scholarly journals Using transient equilibria (TREQ) to measure the thermodynamics of slowly assembling supramolecular systems

2021 ◽  
Author(s):  
Christopher Hennecker ◽  
Christophe Lachance-Brais ◽  
Hanadi Sleiman ◽  
Anthony Mittermaier
Keyword(s):  
Thermal Analysis ◽  
Supramolecular Chemistry ◽  
Molecular Interactions ◽  
Binding Sites ◽  
Thermodynamic Data ◽  
Cyanuric Acid ◽  
Spectroscopic Method ◽  
Analytical Tool ◽  
Supramolecular Systems ◽  
Proof Of Principle

Supramolecular chemistry involves the non-covalent assembly of monomers into materials with unique properties and wide-ranging applications. Thermal analysis is a key analytical tool in this field, as it provides quantitative thermodynamic information on both the structural stability and nature of the underlying molecular interactions. However there exist many supramolecular systems whose kinetics are so slow under conditions approaching equilibrium that thermodynamic data are inaccessible. We have developed a simple and rapid spectroscopic method for extracting thermodynamic parameters from these systems. It is based on repeatedly raising and lowering the temperature during assembly and identifying the points of transient equilibrium as they are passed on the up- and down-scans. In a proof-of-principle application to the co-assembly of polydeoxyadenosine containing 15 adenosines (polyA15) and cyanuric acid (CA), we found that roughly 30% of the CA binding sites on the polyA chains were unoccupied, with implications for the assembly of high-valence systems.

Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites

2019 ◽  
Author(s):  
Michael Olp ◽  
Daniel Sprague ◽  
Stefan Kathman ◽  
Ziyang Xu ◽  
Alexandar Statsyuk ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Site ◽  
Binding Sites ◽  
Computational Prediction ◽  
Chemical Probes ◽  
Computational Docking ◽  
Fragment Screening ◽  
Covalent Inhibitors ◽  
Bet Protein ◽  
Proof Of Principle

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>

scholarly journals Efficient and Flexible Synthesis of New Photoactivatable Propofol Analogs

2020 ◽  
Author(s):  
Kenneth Skinner ◽  
Joseph Wzorek ◽  
Daniel Kahne ◽  
Rachelle Gaudet
Keyword(s):  
Binding Sites ◽  
Transient Receptor Potential ◽  
Receptor Potential ◽  
General Anesthetic ◽  
Bioorthogonal Chemistry ◽  
Functional Assays ◽  
Pain Pathway ◽  
Synthetic Routes ◽  
Transient Receptor ◽  
Proof Of Principle

Propofol is a widely used general anesthetic, which acts by binding to and modulating several neuronal ion channels. We describe the synthesis of photoactivatable propofol analogs functionalized with an alkyne handle for bioorthogonal chemistry. Such tools are useful for detecting and isolating photolabeled proteins. We designed expedient and flexible synthetic routes to three new diazirine-based crosslinkable propofol derivatives, two of which have alkyne handles. As a proof of principle, we show that these compounds activate heterologously expressed Transient Receptor Potential Ankyrin 1 (TRPA1), a key ion channel of the pain pathway, with a similar potency as propofol in fluorescence-based functional assays. This work demonstrates that installation of the crosslinkable and clickable group on a short nonpolar spacer at the para position of propofol does not affect TRPA1 activation, supporting the utility of these chemical tools in identifying and characterizing potentially druggable binding sites in propofolinteracting proteins.

scholarly journals NMR Spectroscopy of supramolecular chemistry on protein surfaces

2020 ◽  
Vol 16 ◽  
pp. 2505-2522
Author(s):  
Peter Bayer ◽  
Anja Matena ◽  
Christine Beuck
Keyword(s):  
Nmr Spectroscopy ◽  
Supramolecular Chemistry ◽  
Molecular Interactions ◽  
Protein Interactions ◽  
Atomic Resolution ◽  
Protein Protein Interactions ◽  
Protein Surfaces ◽  
Interaction Partners ◽  
Binding Pockets ◽  
Nmr Methods

As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.

