1
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Diehl CJ, Salerno A, Ciulli A. Ternary Complex-Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo-PROTACs. Angew Chem Int Ed Engl 2024; 63:e202319456. [PMID: 38626385 DOI: 10.1002/anie.202319456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/18/2024]
Abstract
Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof-of-concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL-targeting Homo-PROTACs as model system, and show that the formation of a VHL2 : Homo-PROTAC ternary complex reversibly assembled using thiol-disulfide exchange chemistry leads to amplification of potent VHL Homo-PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo-PROTAC degraders. We anticipate future applications of ternary-complex directed DCC to early PROTAC screenings and expansion to other proximity-inducing modalities beyond PROTACs.
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Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessandra Salerno
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
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2
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Alena-Rodriguez M, Fernandez-Villamarin M, Alfonso I, Mendes PM. Discovery of selective monosaccharide receptors via dynamic combinatorial chemistry. Org Biomol Chem 2024; 22:3854-3859. [PMID: 38639197 PMCID: PMC11095087 DOI: 10.1039/d4ob00015c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
The molecular recognition of saccharides by synthetic hosts has become an appealing but elusive task in the last decades. Herein, we combine Dynamic Combinatorial Chemistry (DCC) for the rapid self-assembly and screening of virtual libraries of receptors, with the use of ITC and NMR to validate the hits and molecular modelling to understand the binding mechanisms. We discovered a minimalistic receptor, 1F (N-benzyl-L-phenylalanine), with considerable affinity for fructose (Ka = 1762 M-1) and remarkable selectivity (>50-fold) over other common monosaccharides. The approach accelerates the discovery process of receptors for saccharides.
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Affiliation(s)
- Miguel Alena-Rodriguez
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, UK.
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Marcos Fernandez-Villamarin
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, UK.
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, UK.
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3
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Lin X, Jia S, Ye H, He P, You L. Neighboring Effects of Sulfur Oxidation State on Dynamic Covalent Bonds and Assemblies. Org Lett 2024; 26:3640-3645. [PMID: 38635892 DOI: 10.1021/acs.orglett.4c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The impact of a varied sulfur oxidation state (sulfide, sulfoxide, and sulfone) on imine dynamic covalent chemistry is presented. The role of noncovalent interactions, including chalcogen bonds and CH hydrogen bonds, on aldehyde/imine structures and imine exchange reactions was elucidated through experimental and computational evidence. The change in the sulfur oxidation state and diamine linkage further allowed the regulation of imine macrocycles, providing a platform for controlling molecular assemblies.
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Affiliation(s)
- Xin Lin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuaipeng Jia
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Peng He
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- College of Chemistry and Material Science, Fujian Normal University, Fuzhou, 350007, China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Exapicheidou IA, Shams A, Ibrahim H, Tsarenko A, Backenköhler M, Hamed MM, Diamanti E, Volkamer A, Slotboom DJ, Hirsch AKH. Hit optimization by dynamic combinatorial chemistry on Streptococcus pneumoniae energy-coupling factor transporter ECF-PanT. Chem Commun (Camb) 2024; 60:870-873. [PMID: 38164786 DOI: 10.1039/d3cc04738e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Herein, we present the first application of target-directed dynamic combinatorial chemistry (tdDCC) to the whole complex of the highly dynamic transmembrane, energy-coupling factor (ECF) transporter ECF-PanT in Streptococcus pneumoniae. In addition, we successfully employed the tdDCC technique as a hit-identification and -optimization strategy that led to the identification of optimized ECF inhibitors with improved activity. We characterized the best compounds regarding cytotoxicity and performed computational modeling studies on the crystal structure of ECF-PanT to rationalize their binding mode. Notably, docking studies showed that the acylhydrazone linker is able to maintain the crucial interactions.
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Affiliation(s)
- Ioulia Antonia Exapicheidou
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Hamza Ibrahim
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Aleksei Tsarenko
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Michael Backenköhler
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
| | - Andrea Volkamer
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
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5
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Cougnon FBL, Stefankiewicz AR, Ulrich S. Dynamic covalent synthesis. Chem Sci 2024; 15:879-895. [PMID: 38239698 PMCID: PMC10793650 DOI: 10.1039/d3sc05343a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/10/2023] [Indexed: 01/22/2024] Open
Abstract
Dynamic covalent synthesis aims to precisely control the assembly of simple building blocks linked by reversible covalent bonds to generate a single, structurally complex, product. In recent years, considerable progress in the programmability of dynamic covalent systems has enabled easy access to a broad range of assemblies, including macrocycles, shape-persistent cages, unconventional foldamers and mechanically-interlocked species (catenanes, knots, etc.). The reversibility of the covalent linkages can be either switched off to yield stable, isolable products or activated by specific physico-chemical stimuli, allowing the assemblies to adapt and respond to environmental changes in a controlled manner. This activatable dynamic property makes dynamic covalent assemblies particularly attractive for the design of complex matter, smart chemical systems, out-of-equilibrium systems, and molecular devices.
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Affiliation(s)
- Fabien B L Cougnon
- Department of Chemistry and Nanoscience Centre, University of Jyväskylä Jyväskylä Finland
| | - Artur R Stefankiewicz
- Centre for Advanced Technology and Faculty of Chemistry, Adam Mickiewicz University Poznań Poland
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM Montpellier France
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6
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Song H, Guo Y, Zhang G, Shi L. Tailored Water-Soluble Covalent Organic Cages for Encapsulation of Pyrene and Information Encryption. Int J Mol Sci 2023; 24:17541. [PMID: 38139371 PMCID: PMC10743434 DOI: 10.3390/ijms242417541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Forming pyridine salts to construct covalent organic cages is an effective strategy for constructing covalent cage compounds. Covalent organic cages based on pyridine salt structures are prone to form water-soluble supramolecular compounds. Herein, we designed and synthesized a triangular prism-shaped hexagonal cage with a larger cavity and relatively flexible conformation. The supramolecular cage structure was also applied to the encapsulation of pyrene and information encryption.
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Affiliation(s)
| | | | - Guorui Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China; (H.S.); (Y.G.)
| | - Linlin Shi
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China; (H.S.); (Y.G.)
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7
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van Dam A, van Schendel R, Gangarapu S, Zuilhof H, Smulders MMJ. DFT Study of Imine-Exchange Reactions in Iron(II)-Coordinated Pincers. Chemistry 2023; 29:e202301795. [PMID: 37560922 DOI: 10.1002/chem.202301795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/11/2023]
Abstract
The imine bond is among the most applied motifs in dynamic covalent chemistry. Although its uses are varied and often involve coordination to a transition metal for stability, mechanistic studies on imine exchange reactions so far have not included metal coordination. Herein, we investigated the condensation and transimination reactions of an Fe2+ -coordinated diimine pyridine pincer, employing wB97XD/6-311G(2d,2p) DFT calculations in acetonitrile. We first experimentally confirmed that Fe2+ is strongly coordinated by these pincers, and is thus a justified model ion. When considering a four-membered ring-shaped transition state for proton transfers, the required activation energies for condensation and transimination reaction exceeded the values expected for reactions known to be spontaneous at room temperature. The nature of the incoming and exiting amines and the substituents on the para-position of the pincer had no effect on this. Replacing Fe2+ with Zn2+ or removing it altogether did not reduce it either. However, the addition of two ethylamine molecules lowered the energy barriers to be compatible with experiment (19.4 and 23.2 kcal/mol for condensation and transimination, respectively). Lastly, the energy barrier of condensation of a non-coordinated pincer was significantly higher than found for Fe2+ -coordinating pincers, underlining the catalyzing effect of metal coordination on imine exchange reactions.
