Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19. We present here structural models and dynamics of the helicase in complex with its native substrates based on thorough analysis of homologous sequences and existing experimental structures. We performed and analysed microseconds of molecular dynamics (MD) simulations, and our model provides valuable insights to the binding of the ATP and ssRNA at the atomic level. We identify the principal motions characterising the enzyme and highlight the effect of the natural substrates on this dynamics. Furthermore, allosteric binding sites are suggested by our pocket analysis. Our obtained structural and dynamical insights are important for subsequent studies of the catalytic function and for the development of specific inhibitors at our characterised binding pockets for this promising COVID-19 drug target.

The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19.     

Synthesis-enabled exploration of chiral and polar multivalent quaternary sulfides

An innovative method of synthesis is reported for the large and diverse (RE)₆(TM)_x(Tt)₂S₁₄ (RE = rare-earth, TM = transition metals, Tt = Si, Ge, and Sn) family of compounds (∼1000 members, ∼325 contain Si), crystallizing in the noncentrosymmetric, chiral, and polar P6₃ space group. Traditional synthesis of such phases involves the annealing of elements or binary sulfides at elevated temperatures. The atomic mixing of refractory components technique, presented here, allows the synthesis of known members and vastly expands the family to nearly the entire transition metal block, including 3d, 4d, and 5d TMs with oxidation states ranging from 1+ to 4+. Arc-melting of the RE, TM, and tetrel elements of choice forms an atomically-mixed precursor, which readily reacts with sulfur providing bulk powders and large single crystals of the target quaternary sulfides. Detailed in situ and ex situ experiments show the mechanism of formation, which involves multiphase binary sulfide intermediates. Crystal structures and metal oxidation states were corroborated by a combination of single crystal X-ray diffraction, elemental analysis, EPR, NMR, and SQUID magnetometry. The potential of La₆(TM)_x(Tt)₂S₁₄ compounds for non-linear optical applications was also demonstrated.

Synthesis from atomically-mixed precursors opens up a phase space to hundreds of chiral and polar sulfide semiconductors with almost any transition metal in variable oxidation states.     

Synthesis and In Vitro Characterization of Selective Cannabinoid CB2 Receptor Agonists: Biological Evaluation against Neuroblastoma Cancer Cells

1,8-naphthyridine-3-carboxamide structures were previously identified as a promising scaffold from which to obtain CB2R agonists with anticancer and anti-inflammatory activity. This work describes the synthesis and functional characterization of new 1,8-naphthyridin-2(1H)-one-3-carboxamides with high affinity and selectivity for CB2R. The new compounds were able to pharmacologically modulate the cAMP response without modulating CB2R-dependent β-arrestin2 recruitment. These structures were also evaluated for their anti-cancer activity against SH-SY5Y and SK-N-BE cells. They were able to reduce the cell viability of both neuroblastoma cancer cell lines with micromolar potency (IC₅₀ of FG158a = 11.8 μM and FG160a = 13.2 μM in SH-SY5Y cells) by a CB2R-mediated mechanism. Finally, in SH-SY5Y cells one of the newly synthesized compounds, FG158a, was able to modulate ERK1/2 expression by a CB2R-mediated effect, thus suggesting that this signaling pathway might be involved in its potential anti-cancer effect.     

Effect of spatial heterogeneity on level of rejuvenation in Ni80P20 metallic glass

Understanding the relation between spatial heterogeneity and structural rejuvenation is one of the hottest topics in the field of metallic glasses (MGs). In this work, molecular dynamics (MD) simulation is implemented to discover the effects of initial spatial heterogeneity on the level of rejuvenation in the Ni$_{80}$P$_{20 }$MGs. For this purpose, the samples are prepared with cooling rates of $10^{10}$ K/s-$10^{12}$ K/s to make glassy alloys with different atomic configurations. Firstly, it is found that the increase in the cooling rate leads the Gaussian-type shear modulus distribution to widen, indicating the aggregations in both elastically soft and hard regions. After the primary evaluations, the elastostatic loading is also used to transform structural rejuvenation into the atomic configurations. The results indicate that the sample with intermediate structural heterogeneity prepared with 10$^{11}$ K/s exhibits the maximum structural rejuvenation which is due to the fact that the atomic configuration in an intermediate structure contains more potential sites for generating the maximum atomic rearrangement and loosely packed regions under an external excitation. The features of atomic rearrangement and structural changes under the rejuvenation process are discussed in detail.     

