1
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Chen FJ, Lin W, Chen FE. Non-symmetric stapling of native peptides. Nat Rev Chem 2024; 8:304-318. [PMID: 38575678 DOI: 10.1038/s41570-024-00591-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Stapling has emerged as a powerful technique in peptide chemistry. It enables precise control over peptide conformation leading to enhanced properties such as improved stability and enhanced binding affinity. Although symmetric stapling methods have been extensively explored, the field of non-symmetric stapling of native peptides has received less attention, largely as a result of the formidable challenges it poses - in particular the complexities involved in achieving the high chemo-selectivity and site-selectivity required to simultaneously modify distinct proteinogenic residues. Over the past 5 years, there have been significant breakthroughs in addressing these challenges. In this Review, we describe the latest strategies for non-symmetric stapling of native peptides, elucidating the protocols, reaction mechanisms and underlying design principles. We also discuss current challenges and opportunities this field offers for future applications, such as ligand discovery and peptide-based therapeutics.
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Affiliation(s)
- Fa-Jie Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
| | - Wanzhen Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, P. R. China
| | - Fen-Er Chen
- College of Chemistry, Fuzhou University, Fuzhou, P. R. China.
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China.
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Fudan University, Shanghai, P. R. China.
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2
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Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [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] [Indexed: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
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Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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3
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Liu B, Rodriguez J, J Kilgallon L, Wang W, Wang Y, Wang A, Dai Y, Nguyen HVT, Pentelute BL, Johnson JA. An organometallic swap strategy for bottlebrush polymer-protein conjugate synthesis. Chem Commun (Camb) 2024; 60:4238-4241. [PMID: 38529790 PMCID: PMC11008127 DOI: 10.1039/d4cc00293h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Polymer-protein bioconjugation offers a powerful strategy to alter the physical properties of proteins, and various synthetic polymer compositions and architectures have been investigated for this purpose. Nevertheless, conjugation of molecular bottlebrush polymers (BPs) to proteins remains an unsolved challenge due to the large size of BPs and a general lack of methods to transform the chain ends of BPs into functional groups suitable for bioconjugation. Here, we present a strategy to address this challenge in the context of BPs prepared by "graft-through" ring-opening metathesis polymerization (ROMP), one of the most powerful methods for BP synthesis. Quenching ROMP of PEGylated norbornene macromonomers with an activated enyne terminator facilitates the transformation of the BP Ru alkylidene chain ends into Pd oxidative addition complexes (OACs) for facile bioconjugation. This strategy is shown to be effective for the synthesis of two BP-protein conjugates (albumin and ERG), setting the stage for a new class of BP-protein conjugates for future therapeutic and imaging applications.
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Affiliation(s)
- Bin Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Jacob Rodriguez
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Landon J Kilgallon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Wencong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Yuyan Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Aiden Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Yutong Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Hung V-T Nguyen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology Cambridge, MA, 02142, USA
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology Cambridge, MA, 02142, USA
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4
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Aslam S, Zulfiqar F, Hameed W, Qureshi S, Zaroon, Bashir H. Fusion proteins development strategies and their role as cancer therapeutic agents. Biotechnol Appl Biochem 2024; 71:81-95. [PMID: 37822167 DOI: 10.1002/bab.2523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023]
Abstract
Cancer continues to be leading cause of morbidity and mortality despite decades of research and advancement in chemotherapy. Most tumors can be reduced via standard oncology treatments, such as chemotherapy, radiotherapy, and surgical resection, and they frequently recur. Significant progress has been made since targeted cancer therapy inception in creation of medications that exhibit improved tumor-selective action. Particularly in preclinical and clinical investigations, fusion proteins have shown strong activity and improved treatment outcomes for a number of human cancers. Synergistically combining many proteins into one complex allows the creation of synthetic fusion proteins with enhanced characteristics or new capabilities. Signal transduction pathways are important for onset, development, and spread of cancer. As result, signaling molecules are desirable targets for cancer therapies, and significant effort has been made into developing fusion proteins that would act as inhibitors of these pathways. A wide range of biotechnological and medicinal applications are made possible by fusion of protein domains that improves bioactivities or creates new functional combinations. Such proteins may function as immune effectors cell recruiters to tumors or as decoy receptors for various ligands. In this review article, we have outlined the standard methods for creating fusion proteins and covered the applications of fusion proteins in treatment of cancer. This article also highlights the role of fusion proteins in targeting the signaling pathways involved in cancer for effective treatment.
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Affiliation(s)
- Shakira Aslam
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Warda Hameed
- King Edward Medical University, Lahore, Pakistan
| | - Shahnila Qureshi
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Zaroon
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hamid Bashir
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
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5
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Zhang J, Liu J, Li X, Ju Y, Li Y, Zhang G, Li Y. Unexpected Cyclization Product Discovery from the Photoinduced Bioconjugation Chemistry between Tetrazole and Amine. J Am Chem Soc 2024; 146:2122-2131. [PMID: 38190443 DOI: 10.1021/jacs.3c11574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Bioconjugation chemistry has emerged as a powerful tool for the modification of diverse biomolecules under mild conditions. Tetrazole, initially proposed as a bioorthogonal photoclick handle for 1,3-dipolar cyclization with alkenes, was later demonstrated to possess broader photoreactivity with carboxylic acids, serving as a versatile bioconjugation and photoaffinity labeling probe. In this study, we unexpectedly discovered and validated the photoreactivity between tetrazole and primary amine to afford a new 1,2,4-triazole cyclization product. Given the significance of functionalized N-heterocycles in medicinal chemistry, we successfully harnessed the serendipitously discovered reaction to synthesize both pharmacologically relevant DNA-encoded chemical libraries (DELs) and small molecule compounds bearing 1,2,4-triazole scaffolds. Furthermore, the mild reaction conditions and stable 1,2,4-triazole linkage found broad application in photoinduced bioconjugation scenarios, spanning from intramolecular peptide macrocyclization and templated DNA reaction cross-linking to intermolecular photoaffinity labeling of proteins. Triazole cross-linking products on lysine side chains were identified in tetrazole-labeled proteins, refining the comprehensive understanding of the photo-cross-linking profiles of tetrazole-based probes. Altogether, this tetrazole-amine bioconjugation expands the current bioconjugation toolbox and creates new possibilities at the interface of medicinal chemistry and chemical biology.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Jinlu Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yunzhu Ju
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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6
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Gurunathan S, Thangaraj P, Wang L, Cao Q, Kim JH. Nanovaccines: An effective therapeutic approach for cancer therapy. Biomed Pharmacother 2024; 170:115992. [PMID: 38070247 DOI: 10.1016/j.biopha.2023.115992] [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: 08/26/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Cancer vaccines hold considerable promise for the immunotherapy of solid tumors. Nanomedicine offers several strategies for enhancing vaccine effectiveness. In particular, molecular or (sub) cellular vaccines can be delivered to the target lymphoid tissues and cells by nanocarriers and nanoplatforms to increase the potency and durability of antitumor immunity and minimize negative side effects. Nanovaccines use nanoparticles (NPs) as carriers and/or adjuvants, offering the advantages of optimal nanoscale size, high stability, ample antigen loading, high immunogenicity, tunable antigen presentation, increased retention in lymph nodes, and immunity promotion. To induce antitumor immunity, cancer vaccines rely on tumor antigens, which are administered in the form of entire cells, peptides, nucleic acids, extracellular vesicles (EVs), or cell membrane-encapsulated NPs. Ideal cancer vaccines stimulate both humoral and cellular immunity while overcoming tumor-induced immune suppression. Herein, we review the key properties of nanovaccines for cancer immunotherapy and highlight the recent advances in their development based on the structure and composition of various (including synthetic and semi (biogenic) nanocarriers. Moreover, we discuss tumor cell-derived vaccines (including those based on whole-tumor-cell components, EVs, cell membrane-encapsulated NPs, and hybrid membrane-coated NPs), nanovaccine action mechanisms, and the challenges of immunocancer therapy and their translation to clinical applications.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Biotechnology, Rathinam College of Arts and Science, Eachanari, Coimbatore 641 021, Tamil Nadu, India.
