1
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Ghosh A, Zhao Y. Site-Selective Functionalization of Molecularly Imprinted Nanoparticles to Recognize Lysine-Rich Peptides. Biomacromolecules 2024; 25:6188-6194. [PMID: 39092916 DOI: 10.1021/acs.biomac.4c00905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Sequence-selective binding of peptides has been a long-standing goal of chemists. As one of the most abundant amino acids in proteins, lysine plays an important role in protein functions as well as in antimicrobial and cell-penetrating peptides. Herein, we report molecularly imprinted nanoparticles (NPs) with high sequence selectivity for lysine-rich peptides. The NPs are prepared from molecular imprinting of cross-linkable surfactant micelles and postmodification of the imprinted pockets by photoaffinity labeling. The method allows carboxylic acids to be installed precisely near the lysine amino side chains, greatly enhancing the binding strengths of lysine-rich peptides. Small variations in the peptide sequence can be distinguished, and the binding affinity correlates positively with the number of lysine groups in model tripeptides. The method applies to complex lysine-rich biological peptides, achieving hundreds of nanomolar binding affinities and excellent binding specificities.
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Affiliation(s)
- Avijit Ghosh
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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2
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Zanela TMP, Zangiabadi M, Zhao Y, Underbakke ES. Molecularly imprinted nanoparticles reveal regulatory scaffolding features in Pyk2 tyrosine kinase. RSC Chem Biol 2024; 5:447-453. [PMID: 38725907 PMCID: PMC11078204 DOI: 10.1039/d3cb00228d] [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: 11/27/2023] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Pyk2 is a multi-domain non-receptor tyrosine kinase that serves dual roles as a signaling enzyme and scaffold. Pyk2 activation involves a multi-stage cascade of conformational rearrangements and protein interactions initiated by autophosphorylation of a linker site. Linker phosphorylation recruits Src kinase, and Src-mediated phosphorylation of the Pyk2 activation loop confers full activation. The regulation and accessibility of the initial Pyk2 autophosphorylation site remains unclear. We employed peptide-binding molecularly imprinted nanoparticles (MINPs) to probe the regulatory conformations controlling Pyk2 activation. MINPs differentiating local structure and phosphorylation state revealed that the Pyk2 autophosphorylation site is protected in the autoinhibited state. Activity profiling of Pyk2 variants implicated FERM and linker residues responsible for constraining the autophosphorylation site. MINPs targeting each Src docking site disrupt the higher-order kinase interactions critical for activation complex maturation. Ultimately, MINPs targeting key regulatory motifs establish a useful toolkit for probing successive activational stages in the higher-order Pyk2 signaling complex.
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Affiliation(s)
- Tania M Palhano Zanela
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University Ames IA 50011 USA
| | - Milad Zangiabadi
- Department of Chemistry, Iowa State University Ames Iowa 50011 USA
| | - Yan Zhao
- Department of Chemistry, Iowa State University Ames Iowa 50011 USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University Ames IA 50011 USA
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3
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Cecconello A, Tonolo F, Rilievo G, Molinari S, Talpe A, Cozza G, Venerando A, Kariyawasam IDH, Govardhan GT, Arusei RJ, Magro M, Vianello F. Highly specific colloidal ɣ-Fe 2O 3-DNA hybrids: From bioinspired recognition to large-scale lactoferrin purification. Colloids Surf B Biointerfaces 2024; 234:113700. [PMID: 38104467 DOI: 10.1016/j.colsurfb.2023.113700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
The industry transfer of laboratory-use magnetic separation is still hampered by the lack of suitable nanoparticles, both in terms of their features and large-scale availability. Surface Active Maghemite Nanoparticles (SAMNs) characterized by a unique surface chemistry, low environmental impact, scalable synthesis and functionalization were used to develop a bio-inspired lactoferrin (LF) recognition system. Based on the LF affinity for DNA, a self-assembly process was optimized for obtaining a SAMN@DNA hybrid displaying chemical and colloidal stability and LF specificity. SAMN@DNA was successfully tested for the affinity purification of LF from crude bovine whey. Advantages, such as high selectivity and loading capacity, nanoparticle re-usability, outstanding purity (96 ± 1%), preservation of protein conformation and short operational time, were highlighted. Finally, scalability was demonstrated by an automatic system performing continuous purification of LF from 100 liters day-1 of whey. This study responds to essential prerequisites, such as efficiency, re-usability and industrialization feasibility.
