Discovery of 2-Amide-3-methylester Thiophenes that Target SARS-CoV-2 Mac1 and Repress Coronavirus Replication, Validating Mac1 as an Antiviral Target.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed. Here, we describe small-molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation-mediated innate immune responses. Three high-throughput screening hits had the same 2-amide-3-methylester thiophene scaffold. We studied the compound binding mode using X-ray crystallography, allowing us to design analogues. Compound 27 (MDOLL-0229) had an IC50 of 2.1 µM and was selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human proteins. The improved potency allowed testing of its effect on virus replication, and indeed, 27 inhibited replication of both murine hepatitis virus (MHV) prototypes CoV and SARS-CoV-2. Sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1-targeted small molecule demonstrated to inhibit coronavirus replication in a cell model.

Highly effective fractionation chemistry to overcome the recalcitrance of softwood lignocellulose.

The efficient fractionation and thus production of individual biomass components are pivotal processes in the biorefinery concept. However, the recalcitrant nature of lignocellulose biomass, especially in the case of softwood, is one of the main obstacles to the wider application of biomass-based chemicals and materials. In this study, the use of aqueous acidic systems in the presence of thiourea was studied for the fractionation of softwood in mild conditions. Despite relatively low temperature (100 °C) and treatment times (30-90 min), notable high lignin removal efficiency (approximately 90 %) was obtained. Chemical characterization and the isolation of minor fraction of cationic, water-soluble lignin indicated that the fractionation proceed via nucleophilic addition of thiourea to lignin, resulting in dissolution of lignin in acidic water in relatively mild conditions. Besides high fractionation efficiency, both fiber and lignin fractions were obtained with bright color, significantly elevating their usability in material applications.

High Oxygen Barrier Polyester from 3,3'-Bifuran-5,5'-dicarboxylic Acid.

An exceptional oxygen barrier polyester prepared from a new biomass-derived monomer, 3,3'-bifuran-5,5'-dicarboxylic acid, is reported. When exposed to air, the furan-based polyester cross-links and gains O2 permeability 2 orders of magnitude lower than initially, resulting in performance comparable to the best polymers in this class, such as ethylene-vinyl alcohol copolymers. The cross-links hinder the crystallization of amorphous samples, also rendering them insoluble. The process was observable via UV-vis measurements, which showed a gradual increase of absorbance between wavelengths of 320 and 520 nm in free-standing films. The structural trigger bringing about these changes appears subtle: the polyester containing 5,5'-disubstituted 3,3'-bifuran moieties cross-linked, whereas the polyester with 5,5'-disubstituted 2,2'-bifuran moieties was inert. The 3,3'-bifuran-based polyester is effectively a semicrystalline thermoplastic, which is slowly converted into a cross-linked material with intriguing material properties once sufficiently exposed to ambient air.

Discovery of 2-amide-3-methylester thiophenes that target SARS-CoV-2 Mac1 and repress coronavirus replication, validating Mac1 as an anti-viral target.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed to combat additional SARS-CoV-2 variants or novel CoVs. Here, we describe small molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation mediated innate immune responses. The compounds inhibiting Mac1 were discovered through high-throughput screening (HTS) using a protein FRET-based competition assay and the best hit compound had an IC50 of 14 µM. Three validated HTS hits have the same 2-amide-3-methylester thiophene scaffold and the scaffold was selected for structure-activity relationship (SAR) studies through commercial and synthesized analogs. We studied the compound binding mode in detail using X-ray crystallography and this allowed us to focus on specific features of the compound and design analogs. Compound 27 (MDOLL-0229) had an IC50 of 2.1 µM and was generally selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human ADP-ribose binding proteins. The improved potency allowed testing of its effect on virus replication and indeed, 27 inhibited replication of both MHVa prototype CoV, and SARS-CoV-2. Furthermore, sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1 targeted small molecule demonstrated to inhibit coronavirus replication in a cell model. This, together with its well-defined binding mode, makes 27 a good candidate for further hit/lead-optimization efforts.