| | - Pratheep Thangaraj
- Department of Biotechnology, Rathinam College of Arts and Science, Eachanari, Coimbatore 641 021, Tamil Nadu, India
| | - Lin Wang
- Research and Development Department, Qingdao Haier Biotech Co., Ltd., Qingdao, China
| | - Qilong Cao
- Research and Development Department, Qingdao Haier Biotech Co., Ltd., Qingdao, China
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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7
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Abellanas-Perez P, Carballares D, Rocha-Martin J, Fernandez-Lafuente R. The effects of the chemical modification on immobilized lipase features are affected by the enzyme crowding in the support. Biotechnol Prog 2024; 40:e3394. [PMID: 37828788 DOI: 10.1002/btpr.3394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
In this article, we have analyzed the interactions between enzyme crowding on a given support and its chemical modification (ethylenediamine modification via the carbodiimide route and picryl sulfonic (TNBS) modification of the primary amino groups) on the enzyme activity and stability. Lipase from Thermomyces lanuginosus (TLL) and lipase B from Candida antarctica (CALB) were immobilized on octyl-agarose beads at two very different enzyme loadings, one of them exceeding the capacity of the support, one well under this capacity. Chemical modifications of the highly loaded and lowly loaded biocatalysts gave very different results in terms of activity and stability, which could increase or decrease enzyme activity depending on the enzyme support loading. For example, both lowly loaded biocatalysts increased their activity after modification while the effect was the opposite for the highly loaded biocatalysts. Additionally, the modification with TNBS of highly loaded CALB biocatalyst increased its stability while decrease the activity.
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Affiliation(s)
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, Madrid, Spain
| | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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8
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Kim S, Kim S, Kim S, Kim N, Lee SW, Yi H, Lee S, Sim T, Kwon Y, Lee HS. Affinity-Directed Site-Specific Protein Labeling and Its Application to Antibody-Drug Conjugates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306401. [PMID: 38032124 PMCID: PMC10811483 DOI: 10.1002/advs.202306401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Chemically modified proteins have diverse applications; however, conventional chemo-selective methods often yield heterogeneously labeled products. To address this limitation, site-specific protein labeling holds significant potential, driving extensive research in this area. Nevertheless, site-specific modification of native proteins remains challenging owing to the complexity of their functional groups. Therefore, a method for site-selective labeling of intact proteins is aimed to design. In this study, a novel approach to traceless affinity-directed intact protein labeling is established, which leverages small binding proteins and genetic code expansion technology. By applying this method, a site-specific antibody labeling with a drug, which leads to the production of highly effective antibody-drug conjugates specifically targeting breast cancer cell lines is achieved. This approach enables traceless conjugation of intact target proteins, which is a critical advantage in pharmaceutical applications. Furthermore, small helical binding proteins can be easily engineered for various target proteins, thereby expanding their potential applications in diverse fields. This innovative approach represents a significant advancement in site-specific modification of native proteins, including antibodies. It also bears immense potential for facilitating the development of therapeutic agents for various diseases.
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Affiliation(s)
- Sooin Kim
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Sanggil Kim
- New Drug Development CenterOsong Medical Innovation Foundation123 Osongsaengmyeong‐ro, Heungdeok‐guCheongjuChungbuk28160Republic of Korea
| | - Sangji Kim
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Namkyoung Kim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Sang Won Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Hanbin Yi
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Seungeun Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Taebo Sim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Yongseok Kwon
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Hyun Soo Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
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9
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Chen S, Yan K, Liu B. PDB-BRE: A ligand-protein interaction binding residue extractor based on Protein Data Bank. Proteins 2024; 92:145-153. [PMID: 37750380 DOI: 10.1002/prot.26596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/13/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Proteins typically exert their biological functions by interacting with other biomolecules or ligands. The study of ligand-protein interactions is crucial in elucidating the biological mechanisms of proteins. Most existing studies have focused on analyzing ligand-protein interactions, and they ignore the additional situational of inserted and modified residues. Besides, the resources often support only a single ligand type and cannot obtain satisfied results in analyzing novel complexes. Therefore, it is important to develop a general analytical tool to extract the binding residues of ligand-protein interactions in complexes fully. In this study, we propose a ligand-protein interaction binding residue extractor (PDB-BRE), which can be used to automatically extract interacting ligand or protein-binding residues from complex three-dimensional (3D) structures based on the RCSB Protein Data Bank (RCSB PDB). PDB-BRE offers a notable advantage in its comprehensive support for analyzing six distinct types of ligands, including proteins, peptides, DNA, RNA, mixed DNA and RNA entities, and non-polymeric entities. Moreover, it takes into account the consideration of inserted and modified residues within complexes. Compared to other state-of-the-art methods, PDB-BRE is more suitable for massively parallel batch analysis, and can be directly applied for downstream tasks, such as predicting binding residues of novel complexes. PDB-BRE is freely available at http://bliulab.net/PDB-BRE.
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Affiliation(s)
- Shutao Chen
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Ke Yan
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
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10
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Delgado JAC, Tian YM, Marcon M, König B, Paixão MW. Side-Selective Solid-Phase Metallaphotoredox N(in)-Arylation of Peptides. J Am Chem Soc 2023; 145:26452-26462. [PMID: 37976043 DOI: 10.1021/jacs.3c10792] [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: 11/19/2023]
Abstract
Postsynthetic diversification of peptides through selective modification of endogenous amino acid side chains has enabled significant advances in peptide drug discovery while expanding the biological and medical chemistry space. However, current tools have been focused on the modification of reactive polar and ionizable side chains, whereas the decoration of aromatic systems (e.g., the N(in) of the tryptophan) has been a long-standing challenge. Here, we introduce metallaphotocatalysis in solid-phase peptide synthesis for the on-resin orthogonal N-arylation of relevant tryptophan-containing peptides. The protocol allows the chemoselective introduction of a new C(sp2)-N bond at the N(in) of tryptophan in biologically active protected peptide sequences in the presence of native redox-sensitive side chains. The fusion of metallaphotocatalysis with solid-phase peptide synthesis opens new perspectives in diversifying native amino acid side chains.
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Affiliation(s)
- José A C Delgado
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos─UFSCar, Rodovia Washington Luís, km 235, SP-310, São Carlos, São Paulo 13565-905, Brazil
- Institute of Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Ya-Ming Tian
- Institute of Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Michela Marcon
- Institute of Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Burkhard König
- Institute of Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Márcio W Paixão
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos─UFSCar, Rodovia Washington Luís, km 235, SP-310, São Carlos, São Paulo 13565-905, Brazil
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11
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Almeida-Pinto J, Lagarto MR, Lavrador P, Mano JF, Gaspar VM. Cell Surface Engineering Tools for Programming Living Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304040. [PMID: 37823678 DOI: 10.1002/advs.202304040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/10/2023] [Indexed: 10/13/2023]
Abstract
Breakthroughs in precision cell surface engineering tools are supporting the rapid development of programmable living assemblies with valuable features for tackling complex biological problems. Herein, the authors overview the most recent technological advances in chemically- and biologically-driven toolboxes for engineering mammalian cell surfaces and triggering their assembly into living architectures. A particular focus is given to surface engineering technologies for enabling biomimetic cell-cell social interactions and multicellular cell-sorting events. Further advancements in cell surface modification technologies may expand the currently available bioengineering toolset and unlock a new generation of personalized cell therapeutics with clinically relevant biofunctionalities. The combination of state-of-the-art cell surface modifications with advanced biofabrication technologies is envisioned to contribute toward generating living materials with increasing tissue/organ-mimetic bioactivities and therapeutic potential.
