1
|
Ghosh A, Zhao Y. Nanoparticles that Distinguish Chemical and Supramolecular Contexts of Lysine for Single-Site Functionalization of Protein. NANO LETTERS 2024. [PMID: 38976835 DOI: 10.1021/acs.nanolett.4c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Lysine is one of the most abundant residues on the surface of proteins and its site-selective functionalization is extremely challenging. The existing methods of functionalization rely on differential reactivities of lysine on a protein, making it impossible to label less reactive lysines selectively. We here report polymeric nanoparticles that mimic enzymes involved in the posttranslational modifications of proteins that distinguish the chemical and supramolecular contexts of a lysine and deliver the labeling reagent precisely to its ε amino group. The nanoparticles are prepared through molecular imprinting of cross-linkable surfactant micelles, plus an in situ, on-micelle derivatization of the peptide template prior to the imprinting. The procedures encode the polymeric nanoparticles with all the supramolecular information needed for sequence identification and precise labeling, allowing single-site functionalization of a predetermined lysine on the target protein in a mixture.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
Affiliation(s)
- Yan Zhao
- Department of ChemistryIowa State UniversityAmesIA 50011–3111USA
| |
Collapse
|
3
|
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).
Collapse
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.
| | | | | | | | | |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Silva MS, Tavares APM, de Faria HD, Sales MGF, Figueiredo EC. Molecularly Imprinted Solid Phase Extraction Aiding the Analysis of Disease Biomarkers. Crit Rev Anal Chem 2020; 52:933-948. [DOI: 10.1080/10408347.2020.1843131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matheus Siqueira Silva
- Laboratory of Toxicant and Drug Analyses, Federal University of Alfenas, Alfenas, Brazil
| | - Ana P. M. Tavares
- BioMark/ISEP, School of Engineering of the Polytechnic School of Porto, Porto, Portugal
- BioMark/UC, Department of Chemical Engineering, Faculty of Sciences and Technology of the University of Coimbra, Coimbra, Portugal
| | - Henrique Dipe de Faria
- Laboratory of Toxicant and Drug Analyses, Federal University of Alfenas, Alfenas, Brazil
| | - Maria Goreti Ferreira Sales
- BioMark/ISEP, School of Engineering of the Polytechnic School of Porto, Porto, Portugal
- BioMark/UC, Department of Chemical Engineering, Faculty of Sciences and Technology of the University of Coimbra, Coimbra, Portugal
| | | |
Collapse
|
6
|
Zhang Q, Chen Y, Lu R, Yao Y, Li C, Yu Y, Zhang S. Cross-linked small-molecule capsules with excitation wavelength-dependent photoluminescence and high loading capacity: design, synthesis and application in imaging-guided drug delivery. J Mater Chem B 2020; 8:2719-2725. [PMID: 32149293 DOI: 10.1039/c9tb02465d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cross-linked small-molecule micelles (cSMs) have found applications in many fields but their low loading capacity and non-fluorescence property hindered their further development. Herein, water-soluble organic nanoparticles were applied as templates to "stretch" the hydrophobic core of cSMs and photo-cross-linking was employed to supply photoluminescence. The resulting cross-linked small-molecule capsules (cSCs) not only reserve the superior properties of cSMs of accurate monomer, easy functionalization and robust stability, but also achieve high drug loading capacity and excitation wavelength-dependent fluorescence, where the drug loading contents (DLCs) for various hydrophobic drugs were more than 30-fold higher than that of cSMs, and the maximum quantum yield could be as high as 12.0%. Featuring these superiorities, the cSCs hold promising potential in many fields and an example of doxorubicin-loaded cSCs (DOX@cSCs) for multichannel imaging-guided drug delivery is shown in this work.
Collapse
Affiliation(s)
- Qian Zhang
- National Engineering Research Centre for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Yun Chen
- National Engineering Research Centre for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Ruilin Lu
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| | - Yongchao Yao
- National Engineering Research Centre for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Chuanqi Li
- National Engineering Research Centre for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Yunlong Yu
- National Engineering Research Centre for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Shiyong Zhang
- National Engineering Research Centre for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China. and College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Yao Y, Xu D, Zhu Y, Dai X, Yu Y, Luo J, Zhang S. Dandelion flower-like micelles. Chem Sci 2019; 11:757-762. [PMID: 34123049 PMCID: PMC8146335 DOI: 10.1039/c9sc05741b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/23/2019] [Indexed: 11/21/2022] Open
Abstract
Dandelion flower-like micelles (DFMs) were prepared by self-assembly of polycaprolactone (PCL) functionalized surface cross-linked micelles (SCMs). Upon reductive stimuli, the SCMs can be released from the DFMs by non-Brownian motion at an average speed of 19.09 μm s-1. Similar to the property of dandelion flowers dispersing their seeds over a long distance, the DFMs demonstrated enhanced multicellular tumor spheroid (MTS) penetration, a useful property in the treatment of many diseases including cancer, infection-of-biofilm diseases and ocular problems.
