Equilibrium Effective Molarity As a Key Concept in Ring-Chain Equilibria, Dynamic Combinatorial Chemistry, Cooperativity and Self-assembly

2016 ◽  
pp. 1-76 ◽  
Author(s):  
S. Di Stefano ◽  
G. Ercolani
Keyword(s):  
Combinatorial Chemistry ◽  
Self Assembly ◽  
Dynamic Combinatorial Chemistry ◽  
Effective Molarity

scholarly journals Enzyme-mediated dynamic combinatorial chemistry allows out-of-equilibrium template-directed synthesis of macrocyclic oligosaccharides

2019 ◽  
Vol 10 (43) ◽  
pp. 9981-9987 ◽  
Author(s):  
Dennis Larsen ◽  
Sophie R. Beeren
Keyword(s):  
Dynamic System ◽  
Combinatorial Chemistry ◽  
Self Assembly ◽  
Dynamic Combinatorial Chemistry ◽  
Directed Synthesis

Artificial templates can control out-of-equilibrium self-assembly in an enzyme-mediated dynamic system of cyclodextrins, even allowing access to products not selected in Nature.

scholarly journals Applications of dynamic combinatorial chemistry for the determination of effective molarity

2015 ◽  
Vol 6 (1) ◽  
pp. 144-151 ◽  
Author(s):  
Maria Ciaccia ◽  
Irene Tosi ◽  
Laura Baldini ◽  
Roberta Cacciapaglia ◽  
Luigi Mandolini ◽  
...  
Keyword(s):  
Combinatorial Chemistry ◽  
Dynamic Combinatorial Chemistry ◽  
Effective Molarity

Chain-stoppers give rise to ring-chain equilibria in dynamic libraries allowing determination of thermodynamic effective molarities for macrocylisation reactions.

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

2011 ◽  
Vol 64 (6) ◽  
pp. 671 ◽  
Author(s):  
Chandramathi R. Sherman Durai ◽  
Margaret M. Harding
Keyword(s):  
Nucleic Acids ◽  
Combinatorial Chemistry ◽  
Self Assembly ◽  
Block Design ◽  
Quadruplex Dna ◽  
Dynamic Combinatorial Chemistry ◽  
Lead Compounds ◽  
Dna And Rna ◽  
Target Nucleic Acid ◽  
Dna Quadruplex

Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.

scholarly journals Biomimetic selenocystine based dynamic combinatorial chemistry for thiol-disulfide exchange

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Andrea Canal-Martín ◽  
Ruth Pérez-Fernández
Keyword(s):  
Glucose Oxidase ◽  
Combinatorial Chemistry ◽  
Self Assembly ◽  
Equilibrium Composition ◽  
Competitive Inhibitor ◽  
Rnase A ◽  
Disulfide Exchange ◽  
Dynamic Combinatorial Chemistry ◽  
Physiological Conditions ◽  
Ph Conditions

AbstractDynamic combinatorial chemistry applied to biological environments requires the exchange chemistry of choice to take place under physiological conditions. Thiol-disulfide exchange, one of the most popular dynamic combinatorial chemistries, usually needs long equilibration times to reach the required equilibrium composition. Here we report selenocystine as a catalyst mimicking Nature’s strategy to accelerate thiol-disulfide exchange at physiological pH and low temperatures. Selenocystine is able to accelerate slow thiol-disulfide systems and to promote the correct folding of an scrambled RNase A enzyme, thus broadening the practical range of pH conditions for oxidative folding. Additionally, dynamic combinatorial chemistry target-driven self-assembly processes are tested using spermine, spermidine and NADPH (casting) and glucose oxidase (molding). A non-competitive inhibitor is identified in the glucose oxidase directed dynamic combinatorial library.