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Affiliation(s)
- José Almeida-Pinto
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Matilde R Lagarto
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Pedro Lavrador
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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12
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Abstract
The host immune system possesses an intrinsic ability to target and kill cancer cells in a specific and adaptable manner that can be further enhanced by cancer immunotherapy, which aims to train the immune system to boost the antitumor immune response. Several different categories of cancer immunotherapy have emerged as new standard cancer therapies in the clinic, including cancer vaccines, immune checkpoint inhibitors, adoptive T cell therapy, and oncolytic virus therapy. Despite the remarkable survival benefit for a subset of patients, the low response rate and immunotoxicity remain the major challenges for current cancer immunotherapy. Over the last few decades, nanomedicine has been intensively investigated with great enthusiasm, leading to marked advancements in nanoparticle platforms and nanoengineering technology. Advances in nanomedicine and immunotherapy have also led to the emergence of a nascent research field of nano-immunotherapy, which aims to realize the full therapeutic potential of immunotherapy with the aid of nanomedicine. In particular, nanocarriers present an exciting opportunity in immuno-oncology to boost the activity, increase specificity, decrease toxicity, and sustain the antitumor efficacy of immunological agents by potentiating immunostimulatory activity and favorably modulating pharmacological properties. This review discusses the potential of nanocarriers for cancer immunotherapy and introduces preclinical studies designed to improve clinical cancer immunotherapy modalities using nanocarrier-based engineering approaches. It also discusses the potential of nanocarriers to address the challenges currently faced by immuno-oncology as well as the challenges for their translation to clinical applications.
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Affiliation(s)
- Isra Rana
- College of Pharmacy, Chonnam National University, Gwangju, 61186, South Korea
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Jaeeun Oh
- Department of Biological Sciences, Inha University, Incheon, 22212, South Korea
| | - Juwon Baig
- Department of Biological Sciences, Inha University, Incheon, 22212, South Korea
| | - Jeong Hyun Moon
- Department of Biological Sciences, Inha University, Incheon, 22212, South Korea
| | - Sejin Son
- Department of Biological Sciences, Inha University, Incheon, 22212, South Korea.
- Department of Biological Sciences and Bioengineering, Inha University/Industry-Academia Interactive R&E Center for Bioprocess Innovation, Inha University, Incheon, South Korea.
| | - Jutaek Nam
- College of Pharmacy, Chonnam National University, Gwangju, 61186, South Korea.
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13
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Pereira FAR, Macedo-Filho A, Silva AM, Frazão NF, Sarmento RG, Lima KAL, Melo JJS, Pereira Junior ML, Ribeiro Junior LA, Freire VN. On the structural, electronic, and optical properties of L-histidine crystal: a DFT study. J Mol Model 2023; 29:205. [PMID: 37294345 DOI: 10.1007/s00894-023-05580-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023]
Abstract
CONTEXT The monoclinic L-histidine crystal is critical for protein structure and function and is also found in the myelin of brain nerve cells. This study numerically examines its structural, electronic, and optical properties. Our findings indicate that the L-histidine crystal has an insulating band gap of approximately 4.38 eV. Additionally, electron and hole effective masses range between 3.92[Formula: see text]-15.33[Formula: see text] and 4.16[Formula: see text]-7.53[Formula: see text], respectively. Furthermore, our investigation suggests that the L-histidine crystal is an excellent UV collector due to its strong optical absorption activity for photon energies exceeding 3.5 eV. METHODS To investigate the structural, electronic, and optical properties of L-histidine crystals, we used the Biovia Materials Studio software to conduct Density Functional Theory (DFT) simulations as implemented in the CASTEP code. Our DFT calculations were performed using the generalized gradient approximation (GGA) as parameterized by the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional, with an additional dispersion energy correction (PBE [Formula: see text] TS) based on the model proposed by Tkatchenko and Scheffler to describe van der Waals interactions. Additionally, we employed the norm-conserving pseudopotential to treat core electrons.
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Affiliation(s)
- F A R Pereira
- PPGQ-GERATEC, State University of Piauí, 64002-150, Teresina, PI, Brazil
| | - A Macedo-Filho
- PPGQ-GERATEC, State University of Piauí, 64002-150, Teresina, PI, Brazil
- Department of Physics, State University of Piauí, 64002-150, Teresina, PI, Brazil
| | - A M Silva
- Campus Prof. Antonio Geovanne Alves de Sousa, State University of Piauí, 64260-000, Piripiri, PI, Brazil
| | - N F Frazão
- Center for Education and Health, Federal University of Campina Grande, 581750-000, Cuité, PB, Brazil
| | - R G Sarmento
- Campus Minister Petrônio Portella, Federal University of Piauí, 64049-550, Teresina, PI, Brazil
| | - K A L Lima
- PPGQ-GERATEC, State University of Piauí, 64002-150, Teresina, PI, Brazil
| | - J J S Melo
- Department of Physics, Federal Institute of Maranhão, Monte Castelo Campus, 65030-005, São Luis, MA, Brazil
| | - M L Pereira Junior
- Department of Electrical Engineering, Faculty of Technology, University of Brasília, 70910-900, Brasília, Brazil.
| | - L A Ribeiro Junior
- Institute of Physics, University of Brasilia, 70910-900, Brasília, Brazil
| | - V N Freire
- Department of Physics, Federal University of Ceará, 60455-760, Fortaleza, CE, Brazil
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14
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Kulik L, Renner B, Laskowski J, Thurman JM, Michael Holers V. Highly pathogenic natural monoclonal antibody B4-IgM recognizes a post-translational modification comprised of acetylated N-terminal methionine followed by aspartic or glutamic acid. Mol Immunol 2023; 157:112-128. [PMID: 37018938 DOI: 10.1016/j.molimm.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 04/05/2023]
Abstract
The natural monoclonal antibody B4-IgM recognizes murine annexin 4 (mAn4) and exacerbates ischemia-reperfusion injury in many mouse models. During apoptosis, the intracellular mAn4 protein translocates to the membrane surface, remaining attached to the outer membrane leaflet where it is recognized by the anti-mAn4 B4-IgM antibody. B4-IgM does not recognize human annexin 4 (hAn4). However, the B4-IgM antibody epitope was detected by Western blot of unknown human proteins and by flow cytometry on all studied human cell lines undergoing apoptosis and on a minor subset of healthy cells. The B4-IgM antibody also recognizes the epitope on necrotic cells in cytoplasmic proteins, apparently entering through pores large enough to allow natural antibodies to penetrate the cells and bind to the epitope expressed on self-proteins. Using proteomics and site-directed mutagenesis, we found that B4-IgM binds to an epitope with post-translationally modified acetylated N-terminal methionine, followed by either glutamic or aspartic acid. The epitope is not induced by apoptosis or injury because this modification can also occur during protein translation. This finding reveals an additional novel mechanism whereby injured cells are detected by natural antibodies that initiate pathogenic complement activation through the recognition of epitopes that are shared across multiple proteins found in variable cell lines.
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15
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Chen X, Josephson B, Davis BG. Carbon-Centered Radicals in Protein Manipulation. ACS CENTRAL SCIENCE 2023; 9:614-638. [PMID: 37122447 PMCID: PMC10141601 DOI: 10.1021/acscentsci.3c00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/03/2023]
Abstract
Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.
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Affiliation(s)
- Xuanxiao Chen
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
| | - Brian Josephson
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
| | - Benjamin G. Davis
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, U.K.
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16
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Davies LJ, Shuttleworth LM, Zhang X, Peng S, Nitsche C. Bioorthogonal Peptide Macrocyclization Using Oxime Ligation. Org Lett 2023; 25:2806-2809. [PMID: 37053571 DOI: 10.1021/acs.orglett.3c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The biocompatible synthesis of constrained peptides is challenging. Oxime ligation is a bioorthogonal technique frequently used for protein bioconjugation. We report a straightforward method to install N-terminal ketones and aminooxy side chains during standard solid-phase peptide synthesis. Cyclization occurs spontaneously after acidic cleavage or in aqueous buffer. We demonstrate the facile synthesis of protease inhibitors with varying conformational constraint. The most constrained peptide displayed an activity 2 orders of magnitude higher than its linear analog.
