1
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Kovalová A, Prouza V, Zavřel M, Hájek M, Dzijak R, Magdolenová A, Pohl R, Voburka Z, Parkan K, Vrabel M. Selection of Galectin-Binding Ligands from Synthetic Glycopeptide Libraries. Chempluschem 2024; 89:e202300567. [PMID: 37942669 DOI: 10.1002/cplu.202300567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
Galectins, a class of carbohydrate-binding proteins, play a crucial role in various physiological and disease processes. Therefore, the identification of ligands that efficiently bind these proteins could potentially lead to the development of new therapeutic compounds. In this study, we present a method that involves screening synthetic click glycopeptide libraries to identify lectin-binding ligands with low micromolar affinity. Our methodology, initially optimized using Concanavalin A, was subsequently applied to identify binders for the therapeutically relevant galectin 1. Binding affinities were assessed using various methods and showed that the selected glycopeptides exhibited enhanced binding potency to the target lectins compared to the starting sugar moieties. This approach offers an alternative means of discovering galectin-binding ligands as well as other carbohydrate-binding proteins, which are considered important therapeutic targets.
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Affiliation(s)
- Anna Kovalová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Vít Prouza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, Prague, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Miroslav Hájek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Alžbeta Magdolenová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Zdeněk Voburka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
| | - Kamil Parkan
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, Prague, Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague, Czech Republic
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2
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Bibekar P, Krapp L, Peraro MD. PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces. J Chem Theory Comput 2024; 20:2985-2991. [PMID: 38602504 PMCID: PMC11044267 DOI: 10.1021/acs.jctc.3c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
The Protein Structure Transformer (PeSTo), a geometric transformer, has exhibited exceptional performance in predicting protein-protein binding interfaces and distinguishing interfaces with nucleic acids, lipids, small molecules, and ions. In this study, we introduce PeSTo-Carbs, an extension of PeSTo specifically engineered to predict protein-carbohydrate binding interfaces. We evaluate the performance of this approach using independent test sets and compare them with those of previous methods. Furthermore, we highlight the model's capability to specialize in predicting interfaces involving cyclodextrins, a biologically and pharmaceutically significant class of carbohydrates. Our method consistently achieves remarkable accuracy despite the scarcity of available structural data for cyclodextrins.
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Affiliation(s)
- Parth Bibekar
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Lucien Krapp
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss
Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss
Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
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3
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Zhang YW, Lin NP, Guo X, Szabo-Fresnais N, Ortoleva PJ, Chou DHC. Omniligase-1-Mediated Phage-Peptide Library Modification and Insulin Engineering. ACS Chem Biol 2024; 19:506-515. [PMID: 38266161 DOI: 10.1021/acschembio.3c00685] [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: 01/26/2024]
Abstract
Chemical and enzymatic modifications of peptide-displayed libraries have been successfully employed to expand the phage display library. However, the requirement of specific epitopes and scaffolds has limited the scope of protein engineering using phage display. In this study, we present a novel approach utilizing omniligase-1-mediated selective and specific ligation on the phage pIII protein, offering a high conversion rate and compatibility with commercially available phage libraries. We applied this method to perform high-throughput engineering of insulin analogues with randomized B chain C-terminal regions. Insulin analogues with different B chain C-terminal segments were selected and exhibited biological activity equivalent to that of human insulin. Molecular dynamics studies of insulin analogues revealed a novel interaction between the insulin B27 residue and insulin receptor L1 domain. In summary, our findings highlight the potential of omniligase-1-mediated phage display in the development and screening of disulfide-rich peptides and proteins. This approach holds promise for the creation of novel insulin analogues with enhanced therapeutic properties and exhibits potential for the development of other therapeutic compounds.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nai-Pin Lin
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
| | - Xu Guo
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicolas Szabo-Fresnais
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Peter J Ortoleva
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
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4
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Lopez-Morales J, Vanella R, Appelt EA, Whillock S, Paulk AM, Shusta EV, Hackel BJ, Liu CC, Nash MA. Protein Engineering and High-Throughput Screening by Yeast Surface Display: Survey of Current Methods. SMALL SCIENCE 2023; 3:2300095. [PMID: 39071103 PMCID: PMC11271970 DOI: 10.1002/smsc.202300095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024] Open
Abstract
Yeast surface display (YSD) is a powerful tool in biotechnology that links genotype to phenotype. In this review, the latest advancements in protein engineering and high-throughput screening based on YSD are covered. The focus is on innovative methods for overcoming challenges in YSD in the context of biotherapeutic drug discovery and diagnostics. Topics ranging from titrating avidity in YSD using transcriptional control to the development of serological diagnostic assays relying on serum biopanning and mitigation of unspecific binding are covered. Screening techniques against nontraditional cellular antigens, such as cell lysates, membrane proteins, and extracellular matrices are summarized and techniques are further delved into for expansion of the chemical repertoire, considering protein-small molecule hybrids and noncanonical amino acid incorporation. Additionally, in vivo gene diversification and continuous evolution in yeast is discussed. Collectively, these techniques enhance the diversity and functionality of engineered proteins isolated via YSD, broadening the scope of applications that can be addressed. The review concludes with future perspectives and potential impact of these advancements on protein engineering. The goal is to provide a focused summary of recent progress in the field.
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Affiliation(s)
- Joanan Lopez-Morales
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland; Swiss Nanoscience Institute, University of Basel, Basel 4056, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Elizabeth A Appelt
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah Whillock
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alexandra M Paulk
- Program in Mathematical, Computational, and Systems Biology, University of California, Irvine, CA 92697-2280, USA; Center for Synthetic Biology, University of California, Irvine, CA 92697, USA; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benjamin J Hackel
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chang C Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA; Center for Synthetic Biology, University of California, Irvine, CA 92697, USA; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Michael A Nash
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland; Swiss Nanoscience Institute, University of Basel, Basel 4056, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
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5
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Zhang YW, Zheng N, Chou DHC. Serine-mediated hydrazone ligation displaying insulin-like peptides on M13 phage pIII. Org Biomol Chem 2023; 21:8902-8909. [PMID: 37905463 DOI: 10.1039/d3ob01487h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Phage display has emerged as a tool for the discovery of therapeutic antibodies and proteins. However, the effective display and engineering of structurally complex proteins, such as insulin, pose significant challenges due to the sequence of insulin, which is composed of two peptide chains linked by three disulfide bonds. In this study, we developed a new approach for the display of insulin-like peptides on M13 phage pIII, employing N-terminal serine-mediated hydrazone ligation. The insulin-displaying phage retains the biological binding affinity of human insulin. To address the viability loss after ligation, we introduced a trypsin-cleavable spacer on pIII, enabling insulin-displayed phage library selection. This method offers a general pathway for the display of structurally complex proteins on pIII, enhancing the practicality of selecting chemically modified phage libraries and opening avenues for the engineering of new insulin analogs for the treatment of diabetes by using phage display.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nan Zheng
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA.
