Tricationic pyridium porphyrins appending different peripheral substituents: experimental and DFT studies on their interactions with DNA

Four tricationic pyridium porphyrins appending hydroxyphenyl, methoxyphenyl, propionoxyphenyl or carboxyphenyl group at meso-20-position of porphyrin core have been synthesized and their abilities to bind and cleave DNA have been investigated. Using a combination of absorption, fluorescence, circular dichroism (CD) spectra, thermal DNA denaturation as well as viscosity measurements, their binding modes and intrinsic binding constants (K_b) to calf DNA (CT DNA) were comparatively studied and also compared with those of 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP). The results suggest that the K_b values of these porphyrins are greatly influenced by the number of positive charges and steric hindrance. Theoretical calculations applying the density functional theory (DFT) have been carried out and explain their DNA-binding properties reasonably. The efficiency of DNA photocleavage by these porphyrins shows high dependence on the values of K_b.     

Mechanical properties of armchair silicene nanoribbons with edge cracks: a molecular dynamics study

Silicene has been proven to be a promising material with attractive electronic properties. During the synthesis of silicene, structural defects such as edge crack are likely to be generated and such defects in silicene have impacts on its properties. Herein, molecular dynamics simulations were performed to investigate the mechanical properties of the armchair silicene nanoribbons (ASiNRs) with edge cracks. Our results showed that the mechanical properties of the ASiNRs decrease because of the existence of edge crack. Both the pristine ASiNRs and the ASiNRs with edge cracks show brittle fracture behaviours. The crack length plays an important role in determining the critical strain and fracture strength of the ASiNRs. Moreover, we investigated the effects of strain rate and temperature on the mechanical properties of the ASiNRs with edge cracks. We observed that the increasing strain rate increases the critical strain and fracture strength while decreasing the Young’s modulus. Low-strain rates also changes the expanded directions of cracks in the ASiNRs. We also found that the increasing temperature could significantly decrease the mechanical properties of the ASiNRs with edge cracks.     

The structure and stability of B36N36 cages: a computational study

The structure and stability of 22 B₃₆N₃₆ cage molecules containing four-membered (F ₄), five-membered (F ₅), six-membered (F ₆), eight-membered (F ₈) and 12-membered (F ₁₂) rings have been computed at the B3LYP/6-31G* level of density functional theory. The most stable structure (1) has T _d symmetry with six F ₄ and 32 F ₆ rings, following the isolated square rule, while the fullerene-like structures (12 F ₅ and 26 F ₆) and also structures with F ₈ and F ₁₂ are much higher in energy. Figure The T _d symmetrical structure (1) with six F ₄ and thirty-two F ₆ rings is the most stable B₃₆N₃₆ cage.     

C3d-M28增强伪狂犬病毒gC基因体液免疫

研究补体C3d的受体结合功能区(M28)对伪狂犬病毒gC基因DNA疫苗免疫增强作用。将4拷贝的M28基因与伪狂犬病毒gC基因串联后,克隆到载体pcDNA3.1中,构建融合表达的重组质粒(sgC-M284)。BALB/c小鼠免疫试验表明,sgC-M284免疫组比单独表达伪狂犬病毒gC蛋白的重组质粒(sgC)免疫组产生的ELISA抗体高17倍,对致死剂量(316LD50)伪狂犬病毒攻毒的保护率提高了63%。gC基因与M28基因融合表达诱导产生的IL-4水平接近了伪狂犬灭活疫苗免疫组的产生的IL-4水平,显著增强了基于Th2途径的体液免疫反应。     

Non-equilibrium molecular dynamics study on radial thermal conductivity and thermal rectification of graphene

In the present study, the radial thermal rectification and thermal conductivity of the graphene were investigated by non-equilibrium molecular dynamics simulation and then corrected by quantum correction to make it closer to the fact. The Optimised three-body Tersoff potential is employed in order to simulate the interactions between the carbon atoms in the graphene sheet. A circular region in the centre and the one at the graphene edge are selected as hot and cold bath to generate radial temperature gradient. It is observed that the heat current passes through radially inward direction than outward with the same temperature gradient and hence there is a radial thermal rectification in graphene. Also, temperature distribution and heat flux are theoretically introduced as a function of distance from the graphene centre and then it is confirmed by the molecular dynamics simulation data. Finally, the influence of temperature gradient and size of graphene on radial thermal rectification and the impact of size on the radial thermal conductivity is investigated.     

