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Williams ET, Schiefelbein K, Schuster M, Ahmed IMM, De Vries M, Beveridge R, Zerbe O, Hartrampf N. Rapid flow-based synthesis of post-translationally modified peptides and proteins: a case study on MYC's transactivation domain. Chem Sci 2024; 15:8756-8765. [PMID: 38873065 PMCID: PMC11168107 DOI: 10.1039/d4sc00481g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 05/04/2024] [Indexed: 06/15/2024] Open
Abstract
Protein-protein interactions of c-Myc (MYC) are often regulated by post-translational modifications (PTMs), such as phosphorylation, and crosstalk thereof. Studying these interactions requires proteins with unique PTM patterns, which are challenging to obtain by recombinant methods. Standard peptide synthesis and native chemical ligation can produce such modified proteins, but are time-consuming and therefore typically limited to the study of individual PTMs. Herein, we report the development of flow-based methods for the rapid synthesis of phosphorylated MYC sequences (up to 84 AA), and demonstrate the versatility of this approach for the incorporation of other PTMs (N ε-methylation, sulfation, acetylation, glycosylation) and combinations thereof. Peptides containing up to seven PTMs and phosphorylation at up to five sites were successfully prepared and isolated in high yield and purity. We further produced ten PTM-decorated analogues of the MYC Transactivation Domain (TAD) to screen for binding to the tumor suppressor protein, Bin1, using heteronuclear NMR and native mass spectrometry. We determined the effects of phosphorylation and glycosylation on the strength of the MYC:Bin1 interaction, and reveal an influence of MYC sequence length on binding. Our platform for the rapid synthesis of MYC sequences up to 84 AA with distinct PTM patterns thus enables the systematic study of PTM function at a molecular level, and offers a convenient way for expedited screening of constructs.
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Affiliation(s)
- Elyse T Williams
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kevin Schiefelbein
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ikhlas M M Ahmed
- Department for Pure and Applied Chemistry, University of Strathclyde 295 Cathedral St Glasgow G1 1XL UK
| | - Marije De Vries
- Department for Pure and Applied Chemistry, University of Strathclyde 295 Cathedral St Glasgow G1 1XL UK
| | - Rebecca Beveridge
- Department for Pure and Applied Chemistry, University of Strathclyde 295 Cathedral St Glasgow G1 1XL UK
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nina Hartrampf
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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2
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Grunhaus D, Molina ER, Cohen R, Stein T, Friedler A, Hurevich M. Accelerated Multiphosphorylated Peptide Synthesis. Org Process Res Dev 2022; 26:2492-2497. [PMID: 36032360 PMCID: PMC9397535 DOI: 10.1021/acs.oprd.2c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Preparing phosphorylated peptides with multiple adjacent
phosphorylations
is synthetically difficult, leads to β-elimination, results
in low yields, and is extremely slow. We combined synthetic chemical
methodologies with computational studies and engineering approaches
to develop a strategy that takes advantage of fast stirring, high
temperature, and a very low concentration of 1,8-diazabicyclo[5.4.0]undec-7-ene
(DBU) to produce multiphosphorylated peptides at an extremely rapid
time and high purity.
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Affiliation(s)
- Dana Grunhaus
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Estefanía Rossich Molina
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Roni Cohen
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Tamar Stein
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Mattan Hurevich
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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3
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Grunhaus D, Friedler A, Hurevich M. Automated Synthesis of Heavily Phosphorylated Peptides. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dana Grunhaus
- The Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram Jerusalem 9190401 Israel
| | - Assaf Friedler
- The Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram Jerusalem 9190401 Israel
| | - Mattan Hurevich
- The Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram Jerusalem 9190401 Israel
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4
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Samarasimhareddy M, Mayer G, Hurevich M, Friedler A. Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms. Org Biomol Chem 2020; 18:3405-3422. [DOI: 10.1039/d0ob00499e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.