Syntheses of Thiophene and Thiazole-Based Building Blocks and Their Utilization in the Syntheses of A-D-A Type Organic Semiconducting Materials with Dithienosilolo Central Unit.

Dithienosilole moiety is an electron donating unit, and it has been applied, for example, as a part of small molecular and polymeric electron donors in high performance organic photovoltaic cells. Herein, we report efficient synthetic routes to two symmetrical, dithienosilolo-central-unit-based A-D-A type organic semiconducting materials DTS(Th 2 FBTTh) 2 and DTS(ThFBTTh) 2 . Fine-tuned conditions in Suzuki-Miyaura couplings were tested and utilized. The effect of inserting additional hexylthiophene structures symmetrically into the material backbone was investigated, and it was noted that contrary to commonly accepted fact, the distance between electron donor and acceptor seems to play a bigger role in lowering the E gap value of the molecule than just extending the length of the conjugated backbone. We searched for precedent cases from the literature, and these are compared to our findings. The optical properties of the materials were characterized with UV-vis spectroscopy. Majority of the intermediate compounds along the way to final products were produced with excellent yields. Our results offer highly efficient routes to many heterocyclic structures but also give new insights into the design of organic semiconducting materials.

Sidestream materials show potential as top-dressed soil improvers for peatland forests.

The effects of top-dressing of several industrial and farming sidestream materials on the growth of downy birch (Betula pubescens Ehrh.) and Scots pine (Pinus sylvestris L.) seedlings in natural sphagnum peat soil were evaluated. Wood fly ash, industrial filter cake waste, mine tailings sand (quartz feldspar from lithium orebody), and digestate and liquid reject of cow manure from a biogas plant were studied for their physical and chemical properties, as well as for their effects as soil ameliorants on seedling growth during one growing period in a greenhouse. Each material was top-dressed on unfertilised peat in pots in quantities that corresponded to the amounts of ash used in Finnish peatland forest fertilisation (2-6 t ha-1). During growing, the pH of percolate water from the growing pots was below 4, and in the treatments with filter cake even below 3. However, no clear impairment of seedling growth due to acidity was observed. In all treatments, birch and pine seedlings grew at least as well as in the unfertilised peat (control treatment). Growth was strongest in the peat top-dressed with additives originating from cow manure, in which the high N and P contents promoted growth so much that foliar N was found to be diluted with respect to a high P content in the birch seedlings. No harmful concentrations of heavy metal residues were observed from the materials used. Overall, the results suggest that all the used sidestream materials show potential as soil improvers on forested peatlands.

Renewable Furfural-Based Polyesters Bearing Sulfur-Bridged Difuran Moieties with High Oxygen Barrier Properties.

With the goal of achieving high barrier with bio-based materials, for example, for packaging applications, a series of novel furfural-based polyesters bearing sulfide-bridged difuran dicarboxylic acid units with high oxygen barrier properties were synthesized and characterized. For the novel poly(alkylene sulfanediyldifuranoate)s, a 11.2-1.9× higher barrier improvement factor compared to amorphous poly(ethylene terephthalate) was observed which places the novel polyesters in the top class among previously reported 2,5-furandicarboxylic acid (FDCA) and 2,2'-bifuran-based polyesters. Titanium-catalyzed polycondensation reactions between the novel synthesized monomer, dimethyl 5,5'-sulfanediyldi(furan-2-carboxylate), and four different diols, ethylene glycol, 1,3-propanediol, 1,4-butanediol, and 1,5-pentanediol, afforded difuran polyesters with high intrinsic viscosities (0.76-0.90 dL/g). These polyesters had good thermal stability, decomposing at 342-363 and 328-570 °C under nitrogen and air, respectively, which allowed processing them into free-standing films via melt-pressing. In tensile testing of the film specimens, tensile moduli in the range of 0.4-2.6 GPa were recorded, with higher values observed for the polyesters with shorter diol units. Interestingly, besides the low oxygen permeability, the renewable sulfide-bridged furan monomer also endowed the polyesters with slight UV shielding effect, with cutoff wavelengths of ca. 350 nm, in contrast to FDCA-based polyesters, which lack significant UV light absorption at over 300 nm.