Zwitterionic polymers functionalised nanoporous graphene for water desalination: a molecular dynamics study

In this paper, one nanoporous graphene grafting several zwitterionic polymer chains was designed as the osmosis membrane for seawater desalination. Using molecular dynamics simulation, the efficiency and mechanism of salt rejection were discussed. The simulated results showed that the zwitterionic polymer chains on nanoporous graphene can form the charge channel to block Na⁺ and Cl^? ions pass through, and the slat rejection efficiency of functionalised graphene can reach to about 90%. In the simulation, the steric hindrance and electrostatic interaction are the main factors for the salt rejection. With time evolution, the charge channel formed by the soft polymer chains can decrease the effective pore area of membrane, leading to the increase of steric hindrance; the positive and negative centres of polymer chains can adsorb Na⁺ and Cl^? ions under electrostatic interaction in the solution, contributing into the increase of charge density above the membrane. These conclusions are consistent with experimental report. Our designed osmosis membrane about the graphene is helpful for improving the potential application of defect graphene in water desalination and reducing the trouble of obtaining appropriate graphene sheet with small aperture.     

Substrate binding and catalytic mechanism in phospholipase C from Bacillus Cereus: A molecular mechanics and molecular dynamics study

For the first time a consistent catalytic mechanism of phospholipase C from Bacillus cereus is reported based on molecular mechanics calculations. We have identified the position of the nucleophilic water molecule, which is directly involved in the hydrolysis of the natural substrate, phosphatidylcholine, in phospholipase C. This catalytically essential water molecule, after being activated by an acidic residue (Asp55), performs the nucleophilic attack on the phosphorus atom in the substrate, leading to a trigonal bipyramidal pentacoordinated intermediate (and structurally similar transition state). The subsequent collapse of the intermediate, regeneration of the enzyme, and release of the products has to involve a not yet identified second water molecule. The catalytic mechanism reported here is based on a series of molecular mechanics calculations. First, the x-ray structure of phospholipase C from B. cereus including a docked substrate molecule was subjected to a stepwise molecular mechanics energy minimization. Second, the location of the nucleophilic water molecule in the active site of the fully relaxed enzyme–substrate complex was determined by evaluation of nonbonded interaction energies between the complex and a water molecule. The nucleophilic water molecule is positioned at a distance (3.8 Å) from the phosphorus atom in the substrate, which is in good agreement with experimentally observed distances. Finally, the stability of the complex between phospholipase C, the substrate, and the nucleophilic water molecule was verified during a 100 ps molecular dynamics simulation. During the simulation the substrate undergoes a conformational change, but retains its localization in the active site. The contacts between the enzyme, the substrate, and the nucleophilic water molecule display some fluctuations, but remain within reasonable limits, thereby confirming the stability of the enzyme–substrate–water complex. The protocol developed for energy minimization of phospholipase C containing three zinc ions located closely together at the bottom of the active site cleft is reported in detail. In order to handle the strong electrostatic interactions in the active site realistically during energy minimization, delocalization of the charges from the three zinc ions was considered. Therefore, quantum mechanics calculations on the zinc ions and the zinc-coordinating residues were carried out prior to the molecular mechanics calculations, and two different sets of partial atomic charges (MNDO-Mulliken and AM1-ESP) were applied. After careful assignment of partial atomic charges, a complete energy minimization of the protein was carried out by a stepwise procedure without explicit solvent molecules. Energy minimization with either set of charges yielded structures, which were very similar both to the x-ray structure and to each other, although using AM1-ESP partial atomic charges and a dielectric constant of 4, yielded the best protein structure. © 1997 John Wiley and Sons, Inc. Biopoly 42: 319–336, 1997     

Synthesis,molecular docking and ADMET study of ionic liquid as anticancer inhibitors of DNA and COX-2, TOPII enzymes

Abstract

A new ionic liquid was synthesized by the reaction of caprolactam with salicylic acid (CL-SA) and characterized by analysis of spectroscopic and DSC data. The optimized geometry and the electrostatic potential map of CL-SA were calculated with DFT method using the wb97xd/6-31++G(d,p) level of theory. Molecular docking study of the CL-SA was carried out to clarify the probable binding modes between the title compound and DNA and COX-2 and TOPII enzymes. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized ionic liquid which expressed good oral drug-like behavior and non-toxic nature. It was revealed that the compound has a potential to become a lead molecule in drug discovery process.

Communicated by Ramaswamy H. Sarma     

Substrate-enzyme interactions and catalytic mechanism in phospholipase C: a molecular modeling study using the GRID program.

Based on the high-resolution X-ray crystallographic structure of phospholipase C from Bacillus cereus, the orientation of the phosphatidylcholine substrate in the active site of the enzyme is proposed. The proposal is based on extensive calculations using the GRID program and molecular mechanics geometry relaxations. The substrate model has been constructed by successively placing phosphate, choline and diacylglycerol moieties in the positions indicated from GRID calculations. On the basis of the resulting orientation of a complete phosphatidylcholine molecule, we propose a mechanism for the hydrolysis of the substrate.     

