Is PF-00835231 a Pan-SARS-CoV-2 Mpro Inhibitor? A Comparative Study

The COVID-19 outbreak continues to spread worldwide at a rapid rate. Currently, the absence of any effective antiviral treatment is the major concern for the global population. The reports of the occurrence of various point mutations within the important therapeutic target protein of SARS-CoV-2 has elevated the problem. The SARS-CoV-2 main protease (Mpro) is a major therapeutic target for new antiviral designs. In this study, the efficacy of PF-00835231 was investigated (a Mpro inhibitor under clinical trials) against the Mpro and their reported mutants. Various in silico approaches were used to investigate and compare the efficacy of PF-00835231 and five drugs previously documented to inhibit the Mpro. Our study shows that PF-00835231 is not only effective against the wild type but demonstrates a high affinity against the studied mutants as well.     

Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors

A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to C and D rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Thus, it was shown that the order of addition of reagents affects the composition of the reaction products: when sulfochlorides are added to berberrubine, their corresponding 9-O-sulfonates are predominantly formed; when berberrubine is added to pre-generated sulfenes, sultones are the only products. The reaction was shown to proceed stereo-selectively and the cycle configuration was confirmed by 2D NMR spectroscopy. The inhibitory activity of the synthesized sultones and their 12-brominated analogs against the DNA-repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1), an important target for a potential antitumor therapy, was studied. All derivatives were active in the micromolar and submicromolar range, in contrast to the acyclic analogs and 9-O-sulfonates, which were inactive. The significance of the sultone cycle and bromine substituent in binding with the enzyme was confirmed using molecular modeling. The active inhibitors are mostly non-toxic to the HeLa cancer cell line, and several ligands show synergy with topotecan, a topoisomerase 1 poison in clinical use. Thus, novel berberine derivatives can be considered as candidates for adjuvant therapy against cancer.     

Rutin and Quercetin Decrease Cholesterol in HepG2 Cells but Not Plasma Cholesterol in Hamsters by Oral Administration

Rutin (R) and quercetin (Q) are two widespread dietary flavonoids. Previous studies regarding the plasma cholesterol-lowering activity of R and Q generated inconsistent results. The present study was therefore carried out to investigate the effects of R and Q on cholesterol metabolism in both HepG2 cells and hypercholesterolemia hamsters. Results from HepG2 cell experiments demonstrate that both R and Q decreased cholesterol at doses of 5 and 10 µM. R and Q up-regulated both the mRNA and protein expression of sterol regulatory element binding protein 2 (SREBP2), low-density lipoprotein receptor (LDLR), and liver X receptor alpha (LXRα). The immunofluorescence study revealed that R and Q increased the LDLR expression, while only Q improved LDL-C uptake in HepG2 cells. Results from hypercholesterolemia hamsters fed diets containing R (5.5 g/kg diet) and Q (2.5 g/kg diet) for 8 weeks demonstrate that both R and Q had no effect on plasma total cholesterol. In the liver, only Q reduced cholesterol significantly. The discrepancy between the in vitro and in vivo studies was probably due to a poor bioavailability of flavonoids in the intestine. It was therefore concluded that R and Q were effective in reducing cholesterol in HepG2 cells in vitro, whereas in vivo, the oral administration of the two flavonoids had little effect on plasma cholesterol in hamsters.     

Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology

BackgroundIn this study, the network pharmacological methods were used to predict the target of effective components of compounds in Zisheng Shenqi Decoction (ZSD, or Nourishing Kidney Qi Decoction) in the treatment of gouty arthritis (GA).MethodThe main effective components and corresponding key targets of herbs in the ZSD were discerned through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis (TCMSP), Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine (BATMAN-TCM) database. UniProt database and Swiss Target Prediction (STP) database was used to rectify and unify the target names and supply the target information. The targets related to GA were obtained by using GeneCards database. After we discovered the potential common targets between ZSD and GA, the interaction network diagram of “ZSD-component-GA-target” was constructed by Cytoscape software (Version 3.7.1). Subsequently, the Protein-protein interaction (PPI) network of ZSD effective components-targets and GA-related targets was constructed by Search Tool for the Retrieval of Interacting Genes Database (STRING). Bioconductor package “org.Hs.eg.db” and “cluster profiler” package were installed in R software (Version 3.6.0) which used for Gene Ontology analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis.Results146 components and 613 targets of 11 herbal medicines in the ZSD were got from TCMSP database and BATMAN-TCM database. 987 targets of GA were obtained from GeneCards database. After intersected and removed duplications, 132 common targets between ZSD and GA were screened out by Cytoscape software (Version 3.7.1). These common targets derived from 81 effective components of 146 components, such as quercetin, stigmasterol and kaempferol. They were closely related to anti-inflammatory, analgesic and anti oxidative stress and the principal targets comprised of Purinergic receptor P2X, ligand-gated ion channel 7 (P2x7R), Nod-like receptor protein 3 (NLRP3) and IL-1β. GO enrichment analysis and KEGG pathway enrichment analysis by R software (Version 3.6.0) showed that the key target genes had close relationship with oxidative stress, reactive oxygen species (ROS) metabolic process and leukocyte migration in aspects of biological process, cell components and molecular function. It also indicated that ZSD could decrease inflammatory reaction, alleviate ROS accumulation and attenuate pain by regulating P2 × 7R and NOD like receptor signaling pathway of inflammatory reaction.ConclusionA total of 81 effective components and 132 common target genes between ZSD and GA were screened by network pharmacology. The PPI network, GO enrichment analysis and KEGG pathway enrichment analysis suggested that ZSD can exerte anti-inflammatory and analgesic effects on the treatment of GA by reducing decreasing inflammatory reaction, alleviating ROS accumulation, and attenuating pain. The possible molecular mechanism of it mainly involved multiple components, multiple targets and multiple signaling pathways, which provided a comprehensive understanding for further study. In general, the network pharmacological method applied in this study provides an alternative strategy for the mechanism of ZSD in the treatment of GA.     

SO2 Resisting Pd-doped Pr1-xCexMnO3 Perovskites for Efficient Denitration at Low Temperature

H₂-SCR is served as the promising technology for the controlling of NO_x emission, and the Pd-based derivative catalyst exhibited high NO_x reduction performance. Effectively regulating the electronic configuration of the active component is favorable to the rational optimization of noble Pd. In this work, a series of Pr_1-xCe_xMn_1-yPd_yO₃@Ni were successfully synthesized and exhibited superior NO conversion efficiency at low temperatures. 92.7 % conversion efficiency was achieved at 200 °C over Pr_0.9Ce_0.1Mn_0.9Pd_0.1O₃@Ni in the presence of 4 % O₂ with a GHSV of 32000 h⁻¹. Meanwhile, the outstanding performance was obtained in the resistance to SO₂ (200 ppm) and H₂O (8 %). Deduced from the results of XRD, Raman, XPS, and H₂-TPR, the modification of d orbit states in palladium was confirmed originating from the incorporation in the B site of Pr_0.9Ce_0.1Mn_0.9Pd_0.1O₃. The existence of higher valence (Pd³⁺ and Pd⁴⁺) than the bivalence in Pr_0.9Ce_0.1Mn_0.9Pd_0.1O₃ catalyst was evidenced by XPS analysis. Our research provides a new sight into the H₂-SCR through the higher utilization of Pd.     

Synthesis,characterization and biological activity evaluation of new 3- methyl and 4- fluoro isoindoline-1, 3-dione/phthalimide analogues

The convenient route for the synthesis of a series of new Isoindoline-1, 3-dione/phthalimide analogues by condensation of substituted phthalic anhydride with an appropriate Ar-amine is described. Selective phthalimide derivatives were evaluated for their preliminary biological activities against Gram-positive, Gram-negative and fungi strains. These encouraging results could be helpful for the development of new antibacterial or antifungal agents.     

Acetylene Derivatives of Cationic Diazaoxatriangulenes and Diaza [4]Helicenes - Access to Red Emitters and Planar Chiral Stereochemical Traits

