Protein crystal’s shape and polymorphism prediction within the limits resulting from the exploration of the Miyazawa–Jernigan matrix

A computer study of the prediction of the protein crystal’s shape and polymorphism of crystal’s structures within the limits resulting from the exploration of the Miyazawa–Jernigan matrix is presented. In this study, a coarse-graining procedure was applied to prepare a two-dimensional growth unit, where instead of full atom representation of the protein a two-type (hydrophobic–hydrophilic, HP) aminoacidal representation was used. The interaction energies between hydrophobic ($E_{\text{HH}}$) aminoacids were chosen from the well-known HP-type models ($E_{\text{HH}}\in [-4\text{,}-3\text{,}-2.3\text{,}-1]$), whereas interaction energies between hydrophobic and hydrophilic aminoacids ($E_{\text{HP}}$) as well as interaction energies between hydrophilic aminoacids ($E_{\text{PP}}$) were chosen from the range: $<-1\text{,}1>$, but not all values from this range fulfiled limitations resulting from the exploration of the Miyazawa–Jernigan matrix. Exploring every positively vetted combinations of energy interactions a polymorphism of the unit cell was observed what led to the fact that different final crystal’s shapes were obtained.     

Tocopheramine succinate and tocopheryl succinate: Mechanism of mitochondrial inhibition and superoxide radical production

Tocopherols (TOH) are lipophilic antioxidants which require the phenolic OH group for their redox activity. In contrast, non-redox active esters of α-TOH with succinate (α-TOS) were shown to possess proapoptotic activity in cancer cells. It was suggested that this activity is mediated via mitochondrial inhibition with subsequent ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ production triggering apoptosis and that the modification of the linker between the succinate and the lipophilic chroman may modulate this activity. However, the specific mechanism and the influence of the linker are not clear yet on the level of the mitochondrial respiratory chain. Therefore, this study systematically compared the effects of α-TOH acetate (α-TOA), α-TOS and α-tocopheramine succinate (α-TNS) in cells and submitochondrial particles (SMP). The results showed that not all cancer cell lines are highly sensitive to α-TOS and α-TNS. In HeLa cells α-TNS did more effectively reduce cell viability than α-TOS. The complex I activity of SMP was little affected by α-TNS and α-TOS while the complex II activity was much more inhibited (IC₅₀ = 42 ± 8 μM α-TOS, 106 ± 8 μM α-TNS, respectively) than by α-TOA (IC₅₀ >1000 μM). Also the complex III activity was inhibited by α-TNS (IC₅₀ = 137 ± 6 μM) and α-TOS (IC₅₀ = 315 ± 23 μM). Oxygen consumption of NADH- or succinate-respiring SMP, involving the whole electron transfer machinery, was dose-dependently decreased by α-TOS and α-TNS, but only marginal effects were observed in the presence of α-TOA. In contrast to the similar inhibition pattern of α-TOS and α-TNS, only α-TOS triggered ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ formation in succinate- and NADH-respiring SMP. Inhibitor studies excluded complex I as ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ source and suggested an involvement of complex III in ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ production. In cancer cells only α-TOS was reproducibly able to increase ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ levels above the background level but neither α-TNS nor α-TOA. Furthermore, the stability of α-TNS in liver homogenates was significantly lower than that of α-TOS. In conclusion, this suggests that α-TNS although it has a structure similar to α-TOS is not acting via the same mechanism and that for α-TOS not only complex II but also complex III interactions are involved.     

Photosynthetic adaptation of soybean due to varying effectiveness of N2 fixation by two distinct Bradyrhizobium japonicum strains

Rhizobial N₂ fixation is a costly biochemical process, which takes 6–14% of current photosynthate (C) from legumes, without compromising grain productivity. In addition to the effects of leaf N nutrition, rhizobial symbiosis could stimulate photosynthesis due to the removal of C sink limitation by nodule activity. To test that hypothesis, we compared the photosynthetic capacity of soybean plants inoculated with two different strains of Bradyrhizobium japonicum (CPAC 390 or CPAC 7), varying in the effectiveness to fix N₂, with plants fertilized with NO₃⁻. Nodulated plants had 14–31% higher rates of photosynthesis and accumulated less starch in the leaves than N-fertilized plants. There was evidence that B. japonicum CPAC 390 had higher carbon costs of N₂ fixation compared with CPAC 7, but the increases in carbon costs were accompanied by higher rates of photosynthesis. By applying a biochemical model of leaf photosynthesis, including the limitations of Rubisco activity $(V_{{\text{C}}_{\text{max}}})$, electron transport rates (J) and triose-P utilization (TPU), we show that soybean plants adapt their photosynthetic capacity to support the stronger carbon sink created by faster rates of N₂ fixation. We observed that plants associated with CPAC 7 (of low effectiveness to fix N₂) increased their photosynthesis by removing sink limitation solely (with a constant $V_{{\text{C}}_{\text{max}}}$) whereas plants associated with CPAC 390 (of high effectiveness to fix N₂) increased their photosynthesis by sink stimulation. Based on the model, we propose that sink stimulation is governed by a positive feedback between TPU and Rubisco activation, resulting in an increased $V_{{\text{C}}_{\text{max}}}$.     

Synthesis and optimization of novel (3S,5R)-5-(2,2-dimethyl-5-oxo-4-phenylpiperazin-1-yl)piperidine-3-carboxamides as orally active renin inhibitors

We report synthesis and optimization of a series of (3S,5R)-5-(2,2-dimethyl-5-oxo-4-phenylpiperazin-1-yl)piperidine-3-carboxamides as renin inhibitors. Chemical modification of ${{\text{P}}_1}^{\prime }$, ${{\text{P}}_2}^{\prime }$ and P₃ portions led to a promising 3,5-disubstituted piperidine 32o showing high renin inhibitory activity and favorable oral exposure in both rats and cynomolgus monkeys with acceptable CYP and hERG current inhibition. Compound 32o exhibited a significant blood pressure lowering effect by oral administration in two hypertensive animal models, double transgenic rats and furosemide pretreated cynomolgus monkeys.