Molecular Dynamics Study of N-Dodecyl-N,N-Dimethyl-3-Ammonio-1-Propanesulfonate Mono-Layer Adsorbed at the Air/Water Interface

Molecular dynamics (MD) simulation has been carried out to investigate the properties of a mono-layer of N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (SB12-3) adsorbed at the air/water interface. The simulation results show that SB12-3 can form a closely packed mono-layer at the air/water interface, the anionic sulfonic groups of the hydrophilic head group have stronger interactions with the water molecules by comparison with the cationic quaternary nitrogen of the hydrophilic head group, and water molecules can gather more easily and aggregate around the sulfonic groups. With the addition of the Ca²⁺ ions, the number of hydrogen bonds between the SB12-3 surfactant molecules and water molecules remains almost unchanged, which may explain the salt resistance behavior for SB12-3 especially for di-valent ions. The hydrophobic tail in SB12-3 is more ordered in the beginning of the chain.     

Design,Synthesis, Biological Evaluation,and Molecular Modeling of 2-Difluoromethylbenzimidazole Derivatives as Potential PI3Kα Inhibitors

PI3Kα is one of the potential targets for novel anticancer drugs. In this study, a series of 2-difluoromethylbenzimidazole derivatives were studied based on the combination of molecular modeling techniques 3D-QSAR, molecular docking, and molecular dynamics. The results showed that the best comparative molecular field analysis (CoMFA) model had q² = 0.797 and r² = 0.996 and the best comparative molecular similarity indices analysis (CoMSIA) model had q² = 0.567 and r² = 0.960. It was indicated that these 3D-QSAR models have good verification and excellent prediction capabilities. The binding mode of the compound 29 and 4YKN was explored using molecular docking and a molecular dynamics simulation. Ultimately, five new PI3Kα inhibitors were designed and screened by these models. Then, two of them (86, 87) were selected to be synthesized and biologically evaluated, with a satisfying result (22.8 nM for 86 and 33.6 nM for 87).     

On the interaction of bovine serum albumin with ionic surfactants: temperature induced EPR changes of a maleimide nitroxide reflect local protein dynamics and probe solvent accessibility

The interaction of bovine serum albumin (BSA) with the ionic surfactants sodium dodecylsulfate (SDS, anionic), cetyltrimethylammonium chloride (CTAC, cationic) and N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS, zwitterionic) was studied by electron paramagnetic resonance (EPR) spectroscopy of spin label covalently bound to the single free thiol group of the protein. EPR spectra simulation allows to monitor the protein dynamics at the labeling site and to estimate the changes in standard Gibbs free energy, enthalpy and entropy for transferring the nitroxide side chain from the more motionally restricted to the less restricted component. Whereas SDS and CTAC showed similar increases in the dynamics of the protein backbone for all measured concentrations, HPS presented a smaller effect at concentrations above 1.5mM. At 10mM of surfactants and 0.15 mM BSA, the standard Gibbs free energy change was consistent with protein backbone conformations more expanded and exposed to the solvent as compared to the native protein, but with a less pronounced effect for HPS. In the presence of the surfactants, the enthalpy change, related to the energy required to dissociate the nitroxide side chain from the protein, was greater, suggesting a lower water activity. The nitroxide side chain also detected a higher viscosity environment in the vicinity of the paramagnetic probe induced by the addition of the surfactants. The results suggest that the surfactant-BSA interaction, at higher surfactant concentration, is affected by the affinities of the surfactant to its own micelles and micelle-like aggregates. Complementary DLS data suggests that the temperature induced changes monitored by the nitroxide probe reflects local changes in the vicinity of the single thiol group of Cys-34 BSA residue.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

DCN1-UBE2M相互作用抑制剂的3D-QSAR、分子对接和分子动力学研究

类泛素化是一种蛋白质翻译后修饰,其异常会导致神经退行性疾病和多种肿瘤的发生,因此它被视为有希望的抗肿瘤靶标.研究表明,抑制DCN1-UBE2M相互作用可选择性阻遏类泛素化.本文基于哌啶基脲类DCN1-UBE2M相互作用抑制剂进行3D-QSAR、分子对接和分子动力学模拟研究.利用3D-QSAR中的CoMFA和CoMSIA...     

Molecular dynamics simulation on HP1 protein binding by histone H3 tail methylation and phosphorylation

Trimethylation of histone H3 lysine 9 is important for recruiting heterochromatin protein 1 (HP1) to discrete regions of the genome, thereby regulating gene expression, chromatin packaging, and heterochromatin formation. Phosphorylation of histone H3 has been linked with mitotic chromatin condensation. During mitosis in vivo, H3 lysine 9 methylation and serine 10 phosphorylation can occur concomitantly on the same histone tail, whereas the influence of phosphorylation to trimethylation H3 tail recruiting HP1 remains controversial. In this work, molecular dynamics simulation of HP1 complexed with both trimethylated and phosphorylated H3 tail were performed and compared with the results from the previous methylated H3‐HP1 trajectory. It is clear from the 10‐ns dynamics simulation that two adjacent posttranslational modifications directly increase the flexibility of the H3 tail and weaken HP1 binding to chromatin. A combinatorial readout of two adjacent posttranslational modifications—a stable methylation and a dynamic phosphorylation mark—establish a regulatory mechanism of protein–protein interactions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Molecular dynamics simulation of organic glass formers: I. ortho-terphenyl and 1,3,5-tri-α-naphthyl benzene

