X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno‐oncology.     

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Insight into the Urea Binding and K166R Mutation Stabilizing Mechanism of TlpB: Molecular Dynamics and Principal Component Analysis Study

Chemoreceptor TlpB(Tlp=transducer-like protein), which has been demonstrated to respond to pH sensing function, is crucial for the survival of Helicobacter pylori(H. pylori) in host stomach. Urea was proposed to be essential for TlpB's pH sensing function via binding with the Per-ARNT-Sim(PAS) domain of TlpB. Additionally, K166R mutation of the TlpB protein has also been proven to have a similar effect on TlpB pH sensing as urea binding. Although X-ray crystallographic studies have been carried out for urea-bound TlpB, the molecular mechanism for the stabilization of TlpB induced by urea binding and K166R mutation remains to be elucidated. In this study, molecular dynamics simulations combined with principal component analysis(PCA) for the simulation results were used to gain an insight into the molecular mechanism of the stabilization of urea on TlpB protein. The formed H-bonds and salt-bridges surrounding Asp114, which were induced by both urea binding and K166R mutation of TlpB, were important to the stabilization of TlpB by urea. The similarity between the urea binding and K166R mutation as well as their differences in effect has been explicitly demonstrated with computer simulations at atomic-level. The findings may pave the way for the further researches of TlpB.     

聚乙烯唑啉作用下甲烷水合物分解的分子动力学模拟

利用分子动力学模拟系统研究了不同质量浓度下(1.25%、2.50%、6.06%)聚乙烯唑啉(PEtO)对甲烷水合物的分解作用. 模拟体系为甲烷水合物2′2′2的超胞和聚合物对接体系. 模拟发现水分子间氢键构架的水合物笼型结构在PEtO的作用下出现扭曲, 最终导致水合物笼型结构完全坍塌. 通过氧原子径向分布函数、均方位移以及扩散系数比较不同浓度PEtO的作用, 证实在一定浓度范围内, PEtO的浓度越高, 其水合物分解作用越强. 此外, PEtO 具有一定的可生物降解性. PEtO 对水合物的作用为: PEtO 吸附在水合物表面, 其中的酰胺基(N―C＝O)与成笼的水分子形成氢键, 破坏邻近的笼形结构, 令水合物分解; PEtO不断分解表面的水合物, 直到水合物笼完全分解.     

(R)-2-硫代四氢噻唑-4-羧酸及其酯的合成

L-半胱氨酸盐酸盐与二硫化碳, 氢氧化钠在硝酸铅存在下进行成环反应得到(R)-四氢噻唑-2-硫酮-4-羧酸产率76% , 后者与 醇在硫酸铁水合物催化下反应得到(R)-四氢噻唑-2-硫酮-4-羧酸酯, 产率40～82% .     

Synthesis and Crystal Structure of 5（R）-（1R,2S,5R）-Menthoxy-4（R）- N-cyclohexylaminobutyrolactone

1INTRODUCTION Substitutedγ-butyrolactones are a group of impor-tant compounds containing unique carbon skeleton of butyrolactone which is widely present in many natural products and have received considerable interest because of their biological and medicinal properties[1～4].Therefore,much attention has been paid to the new asymmetric methods for synthesi-zing these interesting compounds[5～11].The prece-ding results led us to explore the possibility of using cyclohexylamine to convert5(…     

(XN)4R4簇合物的结构与化学键

用密度泛函理论,在B3LYP/6-311G水平上,对(XN)4R4 (X=C,Si,Ge;R=H,CH3,NH2,OH)及合成的先驱化合物(XN)2R2进行几何构型、电子结构、振动频率和化学反应焓变等进行了研究.结果表明,(RCN)4比(CNR)4更稳定.所有簇合物的零点能EZP值,R=H时最小,R=CH3时最大,R配位原子依次为C、N和O时,EZP值逐渐减小.     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Conformational Analysis of Germacrane Sesquiterpene Lactones. 1(10)Z,4E- and 1(10)E,4Z-Germacranolides

Molecular mechanics was used to study the structures of 1(10)Z,4E- and 1(10)E,4Z-germacranolides. Possible conformers, their probabilities, and barriers to conformational transitions were determined     

Activation of β2-Adrenergic Receptor Induced by Three Catecholamine Agonists: a Docking and Molecular Dynamics Study

We studied the activation of β₂-adrenergic receptor(β₂AR) by norepinephrine, epinephrine and isoproterenol using docking and molecular dynamics(MD) simulation. The simulation was done on the assumption that β₂AR was surrounded with explicit water and infinite lipid bilayer membrane at body temperature. So the result should be close to that under the physiological conditions. We calculated the structure of binding sites in β₂AR for the three activators. We also simulated the change of the conformation of β₂AR in the transmembrane regions(TMs), in the molecular switches, and in the conserved DRY(Aspartic acid, Arginine and Tyrosine) motif. This study provides detailed information concerning the structure of β₂AR during activation process.     

