1
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Qi D, Shi X, Lin C, Holzhausen F, Ville L, Sun X, Luo J, Pitkänen L, Zhu Y, Rosenholm J, Jalkanen S, Li J. Self-Adaptive Synthesis of Non-Covalent Crosslinkers while Folding Single-Chain Polymers. Angew Chem Int Ed Engl 2024:e202408670. [PMID: 38943429 DOI: 10.1002/anie.202408670] [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: 05/07/2024] [Revised: 06/13/2024] [Accepted: 06/27/2024] [Indexed: 07/01/2024]
Abstract
Peptide folding is a dynamic process driven by non-covalent cross-linking leading to functional nanostructures for essential biochemical activities. However, replicating this process in synthetic systems is challenging due to the difficulty in mimicking nature's real-time regulation of non-covalent crosslinking for single-chain polymer folding. Here, we address this by employing anionic dithiol building blocks to create macrocyclic disulfides as non-covalent crosslinkers that adapted to the folding process. Initially, small macrocycles facilitated a low degree folding of a polycation. Then, this preorganized structure catalysed the production of larger macrocycles that enhanced the folding conversely. The self-adaptive synthesis was verified through the encapsulation of an anticancer drug, showing an updated production distribution of non-covalent crosslinkers and maximizing drug-loading efficiency against drug-resistant cancer in vitro. Our research advances the understanding of molecular systems by exploring species evolution via the structural dynamics of polymer folding. Additionally, adaptive synthesis enables controlled, sequential folding of synthetic polymers, with the potential to mimic protein functions.
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Affiliation(s)
- Dawei Qi
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, FI-20520, Turku, Finland
| | - Xuncheng Shi
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, FI-20520, Turku, Finland
| | - Caihong Lin
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, FI-20520, Turku, Finland
| | - Ferdinand Holzhausen
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, FI-20520, Turku, Finland
| | - Liljeström Ville
- Nanomicroscopy Center, OtaNano, Aalto University, Espoo, 00076, Aalto, Finland
| | - Xun Sun
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Jinghui Luo
- Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Leena Pitkänen
- Department of Bioproducts and Biosystems, Aalto University, 02150, Espoo, Finland
| | - Ya Zhu
- Department of Bioproducts and Biosystems, Aalto University, 02150, Espoo, Finland
| | - Jessica Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, FI-20520, Turku, Finland
| | - Jianwei Li
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, FI-20520, Turku, Finland
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2
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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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3
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Peker T, Zagiel B, Rocard L, Bich C, Sachon E, Moumné R. Analytical Tools for Dynamic Combinatorial Libraries of Cyclic Peptides. Chembiochem 2023; 24:e202300688. [PMID: 37815502 DOI: 10.1002/cbic.202300688] [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: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase.
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Affiliation(s)
- Taleen Peker
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Benjamin Zagiel
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Lou Rocard
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Emmanuelle Sachon
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- MS3U Platform, Fédération de Chimie Moléculaire de Paris Centre - FR2769, Sorbonne Université, 4 Place Jussieu, 75005, Paris, France
| | - Roba Moumné
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
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4
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Qi Y, Ramström O. Polymerization, Stimuli-induced Depolymerization, and Precipitation-driven Macrocyclization in a Nitroaldol Reaction System. Chemistry 2022; 28:e202201863. [PMID: 35971799 PMCID: PMC9826525 DOI: 10.1002/chem.202201863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Indexed: 01/11/2023]
Abstract
Dynamic covalent polymers of different topology have been synthesized from an aromatic dialdehyde and α,ω-dinitroalkanes via the nitroaldol reaction. All dinitroalkanes yielded dynamers with the dialdehyde, where the length of the dinitroalkane chain played a vital role in determining the structure of the final products. For longer dinitroalkanes, linear dynamers were produced, where the degree of polymerization reached a plateau at higher feed concentrations. In the reactions involving 1,4-dinitrobutane and 1,5-dinitropentane, specific macrocycles were formed through depolymerization of the linear chains, further driven by precipitation. At lower temperature, the same systemic self-sorting effect was also observed for the 1,6-dinitrohexane-based dynamers. Moreover, the dynamers showed a clear adaptive behavior, displaying depolymerization and rearrangement of the dynamer chains in response to alternative building blocks as external stimuli.