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6
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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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7
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Leusmann S, Ménová P, Shanin E, Titz A, Rademacher C. Glycomimetics for the inhibition and modulation of lectins. Chem Soc Rev 2023; 52:3663-3740. [PMID: 37232696 PMCID: PMC10243309 DOI: 10.1039/d2cs00954d] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 05/27/2023]
Abstract
Carbohydrates are essential mediators of many processes in health and disease. They regulate self-/non-self- discrimination, are key elements of cellular communication, cancer, infection and inflammation, and determine protein folding, function and life-times. Moreover, they are integral to the cellular envelope for microorganisms and participate in biofilm formation. These diverse functions of carbohydrates are mediated by carbohydrate-binding proteins, lectins, and the more the knowledge about the biology of these proteins is advancing, the more interfering with carbohydrate recognition becomes a viable option for the development of novel therapeutics. In this respect, small molecules mimicking this recognition process become more and more available either as tools for fostering our basic understanding of glycobiology or as therapeutics. In this review, we outline the general design principles of glycomimetic inhibitors (Section 2). This section is then followed by highlighting three approaches to interfere with lectin function, i.e. with carbohydrate-derived glycomimetics (Section 3.1), novel glycomimetic scaffolds (Section 3.2) and allosteric modulators (Section 3.3). We summarize recent advances in design and application of glycomimetics for various classes of lectins of mammalian, viral and bacterial origin. Besides highlighting design principles in general, we showcase defined cases in which glycomimetics have been advanced to clinical trials or marketed. Additionally, emerging applications of glycomimetics for targeted protein degradation and targeted delivery purposes are reviewed in Section 4.
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Affiliation(s)
- Steffen Leusmann
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Petra Ménová
- University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Elena Shanin
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
| | - Alexander Titz
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
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8
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Kugler M, Hadzima M, Dzijak R, Rampmaier R, Srb P, Vrzal L, Voburka Z, Majer P, Řezáčová P, Vrabel M. Identification of specific carbonic anhydrase inhibitors via in situ click chemistry, phage-display and synthetic peptide libraries: comparison of the methods and structural study. RSC Med Chem 2023; 14:144-153. [PMID: 36760748 PMCID: PMC9890587 DOI: 10.1039/d2md00330a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The development of highly active and selective enzyme inhibitors is one of the priorities of medicinal chemistry. Typically, various high-throughput screening methods are used to find lead compounds from a large pool of synthetic compounds, and these are further elaborated and structurally refined to achieve the desired properties. In an effort to streamline this complex and laborious process, new selection strategies based on different principles have recently emerged as an alternative. Herein, we compare three such selection strategies with the aim of identifying potent and selective inhibitors of human carbonic anhydrase II. All three approaches, in situ click chemistry, phage-display libraries and synthetic peptide libraries, led to the identification of more potent inhibitors when compared to the parent compounds. In addition, one of the inhibitor-peptide conjugates identified from the phage libraries showed greater than 100-fold selectivity for the enzyme isoform used for the compound selection. In an effort to rationalize the binding properties of the conjugates, we performed detailed crystallographic and NMR structural analysis, which revealed the structural basis of the compound affinity towards the enzyme and led to the identification of a novel exosite that could be utilized in the development of isoform specific inhibitors.
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Affiliation(s)
- Michael Kugler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Martin Hadzima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University Albertov 6 12800 Praha 2 Czech Republic
| | - Rastislav Dzijak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Robert Rampmaier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Zdeněk Voburka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 16000 Prague Czech Republic
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9
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Ng S, Brueckner AC, Bahmanjah S, Deng Q, Johnston JM, Ge L, Duggal R, Habulihaz B, Barlock B, Ha S, Sadruddin A, Yeo C, Strickland C, Peier A, Henry B, Sherer EC, Partridge AW. Discovery and Structure-Based Design of Macrocyclic Peptides Targeting STUB1. J Med Chem 2022; 65:9789-9801. [PMID: 35853179 DOI: 10.1021/acs.jmedchem.2c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent evidence suggests that deletion of STUB1─a pivotal negative regulator of interferon-γ sensing─may potentially clear malignant cells. However, current studies rely primarily on genetic approaches, as pharmacological inhibitors of STUB1 are lacking. Identifying a tool compound will be a step toward validating the target in a broader therapeutic sense. Herein, screening more than a billion macrocyclic peptides resulted in STUB1 binders, which were further optimized by a structure-enabled in silico design. The strategy to replace the macrocyclic peptides' hydrophilic and solvent-exposed region with a hydrophobic scaffold improved cellular permeability while maintaining the binding conformation. Further substitution of the permeability-limiting terminal aspartic acid with a tetrazole bioisostere retained the binding to a certain extent while improving permeability, suggesting a path forward. Although not optimal for cellular study, the current lead provides a valuable template for further development into selective tool compounds for STUB1 to enable target validation.
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Affiliation(s)
- Simon Ng
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Soheila Bahmanjah
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jennifer M Johnston
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lan Ge
- Cell Sciences Innovation, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ruchia Duggal
- ADME Group 2, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Bahanu Habulihaz
- PPDM ADME Transporters & In Vitro Technology, Merck & Co., Inc., 126 East Lincoln Ave, Rahway, New Jersey 07065, United States
| | - Benjamin Barlock
- ADME Group 2, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Sookhee Ha
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ahmad Sadruddin
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Constance Yeo
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Corey Strickland
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Andrea Peier
- Screening & Compound Profiling, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian Henry
- Quantitative Biosciences, MSD, 8 Biomedical Grove, Singapore 138665
| | - Edward C Sherer
- Computational & Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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10
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Chen FJ, Zheng M, Nobile V, Gao J. Fast and Cysteine-Specific Modification of Peptides, Proteins and Bacteriophage Using Chlorooximes. Chemistry 2022; 28:e202200058. [PMID: 35167137 PMCID: PMC8986619 DOI: 10.1002/chem.202200058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 12/21/2022]
Abstract
This work reports a novel chlorooxime mediated modification of native peptides and proteins under physiologic conditions. This method features fast reaction kinetics (apparent k2 =306±4 M-1 s-1 for GSH) and exquisite selectivity for cysteine residues. This cysteine conjugation reaction can be carried out with just single-digit micromolar concentrations of the labeling reagent. The conjugates show high stability towards acid, base, and external thiol nucleophiles. A nitrile oxide species generated in situ is likely involved as the key intermediate. Furthermore, a bis-chlorooxime reagent is synthesized to enable facile Cys-Cys stapling in native peptides and proteins. This highly efficient cysteine conjugation and stapling was further implemented on bacteriophage to construct chemically modified phage libraries.
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Affiliation(s)
- Fa-Jie Chen
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Mengmeng Zheng
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Vincent Nobile
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Jianmin Gao
- Department of Chemistry Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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11
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Engineered protein-small molecule conjugates empower selective enzyme inhibition. Cell Chem Biol 2022; 29:328-338.e4. [PMID: 34363759 PMCID: PMC8807807 DOI: 10.1016/j.chembiol.2021.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
Potent, specific ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. In this platform, a fibronectin protein library is displayed on yeast with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enrich specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibit potent, specific inhibition of carbonic anhydrase isoforms with efficacy superior to that of acetazolamide or protein alone, including an 80-fold specificity increase and 9-fold potency gain. PriSMs are engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveal platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.