定点突变提高IL-4免疫毒素对淋巴瘤的选择性和杀伤活性

采用软件分析选择与IL-4分子结合与活性相关的重要位点13T,121R,通过定点突变得到IL-4突变基因cpIL4(13D121E),将其与绿脓杆菌外毒素突变基因PE38KDEL融合,成功地构建了编码免疫毒素cpIL4(13D121E)-PE38KDEL的融合基因.该基因在原核表达系统中得到了高效表达,表达量占细胞全蛋白的30%以上.表达产物经亲和色谱和阴离子交换色谱纯化后,进行细胞毒性实验,证明其对表达型IL-4受体的淋巴瘤细胞Daudi具有良好的细胞毒作用,活性是同类型IL-4免疫毒素的2倍,而对表达型IL-4受体的内皮细胞活性较低.     

Synthesis and Conformational Properties of Bis（calix [4] arene）

The bis(calix [4] arene)3 was synthesized in moderate yield by the reaction of p-tert-butylcalix [4] arene (1) with 1,4-bis(chloromethyl) benzene (2). The conformation of all alkylated product 4 was investigated by the variable-temperature ^1H-NMR.     

Synthesis and Crystal Structure of （R）-4-Hydroxymethyl-2-thioxo Thiazolidine and Its Asymmetric Catalysis

(R)-4-Hydroxymethyl-2-thioxo thiazolidine as a new chiral catalyst in the asymmetric addition of diethyl-zinc to benzaldehyde was synthesized from (R)-4-hydroxymethyl-2-thioxo thiazolidine carboxylic acid and its crystal structure was determined by X-ray diffraction method. The compound was crystallized in the orthorhombic system, space group P212121 with unit cell dimensions a=0.67253(12) nm; b=0.89164(17) rim; c=1.06146(19) nm, volume 0.6365(2) nm3; Z=4, calculated denisity 1.557 Mg/m3; absorption coefficient 0.733 mm-1; F(000)=312. The X-ray crystal structure analysis reveals that the compound has a thione group.     

Design of Novel IRAK4 Inhibitors Using Molecular Docking,Dynamics Simulation and 3D-QSAR Studies

Treatment of several autoimmune diseases and types of cancer has been an intense area of research over the past two decades. Many signaling pathways that regulate innate and/or adaptive immunity, as well as those that induce overexpression or mutation of protein kinases, have been targeted for drug discovery. One of the serine/threonine kinases, Interleukin-1 Receptor Associated Kinase 4 (IRAK4) regulates signaling through various Toll-like receptors (TLRs) and interleukin-1 receptor (IL1R). It controls diverse cellular processes including inflammation, apoptosis, and cellular differentiation. MyD88 gain-of-function mutations or overexpression of IRAK4 has been implicated in various types of malignancies such as Waldenström macroglobulinemia, B cell lymphoma, colorectal cancer, pancreatic ductal adenocarcinoma, breast cancer, etc. Moreover, over activation of IRAK4 is also associated with several autoimmune diseases. The significant role of IRAK4 makes it an interesting target for the discovery and development of potent small molecule inhibitors. A few potent IRAK4 inhibitors such as PF-06650833, RA9 and BAY1834845 have recently entered phase I/II clinical trial studies. Nevertheless, there is still a need of selective inhibitors for the treatment of cancer and various autoimmune diseases. A great need for the same intrigued us to perform molecular modeling studies on 4,6-diaminonicotinamide derivatives as IRAK4 inhibitors. We performed molecular docking and dynamics simulation of 50 ns for one of the most active compounds of the dataset. We also carried out MM-PBSA binding free energy calculation to identify the active site residues, interactions of which are contributing to the total binding energy. The final 50 ns conformation of the most active compound was selected to perform dataset alignment in a 3D-QSAR study. Generated RF-CoMFA (q² = 0.751, ONC = 4, r² = 0.911) model revealed reasonable statistical results. Overall results of molecular dynamics simulation, MM-PBSA binding free energy calculation and RF-CoMFA model revealed important active site residues of IRAK4 and necessary structural properties of ligand to design more potent IRAK4 inhibitors. We designed few IRAK4 inhibitors based on these results, which possessed higher activity (predicted pIC₅₀) than the most active compounds of the dataset selected for this study. Moreover, ADMET properties of these inhibitors revealed promising results and need to be validated using experimental studies.     