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Affiliation(s)
- Mamidi Samarasimhareddy
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| | - Guy Mayer
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| | - Mattan Hurevich
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
| | - Assaf Friedler
- The Institute of Chemistry
- Edmond J. Safra Campus
- Givat Ram
- The Hebrew University of Jerusalem
- Jerusalem
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5
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Qvit N, Disatnik MH, Sho J, Mochly-Rosen D. Selective Phosphorylation Inhibitor of Delta Protein Kinase C-Pyruvate Dehydrogenase Kinase Protein-Protein Interactions: Application for Myocardial Injury in Vivo. J Am Chem Soc 2016; 138:7626-35. [PMID: 27218445 PMCID: PMC5065007 DOI: 10.1021/jacs.6b02724] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein kinases regulate numerous cellular processes, including cell growth, metabolism, and cell death. Because the primary sequence and the three-dimensional structure of many kinases are highly similar, the development of selective inhibitors for only one kinase is challenging. Furthermore, many protein kinases are pleiotropic, mediating diverse and sometimes even opposing functions by phosphorylating multiple protein substrates. Here, we set out to develop an inhibitor of a selective protein kinase phosphorylation of only one of its substrates. Focusing on the pleiotropic delta protein kinase C (δPKC), we used a rational approach to identify a distal docking site on δPKC for its substrate, pyruvate dehydrogenase kinase (PDK). We reasoned that an inhibitor of PDK's docking should selectively inhibit the phosphorylation of only PDK without affecting phosphorylation of the other δPKC substrates. Our approach identified a selective inhibitor of PDK docking to δPKC with an in vitro Kd of ∼50 nM and reducing cardiac injury IC50 of ∼5 nM. This inhibitor, which did not affect the phosphorylation of other δPKC substrates even at 1 μM, demonstrated that PDK phosphorylation alone is critical for δPKC-mediated injury by heart attack. The approach we describe is likely applicable for the identification of other substrate-specific kinase inhibitors.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford CA 94305-5174 USA
| | - Marie-Hélène Disatnik
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford CA 94305-5174 USA
| | - Jie Sho
- Kunming Biomed International Chenggong, Kunming, P.R. China
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford CA 94305-5174 USA
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6
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Qvit N, Schechtman D, Pena DA, Berti DA, Soares CO, Miao Q, Liang LA, Baron LA, Teh-Poot C, Martínez-Vega P, Ramirez-Sierra MJ, Churchill E, Cunningham AD, Malkovskiy AV, Federspiel NA, Gozzo FC, Torrecilhas AC, Manso Alves MJ, Jardim A, Momar N, Dumonteil E, Mochly-Rosen D. Scaffold proteins LACK and TRACK as potential drug targets in kinetoplastid parasites: Development of inhibitors. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2016; 6:74-84. [PMID: 27054066 PMCID: PMC4805777 DOI: 10.1016/j.ijpddr.2016.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/04/2016] [Accepted: 02/08/2016] [Indexed: 01/15/2023]
Abstract
Parasitic diseases cause ∼500,000 deaths annually and remain a major challenge for therapeutic development. Using a rational design based approach, we developed peptide inhibitors with anti-parasitic activity that were derived from the sequences of parasite scaffold proteins LACK (Leishmania's receptor for activated C-kinase) and TRACK (Trypanosomareceptor for activated C-kinase). We hypothesized that sequences in LACK and TRACK that are conserved in the parasites, but not in the mammalian ortholog, RACK (Receptor for activated C-kinase), may be interaction sites for signaling proteins that are critical for the parasites' viability. One of these peptides exhibited leishmanicidal and trypanocidal activity in culture. Moreover, in infected mice, this peptide was also effective in reducing parasitemia and increasing survival without toxic effects. The identified peptide is a promising new anti-parasitic drug lead, as its unique features may limit toxicity and drug-resistance, thus overcoming central limitations of most anti-parasitic drugs. Identified unique short sequences conserved in parasite but not in host orthologue. Peptides corresponding to these sequences are active anti-parasitic drug lead. Cyclization of the peptides generates drug leads for in vivo proof of concept.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305, USA.
| | - Deborah Schechtman
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305, USA; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | | | | | | | - Qianqian Miao
- National Reference Centre for Parasitology, Research Institute of the McGill University, Montreal, Canada
| | - Liying Annie Liang
- National Reference Centre for Parasitology, Research Institute of the McGill University, Montreal, Canada
| | - Lauren A Baron
- Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Christian Teh-Poot
- Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Pedro Martínez-Vega
- Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Maria Jesus Ramirez-Sierra
- Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Eric Churchill
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Anna D Cunningham
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Andrey V Malkovskiy
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Nancy A Federspiel
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Fabio Cesar Gozzo
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
| | | | | | - Armando Jardim
- Institute of Parasitology and Centre for Host-Parasite Interactions, McGill University, Québec, Canada
| | - Ndao Momar
- National Reference Centre for Parasitology, Research Institute of the McGill University, Montreal, Canada
| | - Eric Dumonteil
- Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA 94305, USA
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7
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Qvit N, Kornfeld OS. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation. J Vis Exp 2016:e53589. [PMID: 26863382 DOI: 10.3791/53589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a systematic screen for the most biological active conformation. This method provides a general, fast, and facile way to synthesize cyclic peptides.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University School of Medicine;
| | - Opher S Kornfeld
- Department of Chemical and Systems Biology, Stanford University School of Medicine
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