1
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Zhang G, Zhu TF. Mirror-image trypsin digestion and sequencing of D-proteins. Nat Chem 2024; 16:592-598. [PMID: 38238467 DOI: 10.1038/s41557-023-01411-x] [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: 02/21/2023] [Accepted: 11/28/2023] [Indexed: 04/07/2024]
Abstract
The development of mirror-image biology systems and related applications is hindered by the lack of effective methods to sequence mirror-image (D-) proteins. Although natural-chirality (L-) proteins can be sequenced by bottom-up liquid chromatography-tandem mass spectrometry (LC-MS/MS), the sequencing of long D-peptides and D-proteins with the same strategy requires digestion by a site-specific D-protease before mass analysis. Here we apply solid-phase peptide synthesis and native chemical ligation to chemically synthesize a mirror-image version of trypsin, a widely used protease for site-specific protein digestion. Using mirror-image trypsin digestion and LC-MS/MS, we sequence a mirror-image large subunit ribosomal protein (L25) and a mirror-image Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), and distinguish between different mutants of D-Dpo4. We also perform writing and reading of digital information in a long D-peptide of 50 amino acids. Thus, mirror-image trypsin digestion in conjunction with LC-MS/MS may facilitate practical applications of D-peptides and D-proteins as potential therapeutic and informational tools.
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Affiliation(s)
- Guanwei Zhang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- School of Life Sciences, New Cornerstone Science Laboratory, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Ting F Zhu
- School of Life Sciences, New Cornerstone Science Laboratory, Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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2
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Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
A combinatorial approach toward novel functional WW domains based on coiled-coil-mediated reconstitution of split WW domains is presented. As such, an ATP-binding WW domain was found from a 4-by-6 library of N- and C-terminal WW domain fragments.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Florian R. Häge
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
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3
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Fan C, Deng Q, Zhu TF. Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase. Nat Biotechnol 2021; 39:1548-1555. [PMID: 34326549 DOI: 10.1038/s41587-021-00969-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Natural DNA is exquisitely evolved to store genetic information. The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day. These next-generation mirror-image molecular tools may transform the development of advanced mirror-image biology systems and pave the way for the realization of the mirror-image central dogma and exploration of their applications.
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Affiliation(s)
- Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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4
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Fankhauser D, Alissandratos A, Liutkus M, Easton CJ. Easy Production of "Difficult Peptides" Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site. Chemistry 2021; 27:17487-17494. [PMID: 34651362 DOI: 10.1002/chem.202103161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 11/08/2022]
Abstract
Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.
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Affiliation(s)
- Daniel Fankhauser
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Mantas Liutkus
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
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5
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Kasim JK, Kavianinia I, Harris PWR, Brimble MA. Three Decades of Amyloid Beta Synthesis: Challenges and Advances. Front Chem 2019; 7:472. [PMID: 31334219 PMCID: PMC6614915 DOI: 10.3389/fchem.2019.00472] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/19/2019] [Indexed: 01/09/2023] Open
Abstract
Aggregation of the pathological amyloid beta (Aβ) isoform Aβ1−42 into senile plaques is a neuropathological hallmark of Alzheimer's disease (AD). The biochemical significance of this phenomenon therefore necessitates the need for ready access to Aβ1−42 for research purposes. Chemical synthesis of the peptide, however, is technically difficult to perform given its propensity to aggregate both on resin during solid phase peptide synthesis and in solution during characterization. This review presents a chronological summary of key publications in the field of Aβ1−42 synthesis, dating back from its maiden synthesis by Burdick et al. Challenges associated with the preparation of Aβ1−42 were identified, and the solutions designed over the course of time critically discussed herein. Ultimately, the intention of this review is to provide readers with an insight into the progress that has been made in the last three decades, and how this has advanced broader research in AD.