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Affiliation(s)
- Lani J Davies
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Laura M Shuttleworth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Xiaobai Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sherry Peng
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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17
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Ahmad R, Tyryshkin AM, Xie L, Hansen WA, Yachnin BJ, Emge TJ, Mashrai A, Khare SD, Knapp S. A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly. J Inorg Biochem 2023; 244:112206. [PMID: 37030124 DOI: 10.1016/j.jinorgbio.2023.112206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu++ and Zn++ in bidentate (N2) and tridentate (N2S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn++, Cu++, and Co++. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H2O/HO-, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.
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Affiliation(s)
- Raheel Ahmad
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - Alexei M Tyryshkin
- Department of Marine and Coastal Sciences, Rutgers The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, United States of America
| | - Lingjun Xie
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - William A Hansen
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Brahm J Yachnin
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Thomas J Emge
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - Ashraf Mashrai
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Sagar D Khare
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America.
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18
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Ono S, Koga M, Arimura Y, Hatakeyama T, Kobayashi M, Sagara JI, Nakai T, Horino Y, Kuroda H, Oyama H, Arima K. Site-Selective Incorporation of a Functional Group into Lys175 in the Vicinity of the Active Site of Chymotrypsin by Using Peptidyl α-Aminoalkylphosphonate Diphenyl Ester-Derivatives. Molecules 2023; 28:molecules28073150. [PMID: 37049913 PMCID: PMC10096113 DOI: 10.3390/molecules28073150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
We previously reported that Lys175 in the region of the active site of chymotrypsin (Csin) could be site-selectively modified by using an N-hydroxy succinimide (NHS) ester of the peptidyl derivative containing 1-amino-2-ethylphenylphosphonate diphenyl ester [NHS-Suc-Ala-Ala-PheP(OPh)2]. In this study, the Lys175-selective modification method was expanded to incorporate functional groups into Lys 175 in Csin. Two types of peptidyl phosphonate derivatives with the dansyl group (Dan) as a functional molecule, Dan-β-Ala-[Asp(NHS) or Glu(NHS)]-Ala-Ala-(R)-PheP(OPh)2 (DanD and DanE, respectively), were synthesized, and their action was evaluated when modifying Lys175 in Csin. Ion-exchange chromatography (IEC), fluorescence spectroscopy, and LC-MS/MS were used to analyze the products from the reaction of Csin with DanD or DanE. By IEC and LC-MS/MS, the results showed that DanE reacted with Csin more effectively than DanD to produce the modified Csin (DanMCsin) bearing Dan at Lys175. DanMCsin exhibited an enzymatic activity corresponding to 1/120 of Csin against Suc-Ala-Ala-Phe-pNA. In addition, an effect of Lys175 modification on the access of the proteinaceous Bowman–Birk inhibitor to the active site of DanMCsin was investigated. In conclusion, by using a peptidyl derivative containing 1-amino-2-ethylphenylphosphonate diphenyl ester, we demonstrated that a functional group could be incorporated into Lys175 in Csin.
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Affiliation(s)
- Shin Ono
- Applied Chemistry, Kanazawa Institute of Technology, Hakusan 924-0838, Ishikawa, Japan
| | - Masato Koga
- Applied Chemistry, Kanazawa Institute of Technology, Hakusan 924-0838, Ishikawa, Japan
| | - Yuya Arimura
- Applied Chemistry, Kanazawa Institute of Technology, Hakusan 924-0838, Ishikawa, Japan
| | - Takahiro Hatakeyama
- Applied Chemistry, Kanazawa Institute of Technology, Hakusan 924-0838, Ishikawa, Japan
| | - Mai Kobayashi
- Applied Chemistry, Kanazawa Institute of Technology, Hakusan 924-0838, Ishikawa, Japan
| | - Jun-ichi Sagara
- Applied Bioengineering, Kanazawa Institute of Technology, Hakusan 924-0838, Ishikawa, Japan
| | - Takahiko Nakai
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
| | - Yoshikazu Horino
- Department of Applied Chemistry and Bioscience, Chitose Institute of Science and Technology, Chitose 066-8655, Hokkaido, Japan
| | - Hirofumi Kuroda
- Department of General Education, National Institute of Technology, Ishikawa College, Tsubata 929-0392, Ishikawa, Japan
| | - Hiroshi Oyama
- Faculty of Science and Engineering, Setsunan University, Hirakata 572-8508, Osaka, Japan
| | - Kazunari Arima
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima 890-0065, Kagoshima, Japan
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19
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Jun JV, Petri YD, Erickson LW, Raines RT. Modular Diazo Compound for the Bioreversible Late-Stage Modification of Proteins. J Am Chem Soc 2023; 145:6615-6621. [PMID: 36920197 PMCID: PMC10175043 DOI: 10.1021/jacs.2c11325] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
We introduce a versatile strategy for the bioreversible modification of proteins. Our strategy is based on a tricomponent molecule, synthesized in three steps, that incorporates a diazo moiety for chemoselective esterification of carboxyl groups, a pyridyl disulfide group for late-stage functionalization with thiolated ligands, and a self-immolative carbonate group for esterase-mediated cleavage. Using cytochrome c (Cyt c) and the green fluorescent protein (GFP) as models, we generated protein conjugates modified with diverse domains for cellular delivery that include a small molecule, targeting and cell-penetrating peptides (CPPs), and a large polysaccharide. As a proof of concept, we used our strategy to effect the delivery of proteins into the cytosol of live mammalian cells in the presence of serum. The cellular delivery of functional Cyt c, which induces apoptosis, highlighted the advantage of bioreversible conjugation on a carboxyl group versus irreversible conjugation on an amino group. The ease and utility of this traceless modification provide new opportunities for chemical biologists.
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20
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Jia Y, Yan X, Li X, Zhang S, Huang Y, Zhang D, Li Y, Qi B. Soy protein–phlorizin conjugate prepared by tyrosinase catalysis: Identification of covalent binding sites and alterations in protein structure and functionality. Food Chem 2023; 404:134610. [DOI: 10.1016/j.foodchem.2022.134610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
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21
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Zhang Y, Tan J, Chen Y. Visible-light-induced protein labeling in live cells with aryl azides. Chem Commun (Camb) 2023; 59:2413-2420. [PMID: 36744609 DOI: 10.1039/d2cc06987c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Chemical labeling of proteins in live cells helps to probe their native functions in biological systems. Aryl azides are chemically inert under physiological conditions, but they are activated by certain external stimuli. Recently, photocatalytic live-cell applications of aryl azides by visible light irradiation have become a burgeoning new field in chemical biology. In this Feature Article, we focus on the recent progress of protein labeling in live cells with aryl azides induced by visible-light irradiation. Light irradiation activates aryl azides to generate highly reactive intermediates, which enables protein labeling for protein functionalization, crosslinking, and profiling. The activation mechanism of aryl azides by light irradiation is categorized as photolysis, energy-transfer, and electron-transfer. The extracellular and intracellular protein labeling applications in live cells with aryl azides induced by visible light are discussed, including recent advances in red-light-induced extracellular protein labeling.
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Affiliation(s)
- Yixin Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China.
| | - Jiawei Tan
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China.
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China. .,School of Physical Science and Technology ShanghaiTech University, 100 Haike Road, Shanghai 201210, P. R. China.,School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, P. R. China
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22
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Chu X, Li B, Liu HY, Sun X, Yang X, He G, Zhou C, Xuan W, Liu SL, Chen G. Bioconjugation via Hetero-Selective Clamping of Two Different Amines with ortho-Phthalaldehyde. Angew Chem Int Ed Engl 2023; 62:e202212199. [PMID: 36398699 DOI: 10.1002/anie.202212199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 11/19/2022]
Abstract
Amino groups are common in both natural and synthetic compounds and offer a very attractive class of endogenous handles for bioconjugation. However, the ability to differentiate two types of amino groups and join them with high hetero-selectivity and efficiency in a complex setting remains elusive. Herein, we report a new method for bioconjugation via one-pot chemoselective clamping of two different amine nucleophiles using a simple ortho-phthalaldehyde (OPA) reagent. Various α-amino acids, aryl amines, and secondary amines can be crosslinked to the ϵ-amino side chain of lysine on peptides or proteins with high efficiency and hetero-selectivity. This method offers a simple and powerful means to crosslink small molecule drugs, imaging probes, peptides, proteins, carbohydrates, and even virus particles without any pre-functionalization.
