One-Pot Facile Synthesis of Substituted Isoindolinones via an Ugi Four-Component Condensation/Diels−Alder Cycloaddition/ Deselenization−Aromatization Sequence

A versatile one-pot synthesis of substituted isoindolinones from 2-furaldehydes, amines, 2-(phenylselanyl)acrylic acids, and isocyanides is described. The tandem process involves the Ugi four-component condensation, intramolecular Diels−Alder cycloaddition, and subsequent deselenization−aromatization promoted by BF3−OEt2. The procedure is general and efficient and the substrates are easily available

Hierarchical Feedback Modules and Reaction Hubs in Cell Signaling Networks

<div><p>Despite much effort, identification of modular structures and study of their organizing and functional roles remain a formidable challenge in molecular systems biology, which, however, is essential in reaching a systematic understanding of large-scale cell regulation networks and hence gaining capacity of exerting effective interference to cell activity. Combining graph theoretic methods with available dynamics information, we successfully retrieved multiple feedback modules of three important signaling networks. These feedbacks are structurally arranged in a hierarchical way and dynamically produce layered temporal profiles of output signals. We found that global and local feedbacks act in very different ways and on distinct features of the information flow conveyed by signal transduction but work highly coordinately to implement specific biological functions. The redundancy embodied with multiple signal-relaying channels and feedback controls bestow great robustness and the reaction hubs seated at junctions of different paths announce their paramount importance through exquisite parameter management. The current investigation reveals intriguing general features of the organization of cell signaling networks and their relevance to biological function, which may find interesting applications in analysis, design and control of bio-networks.</p></div

The functional redundancy test and the parameter sensitivity analysis of crucial proteins in the GPCR signaling network.

<p>(A) Functional redundancy in the forward module of the GPCR signaling network. Two pathways being PLC<i>β</i>3 or PLC<i>β</i>4 dependent, fork at G<i>α</i>q-GTP and converge at IP3. Their function shows redundancy since the concentration of IP3 still reaches as much as 80 percent of the original amplitude even if removing one of them from the signaling network. But when they are both removed, signal only reaches half of the original amplitude indicating the complementarity between the two paths in conducting signals. (B) Sensitivity to parameters of the reaction hub in the forward module of the GPCR signaling network. The reaction rate K08 is the synthetic rate of G<i>α</i>q-GTP and G<i>βγ</i>. Both products are essential for signal forwarding.</p

The Simplified schematics of the three signaling networks.

<p>(A) The sketch is related to the GPCR signaling pathway. The pathway in blue are the skeleton of the forward module depicting how signals propagate forward. Feedback modules in red indicate multiple regulations. The RGS in Module 3 drive two proteins: G<i>α</i>i-GTP and G<i>α</i>q-GTP into the off state: G<i>α</i>i-GDP and G<i>α</i>q-GDP. Reactions in Module 2 constitute a reaction chain, that is: IP3—> IP4—> IP5—> PIP2, and hence reduce the concentration of IP3. Module 2 and 3 are local feedbacks while Module 4 and 5 are working together serving as a global feedback module (B) The skeleton of the EGFR induced MAPK signaling network. Module 4, 5, 6 are three joint dephosphorylation feedback cycles. Module 4 is engaged in the dephosphorylation of ERK-PP, while Module 5 and 6 are able to convert MEK-PP and Raf* to MEK and Raf. Module 8 is also a local feedback serving as a buffer for the highly regulated compounds: (EGF-EGFR*)₂-GAP-Grb2-Sos, (EGF-EGFR*)₂-GAP-Shc*-Grb2-Sos. It also takes in the upstream protein Ras-GTP* and feeds the Ras-GDP back. Two global feedback modules reside near the end of the network. (C) A simplified plot of the JAK/STAT signaling network. The binding of the IFN-<i>γ</i> to its receptor causes activation of the transcription factor (STAT1n*)₂. The expression product SOCS1 suppresses signaling. SHP-2, serving as a tyrosine phosphatase in Module 3, can directly sequester the activation of (IFN-R-JAK*)₂. PPN (nuclear phosphatase TC45) involved in Module 2, and PPX (cytoplasmic phosphatase) embedded in Module 1 act in the same way to capture (STAT1n*)₂ or (STAT1c*)₂ and feed the inactive STAT1 back to the forward module.</p

Reaction cycles in the toy model.

<p>Reaction cycles in the toy model.</p

The redundancy test and the parameter sensitivity analysis of the MAPK signaling networks.

<p>(A) Two pathways from (EGF-EGFR*)₂-GAP to (EGF-EGFR*)₂-GAP-Grb2-Sos are both Shc independent. The blue and green curves indicate that removing either path has similar impact on the concentration of ERK-PP. (B) The sensitivity analysis for the reaction generating (EGF-EGFR*)₂-GAP. A small change in the reaction rate has a big effect on the output signal. A bifurcation is observed when k18 is less than 2.1e-5. (C) Sensitivity analysis of the binding rate of Ras-GDP to (EGF-EGFR*)₂-GAP-Grb2-Sos. (D) Sensitivity analysis of the binding rate of Ras-GDP to (EGF-EGFR*)₂-GAP-Shc*-Grb2-Sos. Another bifurcation is observed at the rate 2.0e-0.5.</p

The dynamical behavior of the target protein in the three signaling systems.

<p>(A) The IP3 concentration of the GPCR pathway over time by deleting individual feedback modules from the full network. All feedback modules in red act at different time scales and in different ways. (B) The ERK-PP concentration over time by deleting individual feedback modules from the whole MAPK network. Different feedback modules carry out different but synergetic functional duties during cell signaling. (C) The change of the (STAT1n*)₂ concentration over time by deleting individual feedbacks from the whole JAK/STAT network. The upstream local feedback (R09) delays the response significantly, and the feedback module (Module 3) directly linked to the target attenuates the output signal. (D) The change of Ca²⁺ concentration over time in the GPCR signaling system. Note that the faster the increase of [IP3], the shorter the response time and the higher the amplitude of the Ca²⁺ spark. A quick time response of IP3 determines the profile of the Ca²⁺ spark; and the amplitude of IP3 concentration does not seem to be of primary importance.</p

Edges in the toy model.

<p>S and E represent the start and the end of each edge and numbers in italics are indices.</p><p>Edges in the toy model.</p

The decomposition of the GPCR, the MAPK and the JAK/STAT signaling system.

<p>(A) The decomposition result of the GPCR mediated IP3-Ca²⁺ signal transduction pathway. One signaling forward module and four feedback modules are plotted. Green nodes are inputs of the networks, while red ones represent outputs; ovals symbolize reactants and products and squares functional nodes representing specific reactions. The edges connecting ovals to squares associate the participants to each reaction. In addition, a bi-directional line indicates that the reaction is reversible. (B) The decomposition result of the MAPK signaling network. The full network is decomposed into one big forward module, and seven feedback modules. (C) The decomposition result of the JAK/STAT signaling network. One main route constitutes the forward module. Module 1 and 2 are mid-ranged feedback controllers. A local feedback loop and the global gene regulation feedback module are combined in Module 3.</p

The toy model employed in the method for illustrating of our method.

<p>The toy model employed in the method for illustrating of our method.</p