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Affiliation(s)
- Johanes K Kasim
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Iman Kavianinia
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Paul W R Harris
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Margaret A Brimble
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
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6
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Yoshiya T, Tsuda S, Masuda S. Development of Trityl Group Anchored Solubilizing Tags for Peptide and Protein Synthesis. Chembiochem 2019; 20:1906-1913. [DOI: 10.1002/cbic.201900105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Taku Yoshiya
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
| | - Shugo Tsuda
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
| | - Shun Masuda
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
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7
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Takayama R, Hayakawa S, Hinou H, Albericio F, Garcia-Martin F. Further applications of classical amide coupling reagents: Microwave-assisted esterification on solid phase. J Pept Sci 2018; 24:e3111. [DOI: 10.1002/psc.3111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Risa Takayama
- Graduate School of Life Science; Hokkaido University; N21, W11, Kita-ku Sapporo 001-0021 Japan
| | - Shun Hayakawa
- Graduate School of Life Science; Hokkaido University; N21, W11, Kita-ku Sapporo 001-0021 Japan
| | - Hiroshi Hinou
- Graduate School of Life Science; Hokkaido University; N21, W11, Kita-ku Sapporo 001-0021 Japan
- Faculty of Advanced Life Science; Hokkaido University; N21, W11, Kita-ku Sapporo 001-0021 Japan
- Medicinal Chemistry Pharmaceuticals, Company Ltd.; N21, W12, Kita-ku Sapporo 001-0021 Japan
| | - Fernando Albericio
- Department of Organic Chemistry and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine; University of Barcelona; Barcelona 080028 Spain
- School of Chemistry and Physics; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Fayna Garcia-Martin
- Graduate School of Life Science; Hokkaido University; N21, W11, Kita-ku Sapporo 001-0021 Japan
- Faculty of Advanced Life Science; Hokkaido University; N21, W11, Kita-ku Sapporo 001-0021 Japan
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8
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9
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Tsuda S, Mochizuki M, Ishiba H, Yoshizawa-Kumagaye K, Nishio H, Oishi S, Yoshiya T. Easy-to-Attach/Detach Solubilizing-Tag-Aided Chemical Synthesis of an Aggregative Capsid Protein. Angew Chem Int Ed Engl 2018; 57:2105-2109. [DOI: 10.1002/anie.201711546] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/20/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hiroyuki Ishiba
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Kumiko Yoshizawa-Kumagaye
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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10
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Tsuda S, Mochizuki M, Ishiba H, Yoshizawa-Kumagaye K, Nishio H, Oishi S, Yoshiya T. Easy-to-Attach/Detach Solubilizing-Tag-Aided Chemical Synthesis of an Aggregative Capsid Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hiroyuki Ishiba
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Kumiko Yoshizawa-Kumagaye
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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11
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ten Brummelhuis N, Wilke P, Börner HG. Identification of Functional Peptide Sequences to Lead the Design of Precision Polymers. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700632] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/26/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Niels ten Brummelhuis
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Patrick Wilke
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Hans G. Börner
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
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12
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Jiang W, Zhang B, Fan C, Wang M, Wang J, Deng Q, Liu X, Chen J, Zheng J, Liu L, Zhu TF. Mirror-image polymerase chain reaction. Cell Discov 2017; 3:17037. [PMID: 29051832 PMCID: PMC5643884 DOI: 10.1038/celldisc.2017.37] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/03/2017] [Accepted: 09/03/2017] [Indexed: 01/30/2023] Open
Abstract
The construction of mirror-image biological systems may open the next frontier for biomedical technology development and discovery. Here we have designed and chemically synthesized a mutant version of the thermostable Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) consisting of d-amino acids. With a total peptide length of 358 amino acid residues, it is the largest chemically synthesized d-amino acid protein reported to date. We show that the d-polymerase is able to amplify a 120-bp l-DNA sequence coding for the Escherichia coli 5S ribosomal RNA gene rrfB by mirror-image polymerase chain reaction, and that both the natural and mirror-image systems operate with strict chiral specificity. The development of efficient miPCR systems may lead to many practical applications, such as mirror-image systematic evolution of ligands by exponential enrichment for the selection of therapeutically promising nuclease-resistant l-nucleic acid aptamers.
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Affiliation(s)
- Wenjun Jiang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Baochang Zhang
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Min Wang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Jiaxing Wang
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Xianyu Liu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ji Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Jishen Zheng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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13
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 631] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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14
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Pathogenic Aβ A2V versus protective Aβ A2T mutation: Early stage aggregation and membrane interaction. Biophys Chem 2017; 229:11-18. [PMID: 28502484 DOI: 10.1016/j.bpc.2017.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 11/20/2022]
Abstract
We investigated the effects of punctual A-to-V and A-to-T mutations in the amyloid precursor protein APP, corresponding to position 2 of Aβ1-42. Those mutations had opposite effects on the onset and progression of Alzheimer disease, the former inducing early AD pathology and the latter protecting against the onset of the disease. We applied Static and Dynamic Light Scattering and Circular Dichroism, to study the different mutants in the early stages of the aggregation process, essential for the disease. Comparative results showed that the aggregation pathways differ in the kinetics and extent of the process, in the size of the aggregates and in the evolution of the secondary structure, resulting in fibrils of different morphology, as seen by AFM. Mutated peptides had comparable toxic effects on N2a cells. Moreover, as assessed by X-ray scattering, all of them displayed disordering effects on the internal structure of mixed phospholipids-gangliosides model membranes.