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Affiliation(s)
- Annemieke van Dam
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Robin van Schendel
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Satesh Gangarapu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
- School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Tianjin, 300072, P.R. China
| | - Maarten M J Smulders
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
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8
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You L. Dual reactivity based dynamic covalent chemistry: mechanisms and applications. Chem Commun (Camb) 2023; 59:12943-12958. [PMID: 37772969 DOI: 10.1039/d3cc04022d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Dynamic covalent chemistry (DCC) focuses on the reversible formation, breakage, and exchange of covalent bonds and assemblies, setting a bridge between irreversible organic synthesis and supramolecular chemistry and finding wide utility. In order to enhance structural and functional diversity and complexity, different types of dynamic covalent reactions (DCRs) are placed in one vessel, encompassing orthogonal DCC without crosstalk and communicating DCC with a shared reactive functional group. As a means of adding tautomers, widespread in chemistry, to interconnected DCRs and combining the features of orthogonal and communicating DCRs, a concept of dual reactivity based DCC and underlying structural and mechanistic insights are summarized. The manipulation of the distinct reactivity of structurally diverse ring-chain tautomers allows selective activation and switching of reaction pathways and corresponding DCRs (C-N, C-O, and C-S) and assemblies. The coupling with photoswitches further enables light-mediated formation and scission of multiple types of reversible covalent bonds. To showcase the capability of dual reactivity based DCC, the versatile applications in dynamic polymers and luminescent materials are presented, paving the way for future functionalization studies.
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Affiliation(s)
- Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
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9
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Bouffard J, Coelho F, Sakai N, Matile S. Dynamic Phosphorus: Thiolate Exchange Cascades with Higher Phosphorothioates. Angew Chem Int Ed Engl 2023:e202313931. [PMID: 37847524 DOI: 10.1002/anie.202313931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/18/2023]
Abstract
In this study, we introduce phosphorus, a pnictogen, as an exchange center for dynamic covalent chemistry. Cascade exchange of neutral phosphorotri- and -tetrathioates with thiolates is demonstrated in organic solvents, aqueous micellar systems, and in living cells. Exchange rates increase with the pH value, electrophilicity of the exchange center, and nucleophilicity of the exchangers. Molecular walking of the dynamic phosphorus center along Hammett gradients is simulated by the sequential addition of thiolate exchangers. Compared to phosphorotrithioates, tetrathioates are better electrophiles with higher exchange rates. Dynamic phosphorotri- and -tetrathioates are non-toxic to HeLa Kyoto cells and participate in the dynamic networks that account for thiol-mediated uptake into living cells.
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Affiliation(s)
- Jules Bouffard
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Filipe Coelho
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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10
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Grenier D, Audebert S, Preto J, Guichou JF, Krimm I. Linkers in fragment-based drug design: an overview of the literature. Expert Opin Drug Discov 2023; 18:987-1009. [PMID: 37466331 DOI: 10.1080/17460441.2023.2234285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023]
Abstract
INTRODUCTION In fragment-based drug design, fragment linking is a popular strategy where two fragments binding to different sub-pockets of a target are linked together. This attractive method remains challenging especially due to the design of ideal linkers. AREAS COVERED The authors review the types of linkers and chemical reactions commonly used to the synthesis of linkers, including those utilized in protein-templated fragment self-assembly, where fragments are directly linked in the presence of the protein. Finally, they detail computational workflows and software including generative models that have been developed for fragment linking. EXPERT OPINION The authors believe that fragment linking offers key advantages for compound design, particularly for the design of bivalent inhibitors linking two distinct pockets of the same or different subunits. On the other hand, more studies are needed to increase the potential of protein-templated approaches in FBDD. Important computational tools such as structure-based de novo software are emerging to select suitable linkers. Fragment linking will undoubtedly benefit from developments in computational approaches and machine learning models.
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Affiliation(s)
- Dylan Grenier
- Team Small Molecules for Biological Targets, Centre de Recherche En Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France
| | - Solène Audebert
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Jordane Preto
- Team Small Molecules for Biological Targets, Centre de Recherche En Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France
| | - Jean-François Guichou
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Isabelle Krimm
- Team Small Molecules for Biological Targets, Centre de Recherche En Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France
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11
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van Hurne S, Kisters M, Smulders MMJ. Covalent adaptable networks using boronate linkages by incorporating TetraAzaADamantanes. Front Chem 2023; 11:1148629. [PMID: 36909710 PMCID: PMC9995436 DOI: 10.3389/fchem.2023.1148629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Boronic esters prepared by condensation of boronic acids and diols have been widely used as dynamic covalent bonds in the synthesis of both discrete assemblies and polymer networks. In this study we investigate the potential of a new dynamic-covalent motif, derived from TetraAzaADamantanes (TAADs), with their adamantane-like triol structure, in boronic ester-based covalent adaptable networks (CANs). The TetraAzaADamantane-boronic ester linkage has recently been reported as a more hydrolytically stable boronic ester variant, while still having a dynamic pH response: small-molecule studies found little exchange at neutral pH, while fast exchange occurred at pH 3.8. In this work, bi- and trifunctional TetraAzaADamantane linkers were synthesised and crosslinked with boronic acids to form rubber-like materials, with a Young's modulus of 1.75 MPa. The dynamic nature of the TetraAzaADamantane networks was confirmed by stress relaxation experiments, revealing Arrhenius-like behaviour, with a corresponding activation energy of 142 ± 10 kJ/mol. Increasing the crosslinking density of the material from 10% to 33% resulted in reduced relaxation times, as is consistent with a higher degree of crosslinking within the dynamic networks. In contrast to the reported accelerating effect of acid addition to small-molecule TetraAzaADamantane complexes, within the polymer network the addition of acid increased relaxation times, suggesting unanticipated interactions between the acid and the polymer that cannot occur in the corresponding small-molecules analogues. The obtained boronate-TetraAzaADamantane materials were thermally stable up to 150°C. This thermal stability, in combination with the intrinsically dynamic bonds inside the polymer network, allowed these materials to be reprocessed and healed after damage by hot-pressing.
