Computational design, synthesis and biological evaluation of PDE5 inhibitors based on N2,N4-diaminoquinazoline and N2,N6-diaminopurine scaffolds.

We report the synthesis, and characterization of twenty-nine new inhibitors of PDE5. Structure-based design was employed to modify to our previously reported 2,4-diaminoquinazoline series. Modification include scaffold hopping to 2,6-diaminopurine core as well as incorporation of ionizable groups to improve both activity and solubility. The prospective binding mode of the compounds was determined using 3D ligand-based similarity methods to inhibitors of known binding mode, combined with a PDE5 docking and molecular dynamics based-protocol, each of which pointed to the same binding mode. Chemical modifications were then designed to both increase potency and solubility as well as validate the binding mode prediction. Compounds containing a quinazoline core displayed IC50s ranging from 0.10 to 9.39 µM while those consisting of a purine scaffold ranging from 0.29 to 43.16 µM. We identified 25 with a PDE5 IC50 of 0.15 µM, and much improved solubility (1.77 mg/mL) over the starting lead. Furthermore, it was found that the predicted binding mode was consistent with the observed SAR validating our computationally driven approach.

Theoretical Investigation of the Enantioselective [4 + 2] Cycloaddition Reaction of o-Hydroxystyrene and Azlactone.

Theoretical studies have been undertaken to rationalize the origin of the enantioselective Diels-Alder reaction (DA) of o-hydroxystyrene and azlactone catalyzed by (a) chiral BINOL-phosphoric acid (CPA) and (b) CPA and chiral guanidine (TBO). The sequence of events leading to increased enantioselectivity under the latter conditions have been studied using density functional theory (DFT) methods. The computational results indicate that both the mono- and co-catalytic processes proceed via stepwise [4 + 2] cycloaddition reactions involving three steps, which are (1) C-C bond formation, (2) C-O bond formation, and (3) the opening of the azlactone ring. This results in the formation of an oxygenous cycle with one chiral center. The origin of greater enantioselectivity under the latter catalytic conditions are discussed in terms of the structural characteristics and energetics of the intermediates and transition states formed on the potential energy surface of the competing reactions.

Effects of Seeding Layer Annealing Temperature on Physical and Morphological Structure of Ga/F Co-Doped ZnO Nanostructures.

In this work, effects of annealing temperature of seeding layer on structural properties and morphologies of Ga/F co-doped ZnO nanostructures synthesized by hydrothermal process were investigated by varying the annealing temperature of seed layer as 300-500 °C. The ZnO seeding layers were deposited onto cleaned glass substrates by dip-coating technique using zinc acetate dehydrate (CH3COO)2Zn·2H2O as starting coating precursor. The Ga/F co-doped ZnO nanostructures were then grown on these seed layers by conventional hydrothermal process using Zn(NO3)2, NH4F, GaN3O9 and hexamethyltetramine as Zn, F and Ga sources, respectively. Effect of seed layer annealing temperature on morphologies, structural and Photoluminescence properties was investigated by X-ray diffraction (XRD), Field emission scanning electron microscope (FE-SEM), and Photoluminescence spectra, respectively. Variation of annealing temperature of seed layers can significantly result to the difference in morphological, structure and shape of the as-synthesized nanostructure products. It is found that the increase in annealing temperature leads to alternation in their shape from vertically-aligned nanosheets to nanorods with their average size ranging from 50 to 200 nm. Furthermore, the luminescence could be ascribed to the different contributions of the defect emissions, such asthe increase in the oxygen vacancy (VO) emissionor the decrease of the Zinc vacancy (Vzn). However, it can be speculated from the photoluminescence that the incorporated Ga and F substitute into ZnO.

Synthesis and Immunological Studies of the Lipomannan Backbone Glycans Found on the Surface of Mycobacterium tuberculosis.