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15
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Total chemical synthesis of a thermostable enzyme capable of polymerase chain reaction. Cell Discov 2017; 3:17008. [PMID: 28265464 PMCID: PMC5335361 DOI: 10.1038/celldisc.2017.8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/06/2017] [Indexed: 01/30/2023] Open
Abstract
Polymerase chain reaction (PCR) has been a defining tool in modern biology. Towards realizing mirror-image PCR, we have designed and chemically synthesized a mutant version of the 352-residue thermostable Sulfolobus solfataricus P2 DNA polymerase IV with l-amino acids and tested its PCR activity biochemically. To the best of our knowledge, this enzyme is the largest chemically synthesized protein reported to date. We show that with optimization of PCR conditions, the fully synthetic polymerase is capable of amplifying template sequences of up to 1.5 kb. The establishment of this synthetic route for chemically synthesizing DNA polymerase IV is a stepping stone towards building a d-enzyme system for mirror-image PCR, which may open up an avenue for the creation of many mirror-image molecular tools such as mirror-image systematic evolution of ligands by exponential enrichment.
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16
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Wang Z, Xu W, Liu L, Zhu TF. A synthetic molecular system capable of mirror-image genetic replication and transcription. Nat Chem 2016; 8:698-704. [PMID: 27325097 DOI: 10.1038/nchem.2517] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 03/21/2016] [Indexed: 02/07/2023]
Abstract
The overwhelmingly homochiral nature of life has left a puzzle as to whether mirror-image biological systems based on a chirally inverted version of molecular machinery could also have existed. Here we report that two key steps in the central dogma of molecular biology, the template-directed polymerization of DNA and transcription into RNA, can be catalysed by a chemically synthesized D-amino acid polymerase on an L-DNA template. We also show that two chirally mirrored versions of the 174-residue African swine fever virus polymerase X could operate in a racemic mixture without significant enantiomeric cross-inhibition to the activity of each other. Furthermore, we demonstrate that a functionally active L-DNAzyme could be enzymatically produced using the D-amino acid polymerase. The establishment of such molecular systems with an opposite handedness highlights the potential to exploit enzymatically produced mirror-image biomolecules as research and therapeutic tools.
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Affiliation(s)
- Zimou Wang
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Weiliang Xu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ting F Zhu
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China
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17
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Amyloid-β peptides in interaction with raft-mime model membranes: a neutron reflectivity insight. Sci Rep 2016; 6:20997. [PMID: 26880066 PMCID: PMC4754687 DOI: 10.1038/srep20997] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/14/2016] [Indexed: 12/11/2022] Open
Abstract
The role of first-stage β–amyloid aggregation in the development of the Alzheimer disease, is widely accepted but still unclear. Intimate interaction with the cell membrane is invoked. We designed Neutron Reflectometry experiments to reveal the existence and extent of the interaction between β–amyloid (Aβ) peptides and a lone customized biomimetic membrane, and their dependence on the aggregation state of the peptide. The membrane, asymmetrically containing phospholipids, GM1 and cholesterol in biosimilar proportion, is a model for a raft, a putative site for amyloid-cell membrane interaction. We found that the structured-oligomer of Aβ(1-42), its most acknowledged membrane-active state, is embedded as such into the external leaflet of the membrane. Conversely, the Aβ(1-42) unstructured early-oligomers deeply penetrate the membrane, likely mimicking the interaction at neuronal cell surfaces, when the Aβ(1-42) is cleaved from APP protein and the membrane constitutes a template for its further structural evolution. Moreover, the smaller Aβ(1-6) fragment, the N-terminal portion of Aβ, was also used. Aβ N-terminal is usually considered as involved in oligomer stabilization but not in the peptide-membrane interaction. Instead, it was seen to remove lipids from the bilayer, thus suggesting its role, once in the whole peptide, in membrane leakage, favouring peptide recruitment.
