Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions. (1) We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5-HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist- and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region.     

LigDockCSA: protein-ligand docking using conformational space annealing

Protein–ligand docking techniques are one of the essential tools for structure‐based drug design. Two major components of a successful docking program are an efficient search method and an accurate scoring function. In this work, a new docking method called LigDockCSA is developed by using a powerful global optimization technique, conformational space annealing (CSA), and a scoring function that combines the AutoDock energy and the piecewise linear potential (PLP) torsion energy. It is shown that the CSA search method can find lower energy binding poses than the Lamarckian genetic algorithm of AutoDock. However, lower‐energy solutions CSA produced with the AutoDock energy were often less native‐like. The loophole in the AutoDock energy was fixed by adding a torsional energy term, and the CSA search on the refined energy function is shown to improve the docking performance. The performance of LigDockCSA was tested on the Astex diverse set which consists of 85 protein–ligand complexes. LigDockCSA finds the best scoring poses within 2 Å root‐mean‐square deviation (RMSD) from the native structures for 84.7% of the test cases, compared to 81.7% for AutoDock and 80.5% for GOLD. The results improve further to 89.4% by incorporating the conformational entropy. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Simulation of chlorination reaction behavior of hull wastes by using the HSC code

Nitrofurantoin (NFN) radiolabeling with technetium-99m (^99mTc) was investigated using different concentration of the NFN, sodium pertechnetate (Na^99mTcO₄), reducing agent (SnCl₂) at different pH ranges (5.1–6.00). The suitability of the ^99mTc-NFN was evaluated in terms of the radiochemical purity (RCP) yield, in vitro stability in saline, serum, in vitro binding with E. coli, biodistribution in E. coli infected model rat (ERT), and scintigraphic accuracy in E. coli infected model rabbit (EBT). The superlative radiochemical succumb at 2.5 mg NFN, 125 μL of SnCl₂ (1 μg/μL in 0.01 N HCl), 2.5 mCi of Na^99mTcO₄, at pH 5.2 at 30, 60, 90, and 120 min after reconstitution was 64.50 ± 0.11, 97.50 ± 0.16, 94.25 ± 0.10, 92.15 ± 0.14 and 90.75 ± 0.0.13%. The complex was found stable in saline and serum for 90% up to 120 min and showed 50–65% in vitro binding with E. coli. The absorption of the ^99mTc-NFN, primarily at E. Coli infected (ECT) muscle of ERT was lower but after 60 min it went up to 7.25 ± 0.17%. The absorption in the blood, liver, spleen, stomach, intestines, inflamed muscle (N.T1) and normal muscle (N.T2) went down while in the kidney and urine it went up with time. The ratio of the ECT/N.T1 was 7:1 and N.T2/N.T1 was 2:1. The Whole Body Static (WBS) imaging of the ERB confirmed the suitability of the ^99mTc-NFN as radiotracer. The superlative radiochemical succumb, significant in vitro stability in saline and serum, in vitro binding with E. coli, ideal biodistribution and scintigraphic accuracy confirmed the viability of the ^99mTc-NFN as radiotracer for infection.     

Controlled loading of cryoprotectants (CPAs) to oocyte with linear and complex CPA profiles on a microfluidic platform

Oocyte cryopreservation has become an essential tool in the treatment of infertility by preserving oocytes for women undergoing chemotherapy. However, despite recent advances, pregnancy rates from all cryopreserved oocytes remain low. The inevitable use of the cryoprotectants (CPAs) during preservation affects the viability of the preserved oocytes and pregnancy rates either through CPA toxicity or osmotic injury. Current protocols attempt to reduce CPA toxicity by minimizing CPA concentrations, or by minimizing the volume changes via the step-wise addition of CPAs to the cells. Although the step-wise addition decreases osmotic shock to oocytes, it unfortunately increases toxic injuries due to the long exposure times to CPAs. To address limitations of current protocols and to rationally design protocols that minimize the exposure to CPAs, we developed a microfluidic device for the quantitative measurements of oocyte volume during various CPA loading protocols. We spatially secured a single oocyte on the microfluidic device, created precisely controlled continuous CPA profiles (step-wise, linear and complex) for the addition of CPAs to the oocyte and measured the oocyte volumetric response to each profile. With both linear and complex profiles, we were able to load 1.5 M propanediol to oocytes in less than 15 min and with a volumetric change of less than 10%. Thus, we believe this single oocyte analysis technology will eventually help future advances in assisted reproductive technologies and fertility preservation.     