Reliability of Clinician-Based (GRBAS and CAPE-V) and Patient-Based (V-RQOL and IPVI) Documentation of Voice Disorders

This study examined the reliability of two methods for documenting voice quality by clinicians and compared the methods for documenting patients' perceptions of voice quality. It involved a prospective reliability study and a retrospective chart review. Reliability of two clinician-based voice assessment protocols-Grade, Roughness, Breathiness, Asthenia, Strain (GRBAS) and Consensus Auditory Perceptual Evaluation-Voice (CAPE-V)-was evaluated. These two protocols were then compared after use in voice assessments of 42 males and 61 females performed by a certified speech-language pathologist specializing in the assessment of voice disorders. In addition, two patient-based scales (Voice Related Quality of Life, or V-RQOL, and Iowa Patient's Voice Index, or IPVI) obtained from the same patients were compared with each other and with the clinician-based scales. Reliability of clinicians' ratings of overall severity of dysphonia using GRBAS and CAPE-V scales was very good (r>0.80). Agreement between V-RQOL Total scores and IPVI ratings of the patient's perceptions of impact of dysphonia was less strong (Spearman's r=-0.76). There was relatively weak agreement between patient-based and clinician-based scales. Clinician's perceptions of dysphonia appeared to be reliable and unaffected by rating tool, as indicated by the high level of agreement between the two rating systems when they were used together. The CAPE-V system appeared to be more sensitive to small differences within and among patients than the GRBAS system. The V-RQOL and IPVI approaches to documenting patient's perceptions of dysphonia agreed less well possibly due to differences in patient dependence on voice and on interpretation of the rating tool items. The differences between clinician-based and patient-based data support the conclusion that clinicians and patients experience and consider dysphonia very differently.     

Distinct Mechanisms of Cytotoxicity in Novel Nitrogenous Heterocycles: Future Directions for a New Anti-Cancer Agent

Electron-rich, nitrogenous heteroaromatic compounds interact more with biological/cellular components than their non-nitrogenous counterparts. The strong intermolecular interactions with proteins, enzymes, and receptors confer significant biological and therapeutic properties to the imidazole derivatives, giving rise to a well-known and extensively used range of therapeutic drugs used for infections, inflammation, and cancer, to name a few. The current study investigates the anti-cancer properties of fourteen previously synthesized nitrogenous heterocycles, derivatives of imidazole and oxazolone, on a panel of cancer cell lines and, in addition, predicts the molecular interactions, pharmacokinetic and safety profiles of these compounds. Method: The MTT and CellTiter-Glo^® assays were used to screen the imidazole and oxazolone derivatives on six cancer cell lines: HL60, MDA-MB-321, KAIMRC1, KMIRC2, MCF-10A, and HCT8. Subsequently, in vitro tubulin staining and imaging were performed, and the level of apoptosis was measured using the Promega ApoTox-Glo^® triplex assay. Furthermore, several computational tools were utilized to investigate the pharmacokinetics and safety profile, including PASS Online, SEA Search, the QikProp tool, SwissADME, ProTox-II, and an in silico molecular docking study on tubulin to identify the critical molecular interactions. Results: In vitro analysis identified compounds 8 and 9 to possess the most significant potent cytotoxic activity on the HL60 and MDA-MB-231 cell lines, supported by PASS Online anti-cancer predictions with pa scores of 0.413 and 0.434, respectively. In addition, compound 9 induced caspase 3/7 dependent-apoptosis and interfered with tubulin polymerization in the MDA-MB-231 cell line, consistent with in silico docking results, identifying binding similarity to the native ligand colchicine. All the derivatives, including compounds 8 and 9, had acceptable pharmacokinetics; however, the safety profile was suboptimal for all the tested derivates except compound 4. Conclusion: The imidazole derivative compound 9 is a promising anti-cancer agent that switches on caspase-dependent apoptotic cell death and modulates microtubule function. Therefore, it could be a lead compound for further drug optimization and development.     

