ABSTRACT
Mathematical modelling of molecular systems can be extremely helpful in elucidating complex phenomena in (bio)chemistry. However, equilibrium conditions in systems consisting of more than two components, such as for molecular glues bound to two proteins, can typically not be analytically determined without assumptions and (semi-)numerical models are not trivial to derive by the non-expert. Here we present a framework for equilibrium models, geared towards molecular glues and other contemporary multicomponent chemical biology challenges. The framework utilizes a general derivation method capable of generating custom mass-balance models for equilibrium conditions of complex molecular systems, based on the simple, reversible biomolecular reactions describing these systems. Several chemical biology concepts are revisited via the framework to demonstrate the simplicity, generality and validity of the approach. The ease of use of the framework and the ability to both analyze systems and gain additional insights in the underlying parameters driving equilibria formation strongly aids the analysis and understanding of biomolecular systems. New directions for research and analysis are brought forward based on the model formation and system and parameter analysis. This conceptual framework severely reduces the time and expertise requirements which currently impede the broad integration of such valuable equilibrium models into molecular glue development and chemical biology research.
ABSTRACT
Scaffold proteins operate as organizing hubs to enable high-fidelity signaling, fulfilling crucial roles in the regulation of cellular processes. Bottom-up construction of controllable scaffolding platforms is attractive for the implementation of regulatory processes in synthetic biology. Here, we present a modular and switchable synthetic scaffolding system, integrating scaffold-mediated signaling with switchable kinase/phosphatase input control. Phosphorylation-responsive inhibitory peptide motifs were fused to 14-3-3 proteins to generate dimeric protein scaffolds with appended regulatory peptide motifs. The availability of the scaffold for intermolecular partner protein binding could be lowered up to 35-fold upon phosphorylation of the autoinhibition motifs, as demonstrated using three different kinases. In addition, a hetero-bivalent autoinhibitory platform design allowed for dual-kinase input regulation of scaffold activity. Reversibility of the regulatory platform was illustrated through phosphatase-controlled abrogation of autoinhibition, resulting in full recovery of 14-3-3 scaffold activity.
Subject(s)
14-3-3 Proteins , Peptides , 14-3-3 Proteins/chemistry , Peptides/metabolism , Phosphoric Monoester Hydrolases/metabolism , Phosphorylation , Protein BindingABSTRACT
Covering: 1978 to 2019 The synthetically challenging [3.3.3]propellane core has caught a lot of attention over the last 50 years. This comprehensive review details all synthetic strategies reported in the period 1978-2019 to facilitate the synthesis of carbocyclic [3.3.3]propellanes. The described strategies span from acid-catalyzed rearrangements and photo-mediated cycloadditions of ketones, heteropropellanes and dispiroundecanes to thermal rearrangements of acetylenes and alkenes. Other approaches, such as radical reactions with halogenated alkenes, domino cyclizations, the smart use of epoxide-carbonyl rearrangements and intramolecular palladium-catalyzed ring contractions are discussed as well. A special section is dedicated to triptindanes, a subclass of [3.3.3]propellanes which are of interest to material sciences.
Subject(s)
Biological Products/chemistry , Bridged-Ring Compounds/chemistry , Photochemistry/methods , Alkynes , Biological Products/chemical synthesis , Bridged-Ring Compounds/chemical synthesis , Bridged-Ring Compounds/metabolism , Catalysis , Cyclization , Cycloaddition Reaction , Epoxy Compounds/chemistry , Ketones/chemistry , Molecular Structure , Palladium , Polycyclic Sesquiterpenes/chemical synthesis , Polycyclic Sesquiterpenes/chemistry , Polycyclic Sesquiterpenes/metabolismABSTRACT
A diverse set of highly substituted 4-aminoquinolines was synthesized from ynamides, triflic anhydride, 2-chloropyridine, and readily accessible amides in a mild one-step procedure.
ABSTRACT
Covering: up to 2014. Xanthone dimers are a widespread, structurally-diverse family of natural products frequently found in plants, fungi and lichens. They feature an intriguing variety of linkages between the component xanthones (benzannulated chromanones). These synthetically elusive secondary metabolites are of great interest due to their broad array of bioactivities, which has led to the xanthones being designated as 'privileged structures'. We seek herein to give an overview of all reliably-described xanthone dimers, their structures, occurrence, and the bioactivities established to date. The possible biosynthetic pathways leading to members of this family are also discussed in light of our current knowledge.
Subject(s)
Biological Products , Xanthones/chemistry , Fungi/chemistry , Lichens/chemistry , Molecular Structure , Plants/chemistryABSTRACT
Double or nothing! Recently the total synthesis of secalonic acids A and D was reported. This work and other natural product syntheses with a dimerization step as a common feature are featured in this Highlight. The significant biological activity of the secalonic acids and the fact that their synthesis has fascinated synthetic chemists for the past forty years make this work a milestone in natural product synthesis.