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Marine JE, Song S, Liang X, Rudick JG. Synthesis and Self-Assembly of Bundle-Forming α-Helical Peptide-Dendron Hybrids. Biomacromolecules 2016; 17:336-44. [PMID: 26674475 PMCID: PMC4710556 DOI: 10.1021/acs.biomac.5b01452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Dendronized helix bundle assemblies combine the sequence diversity and folding properties of proteins with the tailored physical properties of dendrimers. Assembly of peptide-dendron hybrids into α-helical bundles encapsulates the helix bundle motif in a dendritic sheath that will allow the functional, protein-like domain to be transplanted to nonbiological environments. A bioorthogonal graft-to synthetic strategy for preparing helix bundle-forming peptide-dendron hybrids is described herein for hybrids 1a, 1b, and 2. Titration experiments monitored by circular dichroism spectroscopy support our self-assembly model for how the peptide-dendron hybrids self-assemble into α-helical bundles with the dendrons on outside of the bundle.
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Affiliation(s)
- Jeannette E. Marine
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Shuang Song
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Xiaoli Liang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Jonathan G. Rudick
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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Behrendt R, White P, Offer J. Advances in Fmoc solid-phase peptide synthesis. J Pept Sci 2016; 22:4-27. [PMID: 26785684 PMCID: PMC4745034 DOI: 10.1002/psc.2836] [Citation(s) in RCA: 411] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]
Abstract
Today, Fmoc SPPS is the method of choice for peptide synthesis. Very-high-quality Fmoc building blocks are available at low cost because of the economies of scale arising from current multiton production of therapeutic peptides by Fmoc SPPS. Many modified derivatives are commercially available as Fmoc building blocks, making synthetic access to a broad range of peptide derivatives straightforward. The number of synthetic peptides entering clinical trials has grown continuously over the last decade, and recent advances in the Fmoc SPPS technology are a response to the growing demand from medicinal chemistry and pharmacology. Improvements are being continually reported for peptide quality, synthesis time and novel synthetic targets. Topical peptide research has contributed to a continuous improvement and expansion of Fmoc SPPS applications.
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Affiliation(s)
- Raymond Behrendt
- Novabiochem, Merck & CieIm Laternenacker 58200SchaffhausenSwitzerland
| | - Peter White
- Novabiochem, Merck Chemicals LtdPadge RoadBeestonNG9 2JRUK
| | - John Offer
- The Francis Crick Institute215 Euston RoadLondonNW1 2BEUK
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20
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The cell-permeable Aβ1-6A2VTAT(D) peptide reverts synaptopathy induced by Aβ1-42wt. Neurobiol Dis 2015; 89:101-11. [PMID: 26721320 DOI: 10.1016/j.nbd.2015.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023] Open
Abstract
Alzheimer disease (AD) is the most prevalent form of dementia. Loss of hippocampal synapses is the first neurodegenerative event in AD. Synaptic loss has been associated with the accumulation in the brain parenchyma of soluble oligomeric forms of amyloid β peptide (Aβ1-42wt). Clinical observations have shown that a mutation in the APP protein (A673V) causes an early onset AD-type dementia in homozygous carriers while heterozygous carriers are unaffected. This mutation leads to the formation of mutated Aβ peptides (Aβ1-42A2V) in homozygous patients, while in heterozygous subjects both Aβ1-42wt and Aβ1-42A2V are present. To better understand the impact of the A673V mutation in AD, we analyzed the synaptotoxic effect of oligomers formed by aggregation of different Aβ peptides (Aβ1-42wt or Aβ1-42A2V) and the combination of the two Aβ1-42MIX (Aβ1-42wt and Aβ1-42A2V) in an in vitro model of synaptic injury. We showed that Aβ1-42A2V oligomers are more toxic than Aβ1-42wt oligomers in hippocampal neurons, confirming the results previously obtained in cell lines. Furthermore, we reported that oligomers obtained by the combination of both wild type and mutated peptides (Aβ1-42MIX) did not exert synaptic toxicity. We concluded that the combination of Aβ1-42wt and Aβ1-42A2V peptides hinders the toxicity of Aβ1-42A2V and counteracts the manifestation of synaptopathy in vitro. Finally we took advantage of this finding to generate a cell-permeable peptide for clinical application, by fusing the first six residues of the Aβ1-42A2V to the TAT cargo sequence (Aβ1-6A2VTAT(D)). Noteworthy, the treatment with Aβ1-6A2VTAT(D) confers neuroprotection against both in vitro and in vivo synaptopathy models. Therefore Aβ1-6A2VTAT(D) may represent an innovative therapeutic tool to prevent synaptic degeneration in AD.
