkylation, oxidative photocydization and cyanation reaction of mesylate.     

Markov State Models and Molecular Dynamics Simulations Provide Understanding of the Nucleotide-Dependent Dimerization-Based Activation of LRRK2 ROC Domain

Mutations in leucine-rich repeat kinase 2 (LRRK2) are recognized as the most frequent cause of Parkinson’s disease (PD). As a multidomain ROCO protein, LRRK2 is characterized by the presence of both a Ras-of-complex (ROC) GTPase domain and a kinase domain connected through the C-terminal of an ROC domain (COR). The bienzymatic ROC–COR–kinase catalytic triad indicated the potential role of GTPase domain in regulating kinase activity. However, as a functional GTPase, the detailed intrinsic regulation of the ROC activation cycle remains poorly understood. Here, combining extensive molecular dynamics simulations and Markov state models, we disclosed the dynamic structural rearrangement of ROC’s homodimer during nucleotide turnover. Our study revealed the coupling between dimerization extent and nucleotide-binding state, indicating a nucleotide-dependent dimerization-based activation scheme adopted by ROC GTPase. Furthermore, inspired by the well-known R1441C/G/H PD-relevant mutations within the ROC domain, we illuminated the potential allosteric molecular mechanism for its pathogenetic effects through enabling faster interconversion between inactive and active states, thus trapping ROC in a prolonged activated state, while the implicated allostery could provide further guidance for identification of regulatory allosteric pockets on the ROC complex. Our investigations illuminated the thermodynamics and kinetics of ROC homodimer during nucleotide-dependent activation for the first time and provided guidance for further exploiting ROC as therapeutic targets for controlling LRRK2 functionality in PD treatment.     

Novel c-Jun N-Terminal Kinase (JNK) Inhibitors with an 11H-Indeno[1,2-b]quinoxalin-11-one Scaffold

c-Jun N-terminal kinase (JNK) plays a central role in stress signaling pathways implicated in important pathological processes, including rheumatoid arthritis and ischemia-reperfusion injury. Therefore, inhibition of JNK is of interest for molecular targeted therapy to treat various diseases. We synthesized 13 derivatives of our reported JNK inhibitor 11H-indeno[1,2-b]quinoxalin-11-one oxime and evaluated their binding to the three JNK isoforms and their biological effects. Eight compounds exhibited submicromolar binding affinity for at least one JNK isoform. Most of these compounds also inhibited lipopolysaccharide (LPS)-induced nuclear factor-κB/activating protein 1 (NF-κB/AP-1) activation and interleukin-6 (IL-6) production in human monocytic THP1-Blue cells and human MonoMac-6 cells, respectively. Selected compounds (4f and 4m) also inhibited LPS-induced c-Jun phosphorylation in MonoMac-6 cells, directly confirming JNK inhibition. We conclude that indenoquinoxaline-based oximes can serve as specific small-molecule modulators for mechanistic studies of JNKs, as well as potential leads for the development of anti-inflammatory drugs.     

基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

Promising Chemotherapy for Malignant Pediatric Brain Tumor in Recent Biological Insights

Brain tumors are the most widespread malignancies in children around the world. Chemotherapy plays a critical role in the treatment of these tumors. Although the current chemotherapy process has a remarkable outcome for a certain subtype of brain tumor, improving patient survival is still a major challenge. Further intensive treatment with conventional non-specific chemotherapy could cause additional adverse reactions without significant advancement in survival. Recently, patient derived brain tumor, xenograft, and whole genome analysis using deep sequencing technology has made a significant contribution to our understanding of cancer treatment. This realization has changed the focus to new agents, targeting the molecular pathways that are critical to tumor survival or proliferation. Thus, many novel drugs targeting epigenetic regulators or tyrosine kinase have been developed. These selective drugs may have less toxicity in normal cells and are expected to be more effective than non-specific chemotherapeutics. This review will summarize the latest novel targets and corresponding candidate drugs, which are promising chemotherapy for brain tumors according to the biological insights.     

Anti-Inflammatory Effects of Spiramycin in LPS-Activated RAW 264.7 Macrophages

Drug repurposing is a simple concept with a long history, and is a paradigm shift that can significantly reduce the costs and accelerate the process of bringing a new small-molecule drug into clinical practice. We attempted to uncover a new application of spiramycin, an old medication that was classically prescribed for toxoplasmosis and various other soft-tissue infections; specifically, we initiated a study on the anti-inflammatory capacity of spiramycin. For this purpose, we used murine macrophage RAW 264.7 as a model for this experiment and investigated the anti-inflammatory effects of spiramycin by inhibiting the production of pro-inflammatory mediators and cytokines. In the present study, we demonstrated that spiramycin significantly decreased nitric oxide (NO), interleukin (IL)-1β, and IL-6 levels in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. Spiramycin also inhibited the expression of NO synthase (iNOS), potentially explaining the spiramycin-induced decrease in NO production. In addition, spiramycin inhibited the phosphorylation of mitogen-activated protein kinases (MAPKs); extracellular signal-regulated kinase (ERK) and c-Jun N terminal kinase (JNK) as well as the inactivation and subsequent nuclear translocation of nuclear factor κB (NF-κB). This indicated that spiramycin attenuates macrophages’ secretion of IL-6, IL-1β, and NO, inducing iNOS expression via the inhibition of the NF-κB and MAPK signaling pathways. Finally, we tested the potential application of spiramycin as a topical material by human skin primary irritation tests. It was performed on the normal skin (upper back) of 31 volunteers to determine whether 100 μM and μM of spiramycin had irritation or sensitization potential. In these assays, spiramycin did not induce any adverse reactions. In conclusion, our results demonstrate that spiramycin can effectively attenuate the activation of macrophages, suggesting that spiramycin could be a potential candidate for drug repositioning as a topical anti-inflammatory agent.