Effects of compost, biochar and ash mixed in till soil cover of mine tailings on plant growth and bioaccumulation of elements: A growing test in a greenhouse.

Mine closures necessitate vegetation restoration to cover tailings fields and reduce environmental risks. Sole use of forest soil as growth medium provides only low fertility and slow plant growth especially in the harsh boreal climate conditions. This preliminary study examines the feasibility of recyclable waste materials added to forest till soil for improving vegetation success on reclaimed mine tailings. One compost type, three biochar types (Bc1-3) and two ash types (Ash1-2) were studied for physical and chemical properties as well as their effects on the growth and element accumulation of timothy (Phleum pratense L.), white clover (Trifolium repens L.) and Scots pine (Pinus sylvestris L.) during one growing period in a greenhouse. Oxidized surface tailings soil and Ash2 were the finest media components while compost and Ash1 were the coarsest. Tailings soil also had the highest salt contents and electrical conductivity, while in till soil they were at the lowest levels. Timothy and white clover germinated well in moist pure tailings soil but grew poorest in it. White clover grew poorly also in pure till soil. Best biomass growth was in the mixture of till, compost and Bc2 (from sewage sludge and woodchips). Planted pine seedlings grew relatively well in all media during the first growing season but Ash1 (from wood and peat) tended to promote height growth and pure till soil root biomass. In media containing Ash1, pine tissues accumulated B, Ca, Mg, K, Na and S. Elevated As content in tailings soil accumulated in plant shoot tissues slightly; only in the old needles of pine were As levels elevated. The results suggest that till and tailings media with compost added as a nitrogen source can promote adequate plant growth during initial growing seasons. Suitable types of biochar and ash amendments can further expedite plant establishment.

Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs.

The scaffold of TIQ-A, a previously known inhibitor of human poly-ADP-ribosyltransferase PARP1, was utilized to develop inhibitors against human mono-ADP-ribosyltransferases through structure-guided design and activity profiling. By supplementing the TIQ-A scaffold with small structural changes, based on a PARP10 inhibitor OUL35, selectivity changed from poly-ADP-ribosyltransferases towards mono-ADP-ribosyltransferases. Binding modes of analogs were experimentally verified by determining complex crystal structures with mono-ADP-ribosyltransferase PARP15 and with poly-ADP-ribosyltransferase TNKS2. The best analogs of the study achieved 10-20-fold selectivity towards mono-ADP-ribosyltransferases PARP10 and PARP15 while maintaining micromolar potencies. The work demonstrates a route to differentiate compound selectivity between mono- and poly-ribosyltransferases of the human ARTD family.

Amending mine tailing cover with compost and biochar: effects on vegetation establishment and metal bioaccumulation in the Finnish subarctic.

In the northern boreal zone, revegetation and landscaping of closed mine tailings are challenging due to the high concentrations of potentially toxic elements; the use of nutrient-poor, glacigenic cover material (till); cool temperatures; and short growing period. Recycled waste materials such as biochar (BC) and composted sewage sludge (CSS) have been suggested to improve soil forming process and revegetation success as well as decrease metal bioavailability in closed mine tailing areas. We conducted two field experiments in old iron mine tailings at Rautuvaara, northern Finland, where the native mine soil or transported cover till soil had not supported plant growth since the mining ended in 1989. The impacts of CSS and spruce (Picea abies)-derived BC application to till soil on the survival and growth of selected plant species (Pinus sylvestris, Salix myrsinifolia, and grass mixture containing Festuca rubra, Lolium perenne, and Trifolium repens) were investigated during two growing seasons. In addition, the potential of BC to reduce bioaccumulation of metals in plants was studied. We found that (1) organic amendment like CSS markedly enhanced the plant growth and is therefore needed for vegetation establishment in tailing sites that contained only transported till cover, and (2) BC application to till soil-CSS mixture further facilitated the success of grass mixtures resulting in 71-250% higher plant biomass. On the other hand, (3) no effects on P. sylvestris or S. myrsinifolia were recorded during the first growing seasons, and (4) accumulation of metals in cover plants was negligible and BC application to till further decreased the accumulation of Al, Cr, and Fe in the plant tissues.