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Affiliation(s)
- Simon van Hurne
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands
| | - Marijn Kisters
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands
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12
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Jin X, Jiang H, Chen Y, Han X, Sun K, Shi L, Hao XQ, Song MP. A Cavity-Tailored Metal-Organic Tetrahedral Nanocage and Gas Adsorption Property. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:4402. [PMID: 36558254 PMCID: PMC9783787 DOI: 10.3390/nano12244402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Porous organometallic nanomaterials are a new class of materials based on a three-dimensional structure. They have excellent applications in different fields, but their applications in gas storage and separation have not been fully developed. CO2 adsorption storage and hydrocarbon separation has been a challenging industrial problem. Several typical molecular adsorbents have been used to study the separation, but the problems of long-term stability, high selectivity and synthetic complexity of these adsorbents remain to be solved. Here, we have designed and synthesized tetrahedral metal supramolecular nanocage with custom cavities based on the unique rigid structure of triptycene derivatives. Using the unique discrete porous structure of tetrahedral metal nanocages, the gas adsorption and separation performance of the metal supramolecular nanocage was investigated. By analyzing the adsorption and desorption isotherms and the multi-component competitive adsorption curves, we noticed that the tetrahedral supramolecular nanocages had good CO2 storage capacity and good separation capacity for C2H2/CO2 and C2H2/N2. All these indicate that porous organic metal nanomaterials are expected to be a new energy saving separation material.
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Affiliation(s)
- Xin Jin
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hui Jiang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Yi Chen
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xin Han
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Ken Sun
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- College of Energy and Power Engineering, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Linlin Shi
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xin-Qi Hao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Mao-Ping Song
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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13
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Lianglu J, Hu W, Zhu X, Zhang HY, Shi L, Hao XQ, Song MP. Synthesis of a Tetrahedral Metal-Organic Supramolecular Cage with Dendritic Carbazole Arms. Int J Mol Sci 2022; 23:15580. [PMID: 36555222 PMCID: PMC9779595 DOI: 10.3390/ijms232415580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
In recent years, incredible endeavors have been devoted to the design and self-assembly of discrete metal-organic cages (MOCs) with expanding intricacy and functionality. The controlled synthesis of metal-organic supramolecular cages with large branched chains remains an interesting and challenging work in supramolecular chemistry. Herein, a tetrahedral metal-organic supramolecular cage (ZnII4L4) containing 12 dendritic carbazole arms is unprecedentedly constructed through coordination-driven subcomponent self-assembly and characterized in different ways. Interestingly, tetrahedral supramolecular Cage-1 exhibited the potential for aggregation-induced emission (AIE) performance and stimulus-responsive luminescence features, and it achieved color-tunable photoluminescence due to the introduction of dendritic carbazole arms. Crucially, owing to the great photophysical properties of Cage-1 in solution, Cage-1 was enabled to act as a fluorescent ink for the vapor-responsive recording and wiping of information.
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Affiliation(s)
- Juanzi Lianglu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Weinan Hu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xinju Zhu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Yu Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- School of Basic Medical Science, Zhengzhou University, Zhengzhou 450001, China
| | - Linlin Shi
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Xin-Qi Hao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Mao-Ping Song
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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14
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Wu Y, Liu C, Hu L. Fragment-Based Dynamic Combinatorial Chemistry for Identification of Selective α-Glucosidase Inhibitors. ACS Med Chem Lett 2022; 13:1791-1796. [PMID: 36385930 PMCID: PMC9661702 DOI: 10.1021/acsmedchemlett.2c00405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022] Open
Abstract
Efforts to combine advantages of fragment-based drug design (FBDD) and dynamic combinatorial chemistry (DCC) for the development of selective α-glucosidase inhibitors were described. Starting from 5 rationally designed fragments, two iterative dynamic combinatorial libraries (DCLs) comprising 29 acylhydrazone products were generated and screened using α-glucosidase and α-amylase as the templates. The optimal ligand identified showed substantial α-glucosidase inhibition with high selectivity over α-amylase as well as low cytotoxicity. Furthermore, inhibition type and detailed ligand/enzyme binding interactions were elucidated by the binding kinetic study and docking simulation, respectively.
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Affiliation(s)
- Yao Wu
- School of Pharmacy, Jiangsu
University, 301 Xuefu Road, 212013 Zhenjiang, China
| | - Changming Liu
- School of Pharmacy, Jiangsu
University, 301 Xuefu Road, 212013 Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu
University, 301 Xuefu Road, 212013 Zhenjiang, China
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15
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. Angew Chem Int Ed Engl 2022; 61:e202211510. [PMID: 36112310 PMCID: PMC9827864 DOI: 10.1002/anie.202211510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 01/12/2023]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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16
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202211510. [PMID: 38505687 PMCID: PMC10947266 DOI: 10.1002/ange.202211510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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17
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Tiemann M, Nawrotzky E, Schmieder P, Wehrhan L, Bergemann S, Martos V, Song W, Arkona C, Keller BG, Rademann J. A Formylglycine-Peptide for the Site-Directed Identification of Phosphotyrosine-Mimetic Fragments. Chemistry 2022; 28:e202201282. [PMID: 35781901 PMCID: PMC9804470 DOI: 10.1002/chem.202201282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Indexed: 01/05/2023]
Abstract
Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for the sensitive detection of fragments binding to a spatially defined protein site . Formylglycine peptide 3 was derived from a phosphotyrosine-containing peptide substrate of protein tyrosine phosphatase PTP1B by replacing the phosphorylated amino acid with the reactive electrophile. Fragment ligation with formylglycine occurred in situ in aqueous physiological buffer. Structures and kinetics were validated by NMR spectroscopy. Screening and hit validation revealed fluorinated and non-fluorinated hit fragments being able to replace the native phosphotyrosine residue. The formylglycine probe identified low-affinity fragments with high spatial resolution as substantiated by molecular modelling. The best fragment hit, 4-amino-phenyl-acetic acid, was converted into a cellularly active, nanomolar inhibitor of the protein tyrosine phosphatase SHP2.
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Affiliation(s)
- Markus Tiemann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Eric Nawrotzky
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Peter Schmieder
- Leibniz Institute of Molecular Pharmacology (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Leon Wehrhan
- Department of Biology, Chemistry, PharmacyInstitute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Silke Bergemann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Vera Martos
- Leibniz Institute of Molecular Pharmacology (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Wei Song
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Christoph Arkona
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Bettina G. Keller
- Department of Biology, Chemistry, PharmacyInstitute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Jörg Rademann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
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18
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Tunable gregation-induced fluorescent and pressure-responsive luminescence supramolecular cages achieved by subcomponent self-assembly. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Furka Á. Forty years of combinatorial technology. Drug Discov Today 2022; 27:103308. [PMID: 35760283 DOI: 10.1016/j.drudis.2022.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Combinatorial technology has been facilitating the synthesis and screening of large molecular libraries containing millions of organic compounds ever since its introduction 40 years ago. It has changed the paradigms of pharmaceutical research from focusing on single compounds to focusing on immense collections of compounds. It inspired the development of dynamic combinatorial libraries, fragment-based drug discovery and virtual library screening. Combinatorial technology was revitalized by the development of DNA encoding. Amplification of DNA oligomers plus next-generation sequencing has made it possible to successfully screen billions of compounds in a single process.
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Affiliation(s)
- Árpád Furka
- Eötvös Loránd University Budapest Hungary, 1077 Rozsa u. 23-25, Budapest, Hungary.
