Reconstitution of RNA cap methylation reveals different features of SARS-CoV-2 and SARS-CoV methyltransferases.

Cap RNA methylations play important roles in the replication, evasion of host RNA sensor recognition, and pathogenesis. Coronaviruses possess both guanine N7- and 2'-O-ribose methyltransferases (N7-MTase and 2'-O-MTase) encoded by nonstructural protein (nsp) 14 and nsp16/10 complex, respectively. In this study, we reconstituted the two-step RNA methylations of N7-MTase and 2'-O-MTase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and demonstrated its common and different features in comparison with that of SARS-CoV. We revealed that the nsp16/10 2'-O-MTase of SARS-CoV-2 has a broader substrate selectivity than the counterpart of SARS-CoV and can accommodate both unmethylated and uncapped RNA substrates in a sequence-independent manner. Most intriguingly, the substrate selectivity of nsp16/10 complex is not determined by the apoenzyme of nsp16 MTase but by its cofactor nsp10. These results provide insight into the unique features of SARS-CoV-2 MTases and may help develop strategies to precisely intervene in the methylation pathway and pathogenesis of SARS-CoV-2.

Honeycomb-patterned phthalocyanine films with photo-active antibacterial activities.

We report honeycomb-patterned phthalocyanine (Pc) films fabricated by self-assembly of dodecyloxy-azo-Zinc phthalocyanine (daZnPc) using the breath figure (BF) technique. These ultrathin Pc films exhibit a robust photo-dependent antibacterial effect against Escherichia coli (E. coli).

Phosphorescent Ir(III) complexes with both cyclometalate chromophores and phosphine-silanolate ancillary: concurrent conversion of organosilane to silanolate.

Ir(III) metal complexes with general formula [(C^N)2Ir(P^SiO)], where (C^N)H is 2-phenylisoquinoline (1), 2-phenylpyridine (2) or 2-(2,4-difluorophenyl)pyridine (3), and (P^SiO)H is an organosilanolate ancillary chelate with either diphenylsilyl (a) or dimethylsilyl (b) substituent, were synthesized, among which the structure of 3a was also confirmed using single-crystal X-ray diffraction analyses. These complexes exhibit bright phosphorescence in the region of 489-632 nm in solution at room temperature, showing the first successful example of using organosilanolate as an ancillary chelate. For application, organic light emitting diodes (OLEDs) using phosphors 3a and 3b doped in N,N'-dicarbazolyl-3,5-benzene (mCP) exhibited a maximum brightness of 50,800 cd m(-2) at 800 mA cm(-2) (12 V) with η(ext) of 10.1% and a brightness of 45,900 cd m(-2) at 700 mA cm(-2) (14.5 V) with η(ext) of 10.2%, respectively.

Structural basis of specific binding between Aurora A and TPX2 by molecular dynamics simulations.

In the present study, the impacts of G198N and W128F mutations on the recognition between Aurora A and targeting protein of Xenopus kinesin-like protein 2 (TPX2) were investigated using molecular dynamics (MD) simulations, free energy calculations, and free energy decomposition analysis. The predicted binding free energy of the wild-type complex is more favorable than those of three mutants, indicating that both single and double mutations are unfavorable for the Aurora A and TPX2 binding. It is also observed that the mutations alternate the binding pattern between Aurora A and TPX2, especially the downstream of TPX2. An intramolecular hydrogen bond between the atom OD of Asp11(TPX2) and the atom HE1 of Trp34(TPX2) disappear in three mutants and thus lead to the instability of the secondary structure of TPX2. The combination of different molecular modeling techniques is an efficient way to understand how mutation has impacts on the protein-protein binding and our work gives valuable information for the future design of specific peptide inhibitors for Aurora A.

Photocontrollable J-aggregation of a diarylethene-phthalocyanine hybrid and its aggregation-stabilized photochromic behavior.

The photocontrollable J-aggregation of a diarylethene-phthalocyanine hybrid (T-ZnPc) and its aggregation-stabilized photochromic behavior were investigated by various techniques. T-ZnPc initially exhibited slight J-aggregation tendency in solvents such as chloroform and toluene through conformational planarization effect, but formed much stronger J-aggregates upon the illumination of 254 nm UV light. In darkness, the UV-irradiated solutions gradually returned to their initial state. These phenomena can be explained by the pronounced change in molecular planarity accompanying the reversible isomerization of the diarylethene units of T-ZnPc. Besides, we have found that the thermal stability of the closed-ring diarylethene isomers in molecularly dispersed T-ZnPc is much poorer than that in aggregates. As long as the aggregates were broken, they converted to corresponding open-ring form instantly. This study provided an example of fully photocontrollable aggregation of phthalocyanines and paved a new way for improving the stability of the photochromic systems.