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Affiliation(s)
- Alessandro Cecconello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Federica Tonolo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Graziano Rilievo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Simone Molinari
- Museum of Nature and Humankind, Mineralogy Section Alessandro Guastoni, University of Padua, Via Giotto 1, 35121 Padua, Italy
| | - Arthur Talpe
- Catholic University of Leuven, Oude Markt 13, 3000 Leuven, Belgium
| | - Giorgio Cozza
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padova, Italy
| | - Andrea Venerando
- Department of Agrifood, Environmental and Animal Sciences, University of Udine, Via Palladio 8, 33100 Udine, Italy
| | | | - Gayathri Tiruchi Govardhan
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Ruth Jepchirchir Arusei
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, PD, Italy
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4
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Pan YC, Tian JH, Guo DS. Molecular Recognition with Macrocyclic Receptors for Application in Precision Medicine. Acc Chem Res 2023; 56:3626-3639. [PMID: 38059474 DOI: 10.1021/acs.accounts.3c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Macrocyclic receptors can serve as alternatives to natural recognition systems as recognition tools. They provide effectively preorganized cavities to encapsulate guests via host-guest interactions, thereby affecting the physiochemical properties of the guests. Macrocyclic receptors exhibit chemical and thermal stabilities higher than those of natural receptors and thus are expected to resist degradation inside the body. This reduces the risk of harmful degradation byproducts and ensures optimal levels of effectiveness. Macrocyclic receptors have precise molecular weights and well-defined structures; this ensures their batch-to-batch reproducibility, which is critical for ensuring quality and effectiveness levels. Moreover, macrocyclic receptors exhibit broad modification tunabilities, rendering them adaptable to various guests. Molecular recognition is the basis of numerous biological processes. Macrocyclic receptors may display considerable potential for application in diagnosing and treating diseases, depending on the host-guest recognition of bioactive molecules. However, the binding affinities and selectivities of macrocyclic receptors toward bioactive molecules are generally insufficient, which may lead to problems such as low diagnosis accuracies, off-target leaking, and interference with normal functions. Therefore, addressing the challenge of the strong and specific complexation of bioactive molecules and macrocyclic receptors is imperative.To overcome this challenge, we proposed the innovative strategies of longitudinal cavity extension and coassembled heteromultivalent recognition for application in the recognition of small molecules and biomacromolecules, respectively. The deepened cavity provides a stronger hydrophobic effect and a larger interaction area while maintaining the framework rigidity. By coassembling two macrocyclic amphiphiles into one ensemble, we achieved the desired heteromultivalent recognition. This strategy affords the necessary binding properties while preventing the requirement of tedious steps and site mismatch in covalent synthesis. Using these two strategies, we achieved specific and strong binding of macrocyclic receptors to various bioactive molecules including biomarkers, drugs, and disease-related peptides/proteins. We then applied these macrocyclic receptor-based recognition systems in biosensing and bioimaging, drug delivery, and therapeutics.In this Account, we summarize the strategies we used in the recognition of small molecules and biomacromolecules. Thereafter, we discuss their applications in precision medicine, involving the (1) sensing of biomarkers and imaging of lesion sites, which are critical in the early screening of diseases and accurate diagnoses; (2) precise loading and targeted delivery of drugs, which are crucial in improving their therapeutic efficacies and reducing their side effects; and (3) capture and removal of disease-related biomacromolecules, which are significant for precise intervention in life processes. Finally, we propose recommendations for the further development of macrocyclic receptor-based recognition systems in biomedicine. Macrocyclic receptors exhibit considerable potential for research, and continued investigation may not only expand the applications of supramolecular chemistry but also open novel avenues for the development of precision medicine.
