Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors

Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research.     

来源于天然产物的基质金属蛋白酶(MMPs)抑制剂

基质金属蛋白酶（MMPs）参与一系列重大疾病的病理过程,基质金属蛋白酶抑制剂具有广阔的药用前景。本文概述了基质金属蛋白酶抑制剂的研究历史和最新的研究理念。重点回顾总结了天然产物中基质金属蛋白酶的活性抑制成分和对基质金属蛋白酶转录表达抑制的天然产物成分以及这些化合物的抗癌效果。     

A concise synthesis of 2,5-dideoxy-2,5-imino-d-mannitol (DMDP) and HomoDMDP from l-xylose

A short and practical procedure for the preparation of C-2 substituted polyhydroxypyrrolidines is described. The C-2 substituent is introduced by a stereoselective addition of a Grignard reagent to a 2,3,5-protected aldofuranose and the cyclization to the pyrrolidine ring system is performed through a bis-mesylation/double nucleophilic displacement sequence. The efficiency of the methodology was demonstrated by its application to the synthesis of HomoDMDP and DMDP.     

二氢异喹啉类BACE1抑制剂的特征结构及结合模式研究

β-分泌酶(BACE1)是水解淀粉样前体蛋白生成β-淀粉样多肽的关键限速酶,近年来已成为治疗阿尔茨海默症的一个理想靶点。本文以34个二氢异喹啉类BACE1抑制剂为研究对象,采用比较分子相似性指数(CoMSIA)法定量研究其结构与生物活性间的构效关系,并建立可靠的3D-QSAR预测模型,运用分子对接法分析其与受体BACE1间的结合模式。结果显示,基于立体场、疏水场和氢键供体场建立的CoMSIA模型稳定性良好、预测能力强(Q~2=0.47,R_(ncv)~2=0.93,R_(pre)~2=0.95)。本研究所得模型和信息较好地解释了二氢异喹啉类BACE1抑制剂的结构特征及其与受体间的结合模式,为后续新型BACE1抑制剂的设计开发提供理论指导。     

糖原合成激酶-3β马来酰胺类抑制剂构效关系的理论研究

建立糖原合成激酶-3β(GSK-3β)抑制剂的三维构效关系,可预测新的糖原合成激酶-3β抑制剂.通过确定分子的药效构象,与选定的模板分子进行叠合,采用比较分子力场分析法(Co MFA)和比较分子相似性指数分析法(Co MSIA)分别建立38个糖原合成激酶-3β抑制剂的3D-QSAR模型.比较分子力场分析法所建立的模型的决定系数q2=0.711,非交叉验证系数r2=0.887,标准偏差ES=0.411,显著系数F=109.856;比较分子相似性指数分析法所建立模型的决定系数q2=0.605,非交叉验证系数r2=0.931,标准偏差ES=0.326,显著系数F=122.122.该模型在一定程度上反映了结合部位的性质要求,解释马来酰胺类抑制剂的构效关系,具有较好的预测能力.     

Deactivation of Mcl‐1 by Dual‐Function Small‐Molecule Inhibitors Targeting the Bcl‐2 Homology 3 Domain and Facilitating Mcl‐1 Ubiquitination

By means of limited proteolysis assay, three‐dimensional NMR, X‐ray crystallography and alanine mutations, a dynamic region at the Q221R222N223 motif in the Bcl‐2 homology 3 (BH3) domain of Mcl‐1 has been identified as a conformational switch which controls Mcl‐1 ubiquitination. Noxa^BH3 binding biases the QRN motif toward a helical conformation, thus leading to an enhanced in vitro ubiquitination of Mcl‐1. In contrast, Bim^BH3 binding biases the QRN motif toward a nonhelical conformation, thus leading to the inhibition of ubiquitination. A dual function Mcl‐1 inhibitor, which locates at the BH3 domain of Mcl‐1 and forms hydrogen bond with His224 to drive a helical QRN conformation, so that it not only interferes with the pro‐apoptotic partners, but also facilitates Mcl‐1 ubiquitination in living cells, is described. As a result, this inhibitor manifests a more effective apoptosis induction in Mcl‐1‐dependent cancer cells than other inhibitors exhibiting a similar binding affinity with it.     

Mirror‐Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide

Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror‐image packing can enable opposite enantiomers to be accommodated in an enzyme's active site. Reported here is a series of crystallographic studies of complexes between an enzyme and a potent experimental herbicide whose chiral center forms an essential part of the inhibitor pharmacophore. Initial studies with a racemate at 1.85 Å resolution failed to identify the chirality of the bound inhibitor, however, by extending the resolution to 1.1 Å and by analyzing high‐resolution complexes with the enantiopure compounds, we determined that both enantiomers make equivalent pseudosymmetric interactions in the active site, thus mimicking an achiral reaction intermediate.     

自适应模糊偏最小二乘方法在药物构效关系建模中的应用

作为一种局部逼近方法,自适应神经模糊推理系统(ANFIS)适于为药物定量构效关系(QSAR)建模。描述药物分子结构的参数较多,常存在耦合关系,会增加建模难度,并影响模型的预报性能。为此,将ANFIS和偏最小二乘(PLS)相结合,先由PLS从样本数据中提取成分,再由ANFIS实现每对成分间的非线性映射,并基于输出误差进一步修正所提取的成分,使之对因变量具有最优的解释能力,由此构建为EB-AFPLS方法。该法已成功地应用于HIV-1蛋白酶抑制剂的QSAR建模,效果良好,显示出很强的学习能力,所建模型的预报性能也优于其它方法。     

Critical conditions for improved fermentability during overliming of acid hydrolysates from spruce

Bioethanol can be produced from wood via acid hydrolysis, but detoxification is needed to achieve good fermentability. Overliming was investigated in a factorial designed experiment, in which pH and temperature were varied. Degradation of inhibitory furan aldehydes was more extensive compared to monosaccharides. Too harsh conditions led to massive degradation of sugars and formation of inhibiting acids and phenols. The ethanol productivity and yield after optimal overliming reached levels exceeding reference fermentations of pure glucose. A novel metric, the balanced ethanol yield, which takes both ethanol production and losses of fermentable sugars into account, was introduced and showed the optimal conditions within the investigated range. The findings allow process technical and economical considerations to govern the choice of conditions for overliming.     

Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition

Fat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors by applying scaffold hopping approach. Using this novel scaffold, different derivatives were designed by extending scaffold structure with potential functional groups. Molecular docking simulations were carried out by using two different docking algorithm implemented in CDOCKER (flexible docking) and AutoDock programs (rigid docking). Analyzing results of rigid and flexible docking, compound MU06 was selected based on different properties and predicted binding affinities for further analysis. Molecular dynamics simulation of FTO/MU06 complex was performed to characterize structure rationale and binding stability. Certainly, Arg96 and His231 residue of FTO protein showed stable interaction with inhibitor MU06 throughout the production dynamics phase. Three residues of FTO protein (Arg96, Asp233, and His231) were found common in making H-bond interactions with MU06 during molecular dynamics simulation and CDOCKER docking.