The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations.

Aurora kinase family is one of the emerging targets in oncology drug discovery and several small molecules targeting aurora kinases have been discovered and evaluated under early phase I/II trials. Among them, PHA-739358 (compound 1r) is a 3-aminopyrazole derivative with strong activity against Aurora A under early phase II trial. Inhibitory potency of compound 1r (the benzylic substituent at the pro-R position) is 30 times over that of compound 1s (the benzylic substituent at the pro-S position). In present study, the mechanism of how different configurations influence the binding affinity was investigated using molecular dynamics (MD) simulations, free energy calculations and free energy decomposition analysis. The predicted binding free energies of these two complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals contribution is important for distinguishing the binding affinities of these two inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the benzylic substituent could form different binding patterns with protein, thus leading to variant inhibitory potency of compounds 1r and 1s. The combination of different molecular modeling techniques is an efficient way to interpret the chirality effects of inhibitors and our work gives valuable information for the chiral drug design in the near future.

Octathienyl/phenyl-substituted zinc phthalocyanines J-aggregated through conformational planarization.

A novel family of thiophene-decorated phthalocyanines (M-TPcs) was efficiently synthesized, during which the key intermediate of these compounds was purified through a chemical approach. In the optimized geometries of M-TPcs, the peripherally linked thiophene rings are tilted from the Pc core, which oppose aggregation considering the mutual steric hindrance. However, Zn-TPc formed J-aggregates in many solvents while Ni-TPc and Cu-TPc did not. Octaphenyl-substituted zinc Pc (Zn-PPc) showed similar J-aggregation behavior as Zn-TPc. This unusual J-aggregation was attributed to the conformational planarization of the corresponding molecules.

Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations.

Glycogen synthase kinase 3 (GSK-3) is an attractive target for the treatment of diabetes, and paullones have been reported to be effective inhibitors of GSK-3. However, it is still a challenging task to improve selectivity among protein kinases, especially cyclin-dependent kinases (CDKs). Here we investigated the mechanism that enables paullones to selectively inhibit GSK-3 rather than cyclin-dependent kinase 5 (CDK5) using sequence alignment, molecular dynamics simulations, free-energy calculations and free-energy decomposition analysis. The results indicate that the interaction between paullones and Val135 of GSK-3 is obviously stronger than that between paullones and Cys83 of CDK5, suggesting that paullones could be utilized as potent selective inhibitors. Meanwhile, we observed that the decrease in the interaction between paullones and the Asp86 of CDK5 favors their selectivity towards GSK-3 rather than CDK5, as demonstrated using 1-azakenpaullone as an example. Although substitution at position 9 and replacement at position 2 may influence the activity of GSK-3, they only have a minor effect on the selectivity. We expect that the information obtained here could prove useful for developing specific paullone inhibitors of GSK-3.

Free-standing array of multi-walled carbon nanotubes on silicon (111) by a field-inducing self-assembly process.

In this paper, the authors bring forward a novel method named as the field-inducing self-assembly process in which free-standing MWCNTs array can be assembled perpendicularly on silicon (111) wafer. The density of free-standing MWCNTs array is controllable by adjusting the DC voltage from 0 V to 40 V. Preferential MWCNTs array is obtained by the condensation reaction between carboxylic group of MWCNTs end and hydroxyl group of silicon electrode surface under a low DC field. And the MWCNTs array can exhibit excellent field emission property.

Studies on two types of PTP1B inhibitors for the treatment of type 2 diabetes: Hologram QSAR for OBA and BBB analogues.

Hologram quantitative structure-activity relationships (HQSAR) analysis were conducted on two series of PTP1B inhibitors, 39 2-(oxalylamino) benzoic acid (OBA) analogues and 60 benzofuran and benzothiophene biphenyls (BBB) analogues. The optimal HQSAR model of the OBA analogue has q(2)=0.592 and r(2)=0.940, while the optimal HQSAR model for the BBB analogues shows q(2)=0.667 and r(2)=0.863. Two models were employed to predict the biological activities of two test sets. For OBA analogues, the optimal model was validated by an external test set of six compounds with satisfactory predictive r(2) value of 0.786. For BBB analogues, the optimal model shows satisfactory predictive r(2) value of 0.866 for an external test set of 10 compounds. The contribution maps derived from the optimal HQSAR models are consistent with the biological activities of the studied compounds. Two virtual combinatorial libraries were designed and screened by the optimal HQSAR models and potential candidates with high predictive biological activities were discovered. This work may provide valuable information for future design of more promising inhibitors for PTP1B.

