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.     

Point Mutations of Nicotinic Receptor α1 Subunit Reveal New Molecular Features of G153S Slow-Channel Myasthenia

Slow-channel congenital myasthenic syndromes (SCCMSs) are rare genetic diseases caused by mutations in muscle nicotinic acetylcholine receptor (nAChR) subunits. Most of the known SCCMS-associated mutations localize at the transmembrane region near the ion pore. Only two SCCMS point mutations are at the extracellular domains near the acetylcholine binding site, α1(G153S) being one of them. In this work, a combination of molecular dynamics, targeted mutagenesis, fluorescent Ca²⁺ imaging and patch-clamp electrophysiology has been applied to G153S mutant muscle nAChR to investigate the role of hydrogen bonds formed by Ser 153 with C-loop residues near the acetylcholine-binding site. Introduction of L199T mutation to the C-loop in the vicinity of Ser 153 changed hydrogen bonds distribution, decreased acetylcholine potency (EC₅₀ 2607 vs. 146 nM) of the double mutant and decay kinetics of acetylcholine-evoked cytoplasmic Ca²⁺ rise (τ 14.2 ± 0.3 vs. 34.0 ± 0.4 s). These results shed light on molecular mechanisms of nAChR activation-desensitization and on the involvement of such mechanisms in channelopathy genesis.     

Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone–Wales Defects as Drug Carriers: A Molecular Dynamics Approach

Doxorubicin (DOX), a recognized anticancer drug, forms stable associations with carbon nanotubes (CNTs). CNTs when properly functionalized have the ability to anchor directly in cancerous tumors where the release of the drug occurs thanks to the tumor slightly acidic pH. Herein, we study the armchair and zigzag CNTs with Stone–Wales (SW) defects to rank their ability to encapsulate DOX by determining the DOX-CNT binding free energies using the MM/PBSA and MM/GBSA methods implemented in AMBER16. We investigate also the chiral CNTs with haeckelite defects. Each haeckelite defect consists of a pair of square and octagonal rings. The armchair and zigzag CNT with SW defects and chiral nanotubes with haeckelite defects predict DOX-CNT interactions that depend on the length of the nanotube, the number of present defects and nitrogen doping. Chiral nanotubes having two haeckelite defects reveal a clear dependence on the nitrogen content with DOX-CNT interaction forces decreasing in the order 0N > 4N > 8N. These results contribute to a further understanding of drug-nanotube interactions and to the design of new drug delivery systems based on CNTs.     

Comparative study on transport properties of N-, P-, and As-doped SiC nanowires: Calculated based on first principles

According to the one-dimensional quantum state distribution, carrier scattering, and fixed range hopping model, the structural stability and electron transport properties of N-, P-, and As-doped SiC nanowires(N-SiCNWs, P-SiCNWs, and As-SiCNWs) are simulated by using the first principles calculations. The results show that the lattice structure of NSiCNWs is the most stable in the lattice structures of the above three kinds of doped SiCNWs. At room temperature,for unpassivated SiCNWs, the doping effect of P and As are better than that of N. After passivation, the conductivities of all doped SiCNWs increase by approximately two orders of magnitude. The N-SiCNW has the lowest conductivity. In addition, the N-, P-, As-doped SiCNWs before and after passivation have the same conductivity–temperature characteristics,that is, above room temperature, the conductivity values of the doped SiCNWs all increase with temperature increasing.These results contribute to the electronic application of nanodevices.     

Experimental and Theoretical Mechanistic Study on the Thermal Decomposition of 3,3-diphenyl-4-(trichloromethyl)-5-nitropyrazoline

The present paper is a continuation of comprehensive study regarding to synthesis and properties of pyrazoles and their derivatives. In its framework an experimental and theoretical studies of thermal decomposition of the 3,3-diphenyl-4-(trichloromethyl)-5-nitropyrazoline were performed. It was found, that the decompositions of the mentioned pyrazoline system in the solution and at the melted state proceed via completely different molecular mechanisms. These mechanisms have been explained in the framework of the Molecular Electron Density Theory (MEDT) with the computational level of B3LYP/6-31G(d). A Bonding Evolution Theory (BET) examination of dehydrochlorination of the 3,3-diphenyl-4-(trichloromethyl)-5-nitropyrazoline permits elucidation of the molecular mechanism. It was found, that on the contrary for most known HCl extrusion processes in solution, this reaction is realised via single-step mechanism.     