Formation and Trapping of the Thermodynamically Unfavoured Inverted-Hemicucurbit[6]uril

2019 ◽  
Author(s):  
Elena Prigorchenko ◽  
Sandra Kaabel ◽  
Triin Narva ◽  
Anastassia Baškir ◽  
Maria Fomitšenko ◽  
...  
Keyword(s):  
Complex Formation ◽  
Combinatorial Chemistry ◽  
Trifluoroacetic Acid ◽  
Chloride Anion ◽  
Binding Affinities ◽  
Dynamic Covalent Chemistry ◽  
Reaction Selectivity ◽  
Low Concentration ◽  
Dynamic Combinatorial Chemistry ◽  
First Time

Amplification of a thermodynamically unfavoured macrocyclic product through the directed shift of the equilibrium between dynamic covalent chemistry library members is difficult to achieve. We show for the first time that during condensation of formaldehyde and <i>cis</i>-<i>N,N'</i>-cyclohexa-1,2-diylurea formation of <i>inverted-cis</i>-cyclohexanohemicucurbit[6]uril (<i>i-cis</i>-cycHC[6]) can be induced at the expense of thermodynamically favoured <i>cis</i>-cyclohexanohemicucurbit[6]uril (<i>cis</i>-cycHC[6]). The formation of <i>i-cis-</i>cycHC[6] is enhanced in low concentration of the templating chloride anion and suppressed in excess of this template. We found that reaction selectivity is governed by the solution-based template-aided dynamic combinatorial chemistry and continuous removal of the formed cycHC[6] macrocycles from the equilibrating solution by precipitation. Notably, the <i>i-cis</i>-cycHC[6] was isolated with 33% yield. Different binding affinities of three diastereomeric <i>i-cis</i>-, <i>cis</i>-cycHC[6] and their chiral isomer (<i>R,R</i>)-cycHC[6] for trifluoroacetic acid demonstrate the influence of macrocycle geometry on complex formation.

scholarly journals Adventures in molecular recognition. The ins and outs of templating

2000 ◽  
Vol 72 (12) ◽  
pp. 2265-2274 ◽  
Author(s):  
Jeremy K. M. Sanders
Keyword(s):  
Molecular Recognition ◽  
Combinatorial Chemistry ◽  
Biological Systems ◽  
Design Approach ◽  
Supramolecular Systems ◽  
Disulfide Exchange ◽  
Dynamic Combinatorial Chemistry ◽  
Evolutionary Features ◽  
Selection Approach ◽  
Porphyrin Dimers

Two different approaches are described for the creation of supramolecular systems potentially capable of recognition and catalysis. Using the design approach, we have been able to accelerate and influence two different Diels­Alder reactions within the cavities of porphyrin dimers and trimers; this is templating from the outside inwards. The selection approach is a synthetic chemical attempt to capture some of the key evolutionary features of biological systems: dynamic combinatorial chemistry is used to create equilibrating mixtures of potential receptors, and then a template is used to select and amplify the desired system. Five potential reactions for such dynamic chemistry are discussed: base-catalyzed transesterification, hydrazone exchange, disulfide exchange, alkene metathesis, and Pd-catalyzed allyl exchange, and preliminary templating results (inside outwards) are presented.

Structure-Based Design of Inhibitors of the Aspartic Protease Endothiapepsin by Exploiting Dynamic Combinatorial Chemistry

2014 ◽  
Vol 53 (12) ◽  
pp. 3259-3263 ◽  
Author(s):  
Milon Mondal ◽  
Nedyalka Radeva ◽  
Helene Köster ◽  
Ahyoung Park ◽  
Constantinos Potamitis ◽  
...  
Keyword(s):  
Combinatorial Chemistry ◽  
Aspartic Protease ◽  
Dynamic Combinatorial Chemistry

Dynamic combinatorial chemistry with diselenides and disulfides in water

2014 ◽  
Vol 50 (28) ◽  
pp. 3716-3718 ◽  
Author(s):  
Brian Rasmussen ◽  
Anne Sørensen ◽  
Henrik Gotfredsen ◽  
Michael Pittelkow
Keyword(s):  
Combinatorial Chemistry ◽  
Reversible Reaction ◽  
Dynamic Combinatorial Chemistry

Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water at physiological pH.

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