(R)-N-乙酰基-四氢噻唑-2-硫酮-4-甲酰TT的合成及其晶体结构

由N-乙酰(R)-四氢噻唑-2-硫酮-4-羧酸在三聚氯氰及三乙胺存在下与四氢噻唑-2-硫酮反应得到标题化合物，[α]^2^0~D +11.18°。用X射线衍射法测得其晶体结构，属单斜晶系，空间群为P2~1/c。晶体学数据：a=0.9959(4)nm，b=1.1469(4)nm，c=1.1108(3)nm，β=92.72(3)°，V=1.2673(8)nm^3，Z=4。分子中两个C=O基，两个C=S基团处于C(1)-N(1)-C(4)及C(6)-N(2)-C(7)键两侧呈反式。用PM3分子轨道方法研究了该化合物的电子结构，电荷和键序分布，得到该化合物前线轨道性质。     

（R）—四氢噻唑—2—硫酮—4—羧酸的合成及其晶体结构

由Ｌ－半胱氨酸盐酸盐与二硫化碳在ＮａＯＨ及ＣｕＳＯ４．Ｈ２Ｏ存在下反应得到（Ｒ）－四氢噻唑－２－硫酮－４－羧酸，「α」＾２０Ｄ－８７．５°，产率６６％。用Ｘ射线衍射法测得其晶体结构，属正交晶系，Ｐｚ１ｚ１ｚ１空间群，晶体学参数：α＝０．５０２９（２）ｎｍ，ｂ＝０．７７４９９（５）ｎｍ，ｃ＝１．６３００（５）ｎｍ，Ｖ＝０．６３５０（５）ｎｍ＾３，Ｚ＝４。用分子轨道方法研究了该化合物的电子结构，得到其     

树形大分子基药物传输系统结合强度及构型的分子动力学研究

采用全原子分子动力学方法系统研究了聚酰胺(PAMAM)型树形大分子非共价搭载4种抗癌药物分子(CE6,DOX,MTX及SN38)的药物传输复合体系.考察了药物分子种类、数量及树形大分子的代数和聚乙二醇化表面修饰对复合体系的结合强度、尺寸及溶剂中扩散行为的影响.研究发现,PAMAM自身变形能对药物-PAMAM间的结合有重要影响.搭载较多的药物分子可以使PAMAM自身增大,但同样搭载条件下经过聚乙二醇化修饰过的PAMAM变化并不明显.PAMAM分子表面的聚乙二醇化可以更高的强度结合更多的药物分子,并减缓其扩散速度,因而提高药物分子的搭载效率和体内滞留时间.为新型树形大分子基药物传输体系的设计提供理论依据.     

Simultaneous Determination of Sunset Yellow and Ponceau 4R in Gelatin Powder by Derivative Spectrophotometry and Partial Least-Squares Multivariate Spectrophotometric Calibration

ABSTRACT

Two methods for the simultaneous determination of Sunset Yellow and Ponceau 4R in gelatin powders by first derivative spectrophotometry and by partial least-squares multivariate spectrophotometric calibration are described. These procedures do not require any separation step. These methods were applied to determine both colorants in commercial gelatin powders and the results obtained were compared. A good statistical agreement was obtained between the results.     

Deciphering Conformational Changes of the GDP-Bound NRAS Induced by Mutations G13D,Q61R,and C118S through Gaussian Accelerated Molecular Dynamic Simulations

The conformational changes in switch domains significantly affect the activity of NRAS. Gaussian-accelerated molecular dynamics (GaMD) simulations of three separate replicas were performed to decipher the effects of G13D, Q16R, and C118S on the conformational transformation of the GDP-bound NRAS. The analyses of root-mean-square fluctuations and dynamics cross-correlation maps indicated that the structural flexibility and motion modes of the switch domains involved in the binding of NRAS to effectors are highly altered by the G13D, Q61R, and C118Smutations. The free energy landscapes (FELs) suggested that mutations induce more energetic states in NRAS than the GDP-bound WT NRAS and lead to high disorder in the switch domains. The FELs also indicated that the different numbers of sodium ions entering the GDP binding regions compensate for the changes in electrostatic environments caused by mutations, especially for G13D. The GDP–residue interactions revealed that the disorder in the switch domains was attributable to the unstable hydrogen bonds between GDP and two residues, V29 and D30. This work is expected to provide information on the energetic basis and dynamics of conformational changes in switch domains that can aid in deeply understanding the target roles of NRAS in anticancer treatment.     

Spectrophotometric Simultaneous Determination of Amaranth,Ponceau 4R,Allura Red and Red 2G by Partial Least Squares and Principal Component Regression Multivariate Calibration

ABSTRACT

The multivariate calibration methods, partial least square regression type 1 (PLS 1) and principal component regression (PCR), were proposed for the simultaneous spectrophotometry determination of Amaranth (E-123), Ponceau 4R (E-124), Allura red (E-129) and Red 2G (E-128) in their mixtures. The parameters of the chemometric procedures were optimized and the proposed method was validated with synthetic samples and applied to analyze these dyes in spiked samples of beverages with satisfactory results.