Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package

Formosanin C inhibits pulmonary metastasis by targeting stearyl CoA desaturase-1

BACKGROUND

Cisplatin (DDP) as the first-line drug has been used in cancer therapy. However, side effects and drug resistance are the challenges of DDP. Disordered lipid metabolism is related to DDP resistance.

STUDY DESIGN

In this study, formosanin C (FC) as the main compound of Rhizoma Paridis saponins (RPS) inhibits pulmonary metastasis by targeting stearyl CoA desaturase-1.

METHODS AND RESULTS

RPS prolonged the survival period of mice, reduced pulmonary metastases and alleviated colon toxicity caused by DDP. FC as the main compound of RPS enhanced the anti-tumor and anti-metastatic effects of DDP. FC decreased the mRNA level of SCD1 and the content of lipid droplets (LDs) in lung cancer cells. Molecular dynamics and isothermal titration calorimetry verified the binding stability and spontaneously between FC and SCD1. SiSCD1 reduced the content of LDs in cell lines and increased mitochondria (mtROS), which was consistent with the results of FC treatment. The combination group decreased DNA repair associated protein as well as DDP resistance markers such as ERCC1 and 53bp1, and increased DNA damage marker like γH2AX, which indirectly confirmed the occurrence of mtROS. In addition, FC combination with DDP also affected epithelial-mesenchymal transition-related protein like VIM and CDH1 in vivo experiments, and thereby inhibited pulmonary metastasis.

CONCLUSION

Our research indicated that the FC as the main compound of RPS targeted the CY2 domain of SCD1, inhibited lipid metabolism in mice, and thereby suppressed cancer metastases. This provided support for use of FC to treat cancer based on lipid metabolism pathway.

Divide-and-Conquer Linear-Scaling Quantum Chemical Computations

Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.

ULYSSES: An Efficient and Easy to Use Semiempirical Library for C+

We introduce ULYSSES, a user-friendly and robust C++ library for semiempirical quantum chemical calculations. In its current version, ULYSSES is equipped with a large set of different semiempirical models, most of which are based on the Neglect of Diatomic Differential Overlap (NDDO) approximation. Empirical corrections for dispersion and hydrogen bonding are available for most methods, so that higher quality is achieved in the calculation of energies of nonbonded complexes. The library is furthermore equipped with geometry optimization, as well as modules for calculating molecular properties of general interest. Ideal gas thermodynamics is available and allows single structure as well as conformer (multistructure) averaged properties to be calculated. We offer the possibility to use several vibrational partition functions according to the nature of interactions being studied: for covalent systems, the traditional harmonic oscillator approximation is available; for nonbonded complexes, we systematically extended the partition function proposed by Grimme for all thermodynamic functions. The library is also capable of running Born-Oppenheimer molecular dynamics.