SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks

Several software tools for the simulation and analysis of biochemical reaction networks have been developed in the last decades; however, assessing and comparing their computational performance in executing the typical tasks of computational systems biology can be limited by the lack of a standardized benchmarking approach. To overcome these limitations, we propose here a novel tool, named SMGen, designed to automatically generate synthetic models of reaction networks that, by construction, are characterized by relevant features (e.g., system connectivity and reaction discreteness) and non-trivial emergent dynamics of real biochemical networks. The generation of synthetic models in SMGen is based on the definition of an undirected graph consisting of a single connected component that, generally, results in a computationally demanding task; to speed up the overall process, SMGen exploits a main–worker paradigm. SMGen is also provided with a user-friendly graphical user interface, which allows the user to easily set up all the parameters required to generate a set of synthetic models with any number of reactions and species. We analysed the computational performance of SMGen by generating batches of symmetric and asymmetric reaction-based models (RBMs) of increasing size, showing how a different number of reactions and/or species affects the generation time. Our results show that when the number of reactions is higher than the number of species, SMGen has to identify and correct a large number of errors during the creation process of the RBMs, a circumstance that increases the running time. Still, SMGen can generate synthetic models with hundreds of species and reactions in less than 7 s.

Untethering sparteine: 1,3-diamine ligand for asymmetric synthesis in water

Chiral ligands are the toolbox for asymmetric synthesis to access 3D molecular world. Enabling efficient asymmetric reaction in water is a big challenge. As moisture/air stable and strong binding moieties, amines, compared to imine and phosphine ligands, are ideal candidates to accommodate asymmetric transformations in water. Known amine ligands like Proline analogues and Cinchona alkaloids showed excellent asymmetric induction. Sparteine, an alkaloid studied originated in 1968, had never been considered as a privileged catalyst due to its structure defection which led to poor reaction compatibility and unsatisfactory stereoselectivity. Here, we report the design of a chiral diamine catalyst untethering one of the sparteine rings. The diamine catalyst was easily accessed in two steps on 100 gram-scale. This chiral ligand was proved to be efficient for addition reactions in water providing products with excellent yields and enantiomeric ratios. This pluripotent catalyst has also shown good reactivity/enantioselectivity under organocatalysis, Cu and Pd-catalysed conditions. We anticipate that the ligand would allow further development of other catalysts for important yet challenging green stereoselective transformations.

Synthesis and Evaluation of C2-Symmetric SPIROL-Based bis-Oxazoline Ligands

This communication describes the synthesis of new bis-oxazoline chiral ligands (SPIROX) derived from the C2-symmetric spirocyclic scaffold (SPIROL). The readily available (R,R,R)-SPIROL (2) previously developed by our group was subjected to a three-step sequence that provided key diacid intermediate (R,R,R)-7 in 75% yield. This intermediate was subsequently coupled with (R)- and (S)-phenylglycinols to provide diastereomeric products, the cyclization of which led to two diastereomeric SPIROX ligands (R,R,R,R,R)-3a and (R,R,R,S,S)-3b in 85% and 79% yield, respectively. The complexation of (R,R,R,R,R)-3a and (R,R,R,S,S)-3b with CuCl and Cu(OTf)2 resulted in active catalysts that promoted the asymmetric reaction of α-diazopropionate and phenol. The resultant O–H insertion product was formed in 88% yield, and with excellent selectivity (97% ee) when ligand (R,R,R,R,R)-3a was used.

Catalytic Asymmetric Amino Acid and Its Derivatives by Chiral Aldehyde Catalysis

Amine acid transformation is an important chemical process in biological systems. As a well-developed and acknowledged tool, chiral aldehyde catalysis provides good catalytic activation and stereoselective control abilities in the asymmetric reaction of N-unprotected amino acid esters and amino acid esters analogs, in which the key to success is the design of the catalysts derived from chiral BINOL aldehyde, which is based on the face control of enolate intermediates. In this review, one of the co-catalytic systems that combined with a transition metal to form a multiplex catalytic system and the well-established multiplex stereocenters of chiral aldehyde catalysis have been reviewed. Finally, a novel organocatalysis is prospected.

