1
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Siow A, Harris PWR. Leveraging the Mukaiyama oxidation-reduction condensation reaction for on-resin aryl thio-esterification for bio-conjugation. Org Biomol Chem 2024. [PMID: 39189104 DOI: 10.1039/d4ob01230e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
A room-temperature Mukaiyama oxidation-reduction condensation inspired thioesterification methodology has been developed to afford aryl Cα-terminal peptide thioesters on-resin. The conditions herein feature mild reactions compatible with all Fmoc-SPPS protocols offering direct access to this critical arylthioester scaffold. This one-pot synthesis to aryl-thioester functionalised peptides facilitates peptide/protein synthesis by native chemical ligation.
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Affiliation(s)
- Andrew Siow
- School of Biological Sciences, School of Chemical Sciences and Maurice Wilkins Centre for Molecular Biodiversity. The University of Auckland, The University of Auckland, 3b and 23 Symonds Street, Auckland 1010, New Zealand.
| | - Paul W R Harris
- School of Biological Sciences, School of Chemical Sciences and Maurice Wilkins Centre for Molecular Biodiversity. The University of Auckland, The University of Auckland, 3b and 23 Symonds Street, Auckland 1010, New Zealand.
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2
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Lawrence N, Handley TNG, de Veer SJ, Harding MD, Andraszek A, Hall L, Raven KD, Duffy S, Avery VM, Craik DJ, Malins LR, McMorran BJ. Enhancing the Intrinsic Antiplasmodial Activity and Improving the Stability and Selectivity of a Tunable Peptide Scaffold Derived from Human Platelet Factor 4. ACS Infect Dis 2024; 10:2899-2912. [PMID: 39087267 PMCID: PMC11320574 DOI: 10.1021/acsinfecdis.4c00276] [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: 04/09/2024] [Revised: 06/12/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024]
Abstract
The control of malaria, a disease caused by Plasmodium parasites that kills over half a million people every year, is threatened by the continual emergence and spread of drug resistance. Therefore, new molecules with different mechanisms of action are needed in the antimalarial drug development pipeline. Peptides developed from host defense molecules are gaining traction as anti-infectives due to theood of inducing drug resistance. Human platelet factor 4 (PF4) has intrinsic activity against P. falciparum, and a macrocyclic helix-loop-helix peptide derived from its active domain recapitulates this activity. In this study, we used a stepwise approach to optimize first-generation PF4-derived internalization peptides (PDIPs) by producing analogues with substitutions to charged and hydrophobic amino acid residues or with modifications to terminal residues including backbone cyclization. We evaluated the in vitro activity of PDIP analogues against P. falciparum compared to their overall helical structure, resistance to breakdown by serum proteases, selective binding to negatively charged membranes, and hemolytic activity. Next, we combined antiplasmodial potency-enhancing substitutions that retained favorable membrane and cell-selective properties onto the most stable scaffold to produce a backbone cyclic PDIP analogue with four-fold improved activity against P. falciparum compared to first-generation peptides. These studies demonstrate the ability to modify PDIP to select for and combine desirable properties and further validate the suitability of this unique peptide scaffold for developing a new molecule class that is distinct from existing antimalarial drugs.
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Affiliation(s)
- Nicole Lawrence
- Institute
for Molecular Bioscience and Australian Research Council Centre of
Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas N. G. Handley
- Department
of Radiopharmaceutical Sciences, Cancer Imaging, The Peter MacCallum Cancer Centre, Victoria 3000, Australia
- Sir
Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia
| | - Simon J. de Veer
- Institute
for Molecular Bioscience and Australian Research Council Centre of
Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maxim D. Harding
- Institute
for Molecular Bioscience and Australian Research Council Centre of
Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alicja Andraszek
- Institute
for Molecular Bioscience and Australian Research Council Centre of
Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lachlan Hall
- Institute
for Molecular Bioscience and Australian Research Council Centre of
Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Karoline D. Raven
- The
John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Sandra Duffy
- Discovery
Biology, Centre for Cellular Phenomics, School of Environment and
Science, Griffith University, Nathan, Queensland 4111, Australia
| | - Vicky M. Avery
- Discovery
Biology, Centre for Cellular Phenomics, School of Environment and
Science, Griffith University, Nathan, Queensland 4111, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience and Australian Research Council Centre of
Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lara R. Malins
- Research
School of Chemistry and Australian Research Council Centre of Excellence
for Innovations in Peptide and Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Brendan J. McMorran
- The
John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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3
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Wang N, Mcneer NA, Eton E, Fass J, Kentsis A. Proteomic Barcoding Platform for Macromolecular Screening and Delivery. J Proteome Res 2024; 23:2067-2077. [PMID: 38776430 DOI: 10.1021/acs.jproteome.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.
