1
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Niogret G, Chériaux C, Bonhomme F, Levi-Acobas F, Figliola C, Ulrich G, Gasser G, Hollenstein M. A toolbox for enzymatic modification of nucleic acids with photosensitizers for photodynamic therapy. RSC Chem Biol 2024; 5:841-852. [PMID: 39211468 PMCID: PMC11353023 DOI: 10.1039/d4cb00103f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024] Open
Abstract
Photodynamic therapy (PDT) is an approved cancer treatment modality. Despite its high efficiency, PDT is limited in terms of specificity and by the poor solubility of the rather lipophilic photosensitizers (PSs). In order to alleviate these limitations, PSs can be conjugated to oligonucleotides. However, most conjugation methods often involve complex organic synthesis and result in the appendage of single modifications at the 3'/5' termini of oligonucleotides. Here, we have investigated the possibility of bioconjugating a range of known PSs by polymerase-mediated synthesis. We have prepared a range of modified nucleoside triphosphates by different conjugation methods and investigated the substrate tolerance of these nucleotides for template-dependent and -independent DNA polymerases. This method represents a mild and versatile approach for the conjugation of single or multiple PSs onto oligonucleotides and can be useful to further improve the efficiency of the PDT treatment.
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Affiliation(s)
- Germain Niogret
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids 28, rue du Docteur Roux 75724 Paris Cedex 15 France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Camille Chériaux
- Institut de Chimie et Procédés pour L'Energie, L'Environnement et La Santé (ICPEES), Groupe de Chimie Organique pour Les Matériaux, La Biologie et L'Optique (COMBO), CNRS UMR 7515, École de Chimie, Polymères, Matériaux de Strasbourg (ECPM) 25, Rue Becquerel 67087 Strasbourg Cedex 02 France
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Unité de Chimie Biologique Epigénétique 28, rue du Docteur Roux 75724 Paris Cedex 15 France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids 28, rue du Docteur Roux 75724 Paris Cedex 15 France
| | - Carlotta Figliola
- Institut de Chimie et Procédés pour L'Energie, L'Environnement et La Santé (ICPEES), Groupe de Chimie Organique pour Les Matériaux, La Biologie et L'Optique (COMBO), CNRS UMR 7515, École de Chimie, Polymères, Matériaux de Strasbourg (ECPM) 25, Rue Becquerel 67087 Strasbourg Cedex 02 France
| | - Gilles Ulrich
- Institut de Chimie et Procédés pour L'Energie, L'Environnement et La Santé (ICPEES), Groupe de Chimie Organique pour Les Matériaux, La Biologie et L'Optique (COMBO), CNRS UMR 7515, École de Chimie, Polymères, Matériaux de Strasbourg (ECPM) 25, Rue Becquerel 67087 Strasbourg Cedex 02 France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids 28, rue du Docteur Roux 75724 Paris Cedex 15 France
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2
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Soxpollard N, Strauss S, Jungmann R, MacPherson IS. Selection of antibody-binding covalent aptamers. Commun Chem 2024; 7:174. [PMID: 39117896 PMCID: PMC11310417 DOI: 10.1038/s42004-024-01255-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Aptamers are oligonucleotides with antibody-like binding function, selected from large combinatorial libraries. In this study, we modified a DNA aptamer library with N-hydroxysuccinimide esters, enabling covalent conjugation with cognate proteins. We selected for the ability to bind to mouse monoclonal antibodies, resulting in the isolation of two distinct covalent binding motifs. The covalent aptamers are specific for the Fc region of mouse monoclonal IgG1 and are cross-reactive with mouse IgG2a and other IgGs. Investigation into the covalent conjugation of the aptamers revealed a dependence on micromolar concentrations of Cu2+ ions which can be explained by residual catalyst remaining after modification of the aptamer library. The aptamers were successfully used as adapters in the formation of antibody-oligonucleotide conjugates (AOCs) for use in detection of HIV protein p24 and super-resolution imaging of actin. This work introduces a new method for the site-specific modification of native monoclonal antibodies and may be useful in applications requiring AOCs or other antibody conjugates.
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Affiliation(s)
- Noah Soxpollard
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawaii, Honolulu, HI, 96813, USA
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Iain S MacPherson
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawaii, Honolulu, HI, 96813, USA.
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3
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Majumdar B, Sarma D, Yu Y, Lozoya-Colinas A, Chaput JC. Increasing the functional density of threose nucleic acid. RSC Chem Biol 2024; 5:41-48. [PMID: 38179195 PMCID: PMC10763562 DOI: 10.1039/d3cb00159h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical strategies that augment genetic polymers with amino acid residues that are overrepresented on the paratope surface of an antibody offer a promising route for enhancing the binding properties of nucleic acid aptamers. Here, we describe the chemical synthesis of α-l-threofuranosyl cytidine nucleoside triphosphate (tCTP) carrying either a benzyl or phenylpropyl side chain at the pyrimidine C-5 position. Polymerase recognition studies indicate that both substrates are readily incorporated into a full-length α-l-threofuranosyl nucleic acid (TNA) product by extension of a DNA primer-template duplex with an engineered TNA polymerase. Similar primer extension reactions performed using nucleoside triphosphate mixtures containing both C-5 modified tCTP and C-5 modified tUTP substrates enable the production of doubly modified TNA strands for a panel of 20 chemotype combinations. Kinetic measurements reveal faster on-rates (kon) and tighter binding affinity constants (Kd) for engineered versions of TNA aptamers carrying chemotypes at both pyrimidine positions as compared to their singly modified counterparts. These findings expand the chemical space of evolvable non-natural genetic polymers by offering a path for improving the quality of biologically stable TNA aptamers for future clinical applications.