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12
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Wen P, Jia P, Fan Q, McCarty BJ, Tang W. Streamlined Iterative Assembly of Thio-Oligosaccharides by Aqueous S-Glycosylation of Diverse Deoxythio Sugars. CHEMSUSCHEM 2022; 15:e202102483. [PMID: 34911160 PMCID: PMC9100857 DOI: 10.1002/cssc.202102483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/13/2021] [Indexed: 06/14/2023]
Abstract
A streamlined iterative assembly of thio-oligosaccharides was developed by aqueous glycosylation. Facile syntheses of various deoxythio sugars with the sulfur on different positions from commercially available starting materials were described. These syntheses featured efficient chemical methods including our recently reported BTM-catalyzed site-selective acylation. The resulting deoxythio sugars could then be used for the Ca(OH)2 -promoted protecting group-free S-glycosylation in water at room temperature. The aqueous glycosylation reaction proceeded smoothly to afford the corresponding 1,2-trans S-glycosides in good yields with high chemo- and stereoselectivity. An appropriate choice of protecting groups for the thiol in the glycosyl donor was necessary for the development of iterative synthesis of thio-oligosaccharides. The aqueous glycosylation was then applied to the synthesis of a trimannoside moiety of N-linked glycans core region.
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Affiliation(s)
- Peng Wen
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Peijing Jia
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Qiuhua Fan
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bethany J McCarty
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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13
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Richards SJ, Gibson MI. Toward Glycomaterials with Selectivity as Well as Affinity. JACS AU 2021; 1:2089-2099. [PMID: 34984416 PMCID: PMC8717392 DOI: 10.1021/jacsau.1c00352] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Indexed: 05/08/2023]
Abstract
Multivalent glycosylated materials (polymers, surfaces, and particles) often show high affinity toward carbohydrate binding proteins (e.g., lectins) due to the nonlinear enhancement from the cluster glycoside effect. This affinity gain has potential in applications from diagnostics, biosensors, and targeted delivery to anti-infectives and in an understanding of basic glycobiology. This perspective highlights the question of selectivity, which is less often addressed due to the reductionist nature of glycomaterials and the promiscuity of many lectins. The use of macromolecular features, including architecture, heterogeneous ligand display, and the installation of non-natural glycans, to address this challenge is discussed, and examples of selectivity gains are given.
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Affiliation(s)
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Medical School, University of Warwick, Coventry CV4 7AL, U.K.
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14
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Jang H, Lee C, Hwang Y, Lee SJ. Concanavalin A: coordination diversity to xenobiotic metal ions and biological consequences. Dalton Trans 2021; 50:17817-17831. [PMID: 34806716 DOI: 10.1039/d1dt03501k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding ability of lectins has gained attention owing to the carbohydrate-specific interactions of these proteins. Such interactions can be applied to diverse fields of biotechnology, including the detection, isolation, and concentration of biological target molecules. The physiological aspects of the lectin concanavalin A (ConA) have been intensively studied through structural and functional investigations. X-ray crystallography studies have proven that ConA has two β-sheets and a short α-helix and that it exists in the form of a metalloprotein containing Mn2+ and Ca2+. These heterometals are coordinated with side chains located in a metal-coordinated domain (MCD), and they affect the structural environment in the carbohydrate-binding domain (CBD), which interacts with carbohydrates through hydrogen bonds. Recent studies have shown that ConA can regulate biophysical interactions with glycoproteins in virus envelopes because it specifically interacts with diverse polysaccharides through its CBD (Tyr, Asn, Asp, and Arg residues positioned next to the MCD). Owing to their protein-protein interaction abilities, ConA can form diverse self-assembled complexes including monomers, dimers, trimers, and tetramers, thus affording unique results in different applications. In this regard, herein, we present a review of the structural modifications in ConA through metal-ion coordination and their effect on complex formation. In recent approaches, ConA has been applied for viral protein detection, on the basis of the interactions of ConA. These aspects indicate that lectins should be thoroughly investigated with respect to their biophysical interactions, for avoiding unexpected changes in their interaction abilities.
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Affiliation(s)
- Hara Jang
- Department of Chemistry and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Chaemin Lee
- Department of Chemistry and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Yunha Hwang
- Department of Chemistry and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Seung Jae Lee
- Department of Chemistry and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea.
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15
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Wong JYK, Mukherjee R, Miao J, Bilyk O, Triana V, Miskolzie M, Henninot A, Dwyer JJ, Kharchenko S, Iampolska A, Volochnyuk DM, Lin YS, Postovit LM, Derda R. Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL. Chem Sci 2021; 12:9694-9703. [PMID: 34349940 PMCID: PMC8294009 DOI: 10.1039/d1sc01916c] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
In this manuscript, we developed a two-fold symmetric linchpin (TSL) that converts readily available phage-displayed peptides libraries made of 20 common amino acids to genetically-encoded libraries of bicyclic peptides displayed on phage. TSL combines an aldehyde-reactive group and two thiol-reactive groups; it bridges two side chains of cysteine [C] with an N-terminal aldehyde group derived from the N-terminal serine [S], yielding a novel bicyclic topology that lacks a free N-terminus. Phage display libraries of SX1CX2X3X4X5X6X7C sequences, where X is any amino acid but Cys, were converted to a library of bicyclic TSL-[S]X1[C]X2X3X4X5X6X7[C] peptides in 45 ± 15% yield. Using this library and protein morphogen NODAL as a target, we discovered bicyclic macrocycles that specifically antagonize NODAL-induced signaling in cancer cells. At a 10 μM concentration, two discovered bicyclic peptides completely suppressed NODAL-induced phosphorylation of SMAD2 in P19 embryonic carcinoma cells. The TSL-[S]Y[C]KRAHKN[C] bicycle inhibited NODAL-induced proliferation of NODAL-TYK-nu ovarian carcinoma cells with apparent IC50 of 1 μM. The same bicycle at 10 μM concentration did not affect the growth of the control TYK-nu cells. TSL-bicycles remained stable over the course of the 72 hour-long assays in a serum-rich cell-culture medium. We further observed general stability in mouse serum and in a mixture of proteases (Pronase™) for 21 diverse bicyclic macrocycles of different ring sizes, amino acid sequences, and cross-linker geometries. TSL-constrained peptides to expand the previously reported repertoire of phage-displayed bicyclic architectures formed by cross-linking Cys side chains. We anticipate that it will aid the discovery of proteolytically stable bicyclic inhibitors for a variety of protein targets.
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Affiliation(s)
- Jeffrey Y-K Wong
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Olena Bilyk
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | | | - John J Dwyer
- Ferring Research Institute San Diego California 92121 USA
| | | | - Anna Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University Medford MA 02155 USA
| | - Lynne-Marie Postovit
- Department of Experimental Oncology, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
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16
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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17
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Ekanayake AI, Sobze L, Kelich P, Youk J, Bennett NJ, Mukherjee R, Bhardwaj A, Wuest F, Vukovic L, Derda R. Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores. J Am Chem Soc 2021; 143:5497-5507. [PMID: 33784084 DOI: 10.1021/jacs.1c01186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs "early stage" incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts peptide libraries displayed on phage to 1,3-diketone bearing macrocyclic peptides (DKMP): shelf-stable precursors for Knorr pyrazole synthesis. Ligation of diverse hydrazine derivatives onto DKMP libraries displayed on phage that carries silent DNA-barcodes yields macrocyclic libraries in which the amino acid sequence and the pharmacophore are encoded by DNA. Selection of this library against carbonic anhydrase enriched macrocycles with benzenesulfonamide pharmacophore and nanomolar Kd. The methodology described in this manuscript can graft diverse pharmacophores into many existing genetically encoded phage libraries and significantly increase the value of such libraries in molecular discoveries.