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Affiliation(s)
- Ning Wang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Nicole A Mcneer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Elliot Eton
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Josh Fass
- Tri-I PhD Program in Computational Biology and Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
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4
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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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5
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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6
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Su DD, Ali LMA, Coste M, Laroui N, Bessin Y, Barboiu M, Bettache N, Ulrich S. Structure-Activity Relationships in Nucleic-Acid-Templated Vectors Based on Peptidic Dynamic Covalent Polymers. Chemistry 2023; 29:e202202921. [PMID: 36342312 PMCID: PMC10108046 DOI: 10.1002/chem.202202921] [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: 09/19/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
The use of nucleic acids as templates, which can trigger the self-assembly of their own vectors represent an emerging, simple and versatile, approach toward the self-fabrication of tailored nucleic acids delivery vectors. However, the structure-activity relationships governing this complex templated self-assembly process that accompanies the complexation of nucleic acids remains poorly understood. Herein, the class of arginine-rich dynamic covalent polymers (DCPs) composed of different monomers varying the number and position of arginines were studied. The combinations that lead to nucleic acid complexation, in saline buffer, using different templates, from short siRNA to long DNA, are described. Finally, a successful peptidic DCP featuring six-arginine repeating unit that promote the safe and effective delivery of siRNA in live cancer cells was identified.
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Affiliation(s)
- Dan-Dan Su
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France.,Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
| | - Lamiaa M A Ali
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France.,Department of Biochemistry Medical Research Institute, University of Alexandria, 21561, Alexandria, Egypt
| | - Maëva Coste
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Nabila Laroui
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Yannick Bessin
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Mihail Barboiu
- Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
| | - Nadir Bettache
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
| | - Sébastien Ulrich
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM, 34095, Montpellier, France
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7
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Xu Y, Zhu TF. Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs. Science 2022; 378:405-412. [DOI: 10.1126/science.abm0646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To synthesize a chirally inverted ribosome with the goal of building mirror-image biology systems requires the preparation of kilobase-long mirror-image ribosomal RNAs that make up the structural and catalytic core and about two-thirds of the molecular mass of the mirror-image ribosome. Here, we chemically synthesized a 100-kilodalton mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of the full-length mirror-image 5
S
, 16
S
, and 23
S
ribosomal RNAs from enzymatically assembled long mirror-image genes. We further exploited the versatile mirror-image T7 transcription system for practical applications such as biostable mirror-image riboswitch sensor, long-term storage of unprotected kilobase-long
l
-RNA in water, and
l
-ribozyme–catalyzed
l
-RNA polymerization to serve as a model system for basic RNA research.
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Affiliation(s)
- Yuan Xu
- 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, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ting F. Zhu
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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8
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Guo C, Zhang LQ, Jiang W. Biodegrading plastics with a synthetic non-biodegradable enzyme. Chem 2022. [DOI: 10.1016/j.chempr.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Nagano M, Huang Y, Obexer R, Suga H. Chemical peptide macrolactonization via intramolecular
S
‐to‐
S
‐to‐
O
acyl transfer. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Masanobu Nagano
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| | - Yichao Huang
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| | - Richard Obexer
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
| | - Hiroaki Suga
- Graduate School of Science The University of Tokyo Bunkyo‐ku Tokyo Japan
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10
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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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11
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Kossmann C, Ma S, Clemmensen LS, Strømgaard K. Chemical Synthesis of PDZ Domains. Methods Mol Biol 2021; 2256:193-216. [PMID: 34014524 DOI: 10.1007/978-1-0716-1166-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Developments in chemical protein synthesis have enabled the generation of tailor-made proteins including incorporation of many types of modifications into proteins, enhancing our ability to control site-specificity of protein posttranslational modifications (PTMs), modify protein backbones and introduce photocrosslinking probes. For PDZ (postsynaptic density protein, disks large, zonula occludens) protein domains, expressed protein ligation (EPL) has been employed to introduce analogs of cognate amino acids, amide-to-ester bond mutations, and phosphorylations in the study of PDZ domain-mediated protein-protein interactions (PPIs). Here, we present protocols for EPL of PDZ domains focusing on phosphorylation and amide-to-ester modifications in the PDZ domain proteins.