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Affiliation(s)
- Biju Majumdar
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Daisy Sarma
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Yutong Yu
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Adriana Lozoya-Colinas
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
- Department of Chemistry, University of California Irvine CA 92697-3958 USA
- Department of Molecular Biology and Biochemistry, University of California Irvine CA 92697-3958 USA
- Department of Chemical and Biomolecular Engineering, University of California Irvine CA 92697-3958 USA
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4
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Kohn EM, Konovalov K, Gomez CA, Hoover GN, Yik AKH, Huang X, Martell JD. Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS Chem Biol 2023; 18:1976-1984. [PMID: 37531184 DOI: 10.1021/acschembio.3c00183] [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] [Indexed: 08/03/2023]
Abstract
Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirill Konovalov
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christian A Gomez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gillian N Hoover
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew Kai-Hei Yik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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5
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Lin CL, Sojitra M, Carpenter EJ, Hayhoe ES, Sarkar S, Volker EA, Wang C, Bui DT, Yang L, Klassen JS, Wu P, Macauley MS, Lowary TL, Derda R. Chemoenzymatic synthesis of genetically-encoded multivalent liquid N-glycan arrays. Nat Commun 2023; 14:5237. [PMID: 37640713 PMCID: PMC10462762 DOI: 10.1038/s41467-023-40900-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Cellular glycosylation is characterized by chemical complexity and heterogeneity, which is challenging to reproduce synthetically. Here we show chemoenzymatic synthesis on phage to produce a genetically-encoded liquid glycan array (LiGA) of complex type N-glycans. Implementing the approach involved by ligating an azide-containing sialylglycosyl-asparagine to phage functionalized with 50-1000 copies of dibenzocyclooctyne. The resulting intermediate can be trimmed by glycosidases and extended by glycosyltransferases yielding a phage library with different N-glycans. Post-reaction analysis by MALDI-TOF MS allows rigorous characterization of N-glycan structure and mean density, which are both encoded in the phage DNA. Use of this LiGA with fifteen glycan-binding proteins, including CD22 or DC-SIGN on cells, reveals optimal structure/density combinations for recognition. Injection of the LiGA into mice identifies glycoconjugates with structures and avidity necessary for enrichment in specific organs. This work provides a quantitative evaluation of the interaction of complex N-glycans with GBPs in vitro and in vivo.
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Affiliation(s)
- Chih-Lan Lin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Mirat Sojitra
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Eric J Carpenter
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ellen S Hayhoe
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Elizabeth A Volker
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Loretta Yang
- Lectenz Bio, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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6
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Tang L, Huang M, Zhang M, Pei Y, Liu Y, Wei Y, Yang C, Xie T, Zhang D, Zhou R, Song Y, Song J. De Novo Evolution of an Antibody-Mimicking Multivalent Aptamer via a DNA Framework. SMALL METHODS 2023:e2300327. [PMID: 37086150 DOI: 10.1002/smtd.202300327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Multivalent interactions can often endow ligands with more efficient binding performance toward target molecules. Generally speaking, a multivalent aptamer can be constructed via post-assembly based on chemical structural information of target molecules and pre-identified monovalent aptamers derived from traditional systematic evolution of ligands by exponential enrichment (SELEX) technology. However, many target molecules may not have known matched aptamer partners, thus a de novo evolution will be highly desired as an alternative strategy for directed selection of a high-avidity, multivalent aptamer. Here, inspired by the superiority of multivalent interactions between antibodies and antigens, a direct SELEX strategy with a preorganized DNA framework library for an "Antibody-mimicking multivalent aptamer" (Amap) selection to epithelial cell adhesion molecule (EpCAM), a model target protein is reported. The Amap presents a relatively good binding affinity through both aptamer moieties concurrently binding to EpCAM, which has been confirmed by affinity analysis and molecular modeling. Furthermore, dynamic interactions between Amap and EpCAM are directly visualized by magnetic tweezers at the single-molecule level. A nice binding affinity of Amap to EpCAM-positive cancer cells has also been verified, which hints that their Amap-SELEX strategy has the potential to be a new route for de novo evolution of multivalent aptamers.
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Affiliation(s)
- Linlin Tang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, Guangxi, 541004, P. R. China
| | - Mingjiao Zhang
- School of Physics, College of Life Sciences and, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yong Wei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Teng Xie
- School of Physics, College of Life Sciences and, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Dong Zhang
- School of Physics, College of Life Sciences and, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Ruhong Zhou
- School of Physics, College of Life Sciences and, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, P. R. China
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen, 361005, P. R. China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
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7
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Neralkar M, Xu B, Horiya S, Krauss IJ. Large-Scale Synthesis of Man 9GlcNAc 2 High-Mannose Glycan and the Effect of the Glycan Core on Multivalent Recognition by HIV Antibody 2G12. ACS Infect Dis 2022; 8:2232-2241. [PMID: 36278940 DOI: 10.1021/acsinfecdis.2c00442] [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] [Indexed: 01/29/2023]
Abstract
Access to homogeneous high-mannose glycans in high-mg quantities is necessary for carbohydrate-based HIV vaccine development research. We have used directed evolution to design highly antigenic oligomannose clusters that are recognized in low-nM affinity by HIV antibodies. Herein we report an optimized large-scale synthesis of Man9GlcNAc2 including improved building block synthesis and a fully stereoselective 5 + 6 coupling, yielding 290 mg of glycan. We then use this glycan to study the effect of the GlcNAc2 core on the antigenicity of an evolved 2G12-binding glycopeptide, 10F2.