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Affiliation(s)
- Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Lena Sobze
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Jihea Youk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Nicholas J Bennett
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Atul Bhardwaj
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Frank Wuest
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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18
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Islam M, Kehoe HP, Lissoos JB, Huang M, Ghadban CE, Sánchez GB, Lane HZ, Van Deventer JA. Chemical Diversification of Simple Synthetic Antibodies. ACS Chem Biol 2021; 16:344-359. [PMID: 33482061 PMCID: PMC8096149 DOI: 10.1021/acschembio.0c00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibodies possess properties that make them valuable as therapeutics, diagnostics, and basic research tools. However, antibody chemical reactivity and covalent antigen binding are constrained, or even prevented, by the narrow range of chemistries encoded in canonical amino acids. In this work, we investigate strategies for leveraging an expanded range of chemical functionality using yeast displayed antibodies containing noncanonical amino acids (ncAAs) in or near antibody complementarity determining regions (CDRs). To enable systematic characterization of the effects of ncAA incorporation on antibody function, we first investigated whether diversification of a single antibody loop would support the isolation of binding clones against immunoglobulins from three species. We constructed and screened a billion-member library containing canonical amino acid diversity and loop length diversity only within the third complementarity determining region of the heavy chain (CDR-H3). Isolated clones exhibited moderate affinities (double- to triple-digit nanomolar affinities) and, in several cases, single-species specificity, confirming that antibody specificity can be mediated by a single CDR. This constrained diversity enabled the utilization of additional CDRs for the installation of chemically reactive and photo-cross-linkable ncAAs. Binding studies of ncAA-substituted antibodies revealed that ncAA incorporation is reasonably well tolerated, with observed changes in affinity occurring as a function of ncAA side chain identity, substitution site, and the ncAA incorporation machinery used. Multiple azide-containing ncAAs supported copper-catalyzed azide-alkyne cycloaddition (CuAAC) and strain-promoted azide-alkyne cycloaddition (SPAAC) without the abrogation of binding function. Similarly, several alkyne substitutions facilitated CuAAC without the apparent disruption of binding. Finally, antibodies substituted with a photo-cross-linkable ncAA were evaluated for ultraviolet-mediated cross-linking on the yeast surface. Competition-based assays revealed position-dependent covalent linkages, strongly suggesting successful cross-linking. Key findings regarding CuAAC reactions and photo-cross-linking on the yeast surface were confirmed using soluble forms of ncAA-substituted clones. The consistency of findings on the yeast surface and in solution suggest that chemical diversification can be incorporated into yeast display screening approaches. Taken together, our results highlight the power of integrating the use of yeast display and ncAAs in search of proteins with "chemically augmented" binding functions. This includes strategies for systematically introducing small molecule functionality within binding protein structures and evaluating protein-based covalent target binding. The efficient preparation and chemical diversification of antibodies on the yeast surface open up new possibilities for discovering "drug-like" protein leads in high throughput.
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Affiliation(s)
- Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Jacob B. Lissoos
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Manjie Huang
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Christopher E. Ghadban
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Greg B. Sánchez
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Hanan Z. Lane
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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19
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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20
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Hegedüs Z, Hóbor F, Shoemark DK, Celis S, Lian LY, Trinh CH, Sessions RB, Edwards TA, Wilson AJ. Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Chem Sci 2021; 12:2286-2293. [PMID: 34163995 PMCID: PMC8179271 DOI: 10.1039/d0sc05694d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.
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Affiliation(s)
- Zsófia Hegedüs
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Deborah K Shoemark
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Sergio Celis
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Lu-Yun Lian
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool Liverpool L69 3BX UK
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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21
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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22
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Tang JSJ, Schade K, Tepper L, Chea S, Ziegler G, Rosencrantz RR. Optimization of the Microwave Assisted Glycosylamines Synthesis Based on a Statistical Design of Experiments Approach. Molecules 2020; 25:E5121. [PMID: 33158070 PMCID: PMC7663175 DOI: 10.3390/molecules25215121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Glycans carry a vast range of functions in nature. Utilizing their properties and functions in form of polymers, coatings or glycan derivatives for various applications makes the synthesis of modified glycans crucial. Since amines are easy to modify for subsequent reactions, we investigated regioselective amination conditions of different saccharides. Amination reactions were performed according to Kochetkov and Likhoshertov and accelerated by microwave irradiation. We optimized the synthesis of glycosylamines for N-acetyl-d-galactosamine, d-lactose, d-glucuronic acid and l-(-)-fucose using the design of experiments (DoE) approach. DoE enables efficient optimization with limited number of experimental data. A DoE software generated a set of experiments where reaction temperature, concentration of carbohydrate, nature of aminating agent and solvent were investigated. We found that the synthesis of glycosylamines significantly depends on the nature of the carbohydrate and on the reaction temperature. There is strong indication that high temperatures are favored for the amination reaction.
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Affiliation(s)
- Jo Sing Julia Tang
- Fraunhofer Institute for Applied Polymer Research IAP, Biofunctionalized Materials and (Glyco) Biotechnology, Geiselbergstr. 69, 14476 Potsdam, Germany; (J.S.J.T.); (K.S.); (S.C.); (G.Z.)
| | - Kristin Schade
- Fraunhofer Institute for Applied Polymer Research IAP, Biofunctionalized Materials and (Glyco) Biotechnology, Geiselbergstr. 69, 14476 Potsdam, Germany; (J.S.J.T.); (K.S.); (S.C.); (G.Z.)
| | - Lucas Tepper
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany;
| | - Sany Chea
- Fraunhofer Institute for Applied Polymer Research IAP, Biofunctionalized Materials and (Glyco) Biotechnology, Geiselbergstr. 69, 14476 Potsdam, Germany; (J.S.J.T.); (K.S.); (S.C.); (G.Z.)
| | - Gregor Ziegler
- Fraunhofer Institute for Applied Polymer Research IAP, Biofunctionalized Materials and (Glyco) Biotechnology, Geiselbergstr. 69, 14476 Potsdam, Germany; (J.S.J.T.); (K.S.); (S.C.); (G.Z.)
| | - Ruben R. Rosencrantz
- Fraunhofer Institute for Applied Polymer Research IAP, Biofunctionalized Materials and (Glyco) Biotechnology, Geiselbergstr. 69, 14476 Potsdam, Germany; (J.S.J.T.); (K.S.); (S.C.); (G.Z.)
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23
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Iannuzzelli JA, Fasan R. Expanded toolbox for directing the biosynthesis of macrocyclic peptides in bacterial cells. Chem Sci 2020; 11:6202-6208. [PMID: 32953014 PMCID: PMC7480269 DOI: 10.1039/d0sc01699c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
A new suite of unnatural amino acids is reported for directing the biosynthesis of genetically encoded macrocyclic peptides in live bacteria.