Dynamics of above- and belowground responses of silver birch saplings and soil gases to soil freezing and waterlogging during dormancy.

Winter precipitation and soil freeze-thaw events have been predicted to increase in boreal regions with climate change. This may expose tree roots to waterlogging (WL) and soil freezing (Fr) more than in the current climate and therefore affect tree growth and survival. Using a whole-tree approach, we studied the responses of silver birch (Betula pendula Roth.) saplings, growing in mineral soil, to 6-week Fr and WL in factorial combinations during dormancy, with accompanying changes in soil gas concentrations. Physiological activation (dark-acclimated chlorophyll fluorescence and chlorophyll content index) and growth of leaves and shoot elongation and stem diameter growth started earlier in Fr than NoFr (soil not frozen). The starch content of leaves was temporarily higher in Fr than NoFr in the latter part of the growing season. Short and long root production and longevity decreased, and mortality increased by soil Fr, while there were no significant effects of WL. Increased fine root damage was followed by increased compensatory root growth. At the beginning of the growing season, stem sap flow increased fastest in Fr + WL, with some delay in both NoWL (without WL) treatments. At the end of the follow-up growing season, the hydraulic conductance and impedance loss factor of roots were higher in Fr than in NoFr, but there were no differences in above- and belowground biomasses. The concentration of soil carbon dioxide increased and methane decreased by soil Fr at the end of dormancy. At the beginning of the growing season, the concentration of nitrous oxide was higher in WL than in NoWL and higher in Fr than in NoFr. In general, soil Fr had more consistent effects on soil greenhouse gas concentrations than WL. To conclude, winter-time WL alone is not as harmful for roots as WL during the growing season.

Derivatives of a PARP Inhibitor TIQ-A through the Synthesis of 8-Alkoxythieno[2,3-c]isoquinolin-5(4H)-ones.

Thieno[2,3-c]isoquinolin-5(4H)-one is known for its potential as an anti-ischemic agent through the inhibition of poly(ADP-ribose) polymerase 1 (PARP1). However, the compound also inhibits many other enzymes of the PARP family, potentially limiting its usability. The broad inhibition profile, on the other hand, indicates that this molecule backbone could be potentially used as a scaffold for the development of specific inhibitors for certain PARP enzymes. These efforts call for novel synthetic strategies for substituted thieno[2,3-c]isoquinolin-5(4H)-one that could provide the needed selectivity. In this article, an efficient synthetic strategy for 8-alkoxythieno[2,3-c]isoquinolin-5(4H)-ones through eight steps is presented and other tested synthetic pathways are discussed in detail. Synthesis of 7-methoxythieno[2,3-c]isoquinolin-5(4H)-one is also demonstrated to show that the strategy can be applied widely in the syntheses of substituted alkoxythieno[2,3-c]isoquinolin-5(4H)-ones.

Utilizing Furfural-Based Bifuran Diester as Monomer and Comonomer for High-Performance Bioplastics: Properties of Poly(butylene furanoate), Poly(butylene bifuranoate), and Their Copolyesters.

Two homopolyesters and a series of novel random copolyesters were synthesized from two bio-based diacid esters, dimethyl 2,5-furandicarboxylate, a well-known renewable monomer, and dimethyl 2,2'-bifuran-5,5'-dicarboxylate, a more uncommon diacid based on biochemical furfural. Compared to homopolyesters poly(butylene furanoate) (PBF) and poly(butylene bifuranoate) (PBBf), their random copolyesters differed dramatically in that their melting temperatures were either lowered significantly or they showed no crystallinity at all. However, the thermal stabilities of the homopolyesters and the copolyesters were comparable. Based on tensile tests from amorphous film specimens, it was concluded that the elastic moduli, tensile strengths, and elongation at break values for all copolyesters were similar as well, irrespective of the furan:bifuran molar ratio. Tensile moduli of approximately 2 GPa and tensile strengths up to 66 MPa were observed for amorphous film specimens prepared from the copolyesters. However, copolymerizing bifuran units into PBF allowed the glass transition temperature to be increased by increasing the amount of bifuran units. Besides enhancing the glass transition temperatures, the bifuran units also conferred the copolyesters with significant UV absorbance. This combined with the highly amorphous nature of the copolyesters allowed them to be melt-pressed into highly transparent films with very low ultraviolet light transmission. It was also found that furan-bifuran copolyesters could be as effective, or better, oxygen barrier materials as neat PBF or PBBf, which themselves were found superior to common barrier polyesters such as PET.