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Affiliation(s)
- Xin Chu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bo Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Hao-Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiaowei Sun
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiaochen Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Gang He
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| | - Weimin Xuan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China
| | - Gong Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin, 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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23
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Liu H, Li G, Peng Z, Zhang S, Zhou X, Liu Q, Wang J, Liu Y, Jia T. Tagging Peptides with a Redox Responsive Fluorescent Probe Enabled by Photoredox Difunctionalization of Phenylacetylenes with Sulfinates and Disulfides. JACS AU 2022; 2:2821-2829. [PMID: 36590269 PMCID: PMC9795567 DOI: 10.1021/jacsau.2c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/07/2022] [Indexed: 05/09/2023]
Abstract
Herein, we describe a photoredox three-component atom-transfer radical addition (ATRA) reaction of aryl alkynes directly with dialkyl disulfides and alkylsulfinates, circumventing the utilization of chemically unstable and synthetically challenging S-alkyl alkylthiosulfonates as viable addition partners. A vast array of (E)-β-alkylsulfonylvinyl alkylsulfides was prepared with great regio- and stereoselectivity. Moreover, this powerful tactic could be employed to tag cysteine residues of complex polypeptides in solution or on resin merging with solid phase peptide synthesis (SPPS) techniques. A sulfonyl-derived redox responsive fluorescent probe could be conveniently introduced on the peptide, which displays green fluorescence in cells while showing blue fluorescence in medium. The photophysical investigations reveal that the red shift of the emission fluorescence is attested to reduction of carbonyl group to the corresponding hydroxyl moiety. Interestingly, the fluorescence change of tagged peptide could be reverted in cells by treatment of H2O2, arising from the reoxidation of hydroxyl group back to ketone by the elevated level of reactive oxygen species (ROS).
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Affiliation(s)
- Hong Liu
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Guolin Li
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Zhiyuan Peng
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Shishuo Zhang
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Xin Zhou
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Qingchao Liu
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Junfeng Wang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong
Key Laboratory of Marine Materia Medica/Innovation Academy of South
China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xinggang Road, Guangzhou 510301, P. R. China
| | - Yonghong Liu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong
Key Laboratory of Marine Materia Medica/Innovation Academy of South
China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xinggang Road, Guangzhou 510301, P. R. China
- E-mail:
| | - Tiezheng Jia
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94
Weijin Road, Tianjin 300071, P. R. China
- E-mail:
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24
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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25
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Ullrich S, George J, Coram AE, Morewood R, Nitsche C. Biocompatible and Selective Generation of Bicyclic Peptides. Angew Chem Int Ed Engl 2022; 61:e202208400. [PMID: 35852030 DOI: 10.1002/anie.202208400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 01/07/2023]
Abstract
Bicyclic peptides possess superior properties for drug discovery; however, their chemical synthesis is not straightforward and often neither biocompatible nor fully orthogonal to all canonical amino acids. The selective reaction between 1,2-aminothiols and 2,6-dicyanopyridine allows direct access to complex bicyclic peptides in high yield. The process can be fully automated using standard solid-phase peptide synthesis. Bicyclization occurs in water at physiological pH within minutes and without the need for a catalyst. The use of various linkers allows tailored bicyclic peptides with qualities such as plasma stability, conformational preorganization, and high target affinity. We demonstrate this for a bicyclic inhibitor of the Zika virus protease NS2B-NS3 as well as for bicyclic versions of the α-helical antimicrobial peptide aurein 1.2.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Josemon George
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Alexandra E Coram
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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26
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Anticancer peptides mechanisms, simple and complex. Chem Biol Interact 2022; 368:110194. [PMID: 36195187 DOI: 10.1016/j.cbi.2022.110194] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022]
Abstract
Peptide therapy has started since 1920s with the advent of insulin application, and now it has emerged as a new approach in treatment of diseases including cancer. Using anti-cancer peptides (ACPs) is a promising way of cancer therapy as ACPs are continuing to be approved and arrived at major pharmaceutical markets. Traditional cancer treatments face different problems like intensive adverse effects to patient's body, cell resistance to conventional chemical drugs and in some worse cases the occurrence of cell multidrug resistance (MDR) of cancerous tissues against chemotherapy. On the other hand, there are some benefits conceived for peptides usage in treatment of diseases specifically cancer, as these compounds present favorable characteristics such as smaller size, high activity, low immunogenicity, good biocompatibility in vivo, convenient and rapid way of synthesis, amenable to sequence modification and revision and there is no limitation for the type of cargo they carry. It is possible to achieve an optimum molecular and functional structure of peptides based on previous experience and bank of peptide motif data which may result in novel peptide design. Bioactive peptides are able to form pores in cell membrane and induce necrosis or apoptosis of abnormal cells. Moreover, recent researches have focused on the tumor recognizing peptide motifs with the ability to permeate to cancerous cells with the aim of cancer treatment at earlier stages. In this strategy the most important factors for addressing cancer are choosing peptides with easy accessibility to tumor cell without cytotoxicity effect towards normal cells. The peptides must also meet acceptable pharmacokinetic requirements. In this review, the characteristics of peptides and cancer cells are discussed. The various mechanisms of peptides' action proposed against cancer cells make the next part of discussion. It will be followed by giving information on peptides application, various methods of peptide designing along with introducing various databases. Future aspects of peptides for employing in area of cancer treatment come as conclusion at the end.
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27
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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28
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Carboxyl Group-Modified Myoglobin Induces TNF-α-Mediated Apoptosis in Leukemia Cells. Pharmaceuticals (Basel) 2022; 15:ph15091066. [PMID: 36145287 PMCID: PMC9501283 DOI: 10.3390/ph15091066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Previous studies have shown that chemical modification may increase the activity of proteins or confer novel activity to proteins. Some studies have indicated that myoglobin (Mb) is cytotoxic; however, the underlying mechanisms remain unclear. In this study, we investigated whether chemical modification of the carboxyl group by semicarbazide could promote the Mb cytotoxicity in human leukemia U937 cells and the underlying mechanism of semicarbazide-modified myoglobin (SEM-Mb)-induced U937 cell death. The semicarbazide-modified Mb (SEM-Mb) induced U937 cell apoptosis via the production of cleaved caspase-8 and t-Bid, while silencing of FADD abolished this effect. These findings suggest that SEM-Mb can induce U937 cell death by activating the death receptor-mediated pathway. The SEM-Mb inhibited miR-99a expression, leading to increased NOX4 mRNA and protein expression, which promoted SIRT3 degradation, and, in turn, induced ROS-mediated p38 MAPK phosphorylation. Activated p38 MAPK stimulated miR-29a-dependent tristetraprolin (TTP) mRNA decay. Downregulation of TTP slowed TNF-α mRNA turnover, thereby increasing TNF-α protein expression. The SEM-Mb-induced decrease in cell viability and TNF-α upregulation were alleviated by abrogating the NOX4/SIRT3/ROS/p38 MAPK axis or ectopic expression of TTP. Taken together, our results demonstrated that the NOX4/SIRT3/p38 MAPK/TTP axis induces TNF-α-mediated apoptosis in U937 cells following SEM-Mb treatment. A pathway regulating p38 MAPK-mediated TNF-α expression also explains the cytotoxicity of SEM-Mb in the human leukemia cell lines HL-60, THP-1, K562, Jurkat, and ABT-199-resistant U937. Furthermore, these findings suggest that the carboxyl group-modified Mb is a potential structural template for the generation of tumoricidal proteins.