The macrocyclization of recombinant polypeptides by means of genetically encodable non-canonical amino acids has recently provided an attractive strategy for the screening and discovery of macrocyclic peptide inhibitors of protein–protein interactions. Here, we report the development of an expanded suite of electrophilic unnatural amino acids (eUAAs) useful for directing the biosynthesis of genetically encoded thioether-bridged macrocyclic peptides in bacterial cells (E. coli). These reagents are shown to provide efficient access to a broad range of macrocyclic peptide scaffolds spanning from 2 to 20 amino acid residues, with the different eUAAs offering complementary reactivity profiles toward mediating short- vs. long-range macrocyclizations. Swapping of the eUAA cyclization module in a cyclopeptide inhibitor of streptavidin and Keap1 led to compounds with markedly distinct binding affinity toward the respective target proteins, highlighting the effectiveness of this strategy toward tuning the structural and functional properties of bioactive macrocyclic peptides. The peptide cyclization strategies reported here expand opportunities for the combinatorial biosynthesis of natural product-like peptide macrocycles in bacterial cells or in combination with display platforms toward the discovery of selective agents capable of targeting proteins and protein-mediated interactions.
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Affiliation(s)
- Jacob A Iannuzzelli
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA .
| | - Rudi Fasan
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA .
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24
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Jégouzo SAF, Nelson C, Hardwick T, Wong STA, Lau NKK, Neoh GKE, Castellanos-Rueda R, Huang Z, Mignot B, Hirdaramani A, Howitt A, Frewin K, Shen Z, Fox RJ, Wong R, Ando M, Emony L, Zhu H, Holder A, Werling D, Krishnan N, Robertson BD, Clements A, Taylor ME, Drickamer K. Mammalian lectin arrays for screening host-microbe interactions. J Biol Chem 2020; 295:4541-4555. [PMID: 32094229 PMCID: PMC7135977 DOI: 10.1074/jbc.ra120.012783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
Many members of the C-type lectin family of glycan-binding receptors have been ascribed roles in the recognition of microorganisms and serve as key receptors in the innate immune response to pathogens. Other mammalian receptors have become targets through which pathogens enter target cells. These receptor roles have often been documented with binding studies involving individual pairs of receptors and microorganisms. To provide a systematic overview of interactions between microbes and the large complement of C-type lectins, here we developed a lectin array and suitable protocols for labeling of microbes that could be used to probe this array. The array contains C-type lectins from cow, chosen as a model organism of agricultural interest for which the relevant pathogen–receptor interactions have not been previously investigated in detail. Screening with yeast cells and various strains of both Gram-positive and -negative bacteria revealed distinct binding patterns, which in some cases could be explained by binding to lipopolysaccharides or capsular polysaccharides, but in other cases they suggested the presence of novel glycan targets on many of the microorganisms. These results are consistent with interactions previously ascribed to the receptors, but they also highlight binding to additional sugar targets that have not previously been recognized. Our findings indicate that mammalian lectin arrays represent unique discovery tools for identifying both novel ligands and new receptor functions.
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Affiliation(s)
- Sabine A F Jégouzo
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Conor Nelson
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Thomas Hardwick
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - S T Angel Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Noel Kuan Kiat Lau
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Gaik Kin Emily Neoh
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Zhiyao Huang
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Benjamin Mignot
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Aanya Hirdaramani
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Annie Howitt
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kathryn Frewin
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zheng Shen
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rhys J Fox
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rachel Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Momoko Ando
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lauren Emony
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Henderson Zhu
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Angela Holder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom
| | - Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom
| | - Nitya Krishnan
- Department of Infectious Disease and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Brian D Robertson
- Department of Infectious Disease and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Abigail Clements
- Department of Life Sciences and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Maureen E Taylor
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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25
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He B, Dzisoo AM, Derda R, Huang J. Development and Application of Computational Methods in Phage Display Technology. Curr Med Chem 2020; 26:7672-7693. [PMID: 29956612 DOI: 10.2174/0929867325666180629123117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/08/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. METHODS We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. RESULTS We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. CONCLUSION The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.
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Affiliation(s)
- Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.,School of Medicine, Guizhou University, Guiyang 550025, China
| | - Anthony Mackitz Dzisoo
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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26
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Gordon CKL, Wu D, Pusuluri A, Feagin TA, Csordas AT, Eisenstein MS, Hawker CJ, Niu J, Soh HT. Click-Particle Display for Base-Modified Aptamer Discovery. ACS Chem Biol 2019; 14:2652-2662. [PMID: 31532184 PMCID: PMC6929039 DOI: 10.1021/acschembio.9b00587] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Base-modified aptamers
that incorporate non-natural chemical moieties
can achieve greatly improved affinity and specificity relative to
natural DNA or RNA aptamers. However, conventional methods for generating
base-modified aptamers require considerable expertise and resources.
In this work, we have accelerated and generalized the process of generating
base-modified aptamers by combining a click-chemistry strategy with
a fluorescence-activated cell sorting (FACS)-based screening methodology
that measures the affinity and specificity of individual aptamers
at a throughput of ∼107 per hour. Our “click-particle
display (PD)” strategy offers many advantages. First, almost
any chemical modification can be introduced with a commercially available
polymerase. Second, click-PD can screen vast numbers of individual
aptamers on the basis of quantitative on- and off-target binding measurements
to simultaneously achieve high affinity and specificity. Finally,
the increasing availability of FACS instrumentation in academia and
industry allows for easy adoption of click-PD in a broader scientific
community. Using click-PD, we generated a boronic acid-modified aptamer
with ∼1 μM affinity for epinephrine, a target for which
no aptamer has been reported to date. We subsequently generated a
mannose-modified aptamer with nanomolar affinity for the lectin concanavalin
A (Con A). The strong affinity of both aptamers is fundamentally dependent
upon the presence of chemical modifications, and we show that their
removal essentially eliminates aptamer binding. Importantly, our Con
A aptamer exhibited exceptional specificity, with minimal binding
to other structurally similar lectins. Finally, we show that our aptamer
has remarkable biological activity. Indeed, this aptamer is the most
potent inhibitor of Con A-mediated hemagglutination reported to date.
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Affiliation(s)
| | | | | | | | | | | | | | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Hyongsok Tom Soh
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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27
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Keller BG, Rademacher C. Allostery in C-type lectins. Curr Opin Struct Biol 2019; 62:31-38. [PMID: 31838280 DOI: 10.1016/j.sbi.2019.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
C-type lectins are the largest and most diverse family of mammalian carbohydrate-binding proteins. They share a common protein fold, which provides the unifying basis for calcium-mediated carbohydrate recognition. Their involvement in a multitude of biological functions is remarkable. Here, we review the variety of tasks these lectins are involved in alongside with the structural demands on the overall protein architecture. Subtle changes of the protein structure are implemented to cope with such diverse functional requirements. The presence of a high level of structural dynamics over a broad palette of time scales is paired with the presence of secondary binding sites and allosteric coordination of remote sites and renders this lectin fold a highly adaptable scaffold.
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Affiliation(s)
- Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Christoph Rademacher
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.
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28
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Valverde P, Ardá A, Reichardt NC, Jiménez-Barbero J, Gimeno A. Glycans in drug discovery. MEDCHEMCOMM 2019; 10:1678-1691. [PMID: 31814952 PMCID: PMC6839814 DOI: 10.1039/c9md00292h] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 02/06/2023]
Abstract
Glycans are key players in many biological processes. They are essential for protein folding and stability and act as recognition elements in cell-cell and cell-matrix interactions. Thus, being at the heart of medically relevant biological processes, glycans have come onto the scene and are considered hot spots for biomedical intervention. The progress in biophysical techniques allowing access to an increasing molecular and structural understanding of these processes has led to the development of effective therapeutics. Indeed, strategies aimed at designing glycomimetics able to block specific lectin-carbohydrate interactions, carbohydrate-based vaccines mimicking self- and non-self-antigens as well as the exploitation of the therapeutic potential of glycosylated antibodies are being pursued. In this mini-review the most prominent contributions concerning recurrent diseases are highlighted, including bacterial and viral infections, cancer or immune-related pathologies, which certainly show the great promise of carbohydrates in drug discovery.