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Affiliation(s)
- Christin Kossmann
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Sana Ma
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Louise S Clemmensen
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.
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12
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Mailig M, Hymel D, Liu F. Further Exploration of Hydrazine-Mediated Bioconjugation Chemistries. Org Lett 2020; 22:6677-6681. [PMID: 32786214 DOI: 10.1021/acs.orglett.0c02545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrazine group serves as a great anchor for bioconjugation; however, the application of hydrazone ligation has been limited by poor product stability. We aim to resolve such issues by optimizing the recently established pyrazolone ligation and investigating a new pyrazole ligation. We have identified a new, electron-deficient pyrazolone ligation and a regiospecific pyrazole ligation, both offering aqueous buffer stable and chemically inert products possessing triazole-like structures while not involving any heavy metal catalyst.
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Affiliation(s)
- Melrose Mailig
- Novo Nordisk Research Center, 530 Fairview Avenue North, Seattle, Washington 98109, United States
| | - David Hymel
- Novo Nordisk Research Center, 530 Fairview Avenue North, Seattle, Washington 98109, United States
| | - Fa Liu
- Novo Nordisk Research Center, 530 Fairview Avenue North, Seattle, Washington 98109, United States
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13
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Rut W, Zmudzinski M, Snipas SJ, Bekes M, Huang TT, Drag M. Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes. Chem Sci 2020; 11:6058-6069. [PMID: 32953009 PMCID: PMC7477763 DOI: 10.1039/d0sc01347a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Herein we present a workflow for design and synthesis of novel selective Ub-based tools for DUBs. Selectivity is achieved by incorporation of unnatural amino acids into the Ub C-terminal epitope.
Deubiquitinating enzymes (DUBs) are responsible for removing ubiquitin (Ub) from its protein conjugates. DUBs have been implicated as attractive therapeutic targets in the treatment of viral diseases, neurodegenerative disorders and cancer. The lack of selective chemical tools for the exploration of these enzymes significantly impairs the determination of their roles in both normal and pathological states. Commercially available fluorogenic substrates are based on the C-terminal Ub motif or contain Ub coupled to a fluorophore (Z-LRGG-AMC, Ub-AMC); therefore, these substrates suffer from lack of selectivity. By using a hybrid combinatorial substrate library (HyCoSuL) and a defined P2 library containing a wide variety of nonproteinogenic amino acids, we established a full substrate specificity profile for two DUBs—MERS PLpro and human UCH-L3. Based on these results, we designed and synthesized Ub-based substrates and activity-based probes (ABPs) containing selected unnatural amino acids located in the C-terminal Ub motif. Biochemical analysis and cell lysate experiments confirmed the activity and selectivity of engineered Ub-based substrates and probes. Using this approach, we propose that for any protease that recognizes Ub and Ub-like substrates, a highly active and selective unnatural substrate or probe can be engineered.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
| | - Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
| | - Scott J Snipas
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Miklos Bekes
- Department of Biochemistry & Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ; .,Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
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14
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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15
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Qu Q, Gao S, Li YM. Racemic crystal structures of peptide toxins, GsMTx4 prepared by protein total synthesis. J Pept Sci 2018; 24:e3112. [PMID: 30009430 DOI: 10.1002/psc.3112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 01/28/2023]
Abstract
The Piezo channel is a versatile mechanosensitive cation channel that mediates tactile, vascular development, and proprioception. GsMTx4 is the only reported inhibitor specifically targeting Piezo channels. Although the sequence of GsMTx4 is reported, the crystal structure of GsMTx4 is still unknown. Here, we achieved the two-segment synthesis of GsMTx4 and its enantiomer, enGsMTx4, through hydrazide based Native Chemical Ligation, and analyzed the crystal structure of GsMTx4 through the racemic crystallization technology. By analyzing the structure, we found that there is a hydrophobic patch surrounded by aromatic residues and charged residues.