Investigations into novel bacterial drug targets and vaccines are necessary to overcome tuberculosis. Lipomannan (LM), found on the surface of Mycobacterium tuberculosis (Mtb), is actively involved in the pathogenesis and survival of Mtb. Here, we report for the first time a rapid synthesis and biological activities of an LM glycan backbone, α(1-6)mannans. The rapid synthesis is achieved via a regio- and stereoselective ring opening polymerization to generate multiple glycosidic bonds in one simple chemical step, allowing us to finish assembling the defined polysaccharides of 5-20 units within days rather than years. Within the same pot, the polymerization is terminated by a thiol-linker to serve as a conjugation point to carrier proteins and surfaces for immunological experiments. The synthetic glycans are found to have adjuvant activities in vivo. The interactions with DC-SIGN demonstrated the significance of α(1-6)mannan motif present in LM structure. Moreover, surface plasmon resonance (SPR) showed that longer chain of synthetic α(1-6)mannans gain better lectin's binding affinity. The chemically defined components of the bacterial envelope serve as important tools to reveal the interactions of Mtb with mammalian hosts and facilitate the determination of the immunologically active molecular components.

Exploring the catalytic mechanism of dihydropteroate synthase: elucidating the differences between the substrate and inhibitor.

Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made. In this study the mechanistic proposals for DHPS have been systematically investigated using a hybrid QM/MM method. We aimed to compare the energetics associated with SN1 and SN2 processes, whether the SN1 process involves a carbocation or neutral DHP intermediate, uncover the identity of the general base in the catalytic mechanism, and understand the differences in substrate vs. inhibitor reactivity. Our results suggest a reaction that follows an SN1 process with the rate determining step being C-O bond breaking to give a carbocation intermediate. Comparative studies on the inhibitor STZ confirm the experimental observations that it is also a DHPS substrate.

Comparison of feline and human immunodeficiency virus reverse transcriptase enzymes through chemical screening and computational analysis.

Feline immunodeficiency virus (FIV) is a common infection found in domesticated and wild cats worldwide. Despite the wealth of therapeutic understanding of the disease in humans, considerably less information exists regarding the treatment of the disease in felines. Current treatment relies on drugs developed for the related human immunodeficiency virus (HIV) and includes compounds of the popular non-nucleotide reverse transcriptase (NNRTI) class. This is despite FIV-RT being only 67% similar to HIV-1 RT at the enzyme level, increasing to 88% for the allosteric pocket targeted by NNRTIs. The goal of this project was to try to quantify how well the more extensive pharmacological knowledge available for human disease translates to felines. To this end we screened known NNRTIs and 10 diverse pyrimidine analogs identified virtually. We use this chemo-centric probe approach to (a) assess the similarity between the two related RT targets based on the observed experimental inhibition values, (b) try to identify more potent inhibitors at FIV, and (c) gain a better appreciation of the structure-activity relationships (SAR). We found the correlation between IC50s at the two targets to be strong (r2 = 0.87) and identified compound 1 as the most potent inhibitor of FIV with IC50 of 0.030 µM ± 0.009. This compared to FIV IC50 values of 0.22 ± 0.17 µM, 0.040 ± 0.010 µM and >160 µM for known anti HIV-1 RT drugs Efavirenz, Rilpivirine, and Nevirapine, respectively. This knowledge, along with an understanding of the structural origin that give rise to any differences could improve the way HIV drugs are repurposed for FIV.

The Effect of Polyvinyl Alcohol Addition on the Optical Properties and Oxygen Detection Performance of Titanium Dioxide and Methylene Blue Nanocomposite Colorimetric Indicators.

In this study, we investigated the impact of polyvinyl alcohol (PVA) incorporation on the optical properties and oxygen detection performance of a titanium dioxide/methylene blue (TiO2/MB) nanocomposite colorimetric indicator for packaging applications. The nanocomposite was synthesized via mechanical milling of TiO2 nanoparticles with MB and citric acid. PVA, at varying concentrations (0, 3, 9, and 14 wt%), was introduced during the wet milling process to produce a homogeneous composite film. Spin coating was employed to fabricate TiO2/MB nanocomposite films for oxygen detection evaluation. The influence of PVA loading on the films' chemical functionalities and surface morphologies was assessed using Fourier-transform infrared spectroscopy (FTIR) and field-emission scanning electron microscopy (FE-SEM). The indicator's activation process, involving a color change between bleached and colored states, and its recovery time were monitored via optical imaging and UV-VIS-NIR spectrophotometry. The results revealed that a PVA content of 9 wt% yielded well-defined films with enhanced stability of the TiO2/MB nanocomposite's oxygen detection performance.