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Affiliation(s)
- Yu-Chen Pan
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Jia-Hong Tian
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Dong-Sheng Guo
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
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5
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Gu Z, Guo Z, Gao S, Huang L, Liu Z. Hierarchically Structured Molecularly Imprinted Nanotransducers for Truncated HER2-Targeted Photodynamic Therapy of Therapeutic Antibody-Resistant Breast Cancer. ACS NANO 2023. [PMID: 37183805 DOI: 10.1021/acsnano.3c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Antibodies have been a mainstream class of therapeutics for clinical treatment of various diseases, especially cancers. However, mutation in cancer cells leads to resistance to therapeutic antibodies, hyperactivity of proliferation of cancer cells, and difficulty in the development of therapeutic antibodies. Herein, we present a strategy termed molecularly imprinted nanotransducer (MINT) for targeted photodynamic therapy (PDT) of mutated cancers. The MINT is a rationally engineered nanocomposite featuring a core of an upconversion nanoparticle, a shell of a thin layer of molecularly imprinted polymer, and a photosensitizer modified on the surface. As a proof-of-principle, truncated HER2 (P95HER2) overexpressed breast cancer, a challenging cancer lacking effective targeted therapeutics, was used as the cancer model. The designed structure, properties, functions, and anticancer efficacy of MINT were systematically investigated and experimentally confirmed. The MINT could not only specifically target P95HER2+ cancer cells in vitro and in vivo but also efficiently transfer the irradiated light and generate excited-state oxygen, resulting in efficient targeted cancer killing. Therefore, the MINT strategy provides a promising therapeutic for targeted PDT of drug-resistant cancers caused by target mutation.
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Affiliation(s)
- Zikuan Gu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Song Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Lingrui Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
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6
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Zangiabadi M, Ghosh A, Zhao Y. Nanoparticle Scanners for the Identification of Key Sequences Involved in the Assembly and Disassembly of β-Amyloid Peptides. ACS NANO 2023; 17:4764-4774. [PMID: 36857741 DOI: 10.1021/acsnano.2c11186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The aggregation of β-amyloid peptides (Aβ), implied in the development and progression of Alzheimer's disease, is driven by a complex set of intramolecular and intermolecular interactions involving both hydrophobic and polar residues. The key residues responsible for the forward assembling process may be different from those that should be targeted to disassemble already formed aggregates. Molecularly imprinted nanoparticle (MINP) receptors are reported in this work to strongly and selectively bind specific segments of Aβ40. Combined fluorescence spectroscopy, atomic force microscopy (AFM) imaging, and circular dichroism (CD) spectroscopy indicate that binding residues 21-30 near the loop region is most effective at inhibiting the aggregation of monomeric Aβ40, but residues 11-20 that include the internal β strand closer to the N-terminal represent the best target for disaggregating already formed aggregates in the polymerization phase. Once the aggregation proceeds to the saturation phase, binding residues 1-10 has the largest effect on the disaggregation, likely because of the accessibility of these amino acids relative to others to the MINP receptors.
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Affiliation(s)
- Milad Zangiabadi
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Avijit Ghosh
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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7
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Arifuzzaman MD, Bose I, Bahrami F, Zhao Y. Imprinted Polymeric Nanoparticles as Artificial Enzymes for Ester Hydrolysis at Room Temperature and pH 7. CHEM CATALYSIS 2022; 2:2049-2065. [PMID: 38098612 PMCID: PMC10720975 DOI: 10.1016/j.checat.2022.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Natural esterases hydrolyze esters under physiological pHs but chemists often have to use strongly acidic or basic conditions for the same hydrolysis. We report synthetic nanoparticle catalysts that hydrolyze nonactivated alkyl esters at room temperature and neutral pH, with enzyme-like catalytic mechanisms and exquisite substrate selectivity. Unlike natural enzymes that denature easily at elevated temperatures, the synthetic catalysts become more active at higher temperatures.