Development of target-specific multimodality imaging agent by using hollow manganese oxide nanoparticles as a platform

A platform protocol developed based on the hollow manganese oxide nanoparticles provided multimodal diagnostic agents, which allow the selectively detect vulva cancer with T(1)-weighted in vivo MRI.     

Cyclodipeptide-bridged porphyrin dimer supramolecular assemblies

A cyclodipeptide-bridged porphyrin dimer has formed fibrous and toroidal multi-porphyrin array systems by hydrogen bonding-mediated self-assembly.     

Multifunctional hybrid nanoconjugates for efficient in vivo delivery of immunomodulating oligonucleotides and enhanced antitumor immunity

A winning combination: Multifunctional hybrid nanoconjugates (HNCs) based on polymer nanoparticles containing quantum dots (QDs) conjugated with CpG oligonucleotides (as a ligand for TLR9) and STAT3 siRNAs (to suppress the immune response) have been synthesized. These HNCs were shown to synergistically enhance the antitumor immune response in dendritic cells and in tumor-bearing mice.     

Hydrated alizarin complexes: hydrogen bonding and proton transfer

We investigated the hydrogen bonding structures and proton transfer for the hydration complexes of alizarin (Az) produced in a supersonic jet using fluorescence excitation (FE), dispersed laser induced fluorescence (LIF), visible-visible hole burning (HB), and fluorescence detected infrared (FDIR) spectroscopy. The FDIR spectrum of bare Az with two O-H groups exhibits two vibrational bands at 3092 and 3579 cm(-1), which, respectively, correspond to the stretching vibration of O1-H1 that forms a strong intramolecular hydrogen bond with the C9=O9 carbonyl group and the stretching vibration of O2-H2 that is weakly hydrogen-bonded to O1-H1. For the 1:1 hydration complex Az(H(2)O)(1), we identified three conformers. In the most stable conformer, the water molecule forms hydrogen bonds with the O1-H1 and O2-H2 groups of Az as a proton donor and proton acceptor, respectively. In the other conformers, the water binds to the C10=O10 group in two nearly isoenergetic configurations. In contrast to the sharp vibronic peaks in the FE spectra of Az and Az(H(2)O)(1), only broad, structureless absorption was observed for Az(H(2)O)(n) (n≥ 2), indicating a facile decay process, possibly due to proton transfer in the electronic excited state. The FDIR spectrum with the wavelength of the probe laser fixed at the broad band exhibited a broad vibrational band near the O2-H2 stretching vibration frequency of the most stable conformer of Az(H(2)O)(1). With the help of theoretical calculations, we suggest that the broad vibrational band may represent the occurrence of proton transfer by tunnelling in the electronic ground state of Az(H(2)O)(n) (n≥ 2) upon excitation of the O2-H2 vibration.     

Enhanced mid-IR luminescence of Tm3+ ions in Ga2S3 nanocrystals embedded chalcohalide glass ceramics

Chalcohalide glass with a composition of 65GeS₂–25Ga₂S₃–10CsI (in mol%) doped with 0.6 wt% Tm³⁺ ions was prepared by conventional melt–quench method. By heat treating the precursor glass at 20 °C above its glass transition temperature T_g for different durations, IR transparent glass ceramics were obtained. X-ray diffraction (XRD) and scanning electron microscope (SEM) showed that Ga₂S₃ crystallites were precipitated after heat treatment and their grain sizes were in nano-scale and increased with the elongation of heat treated time. Mid-IR luminescence properties of the glass and transparent glass ceramic samples were investigated. The emissions at 2.3 and 3.8 μm corresponding to optical transitions of ³H₄ → ³H₅ and ³H₅ → ³F₄ of Tm³⁺ ions were significantly enhanced by the presence of Ga₂S₃ nanocrystals and reached a maximum after 8 hours treatment.     

High-speed multibit operation of a dual vacancy-type oxide device with extended bi-polar resistive switching behaviors

We investigated the resistive switching behaviors of the metal–copper oxide–metal devices with the enhanced capability in terms of high speed and multi-bit operation. From the analysis of the normal and extended resistive switching behaviors, the voltage-induced resistive changes were modeled and the resistive switching polarity was explained. Also, we proposed and fabricated a dual vacancy-type device structure with an extended resistive switching behavior and demonstrated a high-speed implemental 2-bit multi-bit operation by controlling specifically switch-on voltage pulses.