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29
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Nanovaccines for Cancer Prevention and Immunotherapy: An Update Review. Cancers (Basel) 2022; 14:cancers14163842. [PMID: 36010836 PMCID: PMC9405528 DOI: 10.3390/cancers14163842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Cancer vaccines are a promising immunotherapy-based agents used in cancer therapy. However, monotherapy with these vaccines does not have the sufficient effectiveness in clinical settings. To overcome this challenge, researchers designed nanosystems that increase cancer vaccine efficacy and effectiveness by improving the vaccine's half-life and durability, inducing TME reprogram-ming, and enhancing the anti-tumor immunity with minimum toxicity. This review summarized the structure and different types of cancer nanovaccines and their mechanisms of action in cancer therapy. Moreover, the advantages and drawbacks of these vaccines are discussed. Abstract Cancer immunotherapy has received more and more attention from cancer researchers over the past few decades. Various methods such as cell therapy, immune checkpoint blockers, and cancer vaccines alone or in combination therapies have achieved relatively satisfactory results in cancer therapy. Among these immunotherapy-based methods, cancer vaccines alone have not yet had the necessary efficacy in the clinic. Therefore, nanomaterials have increased the efficacy and ef-fectiveness of cancer vaccines by increasing their half-life and durability, promoting tumor mi-croenvironment (TME) reprogramming, and enhancing their anti-tumor immunity with minimal toxicity. In this review, according to the latest studies, the structure and different types of nanovaccines, the mechanisms of these vaccines in cancer treatment, as well as the advantages and disadvantages of these nanovaccines are discussed.
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30
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Ullrich S, George J, Coram A, Morewood R, Nitsche C. Biocompatible and Selective Generation of Bicyclic Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Ullrich
- Australian National University Research School of Chemistry AUSTRALIA
| | - Josemon George
- Australian National University Research School of Chemistry AUSTRALIA
| | - Alexandra Coram
- Australian National University Research School of Chemistry AUSTRALIA
| | - Richard Morewood
- Australian National University Research School of Chemistry AUSTRALIA
| | - Christoph Nitsche
- Australian National University Research School of Chemistry Sullivans Creek Road ACT 2601 Canberra AUSTRALIA
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31
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Bioconjugates of mercaptocarboxylic acids functionalized AuNP and superoxide dismutase for superoxide electrochemical monitoring. Mikrochim Acta 2022; 189:245. [PMID: 35674988 DOI: 10.1007/s00604-022-05352-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/22/2022] [Indexed: 10/18/2022]
Abstract
The use of gold nanoparticles/superoxide dismutase (AuNP/SOD) bioconjugates is described as building blocks in SOD biosensor development for the quantification of superoxide in cell culture media. AuNP functionalization with 11-mercaptoundecanoic acid (MUA) and 4-mercaptobenzoic acid (MBA) (AuNPMUA and AuNPMBA) was used to improve SOD immobilization through EDC/NHS coupling using their -COOH terminus, leading to the formation of more stable bioconjugates. AuNP and AuNP/SOD bioconjugates were characterized by SEM to determine their size and morphology, UV-Vis for optical properties, FT-IR, and Raman spectroscopies for chemical functional group analysis and EDX for elemental analysis. Electrochemical methods were used to characterize the Au/AuNP-modified electrodes. For the optimization of the biosensor architecture, different AuNP/enzyme bioconjugates were prepared by varying the amount of both enzyme and AuNP, as well as their incubation time. Finally, the biosensors incorporating the bioconjugates were characterized by fixed potential amperometry and voltammetric analysis in order to establish the enzymatic mechanism and to elucidate the best biosensor architecture for monitoring superoxide in cell culture media. The best sensitivity value for superoxide detection corresponded to 41.2 nA µM cm-2, achieved by a biosensor based on AuNPMBA/SOD bioconjugates monitored through fixed potential amperometry at 0.3 V vs. Ag/AgCl, with a limit of detection of 1.0 µM, and overall very good operational stability, maintaining 91% of the initial sensitivity after 30 days. Finally, the optimized biosensor was employed for the quantification of successive additions of superoxide in cell culture media, with excellent recovery values.
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32
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Bagra N, Jain R. Synthesis of 4-(1,2,3-triazol-1-yl)-L-phenylalanines. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2077114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nitin Bagra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
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33
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Roy SK, Purkait A, Shome R, Das S, Das D, Ghosh SS, Jana CK. Proline selective labeling via on-site construction of naphthoxazole (NapOx). Chem Commun (Camb) 2022; 58:5909-5912. [PMID: 35475487 DOI: 10.1039/d2cc01268e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemoselective construction of naphthoxazoles (NapOx) via a three-component annulation reaction enables proline selective labeling of peptides in solution or in solid-phase synthesis. The fluorogenic peptides possess low cytotoxicity, efficient cell membrane permeability and excellent bioimaging potential for biomedical applications.
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Affiliation(s)
- Subhra Kanti Roy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Anisha Purkait
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Rajib Shome
- Department of Biosciences and Engineering, Indian Institute of Technology Guwahati, 781039, India
| | - Saurav Das
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Engineering, Indian Institute of Technology Guwahati, 781039, India
| | - Chandan K Jana
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India.
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34
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Decoene KW, Unal K, Staes A, Zwaenepoel O, Gettemans J, Gevaert K, Winne JM, Madder A. Triazolinedione protein modification: from an overlooked off-target effect to a tryptophan-based bioconjugation strategy. Chem Sci 2022; 13:5390-5397. [PMID: 35655564 PMCID: PMC9093138 DOI: 10.1039/d1sc06942j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/14/2022] [Indexed: 12/30/2022] Open
Abstract
Labelling of tyrosine residues in peptides and proteins has been reported to selectively occur via a 'tyrosine-click' reaction with triazolinedione reagents (TAD). However, we here demonstrate that TAD reagents are actually not selective for tyrosine and that tryptophan residues are in fact also labelled with these reagents. This off-target labelling remained under the radar as it is challenging to detect these physiologically stable but thermally labile modifications with the commonly used HCD and CID MS/MS techniques. We show that selectivity of tryptophan over tyrosine can be achieved by lowering the pH of the aqueous buffer to effect selective Trp-labelling. Given the low relative abundance of tryptophan compared to tyrosine in natural proteins, this results in a new site-selective bioconjugation method that does not rely on enzymes nor unnatural amino acids and is demonstrated for peptides and recombinant proteins.