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Affiliation(s)
| | | | - Foroogh Bahrami
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, U.S.A
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, U.S.A
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8
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Chen K, Zhao Y. Molecular recognition of enzymes and modulation of enzymatic activity by nanoparticle conformational sensors. Chem Commun (Camb) 2022; 58:1732-1735. [PMID: 35029260 DOI: 10.1039/d1cc05699a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regulation of enzyme activity is key to dynamic processes in biology but is difficult to achieve with synthetic systems. We here report molecularly imprinted nanoparticles with strong binding for the N- and C-terminal peptides on lysozyme. Binding affinity for the enzyme correlated with conformational flexibility of the peptides in the protein structure. Significantly, binding at the C-terminus of lysozyme enhanced the performance of the enzyme at elevated temperatures and that at the N-terminus lowered the enzyme activity. These nanoparticles, when clicked onto magnetic nanoparticles, could also be used to fish out the protein of interest from a mixture in a single step.
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Affiliation(s)
- Kaiqian Chen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
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9
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Teixeira SPB, Reis RL, Peppas NA, Gomes ME, Domingues RMA. Epitope-imprinted polymers: Design principles of synthetic binding partners for natural biomacromolecules. SCIENCE ADVANCES 2021; 7:eabi9884. [PMID: 34714673 PMCID: PMC8555893 DOI: 10.1126/sciadv.abi9884] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/07/2021] [Indexed: 05/27/2023]
Abstract
Molecular imprinting (MI) has been explored as an increasingly viable tool for molecular recognition in various fields. However, imprinting of biologically relevant molecules like proteins is severely hampered by several problems. Inspired by natural antibodies, the use of epitopes as imprinting templates has been explored to circumvent those limitations, offering lower costs and greater versatility. Here, we review the latest innovations in this technology, as well as different applications where MI polymers (MIPs) have been used to target biomolecules of interest. We discuss the several steps in MI, from the choice of epitope and functional monomers to the different production methods and possible applications. We also critically explore how MIP performance can be assessed by various parameters. Last, we present perspectives on future breakthroughs and advances, offering insights into how MI techniques can be expanded to new fields such as tissue engineering.
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Affiliation(s)
- Simão P. B. Teixeira
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L. Reis
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nicholas A. Peppas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1801, USA
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Pediatrics, Dell Medical School, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Surgery and Perioperative Care, Dell Medical School, University of Texas at Austin, Austin, TX 78712-1801, USA
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, University of Texas at Austin, Austin, TX 78712-1801, USA
| | - Manuela E. Gomes
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui M. A. Domingues
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
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10
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Pan YC, Yue YX, Hu XY, Li HB, Guo DS. A Supramolecular Antidote to Macromolecular Toxins Prepared through Coassembly of Macrocyclic Amphiphiles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2104310. [PMID: 34418189 DOI: 10.1002/adma.202104310] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Poisoning is a leading cause of admission to medical emergency departments and intensive care units. Supramolecular detoxification, which involves injecting supramolecular receptors that bind with toxins to suppress their biological activity, is an emerging strategy for poisoning treatment; it has few requirements and a broad application scope. However, it is still a formidable challenge to design supramolecular therapeutic materials as an antidote to macromolecular toxins, because the large size, flexible conformation, and presence of multiple and diverse binding sites of biomacromolecules hinder their recognition. Herein, a supramolecular antidote to macromolecular toxins is developed through the coassembly of macrocyclic amphiphiles, relying on heteromultivalent recognition between the coassembled components and toxic macromolecules. The coassembly of amphiphilic cyclodextrin and calixarene strongly and selectively captures melittin, a toxin studied herein; this imparts various therapeutic effects such as inhibiting the interactions of melittin with cell membranes, alleviating melittin cytotoxicity and hemolytic toxicity, reducing the mortality rate of melittin-poisoned mice, and mitigating damage to major organs. The use of the proposed antidote overcomes the limitation of supramolecular detoxification applicability to only small-molecular toxins. The antidote can also detoxify other macromolecular toxins as long as selective and strong binding is achieved because of the coassembling tunability.
