Molecular Simulation of Chemical Reaction Equilibrium by Computationally Efficient Free Energy Minimization

Targeted pharmacokinetics and bioinformatics screening strategy reveals JAK2 as the main target for Xin-Ji-Er-Kang in treatment of MIR injury

BACKGROUND AND PURPOSE

Xin-Ji-Er-Kang (XJEK) is traditional Chinese formula presented excellent protective effects on several heart diseases, but the potential components and targets are still unclear. The aim of this study is to elucidate the effective components of XJEK and reveal its potential mechanism of cardioprotective effect in myocardial ischemia-reperfusion (MIR) injury.

EXPERIMENTAL APPROACH

Firstly, the key compounds in XJEK, plasma and heart tissue were analyzed by high resolution mass spectrometry. Bioinformatics studies were also involved to disclose the potential targets and the binding sites for the key compounds. Secondly, to study the protective effect of XJEK on MIR injury and related mechanism, mice subjected to MIR surgery and gavage administered with XJEK for 6 weeks. Cardiac function parameters and apoptosis level of cardiac tissue were assessed. The potential mechanism was further verified by knock down of target protein in vitro.

RESULTS

Pharmacokinetics studies showed that Sophora flavescens alkaloids, primarily composed with matrine, are the key component of XJEK. And, through bioinformatic analysis, we speculated JAK2 could be the potential target for XJEK, and could form stable hydrogen bonds with matrine. Administration of XJEK and matrine significantly improved heart function and reduced apoptosis of cardiomyocytes by increasing the phosphorylation of JAK2 and STAT3. The anti-apoptosis effect of XJEK and matrine was also observed on AC16 cells, and could be reversed by co-treatment with JAK2 inhibitor AG490 or knock-down of JAK2.

CONCLUSION

XJEK exerts cardioprotective effect on MIR injury, which may be associated with the activation of JAK2/STAT3 signaling pathway.

A systematic review of the molecular simulation of hybrid membranes for performance enhancements and contaminant removals

Number of research on molecular simulation and design has emerged recently but there is currently a lack of review to present these studies in an organized manner to highlight the advances and feasibility. This paper aims to review the development, structural, physical properties and separation performance of hybrid membranes using molecular simulation approach. The hybrid membranes under review include ionic liquid membrane, mixed matrix membrane, and functionalized hybrid membrane for understanding of the transport mechanism of molecules through the different structures. The understanding of molecular interactions, and alteration of pore sizes and transport channels at atomistic level post incorporation of different components in hybrid membranes posing impact to the selective transport of desired molecules are also covered. Incorporation of molecular simulation of hybrid membrane in related fields such as carbon dioxide (CO₂) removal, wastewater treatment, and desalination are also reviewed. Despite the limitations of current molecular simulation methodologies, i.e., not being able to simulate the membrane operation at the actual macroscale in processing plants, it is still able to demonstrate promising results in capturing molecule behaviours of penetrants and membranes at full atomic details with acceptable separation performance accuracy. From the review, it was found that the best performing ionic liquid membrane, mixed matrix membrane and functionalized hybrid membrane can enhance the performance of pristine membrane by 4 folds, 2.9 folds and 3.3 folds, respectively. The future prospects of molecular simulation in hybrid membranes are also presented. This review could provide understanding to the current advancement of molecular simulation approach in hybrid membranes separation. This could also provide a guideline to apply molecular simulation in the related sectors.

A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges

The incorporation of polarizability in classical force-field molecular simulations is an ongoing area of research. We focus here on its application to hydration free energy simulations of organic molecules. In contrast to computationally complex approaches involving the development of explicitly polarizable force fields, we present herein a simple methodology for incorporating polarization into such simulations using standard fixed-charge force fields, which we call the alchemically polarized charges (APolQ) method. APolQ employs a standard classical alchemical free energy change simulation to calculate the free energy difference between a fully polarized solute particle in a condensed phase and its unpolarized state in a vacuum. APolQ can in principle be applied to any microscopically homogeneous system (e.g., pure or mixed solvents). We applied APolQ to hydration free energy data for a test set of 45 neutral solute molecules in the FreeSolv database and compared results obtained using three different water models (SPC/E, TIP3P, and OPC3) and using minimal basis iterative Stockholder (MBIS) and restrained electrostatic potential (RESP) partial charge methodologies. In comparison with AM1-BCC, we found that APolQ outperforms it for the test set. Despite our method using default GAFF parameters, the MBIS partial charges yield absolute average deviations 1.5-1.9 kJ mol-1 lower than using AM1 bond charge correction (AM1-BCC). We conjecture that this method can be further improved by fitting the Lennard-Jones and torsional parameters to partial charges derived using MBIS or RESP methodologies.

Simulations of ionization equilibria in weak polyelectrolyte solutions and gels

This article recapitulates the state of the art regarding simulations of ionization equilibria of weak polyelectrolyte solutions and gels. We start out by reviewing the essential thermodynamics of ionization and show how the weak polyelectrolyte ionization differs from the ionization of simple weak acids and bases. Next, we describe simulation methods for ionization reactions, focusing on two methods: the constant-pH ensemble and the reaction ensemble. After discussing the advantages and limitations of both methods, we review the existing simulation literature. We discuss coarse-grained simulations of weak polyelectrolytes with respect to ionization equilibria, conformational properties, and the effects of salt, both in good and poor solvent conditions. This is followed by a discussion of branched star-like weak polyelectrolytes and weak polyelectrolyte gels. At the end we touch upon the interactions of weak polyelectrolytes with other polymers, surfaces, nanoparticles and proteins. Although proteins are an important class of weak polyelectrolytes, we explicitly exclude simulations of protein ionization equilibria, unless they involve protein-polyelectrolyte interactions. Finally, we try to identify gaps and open problems in the existing simulation literature, and propose challenges for future development.