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.     

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.     

Recent Progress in the $L_p$ Theory for Elliptic and Parabolic Equations with Discontinuous Coefficients

In this paper, we review some results over the last 10-15 years on elliptic and parabolic equations with discontinuous coefficients. We begin with an approach given by N. V. Krylov to parabolic equations in the whole space with $\rm{VMO}_x$ coefficients. We then discuss some subsequent development including elliptic and parabolic equations with coefficients which are allowed to be merely measurable in one or two space directions, weighted $L_p$estimates with Muckenhoupt ($A_p$) weights, non-local elliptic and parabolic equations, as well as fully nonlinear elliptic and parabolic equations.     

Cycloparaphenylene (CPP) series are molecular models for graphene armchair edges: trends in their aromaticity and cyclic conjugation are evaluated

Cycloparaphenylene ([r]CPP) and cyclacene ([r]CA) series are models for short carbon nanotubes. It is shown that armchair edges in model cycloparaphenylenes possess greater aromaticity and cyclic conjugation than do zigzag edges in model cyclacenes. According to Aihara’s bond resonance energy (BRE) and Bosanac and Gutman energy effect (ef) measurements, cycloparaphenylenes are twice as aromatic as cyclacenes. The general solution of all eigenvalues of all members of the cycloparaphenylene series is given. The origin of the recurrence of some eigenvalues are determined.     

Gas-phase 21Ne NMR studies and the nuclear magnetic dipole moment of neon-21

Gas-phase ²¹Ne nuclear magnetic resonance spectra were measured at the natural abundance of ²¹Ne isotope for samples consisting of pressurized neon up to 60 bar at room temperature and applying the magnetic field of the strength B₀ = 11.7574 T. It showed that the nuclear magnetic resonance frequency is linearly dependent on the density of gaseous neon. The resonance frequency was extrapolated to the zero-density point, and it permitted the determination of the ²¹Ne nuclear magnetic moment, μ(²¹Ne) = 0.6617774(10) μ_N. The present value of μ(²¹Ne) is not influenced by the bulk magnetic susceptibility of neon and interactions between neon atoms; therefore, it is more precise and reliable than the previous result obtained for μ(²¹Ne).     

PtII-Catalyzed Hydroxylation of Terminal Aliphatic C(sp3)−H Bonds with Molecular Oxygen

The practical application of Shilov-type Pt catalysis to the selective hydroxylation of terminal aliphatic C−H bonds remains a formidable challenge, due to difficulties in replacing Pt^IV with a more economically viable oxidant, particularly O₂. We report the potential of employing FeCl₂ as a suitable redox mediator to overcome the kinetic hurdles related to the direct use of O₂ in the Pt reoxidation. For the selective conversion of butyric acid to γ-hydroxybutyric acid (GHB), a significantly enhanced catalyst activity and stability (turnover numbers (TON)>30) were achieved under 20 bar O₂ in comparison to current state-of-the-art systems (TON<10). In this regard, essential reaction parameters affecting the overall activity were identified, along with specific additives to attain catalyst stability at longer reaction times. Notably, deactivation by reduction to Pt⁰ was prevented by the addition of monodentate pyridine derivatives, such as 2-fluoropyridine, but also by introducing varying partial pressures of N₂ in the gaseous atmosphere. Finally, stability tests revealed the involvement of Pt^II and FeCl₂ in catalyzing the non-selective overoxidation of GHB. Accordingly, in situ esterification with boric acid proved to be a suitable strategy to maintain enhanced selectivities at much higher conversions (TON>60). Altogether, a useful catalytic system for the selective hydroxylation of primary aliphatic C−H bonds with O₂ is presented.