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Affiliation(s)
- Yu-Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu-Xin Yue
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin-Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Hua-Bin Li
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
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11
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Zhao Y. Substrate Protection in Controlled Enzymatic Transformation of Peptides and Proteins. Chembiochem 2021; 22:2680-2687. [PMID: 34058051 PMCID: PMC8453913 DOI: 10.1002/cbic.202100217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Indexed: 11/07/2022]
Abstract
Proteins are involved in practically every single biological process. The many enzymes involved in their synthesis, cleavage, and posttranslational modification (PTM) carry out highly specific tasks with no usage of protecting groups. Yet, the chemists' strategy of protection/deprotection potentially can be highly useful, for example, when a specific biochemical reaction catalyzed by a broad-specificity enzyme needs to be inhibited, during infection of cells by enveloped viruses, in the invasion and spread of cancer cells, and upon mechanistic investigation of signal-transduction pathways. Doing so requires highly specific binding of peptide substrates in aqueous solution with biologically competitive affinities. Recent development of peptide-imprinted cross-linked micelles allows such protection and affords previously impossible ways of manipulating peptides and proteins in enzymatic transformations.
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Affiliation(s)
- Yan Zhao
- Department of ChemistryIowa State UniversityAmesIA 50011–3111USA
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12
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Mochizuki K, Matsukura L, Ito Y, Miyashita N, Taki M. A medium-firm drug-candidate library of cryptand-like structures on T7 phage: design and selection of a strong binder for Hsp90. Org Biomol Chem 2021; 19:146-150. [PMID: 33095213 DOI: 10.1039/d0ob01855d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized a medium-firm drug-candidate library of cryptand-like structures possessing a randomized peptide linker on the bacteriophage T7. From the macrocyclic library with a 109 diversity, we obtained a binder toward a cancer-related protein (Hsp90) with an antibody-like strong affinity (KD = 62 nM) and the binding was driven by the enthalpy. The selected supramolecular ligand inhibited Hsp90 activity by site-specific binding outside of the well-known ATP-binding pocket on the N-terminal domain (NTD).
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Affiliation(s)
- Kazuto Mochizuki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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13
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Ma F, Zheng X, Li Z. Sequence-selective recognition of cationic amphipathic tripeptides with similar structures in aqueous solutions by cucurbit[7]uril. Phys Chem Chem Phys 2021; 23:13724-13733. [PMID: 34128514 DOI: 10.1039/d1cp01326b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sequence-selective recognition of cationic amphipathic peptides by synthetic receptors is significant to biological applications, but it is still a great challenging task. Here we first study the binding characteristics of receptor cucurbit[7]uril (CB[7]) to the smallest aromatic tripeptides X1GG (X1 = tryptophan (W), phenylalanine (F), and tyrosine (Y)) and basic tripeptides X2GG (X2 = arginine (R), lysine (K), and histidine (H)) by molecular dynamics simulations. The study indicates that the sidechains of aromatic X1 residues can be encapsulated into the CB[7] cavity, while the sidechains of basic X2 residues prefer to locate at the CB[7] portal. Based on that, we consider hydrophobic aromatic residues as the N-terminus, the smallest glycine (G) as the 2nd-residue and basic residues as the C-terminus, and design nine tripeptides X1GX2 (X1 = F, Y, W and X2 = H, K, R). We found that there is a great influence of the C-terminal basic residue of X1GX2 on binding with CB[7] due to the introduction of a new binding site between CB[7] and the sidechain of the C-terminal residue. Interestingly, CB[7] can differentiate WGR and WGK with similar structures efficiently because of their eight orders of magnitude difference in the association constant (Ka). Besides, for WGR, YGR, and YGK with a nanomolar binding affinity (Ka > 109 M-1), on reversing the sequence order of the 2nd-residue and 3rd-residue, their Ka reduces by about at least 1000-fold, implying the sequence dependence of CB[7] on recognizing these tripeptides. These results predict the potential applications of CB[7] in recognizing cationic amphipathic peptides.