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Affiliation(s)
- Pablo Valverde
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
| | - Ana Ardá
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
| | | | - Jesús Jiménez-Barbero
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
- Ikerbasque , Basque Foundation for Science , 48013 Bilbao , Bizkaia , Spain
- Department of Organic Chemistry II , University of the Basque Country , UPV/EHU , 48940 Leioa , Bizkaia , Spain
| | - Ana Gimeno
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
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29
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Chao L, Jongkees S. High-Throughput Approaches in Carbohydrate-Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery. Angew Chem Int Ed Engl 2019; 58:12750-12760. [PMID: 30913359 PMCID: PMC6771893 DOI: 10.1002/anie.201900055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/05/2019] [Indexed: 01/13/2023]
Abstract
Carbohydrates are attached and removed in living systems through the action of carbohydrate-active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high-throughput approaches look at many enzymes at once. Similarly, high-throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high-throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence-activated cell sorting, and metagenomics.
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Affiliation(s)
- Lemeng Chao
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 993581AGUtrechtThe Netherlands
| | - Seino Jongkees
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 993581AGUtrechtThe Netherlands
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30
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Chao L, Jongkees S. High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors, Evolution, and Discovery. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Lemeng Chao
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3581AG Utrecht The Netherlands
| | - Seino Jongkees
- Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences Utrecht University Universiteitsweg 99 3581AG Utrecht The Netherlands
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31
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He B, Chen H, Li N, Huang J. SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data. Int J Biol Sci 2019; 15:1452-1459. [PMID: 31337975 PMCID: PMC6643146 DOI: 10.7150/ijbs.31957] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/09/2019] [Indexed: 01/13/2023] Open
Abstract
SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc.edu.cn/sarotup3.
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang 550025, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang 550025, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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32
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Derda R, Ng S. Genetically encoded fragment-based discovery. Curr Opin Chem Biol 2019; 50:128-137. [DOI: 10.1016/j.cbpa.2019.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
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33
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Chou Y, Kitova EN, Joe M, Brunton R, Lowary TL, Klassen JS, Derda R. Genetically-encoded fragment-based discovery (GE-FBD) of glycopeptide ligands with differential selectivity for antibodies related to mycobacterial infections. Org Biomol Chem 2019; 16:223-227. [PMID: 29255817 DOI: 10.1039/c7ob02783d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Accurate identification of tuberculosis (TB), caused by Mycobacterium tuberculosis, is important for global disease management. Point-of-care serological tests may improve TB diagnosis; however, specificities of available serodiagnostics are sub-optimal. We employed genetically encoded fragment-based discovery (GE-FBD) to select ligands for antibodies directed against the mycobacterial cell wall component lipoarabinomannan (LAM), a potent antigen. GE-FBD employed a phage displayed library of 108 heptapeptides, chemically modified with an arabinofuranosyl hexasaccharide fragment of LAM (Ara6), and the anti-LAM antibody CS-35 as a bait. The selection gave rise to glycopeptides with an enhanced affinity and selectivity for CS-35 but not for 906.4321 antibody, both of which bind to Ara6 with a comparable affinity. Multivalent assays incorporating the discovered ligands Ara6-ANSSFAP, Ara6-DAHATLR and Ara6-TTYVVNP exhibited up to 19-fold discrimination between CS-35 and 906.4321. The use of the Ara6 antigen alone failed to distinguish these antibodies. Thus, GE-FBD gives rise to ligands that differentiate monoclonal antibodies with enhanced specificity. This technology could facilitate the development of effective point-of-care serological tests for mycobacterial and other infections.
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Affiliation(s)
- Ying Chou
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
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34
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Vinals DF, Kitov PI, Tu Z, Zou C, Cairo CW, Lin HCH, Derda R. Selection of galectin-3 ligands derived from genetically encoded glycopeptide libraries. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Pavel I. Kitov
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| | - Zhijay Tu
- Institute of Biological Chemistry, Academia Sinica; Taipei Taiwan
| | - Chunxia Zou
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| | | | | | - Ratmir Derda
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
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35
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Ng S, Bennett NJ, Schulze J, Gao N, Rademacher C, Derda R. Genetically-encoded fragment-based discovery of glycopeptide ligands for DC-SIGN. Bioorg Med Chem 2018; 26:5368-5377. [PMID: 30344001 DOI: 10.1016/j.bmc.2018.08.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/18/2018] [Accepted: 08/27/2018] [Indexed: 11/19/2022]
Abstract
We have employed genetically-encoded fragment-based discovery to identify novel glycopeptides with affinity for the dendritic cell receptor DC-SIGN. Starting from libraries of 108 mannose-conjugated peptides, we identified glycopeptides that exhibited up to a 650-fold increase in multivalent binding affinity for DC-SIGN, which is also preserved in cells. Monovalently, our most potent glycopeptides have a similar potency to a Man3 oligosaccharide, representing a 15-fold increase in activity compared to mannose. These compounds represent the first examples of glycopeptide ligands that target the CRD of DC-SIGN. The natural framework of glycopeptide conjugates and the simplicity of orthogonal conjugation to make these glycopeptides anticipates a promising future for development of DC-SIGN-targeting moieties.
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Affiliation(s)
- Simon Ng
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | - Jessica Schulze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - Nan Gao
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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36
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Ven Chang I, Tsutsumi H, Mihara H. Screening for concanavalin A binders from a mannose-modified α-helix peptide phage library. MOLECULAR BIOSYSTEMS 2018; 13:2222-2225. [PMID: 28967020 DOI: 10.1039/c7mb00495h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mannose-modified lectin-binding peptides were obtained from an α-helical-designed peptide phage library. Concanavalin A (ConA) was used as a representative target protein for the lectin family. The identified glycopeptides could selectively bind to ConA with micromolar affinity. With these results, the methodologies described in this study will enhance the selection of saccharide-modified ligands through the synergistic effects of sugar and peptide units, with better specificity and affinity towards lectin proteins.
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Affiliation(s)
- Iou Ven Chang
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259-B40, Midori-ku, Yokohama 226-8501, Japan
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37
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Bojarová P, Křen V. Sugared biomaterial binding lectins: achievements and perspectives. Biomater Sci 2018; 4:1142-60. [PMID: 27075026 DOI: 10.1039/c6bm00088f] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Lectins, a distinct group of glycan-binding proteins, play a prominent role in the immune system ranging from pathogen recognition and tuning of inflammation to cell adhesion or cellular signalling. The possibilities of their detailed study expanded along with the rapid development of biomaterials in the last decade. The immense knowledge of all aspects of glycan-lectin interactions both in vitro and in vivo may be efficiently used in bioimaging, targeted drug delivery, diagnostic and analytic biological methods. Practically applicable examples comprise photoluminescence and optical biosensors, ingenious three-dimensional carbohydrate microarrays for high-throughput screening, matrices for magnetic resonance imaging, targeted hyperthermal treatment of cancer tissues, selective inhibitors of bacterial toxins and pathogen-recognising lectin receptors, and many others. This review aims to present an up-to-date systematic overview of glycan-decorated biomaterials promising for interactions with lectins, especially those applicable in biology, biotechnology or medicine. The lectins of interest include galectin-1, -3 and -7 participating in tumour progression, bacterial lectins from Pseudomonas aeruginosa (PA-IL), E. coli (Fim-H) and Clostridium botulinum (HA33) or DC-SIGN, receptors of macrophages and dendritic cells. The spectrum of lectin-binding biomaterials covered herein ranges from glycosylated organic structures, calixarene and fullerene cores over glycopeptides and glycoproteins, functionalised carbohydrate scaffolds of cyclodextrin or chitin to self-assembling glycopolymer clusters, gels, micelles and liposomes. Glyconanoparticles, glycan arrays, and other biomaterials with a solid core are described in detail, including inorganic matrices like hydroxyapatite or stainless steel for bioimplants.