Structural insights into the interactions of phorbol ester and bryostatin complexed with protein kinase C: a comparative molecular dynamics simulation study

Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer’s disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the drug development. However, structural details on the binding between PKC and its modulators, especially bryostatin – the highly potent and non-tumor promoting activator for PKCs, are still lacking. Here, we report the first comparative molecular dynamics study aimed at gaining structural insight into the mechanisms by which the PKC delta cys2 activator domain is used in its binding to phorbol ester and bryostatin-1. As anticipated in the phorbol ester binding, hydrogen bonds are formed through the backbone atoms of Thr242, Leu251, and Gly253 of PKC. However, the opposition of H-bond formation between Thr242 and Gly253 may cause the phorbol ester complex to become less stable when compared with the bryostatin binding. For the PKC delta-bryostatin complex, hydrogen bonds are formed between the Gly253 backbone carbonyl and the C30 carbomethoxy substituent of the ligand. Additionally, the indole Nε1 of the highly homologous Trp252 also forms an H-bond to the C20 ester group on bryostatin. Backbone fluctuations also suggest that this latter H-bond formation may abrogate the transient interaction between Trp252 and His269, thus dampening the fluctuations observed on the nearby Zn²⁺-coordinating residues. This new dynamic fluctuation dampening model can potentially benefit future design of new PKC modulators.     

Structural mechanisms of constitutive activation in the C5a receptors with mutations in the extracellular loops: molecular modeling study

Previously we demonstrated by random saturation mutagenesis a set of mutations in the extracellular (EC) loops that constitutively activate the C5a receptor (C5aR) (Klco et al., Nat Struct Mol Biol 2005;12:320-326; Klco et al., J Biol Chem 2006;281:12010-12019). In this study, molecular modeling revealed possible conformations for the extracellular loops of the C5a receptors with mutations in the EC2 loop or in the EC3 loop. Comparison of low-energy conformations of the EC loops defined two distinct clusters of conformations typical either for strongly constitutively active mutants of C5aR (the CAM cluster) or for nonconstitutively active mutants (the non-CAM cluster). In the CAM cluster, the EC3 loop was turned towards the transmembrane (TM) helical bundle and more closely interacted with EC2 than in the non-CAM cluster. This suggested a structural mechanism of constitutive activity where EC3 contacts EC2 leading to EC2 interactions with helix TM3, thus triggering movement of TM7 towards TM2 and TM3. The movement initiates rearrangement of the system of hydrogen bonds between TM2, TM3 and TM7 including formation of the hydrogen bond between the side chains of D82(2.50) in TM2 and N296(7.49) in TM7, which is crucial for formation of the activated states of the C5a receptors (Nikiforovich et al., Proteins: Struct Funct Gene 2011;79:787-802). Since the relative large length of EC3 in C5aR (13 residues) is comparable with those in many other members of rhodopsin family of GPCRs (13-19 residues), our findings might reflect general mechanisms of receptor constitutive activation. The very recent X-ray structure of the agonist-induced constitutively active mutant of rhodopsin (Standfuss et al., Nature 2011;471:656-660) is discussed in view of our modeling results.     

Interfacial adhesion properties of graphene sheet on nanoscale corrugated surface: a molecular dynamics simulation study

Adhesive contacts between graphene sheet (GS) and corrugated substrates made of an ordered array of atomic pillars with variable geometries were investigated by molecular dynamics simulations. Depending on the height and interval distance of the pillars, GS can conformably coat the surface, partially adhere, or remain flat on top of the pillars. The relationship between the geometries of the pillar and the final adhesion configurations of GS was partially established. A critical adsorption energy was determined to achieve stable adsorption configuration of GS on corrugated substrates made of ordered pillar arrays. Besides the geometries of pillars, the effects of initial coating angle of GS were also considered as an important factor that affects the final adsorption configuration. We observed two interesting morphologies of GS, ‘I shape’ and ‘L shape’, which were determined by the initial coating angles.     