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Paradís-Bas M, Tulla-Puche J, Albericio F. The road to the synthesis of "difficult peptides". Chem Soc Rev 2015; 45:631-54. [PMID: 26612670 DOI: 10.1039/c5cs00680e] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The last decade has witnessed a renaissance of peptides as drugs. This progress, together with advances in the structural behavior of peptides, has attracted the interest of the pharmaceutical industry in these molecules as potential APIs. In the past, major peptide-based drugs were inspired by sequences extracted from natural structures of low molecular weight. In contrast, nowadays, the peptides being studied by academic and industrial groups comprise more sophisticated sequences. For instance, they consist of long amino acid chains and show a high tendency to form aggregates. Some researchers have claimed that preparing medium-sized proteins is now feasible with chemical ligation techniques, in contrast to medium-sized peptide syntheses. The complexity associated with the synthesis of certain peptides is exemplified by the so-called "difficult peptides", a concept introduced in the 80's. This refers to sequences that show inter- or intra-molecular β-sheet interactions significant enough to form aggregates during peptide synthesis. These structural associations are stabilized and mediated by non-covalent hydrogen bonds that arise on the backbone of the peptide and-depending on the sequence-are favored. The tendency of peptide chains to aggregate is translated into a list of common behavioral features attributed to "difficult peptides" which hinder their synthesis. In this regard, this manuscript summarizes the strategies used to overcome the inherent difficulties associated with the synthesis of known "difficult peptides". Here we evaluate several external factors, as well as methods to incorporate chemical modifications into sequences, in order to describe the strategies that are effective for the synthesis of "difficult peptides". These approaches have been classified and ordered to provide an extensive guide for achieving the synthesis of peptides with the aforementioned features.
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Affiliation(s)
- Marta Paradís-Bas
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain.
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Marine JE, Liang X, Song S, Rudick JG. Azide-rich peptides via an on-resin diazotransfer reaction. Biopolymers 2015; 104:419-26. [PMID: 25753459 PMCID: PMC4516611 DOI: 10.1002/bip.22634] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 12/19/2022]
Abstract
Azide-containing amino acids are valuable building blocks in peptide chemistry, because azides are robust partners in several bioorthogonal reactions. Replacing polar amino acids with apolar, azide-containing amino acids in solid-phase peptide synthesis can be tricky, especially when multiple azide residues are to be introduced in the amino acid sequence. We present a strategy for effectively incorporating multiple azide-containing residues site-specifically.
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Affiliation(s)
- Jeannette E. Marine
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Xiaoli Liang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Shuang Song
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Jonathan G. Rudick
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, United States
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23
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Messa M, Colombo L, del Favero E, Cantù L, Stoilova T, Cagnotto A, Rossi A, Morbin M, Di Fede G, Tagliavini F, Salmona M. The peculiar role of the A2V mutation in amyloid-β (Aβ) 1-42 molecular assembly. J Biol Chem 2014; 289:24143-52. [PMID: 25037228 DOI: 10.1074/jbc.m114.576256] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We recently reported a novel Aβ precursor protein mutation (A673V), corresponding to position 2 of Aβ1-42 peptides (Aβ1-42A2V), that caused an early onset AD-type dementia in a homozygous individual. The heterozygous relatives were not affected as an indication of autosomal recessive inheritance of this mutation. We investigated the folding kinetics of native unfolded Aβ1-42A2V in comparison with the wild type sequence (Aβ1-42WT) and the equimolar solution of both peptides (Aβ1-42MIX) to characterize the oligomers that are produced in the early phases. We carried out the structural characterization of the three preparations using electron and atomic force microscopy, fluorescence emission, and x-ray diffraction and described the soluble oligomer formation kinetics by laser light scattering. The mutation promoted a peculiar pathway of oligomerization, forming a connected system similar to a polymer network with hydrophobic residues on the external surface. Aβ1-42MIX generated assemblies very similar to those produced by Aβ1-42WT, albeit with slower kinetics due to the difficulties of Aβ1-42WT and Aβ1-42A2V peptides in building up of stable intermolecular interaction.