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Affiliation(s)
- Mahesh Neralkar
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Bokai Xu
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Satoru Horiya
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454, United States
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8
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Li Q, Maola VA, Chim N, Hussain J, Lozoya-Colinas A, Chaput JC. Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities. J Am Chem Soc 2021; 143:17761-17768. [PMID: 34637287 DOI: 10.1021/jacs.1c08649] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Expanding the chemical space of evolvable non-natural genetic polymers (XNAs) to include functional groups that enhance protein target binding affinity offers a promising route to therapeutic aptamers with high biological stability. Here we describe the chemical synthesis and polymerase recognition of 10 chemically diverse functional groups introduced at the C-5 position of α-l-threofuranosyl uridine nucleoside triphosphate (tUTP). We show that the set of tUTP substrates is universally recognized by the laboratory-evolved polymerase Kod-RSGA. Insights into the mechanism of TNA synthesis were obtained from a high-resolution X-ray crystal structure of the postcatalytic complex bound to the primer-template duplex. A structural analysis reveals a large cavity in the enzyme active site that can accommodate the side chain of C-5-modified tUTP substrates. Our findings expand the chemical space of evolvable nucleic acid systems by providing a synthetic route to artificial genetic polymers that are uniformly modified with diversity-enhancing functional groups.
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9
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Redman RL, Krauss IJ. Directed Evolution of 2'-Fluoro-Modified, RNA-Supported Carbohydrate Clusters That Bind Tightly to HIV Antibody 2G12. J Am Chem Soc 2021; 143:8565-8571. [PMID: 34096703 DOI: 10.1021/jacs.1c03194] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carbohydrate binding proteins (CBPs) are attractive targets in medicine and biology. Multivalency, with several glycans binding to several binding pockets in the CBP, is important for high-affinity interactions. Herein, we describe a novel platform for design of multivalent carbohydrate cluster ligands by directed evolution, in which serum-stable 2'-fluoro modified RNA (F-RNA) backbones evolve to present the glycan in optimal clusters. We have validated this method by the selection of oligomannose (Man9) glycan clusters from a sequence pool of ∼1013 that bind to broadly neutralizing HIV antibody 2G12 with 13 to 36 nM affinities.
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Affiliation(s)
- Richard L Redman
- Department of Chemistry, Brandeis University, 415 South Street MS 015, Waltham, Massachusetts 02454, United States
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, 415 South Street MS 015, Waltham, Massachusetts 02454, United States
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10
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Yang C, Wu KB, Deng Y, Yuan J, Niu J. Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers. ACS Macro Lett 2021; 10:243-257. [PMID: 34336395 PMCID: PMC8320758 DOI: 10.1021/acsmacrolett.0c00855] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sequence-controlled polymers are an emerging class of synthetic polymers with a regulated sequence of monomers. In the past decade, tremendous progress has been made in the synthesis of polymers with the sophisticated sequence control approaching the level manifested in biopolymers. In contrast, the exploration of novel functions that can be achieved by controlling synthetic polymer sequences represents an emerging focus in polymer science. This Viewpoint will survey recent advances in the functional applications of sequence-controlled polymers and provide a perspective on the challenges and outlook for pursuing future applications of this fascinating class of macromolecules.
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Affiliation(s)
- Cangjie Yang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kevin B. Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yu Deng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jingsong Yuan
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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11
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Bastida I, Fernández-Tejada A. Synthetic carbohydrate-based HIV-1 vaccines. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 35-36:45-56. [PMID: 33388127 DOI: 10.1016/j.ddtec.2020.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 01/22/2023]
Abstract
An effective prophylactic HIV-1 vaccine is essential in order to contain the HIV/AIDS global pandemic. The discovery of different broadly neutralizing antibodies (bnAbs) in the last decades has enabled the characterization of several minimal epitopes on the HIV envelope (Env) spike, including glycan-dependent fragments. Herein, we provide a brief overview of the progress made on the development of synthetic carbohydrate-based epitope mimics for the elicitation of bnAbs directed to certain regions on Env gp120 protein: the outer domain high-mannose cluster and the variable loops V1V2 and V3. We focus on the design, synthesis and biological evaluation of minimal immunogens and discuss key aspects towards the development of a successful protective vaccine against HIV-1.
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Affiliation(s)
- Iñaki Bastida
- Chemical Immunology Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48169 Derio, Bizkaia, Spain
| | - Alberto Fernández-Tejada
- Chemical Immunology Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48169 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, María Díaz de Haro 13, 48013 Bilbao, Bizkaia, Spain.
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12
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Ochoa S, Milam VT. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020; 25:E4659. [PMID: 33066073 PMCID: PMC7587394 DOI: 10.3390/molecules25204659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.