重组CHO细胞C_(28)株S基因序列的测定及分析

目的测定重组CHO细胞C28株S基因序列,研究其遗传稳定性,并与已全基因序列测定的乙型肝炎病毒的S基因序列进行比较分析,预测和揭示现有疫苗株对当前疾病流行株的防病效果。方法从C28株中选取第22代、24代2、5代2、7代、28代2、9代3、0代、31代3、2代3、3代和34代细胞,根据GenBank中C基因型adr亚型乙型肝炎病毒的全基因序列设计引物。采用酚-氯仿法抽提CHO细胞基因组DNA,用PCR法扩增各代次细胞的S基因,回收700 bp左右的目的片段,克隆至pMD18-T载体上进行序列测定。利用生物学软件MEGA4.1和BioEdit进行S基因序列同源性分析,绘制系统进化树,分析与其他HBV病毒株S基因的同源性。应用实验动物测定C28株生产的重组乙型肝炎疫苗的效价。结果 C28株十一个代次之间S基因序列核苷酸和氨基酸同源性均为100%;C28株十一个代次S基因与其他病毒株S基因比较,与C基因型乙型肝炎病毒同源性最高,与其他基因型乙型肝炎病毒的核苷酸同源性达91.4%～95.1%,氨基酸同源性达84.5%～93.3%。免疫NIH小鼠结果显示5批重组乙型肝炎疫苗的效价均符合标准。结论 C28株S基因在传代及保存过程中具有较高的稳定性,对当前疾病流行株有较好的防病效果。     

基于28S rDNA D2基因序列的几种寄生夜蛾科的多胚跳小蜂的分子系统发育（英文）

本文基于28S rDNA D2部分序列, 用MP和ML方法对几种寄生夜蛾科的多胚跳小蜂Copidosoma spp.进行了系统发育研究,并对其形态和生物学关系进行了讨论。结果表明：寄生金翅夜蛾亚科(Plusiinae)的C. floridanum 和寄生实夜蛾亚科(Heliothinae)的C. primulum关系较近,而以夜蛾亚科(Noctuinae)为寄主的C. truncatellum 和 C. agrotis关系更近。结果提示核基因28S D2区可能对研究多胚跳小蜂种间的系统发育关系很有帮助。     

Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies

Abstract

Acetylcholinesterase (AChE) is an important kind of esterase that plays a key biological role in the central and peripheral nervous systems. Recent research has demonstrated that some fullerene derivatives serve as a new nanoscale class of potent inhibitors of AChE, but the specific inhibition mechanism remains unclear. In the present article, several molecular modeling methods, such as molecular docking, molecular dynamics simulations and molecular mechanics/generalized Born surface area calculations, were used for the investigation of the binding mode and inhibition mechanism of fullerene inhibitions for AChE. Results revealed that fullerene inhibitors block the entrance of substrates by binding with the peripheral anionic site (PAS) region. Thus, fullerene derivatives might mainly serve as competitive inhibitors. The interactions of a fullerene backbone with AChE are at the same level in different single side chain systems and seem to be related to the length or aromaticity of the side chain. The inhibitor with multihydroxyl side chains shows an obviously large electrostatic interaction as it forms additional hydrogen bonds with AChE. Moreover, fullerene derivatives might exhibit noncompetitive inhibition partly by affecting some secondary structures around them. Thus, the destructions of these secondary structures can lead to conformational changes in some important regions, such as the catalytic triad and acyl pocket. The investigation is of great importance to the discovery of good fullerene inhibitors.

Communicated by Ramaswamy H. Sarma     

Application of bioisosterism in design of the semicarbazone derivatives as cruzain inhibitors: a theoretical and experimental study

A series of semicarbazone, thiosemicarbazone, and aminoguanidine derivatives were synthesized and tested as antitrypanosomal agents. The theoretical NMR of the compounds was calculated using molecular modeling techniques (density functional theory (DFT) calculations) and confirmed the formation of the compounds. The ability to inhibit cruzain and Trypanosoma cruzi epimastigote replication was evaluated. Cruzain inhibition ranged between 70 and 75% (100 μM), and IC₅₀ values observed in epimastigote forms of T. cruzi ranged from 20 to 140 μM. Furthermore, the compounds did not present cytotoxicity at concentrations up to 50 and 250 μM in MTT tests. Molecular modeling studies were conducted using DFT method (B3LYP functional and the basis set 6-311G(d,p)) to understand the activity of the compounds, corroborating the observed cruzain inhibitory activity. In docking studies, the obtained analogs showed good complementarity with cruzain active site. In addition, docking results are in accordance with the susceptibility of these analogs to nucleophilic attack of the catalytic Cys25. Taken together, this study shows that this class of compounds can be used as a prototype in the identification of new antichagasic drugs.     

Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations, we investigate the preferential binding of metal ion such as Na⁺ and molecular ions such as tetramethyl ammonium (TMA⁺) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO⁺) to double-stranded DNA. The thermodynamic driving force for a particular molecular ion-DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO⁺. The ion binding processes are found to be entropically favourable. In addition, the contribution of hydrophobic effects towards the entropic stabilisation (in case of TMA⁺) and the effect of hydrogen bonding contributing to enthalpic stabilisation (in case of CHO⁺) have also been investigated.