Carbamation of Starch with Amine Using Dimethyl Carbonate as Coupling Agent.

A one-pot coupling of starch with alkyl amine was studied using dimethyl carbonate (DMC) as the coupling agent. Although reaction occurred without a catalyst (24 h, 70 °C), different catalysts, namely, imidazole, tetramethylguanidine, 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), and combinations thereof were investigated to improve the reaction efficiency. When 20 mol % DBU was used as a catalyst, the degree of substitution (DS) could be improved from 0.05 to 0.15 compared to the noncatalyzed reaction. When the amount of DBU was decreased to 5 mol %, catalytical activity remained, albeit with a slightly lower DS (0.09). Temperature did not have a significant effect on the DS but it could be used to alter the solubility of the product. Based on chemical analysis, the alkyl group was attached to starch by the formation of a carbamate group. As the carbonyl carbon in the carbamate originated from DMC, which, in turn, can be produced from carbon dioxide on an industrial scale, the current study provides a conventional way to utilize carbon dioxide-based chemicals in the functionalization of a natural polymer. DMC is also biodegradable and classified as a nonvolatile organic component, making it an environmentally desirable coupling agent.

UV-Blocking Synthetic Biopolymer from Biomass-Based Bifuran Diester and Ethylene Glycol.

A furan-based synthetic biopolymer composed of a bifuran monomer and ethylene glycol was synthesized through melt polycondensation, and the resulting polyester was found to have promising thermal and mechanical properties. The bifuran monomer, dimethyl 2,2'-bifuran-5,5'-dicarboxylate, was prepared using a palladium-catalyzed, phosphine ligand-free direct coupling protocol. A titanium-catalyzed polycondensation procedure was found effective at polymerizing the bifuran monomer with ethylene glycol. The prepared bifuran polyester exhibited several intriguing properties including high tensile modulus. In addition, the bifuran monomer furnished the polyester with a relatively high glass transition temperature. Films prepared from the new polyester also had excellent oxygen and water barrier properties, which were found to be superior to those of poly(ethylene terephthalate). Moreover, the novel polyester also has good ultraviolet radiation blocking properties.

Carboxymethyl Chitosan and Its Hydrophobically Modified Derivative as pH-Switchable Emulsifiers.

The emulsification properties of carboxymethyl chitosan (CMChi) and hydrophobically modified carboxymethyl chitosan (h-CMChi) were studied as a function of pH and dodecane/water ratio. The pH was varied between 6-10, and the oil/water ratio between 0.1-2.0. In CMChi solution, the emulsion stability increased as the pH was lowered from 10 to 7, and the phase inversion was shifted from oil/water ratio 1.0 to 1.8, respectively. The system behaved differently in pH 6 due to the aggregation of CMChi and the formation of nanoparticles (∼200-300 nm). No phase inversion was observed and the maximum amount of emulsified oil was reached at oil/water ratio 1.2. The h-CMChi showed similar behavior as a function of pH but, due to hydrophobic modification, the phase inversion was shifted to higher values in pH 7-10. In pH 6, the behavior was similar, but the maximum amount of emulsified oil was higher compared to CMChi. The amount of adsorbed particles correlated with the emulsified amount of oil. Reversible emulsification of dodecane was demonstrated by pH adjustment using CMChi and h-CMChi solutions. The formed emulsions were gel-like, suggesting particle-particle interaction.

Effectiveness of N,O-carboxymethyl chitosan on destabilization of Marine Diesel, Diesel and Marine-2T oil for oil spill treatment.