Er-Doped BiVO4/BiFeO3 Nanocomposites Synthesized via Sonochemical Process and Their Piezo-Photocatalytic Application.

In this work, Er-doped BiVO4/BiFeO3 composites are prepared using the sonochemical process with a difference of rare earth loading compositions. The crystallinity and chemical and morphological structure of as-synthesized samples were investigated via X-ray diffraction, Raman scattering, and electron microscopy, respectively. The diffuse reflectance technique was used to extract the optical property and calculate the optical band gap of the composite sample. The piezo-photocatalytic performance was evaluated according to the decomposition of a Rhodamine B organic compound. The decomposition of the organic compound was achieved under ultrasonic bath irradiation combined with light exposure. The Er-doped BiVO4/BiFeO3 composite heterojunction material exhibited significant enhancement of the piezo-photocatalytic activity under both ultrasonic and light irradiation due to the improvement in charge generation and separation. The result indicates that Er dopant strongly affects the phase transformation, change in morphology, and alternation in optical band gap of the BiVO4 matrix. The incorporation of BiFeO3 in the composite form with BiVO4 doped with 1%Er can improve the photocatalytic performance of BiVO4 via piezo-induced charge separation and charge recombination retardment.

Structural and Optical Characterizations of Polymethyl Methacrylate Films with the Incorporation of Ultrafine SiO2/TiO2 Composites Utilized as Self-Cleaning Surfaces.

The structural and optical characterizations of nanocomposite films of polymethyl methacrylate (PMMA) and SiO2/TiO2 composites prepared via the spin-coating technique were investigated using different SiO2:TiO2 ratios. The SiO2/TiO2 nanocomposites were synthesized using the sonochemical process with Si:Ti precursor ratios of 1:0.1, 1:0.5, 1:1, 1:2, 1:4, and 0:1. All characterizations of ultrafine SiO2/TiO2 particles were loaded at 1 wt.% in a PMMA matrix for the fabrication of transparent SiO2/TiO2/PMMA composite films. The phase structure and morphology of SiO2/TiO2/PMMA composite films were monitored using X-ray diffraction, optical microscopy, and field-emission scanning electron microscopy. A surface roughness analysis of SiO2/TiO2/PMMA nanocomposite films was conducted using atomic force microscopy. For optical characterization, transmission properties with different incident angles of SiO2/TiO2/PMMA composite films were analyzed with UV-vis spectrophotometry. The water contact angles of SiO2/TiO2/PMMA composite films were analyzed to identify hydrophilic properties on film surfaces. Photocatalytic reactions in SiO2TiO2 composite films under UV irradiation were evaluated using rhodamine B dye degradation. The optimal condition of SiO2/TiO2/PMMA nanocomposite films was obtained at a 1:1 SiO2:TiO2 ratio in self-cleaning applications, resulting from good particle dispersion and the presence of the TiO2 phase in the composite.

Tailoring the Emission Behavior of WO3 Thin Films by Eu3+ Ions for Light-Emitting Applications.

The article reports the successful fabrication of Eu3+-doped WO3 thin films via the radio-frequency magnetron sputtering (RFMS) technique. To our knowledge, this is the first study showing the tunable visible emission (blue to bluish red) from a WO3:Eu3+ thin film system using RFMS. X-ray diffractograms revealed that the crystalline nature of these thin films increased upto 3 wt% of the Eu3+ concentration. The diffraction peaks in the crystalline films are matched well with the monoclinic crystalline phase of WO3, but for all the films', micro-Raman spectra detected bands related to WO3 monoclinic phase. Vibrational and surface studies reveal the amorphous/semi-crystalline behavior of the 10 wt% Eu3+-doped sample. Valence state determination shows the trivalent state of Eu ions in doped films. In the 400-900 nm regions, the fabricated thin films show an average optical transparency of ~51-85%. Moreover, the band gap energy gradually reduces from 2.95 to 2.49 eV, with an enhancement of the Eu3+-doping content. The doped films, except the one at a higher doping concentration (10 wt%), show unique emissions of Eu3+ ions, besides the band edge emission of WO3. With an enhancement of the Eu3+ content, the concentration quenching process of the Eu3+ ions' emission intensities is visible. The variation in CIE chromaticity coordinates suggest that the overall emission color can be altered from blue to bluish red by changing the Eu3+ ion concentration.