N-Ethylmaleimide-modified actin filaments do not bundle in the presence of α-actinin

1995 ◽  
Vol 73 (1-2) ◽  
pp. 116-122 ◽  
Author(s):  
Aldo Milzani ◽  
Isabella DalleDonne ◽  
Roberto Colombo
Keyword(s):  
Polyethylene Glycol ◽  
Chemical Modification ◽  
Molecular Interactions ◽  
Binding Sites ◽  
Actin Filaments ◽  
Actin Assembly ◽  
Chemically Modified ◽  
C Terminus ◽  
Spatial Reorganization ◽  
Polyethylene Glycol 6000

We show that the modification of actin subdomain 1 by N-ethylmaleimide (NEM), which binds Cys-374 close to the C-terminus of the molecule, inhibits the α-actinin-induced bundling of actin filaments. This effect is not merely related to the block of Cys-374, since N-(1-pyrenyl)iodoacetamide (pyrene-IA) is unable to prevent bundling. Considering that NEM (but not pyrene-IA) influences actin assembly, we suggest that the inhibition of the actin – α-actinin interaction is due to the chemical modification of actin Cys-374 which, by inducing a marked spatial reorganization of actin monomers, is able to modify both the intra- and inter-molecular interactions of this protein. Finally, NEM-modified actin filaments form bundles in the presence of polyethylene glycol 6000 since, in this case, the side by side association of actin filaments does not depend on the accessibility of binding sites nor on the formation of chemical bonds.Key words: chemically modified actin, N-ethylmaleimide, pyrene-IA, Cys-374, actin bundles, α-actinin.

Assessing cooperativity in supramolecular systems

2017 ◽  
Vol 46 (9) ◽  
pp. 2622-2637 ◽  
Author(s):  
Larissa K. S. von Krbek ◽  
Christoph A. Schalley ◽  
Pall Thordarson
Keyword(s):  
Supramolecular Chemistry ◽  
Thermodynamic Analysis ◽  
Supramolecular Systems

In this tutorial review, different aspects of cooperativity in supramolecular chemistry and their thermodynamic analysis are discussed.

Nanophotonics and supramolecular chemistry

Nanophotonics ◽  
2013 ◽  
Vol 2 (4) ◽  
pp. 265-277 ◽  
Author(s):  
Katsuhiko Ariga ◽  
Hirokazu Komatsu ◽  
Jonathan P. Hill
Keyword(s):  
Supramolecular Chemistry ◽  
Self Assembly ◽  
Short Review ◽  
Important Research ◽  
Supramolecular Systems ◽  
Bottom Up ◽  
Practical Applications ◽  
Nanoscience And Nanotechnology

AbstractSupramolecular chemistry has become a key area in emerging bottom-up nanoscience and nanotechnology. In particular, supramolecular systems that can produce a photonic output are increasingly important research targets and present various possibilities for practical applications. Accordingly, photonic properties of various supramolecular systems at the nanoscale are important in current nanotechnology. In this short review, nanophotonics in supramolecular chemistry will be briefly summarized by introducing recent examples of control of photonic responses of supramolecular systems. Topics are categorized according to the fundamental actions of their supramolecular systems: (i) self-assembly; (ii) recognition; (iii) manipulation.

scholarly journals Towards Complex Matter: Supramolecular Chemistry and Self-organization

2009 ◽  
Vol 17 (2) ◽  
pp. 263-280 ◽  
Author(s):  
Jean-Marie Lehn
Keyword(s):  
Supramolecular Chemistry ◽  
Self Assembly ◽  
Building Blocks ◽  
Intermolecular Forces ◽  
Self Organization ◽  
Irreversible Processes ◽  
Continuous Change ◽  
Supramolecular Systems ◽  
Molecular Information ◽  
Complex Matter

Chemistry has developed from molecular chemistry, mastering the combination and recombination of atoms into increasingly complex molecules, to supramolecular chemistry, harnessing intermolecular forces for the generation of informed supramolecular systems and processes through the implementation of molecular information carried by electromagnetic interactions. Supramolecular chemistry is actively exploring systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, on the basis of the molecular information stored in the covalent framework of the components and read out at the supramolecular level through specific molecular recognition interactional algorithms, thus behaving as programmed chemical systems. Supramolecular entities as well as molecules containing reversible bonds are able to undergo a continuous change in constitution by reorganization and exchange of building blocks. This capability defines a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. It takes advantage of dynamic constitutional diversity to allow variation and selection and thus adaptation. The merging of the features of supramolecular systems – information and programmability; dynamics and reversibility; constitution and structural diversity – points towards the emergence of adaptive chemistry. A further development will concern the inclusion of the arrow of time, i.e. of non-equilibrium, irreversible processes and the exploration of the frontiers of chemical evolution towards the establishment of evolutive chemistry, where the features acquired by adaptation are conserved and transmitted. In combination with the corresponding fields of physics and biology, chemistry thus plays a major role in the progressive elaboration of a science of informed, organized, evolutive matter, a science of complex matter.

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