Oil spills are the significant sources of hydrocarbons entering in the receiving aquatic environment. An efficient method to remove hydrocarbons from water resources is adsorption. In this study, water soluble N,O-carboxymethyl chitosan (NO-CS) was synthesized by carboxymethylation of chitosan in a hydro-alcoholic medium at 50°C by chloroacetic acid. The polymer was characterized through degree of deacetylation, degree of substitution, FTIR and 1H NMR. Effectiveness of NO-CS as an adsorbent was studied as a function of dosage, salinity and pH to destabilize the Marine diesel (Oil-1), Diesel (Oil-2) and Marine-2T oil (Oil-3) into small oil droplets of less than 100µm. Optical microscope was used for studying the size of oil droplets and adsorption effect of the oils on this polymer. The destabilization of marine diesel was the most effective among the studied three oils, which showed excellent adsorption at sea water alkalinity and salinity.

The pH sensitive properties of carboxymethyl chitosan nanoparticles cross-linked with calcium ions.

In environmental applications the applied materials are required to be non-toxic and biodegradable. Carboxymethyl chitosan nanoparticles cross-linked with Ca2+ ions (CMC-Ca) fulfill these requirements, and they are also renewable. These nanoparticles were applied to oil-spill treatment in our previous study and here we focused on enhancing their properties. It was found that while the divalent Ca2+ ions are crucial for the formation of the CMC-Ca, the attractive interaction between NH3+ and COO- groups contributed significantly to the formation and stability of the CMC-Ca. The stability decreased as a function of pH due to the deprotonation of the amino groups. Therefore, the nanoparticles were found to be fundamentally pH sensitive in solution, if the pH deviated from the pH (7-9) that was used in the synthesis of the nanoparticles. The pH sensitive CMC-Ca synthesized in pH 7 and 8 were most stable in the studied conditions and could find applications in oil-spill treatment or controlled-release of substances.

Synthesis of Alkaline-Soluble Cellulose Methyl Carbamate Using a Reactive Deep Eutectic Solvent.

This study presents the use of a reactive deep eutectic solvent (DES) for the chemical modification of wood cellulose fibers. DES based on dimethylurea and ZnCl2 was used to synthetize cellulose methyl carbamate (CMeC). This synthesis was performed at elevated temperature under solvent-free conditions. Chemical characterization based on FTIR and NMR indicated that methyl carbamate was successfully introduced to cellulose, and a degree of substitution (DS) of 0.17 was obtained after 3 h of reaction at 150 °C. The product with a DS of 0.17 exhibited good alkaline solubility (in 3 % NaOH solution) after freeze-thawing, whereas the original cellulose fibers were practically insoluble even in 9 % NaOH. As dimethylurea can be produced from CO2 , this method can be used as a sustainable way to obtain novel cellulose materials with desirable properties for use in a wide range of applications.

Synthesis of Benzothiadiazole Derivatives by Applying C-C Cross-Couplings.

The benzothiadiazole moiety has been extensively exploited as a building block in the syntheses of efficient organic semiconducting materials during the past decade. In this paper, parallel synthetic routes to benzothiadiazole derivatives, inspired by previous computational findings, are reported. The results presented here show that various C-C cross-couplings of benzothiadiazole, thiophene, and thiazole derivatives can be efficiently performed by applying Xantphos as a ligand of the catalyst system. Moreover, improved and convenient methods to synthesize important chemical building blocks, e.g., 4,7-dibromo-2,1,3-benzothiadiazole, in good to quantitative yields are presented. Additionally, the feasibility of Suzuki-Miyaura and direct coupling methods are compared in the synthesis of target benzothiadiazole derivatives. The computational characterization of the prepared benzothiadiazole derivatives shows that these compounds have planar molecular backbones and the possibility of intramolecular charge transfer upon excitation. The experimental electrochemical and spectroscopic studies reveal that although the compounds have similar electronic and optical properties in solution, they behave differently in solid state due to the different alkyl side-group substitutions in the molecular backbone. These benzothiadiazole derivatives can be potentially used as building blocks in the construction of more advanced small molecule organic semiconductors with acceptor-donor-acceptor motifs.