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20
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Del Giudice D, Spatola E, Valentini M, Ercolani G, Di Stefano S. Dissipative Dynamic Libraries (DDLs) and Dissipative Dynamic Combinatorial Chemistry (DDCC). CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daniele Del Giudice
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
| | - Emanuele Spatola
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
| | - Matteo Valentini
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
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21
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Villamil V, Saiz C, Mahler G. Thioester deprotection using a biomimetic NCL approach. Front Chem 2022; 10:934376. [PMID: 36072700 PMCID: PMC9441695 DOI: 10.3389/fchem.2022.934376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
The reversibility of the thiol-thioester linkage has been broadly employed in many fields of biochemistry (lipid synthesis) and chemistry (dynamic combinatorial chemistry and material science). When the transthioesterification is followed by a S-to-N acyl transfer to give an amide bond, it is called Native Chemical Ligation (NCL), a high-yield chemoselective process used for peptide synthesis. Recently, we described thioglycolic acid (TGA) as a useful reagent for thioester deprotection both in solution and anchored to a solid-support under mild conditions. Inspired by NCL, in this work, we extended this approach and explored the use of 2-aminothiols for the deprotection of thiols bearing an acyl group. The best results were obtained using cysteamine or L-cysteine in an aqueous buffer pH 8 at room temperature for 30 min. The described approach was useful for S-acetyl, S-butyryl, and S-benzoyl heterocycles deprotection with yields up to 84%. Employing this methodology, we prepared six new analogs 2 of mercaptomethyl bisthiazolidine 1, a useful inhibitor of a wide-range of Metallo-β-Lactamases (MBLs). Compared with the previous methodologies (TGA polymer supported and TGA in solution), the biomimetic deprotection herein described presents better performance with higher yields, shorter reaction times, less time-consuming operations, easier setup, and lower costs.
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Affiliation(s)
- Valentina Villamil
- Laboratorio de Química Farmacéutica (DQO), Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Cecilia Saiz
- Laboratorio de Química Farmacéutica (DQO), Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Graciela Mahler
- Laboratorio de Química Farmacéutica (DQO), Facultad de Química, Universidad de la República, Montevideo, Uruguay
- *Correspondence: Graciela Mahler,
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22
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Wu Y, Zhao S, Liu C, Hu L. Development of urease inhibitors by fragment-based dynamic combinatorial chemistry. ChemMedChem 2022; 17:e202200307. [PMID: 35975876 DOI: 10.1002/cmdc.202200307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/12/2022] [Indexed: 11/07/2022]
Abstract
In this study, fragment-based dynamic combinatorial chemistry (DCC) was explored for the development of novel urease inhibitors. Based on a rationally designed fragment, two iteratively evolved dynamic combinatorial libraries (DCLs) were generated and screened in the presence of urease template. The best ligand identified revealed not only strong urease inhibition but also low cytotoxicity. Additionally, possible inhibitory mechanism was elucidated in the binding kinetic study and docking simulation.
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Affiliation(s)
- Yao Wu
- Jiangsu University School of Pharmacy, College of Pharmacy, CHINA
| | - Shuang Zhao
- Jiangsu University School of Pharmacy, College of Pharmacy, CHINA
| | - Changming Liu
- Jiangsu University School of Pharmacy, College of Pharmacy, CHINA
| | - Lei Hu
- Jiangsu University School of Pharmacy, College of pharmacy, 301 Xuefu Rd., Zhenjiang, China, 212013, Zhenjiang, CHINA
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23
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Bagnolini G, Balboni B, Schipani F, Gioia D, Veronesi M, De Franco F, Kaya C, Jumde RP, Ortega JA, Girotto S, Hirsch AKH, Roberti M, Cavalli A. Identification of RAD51–BRCA2 Inhibitors Using N-Acylhydrazone-Based Dynamic Combinatorial Chemistry. ACS Med Chem Lett 2022; 13:1262-1269. [PMID: 35978685 PMCID: PMC9377020 DOI: 10.1021/acsmedchemlett.2c00063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
![]()
RAD51 is an ATP-dependent recombinase, recruited by BRCA2
to mediate
DNA double-strand breaks repair through homologous recombination and
represents an attractive cancer drug target. Herein, we applied for
the first-time protein-templated dynamic combinatorial chemistry on
RAD51 as a hit identification strategy. Upon design of N-acylhydrazone-based dynamic combinatorial libraries, RAD51 showed
a clear templating effect, amplifying 19 N-acylhydrazones.
Screening against the RAD51–BRCA2 protein–protein interaction
via ELISA assay afforded 10 inhibitors in the micromolar range. Further 19F NMR experiments revealed that 7 could bind
RAD51 and be displaced by BRC4, suggesting an interaction in the same
binding pocket of BRCA2. These results proved not only that ptDCC
could be successfully applied on full-length oligomeric RAD51, but
also that it could address the need of alternative strategies toward
the identification of small-molecule PPI inhibitors.
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Affiliation(s)
- Greta Bagnolini
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123 Saarbrücken, Germany
| | - Beatrice Balboni
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
| | - Fabrizio Schipani
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | - Dario Gioia
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | - Marina Veronesi
- Structural Biophysics and Translational Pharmacology, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | | | - Cansu Kaya
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Ravindra P. Jumde
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123 Saarbrücken, Germany
| | - Jose Antonio Ortega
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | - Stefania Girotto
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
| | - Anna K. H. Hirsch
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology (CCB), Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
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24
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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25
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Matysiak BM, Monreal Santiago G, Otto S. Teaching an Old Compound New Tricks: Reversible Transamidation in Maleamic Acids. Chemistry 2022; 28:e202201043. [PMID: 35488794 PMCID: PMC9401040 DOI: 10.1002/chem.202201043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 12/03/2022]
Abstract
Dynamic combinatorial chemistry is a method widely used for generating responsive libraries of compounds, with applications ranging from chemical biology to materials science. It relies on dynamic covalent bonds that are able to form in a reversible manner in mild conditions, and therefore requires the discovery of new types of these bonds in order to progress. Amides, due to their high stability, have been scarcely used in this field and typically require an external catalyst or harsh conditions for exchange. Compounds able to undergo uncatalysed transamidation at room temperature are still rare exceptions. In this work, we describe reversible amide formation and transamidation in a class of compounds known as maleamic acids. Due to the presence of a carboxylic acid in β‐position, these compounds are in equilibrium with their anhydride and amine precursors in organic solvents at room temperature. First, we show that this equilibrium is responsive to external stimuli: by alternating the additions of a Brønsted acid and a base, we can switch between amide and anhydride several times without side‐reactions. Next, we prove that this equilibrium provides a pathway for reversible transamidation without any added catalyst, leading to thermodynamic distributions of amides at room temperature. Lastly, we use different preparation conditions and concentrations of Brønsted acid to access different library distributions, easily controlling the transition between kinetic and thermodynamic regimes. Our results show that maleamic acids can undergo transamidation in mild conditions in a reversible and tunable way, establishing them as a new addition to the toolbox of dynamic combinatorial chemistry.