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Affiliation(s)
- Steven Ochoa
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Valeria T. Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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13
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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14
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Nguyen DN, Redman RL, Horiya S, Bailey JK, Xu B, Stanfield RL, Temme JS, LaBranche CC, Wang S, Rodal AA, Montefiori DC, Wilson IA, Krauss IJ. The Impact of Sustained Immunization Regimens on the Antibody Response to Oligomannose Glycans. ACS Chem Biol 2020; 15:789-798. [PMID: 32109354 PMCID: PMC7091532 DOI: 10.1021/acschembio.0c00053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The high mannose
patch (HMP) of the HIV envelope protein (Env)
is the structure most frequently targeted by broadly neutralizing
antibodies; therefore, many researchers have attempted to use mimics
of this region as a vaccine immunogen. In our previous efforts, vaccinating
rabbits with evolved HMP mimic glycopeptides containing Man9 resulted in an overall antibody response targeting the glycan core
and linker rather than the full glycan or Manα1→2Man
tips of Man9 glycans. A possible reason could be processing
of our immunogen by host serum mannosidases. We sought to test whether
more prolonged dosing could increase the antibody response to intact
glycans, possibly by increasing the availability of intact Man9 to germinal centers. Here, we describe a study investigating
the impact of immunization regimen on antibody response by testing
immunogen delivery through bolus, an exponential series of mini doses,
or a continuously infusing mini-osmotic pump. Our results indicate
that, with our glycopeptide immunogens, standard bolus immunization
elicited the strongest HIV Env-binding antibody response, even though
higher overall titers to the glycopeptide were elicited by the exponential
and pump regimens. Antibody selectivity for intact glycan was, if
anything, slightly better in the bolus-immunized animals.
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Affiliation(s)
- Dung N. Nguyen
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Richard L. Redman
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Satoru Horiya
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Jennifer K. Bailey
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Bokai Xu
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - J. Sebastian Temme
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Shiyu Wang
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Avital A. Rodal
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Isaac J. Krauss
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
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15
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Kong D, Movahedi M, Mahdavi-Amiri Y, Yeung W, Tiburcio T, Chen D, Hili R. Evolutionary Outcomes of Diversely Functionalized Aptamers Isolated from in Vitro Evolution. ACS Synth Biol 2020; 9:43-52. [PMID: 31774997 DOI: 10.1021/acssynbio.9b00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Expanding the chemical diversity of aptamers remains an important thrust in the field in order to increase their functional potential. Previously, our group developed LOOPER, which enables the incorporation of up to 16 unique modifications throughout a ssDNA sequence, and applied it to the in vitro evolution of thrombin binders. As LOOPER-derived highly modified nucleic acids polymers are governed by two interrelated evolutionary variables, namely, functional modifications and sequence, the evolution of this polymer contrasts with that of canonical DNA. Herein we provide in-depth analysis of the evolution, including structure-activity relationships, mapping of evolutionary pressures on the library, and analysis of plausible evolutionary pathways that resulted in the first LOOPER-derived aptamer, TBL1. A detailed picture of how TBL1 interacts with thrombin and how it may mimic known peptide binders of thrombin is also proposed. Structural modeling and folding studies afford insights into how the aptamer displays critical modifications and also how modifications enhance the structural stability of the aptamer. A discussion of benefits and potential limitations of LOOPER during in vitro evolution is provided, which will serve to guide future evolutions of this highly modified class of aptamers.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Matina Movahedi
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Yasaman Mahdavi-Amiri
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Tristan Tiburcio
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Dickson Chen
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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16
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Odeh F, Nsairat H, Alshaer W, Ismail MA, Esawi E, Qaqish B, Bawab AA, Ismail SI. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules 2019; 25:E3. [PMID: 31861277 PMCID: PMC6982925 DOI: 10.3390/molecules25010003] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems.
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Affiliation(s)
- Fadwa Odeh
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Hamdi Nsairat
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Ezaldeen Esawi
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Baraa Qaqish
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Abeer Al Bawab
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Said I. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
- Qatar Genome Project, Qatar Foundation, Doha 5825, Qatar
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17
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Levi-Acobas F, Katolik A, Röthlisberger P, Cokelaer T, Sarac I, Damha MJ, Leumann CJ, Hollenstein M. Compatibility of 5-ethynyl-2'F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers. Org Biomol Chem 2019; 17:8083-8087. [PMID: 31460550 DOI: 10.1039/c9ob01515a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A modified nucleoside triphosphate bearing two modifications based on a 2'-deoxy-2'-fluoro-arabinofuranose sugar and a uracil nucleobase equipped with a C5-ethynyl moiety (5-ethynyl-2'F-ANA UTP) was synthesized. This nucleotide analog could enzymatically be incorporated into DNA oligonucleotides by primer extension and reverse transcribed to unmodified DNA. This nucleotide could be used in SELEX for the identification of high binding affinity and nuclease resistant aptamers.
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Affiliation(s)
- Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. and Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Adam Katolik
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland and Department of Chemistry, McGill University, 801 Rue Sherbrooke Street West, Montréal, QC H3A 0B8, Canada
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. and Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France and Institut Pasteur, Biomics Platform, C2RT, Paris, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. and Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Street West, Montréal, QC H3A 0B8, Canada
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. and Institut Pasteur, Department of Genome and Genetics, Paris, France
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18
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Nguyen DN, Xu B, Stanfield RL, Bailey JK, Horiya S, Temme JS, Leon DR, LaBranche CC, Montefiori DC, Costello CE, Wilson IA, Krauss IJ. Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities. ACS CENTRAL SCIENCE 2019; 5:237-249. [PMID: 30834312 PMCID: PMC6396197 DOI: 10.1021/acscentsci.8b00588] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 06/01/2023]
Abstract
Up to ∼20% of HIV-infected individuals eventually develop broadly neutralizing antibodies (bnAbs), and many of these antibodies (∼40%) target a region of dense high-mannose glycosylation on gp120 of the HIV envelope protein, known as the "high-mannose patch" (HMP). Thus, there have been numerous attempts to develop glycoconjugate vaccine immunogens that structurally mimic the HMP and might elicit bnAbs targeting this conserved neutralization epitope. Herein, we report on the immunogenicity of glycopeptides, designed by in vitro selection, that bind tightly to anti-HMP antibody 2G12. By analyzing the fine carbohydrate specificity of rabbit antibodies elicited by these immunogens, we found that they differ from some natural human bnAbs, such as 2G12 and PGT128, in that they bind primarily to the core structures within the glycan, rather than to the Manα1 → 2Man termini (2G12) or to the whole glycan (PGT128). Antibody specificity for the glycan core may result from extensive serum mannosidase trimming of the immunogen in the vaccinated animals. This finding has broad implications for vaccine design aiming to target glycan-dependent HIV neutralizing antibodies.
