Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

As the second most abundant cation in the human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn²⁺ coordination with organic compounds and protein side chains using a polarizable atomic multipole-based electrostatic model. We find that the polarization effect plays a determining role in Zn²⁺ coordination geometry in both matrix metalloproteinase (MMP) complexes and zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn²⁺ exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal that the polarization effect on binding is ligand-dependent and thus difficult to incorporate into fixed-charge models implicitly

Production of Formamides from CO and Amines Induced by Porphyrin Rhodium(II) Metalloradical

It is of fundamental importance to transform carbon monoxide (CO) to petrochemical feedstocks and fine chemicals. Many strategies built on the activation of CO bond by π-back bonding from the transition metal center were developed during the past decades. Herein, a new CO activation method, in which the CO was converted to the active acyl-like metalloradical, [(por)­Rh­(CO)]^• (por = porphyrin), was reported. The reactivity of [(por)­Rh­(CO)]^• and other rhodium porphyrin compounds, such as (por)­RhCHO and (por)­RhC­(O)­NH^<i>n</i>Pr, and corresponding mechanism studies were conducted experimentally and computationally and inspired the design of a new conversion system featuring 100% atom economy that promotes carbonylation of amines to formamides using porphyrin rhodium­(II) metalloradical. Following this radical based pathway, the carbonylations of a series of primary and secondary aliphatic amines were examined, and turnover numbers up to 224 were obtained

Production of Formamides from CO and Amines Induced by Porphyrin Rhodium(II) Metalloradical

It is of fundamental importance to transform carbon monoxide (CO) to petrochemical feedstocks and fine chemicals. Many strategies built on the activation of CO bond by π-back bonding from the transition metal center were developed during the past decades. Herein, a new CO activation method, in which the CO was converted to the active acyl-like metalloradical, [(por)­Rh­(CO)]^• (por = porphyrin), was reported. The reactivity of [(por)­Rh­(CO)]^• and other rhodium porphyrin compounds, such as (por)­RhCHO and (por)­RhC­(O)­NH^<i>n</i>Pr, and corresponding mechanism studies were conducted experimentally and computationally and inspired the design of a new conversion system featuring 100% atom economy that promotes carbonylation of amines to formamides using porphyrin rhodium­(II) metalloradical. Following this radical based pathway, the carbonylations of a series of primary and secondary aliphatic amines were examined, and turnover numbers up to 224 were obtained

Production of Formamides from CO and Amines Induced by Porphyrin Rhodium(II) Metalloradical

It is of fundamental importance to transform carbon monoxide (CO) to petrochemical feedstocks and fine chemicals. Many strategies built on the activation of CO bond by π-back bonding from the transition metal center were developed during the past decades. Herein, a new CO activation method, in which the CO was converted to the active acyl-like metalloradical, [(por)­Rh­(CO)]^• (por = porphyrin), was reported. The reactivity of [(por)­Rh­(CO)]^• and other rhodium porphyrin compounds, such as (por)­RhCHO and (por)­RhC­(O)­NH^<i>n</i>Pr, and corresponding mechanism studies were conducted experimentally and computationally and inspired the design of a new conversion system featuring 100% atom economy that promotes carbonylation of amines to formamides using porphyrin rhodium­(II) metalloradical. Following this radical based pathway, the carbonylations of a series of primary and secondary aliphatic amines were examined, and turnover numbers up to 224 were obtained

Additional file 2: Table S1. of A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63

Genes changed >3-fold with BRG1/BRM knockdown. Table S2 Shared genes controlled by both BAF and p63 with fold change > 3. Table S3 Sequencing depth of the ATAC-seq, RNA-seq, and ChIP-seq data generated for this study. (XLSX 78 kb

Additional file 1: of A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63

Includes the supplementary Figures S1–4. Figure S1. BAF is essential for epidermal gene induction. (a) Quantitative RT-PCR analysis demonstrating the knockdown efficiency of BRG1/BRM siRNAs and the suppression of differentiation gene expression in BAF loss compared to control. (b) GO analysis of the significant changed genes (fold change > 3, FDR < 0.01) with BAF knockdown in RNA-seq. (c) Western blot analysis showing the time course of 4-day differentiation induction in primary human keratinocytes, comparing BRG1/BRM loss with control. BRG1/BRM siRNA efficiently knocked down BRG1 and BRM protein levels. The induction of Keratin 1 is significantly impaired with BAF loss, although no significant changes were detected with p63 and p53 protein level relative to tubulin loading control. (d–f) Distribution of total ATAC-seq peaks, and the BAF-dependent ATAC-seq peaks relative to gene promoter, exon, intron and distal regulatory regions. Figure S2. BAF maintains open chromatin regions with p63 binding sites. (a) Scatter plot demonstrating correlation between BAF binding and open chromatin across the genome. (b) RNA expression levels (RPKM) of p53 family transcription factors in human keratinocytes. (c) Pie chart demonstrating the percentage of p63 motif sites at p63 binding sites that became inaccessible with BAF knockdown. (d) RNA expression levels of all expressed TFs in keratinocytes. Gray dots indicate the expression levels of 809 TFs (RPKM > 1 in differentiating human keratinocytes) listed in GO. Representative TFs known to be functional in epidermal differentiation along with CTCF are highlighted in brown and red. (e) ATAC-seq accessibility in KLF4 motif sites in KLF4 binding sites comparing control vs BAF loss conditions. (f) Heatmap showing the fold changes of the shared 236 genes (fold change > 3, FDR < 0.01) controlled by both BAF and p63. (g) Representative RNA-seq data tracks of BAFi, p63i, and CTRLi replicates. Figure S3. BAF loss does not affect nucleosome positioning or genome accessibility at CTCF binding regions. (a) ATAC-seq fragment size distribution. Gray shaded area represents nucleosome-free fragments (<100 bp), and blue shaded area represents mononucleosome fragments (180–247 bp). Schematic illustration of these ATAC-seq fragments is shown on the right. (b, c) V-plot analysis demonstrating the nucleosome positioning at CTCF motif regions comparing control versus BAF loss. (d) Average diagram of nucleosome-free ATAC-seq fragments at CTCF motif regions comparing control and BAF loss. (e) Average diagram of mononucleosome ATAC-seq fragments at CTCF motif regions comparing control and BAF loss. (f) Average diagram of predicted nucleosome binding probability based on DNA sequences using same number of shuffled genomic regions as in p63 motif nucleosome probability analysis. Figure S4. BAF loss impairs p63 binding to its target sites. (a, b) Single nucleotide ATAC accessibility analysis with 1-bp resolution at p63 and CTCF motif regions in their ChIP-seq binding sites, comparing control and BAF loss. (c) Summit-centered heatmap comparing p63 ChIP-seq peaks in control and BAF loss. (d, e) Average diagram of p63 ChIP-seq signal enrichment in the peaks that are overlapped or unique in control. (f) Average diagram of BAF ChIP-seq signal at CTCF sites comparing p63 loss with control conditions. (PDF 3349 kb