A computer code was prepared for the molecular dynamics (MD) simulation of a multimolecular system to atomic resolution. Based on a widely accepted force field and aided by simulated annealing of single molecules, and were computed for ortho-terphenyl and 1,3,5-tri-α-naphthyl benzene across an extended range of temperatures. Although neither the simulation time (40–100 ps) nor the system size (27 and 64 molecules) appeared to affect the computational results to an appreciable extent, it was clear that a longer simulation time or a larger system tended to yield a more consistent set of data. In comparison to experimental observations, simulation was capable of representing to within 2–7%, T_g to within 10 K, and ΔC_p across T_g to within 10%. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 86–93, 1998     

Molecular structure of 1-phenyl-2-trifluoromethyl-3-benzoylaziridine

1-Phenyl-2-trifluoromethyl-3-benzoylaziridine has been studied by X-ray structural analysis. Protons of the aziridine cycle are intrans positions. The C(1)-N(1) bond is the shortest of the corresponding bonds in aziridine derivatives, which have been studied by X-ray structural analysis previously.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1975–1977, October, 1995.     

The Chemistry of Tetrafluoroallene： One－pot Synthesis of Trifluoromethylindolizines from 1,3－Diiodo－1,1,3,3－tetrafluoropropane by 1,3－Dipolar Cycloaddition

Heating a mixture of 1, 3-diiodo-1, 1, 3, 3-tetrafluoropropane (2), K2CO3, pyridinium bromides (3) in CH3CN at 65℃ for 10 h gives the corresponding trifluoromethylindolizines.     

Interaction of giant extracellular Glossoscolex paulistus hemoglobin (HbGp) with zwitterionic surfactant N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS): effects of oligomeric dissociation

The present work focuses on the interaction between the zwitterionic surfactant N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS) and the giant extracellular hemoglobin of Glossoscolex paulistus (HbGp). Electronic optical absorption, fluorescence emission and circular dichroism spectroscopy techniques, together with Gel-filtration chromatography, were used in order to evaluate the oligomeric dissociation as well as the autoxidation of HbGp as a function of the interaction with HPS. A peculiar behavior was observed for the HPS–HbGp interaction: a complex ferric species formation equilibrium was promoted, as a consequence of the autoxidation and oligomeric dissociation processes. At pH 7.0, HPS is more effective up to 1 mM while at pH 9.0 the surfactant effect is more intense above 1 mM. Furthermore, the interaction of HPS with HbGp was clearly less intense than the interaction of this hemoglobin with cationic (CTAC) and anionic (SDS) surfactants. Probably, this lower interaction with HPS is due to two factors: (i) the lower electrostatic attraction between the HPS surfactant and the protein surface ionic sites when compared to the electrostatic interaction between HbGp and cationic and anionic surfactants, and (ii) the low cmc of HPS, which probably reduces the interaction of the surfactant in the monomeric form with the protein. The present work emphasizes the importance of the electrostatic contribution in the interaction between ionic surfactants and HbGp. Furthermore, in the whole HPS concentration range used in this study, no folding and autoxidation decrease induced by this surfactant were observed. This is quite different from the literature data on the interaction between surfactants and tetrameric hemoglobins, that supports the occurrence of this behavior for the intracellular hemoglobins at low surfactant concentration range. Spectroscopic data are discussed and compared with the literature in order to improve the understanding of hemoglobin–surfactant interaction as well as the acid isoelectric point (pI) influence of the giant extracellular hemoglobins on their structure–activity relationship.     

The easy hydrolysis of hexacyanocyclopropane, ethyl 1,2,2,3,3-pentacyanocyclopropane-1-carboxylate, 1,2,2,3,3-pentacyanocyclopropane-1-carboxamide, andN,N-dimethyl-1,2,2,3,3-pentacyanocyclopropane-1-carboxamide tor-1,c-2,c-3-tricyanocyclopropane-t-carboxamide

Hydrolysis of hexacyanocyclopropane (1a), ethyl 1,2,2,3,3-pentacyanocyclopropane-1-carboxylate (1b), 1,2,2,3,3-pentacyanocylopropane-1-carboxamide (1c), andN,N-dimethyl-1,2,2,3,3-pentacyanocylopropane-1-carboxamide (1d) in 95% acetic acid yieldsr-1,c-2,c-3-tricyanocyclopropane-t-1-carboxamide (3). The structure of3 was proved by X-ray diffraction analysis. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 454–456, March, 1998.     

