Binding site identification and role of permanent water molecule of PIM-3 kinase: A molecular dynamics study

Parameterization of General Organic Polymers within the Open Force Field Framework

Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems within the same workflow used for smaller ligands. The monomer format encompasses a subset of the SMIRKS substructure query language to uniquely identify chemical information and repeating charges in underspecified systems through matching atomic connectivity. This workflow is combined with several different approaches for automatic partial-charge generation for larger systems. As an initial proof of concept, a variety of diverse polymeric systems were parametrized with the Open Force Field toolkit, including functionalized proteins, DNA, homopolymers, cross-linked systems, and sugars. Additionally, shape properties and radial distribution functions were computed from molecular dynamics simulations of poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide) homopolymers in aqueous solution and compared to previous simulation results in order to demonstrate a start-to-finish workflow for simulation and property prediction. We expect that these tools will greatly expedite the day-to-day computational research of soft-matter simulations and create a robust atomic-scale polymer specification in conjunction with existing polymer structural notations.

PIM3 Kinase: A Promising Novel Target in Solid Cancers

PIM3 (provirus-integrating Moloney site 3) is a serine/threonine kinase and belongs to the PIM family (PIM1, PIM2, and PIM3). PIM3 is a proto-oncogene that is frequently overexpressed in cancers originating from endoderm-derived tissues, such as the liver, pancreas, colon, stomach, prostate, and breast cancer. PIM3 plays a critical role in activating multiple oncogenic signaling pathways promoting cancer cell proliferation, survival, invasion, tumor growth, metastasis, and progression, as well as chemo- and radiation therapy resistance and immunosuppressive microenvironment. Genetic inhibition of PIM3 expression suppresses in vitro cell proliferation and in vivo tumor growth and metastasis in mice with solid cancers, indicating that PIM3 is a potential therapeutic target. Although several pan-PIM inhibitors entered phase I clinical trials in hematological cancers, there are currently no FDA-approved inhibitors for the treatment of patients. This review provides an overview of recent developments and insights into the role of PIM3 in various cancers and its potential as a novel molecular target for cancer therapy. We also discuss the current status of PIM-targeted therapies in clinical trials.

Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery

With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.

Understanding PIM-1 kinase inhibitor interactions with free energy simulation

The proviral integration site of the Moloney leukemia virus (PIM) family includes three homologous members. PIM-1 kinase is an important target in effective therapeutic interventions of lymphomas, prostate cancer and leukemia. In the current work, we performed free energy calculations to calculate the binding affinities of several inhibitors targeting this protein. The alchemical method with integration and perturbation-based estimators and the end-point methods were compared. The computational results indicated that the alchemical method can accurately predict the binding affinities, while the end-point methods give relatively unreliable predictions. Decomposing the free energy difference into enthalpic and entropic components with MBAR reweighting enabled us to investigate the detailed thermodynamic parameters with which the entropy-enthalpy compensation in this protein-ligand binding case is identified. We then studied the conformational ensemble, and the important protein-ligand interactions were identified. The current work sheds light on the understanding of the PIM-1-kinase-inhibitor interactions at the atomic level and will be useful in the further development of potential drugs.

Heat shock protein 70 protects cardiomyocytes through suppressing SUMOylation and nucleus translocation of phosphorylated eukaryotic elongation factor 2 during myocardial ischemia and reperfusion

Myocardial ischemia and reperfusion (MIR) results in cardiomyocyte apoptosis with severe outcomes, which blocks cardiac tissue recovering from myocardial ischemia diseases. Heat shock protein 70 (HSP70) is one of protective molecule chaperones which could regulate the nucleus translocation of other proteins. In addition, eukaryotic elongation factor 2 (eEF2), which modulates protein translation process, is vital to the recovery of heart during MIR. However, the relationship between HSP70 and eEF2 and its effects on MIR are unclear. The expression and relationship between HSP70 and eEF2 is confirmed by western blot, immunoprecipitation in vitro using cardiomyocyte cell line H9c2 and in vivo rat MIR model. The further investigation was conducted in H9c2 cells with detection for cell-cycle and apoptosis. It is revealed that eEF2 interacted and be regulated by HSP70, which kept eEF2 as dephosphorylated status and preserved the function of eEF2 during MIR. In addition, HSP70 suppressed the nucleus translocation of phosphorylated eEF2, which inhibited cardiomyocyte apoptosis during myocardial reperfusion stage. Furthermore, HSP70 also interacted with C-terminal fragment of eEF2, which could reverse the nucleus translocation and cardiomyocyte apoptosis caused by N-terminal fragment of eEF2. HSP70 draw on advantage and avoid defect of MIR through regulating phosphorylation and nucleus translocation of eEF2.

Expression of Pim-3 in colorectal cancer and its relationship with prognosis

There is increasing evidence suggesting that the establishment of Pim-3 is involved in tumorigenesis. This study aimed to investigate the expression and clinicopathological significance of Pim-3 in colorectal cancer (CRC). Clinical pathology data were collected from 410 CRC patients who received radical resection and were pathologically confirmed at the Sun Yat-Sen University Cancer Center between October 2002 and December 2008. We compared the expression Pim-3 in the primary focus and liver metastasis and investigated the correlations with other clinical-pathological factors. Multivariate analysis showed that perioperative blood transfusion, local invasion, lymph node and liver metastasis, and Pim-3 expression were independent prognostic factors. The expression of Pim-3 in CRC was higher than that in normal tissues. Patients with positive expression had significant decreases in 5-year survival. Pim-3 expression showed a positive correlation with tumor cell differentiation, local infiltration, and lymph node and liver metastasis. In conclusion, Pim-3 might serve as a novel target and prognosis factor for colorectal cancer.