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Affiliation(s)
- Klaas W Decoene
- Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium .,Department of Biomolecular Medicine, Ghent University Ghent Belgium.,VIB Center for Medical Biotechnology Technologiepark-Zwijnaarde 75 9052 Ghent Belgium
| | - Kamil Unal
- Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - An Staes
- Department of Biomolecular Medicine, Ghent University Ghent Belgium.,VIB Center for Medical Biotechnology Technologiepark-Zwijnaarde 75 9052 Ghent Belgium.,VIB Core Facility, VIB Center for Medical Biotechnology Technologiepark-Zwijnaarde 75 9052 Ghent Belgium
| | | | - Jan Gettemans
- Department of Biomolecular Medicine, Ghent University Ghent Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University Ghent Belgium.,VIB Center for Medical Biotechnology Technologiepark-Zwijnaarde 75 9052 Ghent Belgium
| | - Johan M Winne
- Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
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35
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Yu H, Feng J, Zhong F, Wu Y. Chemical Modification for the "off-/on" Regulation of Enzyme Activity. Macromol Rapid Commun 2022; 43:e2200195. [PMID: 35482602 DOI: 10.1002/marc.202200195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/14/2022] [Indexed: 11/07/2022]
Abstract
Enzymes with excellent catalytic performance play important roles in living organisms. Advances in strategies for enzyme chemical modification have enabled powerful strategies for exploring and manipulating enzyme functions and activities. Based on the development of chemical enzyme modifications, incorporating external stimuli-responsive features-for example, responsivity to light, voltage, magnetic force, pH, temperature, redox activity, and small molecules-into a target enzyme to turn "on" and "off" its activity has attracted much attention. The ability to precisely control enzyme activity using different approaches would greatly expand the chemical biology toolbox for clarification and detection of signal transduction and in vivo enzyme function and significantly promote enzyme-based disease therapy. This review summarizes the methods available for chemical enzyme modification mainly for the off-/on control of enzyme activity and particularly highlights the recent progress regarding the applications of this strategy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Huaibin Yu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Jiayi Feng
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Fangrui Zhong
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Yuzhou Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
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36
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Chen FJ, Zheng M, Nobile V, Gao J. Fast and Cysteine-Specific Modification of Peptides, Proteins and Bacteriophage Using Chlorooximes. Chemistry 2022; 28:e202200058. [PMID: 35167137 PMCID: PMC8986619 DOI: 10.1002/chem.202200058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 12/21/2022]
Abstract
This work reports a novel chlorooxime mediated modification of native peptides and proteins under physiologic conditions. This method features fast reaction kinetics (apparent k2 =306±4 M-1 s-1 for GSH) and exquisite selectivity for cysteine residues. This cysteine conjugation reaction can be carried out with just single-digit micromolar concentrations of the labeling reagent. The conjugates show high stability towards acid, base, and external thiol nucleophiles. A nitrile oxide species generated in situ is likely involved as the key intermediate. Furthermore, a bis-chlorooxime reagent is synthesized to enable facile Cys-Cys stapling in native peptides and proteins. This highly efficient cysteine conjugation and stapling was further implemented on bacteriophage to construct chemically modified phage libraries.
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Affiliation(s)
- Fa-Jie Chen
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Mengmeng Zheng
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Vincent Nobile
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Jianmin Gao
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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37
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Pan J, Zhang Z, Mintah BK, Xu H, Dabbour M, Cheng Y, Dai C, He R, Ma H. Effects of nonthermal physical processing technologies on functional, structural properties and digestibility of food protein: A review. J FOOD PROCESS ENG 2022. [DOI: 10.1111/jfpe.14010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jiayin Pan
- School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu China
- Institute of Food Physical Processing Jiangsu University Zhenjiang Jiangsu China
| | - Zhaoli Zhang
- College of Food Science and Engineering Yangzhou University Yangzhou Jiangsu China
| | | | - Haining Xu
- School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu China
- Institute of Food Physical Processing Jiangsu University Zhenjiang Jiangsu China
| | - Mokhtar Dabbour
- Department of Agricultural and Biosystems Engineering Faculty of Agriculture, Benha University Moshtohor Qaluobia Egypt
| | - Yu Cheng
- School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu China
- Institute of Food Physical Processing Jiangsu University Zhenjiang Jiangsu China
| | - Chunhua Dai
- School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu China
- Institute of Food Physical Processing Jiangsu University Zhenjiang Jiangsu China
| | - Ronghai He
- School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu China
- Institute of Food Physical Processing Jiangsu University Zhenjiang Jiangsu China
| | - Haile Ma
- School of Food and Biological Engineering Jiangsu University Zhenjiang Jiangsu China
- Institute of Food Physical Processing Jiangsu University Zhenjiang Jiangsu China
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38
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Wang Y, Xie F, Liu L, Xu X, Fan S, Zhong W, Zhou X. Development of applicable thiol-linked antibody-drug conjugates with improved stability and therapeutic index. Drug Deliv 2022; 29:754-766. [PMID: 35244495 PMCID: PMC8933021 DOI: 10.1080/10717544.2022.2039807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Maleimides are typically applicable for coupling with reactive thiol moieties of antibodies in antibody–drug conjugates (ADCs) via the thiol-Michael click chemistry. Even so, the thiosuccinimide group produced in ADCs is unstable under physiological conditions, which is a unresolved issue in the ADC industry that can cause serious off-target toxicity. Committed to solving the stability defects of traditional thiosuccinimide-containing ADCs, we explored a series of linkers based on the ring-opening hydrolysates of thiosuccinimide. Meanwhile, a type of linkers based on maleamic methyl ester were used to conjugate the popular monomethyl auristatin E to an anti-HER2 antibody to generate the target ADCs, which enhances the stability and do not need to change the structure of the ideal stable metabolite of traditional ADCs. In vivo studies demonstrate that our preferred ADC mil40-12b not only has better efficacy than traditional ADCs but also exhibits better safety parameters in mice. For example, complete tumor regression can still be achieved even when the dose is halved (2.5 mg/kg), and the maximum tolerable dose is increased by 40 mg/kg. This strategy is expected to provide an applicable tool for the construction of thiol-linked ADCs with improved therapeutic index.
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Affiliation(s)
- Yanming Wang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Fei Xie
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Lianqi Liu
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xin Xu
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Shiyong Fan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xinbo Zhou
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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39
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Bhatt M, Shende P. Surface patterning techniques for proteins on nano- and micro-systems: a modulated aspect in hierarchical structures. J Mater Chem B 2022; 10:1176-1195. [PMID: 35119060 DOI: 10.1039/d1tb02455h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The surface patterning of protein using fabrication or the external functionalization of structures demonstrates various applications in the biomedical field for bioengineering, biosensing and antifouling. This review article offers an outline of the existing advances in protein patterning technology with a special emphasis on the current physical and physicochemical methods, including stencil patterning, trap- and droplet-based microfluidics, and chemical modification of surfaces via photolithography, microcontact printing and scanning probe nanolithography. Different approaches are applied for the biological studies of recent trends for single-protein patterning technology, such as robotic printing, stencil printing and colloidal lithography, wherein the concepts of physical confinement, electrostatic and capillary forces, as well as dielectrophoretics, are summarised to understand the design approaches. Photochemical alterations with diazirine, nitrobenzyl and aryl azide functional groups for the implication of modified substrates, such as self-assembled monolayers functionalized with amino silanes, organosilanes and alkanethiols on gold surfaces, as well as topographical effects of patterning techniques for protein functionalization and orientation, are discussed. Analytical methods for the evaluation of protein functionality are also mentioned. Regarding their selectivity, protein pattering methods will be readily used to fabricate modified surfaces and target-specific delivery systems for the transportation of macromolecules such as streptavidin, and albumin. Future applications of patterning techniques include high-throughput screening, the evaluation of intracellular interactions, accurate screening and personalized treatments.
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Affiliation(s)
- Maitri Bhatt
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
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40
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Synthesis of 5‐Alkynyl and 2,5‐Dialkynyl‐L‐histidines. ChemistrySelect 2022. [DOI: 10.1002/slct.202200264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Chemical modification for improving catalytic performance of lipase B from Candida antarctica with hydrophobic proline ionic liquid. Bioprocess Biosyst Eng 2022; 45:749-759. [PMID: 35113231 DOI: 10.1007/s00449-022-02696-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022]
Abstract
In this study, a series of proline ionic liquids with different lengths of hydrophobic alkyl on the side chain were used to modify the Candida Antarctic lipase B (CALB). The catalytic activity, thermal stability and tolerance to methanol and DMSO of the modified enzyme were all improved simultaneously. The optimum temperature changed from 55 to 60 ℃. The hydrophobicity and anion type of the modifier have important influence on the catalytic performance of CALB. CALB modified by [ProC12][H2PO4] has a better effect. Under the optimal conditions, its hydrolysis activity was 3.0 times than that of the native enzyme, the catalytic efficiency Kcat/Km improved 2.8 times in aqueous phase, and the tolerance to organic solvent with strong polarity (50% methanol 2 h) was increased by 6.8 times. Fluorescence spectra and circular dichroism (CD) spectroscopy showed that the introduction of ionic liquids changed the microenvironment near the fluorophores of the enzyme protein, the α-helix decreased and β-sheet increased in the secondary structure of the modified enzymes. The root mean square deviation (RMSD), residue root mean square fluctuation (RMSF), radius of gyration (Rg), and solution accessible surface area (SASA) of [ProC2][Br]-CALB, [ProC12][Br]-CALB and native CALB were obtained for comparison by molecular dynamics simulation. The results of dynamics simulation were in good agreement with enzymology experiment. The introduction of ionic liquids can keep CALB in a better active conformation, and proline ionic liquids with long hydrophobic chains can significantly improve the surface hydrophobicity and overall rigidity of CALB. This research offers a new idea for rapid screening of efficient modifiers and provision of enzymes with high stability and activity for industrial application.
