1
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Wang YF, Wang SM, Zhang X, Nian H, Zheng LS, Wang X, Schreckenbach G, Jiang W, Yang LP, Wang LL. Precise Recognition in Water by an Endo-Functionalized Cavity: Tuning the Complementarity of Binding Sites. Angew Chem Int Ed Engl 2023; 62:e202310115. [PMID: 37814589 DOI: 10.1002/anie.202310115] [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: 07/16/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
Precise binding towards structurally similar substrates is a common feature of biomolecular recognition. However, achieving such selectivity-especially in distinguishing subtle differences in substrates-with synthetic hosts can be quite challenging. Herein, we report a novel design strategy involving the combination of different rigid skeletons to adjust the distance between recognition sites within the cavity, which allows for the highly selective recognition of hydrogen-bonding complementary substrates, such as 4-chromanone. X-ray single-crystal structures and density functional theory calculations confirmed that the distance of endo-functionalized groups within the rigid cavity is crucial for achieving high binding selectivity through hydrogen bonding. The thermodynamic data and molecular dynamics simulations revealed a significant influence of the hydrophobic cavity on the binding affinity. The new receptor possesses both high selectivity and high affinity, which provide valuable insights for the design of customized receptors.
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Affiliation(s)
- Yan-Fang Wang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Song-Meng Wang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Xiaobin Zhang
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Hao Nian
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Li-Shuo Zheng
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Xiaoping Wang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Wei Jiang
- Department of Chemistry, Southern University of Science and Technology, Xueyuan Blvd 1088, Shenzhen, 518055, China
| | - Liu-Pan Yang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Li-Li Wang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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2
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Ferguson Johns HP, Harrison EE, Stingley KJ, Waters ML. Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water. Chemistry 2021; 27:6620-6644. [PMID: 33048395 DOI: 10.1002/chem.202003759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 01/25/2023]
Abstract
Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.
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Affiliation(s)
- Hannah P Ferguson Johns
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily E Harrison
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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3
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Shaurya A, Garnett GAE, Starke MJ, Grasdal MC, Dewar CC, Kliuchynskyi AY, Hof F. An easily accessible, lower rim substituted calix[4]arene selectively binds N, N-dimethyllysine. Org Biomol Chem 2021; 19:4691-4696. [PMID: 33978657 DOI: 10.1039/d1ob00524c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Post-translational modifications (PTMs) are critical controllers of protein functions. One set of important PTMs are N-methylated side chains of lysine and arginine, which exist in several functionally distinct forms. Multiple groups have demonstrated the selective binding of the most hydrophobic family member, trimethyllysine (Kme3), using various macrocyclic hosts, but the selective binding of lower methylation states remains challenging. Herein we report that the installation of a sulfonate ester on the lower rim phenol of p-sulfonatocalix[4]arene efficiently generates a potent, N,N-dimethyllysine (Kme2)-selective host in one step from commercially available starting materials. We characterize its binding behaviors in solution, and examine the relationship between its unusual conformational dynamics and its guest-binding properties.
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Affiliation(s)
- Alok Shaurya
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Graham A E Garnett
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Melissa J Starke
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Mark C Grasdal
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Charlotte C Dewar
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Anton Y Kliuchynskyi
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Fraser Hof
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
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4
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Huang X, Wang X, Quan M, Yao H, Ke H, Jiang W. Biomimetic Recognition and Optical Sensing of Carboxylic Acids in Water by Using a Buried Salt Bridge and the Hydrophobic Effect. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xuan Huang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Mao Quan
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Huan Yao
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Hua Ke
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
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5
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Huang X, Wang X, Quan M, Yao H, Ke H, Jiang W. Biomimetic Recognition and Optical Sensing of Carboxylic Acids in Water by Using a Buried Salt Bridge and the Hydrophobic Effect. Angew Chem Int Ed Engl 2020; 60:1929-1935. [DOI: 10.1002/anie.202012467] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/21/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Huang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Mao Quan
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Huan Yao
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Hua Ke