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Affiliation(s)
- Dung N. Nguyen
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Bokai Xu
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Robyn L. Stanfield
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Jennifer K. Bailey
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Satoru Horiya
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - J. Sebastian Temme
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Deborah R. Leon
- Department
of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02215, United States
| | - Celia C. LaBranche
- Department
of Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - David C. Montefiori
- Department
of Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Catherine E. Costello
- Department
of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02215, United States
| | - Ian A. Wilson
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Isaac J. Krauss
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
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19
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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20
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Mei H, Chaput JC. Expanding the chemical diversity of TNA with tUTP derivatives that are substrates for a TNA polymerase. Chem Commun (Camb) 2018; 54:1237-1240. [PMID: 29340357 DOI: 10.1039/c7cc09130c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Expanding the chemical diversity of threose nucleic acid (TNA) beyond the natural bases would enable the development of TNA polymers with enhanced physicochemical properties. Here, we describe a versatile approach for increasing the chemical diversity of TNA using 5-alkynyl-modified α-l-threofuranosyl uridine triphosphates that are substrates for a TNA polymerase.
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Affiliation(s)
- Hui Mei
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, USA.
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21
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Wang Y, Ng N, Liu E, Lam CH, Perrin DM. Systematic study of constraints imposed by modified nucleoside triphosphates with protein-like side chains for use in in vitro selection. Org Biomol Chem 2018; 15:610-618. [PMID: 27942671 DOI: 10.1039/c6ob02335e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Successful selection of modified DNAzymes depends on the potential for modified nucleoside triphosphates (dNTPs) to replace their unmodified counterparts in enzyme catalyzed primer extension reactions and, once incorporated, to serve as template bases for information transfer prior to PCR amplification. To date, the most densely modified DNAzymes have been selected from three modified dNTPs: 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) to provide several RNA-cleaving DNAzymes with greatly enhanced rate constants compared to unmodified counterparts. Here we report biophysical and enzymatic properties of these three modified nucleosides in the context of specific oligonucleotide sequences to understand how these three modified nucleobases function in combinatorial selection. The base-pairing abilities of oligonucleotides bearing one or three modified nucleosides were investigated by thermal denaturation studies and as templates for enzymatic polymerization with both modified and unmodified dNTPs. While we address certain shortcomings in the use of modified dNTPs, we also provide key evidence of faithful incorporation and enzymatic read-out, which strongly supports their continued use in in vitro selection.
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Affiliation(s)
- Yajun Wang
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Nicole Ng
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Erkai Liu
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Curtis H Lam
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - David M Perrin
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
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22
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MacPherson IS, Temme JS, Krauss IJ. DNA display of folded RNA libraries enabling RNA-SELEX without reverse transcription. Chem Commun (Camb) 2018; 53:2878-2881. [PMID: 28220154 DOI: 10.1039/c6cc09991b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A method for the physical attachment of folded RNA libraries to their encoding DNA is presented as a way to circumvent the reverse transcription step during systematic evolution of RNA ligands by exponential enrichment (RNA-SELEX). A DNA library is modified with one isodC base to stall T7 polymerase and a 5' "capture strand" which anneals to the nascent RNA transcript. This method is validated in a selection of RNA aptamers against human α-thrombin with dissociation constants in the low nanomolar range. This method will be useful in the discovery of RNA aptamers and ribozymes containing base modifications that make them resistant to accurate reverse transcription.
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Affiliation(s)
- I S MacPherson
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Manoa, 651 Ilalo St., Biosciences Building, Suite 325, Honolulu, Hawaii 96813-5525, USA. and Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA.
| | - J S Temme
- Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA.
| | - I J Krauss
- Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA.
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23
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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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24
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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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25
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Abstract
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein. Although yeast, mammalian and Escherichia coli cells can be engineered to produce a homogenous glycoform at all glycosylation sites, there are just a few specific glycan structures that can readily be accessed in this manner. Recently, we reported a novel system for the directed evolution of glycopeptide libraries, which could in principle be decorated with any desired glycan. Our method combines in vitro peptide selection by mRNA display with unnatural amino acid incorporation and chemical attachment of synthetic oligosaccharides. Here, we provide an updated and optimized protocol for this method, which is designed to create glycopeptide mRNA display libraries containing ~1013 sequences and select them for target binding. The target described here is the HIV broadly neutralizing monoclonal antibody 2G12; 2G12 binds to cluster of high-mannose oligosaccharides on the HIV envelope glycoprotein gp120; and glycopeptides that mimic this epitope may be useful in HIV vaccine applications. This method is expected to be readily applicable for other types of glycans and targets of interest in glycobiology.
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26
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Abstract
Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code.