Fabrication of hierarchical CaCO3 mesoporous spheres: particle-mediated self-organization induced by biphase interfaces and SAMs.

Highly ordered hierarchical calcium carbonate is an important phase involved in calcification by a wide variety of invertebrate organisms, and its formation is of technological interest in the development of functional materials. In this article, porous CaCO(3) hierarchical microspheres with a hedgehoglike appearance have been fabricated on the flexible substrate under mild conditions. There are two points that play important roles in the regular organization of the terminal products: one is the biphase interfaces, which are generated by organic solvent n-hexane and an aqueous saturated solution of Ca(OH)(2), and the other is hydroxyl-terminated monolayers assembled on the flexible PET (poly(ethylene terephthalate)) substrate. The SEM images show that novel CaCO(3) hierarchical microspheres consist of densely stacked "shuttles" by the oriented self-organization of CaCO(3) nanoparticles. The IR and XRD spectra indicate that the as-synthesized products are composed of a calcite phase obtained by an ACC (amorphous calcium carbonate)-to-calcite transformation. In view of the results, a nanoparticle-mediated self-organization process induced by biphase interfaces and SAMs template is proposed for the integration of functional materials and nanodevices.

Synthesis, photophysical and photochemical properties of amphiphilic carboxyl phthalocyanine oligomers.

The synthesis and photochemical properties are reported for a series of novel amphiphilic carboxyl polymeric phthalocyanines, with zinc (3a), aluminum (3b), ytterbium (3c) and hydrogen (metal-free, 3d) as the substituted central atom, respectively. The synthesis routes included cyclotetramerization of tetra-phthalonitriles and subsequent hydrolysis of cyano to carboxyl in alkaline solution. All four molecules were verified to be oligomers by viscosity method. Specifically, 3c showed strongest fluorescent emission, which can be elevated by Triton X 100 and CTAB. The singlet oxygen quantum yield (Phi(Delta)) for 3a and 3b were larger than that of 3c and 3d. In the presence of surfactants, nearly 2 folds enhancement of Phi(Delta) was observed as 0.76 and 0.70 for 3a and 3b, respectively. The characteristic photochemical properties of these oligomers suggested potential applications in photodynamic therapy, photocatalysis and photodynamic diagnoses.

Photoinduced multi-electron transfer in the Dn-A system consisting of multi-phthalocyanines linked to one carbon nanotube.

A Dn-A model in which a carbon nanotube (nanoscaled electron acceptor A) is attached with a number of electron donors (Dn), i.e. amino phthalocyanines, was employed to reveal the different nature of photoinduced electron transfer (PeT) in the nanoscaled model from that of a usual one-to-one linked D-A system, which is known to form the single-charge separation state D*+-A*-via well-studied single-electron transfer. For the Dn-A system, however, a one-step multi-electron transfer from multi donors to the same acceptor occurs simultaneously to generate a long-lived multiple-charge separation state Dn*+-A*n- (n>1), which is desirable for efficiently mimicking PSII in photosynthesis.

Prototropic equilibria, tautomerization and electronic absorption properties of dibenzofluorescein in aqueous solution related to its capability as a fluorescence probe.

The protolytic equilibria of 1,2,7,8-dibenzofluorescein in aqueous solution have been characterized by visible absorption and fluorescence spectra. The species involved are identified as dianion, monoanion, neutral form and cation. The neutral form includes both the quinoid and lactone structures. The pKas were calculated by an improved procedure to be 3.14, 4.04 and 6.28, respectively. The absorption spectra for each protolytic form were resolved. The absorption maxima (molar absorption coefficient, x10(5), M(-1) cm(-1)) are 532 nm (0.87) for the dianion, 510 nm (0.39) for the monoanion, 500 nm (0.16) for the neutral form, and 494 nm (0.19) for the cation, respectively. Contrary to the assumption in the literature, we found that the monoanion is highly fluorescent (Phif=0.66, compared to Phif=0.25 for dianion) and its molar ratio can reach 50% at neutral pH. It is therefore concluded that under physiological pH conditions the monoanion plays a major role when it is used as a fluorescence probe.