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Affiliation(s)
- Fenfen Ma
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Xiaoyan Zheng
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Zesheng Li
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
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14
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Li X, Chen K, Zhao Y. Sequence‐Selective Protection of Peptides from Proteolysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiaowei Li
- Department of Chemistry Iowa State University Ames IA 50011-3111 USA
| | - Kaiqian Chen
- Department of Chemistry Iowa State University Ames IA 50011-3111 USA
| | - Yan Zhao
- Department of Chemistry Iowa State University Ames IA 50011-3111 USA
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15
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Li X, Chen K, Zhao Y. Sequence-Selective Protection of Peptides from Proteolysis. Angew Chem Int Ed Engl 2021; 60:11092-11097. [PMID: 33725413 PMCID: PMC8252432 DOI: 10.1002/anie.202102148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 01/06/2023]
Abstract
Proteolysis of proteins and peptides is involved in the infection of cells by enveloped viruses and also in the invasion and spread of cancer cells. Shutting down broad‐specificity proteases, however, is problematic because normal functions by these proteases will be affected. Herein, nanoparticle receptors were prepared from molecular imprinting for complex biological peptides. Their strong and selective binding enabled them to protect their targeted sequences from proteolysis in aqueous solution at stoichiometric amounts. Generality of the method was demonstrated by the protection of hydrophobic and hydrophilic peptides from different proteases, selective protection of a segment of a long peptide, and selective protection of a targeted peptide in a mixture. Most interestingly, two receptors targeting different parts of a long peptide could work in cooperation to protect the overall sequence, highlighting the versatility of the method.
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Affiliation(s)
- Xiaowei Li
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA
| | - Kaiqian Chen
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA
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16
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Ma F, Zheng X, Xie L, Li Z. Sequence-dependent nanomolar binding of tripeptides containing N-terminal phenylalanine by Cucurbit[7]uril: A theoretical study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Li X, Palhano Zanela TM, Underbakke ES, Zhao Y. Controlling Kinase Activities by Selective Inhibition of Peptide Substrates. J Am Chem Soc 2021; 143:639-643. [DOI: 10.1021/jacs.0c11566] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Wang H, Xu X, Pan YC, Yan Y, Hu XY, Chen R, Ravoo BJ, Guo DS, Zhang T. Recognition and Removal of Amyloid-β by a Heteromultivalent Macrocyclic Coassembly: A Potential Strategy for the Treatment of Alzheimer's Disease. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006483. [PMID: 33325586 DOI: 10.1002/adma.202006483] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/20/2020] [Indexed: 06/12/2023]
Abstract
The imbalance of amyloid-β (Aβ) production and clearance causes aggregation of Aβ1-42 monomers to form fibrils and amyloid plaques, which is an indispensable process in the pathogenesis of Alzheimer's disease (AD), and eventually leads to pathological changes and cognitive impairment. Consequently, Aβ1-42 is the most important target for the treatment of AD. However, developing a single treatment method that can recognize Aβ1-42 , inhibit Aβ1-42 fibrillation, eliminate amyloid plaques, improve cognitive impairments, and alleviate AD-like pathology is challenging. Here, a coassembly composed of cyclodextrin (CD) and calixarene (CA) is designed, and it is used as an anti-Aβ therapy agent. The CD-CA coassembly is based on the previously reported heteromultivalent recognition strategy and is able to successfully eliminate amyloid plaques and degrade Aβ1-42 monomers in 5xFAD mice. More importantly, the coassembly improves recognition and spatial cognition deficits, and synaptic plasticity impairment in the 5xFAD mice. In addition, the coassembly ameliorates AD-like pathology including prevention of neuronal apoptosis and oxidant stress, and alteration of M1/M2 microglial polarization states. This supramolecular approach makes full use of both molecular recognition and self-assembly of macrocyclic amphiphiles, and is a promising novel strategy for AD treatment.