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Affiliation(s)
- P Bojarová
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
| | - V Křen
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
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Mendoza C, Emmanuel N, Páez CA, Dreesen L, Monbaliu JCM, Heinrichs B. Transitioning from conventional batch to microfluidic processes for the efficient singlet oxygen photooxygenation of methionine. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.12.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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39
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Abstract
In this report, we describe an efficient way to generate libraries of macrocyclic glycopeptides in one step by reacting phage-displayed libraries of peptides with dichloro-oxime derivatives. We showed that the reactions do not interfere with the ability of phage to replicate in bacteria. The reactions are site-selective for phage-displayed peptides and they do not modify any other proteins of phage. The technology described in this report will be instrumental for genetic selection of macrocyclic glycopeptides for diverse glycan-binding proteins.
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Affiliation(s)
- Simon Ng
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
| | - Ratmir Derda
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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40
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He B, Tjhung KF, Bennett NJ, Chou Y, Rau A, Huang J, Derda R. Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing. Sci Rep 2018; 8:1214. [PMID: 29352178 PMCID: PMC5775325 DOI: 10.1038/s41598-018-19439-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/02/2018] [Indexed: 01/09/2023] Open
Abstract
Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4.5 hours to yield a "naïve" library), and libraries chemically modified by aldehyde ligation and cysteine macrocyclization {M} characterized by paired-end deep sequencing, detected a significant drop in diversity in {L} → {N}, but only a minor compositional difference in {S} → {L} and {N} → {M}. Libraries expressed at the N-terminus of phage protein pIII censored positively charged amino acids Arg and Lys; libraries expressed between pIII domains N1 and N2 overcame Arg/Lys-censorship but introduced new bias towards Gly and Ser. Interrogation of biases arising from cPTM by aldehyde ligation and cysteine macrocyclization unveiled censorship of sequences with Ser/Phe. Analogous analysis can be used to explore library diversity in new display platforms and optimize cPTM of these libraries.
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Affiliation(s)
- Bifang He
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Katrina F Tjhung
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
- The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Nicholas J Bennett
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ying Chou
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Andrea Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jian Huang
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Information in Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ratmir Derda
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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41
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Hou J, Chen R, Liu J, Wang H, Shi Q, Xin Z, Wong SC, Yin J. Multiple microarrays of non-adherent cells on a single 3D stimuli-responsive binary polymer-brush pattern. J Mater Chem B 2018; 6:4792-4798. [DOI: 10.1039/c8tb01441h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hierarchically binary PGAMA/PNIPAM pattern is fabricated, and multiple cell microarrays are formed on this single pattern with the aid of Con A and temperature.
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Affiliation(s)
- Jianwen Hou
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Runhai Chen
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Jingchuan Liu
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Haozheng Wang
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Qiang Shi
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Zhirong Xin
- Department of Polymer
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai
- P. R. China
| | | | - Jinghua Yin
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
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42
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He B, Jiang L, Duan Y, Chai G, Fang Y, Kang J, Yu M, Li N, Tang Z, Yao P, Wu P, Derda R, Huang J. Biopanning data bank 2018: hugging next generation phage display. Database (Oxford) 2018; 2018:4955852. [PMID: 29688378 PMCID: PMC7206649 DOI: 10.1093/database/bay032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/12/2022]
Abstract
Database URL The BDB database is available at http://immunet.cn/bdb.
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Affiliation(s)
- Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Lixu Jiang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Yaocong Duan
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Guoshi Chai
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Yewei Fang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Juanjuan Kang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Min Yu
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Zhongjie Tang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Pengcheng Yao
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Pengcheng Wu
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
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43
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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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44
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Emmanuel N, Mendoza C, Winter M, Horn CR, Vizza A, Dreesen L, Heinrichs B, Monbaliu JCM. Scalable Photocatalytic Oxidation of Methionine under Continuous-Flow Conditions. Org Process Res Dev 2017. [DOI: 10.1021/acs.oprd.7b00212] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | | | - Marc Winter
- Corning
Reactor Technologies, Corning SAS, 7 bis Avenue de Valvins, CS 70156 Samois sur Seine, 77215 Avon Cedex, France
| | - Clemens R. Horn
- Corning
Reactor Technologies, Corning SAS, 7 bis Avenue de Valvins, CS 70156 Samois sur Seine, 77215 Avon Cedex, France
| | - Alessandra Vizza
- Corning
Reactor Technologies, Corning SAS, 7 bis Avenue de Valvins, CS 70156 Samois sur Seine, 77215 Avon Cedex, France
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Lauster D, Glanz M, Bardua M, Ludwig K, Hellmund M, Hoffmann U, Hamann A, Böttcher C, Haag R, Hackenberger CPR, Herrmann A. Multivalent Peptide-Nanoparticle Conjugates for Influenza-Virus Inhibition. Angew Chem Int Ed Engl 2017; 56:5931-5936. [PMID: 28444849 PMCID: PMC5485077 DOI: 10.1002/anie.201702005] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 12/20/2022]
Abstract
To inhibit binding of the influenza A virus to the host cell glycocalyx, we generate multivalent peptide-polymer nanoparticles binding with nanomolar affinity to the virus via its spike protein hemagglutinin. The chosen dendritic polyglycerol scaffolds are highly biocompatible and well suited for a multivalent presentation. We could demonstrate in vitro that by increasing the size of the polymer scaffold and adjusting the peptide density, viral infection is drastically reduced. Such a peptide-polymer conjugate qualified also in an in vivo infection scenario. With this study we introduce the first non-carbohydrate-based, covalently linked, multivalent virus inhibitor in the nano- to picomolar range by ensuring low peptide-ligand density on a larger dendritic scaffold.