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Affiliation(s)
- Yunchuan Qi
- Department of ChemistryUniversity of Massachusetts LowellOne University Ave.LowellMA 01854USA
| | - Olof Ramström
- Department of ChemistryUniversity of Massachusetts LowellOne University Ave.LowellMA 01854USA,Department of Chemistry and Biomedical SciencesLinnaeus UniversitySE-39182KalmarSweden
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5
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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: 5] [Impact Index Per Article: 2.5] [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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6
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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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7
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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: 9] [Impact Index Per Article: 4.5] [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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8
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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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9
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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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10
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Selinger AJ, Cavallin NA, Yanai A, Birol I, Hof F. Template‐Directed Synthesis of Bivalent, Broad‐Spectrum Hosts for Neuromuscular Blocking Agents**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113235] [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)
- Allison J. Selinger
- Department of Chemistry University of Victoria 3800 Finnerty Rd. Victoria BC V8P 5C2 Canada
- Centre for Advanced Materials and Related Technology (CAMTEC) University of Victoria 3800 Finnerty Rd. Victoria BC V8W 2Y2 Canada
| | - Natalie A. Cavallin
- Department of Chemistry University of Victoria 3800 Finnerty Rd. Victoria BC V8P 5C2 Canada
- Centre for Advanced Materials and Related Technology (CAMTEC) University of Victoria 3800 Finnerty Rd. Victoria BC V8W 2Y2 Canada
| | - Anat Yanai
- Canada's Michael Smith Genome Sciences Centre BC Cancer Vancouver BC V5Z 4S6 Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre BC Cancer Vancouver BC V5Z 4S6 Canada
- Department of Medical Genetics University of British Columbia Vancouver BC V6T 1Z3 Canada
| | - Fraser Hof
- Department of Chemistry University of Victoria 3800 Finnerty Rd. Victoria BC V8P 5C2 Canada
- Centre for Advanced Materials and Related Technology (CAMTEC) University of Victoria 3800 Finnerty Rd. Victoria BC V8W 2Y2 Canada
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11
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Selinger AJ, Cavallin NA, Yanai A, Birol I, Hof F. Template-Directed Synthesis of Bivalent, Broad-Spectrum Hosts for Neuromuscular Blocking Agents*. Angew Chem Int Ed Engl 2021; 61:e202113235. [PMID: 34889016 DOI: 10.1002/anie.202113235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Indexed: 12/19/2022]
Abstract
We report on the synthesis of bivalent water-soluble calix[4]arene and calix[5]arene hosts, Super-sCx4 and Super-sCx5 as new broad-spectrum supramolecular binders of neuromuscular blocking agents (NMBAs). Synthesis was achieved using the target bisquaternary amine NMBAs as a template to link two highly anionic p-sulfonatocalixarene building blocks in aqueous solution. Bivalent anionic hosts Super-sCx4 and Super-sCx5 bind by engaging both quaternary amines present on a variety of NMBAs. We report low μM binding to structurally diverse alkyl, steroidal, curarine and benzylisoquinoline NMBAs with high selectivity over the neurotransmitter acetylcholine and a variety of other hydrophobic amines.
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Affiliation(s)
- Allison J Selinger
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.,Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| | - Natalie A Cavallin
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.,Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| | - Anat Yanai
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.,Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
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12
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Canal-Martín A, Navo CD, Sáez E, Molero D, Jiménez-Osés G, Pérez-Fernández R. Nucleophilic catalysis of p-substituted aniline derivatives in acylhydrazone formation and exchange. Org Biomol Chem 2021; 19:7202-7210. [PMID: 34612342 DOI: 10.1039/d1ob00871d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrazone bond formation is a versatile reaction employed in several research fields. It is one of the most popular reversible reactions in dynamic combinatorial chemistry. Under physiological conditions, hydrazone exchange benefits from the addition of a nucleophilic catalyst. We report a mechanistic study and superior performance of electron-rich p-substituted aniline derivatives as catalysts for efficient hydrazone formation and exchange in both protic and aprotic solvents. Rigorous kinetic analyses demonstrate that imine formation with 3-hydroxy-4-nitrobenzaldehyde and aniline derivatives proceeds with unprecedented third-order kinetics in which the aldehyde consistently shows a partial order of two. Computational investigations provide insights into the mechanisms of these transformations.
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Affiliation(s)
- Andrea Canal-Martín
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid 28040, Spain.
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13
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Hoz ADL, Alkorta I, Elguero J. The mechanism of the reaction of hydrazines with α,β-unsaturated carbonyl compounds to afford hydrazones and 2-pyrazolines (4,5-dihydro-1H-pyrazoles): Experimental and theoretical results. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Han GS, Domaille DW. Tuning the exchange dynamics of boronic acid hydrazones and oximes with pH and redox control. Org Biomol Chem 2021; 19:4986-4991. [PMID: 34008683 DOI: 10.1039/d1ob00191d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Dynamic bonds continually form and dissociate at equilibrium. Carbonyl compounds with proximal boronic acids, including 2-formylphenylboronic acid (2-FPBA), have been reported to form highly dynamic covalent hydrazone and oxime bonds in physiological conditions, but strategies to tune the dynamics have not yet been reported. Here, we characterize the dynamics of 2-FPBA-derived hydrazones and oximes and account for both the rapid rate of formation (∼102-103 M-1 s-1) and the relatively fast rate of hydrolysis (∼10-4 s-1) at physiological pH. We further show that these substrates undergo exchange with α-nucleophiles, which can be reversibly paused and restarted with pH control. Finally, we show that oxidation of the arylboronic acid effectively abolishes the rapid dynamics, which slows the forward reaction by more than 30 000 times and increases the hydrolytic half-life from 50 minutes to 6 months at physiological pH. These results set the stage to explore these linkages in dynamic combinatorial libraries, reversible bioconjugation, and self-healing materials.
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Affiliation(s)
- Gun Su Han
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA.
| | - Dylan W Domaille
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA.
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15
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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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Biomimetic selenocystine based dynamic combinatorial chemistry for thiol-disulfide exchange. Nat Commun 2021; 12:163. [PMID: 33420034 PMCID: PMC7794297 DOI: 10.1038/s41467-020-20415-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
Dynamic combinatorial chemistry applied to biological environments requires the exchange chemistry of choice to take place under physiological conditions. Thiol-disulfide exchange, one of the most popular dynamic combinatorial chemistries, usually needs long equilibration times to reach the required equilibrium composition. Here we report selenocystine as a catalyst mimicking Nature's strategy to accelerate thiol-disulfide exchange at physiological pH and low temperatures. Selenocystine is able to accelerate slow thiol-disulfide systems and to promote the correct folding of an scrambled RNase A enzyme, thus broadening the practical range of pH conditions for oxidative folding. Additionally, dynamic combinatorial chemistry target-driven self-assembly processes are tested using spermine, spermidine and NADPH (casting) and glucose oxidase (molding). A non-competitive inhibitor is identified in the glucose oxidase directed dynamic combinatorial library.
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