Photoresponsive J-aggregation behavior of a novel azobenzene-phthalocyanine dyad and its third-order optical nonlinearity.

The photoresponsive J-aggregation behaviors of a novel azobenzene-substituted zinc phthalocyanine (azo-ZnPc dyad) were studied by UV/vis, fluorescence, and (1)H NMR spectroscopy. Upon illumination with 365 nm UV light, the trans-cis isomerization of azobenzene can efficiently reduce the steric hindrance around the peripheral oxygen atom of azo-ZnPc, shortening the possible distance between two phthalocyanine molecules and, consequently, greatly improving the tendency of J-aggregation of azo-ZnPc dyad. The third-order optical nonlinearities of the photoresponsive J-aggregates (before and after illumination) were measured by a Z-scan technique at 532 nm with a pulse duration of 25 ps. The Z-scan spectra revealed that all the samples possessed large positive nonlinear refraction and positive nonlinear absorption, exhibiting a self-focusing effect and reverse saturable absorption, respectively. The second molecular hyperpolarizabilities of the dyad in two conditions were measured to be 3.87 x 10(-30) and 4.82 x 10(-30) esu, respectively. All the results suggest that the azo-ZnPc dyad has potential in the field of nonlinear optics applications.

Photophysical properties of sulfonated dihydroxy phosphorus(V) tetrabenzotriazacorrole.

The photosensitizing properties of a novel phthalocyanine analogue, sulfonated dihydroxy phosphorus(V) tetrabenzotriazacorrole [P(OH)2TBCSn] and a non-sulfonated one [P(OH)2TBC] are reported in this paper. Different from other phthalocyanine derivatives, P(OH)2TBCSn shows little aggregation in aqueous solution. The fluorescence quantum yield (PhiF) of P(OH)2TBCSn is lower than that of the non-sulfonated one. Studies of triplet state photophysics show that the presence of peripheral substituents on the macrocycle enhances the quantum yield of the triplet state. The sulfonated derivative, P(OH)2TBCSn, has a longer triplet lifetime (tauT = 0.234 ms) and higher singlet oxygen quantum yield (PhiDelta = 0.88) than P(OH)2TBC. Together with the ground-state absorption properties, the photosensitizing properties of the new compound suggest that it may be used as an excellent photosensitizer for photodynamic therapy (PDT).

Photophysical properties of dibenzofluorescein and the presence of its tautomers or prototropic forms in organic solvents.

The UV/Vis absorption and fluorescence properties of dibenzofluorescein (DBFL) in organic solvents were measured and used to shed light on the possible presence of its tautomers or various prototropic forms. DBFL in aprotic solvents mainly exists in two tautomeric forms, viz. quinoid and lactone, but neither are efficiently fluorescent. In protic solvents, such as methanol and ethanol, both the monoanion and neutral quinoid are present and showed the highest fluorescence quantum yield. In contrast, DBFL is fully dissociated to the monoanion and dianion in deionized water.

Fluorescence properties of dibenzofluorescein in aqueous solution.

The deprotonation of dibenzofluorescein (DBFL), a long wavelength fluorescence probe, results in the simultaneous occurrence of neutral form, monoanion and dianion under physiological conditions. The fluorescence properties of the former two cannot be measured directly because they are always coexistent with some other species. By measuring the fluorescence under various pHs we computed the fluorescence parameters for each species involved in the prototropic equilibria of DBFL, including each species' emission spectrum, excitation spectrum, emission and excitation maximum, fluorescence quantum yield and lifetime. It was found that the monoanion is the most fluorescent chromospheres (Phif=0.66, compared to Phif=0.25 for dianion, 0.18 for cation and 0.0 for the neutral form). Together with the computed pKas, we are able to suggest that the monoanion plays a major role under physiological conditions when DBFL is used as a fluorescence probe, contrary to the assumption in literature.

Photochemical DNA cleavage by novel water-soluble sulfonated dihydroxy phosphorus(V) tetrabenzotriazacorrole.

The photosensitizing properties of a novel water-soluble phthalocyanine-like photosensitizer, sulfonated dihydroxy phosphorus(V) tetrabenzotriazacorrole {P(OH)(2)TBCS(n)}, have been reported. It is relevant for the use of this dye as photodynamic sensitizer. The compound exhibited significant photocleavage of supercoiled (SC) pUC19 DNA. The photooxygenation and photocleavage to DNA showed high efficiency in generating singlet oxygen.