Phosphoinositide-3-kinase inhibitors: Evaluation of substituted alcohols as replacements for the piperazine sulfonamide portion of AMG 511

Replacement of the piperazine sulfonamide portion of the PI3Kα inhibitor AMG 511 (1) with a range of aliphatic alcohols led to the identification of a truncated gem-dimethylbenzylic alcohol analog, 2-(5-(4-amino-6-methyl-1,3,5-triazin-2-yl)-6-((5-fluoro-6-methoxypyridin-3-yl)amino)pyridin-3-yl)propan-2-ol (7). This compound possessed good in vitro efficacy and pharmacokinetic parameters and demonstrated an EC₅₀ of 239 ng/mL in a mouse liver pharmacodynamic model measuring the inhibition of hepatocyte growth factor (HGF)-induced Akt Ser473 phosphorylation in CD1 nude mice 6 h post-oral dosing.     

Flagellar adhesion and deadhesion in chlamydomonas gametes: Effects of tunicamycin and observations on flagellar tip morphology

The aggregation-dependent loss of flagellar adhesiveness in Chlamydomonas reinhardi has been correlated with changes in flagellar tip morphology during adhesion and deadhesion. As aggregating mt^? and impotent (able to adhere, but not fuse) mt⁺ gametes begin to disaggregate in the presence of the protein synthesis inhibitor cycloheximide, there is a concomitant change in flagellar tip morphology from the activated bulbous form to the nonactivated tapered shape. The requirement of protein-synthetic activity for the maintenance of flagellar adhesiveness during aggregation may be due in part to turnover of proteins involved in formation or stabilization of activated flagellar tips. Incubation of aggregating gametes with tunicamycin indicates that, like protein synthesis inhibitors, this inhibitor of glycosylation also causes adhering gametes to deadhere. The results suggest that protein glycosylation may be essential for maintenance of adhesiveness during aggregation.     

Shimiella gen. nov. and Shimiella gracilenta sp. nov. (Dinophyceae,Kareniaceae), a Kleptoplastidic Dinoflagellate from Korean Waters and its Survival under Starvation

A small dinoflagellate, ~13 μm in cell length, was isolated from Jinhae Bay, Korea. Light microscopy showed that it was similar to the kleptoplastidic dinoflagellate Gymnodinium gracilentum nom. inval. rDNA sequences were obtained and its anatomy and morphology described using light and scanning and transmission electron microscopy. Phylogenetic analyses indicated that it belonged to the family Kareniaceae. However, its large subunit (LSU) rDNA sequences were 5.2–9.5% different from those of the other five genera in the family, and its clade was clearly divergent from that of each genus. Its overall morphology was different from those of the other five genera in the family and from Gymnodinium. Unlike Gymnodinium, this dinoflagellate did not have a horseshoe‐shaped apical groove, nuclear envelope chambers, or a nuclear fibrous connective (NFC). It had an apical line of narrow amphiesmal vesicles and an elongated apical furrow crossing the apex. Cells were covered with polygonal amphiesmal vesicles arranged in 16 rows. Starved cells did not contain their own plastids, eyespots, pyrenoids, peridinin, or fucoxanthin. However, they could survive without added prey for approximately one month using chloroplasts from the cryptophyte prey Teleaulax amphioxeia, indicating kleptoplastidy. Because this taxon is genetically distinct at the generic rank from the other genera in Kareniaceae, it is placed in Shimiella gen. nov., and because G. gracilentum was invalid, the new bionomial S. gracilenta sp. nov. is proposed.     

Structural insights into ligand-binding pocket formation in Nurr1 by molecular dynamics simulations

Abstract

The nuclear receptor Nurr1 (NR4A2) has been identified as a potential target for the treatment of Parkinson’s disease. In contrast to most other nuclear receptors, the X-ray crystal structure of the Nurr1 ligand-binding domain (LBD) lacks any ligand-binding pocket (LBP). However, NMR spectroscopy measurements have revealed that the known Nurr1 agonist docosahexaenoic acid (DHA) binds to a region within the LBD that corresponds to the classical NR ligand-binding pocket (LBP). In order to investigate the structural dynamics of the Nurr1 LBD and to study potential LBP formation, the conformational space of the receptor was sampled using a molecular dynamics (MD) simulation. Docking of DHA into 50,000 LBD structures extracted from the simulation revealed the existence of a transient LBP that is capable to fully harbor the compound. The location of the identified pocket overlaps with the ligand-binding site suggested by NMR experiments. Structural analysis of the protein-ligand complex showed that only modest structural rearrangements within the Nurr1 LBD are required for LBP formation. These findings may support structure-based drug discovery campaigns for the development of receptor-specific agonists.     