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42
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Energy-based fragmentation contribution approach for calculating the fluorescence spectrum of biomacromolecules. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Arumugam K, Shanker RR. Text Mining and Machine Learning Protocol for Extracting Human-Related Protein Phosphorylation Information from PubMed. Methods Mol Biol 2022; 2496:159-177. [PMID: 35713864 DOI: 10.1007/978-1-0716-2305-3_9] [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] [Indexed: 06/15/2023]
Abstract
In the modern health care research, protein phosphorylation has gained an enormous attention from the researchers across the globe and requires automated approaches to process a huge volume of data on proteins and their modifications at the cellular level. The data generated at the cellular level is unique as well as arbitrary, and an accumulation of massive volume of information is inevitable. Biological research has revealed that a huge array of cellular communication aided by protein phosphorylation and other similar mechanisms imply different and diverse meanings. This led to a collection of huge volume of data to understand the biological functions of human evolution, especially for combating diseases in a better way. Text mining, an automated approach to mine the information from an unstructured data, finds its application in extracting protein phosphorylation information from the biomedical literature databases such as PubMed. This chapter outlines a recent text mining protocol that applies natural language parsing (NLP) for named entity recognition and text processing, and support vector machines (SVM), a machine learning algorithm for classifying the processed text related human protein phosphorylation. We discuss on evaluating the text mining system which is the outcome of the protocol on three corpora, namely, human Protein Phosphorylation (hPP) corpus, Integrated Protein Literature Information and Knowledge corpus (iProLink), and Phosphorylation Literature corpus (PLC). We also present a basic understanding on the chemistry and biology that drive the protein phosphorylation process in a human body. We believe that this basic understanding will be useful to advance the existing text mining systems for extracting protein phosphorylation information from PubMed.
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Affiliation(s)
- Krishnamurthy Arumugam
- Department of Management Studies, Coimbatore Institute of Engineering and Technology, Coimbatore, Tamilnadu, India.
| | - Raja Ravi Shanker
- International Business Unit, Alembic Pharmaceuticals Limited, Vadodara, Gujarat, India
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44
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Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
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Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
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45
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Zhang T, Luo P, Lai C, Liu Z, Jin Y, Wang F. Catalyst-free Photochemical Bromination of Unprotected Aromatic Amino Acid Derivatives by Using a Rotating Ultraviolet Photoreactor. Chem Res Chin Univ 2021. [DOI: 10.1007/s40242-021-1413-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Giri P, Pagar AD, Patil MD, Yun H. Chemical modification of enzymes to improve biocatalytic performance. Biotechnol Adv 2021; 53:107868. [PMID: 34774927 DOI: 10.1016/j.biotechadv.2021.107868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022]
Abstract
Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.
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Affiliation(s)
- Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mahesh D Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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47
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Methacrylated zein as a novel biobased macro-crosslinker for PVCL hydrogels. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.124278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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48
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Biedka S, Schmidt BF, Frey NM, Boothman SM, Minden JS, Lucas A. Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis. J Proteome Res 2021; 20:4787-4800. [PMID: 34524823 DOI: 10.1021/acs.jproteome.1c00443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Successful proteome analysis requires reliable sample preparation beginning with protein solubilization and ending with a sample free of contaminants, ready for downstream analysis. Most proteome sample preparation technologies utilize precipitation or filter-based separation, both of which have significant disadvantages. None of the current technologies are able to prepare both intact proteins or digested peptides. Here, we introduce a reversible protein tag, ProMTag, that enables whole proteome capture, cleanup, and release of intact proteins for top-down analysis. Alternatively, the addition of a novel Trypsin derivative to the workflow generates peptides for bottom-up analysis. We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests. For top-down analysis, ProMTag cleanup improves resolution on 2D gels; for bottom-up exploration, this methodology produced reproducible mass spectrometry results, demonstrating that the ProMTag method is a truly universal approach that produces high-quality proteome samples compatible with multiple downstream analytical techniques. Data are available via ProteomeXchange with identifier PXD027799.
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Affiliation(s)
- Stephanie Biedka
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States
| | - Brigitte F Schmidt
- JGS Research Co., Pittsburgh, Pennsylvania 15212, United States.,Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nolan M Frey
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sarah M Boothman
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jonathan S Minden
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States.,Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Amber Lucas
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States
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Abstract
Biopolymers are natural polymers sourced from plants and animals, which include a variety of polysaccharides and polypeptides. The inclusion of biopolymers into biomedical hydrogels is of great interest because of their inherent biochemical and biophysical properties, such as cellular adhesion, degradation, and viscoelasticity. The objective of this Review is to provide a detailed overview of the design and development of biopolymer hydrogels for biomedical applications, with an emphasis on biopolymer chemical modifications and cross-linking methods. First, the fundamentals of biopolymers and chemical conjugation methods to introduce cross-linking groups are described. Cross-linking methods to form biopolymer networks are then discussed in detail, including (i) covalent cross-linking (e.g., free radical chain polymerization, click cross-linking, cross-linking due to oxidation of phenolic groups), (ii) dynamic covalent cross-linking (e.g., Schiff base formation, disulfide formation, reversible Diels-Alder reactions), and (iii) physical cross-linking (e.g., guest-host interactions, hydrogen bonding, metal-ligand coordination, grafted biopolymers). Finally, recent advances in the use of chemically modified biopolymer hydrogels for the biofabrication of tissue scaffolds, therapeutic delivery, tissue adhesives and sealants, as well as the formation of interpenetrating network biopolymer hydrogels, are highlighted.
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Affiliation(s)
- Victoria G. Muir
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason A. Burdick
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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50
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Vaghi L, Monti M, Marelli M, Motto E, Papagni A, Cipolla L. Photoinduced Porcine Gelatin Cross-Linking by Homobi- and Homotrifunctional Tetrazoles. Gels 2021; 7:124. [PMID: 34449602 PMCID: PMC8395868 DOI: 10.3390/gels7030124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Gelatin is a costless polypeptide material of natural origin, able to form hydrogels that are potentially useful in biomaterial scaffold design for drug delivery, cell cultures, and tissue engineering. However, gelatin hydrogels are unstable at physiological conditions, losing their features only after a few minutes at 37 °C. Accordingly, treatments to address this issue are of great interest. In the present work, we propose for the first time the use of bi- and trifunctional tetrazoles, most of them unknown to date, for photoinduced gelatin cross-linking towards the production of physiologically stable hydrogels. Indeed, after UV-B irradiation, aryl tetrazoles generate a nitrilimine intermediate that is reactive towards different functionalities, some of them constitutively present in the amino acid side chains of gelatin. The efficacy of the treatment strictly depends on the structure of the cross-linking agent used, and substantial improved stability was observed by switching from bifunctional to trifunctional cross-linkers.
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Affiliation(s)
- Luca Vaghi
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano—Bicocca, via R. Cozzi 55, 20125 Milano, Italy;
| | - Mauro Monti
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano—Bicocca, via R. Cozzi 55, 20125 Milano, Italy;
| | - Marcello Marelli
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR-SCITEC, Sede Fantoli, via Fantoli 16/15, 20138 Milano, Italy;
| | - Elisa Motto
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano—Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Antonio Papagni
- Dipartimento di Scienza dei Materiali, Università degli Studi di Milano—Bicocca, via R. Cozzi 55, 20125 Milano, Italy;
| | - Laura Cipolla
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano—Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
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