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Affiliation(s)
- Massimo Messa
- From the Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy
| | - Laura Colombo
- From the Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy
| | - Elena del Favero
- Department of Medical Biotechnology and Translational Medicine, University of Milan, V.le F.lli Cervi 93, 20090 Segrate, Italy, and
| | - Laura Cantù
- Department of Medical Biotechnology and Translational Medicine, University of Milan, V.le F.lli Cervi 93, 20090 Segrate, Italy, and
| | - Tatiana Stoilova
- From the Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy
| | - Alfredo Cagnotto
- From the Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy
| | - Alessandro Rossi
- From the Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy
| | - Michela Morbin
- Neurology V and Neuropathology, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133 Milan, Italy
| | - Giuseppe Di Fede
- Neurology V and Neuropathology, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133 Milan, Italy
| | - Fabrizio Tagliavini
- Neurology V and Neuropathology, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133 Milan, Italy
| | - Mario Salmona
- From the Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy,
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24
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Stuhr-Hansen N, Padrah S, Strømgaard K. Facile synthesis of α-hydroxy carboxylic acids from the corresponding α-amino acids. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.05.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Kolesanova EF, Sanzhakov MA, Kharybin ON. Development of the schedule for multiple parallel "difficult" Peptide synthesis on pins. INTERNATIONAL JOURNAL OF PEPTIDES 2013; 2013:197317. [PMID: 24027588 PMCID: PMC3762146 DOI: 10.1155/2013/197317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/09/2013] [Indexed: 12/20/2022]
Abstract
Unified schedule for multiple parallel solid-phase synthesis of so-called "difficult" peptides on polypropylene pins was developed. Increase in the efficiency of 9-fluorenyl(methoxycarbonyl) N-terminal amino-protecting group removal was shown to have a greater influence on the accuracy of the "difficult" peptide synthesis than the use of more efficient amino acid coupling reagents such as aminium salts. Hence the unified schedule for multiple parallel solid-phase synthesis of "difficult" peptides included the procedure for N-terminal amino group deprotection modified by applying a more efficient reagent for the deprotection and the standard procedure of amino acid coupling by carbodiimide method with an additional coupling using aminium salts, if necessary. Amino acid coupling with the help of carbodiimide allows to follow the completeness of the coupling via the bromophenol blue indication, thus providing the accuracy of the synthesis and preventing an overexpenditure of expensive reagents. About 100 biotinylated hepatitis C virus envelope protein fragments, most of which represented "difficult" peptides, were successfully obtained by synthesis on pins with the help of the developed unified schedule.
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Affiliation(s)
- Ekaterina F. Kolesanova
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Ulica, Moscow 119121, Russia
| | - Maxim A. Sanzhakov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Ulica, Moscow 119121, Russia
| | - Oleg N. Kharybin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Ulica, Moscow 119121, Russia
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26
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Expression and purification of chimeric peptide comprising EGFR B-cell epitope and measles virus fusion protein T-cell epitope in Escherichia coli. Protein Expr Purif 2013; 88:7-12. [DOI: 10.1016/j.pep.2012.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/02/2012] [Accepted: 11/16/2012] [Indexed: 01/31/2023]
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27
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Monbaliu JCM, Dive G, Stevens CV, Katritzky AR. Governing Parameters of Long-Range Intramolecular S-to-N Acyl Transfers within (S)-Acyl Isopeptides. J Chem Theory Comput 2013; 9:927-34. [DOI: 10.1021/ct300830k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jean-Christophe M. Monbaliu
- Center for Heterocyclic Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Georges Dive
- Center of Protein Engineering,
Institut de Chimie, University of Liège, Bâtiment B.6, B-4000 Sart Tilman, Liège, Belgium
| | - Christian V. Stevens
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Alan R. Katritzky
- Center for Heterocyclic Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Chemistry Department, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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28
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Synthesis of protected sugar-amino acid hybrid molecules as platform for further derivatization. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.10.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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Abstract
Selected reaction monitoring (SRM) has a long history of use in the area of quantitative MS. In recent years, the approach has seen increased application to quantitative proteomics, facilitating multiplexed relative and absolute quantification studies in a variety of organisms. This article discusses SRM, after introducing the context of quantitative proteomics (specifically primarily absolute quantification) where it finds most application, and considers topics such as the theory and advantages of SRM, the selection of peptide surrogates for protein quantification, the design of optimal SRM co-ordinates and the handling of SRM data. A number of published studies are also discussed to demonstrate the impact that SRM has had on the field of quantitative proteomics.
