Comparative Modelling of Organic Anion Transporting Polypeptides: Structural Insights and Comparison of Binding Modes

To better understand the functionality of organic anion transporting polypeptides (OATPs) and to design new ligands, reliable structural data of each OATP is needed. In this work, we used a combination of homology model with molecular dynamics simulations to generate a comprehensive structural dataset, that encompasses a diverse set of OATPs but also their relevant conformations. Our OATP models share a conserved transmembrane helix folding harbouring a druggable binding pocket in the shape of an inner pore. Our simulations suggest that the conserved salt bridges at the extracellular region between residues on TM1 and TM7 might influence the entrance of substrates. Interactions between residues on TM1 and TM4 within OATP1 family shown their importance in transport of substrates. Additionally, in transmembrane (TM) 1/2, a known conserved element, interact with two identified motifs in the TM7 and TM11. Our simulations suggest that TM1/2-TM7 interaction influence the inner pocket accessibility, while TM1/2-TM11 salt bridges control the substrate binding stability.     

Excited-State Dynamics of Proflavine after Intercalation into DNA Duplex

Proflavine is an acridine derivative which was discovered as one of the earliest antibacterial agents, and it has been proven to have potential application to fields such as chemotherapy, photobiology and solar-energy conversion. In particular, it is well known that proflavine can bind to DNA with different modes, and this may open addition photochemical-reaction channels in DNA. Herein, the excited-state dynamics of proflavine after intercalation into DNA duplex is studied using femtosecond time-resolved spectroscopy, and compared with that in solution. It is demonstrated that both fluorescence and the triplet excited-state generation of proflavine were quenched after intercalation into DNA, due to ultrafast non-radiative channels. A static-quenching mechanism was identified for the proflavine-DNA complex, in line with the spectroscopy data, and the excited-state deactivation mechanism was proposed.     

Design Two Novel Tetrahydroquinoline Derivatives against Anticancer Target LSD1 with 3D-QSAR Model and Molecular Simulation

Lysine-specific demethylase 1 (LSD1) is a histone-modifying enzyme, which is a significant target for anticancer drug research. In this work, 40 reported tetrahydroquinoline-derivative inhibitors targeting LSD1 were studied to establish the three-dimensional quantitative structure–activity relationship (3D-QSAR). The established models CoMFA (Comparative Molecular Field Analysis (q² = 0.778, Rpred2 = 0.709)) and CoMSIA (Comparative Molecular Similarity Index Analysis (q² = 0.764, Rpred2 = 0.713)) yielded good statistical and predictive properties. Based on the corresponding contour maps, seven novel tetrahydroquinoline derivatives were designed. For more information, three of the compounds (D1, D4, and Z17) and the template molecule 18x were explored with molecular dynamics simulations, binding free energy calculations by MM/PBSA method as well as the ADME (absorption, distribution, metabolism, and excretion) prediction. The results suggested that D1, D4, and Z17 performed better than template molecule 18x due to the introduction of the amino and hydrophobic groups, especially for the D1 and D4, which will provide guidance for the design of LSD1 inhibitors.     

The Anisotropic Chemical Reaction Mechanism of 1,3,3-trinitroazetidine (TNAZ) under Different Shock Wave Directions by ReaxFF Reactive Molecular Dynamics Simulations

1,3,3-Trinitroazetidine (TNAZ) has good thermal stability and low shock sensitivity, among other properties, and it has broad prospects in insensitive ammunition applications. In this study, a molecular dynamics calculation based on the ReaxFF-lg force field and multiscale shock technique (MSST) was used to simulate the shock-induced chemical reaction of TNAZ with different shock wave directions. The results showed that the shock sensitivity of TNAZ was in the order of [100] > [010] > [001]. There were significant differences in molecular arrangements in different shock directions, which affected the reaction rate and reaction path in different directions. The molecular arrangement in the [010] and [001] directions formed a “buffer” effect. The formation and cleavage of bonds, formation of small molecules and growth of clusters were analyzed to show the effect of the “buffer”. The polymerization reactions in the [010] and [001] directions appeared later than that in the [100] direction, and the cluster growth in the [010] and [001] directions was slower than that in the [100] direction. In different shock loading directions, the formation and cleavage mechanisms of the N-O bonds of the TNAZ molecules were different, which resulted in differences in the initial reaction path and reaction rate in the three directions     

硅晶体生长固液界面形貌研究

结合杰克逊界面理论、分子动力学模拟(MD)和密度泛函理论(DFT),对硅晶体(100)和(111)面生长过程中固液界面形貌进行研究,包括界面自由能变化、结构变化和生长位置吸附能等。通过杰克逊界面理论计算,发现(100)界面晶相原子和流体相原子在表面各占约50%时吉布斯自由能达到极小值,而(111)界面在表面占比约0%或100%时达到极小值,说明当热力学平衡时,(100)面趋向于粗糙面,(111)面趋向于光滑面;分子动力学模拟显示,随着生长的进行,初始光滑的固液界面在(100)面上会逐渐转变为粗糙界面,而(111)面则始终保持光滑界面生长;且在生长过程中,(100)面的生长速率明显高于(111)面,因为(100)面始终为粗糙面生长;DFT计算发现,(100)面上的所有生长位置吸附能接近,可以实现连续生长,(111)面吸附能则存在明显的差值,生长原子需要吸附在台阶处才能进行层状生长。     