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Affiliation(s)
- Hui Wang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, 300071, P. R. China
| | - XinXin Xu
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, 300071, P. R. China
| | - Yu-Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin, 300071, P. R. China
| | - YuXing Yan
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, 300071, P. R. China
| | - Xin-Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin, 300071, P. R. China
| | - RunWen Chen
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, 300071, P. R. China
| | - Bart Jan Ravoo
- Organic Chemistry Institute and Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster, Busso-Peus-Straße 10, Münster, 48149, Germany
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin, 300071, P. R. China
| | - Tao Zhang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, 300071, P. R. China
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19
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Li X, Zhao Y. Synthetic Glycosidase Distinguishing Glycan and Glycosidic Linkage in Its Catalytic Hydrolysis. ACS Catal 2020; 10:13800-13808. [PMID: 34123483 DOI: 10.1021/acscatal.0c04038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selective hydrolysis of carbohydrates is vital to the processing of these molecules in biology but has rarely been achieved with synthetic catalysts. The challenge is especially difficult because the catalyst needs to distinguish the inversion of a single hydroxyl and the α or β glycosidic bonds that join monosaccharide building blocks. Here we report synthetic glycosidase prepared through molecular imprinting within a cross-linked micelle. The nanoparticle catalyst resembles natural enzymes in dimension, water-solubility, and a hydrophilic/hydrophobic surface-core topology. Its boronic acid-functionalized active site binds its targeted glycoside substrate and an acid cofactor simultaneously, with the acidic group in close proximity to the exocyclic glycosidic oxygen. The hydrophobically anchored acid cofactor is tunable in acidity and causes selective cleavage of the targeted glycoside in mildly acidic water. Selectivity for both the glycan and the α/β glycosidic bond can be rationally designed through the molecular imprinting process.
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Affiliation(s)
- Xiaowei Li
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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20
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Bose I, Zhao Y. pH-Controlled Nanoparticle Catalysts for Highly Selective Tandem Henry Reaction from Mixtures. ACS Catal 2020; 10:13973-13977. [PMID: 34094653 DOI: 10.1021/acscatal.0c03468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nature has a remarkable ability to perform selective transformation of complex biological mixtures into desired products using enzymatic catalysts. We report the preparation of nanoparticle catalysts through molecular imprinting within cross-linked micelles. These catalysts were highly selective for their targeted substrates and could selectively hydrolyze less reactive acetals over more reactive ones even under basic conditions. Their catalytic activity and selectivity were tunable through rational postmodification of the active site. These properties enabled the nanoparticle catalysts to produce the desired β-nitro alcohol from a four-component acetal mixture in a tandem deprotection/Henry reaction that required incompatible acidic and basic catalysts in the two steps.
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Affiliation(s)
- Ishani Bose
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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21
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Zhang N, Hu X, Guan P, Xu Y, Liu Z, Cheng Y. Effect of surface functionality of molecularly imprinted composite nanospheres on specific recognition of proteins. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 116:111076. [PMID: 32806320 DOI: 10.1016/j.msec.2020.111076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/16/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022]
Abstract
The surface functionality of biomaterial plays a primary role in determining its application in biorecognition and drug delivery. In our work, three types of synthetic tailoring polymer nanospheres with hierarchical architecture were constructed to obtain functional polymer layer with disparate chemical motifs for protein adsorption via surface imprinting and grafting copolymerization. In this polymerization system, the structure stability of template protein bovine serum albumin (BSA) is well maintained within a certain range, which facilitated the accurate imprinting and precise identification. A comprehensive protocol for screening different functional layer is proposed through comparing the adsorption behavior, selectivity, identification and responsiveness to medium pH of three functional layers. Our study demonstrates that surface functionality greatly influences the adsorption capacity and selectivity of adsorption material. The functional layer with ionic liquid structure that could only provide multiple non-covalent binding sites is beneficial to the proteins aggregation and extraction, while the anti-nonspecific binding functional layer of biomaterial with zwitterionic structure for specific protein capture is promising to serve as a preferable antigen-antibody communication network, which shows great potential for protein recognition and separation. In summary, our proposed strategy provides a systematic selection criterion of biomaterials for effective application in biosensors.
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Affiliation(s)
- Nan Zhang
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an 710072, PR China; Institute of High Performance Computing, A*STAR, 138632, Singapore
| | - Xiaoling Hu
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an 710072, PR China.
| | - Ping Guan
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Yarong Xu
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Zhuangjian Liu
- Institute of High Performance Computing, A*STAR, 138632, Singapore
| | - Yuan Cheng
- Institute of High Performance Computing, A*STAR, 138632, Singapore.