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Affiliation(s)
- Bartosz M. Matysiak
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747AG Groningen Netherlands
| | - Guillermo Monreal Santiago
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747AG Groningen Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747AG Groningen Netherlands
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26
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Orrillo AG, Furlan RLE. Sulfur in Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2022; 61:e202201168. [PMID: 35447003 DOI: 10.1002/anie.202201168] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Indexed: 12/21/2022]
Abstract
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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Affiliation(s)
- A Gastón Orrillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, Rosario, S2002LRK, Argentina
| | - Ricardo L E Furlan
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, Rosario, S2002LRK, Argentina
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27
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Casciuc I, Osypenko A, Kozibroda B, Horvath D, Marcou G, Bonachera F, Varnek A, Lehn JM. Toward in Silico Modeling of Dynamic Combinatorial Libraries. ACS CENTRAL SCIENCE 2022; 8:804-813. [PMID: 35756377 PMCID: PMC9228562 DOI: 10.1021/acscentsci.2c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 06/15/2023]
Abstract
Dynamic combinatorial libraries (DCLs) display adaptive behavior, enabled by the reversible generation of their molecular constituents from building blocks, in response to external effectors, e.g., protein receptors. So far, chemoinformatics has not yet been used for the design of DCLs-which comprise a radically different set of challenges compared to classical library design. Here, we propose a chemoinformatic model for theoretically assessing the composition of DCLs in the presence and the absence of an effector. An imine-based DCL in interaction with the effector human carbonic anhydrase II (CA II) served as a case study. Support vector regression models for the imine formation constants and imine-CA II binding were derived from, respectively, a set of 276 imines synthesized and experimentally studied in this work and 4350 inhibitors of CA II from ChEMBL. These models predict constants for all DCL constituents, to feed software assessing equilibrium concentrations. They are publicly available on the dedicated website. Models rationally selected two amines and two aldehydes predicted to yield stable imines with high affinity for CA II and provided a virtual illustration on how effector affinity regulates DCL members.
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Affiliation(s)
- Iuri Casciuc
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Artem Osypenko
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Bohdan Kozibroda
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
- Institute
of High Technologies, Taras Shevchenko National
University of Kyiv, 4g
Hlushkova Avenue, 03022 Kyiv, Ukraine
| | - Dragos Horvath
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Gilles Marcou
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Fanny Bonachera
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Alexandre Varnek
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
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28
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Orrillo AG, Furlan RLE. Sulfur in Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alfredo Gastón Orrillo
- Universidad Nacional de Rosario Facultad de Ciencias Bioquimicas y Farmaceuticas Organic Chemistry Suipacha 530 2000 Rosario ARGENTINA
| | - Ricardo L. E. Furlan
- Universidad Nacional de Rosario Facultad de Ciencias Bioquimicas y Farmaceuticas Organic Chemistry Suipacha 530 2000 Rosario ARGENTINA
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29
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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30
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Gay M, Diaz-Lobo M, Gusi-Vives M, Arauz-Garofalo G, Vilanova M, Giralt E, Vilaseca M, Guardiola S. Proteomic tools for the quantitative analysis of artificial peptide libraries: detection and characterization of target-amplified PD-1 inhibitors. Chembiochem 2022; 23:e202200152. [PMID: 35362647 DOI: 10.1002/cbic.202200152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/31/2022] [Indexed: 11/07/2022]
Abstract
We report a quantitative proteomics data analysis pipeline which, coupled to protein-directed dynamic combinatorial chemistry (DDC) experiments, enables the rapid discovery and direct characterization of protein-protein interaction (PPI) modulators. A low-affinity PD-1 binder was incubated with a library of >100 D-peptides under thiol-exchange favoring conditions, in the presence of the target protein PD-1, and we determined the S-linked dimeric species that resulted amplified in the protein samples versus the controls. We chemically synthesized the target dimer candidates and validated them by thermophoresis binding and protein-protein interaction assays. The results provide a proof-of-concept for using this strategy in the high-throughput search of improved drug-like peptide binders that block therapeutically relevant protein-protein interactions.
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Affiliation(s)
- Marina Gay
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Mireia Diaz-Lobo
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Mar Gusi-Vives
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Pharmacology, SPAIN
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Mar Vilanova
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, mas, SPAIN
| | - Ernest Giralt
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Pharmacology, SPAIN
| | - Marta Vilaseca
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Salvador Guardiola
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Pharmacology, Baldiri Reixac, 4, 08028, Barcelona, SPAIN
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31
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Fray M, Mathiron D, Pilard S, Lesur D, Abidi R, Barhoumi-Slimi T, Cragg PJ, BENAZZA M. Heteroglycoclusters through Unprecedented Orthogonal Chemistry Based on N‐Alkylation of N‐Acylhydrazone. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marwa Fray
- LG2A: Laboratoire de Glycochimie des Antimicrobiens et des Agroressources Chemistry 10 Rue Baudelocque 80039 Amiens FRANCE
| | - David Mathiron
- UPJV: Universite de Picardie Jules Verne Analytique 80039 Amiens FRANCE
| | - Serge Pilard
- UPJV: Universite de Picardie Jules Verne Analytique 80039 Amiens FRANCE
| | - David Lesur
- LG2A: Laboratoire de Glycochimie des Antimicrobiens et des Agroressources Analytique 10 Rue Baudelocque 80039 Amiens FRANCE
| | - Rym Abidi
- University of Carthage: Universite de Carthage Chemistry Zarzouna-Bizerte, TN 7021, Tunisia TN 7021 Bizerte TUNISIA
| | - Thouraya Barhoumi-Slimi
- University of Tunis El Manar: Universite de Tunis El Manar Structural Chemistry Faculty of Sciences of Tunis 2092 Tunis TUNISIA
| | - Peter J. Cragg
- University of Brighton School of Applied Sciences BN2 4GJ Brighton UNITED KINGDOM
| | - Mohammed BENAZZA
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources (LG2A UMR7378, CNRS), Université de Picardie Jules Verne Departement of organic Chemistry 10 Rue Baudelocque 80039 Amiens FRANCE
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32
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Carbajo D, Pérez Y, Guerra-Rebollo M, Prats E, Bujons J, Alfonso I. Dynamic Combinatorial Optimization of In Vitro and In Vivo Heparin Antidotes. J Med Chem 2022; 65:4865-4877. [PMID: 35235323 PMCID: PMC8958503 DOI: 10.1021/acs.jmedchem.1c02054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Heparin-like macromolecules
are widely used in clinics as anticoagulant,
antiviral, and anticancer drugs. However, the search of heparin antidotes
based on small synthetic molecules to control blood coagulation still
remains a challenging task due to the physicochemical properties of
this anionic polysaccharide. Here, we use a dynamic combinatorial
chemistry approach to optimize heparin binders with submicromolar
affinity. The recognition of heparin by the most amplified members
of the dynamic library has been studied with different experimental
(SPR, fluorescence, NMR) and theoretical approaches, rendering a detailed
interaction model. The enzymatic assays with selected library members
confirm the correlation between the dynamic covalent screening and
the in vitro heparin inhibition. Moreover, both ex vivo and in vivo blood coagulation assays
with mice show that the optimized molecules are potent antidotes with
potential use as heparin reversal drugs. Overall, these results underscore
the power of dynamic combinatorial chemistry targeting complex and
elusive biopolymers.