Koshland’s model as a method for the analysis of enzymatic deracemization reactions

Koshland’s four-point location model is applied to consider some enzymatic reactions of deracemization. The sequen-tial model is a theory describing the cooperativity of protein subunits. It postulates that the conformation of the protein changes with each binding of a ligand, thus sequentially changing its affinity to ligands at adjacent binding sites. When the substrate binds to the active site of one subunit of the enzyme, the remaining subunits are activated. The possibility of the alternative binding of both substrates and products of the enzymatic reaction can be assessed on the basis of the known data on the structure of all four substituents at the chiral atom and their correspondence to the ligand specificity of the corresponding subsets of the enzyme. The made theoretical conclusions were tested by the example of the enzymatic deracemization of some hydroxyphosphonic acids. The replacement of ethoxyl groups at the phosphorus atom by isopropoxy groups and an increase in the volume of the substituent led to a significant increase in the enantiomeric excess of the hydrolysis product of hydroxyphosphonate. Hence, the conclusion is drawn that the key criterion for the efficient or inefficient passage of the reaction is the ratio of the sizes and the degree of hydrophobicity of the corresponding substituents at the asymmetric reaction center.

Sensitivities of Southeast Asian industries to the local and global business cycles

PurposeThis paper estimates the sensitivities of the output of the manufacturing industries of the four Southeast countries (Indonesia, Malaysia, Philippines, Singapore) to both the country-specific and global business cycle fluctuations. The study investigates whether the business cycle exposures of these industries differ to their nature classified as producing durable or nondurable goods and also to booms and recessions.Design/methodology/approachUsing annual time series data on sectoral manufacturing production indices for major manufacturing industries over the period from 1999 to 2018, this paper uses the seemingly unrelated regression (SUR)–based generalized least square estimator to estimate the exposures of each industry for each of the four countries to local and world business cycle.FindingsThe individual country analysis indicates that generally the sensitivities of the ASEAN manufacturing industries to booms and recessions are different from the pattern observed in the developed countries and Russia. We do not find evidence consistent with the commonly held view among economists and business managers that demand for durable goods flourishes in booms and falls in recessions. Also, very few industries exhibit an asymmetric reaction to booms and busts. However, the analysis of panel data reveals the expected pattern of industrial sensitivities to the local business cycle only.Originality/valueThe paper makes several contributions. Firstly, the model proposed in the paper estimates sensitivities of industries to both the local and global business cycle variations. Secondly, the model enables us to explicitly test the asymmetric reaction of industries to booms and busts. Thirdly, the paper is the first attempt to estimating business cycle exposures for manufacturing industries in emerging markets.

Synthesis of optically active 2-amino-1′-benzyl-2′,5-dioxo-5H-spiro[indeno[1,2-b]pyran-4,3′-indoline]-3-carbonitriles catalyzed by a bifunctional squaramide derived from quinine

The first organocatalytic asymmetric reaction of propylene malononitrile with oxoindole and 1,3-indandione for the synthesis of chiral indeno-spiro compounds has been developed.

Synthetic Studies towards the Total Synthesis of Indole Alkaloids Containing Indolyl Lactam Frameworks

In this account, recent progress on the synthetic studies of several monoterpene indole alkaloids, (±)-mersicarpine, misassigned (±)-tronoharine, and (±)-leuconodines D and E, is summarized. Specifically, the rationale for the design and development of the Lewis acid catalyzed SN1-type substitution and formal [3+3] cycloaddition reaction of indol-2-yl carbinols, and the Pd-catalyzed aerobic oxidative intramolecular Heck cross-coupling of indolyl amides tethered with a terminal olefin functionality, are emphasized. These key reactions set the basis for the rapid construction of the fused ring skeleton containing an all-carbon quaternary center at the indol-2-yl position.1 Introduction2 Synthetic Study of (±)-Mersicarpine3 Synthetic Study of the Misassigned (±)-Tronoharine4 Study of the Asymmetric Reaction of Indol-2-yl Carbinols5 Synthetic Study of (±)-Leuconodines D and E6 Conclusion