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Affiliation(s)
- Qian Qu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,School of Biological and Medical Engineering, Hefei University of Technology, Anhui, Hefei, 230009, China
| | - Shuai Gao
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Li
- School of Biological and Medical Engineering, Hefei University of Technology, Anhui, Hefei, 230009, China
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16
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Total synthesis of snake toxin α-bungarotoxin and its analogues by hydrazide-based native chemical ligation. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Antonatou E, Verleysen Y, Madder A. Singlet oxygen-mediated one-pot chemoselective peptide-peptide ligation. Org Biomol Chem 2018; 15:8140-8144. [PMID: 28914947 DOI: 10.1039/c7ob02245j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We here describe a furan oxidation based site-specific chemical ligation approach using unprotected peptide segments. This approach involves two steps: after photooxidation of a furan-containing peptide, ligation is achieved by reaction of the unmasked keto-enal with C- or N-terminal α-nucleophilic moieties of the second peptide such as hydrazine or hydrazide to form a pyridazinium or pyrrolidinone linkage respectively.
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Affiliation(s)
- Eirini Antonatou
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Gent, Belgium.
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18
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Garabedian A, Baird M, Porter J, Jeanne Dit Fouque K, Shliaha PV, Jensen ON, Williams TD, Fernandez-Lima F, Shvartsburg A. Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms. Anal Chem 2018; 90:2918-2925. [PMID: 29359922 PMCID: PMC6366606 DOI: 10.1021/acs.analchem.7b05224] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Comprehensive characterization of proteomes comprising the same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS), relying on the mobility increment at high electric fields, but not previously by linear IMS on the basis of absolute mobility. We now use complete histone tails with diverse PTMs on alternative sites to demonstrate that high-resolution linear IMS, here trapped IMS (TIMS), broadly resolves the variants of ∼50 residues in full or into binary mixtures quantifiable by tandem MS, largely thanks to orthogonal separations across charge states. Separations using traveling-wave (TWIMS) and/or involving various time scales and electrospray ionization source conditions are similar (with lower resolution for TWIMS), showing the transferability of results across linear IMS instruments. The linear IMS and FAIMS dimensions are substantially orthogonal, suggesting FAIMS/IMS/MS as a powerful platform for proteoform analyses.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
| | - Matthew Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260
| | - Jacob Porter
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
| | | | - Pavel V. Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Todd D. Williams
- Mass Spectrometry Laboratory, University of Kansas, Lawrence, KS 66045
| | | | - Alexandre Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260
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19
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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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20
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Shliaha PV, Baird MA, Nielsen MM, Gorshkov V, Bowman AP, Kaszycki JL, Jensen ON, Shvartsburg AA. Characterization of Complete Histone Tail Proteoforms Using Differential Ion Mobility Spectrometry. Anal Chem 2017; 89:5461-5466. [PMID: 28406606 PMCID: PMC5436587 DOI: 10.1021/acs.analchem.7b00379] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histone proteins are subject to dynamic post-translational modifications (PTMs) that cooperatively modulate the chromatin structure and function. Nearly all functional PTMs are found on the N-terminal histone domains (tails) of ∼50 residues protruding from the nucleosome core. Using high-definition differential ion mobility spectrometry (FAIMS) with electron transfer dissociation, we demonstrate rapid baseline gas-phase separation and identification of tails involving monomethylation, trimethylation, acetylation, or phosphorylation in biologically relevant positions. These are by far the largest variant peptides resolved by any method, some with PTM contributing just 0.25% to the mass. This opens the door to similar separations for intact proteins and in top-down proteomics.
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Affiliation(s)
- Pavel V Shliaha
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Matthew A Baird
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Mogens M Nielsen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Andrew P Bowman
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Julia L Kaszycki
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University , 1845 Fairmount, Wichita, Kansas 67260, United States
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21
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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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22
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Johnston HJ, Boys SK, Makda A, Carragher NO, Hulme AN. Naturally Inspired Peptide Leads: Alanine Scanning Reveals an Actin-Targeting Thiazole Analogue of Bisebromoamide. Chembiochem 2016; 17:1621-7. [PMID: 27304907 PMCID: PMC5096027 DOI: 10.1002/cbic.201600257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 12/29/2022]
Abstract
Systematic alanine scanning of the linear peptide bisebromoamide (BBA), isolated from a marine cyanobacterium, was enabled by solid-phase peptide synthesis of thiazole analogues. The analogues have comparable cytotoxicity (nanomolar) to that of BBA, and cellular morphology assays indicated that they target the actin cytoskeleton. Pathway inhibition in human colon tumour (HCT116) cells was explored by reverse phase protein array (RPPA) analysis, which showed a dose-dependent response in IRS-1 expression. Alanine scanning reveals a structural dependence to the cytotoxicity, actin targeting and pathway inhibition, and allows a new readily synthesised lead to be proposed.