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Affiliation(s)
| | | | - Marta Guerra-Rebollo
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarriá (IQS), Universitat Ramon Llull (URL), Via Augusta 390, 08017 Barcelona, Spain
| | - Eva Prats
- Research and Development Center (CID-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
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33
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Phuong Vu L, Zyulina M, Hingst A, Schnakenburg G, Gütschow M. Combinatorial Assembly, Traceless Generation and In Situ Evaluation of Inhibitors for Therapeutically Relevant Serine Proteases. Bioorg Chem 2022; 121:105676. [DOI: 10.1016/j.bioorg.2022.105676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/02/2022]
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34
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Wu Y, Zhao S, Hu L. Identification of potent α-amylase inhibitors via dynamic combinatorial chemistry. Bioorg Med Chem 2022; 55:116609. [PMID: 35021143 DOI: 10.1016/j.bmc.2022.116609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/31/2021] [Accepted: 01/02/2022] [Indexed: 11/30/2022]
Abstract
In this study, we report for the first time the discovery of potent α-amylase inhibitors using principle of dynamic combinatorial chemistry. The best compound identified exhibited not only high inhibitory efficiency but also low cytotoxicity. The binding mode and possible mechanism are determined in the subsequent kinetic and molecular docking studies.
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Affiliation(s)
- Yao Wu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Shuang Zhao
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China.
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35
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Li Z, Zhang L, Zhou Y, Zha D, Hai Y, You L. Dynamic Covalent Reactions Controlled by Ring‐Chain Tautomerism of 2‐Formylbenzoic Acid. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ziyi Li
- College of Chemistry and Material Science Fujian Normal University Fuzhou Fujian 350007 China
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Ling Zhang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Yuntao Zhou
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Daijun Zha
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Yu Hai
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lei You
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China Fuzhou Fujian 350108 China
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36
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Kawai K, Ikeda K, Sato A, Kabasawa A, Kojima M, Kokado K, Kakugo A, Sada K, Yoshino T, Matsunaga S. 1,2-Disubstituted 1,2-Dihydro-1,2,4,5-tetrazine-3,6-dione as a Dynamic Covalent Bonding Unit at Room Temperature. J Am Chem Soc 2022; 144:1370-1379. [PMID: 35040645 DOI: 10.1021/jacs.1c11665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.
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Affiliation(s)
- Kentaro Kawai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Ikeda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akane Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Kabasawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Masahiro Kojima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kenta Kokado
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - Akira Kakugo
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Tatsuhiko Yoshino
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Shigeki Matsunaga
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12 Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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37
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Jia S, Ye H, You L. Interplay between chalcogen bonds and dynamic covalent bonds. Org Chem Front 2022. [DOI: 10.1039/d2qo00684g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of chalcogen bonds, one type of emerging non-covalent bonding force, and imine bonds, allow the control of the dynamic covalent chemistry with orbital interactions and the reversal of kinetic and thermodynamic selectivity.
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Affiliation(s)
- Shuaipeng Jia
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
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38
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Zhao S, Wu Y, Hu L. Identification and synthesis of selective cholesterol esterase inhibitor using dynamic combinatorial chemistry. Bioorg Chem 2021; 119:105520. [PMID: 34864280 DOI: 10.1016/j.bioorg.2021.105520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022]
Abstract
In this study, the concept of dynamic combinatorial chemistry (DCC) was applied to explore novel cholesterol esterase (CEase) inhibitors. In the presence of enzyme, two substrates (A1H3 and A2H3) were amplified from the dynamic combinatorial library (DCL), which was generated through reversible acylhydrazone formation reaction. In the in vitro biological evaluation, compound A1H3 exhibited not only potent (IC50 in nanomolar range) but also selective inhibition (>120 folds of selectivity for CEase over AChE). Furthermore, the binding pattern and possible binding mechanism were investigated in the kinetic experiment and molecular docking study, respectively.
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Affiliation(s)
- Shuang Zhao
- School of Pharmacy, Jiangsu University, Zhenjiang, 301 Xuefu Rd., Zhenjiang, China
| | - Yao Wu
- School of Pharmacy, Jiangsu University, Zhenjiang, 301 Xuefu Rd., Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, Zhenjiang, 301 Xuefu Rd., Zhenjiang, China.
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39
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Abstract
Although dynamic reactions of imines have been extensively studied, the dynamic behaviors manipulated by chirality remain nearly unexplored. In this work, enantioselective amine exchange reactions were demonstrated as a first example via the reaction of enantiomeric chiral amines such as natural amino acids with a series of innovative axially chiral 1,1'-binaphthyl-2,2'-diamine (BNDA)-based imines that were prepared from the condensation reactions between BNDA and salicylaldehyde (SA) or its derivatives. This enantioselective dynamic behavior can be directly indicated by the degree of the fluorescence response of the R-configuration of imines to the d-enantiomer of chiral amine, because the released BNDA can serve as the fluorescence signal output when the amine exchange reaction occurs, which is far higher than the response to its l-enantiomer under identical experimental conditions. For the S-configuration of chiral imines, the fluorescence response is the opposite. The enantioselective exchange reaction can be tuned by altering the electron-withdrawing or electron-donating capability of the substituent at position 4 or 5 of the SA part of chiral imines. Not only o-OH groups in SA-based imines but also protic solvents used as reaction media were found to be important to the dynamic behavior at high rates.
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Affiliation(s)
- Rui-Xue Ji
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Ning Liu
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jiang-Shan Shen
- Xiamen Key Laboratory of Optoelectronic Materials and Advanced Manufacturing, College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
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40
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Shadfar Z, Yahiaoui O, Collier TA, Fallon T, Allison JR. Illustration of a computational pipeline for evaluating cyclodextrin host-guest complex formation through conformational capture of bullvalene. J Chem Phys 2021; 154:154105. [PMID: 33887942 DOI: 10.1063/5.0045115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cyclodextrins have a diverse range of applications, including as supramolecular hosts, as enzyme active-site analogs, in improving drug solubility and delivery, and in molecular selection. We have investigated their ability to form stable complexes with bullvalenes, unusual organic cage molecules that spontaneously interconvert between numerous degenerate isomers. The shape-shifting nature of substituted bullvalenes raises the potential for dynamic adaptive binding to biological targets. We tested whether β- and γ-cyclodextrins can capture particular bullvalene isomers and whether the preferred binding mode(s) differ between isomers. We first applied our computational host-guest interaction potential energy profiling to determine the best binding mode(s) of unsubstituted bullvalene and each isomer of methylenehydroxybullvalene to β- and γ-cyclodextrin. Subsequent molecular dynamics simulations of the predicted host-guest complexes showed that while unsubstituted bullvalene has a single, albeit ill-defined, binding mode with either cyclodextrin, each isomer of methylenehydroxybullvalene has two possible modes of binding to β-cyclodextrin but only a single, nebulous mode of binding to γ-cyclodextrin. Experimental determination of the binding free energy of each methylenehydroxybullvalene-cyclodextrin complex showed that methylenehydroxybullvalene is more likely to bind to β-cyclodextrin than to γ-cyclodextrin, despite its smaller cavity. Together, our results suggest that β-cyclodextrin, but not γ-cyclodextrin, shows promise for conformational capture of mono-substituted bullvalenes. More broadly, our computational pipeline should prove useful for rapid characterization of cyclodextrin host-guest complexes, avoiding the need for costly synthesis of guest molecules that are unlikely to bind stably, as well as providing detailed atomic-level insight into the nature of complexation.