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30
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Raphel J, Parisi-Amon A, Heilshorn S. Photoreactive elastin-like proteins for use as versatile bioactive materials and surface coatings. JOURNAL OF MATERIALS CHEMISTRY 2012; 22:19429-19437. [PMID: 23015764 PMCID: PMC3449156 DOI: 10.1039/c2jm31768k] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photocrosslinkable, protein-engineered biomaterials combine a rapid, controllable, cytocompatible crosslinking method with a modular design strategy to create a new family of bioactive materials. These materials have a wide range of biomedical applications, including the development of bioactive implant coatings, drug delivery vehicles, and tissue engineering scaffolds. We present the successful functionalization of a bioactive elastin-like protein with photoreactive diazirine moieties. Scalable synthesis is achieved using a standard recombinant protein expression host followed by site-specific modification of lysine residues with a heterobifunctional N-hydroxysuccinimide ester-diazirine crosslinker. The resulting biomaterial is demonstrated to be processable by spin coating, drop casting, soft lithographic patterning, and mold casting to fabricate a variety of two- and three-dimensional photocrosslinked biomaterials with length scales spanning the nanometer to millimeter range. Protein thin films proved to be highly stable over a three-week period. Cell-adhesive functional domains incorporated into the engineered protein materials were shown to remain active post-photo-processing. Human adipose-derived stem cells achieved faster rates of cell adhesion and larger spread areas on thin films of the engineered protein compared to control substrates. The ease and scalability of material production, processing versatility, and modular bioactive functionality make this recombinantly engineered protein an ideal candidate for the development of novel biomaterial coatings, films, and scaffolds.
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Affiliation(s)
- Jordan Raphel
- Department of Materials Science & Engineering, Stanford University. 476 Lomita Mall, McCullough Building 246, Stanford, CA 94035, USA
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31
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A Single Pseudoproline and Microwave Solid Phase Peptide Synthesis Facilitates an Efficient Synthesis of Human Amylin 1–37. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9325-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Lüttenberg S, Sondermann F, Scherkenbeck J. Anthelmintic PF1022A: stepwise solid-phase synthesis of a cyclodepsipeptide containing N-methyl amino acids. Tetrahedron 2012; 68:2068-2073. [PMID: 32287426 PMCID: PMC7111844 DOI: 10.1016/j.tet.2011.12.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/04/2011] [Accepted: 12/10/2011] [Indexed: 11/18/2022]
Abstract
Cyclodepsipeptides of the enniation-, PF1022-, and verticilide-family represent a diverse class of highly interesting natural products with respect to their manifold biological activities. However, until now no stepwise solid-phase synthesis has been accomplished due to the difficult combination of N-methyl amino acids and hydroxycarboxylic acids. We report here the first stepwise solid-phase synthesis of the anthelmintic cyclooctadepsipeptide PF1022A based on an Fmoc/THP-ether protecting group strategy on Wang-resin. The standard conditions of our synthesis allow an unproblematic adaption to an automated peptide synthesizer.
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Key Words
- ACN, acetonitrile
- BOPCl, N,N′-bis(2-oxo-3-oxazolidinyl)phosphinic chloride
- Boc, tert-butyloxycarbonyl
- DCM, dichloromethane
- DEAD, diethylazodicarboxylate
- DHP, 3,4-dihydro-2H-pyrane
- DIC, N,N′-diisopropylcarbodiimide
- DIEA, diisopropylethylamine
- DMAP, 4-dimethylaminopyridine
- DMF, dimethylformamide
- DMSO, dimethylsulfoxide
- EDCI, 1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide methiodide
- Fmoc, 9-Fluorenyl-methoxycarbonyl
- HATU, N,N,N′,N′-tetramethyl-O-(7-azabenzo-triazol-1-yl)uroniumhexa-fluorophosphate
- HOAt, 1-hydroxy-7-azabenzotriazole
- HOBt, 1-hydroxy-benzotriazole
- MeOH, methanol
- TEA, triethylamine
- TFA, trifluoro acetic acid
- THF, tetrahydrofuran
- THP, tetrahydropyranyl
- TPP, triphenylphosphane
- p-TsOH, para-toluenesulfonic acid
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Affiliation(s)
- Sebastian Lüttenberg
- Bergische Universität Wuppertal, Fachgruppe Chemie, Gaußstraße 20, D-42119 Wuppertal, Germany
| | - Frank Sondermann
- Bergische Universität Wuppertal, Fachgruppe Chemie, Gaußstraße 20, D-42119 Wuppertal, Germany
| | - Jürgen Scherkenbeck
- Bergische Universität Wuppertal, Fachgruppe Chemie, Gaußstraße 20, D-42119 Wuppertal, Germany
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Butterfield S, Hejjaoui M, Fauvet B, Awad L, Lashuel HA. Chemical strategies for controlling protein folding and elucidating the molecular mechanisms of amyloid formation and toxicity. J Mol Biol 2012; 421:204-36. [PMID: 22342932 DOI: 10.1016/j.jmb.2012.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 12/12/2022]