A novel potent autophagy inhibitor ECDD-S27 targets vacuolar ATPase and inhibits cancer cell survival.

Autophagy is a conserved lysosomal-dependent cellular degradation process and its dysregulation has been linked to numerous diseases including neurodegeneration, infectious diseases, and cancer. Modulation of autophagy is therefore considered as an attractive target for disease intervention. We carried out a high-content image analysis screen of natural product-derived compounds to discover novel autophagy modulating molecules. Our screen identified ECDD-S27 as the most effective compound for increasing the number of autophagic vacuoles inside cells. The structure of ECDD-S27 revealed that it is a derivative of cleistanthin A, a natural arylnaphthalene lignan glycoside found in plants. ECDD-S27 increases the number of autophagic vacuoles by inhibiting the autophagic flux and is able to restrict the survival of different cancer cells at low nanomolar concentrations. Molecular docking and SERS analysis showed that ECDD-S27 may potentially target the V-ATPase. Upon treatment of various cancer cells with ECDD-S27, the V-ATPase activity is potently inhibited thereby resulting in the loss of lysosomal acidification. Taken together, these data indicated that ECDD-S27 retards the autophagy pathway by targeting the V-ATPase and inhibits cancer cell survival. The observed antitumor activity without cytotoxicity to normal cells suggests the therapeutic potential warranting further studies on lead optimization of the compound for cancer treatment.

Influence of Ethanol as a Co-Solvent in Cyclodextrin Inclusion Complexation: A Molecular Dynamics Study.

Molecular dynamics (MD) simulations were used to investigate the dynamics and host-guest interactions of the inclusion complexes between a potent anti-HIV agent, UC781, and three different types of cyclodextrins (CDs) including ßCD, 2,6-dimethyl-ßCD (MßCD), and 2-hydroxypropyl-ßCD (HPßCD) in aqueous solution with ethanol (EtOH) as a co-solvent. The MD simulation results revealed that EtOH as the co-solvent and the type of cyclodextrin affected the inclusion complex formation. From this study, UC781/MßCD provided the most stable inclusion complex. The competition for the cavity of ßCD between UC781 and EtOH and the ensuing occupation of ßCD cavities by EtOH resulted in a weaker interaction between ßCD and UC781. In HPßCD, a supramolecular complex of UC781-HPßCD-EtOH was formed. The EtOH could easily fill the residual void space of the interior of unoccupied HPßCD due to the movement of UC781. In MßCD, the strong hydrogen bond interactions between the UC781 amide group and the secondary hydroxyl groups of MßCD significantly stabilized the inclusion complex in the presence of EtOH.

Molecular dynamics simulations of UC781-cyclodextrins inclusion complexes in aqueous solution.

The inclusion complexes of highly potent anti-HIV agent, UC781, with ß-cyclodextrin (ßCD), 2,6-dimethyl-ß-cyclodextrin (MßCD), and 2-hydroxypropyl-ß-cyclodextrin (HPßCD) in aqueous solution were investigated by molecular dynamics simulations. Simulations show that the phenyl ring of UC781 is trapped inside CD cavities, while the NH group of UC781 interacts with secondary hydroxyl groups at the wider rim of CDs. The different types of CDs directly affect the binding energy and the stability of the inclusion complexes. MßCD provides the most stable inclusion complex of UC781 among all CDs in this study due to the effect of methoxy groups (-OCH(3)) at C2 and C6 positions on the glucopyranose of CDs. Structure analysis of CDs and the orientation of UC781 inside CD cavities as well as the effects of aqueous solution to the inclusion complexes of UC781/CDs are discussed. Results of this study have provided an agreeable output; therefore, a reliable prediction method for other drug/CD inclusion complex formations is introduced.