1
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Henry C, Kruell JA, Wilson RM, Chang CF, Woo CM, Koehler AN. A Versatile Isocyanate-Mediated Strategy for Appending Chemical Tags onto Drug-Like Small Molecules. Bioconjug Chem 2023; 34:2181-2186. [PMID: 38052453 PMCID: PMC10739574 DOI: 10.1021/acs.bioconjchem.3c00352] [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: 08/06/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023]
Abstract
Target identification studies are a major hurdle in probe and drug discovery pipelines due to the need to chemically modify small molecules of interest, which can be time intensive and have low throughput. Here, we describe a versatile and scalable method for attaching chemical moieties to a small molecule, isocyanate-mediated chemical tagging (IMCT). By preparation of a template resin with an isocyanate capture group and a cleavable linker, nucleophilic groups on small molecules can be modified with an enforced one-to-one stoichiometry. We demonstrate a small molecule substrate scope that includes primary and secondary amines, thiols, phenols, benzyl alcohols, and primary alcohols. Cheminformatic analyses predict that IMCT is reactive with more than 25% of lead-like compounds in publicly available databases. To demonstrate that the method can produce biologically active molecules, we generated FKBP12 photoaffinity labeling (PAL) compounds with a wide range of affinities and showed that purified and crude cleavage products can bind to and label FKBP12. This method could be used to rapidly modify small molecules for many applications, including the synthesis of PAL probes, fluorescence polarization probes, pull-down probes, and degraders.
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Affiliation(s)
- Catherine
C. Henry
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- MIT
Center for Precision Cancer Medicine, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Jasmin A. Kruell
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- MIT
Center for Precision Cancer Medicine, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Robert M. Wilson
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- MIT
Center for Precision Cancer Medicine, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Chia-Fu Chang
- Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Angela N. Koehler
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- MIT
Center for Precision Cancer Medicine, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02142, United States
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2
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Synthesis and characterization of chemically fueled supramolecular materials driven by carbodiimide-based fuels. Nat Protoc 2021; 16:3901-3932. [PMID: 34194049 DOI: 10.1038/s41596-021-00563-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Many supramolecular materials in biological systems are driven to a nonequilibrium state by the irreversible consumption of high-energy molecules such as ATP or GTP. As a result, they exhibit unique dynamic properties such as a tunable lifetime, adaptivity or the ability to self-heal. In contrast, synthetic counterparts that exist in or close to equilibrium are controlled by thermodynamic parameters and therefore lack these dynamic properties. To mimic biological materials more closely, synthetic self-assembling systems have been developed that are driven out of equilibrium by chemical reactions. This protocol describes the synthesis and characterization of such an assembly, which is driven by carbodiimide fuels. Depending on the amount of chemical fuel added to the material, its lifetime can be tuned. In the first step, the protocol details the synthesis and purification of the peptide-based precursors for the fuel-driven assemblies by solid-phase peptide synthesis. Then, we explain how to analyze the kinetic response of the precursors to a carbodiimide-based chemical fuel by HPLC and kinetic models. Finally, we detail how to study the emerging assembly's macro- and microscopic properties by time-lapse photography, UV-visible spectroscopy, shear rheology, confocal laser scanning microscopy and electron microscopy. The procedure is described using the example of a colloid-forming precursor Fmoc-E-OH and a fiber-forming precursor Fmoc-AAD-OH to emphasize the differences in characterization depending on the type of assembly. The characterization of a precursor's transient assembly can be done within 5 d. The synthesis and purification of a peptide precursor requires 2 d of work.