Electronic Properties of the Amino Acid Side Chains Contribute to the Structural Preferences in Protein Folding

Abstract

A database of 118 non-redundant proteins was examined to determine the preferences of amino acids for secondary structures: α-helix, β-strand and coil conformations. To better understand how the physicochemical properties of amino acid side chains might influence protein folding, several new scales have been suggested for quantifying the electronic effects of amino acids. These include the pKa at the amino group, localized effect substituent constants (eσ), and a composite of these two scales (ε). Amino acids were also classified into 5 categories on the basis of their electronic properties: O (strong electron donor), U (weak donor), Z (ambivalent), B (weak electron acceptor), and X (strong acceptor). Certain categories of amino acid appeared to be critical for particular conformations, e.g., O and U-type residues for α-helix formation. Pairwise analysis of the database according to these categories revealed significant context effects in the structural preferences. In general, the propensity of an amino acid for a particular conformation was related to the electronic features of the side chain. Linear regression analyses revealed that the electronic properties of amino acids contributed about as much to the folding preferences as hydrophobicity, which is a well-established determinant of protein folding. A theoretical model has been proposed to explain how the electronic properties of the side chain groups might influence folding along the peptide backbone.     

Effects of active site mutations in haemoglobin I from Lucina pectinata: a molecular dynamic study

Haemoglobin I from Lucina pectinata is a monomeric protein consisting of 142 amino acids. Its active site contains a peculiar arrangement of phenylalanine residues (PheB10, PheCD1 and PheE11) and a distal Gln at position E7. Active site mutations at positions B10, E7 and E11 were performed in deoxy haemoglobin I (HbI), followed by 10 ns molecular dynamic simulations. The results showed that the mutations induced changes in domains far from the active site producing more flexible structures than the native HbI. Distance analyses revealed that the heme pocket amino acids at positions E7 and B10 are extremely sensitive to any heme pocket residue mutation. The high flexibility observed by the E7 position suggests an important role in the ligand binding kinetics in ferrous HbI, while both positions play a major role in the ligand stabilisation processes. Furthermore, our results showed that E11Phe plays a pivotal role in protein stability.     

Structure basis of bigelovin as a selective RXR agonist with a distinct binding mode

The nuclear receptor retinoid X receptor (RXR) functions potently in the regulation of homeostasis and cell development, while rexinoids as RXR agonists have proved their therapeutic potential in the treatment of metabolic diseases and cancer. Here, the natural product bigelovin was identified as a selective RXRα agonist. Interestingly, this compound could not transactivate RXRα:RXRα homodimer but could enhance the transactivation of RXRα:peroxisome proliferator-activated receptor γ heterodimer and repress that of RXRα:liver X receptor (LXR) α heterodimer, while it had no effects on RXRα:farnesoid X receptor heterodimer. Considering that the effective role of LXR response element involved transactivation of sterol regulatory element-binding protein-1c mediated by RXRα:LXRα in triglyceride elevation, such LXR response element repressing by bigelovin has obviously addressed its potency for further research. Moreover, our determined crystal structure of the bigelovin-activated RXRα ligand-binding domain with the coactivator human steroid receptor coactivator-1 peptide revealed that bigelovin adopted a distinct binding mode. Compared with the known RXR ligands, bigelovin lacks the acidic moiety in structure, which indicated that the acidic moiety rendered little effects on RXR activation. Our results have thereby provided new insights into the structure-based selective rexinoids design with bigelovin as a potential lead compound.     

ARE CYTOPLASMIC POCKETS (MTR/POCKET) PRESENT IN ALL PHOTOSYNTHETIC EUGLENOID GENERA?1

In 1985, the existence of a cytoplasmic pocket formed from the reservoir membrane in the photosynthetic euglenoid Colacium was described. A band of reinforcing microtubules (MTR) derived from the ventral flagellar root lined the pocket, and a dense fibrillar mesh was associated with the membrane. A comparison of bodonid cytostomes, colorless euglenoid cytostomes, and the reservoir pocket found in Colacium suggested that the three structures were homologous and that photosynthetic euglenoids arose from phagotrophic ancestors. MTR/pockets have since been reported in other photosynthetic euglenoids, including Euglena, Eutreptia, Eutreptiella, Cryptoglena, Tetreutreptia, and Phacus. We found MTR/pockets in three additional taxa, Lepocinclis, Trachelomonas, and Strombomonas, thereby demonstrating the presence of this complex in representatives of all the major photosynthetic genera. A comparison of the MTR/pocket complex across genera indicated a reduction in structural complexity that was consistent with recent phylogenetic schemes based on molecular characters. Three alternative hypotheses of the origin of MTR/pockets in phototrophic euglenoids are presented and discussed.     

An automated decision-tree approach to predicting protein interaction hot spots

Protein-protein interactions can be altered by mutating one or more "hot spots," the subset of residues that account for most of the interface's binding free energy. The identification of hot spots requires a significant experimental effort, highlighting the practical value of hot spot predictions. We present two knowledge-based models that improve the ability to predict hot spots: K-FADE uses shape specificity features calculated by the Fast Atomic Density Evaluation (FADE) program, and K-CON uses biochemical contact features. The combined K-FADE/CON (KFC) model displays better overall predictive accuracy than computational alanine scanning (Robetta-Ala). In addition, because these methods predict different subsets of known hot spots, a large and significant increase in accuracy is achieved by combining KFC and Robetta-Ala. The KFC analysis is applied to the calmodulin (CaM)/smooth muscle myosin light chain kinase (smMLCK) interface, and to the bone morphogenetic protein-2 (BMP-2)/BMP receptor-type I (BMPR-IA) interface. The results indicate a strong correlation between KFC hot spot predictions and mutations that significantly reduce the binding affinity of the interface.