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27
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Behrens AJ, Seabright GE, Crispin M. Targeting Glycans of HIV Envelope Glycoproteins for Vaccine Design. CHEMICAL BIOLOGY OF GLYCOPROTEINS 2017. [DOI: 10.1039/9781782623823-00300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The surface of the envelope spike of the human immunodeficiency virus (HIV) is covered with a dense array of glycans, which is sufficient to impede the host antibody response while maintaining a window for receptor recognition. The glycan density significantly exceeds that typically observed on self glycoproteins and is sufficiently high to disrupt the maturation process of glycans, from oligomannose- to complex-type glycosylation, that normally occurs during glycoprotein transit through the secretory system. It is notable that this generates a degree of homogeneity not seen in the highly mutated protein moiety. The conserved, close glycan packing and divergences from default glycan processing give a window for immune recognition. Encouragingly, in a subset of individuals, broadly neutralizing antibodies (bNAbs) have been isolated that recognize these features and are protective in passive-transfer models. Here, we review the recent advances in our understanding of the glycan shield of HIV and outline the strategies that are being pursued to elicit glycan-binding bNAbs by vaccination.
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Affiliation(s)
- Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Gemma E. Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK
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28
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Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens. Molecules 2017; 22:molecules22020215. [PMID: 28146093 PMCID: PMC5572134 DOI: 10.3390/molecules22020215] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/24/2017] [Indexed: 01/10/2023] Open
Abstract
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This review summarizes these milestones that have pushed the field forward, allowing researchers to generate aptamers that can potentially be applied as therapeutic and diagnostic agents.
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29
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Abstract
Aptamers are nucleic acid-based scaffolds that can bind with high affinity to a variety of biological targets. Aptamers are identified from large DNA or RNA libraries through a process of directed molecular evolution (SELEX). Chemical modification of nucleic acids considerably increases the functional and structural diversity of aptamer libraries and substantially increases the affinity of the aptamers. Additionally, modified aptamers exhibit much greater resistance to biodegradation. The evolutionary selection of modified aptamers is conditioned by the possibility of the enzymatic synthesis and replication of non-natural nucleic acids. Wild-type or mutant polymerases and their non-natural nucleotide substrates that can support SELEX are highlighted in the present review. A focus is made on the efforts to find the most suitable type of nucleotide modifications and the engineering of new polymerases. Post-SELEX modification as a complementary method will be briefly considered as well.
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Affiliation(s)
- Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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30
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Lipi F, Chen S, Chakravarthy M, Rakesh S, Veedu RN. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies. RNA Biol 2016; 13:1232-1245. [PMID: 27715478 PMCID: PMC5207382 DOI: 10.1080/15476286.2016.1236173] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.
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Affiliation(s)
- Farhana Lipi
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Suxiang Chen
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Madhuri Chakravarthy
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Shilpa Rakesh
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Rakesh N Veedu
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
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31
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Bailey JK, Nguyen DN, Horiya S, Krauss IJ. Synthesis of multivalent glycopeptide conjugates that mimic an HIV epitope. Tetrahedron 2016; 72:6091-6098. [PMID: 28190897 PMCID: PMC5300091 DOI: 10.1016/j.tet.2016.07.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Recently, we reported a directed evolution method which enabled us to discover sequences of glycopeptides that bind with picomolar affinity to HIV antibody 2G12 and are of interest as HIV vaccine candidates. In this manuscript, we describe the syntheses of several of these large (~11-12 kDa) glycopeptides by a combination of fast flow peptide synthesis and click chemistry. We also discuss the optimization of their attachment to carrier protein CRM197, affording antigenic and immunogenic conjugates ready for animal vaccination.
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Affiliation(s)
| | | | - Satoru Horiya
- Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA
| | - Isaac J. Krauss
- Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA
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32
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Huang ML, Godula K. Nanoscale materials for probing the biological functions of the glycocalyx. Glycobiology 2016; 26:797-803. [PMID: 26916883 PMCID: PMC5018045 DOI: 10.1093/glycob/cww022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/31/2016] [Accepted: 02/16/2016] [Indexed: 12/23/2022] Open
Abstract
Glycans are among the most intriguing carriers of biological information in living systems. The structures of glycans not only convey the cells' physiological state, but also regulate cellular communication and responses by engaging receptors on neighboring cells and in the extracellular matrix. The assembly of simple monosaccharide building blocks into linear or branched oligo- and polysaccharides gives rise to a large repertoire of diverse glycan structures. Despite their structural complexity, individual glycans rarely engage their protein partners with high affinity. Yet, glycans modulate biological processes with exquisite selectivity and specificity. To correctly evaluate glycan interactions and their biological consequences, one needs to look beyond individual glycan structures and consider the entirety of the cell-surface landscape. There, glycans are presented on protein scaffolds, or are linked directly to membrane lipids, forming a complex, hierarchically organized network with specialized functions, called the glycocalyx. Nanoscale glycomaterials, which can mimic the various components of the glycocalyx, have been instrumental in revealing how the presentation of glycans can influence their biological functions. In this review, we wish to highlight some recent developments in this area, while placing emphasis on the applications of glycomaterials providing new insights into the mechanisms through which glycans mediate cellular functions.