Abstract
It has been more than a century since the first evidence linking the process of amyloid formation to the pathogenesis of Alzheimer's disease. During the last three decades in particular, increasing evidence from various sources (pathology, genetics, cell culture studies, biochemistry, and biophysics) continues to point to a central role for the pathogenesis of several incurable neurodegenerative and systemic diseases. This is in part driven by our improved understanding of the molecular mechanisms of protein misfolding and aggregation and the structural properties of the different aggregates in the amyloid pathway and the emergence of new tools and experimental approaches that permit better characterization of amyloid formation in vivo. Despite these advances, detailed mechanistic understanding of protein aggregation and amyloid formation in vitro and in vivo presents several challenges that remain to be addressed and several fundamental questions about the molecular and structural determinants of amyloid formation and toxicity and the mechanisms of amyloid-induced toxicity remain unanswered. To address this knowledge gap and technical challenges, there is a critical need for developing novel tools and experimental approaches that will not only permit the detection and monitoring of molecular events that underlie this process but also allow for the manipulation of these events in a spatial and temporal fashion both in and out of the cell. This review is primarily dedicated in highlighting recent results that illustrate how advances in chemistry and chemical biology have been and can be used to address some of the questions and technical challenges mentioned above. We believe that combining recent advances in the development of new fluorescent probes, imaging tools that enabled the visualization and tracking of molecular events with advances in organic synthesis, and novel approaches for protein synthesis and engineering provide unique opportunities to gain a molecular-level understanding of the process of amyloid formation. We hope that this review will stimulate further research in this area and catalyze increased collaboration at the interface of chemistry and biology to decipher the mechanisms and roles of protein folding, misfolding, and aggregation in health and disease.
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Affiliation(s)
- Sara Butterfield
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Monbaliu JCM, Katritzky AR. Recent trends in Cys- and Ser/Thr-based synthetic strategies for the elaboration of peptide constructs. Chem Commun (Camb) 2012; 48:11601-22. [DOI: 10.1039/c2cc34434c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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36
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Marchini M, Mingozzi M, Colombo R, Gennari C, Durini M, Piarulli U. Selective O-acylation of unprotected N-benzylserine methyl ester and O,N-acyl transfer in the formation of cyclo[Asp-Ser] diketopiperazines. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Musiol HJ, Moroder L. Two-Chain Insulin from a Single-Chain Branched Depsipeptide Precursor: The End of a Long Journey. Angew Chem Int Ed Engl 2010; 49:7624-6. [DOI: 10.1002/anie.201003018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Musiol HJ, Moroder L. Zweikettiges Insulin aus einer einkettigen, verzweigten Depsipeptidvorstufe - das Ende einer langen Reise. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Tan LT, Goh BPL, Tripathi A, Lim MG, Dickinson GH, Lee SSC, Teo SLM. Natural antifoulants from the marine cyanobacterium Lyngbya majuscula. BIOFOULING 2010; 26:685-95. [PMID: 20658384 DOI: 10.1080/08927014.2010.508343] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Filamentous benthic marine cyanobacteria are a prolific source of structurally unique bioactive secondary metabolites. A total of 12 secondary metabolites, belonging to the mixed polyketide-polypeptide structural class, were isolated from the marine cyanobacterium, Lyngbya majuscula, and were tested to determine if they showed activity against barnacle larval settlement. The assays revealed four compounds, dolastatin 16, hantupeptin C, majusculamide A, and isomalyngamide A, that showed moderate to potent anti-larval settlement activities, with EC(50) values ranging from 0.003 to 10.6 microg ml(-1). In addition, field testing conducted over a period of 28 days (using the modified Phytagel method) based on the cyanobacterial compound, dolastatin 16, showed significantly reduced barnacle settlement as compared to controls at all the concentrations tested. The results of this study highlight the importance of marine cyanobacteria as an underexplored source of potential environmentally friendly antifoulants.
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Affiliation(s)
- Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Singapore.
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