Correlating Sensory Assessment of Smoke-Tainted Wines with Inter-Laboratory Study Consensus Values for Volatile Phenols

Vineyard exposure to wildfire smoke can taint grapes and wine. To understand the impact of this taint, it is imperative that the analytical methods used are accurate and precise. This study compared the variance across nine commercial and research laboratories following quantitative analysis of the same set of smoke-tainted wines. In parallel, correlations between the interlaboratory consensus values for smoke-taint markers and sensory analyses of the same smoke-tainted wines were evaluated. For free guaiacol, the mean accuracy was 94 ± 11% in model wine, while the free cresols and 4-methylguaiacol showed a negative bias and/or decreased precision relative to guaiacol. Similar trends were observed in smoke-tainted wines, with the cresols and glycosidically bound markers demonstrating high variance. Collectively, the interlaboratory results show that data from a single laboratory can be used quantitatively to understand smoke-taint. Results from different laboratories, however, should not be directly compared due to the high variance between study participants. Correlations between consensus compositional data and sensory evaluations suggest the risk of perceivable smoke-taint can be predicted from free cresol concentrations, overcoming limitations associated with the occurrence of some volatile phenols, guaiacol in particular, as natural constituents of some grape cultivars and of the oak used for barrel maturation.     

Optimization of Microwave-Assisted Pectin Extraction from Cocoa Pod Husk

Optimization of pectin extraction from cocoa pod husk was carried out to examine independent variables that affect the quality of pectin obtained and determine the best conditions for the extraction process. In this study, three independent variables thought to contribute to microwave-assisted pectin extraction were used, namely, extraction time (20, 25, and 30 min), microwave power (180, 300, and 450 W), and citric acid concentration (2.5%, 5%, and 10%). Response surface methodology was applied using central composite design (CCD) to examine the effect of independent variables on the parameter measured. Among the seven parameters measured, namely, yield, temperature, moisture content, ash content, equivalent weight, methoxyl content, and galacturonic acid content, the statistical analysis test showed that the model equations that were suitable for predicting response values were temperature, moisture content, and ash content. Therefore, the optimization of conditions was only reviewed for these three parameters. Optimization results concluded that the factors that had the most significant effect on temperature, moisture content, and ash content were extraction time and microwave power. Optimal conditions for pectin extraction were at 30 min extraction time, 450 W microwave power, and 10% solvent concentration, resulting in a temperature of 104 °C, moisture content of 6%, and ash content of 8%. Other parameter values measured under these conditions were a yield of 21.10%, equivalent weight of 602.40 mg/mol, methoxyl content of 6.07%, and galacturonic acid content of 72.86%. Pectin extracted from cocoa pod husk using this method has the potential to be further applied, especially in the food and pharmaceutical industries.     

Polysorbates versus Hydroxypropyl Beta-Cyclodextrin (HPβCD): Comparative Study on Excipient Stability and Stabilization Benefits on Monoclonal Antibodies

Polysorbates (PS 20 and PS 80) are the most widely used surfactants in biopharmaceutical formulations to protect proteins from denaturation, aggregation, and surface adsorption. To date, around 70% of marketed therapeutic antibodies contain either PS 20 or PS 80 in their formulations. However, polysorbates are chemically diverse mixtures, which are prone to degradation by oxidation and hydrolysis to produce peroxides and fatty acids, which, in turn, induce protein oxidation, aggregation, and insoluble particle formation. These will negatively impact protein quality and stability. Thus, polysorbate degradation has emerged as one of the major challenges in the development and commercialization of therapeutic protein products. KLEPTOSE^® HPβCD (hydroxypropyl beta-cyclodextrin), a new multifunctional excipient, has been shown to provide protein stabilization functions in biopharmaceutical downstream processes and in their final formulations. This study aims to evaluate HPβCD, a new molecule of its class, against polysorbates as a stabilizer in biologics formulations. In this study, the chemical stability of KLEPTOSE^® HPβCDs is compared with polysorbates (20 and 80) under various stress conditions. When subjected to heat stress, HPβCDs show little change in product recovery (90.7–100.7% recovery for different HPβCDs), while polysorbates 20 and 80 show significant degradation, with only 11.5% and 7.3% undegraded product remaining, respectively. When subjected to other chemical stressors, namely, autoclave, light, and oxidative stresses, HPβCD remains almost stable, while polysorbates show more severe degradation, with 95.5% to 98.8% remaining for polysorbate 20 and 85.5% to 97.4% remaining for polysorbate 80. Further, profiling characterization and degradation analysis reveal that chemical structures of HPβCDs remain intact, while polysorbates undergo significant hydrolytic degradation and oxidation. Lastly, the physicochemical stability of monoclonal antibodies in formulations is investigated. When subjected to light stress, adalimumab, as a model mAb, formulated in the presence of HPβCD, shows a significant decrease in protein aggregation, and superior monomer and total protein recovery compared to PS 80-containing formulations. HPβCD also reduces both agitation and thermal stress-induced protein aggregation and prevents subvisible particle formation compared to PS 80.