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Affiliation(s)
- Mia L Huang
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0358, USA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0358, USA
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33
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Kong D, Yeung W, Hili R. Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates. ACS COMBINATORIAL SCIENCE 2016; 18:355-70. [PMID: 27275512 DOI: 10.1021/acscombsci.6b00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
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34
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Machida T, Winssinger N. One-Step Derivatization of Reducing Oligosaccharides for Rapid and Live-Cell-Compatible Chelation-Assisted CuAAC Conjugation. Chembiochem 2016; 17:811-5. [DOI: 10.1002/cbic.201600003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Takuya Machida
- Department of Organic Chemistry; NCCR Chemical Biology; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry; NCCR Chemical Biology; University of Geneva; 30 quai Ernest Ansermet 1211 Geneva Switzerland
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35
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Wang Z, Qin C, Hu J, Guo X, Yin J. Recent advances in synthetic carbohydrate-based human immunodeficiency virus vaccines. Virol Sin 2016; 31:110-7. [PMID: 26992403 DOI: 10.1007/s12250-015-3691-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/02/2016] [Indexed: 12/14/2022] Open
Abstract
An effective vaccine for human immunodeficiency virus (HIV) is urgently needed to prevent HIV infection and progression to acquired immune deficiency syndrome (AIDS). As glycosylation of viral proteins becomes better understood, carbohydrate-based antiviral vaccines against special viruses have attracted much attention. Significant efforts in carbohydrate synthesis and immunogenicity research have resulted in the development of multiple carbohydrate-based HIV vaccines. This review summarizes recent advances in synthetic carbohydrate-based vaccines design strategies and the applications of these vaccines in the prevention of HIV.
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Affiliation(s)
- Zhenyuan Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chunjun Qin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jing Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Wuxi Medical School, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqiang Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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36
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Liu CC, Zheng XJ, Ye XS. Broadly Neutralizing Antibody-Guided Carbohydrate-Based HIV Vaccine Design: Challenges and Opportunities. ChemMedChem 2016; 11:357-62. [PMID: 26762799 DOI: 10.1002/cmdc.201500498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 11/12/2022]
Abstract
The HIV envelope (Env) is heavily glycosylated, facilitating the spread and survival of HIV in many ways. Some potent broadly neutralizing antibodies (bnAbs) such as 2G12, PG9, PG16, and PGTs can recognize the conserved glycan residues on Env. The bnAbs, which often emerge after many years of chronic infection, provide insight into the vulnerability of HIV and can therefore guide the design of vaccines. Many carbohydrate-conjugated vaccines have been designed to induce bnAb-like antibodies, but none have yet been successful. The low antigenicity of these vaccines is one possible explanation. New strategies have been applied to obtain high-affinity antigens of glycan-dependent and other bnAbs. However, when used as immunogens in vivo, high-affinity antigens are still insufficient in eliciting bnAb-like antibodies. bnAbs generally possess some unusual features and may therefore be suppressed by the host immune system. In view of this situation, some immunization regimens based on the affinity maturation of antibodies have been tested. Herein we summarize recent studies into the design of carbohydrate-based HIV vaccines and some valuable experiences gained in work with other bnAb-based HIV vaccines.
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Affiliation(s)
- Chang-Cheng Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xiu-Jing Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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37
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Generation of Aptamers with an Expanded Chemical Repertoire. Molecules 2015; 20:16643-71. [PMID: 26389865 PMCID: PMC6332006 DOI: 10.3390/molecules200916643] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 01/03/2023] Open
Abstract
The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved or hitherto unknown properties. In this review, we discuss the nature of the functionalities appended to nucleoside triphosphates and their impact on selection experiments. The properties of the resulting modified aptamers will be described, particularly those integrated in the fields of biomolecular diagnostics, therapeutics, and in the expansion of genetic systems (XNAs).
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38
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Guo C, Watkins CP, Hili R. Sequence-Defined Scaffolding of Peptides on Nucleic Acid Polymers. J Am Chem Soc 2015; 137:11191-6. [DOI: 10.1021/jacs.5b07675] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Chun Guo
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
| | - Christopher P. Watkins
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602-2556, United States
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39
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Renders M, Miller E, Hollenstein M, Perrin D. A method for selecting modified DNAzymes without the use of modified DNA as a template in PCR. Chem Commun (Camb) 2015; 51:1360-2. [PMID: 25487111 DOI: 10.1039/c4cc07588a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Modified DNAzyme selections typically depend on recopying catalytically active modified DNA (mDNA) into cDNA in a PCR amplification step. However mDNA is often a poor template in PCR. Herein we propose a selection method in which the catalytically active, mDNA strand is covalently linked to the unmodified DNA template strand from which it was polymerized. Following selection, the unmodified DNA template is amplified in a PCR instead of the mDNA. This method circumvents the PCR amplification of mDNA.
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Affiliation(s)
- Marleen Renders
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T 1Z1, Canada.
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40
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Abstract
In vitro selection of nucleic acid aptamers, coined SELEX, has led to the discovery of novel therapeutics and aided in the structural and mechanistic understanding of many ligand-biomolecule interactions. A related method, selection with modified aptamers (SELMA), enables selection of DNA aptamers containing bases with a large modification that cannot undergo PCR. A key application of this method is the evolution of aptamers containing carbohydrate modifications. Carbohydrate-binding proteins normally require several copies of the carbohydrate moiety for strong recognition. Whereas it may be difficult to rationally design synthetic scaffolds that cluster glycans in the optimal spacing and orientation for target recognition, SELMA furnishes glycoaptamers with highly optimized glycan clustering, achieving low-nanomolar recognition. Although numerous applications can be envisioned, the protocols and discussions in this article describe procedures involved in applying SELMA to the discovery glycoDNAs that bind to the HIV broadly neutralizing antibody 2G12.