Collapse
Affiliation(s)
- Yongchao Yao
- National Engineering Research Center for Biomaterials, Sichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Deqiu Xu
- College of Chemistry and Environmental Protection Engineering, Southwest Minzu University Chengdu 610041 China
- Sichuan Guojian Inspection Co., Ltd. 646000 Luzhou Sichuan China
| | - Yuhong Zhu
- National Engineering Research Center for Biomaterials, Sichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Xin Dai
- National Engineering Research Center for Biomaterials, Sichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Yunlong Yu
- National Engineering Research Center for Biomaterials, Sichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Jianbin Luo
- College of Chemistry and Environmental Protection Engineering, Southwest Minzu University Chengdu 610041 China
| | - Shiyong Zhang
- National Engineering Research Center for Biomaterials, Sichuan University 29 Wangjiang Road Chengdu 610064 China
| |
Collapse
|
9
|
Chen K, Zhao Y. Effects of nano-confinement and conformational mobility on molecular imprinting of cross-linked micelles. Org Biomol Chem 2019; 17:8611-8617. [PMID: 31528942 PMCID: PMC7474537 DOI: 10.1039/c9ob01440c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Molecular imprinting is a facile method to create guest-complementary binding sites in a cross-linked polymeric network. When performed within cross-linked micelles, the resulting molecularly imprinted nanoparticles (MINPs) exhibited an extraordinary ability to distinguish subtle structural changes in the guest, including the shift of a hydrophilic or hydrophobic group by 1 carbon and addition of a single methylene/methyl group. A high surface-cross-linking density prior to core-cross-linking was key to the high-fidelity imprinting, enhancing both the binding affinity of the imprinted micelle for the template and selectivity among structural analogues. Whereas the imprinted site closely complemented the hydrophilic surface anchoring group and rigid hydrophobic aromatic core, it was expanded significantly for a conformationally mobile small group (i.e., methoxy).
Collapse
Affiliation(s)
- Kaiqian Chen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
| | | |
Collapse
|
10
|
Xiang F, Li B, Zhao P, Tan J, Yu Y, Zhang S. Copper(I)‐Chelated Cross‐Linked Cyclen Micelles as a Nanocatalyst for Azide‐Alkyne Cycloaddition in Both Water and Cells. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fuqing Xiang
- National Engineering Research Centre for BiomaterialsSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Bing Li
- National Engineering Research Centre for BiomaterialsSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Pengxiang Zhao
- Institute of MaterialsChina Academy of Engineering Physics No. 9, Huafengxincun Jiangyou 621908 China General methods
| | - Jiangbing Tan
- National Engineering Research Centre for BiomaterialsSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Yunlong Yu
- National Engineering Research Centre for BiomaterialsSichuan University 29 Wangjiang Road Chengdu 610064 China
| | - Shiyong Zhang
- National Engineering Research Centre for BiomaterialsSichuan University 29 Wangjiang Road Chengdu 610064 China
- College of ChemistrySichuan University 29 Wangjiang Road Chengdu 610064 China
| |
Collapse
|
11
|
Fa S, Zhao Y. General Method for Peptide Recognition in Water through Bioinspired Complementarity. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2019; 31:4889-4896. [PMID: 32921904 PMCID: PMC7486028 DOI: 10.1021/acs.chemmater.9b01613] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A general method for peptide recognition has been elusive despite decades of research. Strong binding and selectivity among closely related peptides are necessary for biological applications but have been difficult to achieve with synthetic receptors. With inspiration from highly specific protein-protein and protein-ligand interactions, protein-sized, water-soluble imprinted nanoparticles were prepared via templated polymerization of peptides within cross-linked micelles. Combination of hydrophobic and polar interactions afforded micromolar to submicromolar binding affinities for selected tripeptides. A "golden pair" of functional monomers was identified to enhance both the affinity and selectivity of binding, and enabled differentiation of subtly different sequences including single-point variation of lysine by arginine and insertion of a single glycine at the N- or C-terminus. Biological peptides (β-amyloid peptides) afforded even stronger binding (tens of nanomolar) due to a larger number of complementary interactions between the host and the guest, opening doors to a wide range of biological applications.
Collapse
Affiliation(s)
- Shixin Fa
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111
| |
Collapse
|
12
|
Hu L, Arifuzzaman MD, Zhao Y. Controlling Product Inhibition through Substrate-Specific Active Sites in Nanoparticle-Based Phosphodiesterase and Esterase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00630] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lan Hu
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - MD Arifuzzaman
- 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
| |
Collapse
|
13
|
Korde BA, Mankar JS, Phule S, Krupadam RJ. Nanoporous imprinted polymers (nanoMIPs) for controlled release of cancer drug. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 99:222-230. [PMID: 30889694 DOI: 10.1016/j.msec.2019.01.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/07/2019] [Accepted: 01/24/2019] [Indexed: 12/14/2022]
Abstract
In this article, a new approach to directly synthesize drug molecule imbedded in the nanometer sized polymer particles is reported. Molecular imprinting is used to prepare polymers for drug specific for selectively loading of a desired drug. Computer simulations were performed to provide mechanistic insights on the binding modalities of model cancer drug, amygdalin with the polymer precursors. Controlled release of amygdalin from nanoMIPs was studied in vitro cell test and monitoring the absorbance at λem of 390 nm by fluorescence. The nanoparticles imprinted with amygdalin (nanoMIPs) showed high drug loading (0.98 mg g-1) and also releases drug in a controlled way without burst release. The polymer releases amygdalin 0.095 μg (5 min), 0.120 μg (30 min), 0.180 μg (180 min), 0.205 μg in 300 min in de-ionized water and similar pattern of release was observed in buffer 2 and 7. The sustained release of drug from nanoMIPs follows Fickian diffusion; and uniformity in nanoMIPs size have significant impact on release of drug. Swelling of nanoMIP is one of the dominant factors influencing the drug release patterns. The imprinting procedure and the studies reported in this study would be highly useful in future for cancer drug administration.
Collapse
Affiliation(s)
- Bhagyashree A Korde
- CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, India
| | - Juili S Mankar
- CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, India
| | - Sumidha Phule
- Department of Biotechnology, Dr B.R. Ambedkar College, Deeksha Bhoomi, Nagpur 440010, India
| | - Reddithota J Krupadam
- CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, India.
| |
Collapse
|