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3
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Brown JS, Ruttinger AW, Vaidya AJ, Alabi CA, Clancy P. Decomplexation as a rate limitation in the thiol-Michael addition of N-acrylamides. Org Biomol Chem 2020; 18:6364-6377. [PMID: 32760955 DOI: 10.1039/d0ob00726a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The thiol-Michael addition is a popular, selective, high-yield "click" reaction utilized for applications ranging from small-molecule synthesis to polymer or surface modification. Here, we combined experimental and quantum mechanical modeling approaches using density functional theory (DFT) to examine the thiol-Michael reaction of N-allyl-N-acrylamide monomers used to prepare sequence-defined oligothioetheramides (oligoTEAs). Experimentally, the reaction was evaluated with two fluorous tagged thiols and several monomers at room temperature (22 °C and 40 °C). Using the Eyring equation, the activation energies (enthalpies) were calculated, observing a wide range of energy barriers ranging from 28 kJ mol-1 to 108 kJ mol-1 within the same alkene class. Computationally, DFT coupled with the Nudged Elastic Band method was used to calculate the entire reaction coordinate of each monomer reaction using the B97-D3 functional and a hybrid implicit-explicit methanol solvation approach. The thiol-Michael reaction is traditionally rate-limited by the propagation or chain-transfer steps. However, our test case with N-acrylamides and fluorous thiols revealed experimental and computational data produced satisfactory agreement only when we considered a previously unconsidered step that we termed "product decomplexation", which occurs as the product physically dissociates from other co-reactants after chain transfer. Five monomers were investigated to support this finding, capturing a range of functional groups varying in alkyl chain length (methyl to hexyl) and aromaticity (benzyl and ethylenephenyl). Increased substrate alkyl chain length increased activation energy, explained by the inductive effect. Aromatic ring-stacking configurations significantly impacted the activation energy and contributed to improved molecular packing density. Hydrogen-bonding between reactants increased the activation energy emphasizing the rate-limitation of the product decomplexation. Our findings begin to describe a new structure-kinetic relationship for thiol-Michael acceptors to enable further design of reactive monomers for synthetic polymers and biomaterials.
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Affiliation(s)
- Joseph S Brown
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Andrew W Ruttinger
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Akash J Vaidya
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Paulette Clancy
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.
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4
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Hussein WM, Skwarczynski M, Toth I. An Isodipeptide Building Block for Microwave-Assisted Solid-Phase Synthesis of Difficult Sequence-Containing Peptides. Methods Mol Biol 2020; 2103:139-150. [PMID: 31879923 DOI: 10.1007/978-1-0716-0227-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microwave technology, in conjunction with the isopeptide strategy including Fmoc-based solid-phase peptide synthesis (SPPS), was used to establish a methodology for time-efficient synthesis of peptides containing difficult sequences. A model difficult sequence-containing peptide (8QSer) was synthesized through this method in 1 day, representing a tenfold reduction in synthesis time compared to the isopeptide method combined with classical SPPS.
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Affiliation(s)
- Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD, Australia.
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5
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Synthetic Evaluation of Standard and Microwave-Assisted Solid Phase Peptide Synthesis of a Long Chimeric Peptide Derived from Four Plasmodium falciparum Proteins. Molecules 2018; 23:molecules23112877. [PMID: 30400576 PMCID: PMC6278645 DOI: 10.3390/molecules23112877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
An 82-residue-long chimeric peptide was synthesised by solid phase peptide synthesis (SPPS), following the Fmoc protocol. Microwave (MW) radiation-assisted synthesis was compared to standard synthesis using low loading (0.20 mmol/g) of polyethylene glycol (PEG) resin. Similar synthetic difficulties were found when the chimeric peptide was obtained via these two reaction conditions, indicating that such difficulties were inherent to the sequence and could not be resolved using MW; by contrast, the number of coupling cycles and total reaction time became reduced whilst crude yield and percentage recovery after purification were higher for MW radiation-assisted synthesis.
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6
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Wen L, Edmunds G, Gibbons C, Zhang J, Gadi MR, Zhu H, Fang J, Liu X, Kong Y, Wang PG. Toward Automated Enzymatic Synthesis of Oligosaccharides. Chem Rev 2018; 118:8151-8187. [DOI: 10.1021/acs.chemrev.8b00066] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Liuqing Wen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Garrett Edmunds
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Christopher Gibbons
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jiabin Zhang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Madhusudhan Reddy Gadi
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Hailiang Zhu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Junqiang Fang
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Xianwei Liu
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Yun Kong
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Peng George Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National Glycoengineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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7
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Shin YH, Gellman SH. Impact of Backbone Pattern and Residue Substitution on Helicity in α/β/γ-Peptides. J Am Chem Soc 2018; 140:1394-1400. [PMID: 29350033 DOI: 10.1021/jacs.7b10868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have evaluated the impact of changes in the chemical structure of peptidic oligomers containing α-, β-, and γ-amino acid residues (α/β/γ-peptides) on the propensities of these oligomers to adopt helical conformations in aqueous and alcoholic solutions. These studies were inspired by our previous discovery that α/β/γ-peptides containing a regular αγααβα hexad repeat adopt an α-helix-like conformation in which the β and γ residues are aligned in a stripe along one side, and the remainder of the helix surface is defined by the α residues. This helix was found to be most stable when the β and γ residues were rigidified with specific cyclic constraints. Relaxation of the β residue constraints caused profound conformational destabilization, but relaxation of the γ residue constraints led to only a moderate drop in helicity. The new work more broadly characterizes the effect of γ residue substitution on helix stability, based on circular dichroism and two-dimensional NMR measurements. We find that even a fully unsubstituted γ residue (derived from γ-aminobutyric acid) supports a moderate helical propensity, which is surprising in light of the strong destabilizing effect of glycine residues on α-helix stability. Additional studies examine the effects of altering sequence in terms of amino acid type, by comparing a prototype with the αγααβα hexad pattern to isomers with irregular arrangements of the α, β, and γ residues along the backbone. The data indicate that the strong helix-forming propensity previously discovered for α/β/γ-peptide 12-mers is retained when sequence is varied, with small variations detected across diverse α-β-γ placements. These structural findings suggest that α/β/γ-peptide scaffolds represent versatile scaffolds for the design of peptidic foldamers that display specific functions.