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Affiliation(s)
- J Sebastian Temme
- Department of Chemistry, Brandeis University, Waltham, Massachusetts
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, Waltham, Massachusetts
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41
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Novoa A, Winssinger N. DNA display of glycoconjugates to emulate oligomeric interactions of glycans. Beilstein J Org Chem 2015; 11:707-19. [PMID: 26113879 PMCID: PMC4462854 DOI: 10.3762/bjoc.11.81] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022] Open
Abstract
Glycans (carbohydrate portion of glycoproteins and glycolipids) frequently exert their function through oligomeric interactions involving multiple carbohydrate units. In efforts to recapitulate the diverse spatial arrangements of the carbohydrate units, assemblies based on hybridization of nucleic acid conjugates have been used to display simplified ligands with tailored interligand distances and valences. The programmability of the assemblies lends itself to a combinatorial display of multiple ligands. Recent efforts in the synthesis and applications of such conjugates are discussed.
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Affiliation(s)
- Alexandre Novoa
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland
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42
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Horiya S, MacPherson IS, Krauss IJ. Recent strategies targeting HIV glycans in vaccine design. Nat Chem Biol 2014; 10:990-9. [PMID: 25393493 PMCID: PMC4431543 DOI: 10.1038/nchembio.1685] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
Abstract
Although efforts to develop a vaccine against HIV have so far met with little success, recent studies of HIV-positive patients with strongly neutralizing sera have shown that the human immune system is capable of producing potent and broadly neutralizing antibodies (bnAbs), some of which neutralize up to 90% of HIV strains. These antibodies bind conserved vulnerable sites on the viral envelope glycoprotein gp120, and identification of these sites has provided exciting clues about the design of potentially effective vaccines. Carbohydrates have a key role in this field, as a large fraction of bnAbs bind carbohydrates or combinations of carbohydrate and peptide elements on gp120. Additionally, carbohydrates partially mask some peptide surfaces recognized by bnAbs. The use of engineered glycoproteins and other glycostructures as vaccines to elicit antibodies with broad neutralizing activity is therefore a key area of interest in HIV vaccine design.
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Affiliation(s)
- Satoru Horiya
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Iain S MacPherson
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Isaac J Krauss
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, USA
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43
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Chiodo F, Enríquez-Navas PM, Angulo J, Marradi M, Penadés S. Assembling different antennas of the gp120 high mannose-type glycans on gold nanoparticles provides superior binding to the anti-HIV antibody 2G12 than the individual antennas. Carbohydr Res 2014; 405:102-9. [PMID: 25573666 DOI: 10.1016/j.carres.2014.07.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 11/16/2022]
Abstract
In order to re-build Man9GlcNAc2 clusters of the HIV gp120 glycoprotein, ∼2 nm gold glyconanoparticles (GNPs) were coated with the synthetic partial structures of Man9, the tetramannoside Manα1-2Manα1-2Manα1-3Manα1- and the pentamannoside Manα1-2Manα1-3[Manα1-2Manα1-6]Manα1-. Their interactions with the anti-HIV broadly neutralizing antibody 2G12 were studied by surface plasmon resonance (SPR)-based biosensors and saturation transfer difference (STD)-NMR spectroscopy. A synergistic effect of the tetra- and pentamannosides multimerized on a same GNP was observed. The assembly of these antennas of the gp120 high-mannose type glycan on GNPs provided superior binding to the anti-HIV antibody 2G12 with respect to GNPs carrying only the individual oligomannosides. The results presented in this work provide new molecular information on the interactions between clusters of oligomannosides and 2G12 that could help in the design of a carbohydrate-based vaccine against HIV.
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Affiliation(s)
- Fabrizio Chiodo
- Laboratory of Glyconanotechnology, Biofunctional Nanomaterials Unit, CIC biomaGUNE, P° de Miramón 182, 28009 San Sebastian, Spain
| | - Pedro M Enríquez-Navas
- Laboratory of Glyconanotechnology, Biofunctional Nanomaterials Unit, CIC biomaGUNE, P° de Miramón 182, 28009 San Sebastian, Spain
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Marco Marradi
- Laboratory of Glyconanotechnology, Biofunctional Nanomaterials Unit, CIC biomaGUNE, P° de Miramón 182, 28009 San Sebastian, Spain; Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), P° de Miramón 182, 28009 San Sebastian, Spain
| | - Soledad Penadés
- Laboratory of Glyconanotechnology, Biofunctional Nanomaterials Unit, CIC biomaGUNE, P° de Miramón 182, 28009 San Sebastian, Spain; Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), P° de Miramón 182, 28009 San Sebastian, Spain.
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44
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Horiya S, Bailey JK, Temme JS, Guillen Schlippe YV, Krauss IJ. Directed evolution of multivalent glycopeptides tightly recognized by HIV antibody 2G12. J Am Chem Soc 2014; 136:5407-15. [PMID: 24645849 PMCID: PMC4004241 DOI: 10.1021/ja500678v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Herein,
we report a method for in vitro selection of multivalent
glycopeptides, combining mRNA display with incorporation of unnatural
amino acids and “click” chemistry. We have demonstrated
the use of this method to design potential glycopeptide vaccines against
HIV. From libraries of ∼1013 glycopeptides containing
multiple Man9 glycan(s), we selected variants that bind
to HIV broadly neutralizing antibody 2G12 with picomolar to low nanomolar
affinity. This is comparable to the strength of the natural 2G12–gp120
interaction, and is the strongest affinity achieved to date with constructs
containing 3–5 glycans. These glycopeptides are therefore of
great interest in HIV vaccine design.
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Affiliation(s)
- Satoru Horiya
- Department of Chemistry, Brandeis University , Waltham, Massachusetts 02454-9110, United States
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