Cationic triangulenes, and related helicenes, constitute a rich class of dyes and fluorophores, usually absorbing and emitting light at low energy, in the orange to red domains. Recently, to broaden the scope of applications, regioselective late-stage functionalizations on these core moieties have been developed. For instance, with the introduction of electron-donating groups (EDGs), important bathochromic shifts are observed pushing absorptions towards or in the near-infrared (NIR) spectral domain while emissive properties disappear essentially completely. Herein, to upset this drawback, acetylene derivatives of cationic diazaoxa triangulenes (DAOTA) and [4]helicenes are prepared (16 examples). Contrary to other EDG-functionalized derivatives, C≡C− functionalized products remain broadly fluorescent, with red-shifted absorptions (Δλ_abs up to 25 nm) and emissions (Δλ_em up to 73 nm, Φ_PL up to 51 %). Quite interestingly, a general dynamic stereoisomerism phenomenon is evidenced for the compounds derived from achiral DAOTA cores. At low temperature in ¹H NMR spectroscopy (218 K), N−CH₂ protons become diastereotopic with chemical shifts differences (Δδ) as high as +1.64 ppm. The signal coalescence occurs around 273 K with a barrier of ∼12 kcal mol⁻¹. This phenomenon is due to planar chiral conformations (S_p and R_p configurations), induced by the geometry of the alkyl (n-propyl) side-chains next to the acetylenic substituents. Ion pairing studies with Δ-TRISPHAT anion not only confirm the occurrence of the chiral conformations but evidence a moderate but definite asymmetric induction from the chiral anion onto the cations. Finally, DFT calculations offer a valuable insight on the geometries, the corresponding stereodynamics and also on the very large difference in NMR for some of the diastereotopic protons.     

Inhomogeneous ‘longitudinal’ plane waves in a deformed elastic material

By definition, a homogeneous isotropic compressible Hadamard material has the property that an infinitesimal longitudinal homogeneous plane wave may propagate in every direction when the material is maintained in a state of arbitrary finite static homogeneous deformation. Here, as regards the wave, homogeneous means that the direction of propagation of the wave is parallel to the direction of eventual attenuation; and longitudinal means that the wave is linearly polarized in a direction parallel to the direction of propagation. In other words, the displacement is of the form u = ncos k(n · x – ct), where n is a real vector. It is seen that the Hadamard material is the most general one for which a longitudinal inhomogeneous plane wave may also propagate in any direction of a predeformed body. Here, inhomogeneous means that the wave is attenuated, in a direction distinct from the direction of propagation; and longitudinal means that the wave is elliptically polarized in the plane containing these two directions, and that the ellipse of polarization is similar and similarly situated to the ellipse for which the real and imaginary parts of the complex wave vector are conjugate semi-diameters. In other words, the displacement is of the form u = {S exp i(S · x – ct)}, where S is a complex vector (or bivector). Then a Generalized Hadamard material is introduced. It is the most general homogeneous isotropic compressible material which allows the propagation of infinitesimal longitudinal inhomogeneous plane circularly polarized waves for all choices of the isotropic directional bivector. Finally, the most general forms of response functions are found for homogeneously deformed isotropic elastic materials in which longitudinal inhomogeneous plane waves may propagate with a circular polarization in each of the two planes of central circular section of the ⁿ -ellipsoid, where is the left Cauchy-Green strain tensor corresponding to the primary pure homogeneous deformation.     

Measurement of energy release rate and energy flux of rapidly bifurcating crack in Homalite 100 and Araldite B by high-speed holographic microscopy

High-speed holographic microscopy is applied to take three successive photographs of fast propagating cracks in Homalite 100 or in Araldite B at the moment of bifurcation. Crack speed at bifurcation is about 540 m/s on Homalite 100, and about 450 m/s on Araldite B. From the photographs, crack speeds immediately before and after bifurcation are obtained, and it is found that discontinuous change of crack speed does not exist at the moment of bifurcation in the case of Homalite 100, but exists in the case of Araldite B. From the photographs, crack opening displacement (COD) is also measured along the cracks as a function of distance r from the crack tips. The measurement results show that the CODs are proportional to √r before bifurcation. After bifurcation, the CODs of mother cracks are proportional to √r, though the CODs of branch cracks are not always proportional to √r. The energy release rate is obtained from the measured CODs, and it is found that energy release rate is continuous at bifurcation point in both cases of Homalite 100 and Araldite B. Energy flux that shows the energy flow toward a crack tip is also obtained.     

Energy release rates in a constrained epoxy disc with Hookean and Mooney–Rivlin materials

Assuming that the disc material can be modeled either as Mooney–Rivlin or as Hookean and the steel ring enclosing the disc as Hookean, the energy release rates as a function of the crack length are evaluated and compared. Two loadings are considered––one in which the surface of the star shape hole in the disc is loaded by a uniform pressure and the other in which the temperature of the composite body is uniformly raised. It is found that the linear and the nonlinear analyses give qualitatively similar results for the two loadings. For each load, the energy release rate increases with an increase in the starter crack length, reaches a maximum value and then decreases gradually.