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Systems chemistry aims to develop molecular systems that display emerging properties arising from their network and absent in their individual constituents. Employing reversible chemistry under thermodynamic control represents a valuable tool for generating dynamic combinatorial libraries of interconverting molecules, which may exhibit intriguing collective behaviour. A simple dynamic combinatorial library was prepared using dithioacetal/thiol/disulfide exchanges. Because of the relative reactivities of these reversible reactions, the library constitutes a two-layer dynamic system with one layer active in an acid medium (thiol/dithioacetal exchange) and one layer active in a basic medium (thiol/disulfide exchange). This property enables the system to respond to momentary changes in acidity of the medium by activating different network regions, channeling some building blocks from one layer to another through shared thiol reagents (nodes). This momentaneous change in wiring affects the final steady state composition of the library, measured the next day, even though the event that caused it vanishes without leaving any residue. Therefore, the final composition of this dynamic system provides information about this transient past perturbation in the environment such as: when it occurred, how long it was, or how intense it was.

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Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.

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CD44 promotes metastasis, chemoresistance, and stemness in different types of cancer and is a target for the development of new anti-cancer therapies. All CD44 isoforms share a common N-terminal domain that binds to hyaluronic acid (HA). Herein, we used a computational approach to design new potential CD44 antagonists and evaluate their target-binding ability. By analyzing 30 crystal structures of the HA-binding domain (CD44HAbd), we characterized a subdomain that binds to 1,2,3,4-tetrahydroisoquinoline (THQ)-containing compounds and is adjacent to residues essential for HA interaction. By computational combinatorial chemistry (CCC), we designed 168,190 molecules and compared their conformers to a pharmacophore containing the key features of the crystallographic THQ binding mode. Approximately 0.01% of the compounds matched the pharmacophore and were analyzed by computational docking and molecular dynamics (MD). We identified two compounds, Can125 and Can159, that bound to human CD44HAbd (hCD44HAbd) in explicit-solvent MD simulations and therefore may elicit CD44 blockage. These compounds can be easily synthesized by multicomponent reactions for activity testing and their binding mode, reported here, could be helpful in the design of more potent CD44 antagonists.

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Peptide-based drug discovery is re-gaining attention in drug discovery. Similarly, combinatorial chemistry continues to be a useful technique for the rapid exploration of chemical space. A current challenge, however, is the enumeration of combinatorial peptide libraries using freely accessible tools. To facilitate the swift enumeration of combinatorial peptide libraries, we introduce herein D-Peptide Builder. In the current version, the user can build up to pentapeptides, linear or cyclic, using the natural pool of 20 amino acids. The user can use non- and/or N-methylated amino acids. The server also enables the rapid visualization of the chemical space of the newly enumerated peptides in comparison with other libraries relevant to drug discovery and preloaded in the server. D-Peptide Builder is freely accessible at http://dpeptidebuilder. quimica.unam.mx:4000/. It is also accessible through the open D-Tools platform (DIFACQUIM Tools for Chemoinformatics https://www.difacquim.com/d-tools/).

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Peptide and peptide-like structures are regaining attention in drug discovery. Previous studies suggest that bioactive peptides have diverse structures and may have physicochemical properties attractive to become hit and lead compounds. However, chemoinformatic studies that characterize such diversity are limited. Herein, we report the physicochemical property profile and chemical space of four synthetic linear and cyclic combinatorial peptide libraries. As a case study, the analysis was focused on penta-peptides. The chemical space of the peptide and N-methylated peptides libraries was compared to compound data sets of pharmaceutical relevance. Results indicated that there is a major overlap in the chemical space of N-methylated cyclic peptides with inhibitors of protein-protein interactions and macrocyclic natural products available for screening. Also, there is an overlap between the chemical space of the synthetic peptides with peptides approved for clinical use (or in clinical trials), and to other approved drugs that are outside the traditional chemical space. Results further support that synthetic penta-peptides are suitable compounds to be used in drug discovery projects.

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The control of the connectivity between nodes of synthetic networks is still largely unexplored. To address this point we take advantage of a simple dynamic chemical system with two exchange levels that are mutually connected and can be activated simultaneously or sequentially. Dithioacetals and disulfides can be exchanged simultaneously under UV light in the presence of a sensitizer. Crossover reactions between both exchange processes produce a fully connected chemical network. On the other hand, the use of acid, base or UV light connects different nodes allowing network rewiring.

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The kinetic and thermodynamic selectivity of acylhydrazone formation in dynamic combinatorial libraries (DCL) is described. Competition reactions were generated from hydrazides: isoniazid, 4-nitro-benzohydrazide, 4-dimethylamino-benzohydrazide, and nicotinic hydrazide as well as the aldehyde derivatives: benzaldehyde and 2-pyridine-carboxaldehyde. The obtained species and the distribution of the DCLs were monitored by 'H-NMR spectroscopy finding that those acylhydrazones containing the 4-dimethylamino-benzohydrazide moiety are both the kinetic and thermodynamic product of their respective libraries. Configurational and coordination dynamics for some of these libraries were also investigated. The obtained results allowed the study of the redistribution of components and the amplification of one or more products using light and metal ions as physical and chemical templates, respectively.