A new study of associating inhomogeneous fluids with classical density functional theory

ABSTRACT

A new density functional for the study of associating inhomogeneous fluids based on Wertheim's first-order thermodynamic perturbation theory is presented and compared to the most currently used associating density functionals. This functional is developed using the weighted density approximation in the range of association of hard spheres. We implement this functional within the framework of classical density functional theory together with modified fundamental measure theory to account for volume exclusion of hard spheres. This approach is tested against molecular simulations from literature of pure associating hard spheres and mixtures of non-associationg and associating hard spheres with different number of bonding sites close to a hard uniform wall. Furthermore, we compare and review our results with the performance of associating functionals from literature, one based on fundamental measure theory and the inhomogeneous version of Wertheim's perturbation theory. Results obtained with classical DFT and the three functionals show excellent agreement with molecular simulations in systems with one hard wall. For the cases of small pores where only one or two layers of fluid are allowed discrepancies between results with classical DFT and molecular simulations were found.     

基于时变Copula模型的 基金收益率相依关系的应用研究

基于时变Copula模型,获得预测方差,确定单个基金收益率序列的边缘分布.利用常见的静态Copula和时变Copula模型对基金收益率序列间两两相依关系进行建模并进行对比分析.应用研究表明,基于MCMC方法的时变Copula模型能更有效地度量基金收益率序列的风险.     

Pentapnictogen heterocyclic monoanions: Structure,stability, and aromaticity

Inorganic planar ring-shape molecules with 4n + 2 π electrons are always the focus of experimental synthesis and theoretical research due to their potential aromaticity and stability. In this work, the whole series of five-membered heterocycle monoanions X _nY_5-n⁻ (X, Y = group 15 elements; n = 1-4) were thoroughly investigated by means of density functional theory calculations. They all have large formation energies and HOMO-LUMO gap energies, suggesting the potential thermodynamic and kinetic stability. Their aromaticities are comparable to that of typical aromatic hydrocarbons. Their thermal stabilities were firmly established by the ab initio molecular dynamics simulations. As most of them are predicted for the first time, their various spectra were simulated for experimental characterization. Furthermore, we demonstrate that these five-membered cyclic anions can be employed as η⁵-ligand to construct novel all-inorganic metallocenes, which may serve as the building blocks of low-dimensional nanomaterials.     

Rational Molecular Design towards Vis/NIR Absorption and Fluorescence by using Pyrrolopyrrole aza‐BODIPY and its Highly Conjugated Structures for Organic Photovoltaics

Pyrrolopyrrole aza‐BODIPY (PPAB) developed in our recent study from diketopyrrolopyrrole by titanium tetrachloride‐mediated Schiff‐base formation reaction with heteroaromatic amines is a highly potential chromophore due to its intense absorption and fluorescence in the visible region and high fluorescence quantum yield, which is greater than 0.8. To control the absorption and fluorescence of PPAB, particularly in the near‐infrared (NIR) region, further molecular design was performed using DFT calculations. This results in the postulation that the HOMO–LUMO gap of PPAB is perturbed by the heteroaromatic moieties and the aryl‐substituents. Based on this molecular design, a series of new PPAB molecules was synthesized, in which the largest redshifts of the absorption and fluorescence maxima up to 803 and 850 nm, respectively, were achieved for a PPAB consisting of benzothiazole rings and terthienyl substituents. In contrast to the sharp absorption of PPAB, a PPAB dimer, which was prepared by a cross‐coupling reaction of PPAB monomers, exhibited panchromatic absorption across the UV/Vis/NIR regions. With this series of PPAB chromophores in hand, a potential application of PPAB as an optoelectronic material was investigated. After identifying a suitable PPAB molecule for application in organic photovoltaic cells based on evaluation using time‐resolved microwave conductivity measurements, a maximized power conversion efficiency of 1.27 % was achieved.