10074-G5

The computational study of ligand binding to a target protein provides mechanistic insight into the molecular determinants of this process and can improve the success rate of in silico drug design. All-atom molecular dynamics (MD) simulations can be used to evaluate the binding free energy, typically by thermodynamic integration, and to probe binding mechanisms, including the description of protein conformational dynamics. The advantages of MD come at a high computational cost, which limits its use. Such cost could be reduced by using coarse-grained models, but their use is generally associated with an undesirable loss of resolution and accuracy. To address the trade-off between speed and accuracy of MD simulations, we describe the use of the recently introduced multi-eGO atomic model for the estimation of binding free energies. We illustrate this approach in the case of the binding of benzene to lysozyme by both thermodynamic integration and metadynamics, showing multiple binding/unbinding pathways of benzene. We then provide equally accurate results for the binding free energy of dasatinib and PP1 to Src kinase by thermodynamic integration. Finally, we show how we can describe the binding of the small molecule 10074-G5 to Aβ42 by single molecule simulations and by explicit titration of the ligand as a function of concentration. These results demonstrate that multi-eGO has the potential to significantly reduce the cost of accurate binding free energy calculations and can be used to develop and benchmark in silico ligand binding techniques.

Colorectal cancer (CRC) is a common cancer worldwide with an increasing annual incidence. Cancer stem cells (CSCs) play important roles in the occurrence, development, recurrence, and metastasis of CRC. The molecular mechanism regulating the development of colorectal CSCs remains unclear. The discovery of human induced pluripotent stem cells (hiPSCs) through somatic cell reprogramming has revolutionized the fields of stem cell biology and translational medicine. In the present study, we converted hiPSCs into cancer stem-like cells by culture with conditioned medium (CM) from CRC cells. These transformed cells, termed hiPSC-CSCs, displayed cancer stem-like properties, including a spheroid morphology and the expression of both pluripotency and CSC markers. HiPSC-CSCs showed tumorigenic and metastatic abilities in mouse models. The epithelial-mesenchymal transition phenotype was observed in hiPSC-CSCs, which promoted their migration and angiogenesis. Interestingly, upregulation of C-MYC was observed during the differentiation of hiPSC-CSCs. Mechanistically, CREB binding protein (CBP) bound to the C-MYC promoter, while histone deacetylase 1 and 3 (HDAC1/3) dissociated from the promoter, ultimately leading to an increase in histone acetylation and C-MYC transcriptional activation during the differentiation of hiPSC-CSCs. Pharmacological treatment with a CBP inhibitor or abrogation of CBP expression with a CRISPR/Cas9-based strategy reduced the stemness of hiPSC-CSCs. This study demonstrates for the first time that colorectal CSCs can be generated from hiPSCs. The upregulation of C-MYC via histone acetylation plays a crucial role during the conversion process. Inhibition of CBP is a potential strategy for attenuating the stemness of colorectal CSCs.