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Affiliation(s)
- Daniel Lauster
- Institut für Biologie, Molekulare BiophysikIRI Life SciencesHumboldt-Universität zu BerlinInvalidenstrasse 4210115BerlinGermany
| | - Maria Glanz
- Leibniz-Institut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse-1013125BerlinGermany
- Humboldt Universität zu BerlinInstitut für ChemieBrook-Taylor-Strasse 212489BerlinGermany
| | - Markus Bardua
- Therapeutische Genregulation und Experimentelle RheumatologieDeutsches Rheuma-Forschungszentrum BerlinCharité 14Universitätsmedizin BerlinCharitéplatz 110117BerlinGermany
| | - Kai Ludwig
- Forschungszentrum für Elektronenmikroskopie and Core Facility BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstrasse 36a14195BerlinGermany
| | - Markus Hellmund
- Institut für Chemie und Biochemie—Organische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Ute Hoffmann
- Therapeutische Genregulation und Experimentelle RheumatologieDeutsches Rheuma-Forschungszentrum BerlinCharité 14Universitätsmedizin BerlinCharitéplatz 110117BerlinGermany
| | - Alf Hamann
- Therapeutische Genregulation und Experimentelle RheumatologieDeutsches Rheuma-Forschungszentrum BerlinCharité 14Universitätsmedizin BerlinCharitéplatz 110117BerlinGermany
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie and Core Facility BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstrasse 36a14195BerlinGermany
| | - Rainer Haag
- Institut für Chemie und Biochemie—Organische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Christian P. R. Hackenberger
- Leibniz-Institut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse-1013125BerlinGermany
- Humboldt Universität zu BerlinInstitut für ChemieBrook-Taylor-Strasse 212489BerlinGermany
| | - Andreas Herrmann
- Institut für Biologie, Molekulare BiophysikIRI Life SciencesHumboldt-Universität zu BerlinInvalidenstrasse 4210115BerlinGermany
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46
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Lauster D, Glanz M, Bardua M, Ludwig K, Hellmund M, Hoffmann U, Hamann A, Böttcher C, Haag R, Hackenberger CPR, Herrmann A. Multivalente Peptid-Nanopartikel-Konjugate zur Hemmung des Influenzavirus. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daniel Lauster
- Institut für Biologie, Molekulare Biophysik; IRI Life Sciences; Humboldt-Universität zu Berlin; Invalidenstr. 42 10115 Berlin Deutschland
| | - Maria Glanz
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Str. 10 13125 Berlin Deutschland
- Humboldt Universität zu Berlin; Institut für Chemie; Brook-Taylor-Str. 2 12489 Berlin Deutschland
| | - Markus Bardua
- Therapeutische Genregulation und Experimentelle Rheumatologie; Deutsches Rheuma-Forschungszentrum Berlin; Charité 14 Universitätsmedizin Berlin; Charitéplatz 1 10117 Berlin Deutschland
| | - Kai Ludwig
- Forschungszentrum für Elektronenmikroskopie und Core Facility BioSupraMol; Institut für Chemie und Biochemie; Freie Universität Berlin; Fabeckstr. 36a 14195 Berlin Deutschland
| | - Markus Hellmund
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustr. 3 14195 Berlin Deutschland
| | - Ute Hoffmann
- Therapeutische Genregulation und Experimentelle Rheumatologie; Deutsches Rheuma-Forschungszentrum Berlin; Charité 14 Universitätsmedizin Berlin; Charitéplatz 1 10117 Berlin Deutschland
| | - Alf Hamann
- Therapeutische Genregulation und Experimentelle Rheumatologie; Deutsches Rheuma-Forschungszentrum Berlin; Charité 14 Universitätsmedizin Berlin; Charitéplatz 1 10117 Berlin Deutschland
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie und Core Facility BioSupraMol; Institut für Chemie und Biochemie; Freie Universität Berlin; Fabeckstr. 36a 14195 Berlin Deutschland
| | - Rainer Haag
- Institut für Chemie und Biochemie - Organische Chemie; Freie Universität Berlin; Takustr. 3 14195 Berlin Deutschland
| | - Christian P. R. Hackenberger
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Str. 10 13125 Berlin Deutschland
- Humboldt Universität zu Berlin; Institut für Chemie; Brook-Taylor-Str. 2 12489 Berlin Deutschland
| | - Andreas Herrmann
- Institut für Biologie, Molekulare Biophysik; IRI Life Sciences; Humboldt-Universität zu Berlin; Invalidenstr. 42 10115 Berlin Deutschland
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47
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Kuriki Y, Komatsu T, Ycas PD, Coulup SK, Carlson EJ, Pomerantz WCK. Meeting Proceedings ICBS2016-Translating the Power of Chemical Biology to Clinical Advances. ACS Chem Biol 2017; 12:869-877. [PMID: 28303709 DOI: 10.1021/acschembio.7b00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yugo Kuriki
- Graduate School
of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toru Komatsu
- Graduate School
of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
- Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Peter D. Ycas
- Department of Chemistry, University of Minnesota, 312 Smith
Hall, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Sara K. Coulup
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Erick J. Carlson
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, 312 Smith
Hall, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
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48
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Weichenberger CX, Pozharski E, Rupp B. Twilight reloaded: the peptide experience. Acta Crystallogr D Struct Biol 2017; 73:211-222. [PMID: 28291756 PMCID: PMC5349433 DOI: 10.1107/s205979831601620x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2024] Open
Abstract
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.
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Affiliation(s)
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bernhard Rupp
- k.k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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49
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Van Deventer JA, Le DN, Zhao J, Kehoe HP, Kelly RL. A platform for constructing, evaluating, and screening bioconjugates on the yeast surface. Protein Eng Des Sel 2016; 29:485-494. [PMID: 27515702 DOI: 10.1093/protein/gzw029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 12/31/2022] Open
Abstract
The combination of protein display technologies and noncanonical amino acids (ncAAs) offers unprecedented opportunities for the high throughput discovery and characterization of molecules suitable for addressing fundamental and applied problems in biological systems. Here we demonstrate that ncAA-compatible yeast display facilitates evaluations of conjugation chemistry and stability that would be challenging or impossible to perform with existing mRNA, phage, or E. coli platforms. Our approach enables site-specific introduction of ncAAs into displayed proteins, robust modification at azide-containing residues, and quantitative evaluation of conjugates directly on the yeast surface. Moreover, screening allows for the selective enrichment of chemically modified constructs while maintaining a genotype-phenotype linkage with encoded azide functionalities. Thus, this platform is suitable for the high throughput characterization and screening of libraries of chemically modified polypeptides for therapeutic lead discovery and other biological applications.
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Affiliation(s)
- James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, 4 Colby Street Room 148, Medford, MA 02155, United States of America.,Koch Institute for Integrative Cancer Research.,Department of Chemical Engineering
| | - Doris N Le
- Koch Institute for Integrative Cancer Research.,Department of Chemical Engineering
| | - Jessie Zhao
- Koch Institute for Integrative Cancer Research.,Department of Chemical Engineering
| | - Haixing P Kehoe
- Chemical and Biological Engineering Department, Tufts University, 4 Colby Street Room 148, Medford, MA 02155, United States of America
| | - Ryan L Kelly
- Koch Institute for Integrative Cancer Research.,Department of Biological Engineering, Massachusetts Institute of Technology, 500 Main Street, Building 76 Room 289, Cambridge, MA 02139, United States of America
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50
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Jongkees SAK, Umemoto S, Suga H. Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides. Chem Sci 2016; 8:1474-1481. [PMID: 28572907 PMCID: PMC5452274 DOI: 10.1039/c6sc04381j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates.
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner. This new strategy can overcome a limitation of ribosomal translation, providing a means to incorporate untranslatable groups such as carbohydrates in amino acid side chains, and will allow for the ribosomal generation of glycopeptides, requiring only the introduction of a free thiol in the molecule to be incorporated. In combination with in vitro selection techniques, this strategy is envisaged to allow the discovery of biologically-active glycopeptides with a near-natural, but hydrolytically stable, thioglycosidic bond.
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Affiliation(s)
- S A K Jongkees
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - S Umemoto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan . .,JST CREST , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan
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