基于虚拟筛选和分子动力学模拟发现新型ULK1抑制剂

Unc-51样自噬激活激酶1（unc-51-like autophagy activating kinase 1,ULK1）作为自噬启动的重要调控因子,是肿瘤治疗的关键靶点之一。首先,以已知ULK1抑制剂为基础构建药效团模型,通过药效团模型筛选、分子对接以及分子力学广义波恩表面积（Molecular Mechanics/Generalized Born Surface Area,MM/GBSA）结合自由能计算等方法,对含有52万多个类药性小分子的数据库进行虚拟筛选,得到具有较高理论亲和力的化合物。随后,50ns的分子动力学模拟验证了蛋白质-配体复合物结合的稳定性,最后10ns的平均结合自由能的计算研究进一步验证了配体的结合能力。结果表明,6个化合物（F5258-0159、F3407-0428、F0529-1100、F0696-3531、F3222-5280、F6525-5596）具有骨架新颖、分子对接分数和结合自由能数值优异及与ULK1的结合状态稳定等特点,可以作为新型潜在的ULK1抑制剂用于肿瘤治疗的研究,也为新型ULK1抑制剂的设计和研发提供新的研究思路。     

Exact solution of the totally asymmetric simple exclusion process: Shock profiles

The microscopic structure of macroscopic shocks in the one-dimensional, totally asymmetric simple exclusion process is obtained exactly from the complete solution of the stationary state of a model system containing two types of particles-first and second class. This nonequilibrium steady state factorizes about any second-class particle, which implies factorization in the one-component system about the (random) shock position. It also exhibits several other interesting features, including long-range correlations in the limit of zero density of the second-class particles. The solution also shows that a finite number of second-class particles in a uniform background of first-class particles form a weakly bound state.     

One-pot,four-component synthesis of benzylpyrazolyl naphthoquinone derivatives and molecular docking studies

A highly efficient, green, one-pot, four-component approach for the synthesis of benzylpyrazolyl naphthoquinone derivatives (5a–p) have been developed by the domino reaction of 2-hydroxy naphthoquinone, aromatic aldehyde, ethyl acetoacetate, and phenyl hydrazine derivatives in water and employed p-toluene sulfonic acid (p-TSA) as the right choice of catalyst at reflux. Docking simulation was performed to position compounds 5a, 5b, and 5g into the anaplastic lymphoma kinase (ALK) structure active site to determine the probable binding model.     

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。     

Analytical solution and meaning of feasible regions in two-component three-way arrays

Although many efforts have been directed to the development of approximation methods for determining the extent of feasible regions in two- and three-way data sets; analytical determination (i.e. using only finite-step direct calculation(s) instead of the less exact numerical ones) of feasible regions in three-way arrays has remained unexplored. In this contribution, an analytical solution of trilinear decomposition is introduced which can be considered as a new direct method for the resolution of three-way two-component systems. The proposed analytical calculation method is applied to the full rank three-way data array and arrays with rank overlap (a type of rank deficiency) loadings in a mode. Close inspections of the analytically calculated feasible regions of rank deficient cases help us to make clearer the information gathered from multi-way problems frequently emerged in physics, chemistry, biology, agricultural, environmental and clinical sciences, etc. These examinations can also help to answer, e.g., the following practical question: “Is two-component three-way data with proportional loading in a mode actually a three-way data array?” By the aid of the additional information resulted from the investigated feasible regions of two-component three-way data arrays with proportional profile in a mode, reasons for the inadequacy of the seemingly trilinear data treatment methods published in the literature (e.g., U-PLS/RBL-LD that was used for extraction of quantitative and qualitative information reported by Olivieri et al. (Anal. Chem. 82 (2010) 4510–4519)) could be completely understood.     

A Facile Synthesis of New 4,6‐Dichloropyridine Derivatives,Their Biological Evaluation for Antimicrobial and Antioxidant Activity,and Docking Studies

A facile synthesis of new 4,6‐dichloropyridine derivatives 5 ( a–f ), 6 ( a–c ), and 7 ( a–c ) were synthesized using both conventional heating and solvent‐free microwave irradiation techniques. The results revealed that the latter method is superior to the conventional heating method. The easy work‐up of the products, rapid reaction, and mild conditions are noticeable features of this protocol. Structural elucidation of the synthesized compounds was made on the basis of various spectroscopic methods. The synthesized compounds were evaluated for their in vitro antimicrobial activity (minimum inhibitory concentration; MIC) against various microbial strains using the agar well‐diffusion method. Among the compounds, 5c showed best antimicrobial activity against most of the employed strains, especially against Staphylococcus aureus, Escherichia coli, Rhizopus arrhizus, and Candida albicans. Compounds 5a , 6a , 6c , 7a , and 7c showed significant antioxidant activity when compared to the other compounds. In addition to this, theoretical docking studies were performed for the highly potent compounds 5a , 6a , 6c , 7a , and 7c against three different drug targets belonging to the oxidoreductase family, and the results were found to be highly satisfactory.     

Exponential repulsion improves structural predictability of molecular docking

Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom‐centered partial charges and standard 6–12 Lennard–Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard–Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. © 2016 Wiley Periodicals, Inc.     

p-TSA-catalyzed one-pot synthesis and docking studies of some 5H-indeno[1,2-b]quinoline-9,11(6H,10H)-dione derivatives as anticonvulsant agents

The present work describes a facile, one-pot three component environment friendly, green synthesis of a series of 5-(4-methoxyphenyl)-7,7-dimethyl-10-phenyl-7,8-dihydro-5H-indeno[1,2-b]quinoline-9,11(6H,10H)-dione derivatives 8(a-n). 1,3-indanedione, aryl-aldehyde and enaminone was thoroughly ground in the presence of catalytic amount of p-toluene sulfonic acid (p-TSA) to give the titled compounds in good yields. All the synthesized derivatives were evaluated for their anticonvulsant activity using the maximal electroshock (MES) method with phenytoin as a standard drug along with their neurotoxicity effect. Derivatives 8b, 8e and 8k exhibited significant anticonvulsant activity (P<0.001). The neurotoxicity study clearly revealed that all the tested compounds are non-toxic at a dose of 40 mg/kg. The molecular modeling studies also predicted good binding interactions of most active molecules with the serotonin 5-HT_2A receptor. Therefore, it can be safely concluded that synthesized derivatives 8(a-n) would represent useful leads for further investigation in the development of a new class of anticonvulsant agents.     

Development of bis-thiobarbiturates as successful urease inhibitors and their molecular modeling studies

Bis-thiobarbiturate derivatives 1–15 have been synthesized, characterized by1 HNMR and EI-MS and screened for urease inhibition. All compounds showed various degree of urease inhibitory activity with IC_(50) values ranging 7.45 0.12 74.24 0.81 mmol/L while the standard thiourea behaved normally(IC_(50) = 21.10 0.12). Compounds 1(IC_(50) = 7.45 0.12 μmol/L), 9(IC_(50) = 18.17 1.03 μmol/L) and 13(IC_(50) = 8.61 0.45 μmol/L) showed excellent urease inhibitory activity in the series. Molecular modeling studies were performed to understand the binding site with the bimetallic nickel center of the enzyme.Structure-activity relationship has also been established for these compounds. This study identified bisthiobarbiturate as a novel class of urease inhibitors.