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

Development of the AMOEBA (atomic multipole optimized energetics for biomolecular simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and <i>J</i>-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments

CD44-Targeted Facile Enzymatic Activatable Chitosan Nanoparticles for Efficient Antitumor Therapy and Reversal of Multidrug Resistance

Nanoparticles are attractive platforms for the delivery of various anticancer therapeutics. Nevertheless, their applications are still limited by the relatively low drug loading capacity and the occurrence of multidrug resistance (MDR) against chemotherapeutics. In this study, we report that the integration of d-α-tocopherol succinate (VES) residue with both chitosan and paclitaxel (PTX) led to significant improvement of drug loading capacity and drug loading efficiency through the enhancement of drug/carrier interaction. After the incorporation of hyaluronic acid containing PEG side chains (HA-PEG), higher serum stability and more efficient cellular uptake were obtained. Due to HA coating, VES residues and the enzymatic responsive drug release property, such facile nanoparticles actively targeted cancer cells that overexpress CD44 receptor and efficiently reversed the MDR of treated cells, but caused no significant toxicity to mouse fibroblast (NIH-3T3). More importantly, with HA-PEG coating, longer blood circulation and more effective tumor accumulation were achieved for prodrug nanoparticles. Finally, superior anticancer activity and excellent safety profile was demonstrated by HA-PEG coated enzymatically activatable prodrug nanoparticles compared to commercially available Taxol formulation

DataSheet1_Combining photodynamic therapy and cascade chemotherapy for enhanced tumor cytotoxicity: the role of CTT2P@B nanoparticles.docx

The mitochondria act as the main producers of reactive oxygen species (ROS) within cells. Elevated levels of ROS can activate the mitochondrial apoptotic pathway, leading to cell apoptosis. In this study, we devised a molecular prodrug named CTT2P, demonstrating notable efficacy in facilitating mitochondrial apoptosis. To develop nanomedicine, we enveloped CTT2P within bovine serum albumin (BSA), resulting in the formulation known as CTT2P@B. The molecular prodrug CTT2P is achieved by covalently conjugating mitochondrial targeting triphenylphosphine (PPh3), photosensitizer TPPOH2, ROS-sensitive thioketal (TK), and chemotherapeutic drug camptothecin (CPT). The prodrug, which is chemically bonded, prevents the escape of drugs while they circulate throughout the body, guaranteeing the coordinated dispersion of both medications inside the organism. Additionally, the concurrent integration of targeted photodynamic therapy and cascade chemotherapy synergistically enhances the therapeutic efficacy of pharmaceutical agents. Experimental results indicated that the covalently attached prodrug significantly mitigated CPT cytotoxicity under dark conditions. In contrast, TPPOH2, CTT2, CTT2P, and CTT2P@B nanoparticles exhibited increasing tumor cell-killing effects and suppressed tumor growth when exposed to light at 660 nm with an intensity of 280 mW cm−2. Consequently, this laser-triggered, mitochondria-targeted, combined photodynamic therapy and chemotherapy nano drug delivery system, adept at efficiently promoting mitochondrial apoptosis, presents a promising and innovative approach to cancer treatment.</p

Tumor Specific and Renal Excretable Star-like Triblock Polymer–Doxorubicin Conjugates for Safe and Efficient Anticancer Therapy

Efficient tumor accumulation and body clearance are two paralleled requirements for ideal nanomedicines. However, it is hard for both to be met simultaneously. The inefficient clearance often restrains the application of drug delivery systems (DDSs), especially for high-dosage administration. In this study, the star-like and block structures are combined to enhance the tumor specific targeting of the parent structures and obtain additional renal excretion property. The influences of polymer architectures and chemical compositions on the physicochemical and biological properties, particularly the simultaneous achievement of tumor accumulation and renal clearance, have been investigated. Among the tested conjugates, an eight-arm triblock star polymer based on poly­(ethylene glycol) (PEG) and poly­(<i>N</i>-(2-hydroxyl) methacrylamide) (PHPMA) is found to simultaneously fulfill the requirements of superior tumor accumulation and efficient renal clearance due to the appropriate micelle size and reversible aggregation process. On the basis of this conjugate, 60 mg/kg of Dox equivalent (much higher than the maximum tolerated dose (MTD) of Dox) can be administered to efficiently suppress tumor growth without causing any obvious toxicity. This work provides a new approach to design polymer–drug conjugates for tumor specific application, which can simultaneously address the efficacy and safety concerns