Influence of temperature and alloying elements on the threshold displacement energies in concentrated Ni–Fe–Cr alloys

Concentrated solid-solution alloys(CSAs) have demonstrated promising irradiation resistance depending on their compositions. Under irradiation, various defects can be produced. One of the most important parameters characterizing the defect production and the resulting defect number is the threshold displacement energies(E_d). In this work, we report the results of E_dvalues in a series of Ni–Fe–Cr concentrated solid solution alloys through molecular dynamics(MD)simulations. Based on several different empirical potentials, we show that the differences in the E_dvalues and its angular dependence are mainly due to the stiffness of the potential in the intermediate regime. The influences of different alloying elements and temperatures on E_dvalues in different CSAs are further evaluated by calculating the defect production probabilities. Our results suggest a limited influence of alloying elements and temperature on E_dvalues in concentrated alloys. Finally, we discuss the relationship between the primary damage and E_dvalues in different alloys. Overall, this work presents a thorough study on the E_dvalues in concentrated alloys, including the influence of empirical potentials,their angular dependence, temperature dependence, and effects on primary defect production.     

Atomistic insights into the selective therapeutic activity of 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a]pyrazin-1(2H)-one towards bromodomain-containing proteins

Cross-target effect has been one of the major mechanisms of drug toxicity, this has necessitated the design of inhibitors that are specifically tailored to target particular biomolecules. 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a] pyrazin-1(2H)-one (Cpd38) is an inhibitor possessing high inhibition rate and tailored specificity towards bromodomain-containing protein 4 (BRD4). In this research, we used an array of computational techniques to provide insight at the atomistic level the specific targeting of BRD4 by Cpd38 relative to the binding of Cpd38 with E1A binding protein P300 (EP300); another bromodomain-containing protein (BCP). Comparatively, binding of Cpd38 improved the conformational stability and compactness of BRD4 protein when compared to the Cpd38 bound EP300. Also, Cpd38 induced a conformational change in the active site of BRD4 that facilitated a complementary pose between Cpd38 and BRD4 suitable for effective atomistic interactions. Expectedly, thermodynamic calculations revealed that the Cpd38-BRD4 system had higher binding energy (−36.11 Kcal/mol) than the Cpd38-EP300 system with a free binding energy of −15.86 Kcal/mol. Noteworthy is the opposing role Trp81 (acting as hydrogen bond acceptor) and Pro1074 (acting as hydrogen bond donor) found on the WPF and LPF loops respectively play in maintaining Cpd38 stability. Furthermore, the hydrogen bond acceptor/donator ratio was approximately 4:1 in Cpd38-BRD4 system compared with 2:1 in Cpd38-EP300 system. Taken together, atomistic insights and structural perspectives detailed in this report supplements the experimental report supporting the improved selectivity of Cpd38 for BRD4 ahead of other BCPs while providing leeway for the future design of BET selective agents with better pharmacological profile.     

Time evolution of the solvated and conformationally relaxed emissive excited state of the anionic form of salophen,a Schiff base

Salophen is a weakly fluorescent Schiff base which forms emissive co-ordination complexes with Zn²⁺ and Al³⁺. The complex with Al³⁺ is significantly more fluorescent than that with Zn²⁺, presumably because the dimeric complex with Zn²⁺ is associated with additional nonradiative channels. This contention has been put to test, through a careful investigation of excited state dynamics of the anionic form of salophen (Sal²⁻), which is the form in which the ligand exists in the complexes. The emissive excited state of the anion (Sal²⁻) has been found to be solvated and conformationally relaxed, over tens of picosecond. It is significantly more fluorescent than the neutral compound, with fluorescence lifetime that is longer by almost two orders of magnitude. Fluorescence lifetime of the anion is in fact longer than that of the complex with Zn²⁺ and slightly less than that of the complex with Al³⁺. So, the earlier hypothesis about additional nonradiative deactivation pathways in the Zn²⁺ complex gains credence from the present study.     

基于逆动力学分析的路面不平度测试研究

通过分析一个简化的履带车辆单扭力轴-负重轮力学模型,建立了扭力轴扭转角与路面不平度的联系方程,基于该方程可以由路面不平度求出扭力轴扭转角,如已知扭转角则可以通过逆动力学分析得到路面不平度. 数值算例结合ADAMS仿真结果验证了该方法用于路面不平度测试的可行性.     

铜、银及铂原子纳米团簇熔点随尺寸非单调变化的分子动力学模拟研究

采用分子动力学方法和原子嵌入法模型势模拟了铜原子、银原子及铂原子纳米团簇的熔化过程,研究了这些金属原子纳米团簇熔点与团簇尺寸的关系,发现各自在小于一定数目原子的金属纳米团簇的熔点不再随尺寸的变小而单调下降,通过对各种团簇溶化前后结构的比较研究,分析了导致这种现象的原因。