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Affiliation(s)
- Zahra Shadfar
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland 0632, New Zealand
| | - Oussama Yahiaoui
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Thomas A Collier
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland 0632, New Zealand
| | - Thomas Fallon
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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41
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Schaufelberger F, Ramström O. Activated Self-Resolution and Error-Correction in Catalytic Reaction Networks*. Chemistry 2021; 27:10335-10340. [PMID: 33780566 DOI: 10.1002/chem.202100208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 01/02/2023]
Abstract
Understanding the emergence of function in complex reaction networks is a primary goal of systems chemistry and origin-of-life studies. Especially challenging is to create systems that simultaneously exhibit several emergent functions that can be independently tuned. In this work, a multifunctional complex reaction network of nucleophilic small molecule catalysts for the Morita-Baylis-Hillman (MBH) reaction is demonstrated. The dynamic system exhibited triggered self-resolution, preferentially amplifying a specific catalyst/product set out of a many potential alternatives. By utilizing selective reversibility of the products of the reaction set, systemic thermodynamically driven error-correction could also be introduced. To achieve this, a dynamic covalent MBH reaction based on adducts with internal H-transfer capabilities was developed. By careful tuning of the substituents, rate accelerations of retro-MBH reactions of up to four orders of magnitude could be obtained. This study thus demonstrates how efficient self-sorting of catalytic systems can be achieved through an interplay of several complex emergent functionalities.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH - Royal Institute of Technology Teknikringen 36, 10044 Stockholm (Sweden)
| | - Olof Ramström
- Department of Chemistry, KTH - Royal Institute of Technology Teknikringen 36, 10044 Stockholm (Sweden).,Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA, 01854, USA.,Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182, Kalmar, Sweden
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42
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Tchakalova V, Lutz E, Lamboley S, Moulin E, Benczédi D, Giuseppone N, Herrmann A. Design of Stimuli-Responsive Dynamic Covalent Delivery Systems for Volatile Compounds (Part 2): Fragrance-Releasing Cleavable Surfactants in Functional Perfumery Applications. Chemistry 2021; 27:13468-13476. [PMID: 34270131 DOI: 10.1002/chem.202102051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 11/11/2022]
Abstract
Amphiphilic imines prepared by condensation of a hydrophobic fragrance aldehyde with a hydrophilic amine derived from a poly(propylene oxide) and poly(ethylene oxide) diblock copolymer were investigated as cleavable surfactant profragrances in applications of functional perfumery. In water, the cleavable surfactants assemble into micelles that allow solubilization of perfume molecules that are not covalently attached to the surfactant. Dynamic headspace analysis on a glass surface showed that solubilized perfume molecules evaporated in a similar manner in the presence of the cleavable surfactant as compared with a non-cleavable reference surfactant. Under application conditions, the cleavable surfactant imine hydrolysed to release the covalently linked fragrance aldehyde. The profragrances were stable during storage in aqueous media, and upon dilution showed a blooming effect for the hydrolytical fragrance release and a more balanced performance of a solubilized perfume by retaining the more volatile fragrances and boosting the evaporation of the less volatile fragrances.
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Affiliation(s)
- Vera Tchakalova
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Eric Lutz
- SAMS research group Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Serge Lamboley
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Emilie Moulin
- SAMS research group Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Daniel Benczédi
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Nicolas Giuseppone
- SAMS research group Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Andreas Herrmann
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
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43
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Lutz E, Moulin E, Tchakalova V, Benczédi D, Herrmann A, Giuseppone N. Design of Stimuli-Responsive Dynamic Covalent Delivery Systems for Volatile Compounds (Part 1): Controlled Hydrolysis of Micellar Amphiphilic Imines in Water. Chemistry 2021; 27:13457-13467. [PMID: 34270124 DOI: 10.1002/chem.202102049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 12/29/2022]
Abstract
Despite their intrinsic hydrolysable character, imine bonds can become remarkably stable in water when self-assembled in amphiphilic micellar structures. In this work, we systematically studied some of these structures and the influence of various parameters that can be used to take control of their hydrolysis, including pH, concentration, the position of the imine function in the amphiphilic structure, relative lengths of the linked hydrophilic and hydrophobic moieties. Thermodynamic and kinetic data led us to the rational design of stable imines in water, partly based on the location of the imine function within the hydrophobic part of the amphiphile and on a predictable quantitative term that we define as the total hydrophilic-lipophilic balance (HLB). In addition, we show that such stable systems are also stimuli-responsive and therefore, of potential interest in trapping and releasing micellar components on demand.
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Affiliation(s)
- Eric Lutz
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Emilie Moulin
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Vera Tchakalova
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Daniel Benczédi
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Andreas Herrmann
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Nicolas Giuseppone
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
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Molęda Z, Zawadzka A, Czarnocki Z, Monjas L, Hirsch AKH, Budzianowski A, Maurin JK. "Clicking" fragment leads to novel dual-binding cholinesterase inhibitors. Bioorg Med Chem 2021; 42:116269. [PMID: 34130217 DOI: 10.1016/j.bmc.2021.116269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022]
Abstract
Cholinesterase inhibitors are potent therapeutics in the treatment of Alzheimer's disease. Among them, dual binding ligands have recently gained a lot of attention. We discovered novel dual-binding cholinesterase inhibitors, using "clickable" fragments, which bind to either catalytic active site (CAS) or peripheral anionic site (PAS) of the enzyme. Copper(I)-catalyzed azide-alkyne cycloaddition allowed to effectively synthesize a series of final heterodimers, and modeling and kinetic studies confirmed their ability to bind to both CAS and PAS. A potent acetylcholinesterase inhibitor with IC50 = 18 nM (compound 23g) was discovered. A target-guided approach to link fragments by the enzyme itself was tested using butyrylcholinesterase.
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Affiliation(s)
- Zuzanna Molęda
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland.
| | - Anna Zawadzka
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Zbigniew Czarnocki
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Leticia Monjas
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | | | - Jan K Maurin
- National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; National Centre for Nuclear Research, 05-400 Otwock-Świerk, Poland
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45
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Tauber C, Wamser R, Arkona C, Tügend M, Abdul Aziz UB, Pach S, Schulz R, Jochmans D, Wolber G, Neyts J, Rademann J. Chemische Evolution antiviraler Wirkstoffe gegen Enterovirus D68 durch Proteintemplat‐gesteuerte Knoevenagelreaktionen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Carolin Tauber
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Rebekka Wamser
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Christoph Arkona
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Marisa Tügend
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Umer Bin Abdul Aziz
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Szymon Pach
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Robert Schulz
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Dirk Jochmans
- Department of Microbiology, Immunology and Transplantation Rega Institute KU Leuven Leuven Belgien
| | - Gerhard Wolber
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation Rega Institute KU Leuven Leuven Belgien
| | - Jörg Rademann
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
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46
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Tauber C, Wamser R, Arkona C, Tügend M, Abdul Aziz UB, Pach S, Schulz R, Jochmans D, Wolber G, Neyts J, Rademann J. Chemical Evolution of Antivirals Against Enterovirus D68 through Protein-Templated Knoevenagel Reactions. Angew Chem Int Ed Engl 2021; 60:13294-13301. [PMID: 33749121 PMCID: PMC8252737 DOI: 10.1002/anie.202102074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 02/06/2023]
Abstract
The generation of bioactive molecules from inactive precursors is a crucial step in the chemical evolution of life, however, mechanistic insights into this aspect of abiogenesis are scarce. Here, we investigate the protein-catalyzed formation of antivirals by the 3C-protease of enterovirus D68. The enzyme induces aldol condensations yielding inhibitors with antiviral activity in cells. Kinetic and thermodynamic analyses reveal that the bioactivity emerges from a dynamic reaction system including inhibitor formation, alkylation of the protein target by the inhibitors, and competitive addition of non-protein nucleophiles to the inhibitors. The most active antivirals are slowly reversible inhibitors with elongated target residence times. The study reveals first examples for the chemical evolution of bio-actives through protein-catalyzed, non-enzymatic C-C couplings. The discovered mechanism works under physiological conditions and might constitute a native process of drug development.