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
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6
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Dumartin M, Septavaux J, Donnier-Maréchal M, Jeamet E, Dumont E, Perret F, Vial L, Leclaire J. The dark side of disulfide-based dynamic combinatorial chemistry. Chem Sci 2020; 11:8151-8156. [PMID: 34094174 PMCID: PMC8163284 DOI: 10.1039/d0sc02399j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
During the last two decades, disulfide-based dynamic combinatorial chemistry has been extensively used in the field of molecular recognition to deliver artificial receptors for molecules of biological interest. Commonly, the nature of library members and their relative amounts are provided from HPLC-MS analysis of the libraries, allowing the identification of potential binders for a target (bio)molecule. By re-investigating dynamic combinatorial libraries generated from a simple 2,5-dicarboxy-1,4-dithiophenol building block in water, we herein demonstrated that multiple analytical tools were actually necessary in order to comprehensively describe the libraries in terms of size, stereochemistry, affinity, selectivity, and finally to get a true grasp on the different phenomena at work within dynamic combinatorial systems. We show that multiple analytical tools are necessary in order to describe the different phenomena within disulfide-based dynamic combinatorial libraries in terms of size, stereochemistry, affinity and selectivity.![]()
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Affiliation(s)
- Mélissa Dumartin
- Univ. Lyon, Univ. Lyon 1, CNRS, INSA, CPE, ICBMS F-69622 Lyon France
| | - Jean Septavaux
- Univ. Lyon, Univ. Lyon 1, CNRS, INSA, CPE, ICBMS F-69622 Lyon France .,Secoya Technologies, Louvain-La-Neuve 1348 Belgium
| | | | - Emeric Jeamet
- Univ. Lyon, Univ. Lyon 1, CNRS, INSA, CPE, ICBMS F-69622 Lyon France
| | - Elise Dumont
- ENS Lyon, Univ. Lyon 1, CNRS, Laboratoire de Chimie F-69364 France.,Institut Universitaire de France 5 rue Descartes 75005 Paris France
| | - Florent Perret
- Univ. Lyon, Univ. Lyon 1, CNRS, INSA, CPE, ICBMS F-69622 Lyon France
| | - Laurent Vial
- Univ. Lyon, Univ. Lyon 1, CNRS, INSA, CPE, ICBMS F-69622 Lyon France
| | - Julien Leclaire
- Univ. Lyon, Univ. Lyon 1, CNRS, INSA, CPE, ICBMS F-69622 Lyon France
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7
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Mullins AG, St. Louis LE, Waters ML. Using changes in speciation in a dynamic combinatorial library as a fingerprint to differentiate the methylation states of arginine. Chem Commun (Camb) 2020; 56:3947-3950. [DOI: 10.1039/d0cc00415d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A dynamic combinatorial library was shown to provide a direct method of sensing methylated arginine and lysine due to differences in speciation. This provides the first sensor array for all the methylation states of arginine.
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Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Lauren E. St. Louis
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Marcey L. Waters
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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8
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Mullins AG, Pinkin NK, Hardin JA, Waters ML. Achieving High Affinity and Selectivity for Asymmetric Dimethylarginine by Putting a Lid on a Box. Angew Chem Int Ed Engl 2019; 58:5282-5285. [DOI: 10.1002/anie.201814645] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/30/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Nicholas K. Pinkin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Joshua A. Hardin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
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9
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Mullins AG, Pinkin NK, Hardin JA, Waters ML. Achieving High Affinity and Selectivity for Asymmetric Dimethylarginine by Putting a Lid on a Box. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Nicholas K. Pinkin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Joshua A. Hardin
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA
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10
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Sapotta M, Hofmann A, Bialas D, Würthner F. A Water-Soluble Perylene Bisimide Cyclophane as a Molecular Probe for the Recognition of Aromatic Alkaloids. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Meike Sapotta
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Anja Hofmann
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - David Bialas
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC); Universität Würzburg; Theodor-Boveri-Weg 97074 Würzburg Germany
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11
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Sapotta M, Hofmann A, Bialas D, Würthner F. A Water-Soluble Perylene Bisimide Cyclophane as a Molecular Probe for the Recognition of Aromatic Alkaloids. Angew Chem Int Ed Engl 2019; 58:3516-3520. [DOI: 10.1002/anie.201813559] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Meike Sapotta
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Anja Hofmann
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - David Bialas
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC); Universität Würzburg; Theodor-Boveri-Weg 97074 Würzburg Germany
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12
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Gruber T. Synthetic Receptors for the Recognition and Discrimination of Post-Translationally Methylated Lysines. Chembiochem 2018; 19:2324-2340. [DOI: 10.1002/cbic.201800398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Gruber
- School of Pharmacy; University of Lincoln; Joseph Banks Laboratories; Green Lane Lincoln LN6 7DL UK
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