Se describe la selectividad cinética y termodinámica de la formación de acil-hidrazona en bibliotecas combinatorias dinámicas (DCL). Se generaron reacciones competitivas a partir de hidrazidas: isoniazida, 4-nitro-benzohidrazida, 4-dimetilamino-benzohidrazida y hidrazida nicotínica; así como a partir de los derivados de aldehído: benzaldehído y 2-piridin-carboxaldehido. Las especies obtenidas y la distribución de los DCLs fueron monitoreados mediante espectroscopia 'H-NMR, encontrándose que las acil-hidrazonas que contenían la 4-dimetilamino-benzohidrazida son tanto el producto cinético, como el termodinámico de sus respectivas bibliotecas. También se investigaron las dinámicas de configuración y de coordinación para algunas de estas bibliotecas. Los resultados obtenidos permitieron estudiar la redistribución de los componentes y la amplificación de uno o más productos usando luz e iones metálicos como plantillas físicas y químicas, respectivamente.

É descrita a seletividade cinética e termodinâmica da formação de acil-hidrazonas em livrarias combinatórias dinâmicas (DLC). Foram geradas reações competitivas a partir das hidrazidas: isoniazida, 4-nitro-benzohidrazida, 4-dimetilamino-benzohidrazida e hidrazida nicotínica; além dos derivados de aldeído: benzaldeído e 2-piridin-carboxaldeído. As espécies obtidas e a distribuição dos DLCs foram monitorados mediante espectroscopia 'H-NMR, foi encontrado que as acil-hidrazonas que continham à 4-dimetilamino-benzohidrazida são tanto o produto cinético como o termodinâmico de suas respectivas livrarias. Também investigaram-se as dinâmicas de configuração e coordenação para algumas destas livrarias. Os resultados obtidos permitem estudar a redistribuicao dos componentes e a amplificação de um ou mais produtos usando luz e íons metálicos como modelos físicos e químicos, respectivamente.

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Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.

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INTRODUCTION: Aptamers are oligonucleotide molecules raised in vitro from large combinatorial libraries of nucleic acids and developed to bind to targets with high affinity and specificity. Whereas novel target molecules are proposed for therapeutic intervention and diagnostic, aptamer technology has a great potential to become a source of lead compounds. AREAS COVERED: In this review, the authors address the current status of the technology and highlight the recent progress in aptamer-based technologies. They also discuss the current major technical limitations of aptamer technology and propose original solutions based on existing technologies that could result in a solid aptamer-discovery platform. EXPERT OPINION: Whereas aptamers have shown to bind to targets with similar affinities and specificities to those of antibodies, aptamers have several advantages that could outweigh antibody technology and open new opportunities for better medical and diagnostic solutions. However, the current status of the aptamer technology suffers from several technical limitations that slowdown the progression of novel aptamers into the clinic and makes the business around aptamers challenging.

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Hydrazones exhibit a versatile chemistry and are of interest for their potential use as functional molecular systems capable of undergoing reversible changes of configuration, i.e. E/Z isomerization. The title compound, C12H12N4O, has an E configuration with respect to the hydrazone C=N bond. The crystal packing is formed by N-H...N and O-H...N hydrogen bonds that give a two-dimensional layer structure and C-H...C interactions associated with layer stacking to produce the three-dimensional supramolecular structure. These intermolecular interactions were analyzed and quantified by the Hirshfeld surface method and the two-dimensional supramolecular arrangement was topologically simplified as a hcb network.

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During the past five years, the three-dimensional structures of 14 different G-protein coupled receptors (GPCRs) have been resolved by X-ray crystallography. The most recently published structures, those of the opioid receptors (ORs), are remarkably important in pain modulation, drug addiction, and mood disorders. These structures, confirmed previously proposed key interactions conferring potency and antagonistic properties, including the well-known interaction with Asp138, conserved in all aminergic GPCRs. In addition, crystallization of the opioid receptors highlighted the potential function of the ECL2 and ICL2 loops. We have previously reported a set of potent and selective kappa opioid receptor peptide agonists, of which ff(D-nle)r-NH2 is among the most potent and selective ones. These peptides were identified from the deconvolution of a 6,250,000 tetrapeptide combinatorial library. A derivative of this set is currently the subject of a phase 2 clinical trial in the United States. In this work, we describe comparative molecular modeling studies of kappa-OR peptide agonists with the co-crystallized antagonist, JDTic, and also report structure-activity relationships of 23 tetrapeptides. The overall binding and contact interactions are sound and interactions known to favor selectivity and potency were observed. Additional modeling studies will reveal conformational changes that the kappa-OR undergoes upon binding to these peptide agonists.

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