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Affiliation(s)
- Carolin Tauber
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Rebekka Wamser
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Christoph Arkona
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Marisa Tügend
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Umer Bin Abdul Aziz
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Szymon Pach
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Robert Schulz
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Dirk Jochmans
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
| | - Gerhard Wolber
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Johan Neyts
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
| | - Jörg Rademann
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
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47
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He M, Lehn JM. Metal Cation-Driven Dynamic Covalent Formation of Imine and Hydrazone Ligands Displaying Synergistic Co-catalysis and Auxiliary Amine Effects. Chemistry 2021; 27:7516-7524. [PMID: 33909937 DOI: 10.1002/chem.202100662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 11/09/2022]
Abstract
Optimizing C=N bond formation and C/N component exchange has major significance in Dynamic Covalent Chemistry (DCC). Imine and hydrazone generation from their aldehyde, amine and hydrazine components showed large accelerations in presence of AgOTf or Zn(OTf)2 , up to 104 for the Zn(II)-(p-anisidine)imine complex. Zn(OTf)2 and auxiliary p-anisidine together accelerated 630 times the formation of the Zn(II)-hydrazone complex, revealing a strong synergistic effect, traced to very fast initial formation of the reactive Zn(II)-imine complex presenting a C=N bond metallo-activated towards reaction with the hydrazine component. Reactions involving more entities showed kinetically faster and thermodynamically simpler outputs due to dynamic competition within a mixture of higher complexity. Catalytic amounts of metal salts and auxiliary amine gave similar marked rate accelerations and turnover, indicating true catalysis. The synergistic effect achieved by combining metallo- and organo-catalysis points to a powerful co-catalysis strategy of bond-formation in DCC through interconnected chemical transformations.
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Affiliation(s)
- Meixia He
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 8 allée Gaspard Monge, 67000, Strasbourg, France
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48
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Jumde RP, Guardigni M, Gierse RM, Alhayek A, Zhu D, Hamid Z, Johannsen S, Elgaher WAM, Neusens PJ, Nehls C, Haupenthal J, Reiling N, Hirsch AKH. Hit-optimization using target-directed dynamic combinatorial chemistry: development of inhibitors of the anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase. Chem Sci 2021; 12:7775-7785. [PMID: 34168831 PMCID: PMC8188608 DOI: 10.1039/d1sc00330e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023] Open
Abstract
Target-directed dynamic combinatorial chemistry (tdDCC) enables identification, as well as optimization of ligands for un(der)explored targets such as the anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase (DXPS). We report the use of tdDCC to first identify and subsequently optimize binders/inhibitors of the anti-infective target DXPS. The initial hits were also optimized for their antibacterial activity against E. coli and M. tuberculosis during subsequent tdDCC runs. Using tdDCC, we were able to generate acylhydrazone-based inhibitors of DXPS. The tailored tdDCC runs also provided insights into the structure-activity relationship of this novel class of DXPS inhibitors. The competition tdDCC runs provided important information about the mode of inhibition of acylhydrazone-based inhibitors. This approach holds the potential to expedite the drug-discovery process and should be applicable to a range of biological targets.
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Affiliation(s)
- Ravindra P Jumde
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Melissa Guardigni
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- D3-PharmaChemistry, Istituto Italiano di Tecnologia Via Morego 30 16163 Genoa Italy
| | - Robin M Gierse
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Alaa Alhayek
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Di Zhu
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Zhoor Hamid
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Sandra Johannsen
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Walid A M Elgaher
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Philipp J Neusens
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Christian Nehls
- RG Biophysics, Research Center Borstel, Leibniz Lung Center Borstel Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center Borstel Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems Borstel Germany
| | - Anna K H Hirsch
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
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49
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Zhao S, Xu J, Zhang S, Han M, Wu Y, Li Y, Hu L. Multivalent butyrylcholinesterase inhibitor discovered by exploiting dynamic combinatorial chemistry. Bioorg Chem 2021; 108:104656. [PMID: 33548731 DOI: 10.1016/j.bioorg.2021.104656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/21/2022]
Abstract
In this study, we report the generation of a polymer-based dynamic combinatorial library (DCL) incorporating exchangeable side chains using acylhydrazone formation reaction. In combination with tetrameric butyrylcholinesterase (BChE), the most potent binding side chain was identified, and the information obtained was further used for the synthesis of a multivalent BChE inhibitor. In the in vitro biological evaluation, this multivalent inhibitor exhibited not only better inhibitory effect than the commercial reference but also high selectivity on BChE over acetylcholinesterase (AChE).
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Affiliation(s)
- Shuang Zhao
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Jintao Xu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Shixin Zhang
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Maochun Han
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Yao Wu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Yusi Li
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, 301 Xuefu Rd., Zhenjiang, China.
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50
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Dutta K, Kanjilal P, Das R, Thayumanavan S. Synergistic Interplay of Covalent and Non-Covalent Interactions in Reactive Polymer Nanoassembly Facilitates Intracellular Delivery of Antibodies. Angew Chem Int Ed Engl 2021; 60:1821-1830. [PMID: 33034131 PMCID: PMC7855684 DOI: 10.1002/anie.202010412] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/23/2020] [Indexed: 01/29/2023]
Abstract
The primary impediments in developing large antibodies as drugs against intracellular targets involve their low transfection efficiency and suitable reversible encapsulation strategies for intracellular delivery with retention of biological activity. To address this, we outline an electrostatics-enhanced covalent self-assembly strategy to generate polymer-protein/antibody nanoassemblies. Through structure-activity studies, we down-select the best performing self-immolative pentafluorophenyl containing activated carbonate polymer for bioconjugation. With the help of an electrostatics-aided covalent self-assembly approach, we demonstrate efficient encapsulation of medium to large proteins (HRP, 44 kDa and β-gal, 465 kDa) and antibodies (ca. 150 kDa). The designed polymeric nanoassemblies are shown to successfully traffic functional antibodies (anti-NPC and anti-pAkt) to cytosol to elicit their bioactivity towards binding intracellular protein epitopes and inducing apoptosis.
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Affiliation(s)
| | | | - Ritam Das
- University of Massachusetts, Amherst, MA, 01003, USA
| | - Sankaran Thayumanavan
- Department of Chemistry, Molecular and Cellular Biology Program, and The Center for Bioactive Delivery-Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, 01003, USA
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