Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane

The emergence of machine learning force fields in drug design

In the field of molecular simulation for drug design, traditional molecular mechanic force fields and quantum chemical theories have been instrumental but limited in terms of scalability and computational efficiency. To overcome these limitations, machine learning force fields (MLFFs) have emerged as a powerful tool capable of balancing accuracy with efficiency. MLFFs rely on the relationship between molecular structures and potential energy, bypassing the need for a preconceived notion of interaction representations. Their accuracy depends on the machine learning models used, and the quality and volume of training data sets. With recent advances in equivariant neural networks and high-quality datasets, MLFFs have significantly improved their performance. This review explores MLFFs, emphasizing their potential in drug design. It elucidates MLFF principles, provides development and validation guidelines, and highlights successful MLFF implementations. It also addresses potential challenges in developing and applying MLFFs. The review concludes by illuminating the path ahead for MLFFs, outlining the challenges to be overcome and the opportunities to be harnessed. This inspires researchers to embrace MLFFs in their investigations as a new tool to perform molecular simulations in drug design.

Is IIIG9 a New Protein with Exclusive Ciliary Function? Analysis of Its Potential Role in Cancer and Other Pathologies

The identification of new proteins that regulate the function of one of the main cellular phosphatases, protein phosphatase 1 (PP1), is essential to find possible pharmacological targets to alter phosphatase function in various cellular processes, including the initiation and development of multiple diseases. IIIG9 is a regulatory subunit of PP1 initially identified in highly polarized ciliated cells. In addition to its ciliary location in ependymal cells, we recently showed that IIIG9 has extraciliary functions that regulate the integrity of adherens junctions. In this review, we perform a detailed analysis of the expression, localization, and function of IIIG9 in adult and developing normal brains. In addition, we provide a 3D model of IIIG9 protein structure for the first time, verifying that the classic structural and conformational characteristics of the PP1 regulatory subunits are maintained. Our review is especially focused on finding evidence linking IIIG9 dysfunction with the course of some pathologies, such as ciliopathies, drug dependence, diseases based on neurological development, and the development of specific high-malignancy and -frequency brain tumors in the pediatric population. Finally, we propose that IIIG9 is a relevant regulator of PP1 function in physiological and pathological processes in the CNS.

Molecular Dynamics Simulation Studies on Structure, Dynamics, and Thermodynamics of Uranyl Nitrate Solution at Various Acid Concentrations

The structural and dynamical characteristics of uranyl ions in an aqueous acidic environment are of immense importance in the field of nuclear fuel reprocessing. In view of that, the structural and dynamical behavior of the uranyl ion in water has been investigated by performing molecular dynamics (MD) simulations using different force fields. All the force fields have depicted similar structural and dynamical properties except the free energy of hydration where the Guilbaud-Wipff (GW) model performs well over the others. The calculated density using MD simulations is found to be in excellent agreement with the measured experimental density, which ensures the accuracy of the adopted GW force field. The calculated surface tension and shear viscosity are seen to be increased with uranyl nitrate concentrations. At a higher concentration of about 4.0 mol/L, the supersaturation effect has been captured by an inflection in the plot of surface tension and shear viscosity against concentration because of the solution heterogeneity, which was correlated by an inflection in the scattering intensity observed by performing the dynamic light scattering experiment. The binding mode of nitrate ions with the uranyl ion is found to be concentration-dependent, and at higher concentration, it is predominantly monodentate.