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22
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Duan L, Zangiabadi M, Zhao Y. Synthetic lectins for selective binding of glycoproteins in water. Chem Commun (Camb) 2020; 56:10199-10202. [PMID: 32748907 PMCID: PMC7484035 DOI: 10.1039/d0cc02892d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although synthetic mimics of lectins can be extremely useful in biological and biomedical research, molecular recognition of carbohydrates has been hampered by their strong solvation in water and subtle structural differences among analogues. Molecularly imprinted nanoparticle receptors were prepared with glycans directly cleaved from glycoproteins. Functionalized with boroxole groups in the binding sites, these water-soluble synthetic lectins bound the parent glycoproteins selectively in water with an association constant of Ka = 104-105 M-1. The strong binding enabled the receptors to protect the targeted glycans from enzymatic cleavage. When clicked onto magnetic nanoparticles, the receptors enabled facile isolation of glycoproteins from a mixture.
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Affiliation(s)
- Likun Duan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
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23
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Padilla-Coley S, Xu H, Morsby J, Gao H, Smith BD. Supramolecular Loading of a Broad Spectrum of Molecular Guests In Hyperbranched Polytriazole Nanoparticles with Cores Containing Multiple Functional Groups. Biomacromolecules 2020; 21:2165-2175. [PMID: 32227988 DOI: 10.1021/acs.biomac.0c00151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This study evaluated the supramolecular properties of a new family of water-soluble hyperbranched polytriazoles that have a unimolecular micelle structure. Two new, structurally related hyperbranched polymers (HBPa and HBPn), with the same size (Dh = 11 nm) and core-shell architecture, were prepared and found to act as nanoscale hosts for a broad spectrum of molecular guests. The globular-shaped hyperbranched polymers were synthesized by a straightforward one-pot polymerization method that permits easy synthetic control of the multiple functional groups within the core. Surrounding the core is a shell of polyethylene glycol chains that promotes solubility in pH 7.4 buffer solution and inhibits self-aggregation of the nanoparticles. The core of HBPa, containing a mixture of anionic carboxylate groups and 1,2,3-triazole rings, could be loaded with cationic hydrophilic (i.e., propidium iodide) or partially hydrophobic (i.e., Hoechst 33342) dyes or drugs, including a binary dye/drug pair (i.e., indocyanine green/mitoxantrone). The core of HBPn, containing a mixture of uncharged 2-pentanone chains and 1,2,3-triazole rings, could be loaded with uncharged and very hydrophobic dyes (i.e., Nile Red) or drugs. Improved aqueous solubility of camptothecin was achieved 10-fold from 8.4 to 75 ng/mL. Additionally, cell toxicity studies showed that HBPn was able to release the camptothecin drug inside A549 cancer cells resulting in increased cell death. Taken together, the results suggest that this new family of water-soluble hyperbranched polytriazoles could be broadly useful as nanocarriers for various applications in therapy, imaging, or a combination of the two (theranostics).
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Affiliation(s)
- Sasha Padilla-Coley
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Hui Xu
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Janeala Morsby
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Haifeng Gao
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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24
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Duan L, Zhao Y. Selective Binding of Dopamine and Epinephrine in Water by Molecularly Imprinted Fluorescent Receptors. Chem Asian J 2020; 15:1035-1038. [PMID: 32043821 PMCID: PMC7480134 DOI: 10.1002/asia.201901783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/06/2020] [Indexed: 01/02/2023]
Abstract
Catecholamines play important roles in biology but their structural similarity makes it challenging to construct synthetic receptors with selective binding. A combination of covalent and noncovalent binding groups in the hydrophobic core of water-soluble nanoparticles enabled them to recognize dopamine and epinephrine with an association constant (Ka ) of 3-4×104 M-1 in water, an order of magnitude higher than those of previously reported synthetic hosts. In addition, minute structural changes among analogues were detected including the addition or removal of a single hydroxyl or methyl group.
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Affiliation(s)
- Likun Duan
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, U.S.A
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, U.S.A
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