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Affiliation(s)
- Heather J Johnston
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Sarah K Boys
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Ashraff Makda
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - Neil O Carragher
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - Alison N Hulme
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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23
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Li YT, Huang YC, Xu Y, Pan M, Li YM. Ubiquitin 7-amino-4-carbamoylmethylcoumarin as an improved fluorogenic substrate for deubiquitinating enzymes. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.05.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Pan M, Gao S, Zheng Y, Tan X, Lan H, Tan X, Sun D, Lu L, Wang T, Zheng Q, Huang Y, Wang J, Liu L. Quasi-Racemic X-ray Structures of K27-Linked Ubiquitin Chains Prepared by Total Chemical Synthesis. J Am Chem Soc 2016; 138:7429-35. [PMID: 27268299 DOI: 10.1021/jacs.6b04031] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quasi-racemic crystallography has been used to determine the X-ray structures of K27-linked ubiquitin (Ub) chains prepared through total chemical synthesis. Crystal structures of K27-linked di- and tri-ubiquitins reveal that the isopeptide linkages are confined in a unique buried conformation, which provides the molecular basis for the distinctive function of K27 linkage compared to the other seven Ub chains. K27-linked di- and triUb were found to adopt different structural conformations in the crystals, one being symmetric whereas the other triangular. Furthermore, bioactivity experiments showed that the ovarian tumor family de-ubiquitinase 2 significantly favors K27-linked triUb than K27-linked diUb. K27-linked triUb represents the so-far largest chemically synthesized protein (228 amino acids) that has been crystallized to afford a high-resolution X-ray structure.
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Affiliation(s)
- Man Pan
- 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
| | - Shuai Gao
- 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
| | - Yong Zheng
- 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
| | - Xiaodan Tan
- 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
| | - Huan Lan
- 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
| | - Xianglong Tan
- 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
| | - Demeng Sun
- 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
| | - Lining Lu
- 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
| | - Tian Wang
- 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
| | - Qingyun Zheng
- 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
| | - Yichao Huang
- 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
| | - Jiawei Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, 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
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25
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Huang Y, Chen C, Gao S, Wang Y, Xiao H, Wang F, Tian C, Li Y. Synthesis of
l
‐ and
d
‐Ubiquitin by One‐Pot Ligation and Metal‐Free Desulfurization. Chemistry 2016; 22:7623-8. [DOI: 10.1002/chem.201600101] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Yi‐Chao Huang
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
- Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Chen‐Chen Chen
- High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230026 P. R. China
| | - Shuai Gao
- Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Ye‐Hai Wang
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
| | - Hua Xiao
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
| | - Feng Wang
- Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Chang‐Lin Tian
- High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230026 P. R. China
| | - Yi‐Ming Li
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
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26
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Huang YC, Fang GM, Liu L. Chemical synthesis of proteins using hydrazide intermediates. Natl Sci Rev 2015. [DOI: 10.1093/nsr/nwv072] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Protein chemical synthesis offers useful and otherwise-difficulty-to-obtain biomacromolecules for biological and pharmaceutical studies. Recently, the hydrazide chemistry has drawn attentions in this field as peptide or protein hydrazides can be used as key intermediates for different synthesis and modification purposes. Besides being a traditional bioorthogonal chemical handle, a hydrazide group can serve as a readily accessible precursor of a thioester. This strategy significantly improves the efficiency and scope of native chemical ligation for protein chemical synthesis. Here we review the chemical transformations of peptide or protein hydrazides and total/semi/enzymatic protein synthesis methods involving peptide or protein hydrazides. Several examples of protein chemical synthesis using peptide hydrazides as key intermediates are described.
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27
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Huang YC, Guan CJ, Tan XL, Chen CC, Guo QX, Li YM. Accelerated Fmoc solid-phase synthesis of peptides with aggregation-disrupting backbones. Org Biomol Chem 2015; 13:1500-6. [PMID: 25476596 DOI: 10.1039/c4ob02260b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we describe an accelerated solid-phase synthetic protocol for ordinary or difficult peptides involving air-bath heating and amide protection. For the Hmsb-based backbone amide protection, an optimized acyl shift condition using 1,4-dioxane was discovered. The efficiency and robustness of the protocol was validated in the course of preparation of classical difficult peptides and ubiquitin protein segments.
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Affiliation(s)
- Yi-Chao Huang
- School of Medical Engineering, Hefei University of Technology, Hefei 230009, China.