Theoretical study on cation-anion interaction and vibrational spectra of 1-allyl-3-methylimidazolium-based ionic liquids

In order to deepen the understanding of the cation-anion interaction in ionic liquids, the structures of cation, anions, and cation-anion ion-pairs of 1-allyl-3-methylimidazolium-based ionic liquids are optimized using density functional theory (DFT), and their most stable geometries are discussed. The structural parameters, hydrogen bonds and interaction energies of 1-allyl-3-methylimidazolium dicyanamide ([Amim]DCA), 1-allyl-3-methylimidazolium chloride ([Amim]Cl), 1-allyl-3-methylimidazolium formate ([Amim]FmO) and 1-allyl-3-methylimidazolium acetate ([Amim]AcO) ion pairs are studied. The vibrational frequencies of [Amim]DCA and [Amim]Cl have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes.     

Binding free energy of several sterols to the N-terminal domain of Niemann-Pick C1-like 1 protein due to mutation: Molecular dynamics study

The membrane protein Niemann-Pick type C1-like 1 (NPC1L1) plays a central role in the absorption of cholesterol in the small intestine. Other sterols, notably vitamin E and vitamin K1 also utilize NPC1L1 as a membrane transporter even though other absorption paths exist. Many NPC1L1 mutations causing the disease due to poor transport of cholesterol are known. It is not clear at this moment if the same mutation can lead to reduced transport behavior with these vitamins. In this study, we have obtained the binding free energies of these two sterols using molecular dynamics simulation and compared these values with the cholesterol-binding free energy. The N-terminal domain (NTD) of the wild as well as the disease-causing two mutations, T61M and L110F, are used for this purpose. The result indicates that the mutations show reduced binding affinity compared to the wild except for the vitamin K1 in the T61M mutant, which has increased binding free energy. Also, we found the similarity of the key amino acids responsible for the change of free energy by mutation between T61M and L110F. At the same time, non-negligible differences exist also.     

Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B_1–282-allosteric inhibitor complex crystal structure lacks α7 (287–298) and moreover there is no available 3D structure of PTP1B_1–298 in open form. As the interaction between α7 and α6–α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B_1–282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7–α6–α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular dynamics study on lattice defects and heat capacity of LiCr1/6Mn11/6O4-d

Heat capacity of spinel LiCr_1/6Mn_11/6O_4-d (d=0, 0.0184)was measured between 5 and 300 K. Both compounds showed no anomaly in the measured temperature range, especially around the room temperature where a structural phase transition is reported for the parent compound LiMn₂O₄. The non-stoichiometric compound LiCr_1/6Mn_11/6O_3.9816 has greater heat capacity than that of the stoichiometric LiCr_1/6Mn_11/6O₄. Molecular dynamics study on the vibrational property of LiMn₂O_4-d revealed that the lattice defects in the non-stoichiometric compound increase the low frequency phonons compared with the stoichiometric compound. It should be related to the greater heat capacity of the non-stoichiometric compound LiCr_1/6Mn_11/6O_3.9816. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular dynamics simulations of aggregation behavior of sodium dodecyl sulfate on SiO2 and CaCO3 surfaces

Molecular dynamics simulations were carried out to investigate the aggregation behavior of anionic surfactant sodium dodecyl sulfate (SDS) on the surfaces of SiO₂ and CaCO₃. The results indicate that SDS molecules formed a spherical micelle structure near the SiO₂ surface; moreover, there were more head groups near the SiO₂ surface. However, they could form a self‐assemble film on the CaCO₃ surface. The self‐assemble film of SDS on the CaCO₃ surface was more stable than that on the SiO₂ surface. Our simulation results have a certain significance to understand the aggregation behavior of SDS on different surfaces on molecular level.     

HIV-1逆转录酶抑制剂的3D-QSAR研究及分子设计

采用Topomer Co MFA方法对24个二芳基苯胺衍生物进行三维定量构效关系研究,建立了3DQSAR模型,所得优化模型的非交叉相关系数、交互验证系数以及外部验证的复相关系数分别为0.928,0.654和0.940,结果表明该模型具有良好的稳定性和预测能力。采用分子对接技术对药物与受体的作用机制进行了研究,结果显示,药物与HIV-1逆转录酶的LYS172,GLU138,LYS101等位点作用明显。运用这些信息进行分子设计,在理论上获得了一些具有较高活性的新的二芳基苯胺类抗艾滋病药物,该QSAR的研究结果可为新药合成提供理论参考。     

Molecular dynamics simulation of poly(3‐hexylthiophene) helical structure In Vacuo and in amorphous polymer surrounding

The stability of poly(3‐hexylthiophene) (P3HT) helical structure has been investigated in vacuo and in amorphous polymer surrounding via molecular dynamics‐based simulations at temperatures below and above the P3HT melting point. The results show that the helical chain remains stable at room temperature both in vacuo and in amorphous surrounding, and promptly loses its structure at elevated temperatures. However, the amorphous surrounding inhibits the destruction of the helix at higher temperatures. In addition, it is shown that the electrostatic interactions do not significantly affect the stability of the helical structure. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2448–2456