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28
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Swain SP, Chou YL, Hou DR. Thioesterifications Free of Activating Agent and Thiol: A Three-Component Reaction of Carboxylic Acids, Thioureas, and Michael Acceptors. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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29
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Li SJ, Qu DL, Wang YH, He Y, Wen M, Guo QX, Shi J, Li YM. Facile and efficient chemical synthesis of APET×2, an ASIC-targeting toxin, via hydrazide-based native chemical ligation. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Bello C, Kikul F, Becker CFW. Efficient generation of peptide hydrazides via direct hydrazinolysis of Peptidyl-Wang-TentaGel resins. J Pept Sci 2015; 21:201-7. [PMID: 25648984 DOI: 10.1002/psc.2747] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 12/21/2014] [Accepted: 12/22/2014] [Indexed: 01/19/2023]
Abstract
Peptide hydrazides are valuable building blocks in peptide and protein chemistry, e.g. as precursors of peptide thioesters that allow the preparation of these important intermediates under mild conditions. Additional robust and versatile methods for the generation of peptide hydrazides from standard solid supports are therefore highly desired in order to facilitate access to peptide thioester via Fmoc-based SPPS. Here, the efficient generation of peptide hydrazides from conventional 4-hydroxymethyl phenol Wang-TentalGel peptidyl resins is described. Direct hydrazinolysis of a 19mer mucin1 peptide gives the protected peptide hydrazide in excellent yields. Testing a series of octapeptides carrying the 20 common proteinogenic amino acids at their C-terminus led to preparation of all corresponding peptide hydrazides in very good to excellent yields and purities. The available set of octapeptides allowed analyzing the influence of the nature of the C-terminal amino acid and of the solvent on the hydrazinolysis reaction. Furthermore, the compatibility of the method with posttranslational modifications (here glycosylation) and with potentially sensitive functional groups in amino acid side chains makes this approach a viable alternative for obtaining peptide hydrazides. It combines the advantages of a straightforward synthesis with stereochemical stability and flexibility, as it provides easy access to the peptide acid and the peptide thioester (via the hydrazide) from the same solid support.
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Affiliation(s)
- Claudia Bello
- Department of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
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31
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Bartolami E, Bessin Y, Bettache N, Gary-Bobo M, Garcia M, Dumy P, Ulrich S. Multivalent DNA recognition by self-assembled clusters: deciphering structural effects by fragments screening and evaluation as siRNA vectors. Org Biomol Chem 2015; 13:9427-38. [DOI: 10.1039/c5ob01404b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fragment self-assembly was used for producing clusters with a variety of scaffolds and ligands, and an effective siRNA vector was identified.
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Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Yannick Bessin
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Nadir Bettache
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Magali Gary-Bobo
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Marcel Garcia
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
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32
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Efficient synthesis of trypsin inhibitor SFTI-1 via intramolecular ligation of peptide hydrazide. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Chen C, Huang Y, Xu L, Zheng Y, Xu H, Guo Q, Tian C, Li Y, Shi J. Thiol-assisted one-pot synthesis of peptide/protein C-terminal thioacids from peptide/protein hydrazides at neutral conditions. Org Biomol Chem 2014; 12:9413-8. [DOI: 10.1039/c4ob01885k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An efficient thiol-assisted one-pot synthesis of peptide/protein C-terminal thioacids was achieved by using peptide/protein hydrazides precursors at neutral pH and room temperature (about 20 °C).
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Affiliation(s)
- Chenchen Chen
- School of Medical Engineering
- School of Chemistry and Chemical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
| | - Yichao Huang
- Department of Chemistry
- Tsinghua University
- Beijing 100084, China
| | - Ling Xu
- Department of Chemistry
- University of Science and Technology of China
- China
| | - Yong Zheng
- Department of Chemistry
- University of Science and Technology of China
- China
| | - Huajian Xu
- School of Medical Engineering
- School of Chemistry and Chemical Engineering
- Hefei University of Technology
- Hefei, China
| | - Qingxiang Guo
- Department of Chemistry
- University of Science and Technology of China
- China
| | - Changlin Tian
- Department of Chemistry
- University of Science and Technology of China
- China
| | - Yiming Li
- School of Medical Engineering
- School of Chemistry and Chemical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
| | - Jing Shi
- Department of Chemistry
- University of Science and Technology of China
- China
| |
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