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Affiliation(s)
- Young-Hee Shin
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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8
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Bartus É, Hegedüs Z, Wéber E, Csipak B, Szakonyi G, Martinek TA. De Novo Modular Development of a Foldameric Protein-Protein Interaction Inhibitor for Separate Hot Spots: A Dynamic Covalent Assembly Approach. ChemistryOpen 2017; 6:236-241. [PMID: 28413758 PMCID: PMC5390796 DOI: 10.1002/open.201700012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions stabilized by multiple separate hot spots are highly challenging targets for synthetic scaffolds. Surface-mimetic foldamers bearing multiple recognition segments are promising candidate inhibitors. In this work, a modular bottom-up approach is implemented by identifying short foldameric recognition segments that interact with the independent hot spots, and connecting them through dynamic covalent library (DCL) optimization. The independent hot spots of a model target (calmodulin) are mapped with hexameric β-peptide helices using a pull-down assay. Recognition segment hits are subjected to a target-templated DCL ligation through thiol-disulfide exchange. The most potent derivative displays low nanomolar affinity towards calmodulin and effectively inhibits the calmodulin-TRPV1 interaction. The DCL assembly of the folded segments offers an efficient approach towards the de novo development of a high-affinity inhibitor of protein-protein interactions.
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Affiliation(s)
- Éva Bartus
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Zsófia Hegedüs
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Brigitta Csipak
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Tamás A. Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
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9
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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10
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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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11
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Deiss F, Yang Y, Matochko WL, Derda R. Heat-enhanced peptide synthesis on Teflon-patterned paper. Org Biomol Chem 2016; 14:5148-56. [DOI: 10.1039/c6ob00898d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we describe the methodology for 96 parallel organic syntheses of peptides on Teflon-patterned paper assisted by heating with an infra-red lamp.
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Affiliation(s)
- Frédérique Deiss
- Department of Chemistry and Alberta Glycomics Centre
- University of Alberta
- Edmonton
- Canada
| | - Yang Yang
- Department of Chemistry and Alberta Glycomics Centre
- University of Alberta
- Edmonton
- Canada
| | - Wadim L. Matochko
- Department of Chemistry and Alberta Glycomics Centre
- University of Alberta
- Edmonton
- Canada
| | - Ratmir Derda
- Department of Chemistry and Alberta Glycomics Centre
- University of Alberta
- Edmonton
- Canada
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12
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Helmer D, Schmitz K. Peptides and Peptide Analogs to Inhibit Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:147-83. [PMID: 27236556 DOI: 10.1007/978-3-319-32805-8_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Protein-protein interactions are governed by relatively few amino acid residues at the binding interface. Peptides derived from these protein regions may serve as mimics of one of the interaction partners in structural studies or as inhibitors to disrupt the respective interaction and investigate its biological consequences. Inhibitory peptides may also be lead structures for drug development if the respective protein-protein interaction is essential for a pathogen or disease mechanism. Binding peptides may be systematically derived from one of the binding partners or found in the screen of combinatorial peptide libraries. Molecular modelling based on structural data helps to refine existing peptides or even design novel binding peptides. This chapter gives an outline of the binding peptide discovery process and subsequent chemical modifications to further enhance affinity and specificity and to increase stability against degradation in vivo. Examples from the past three decades illustrate the great diversity of applications for protein binding peptides and peptide analogs.
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Affiliation(s)
- Dorothea Helmer
- Technische Universität Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Katja Schmitz
- Technische Universität Darmstadt, Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
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13
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Peterson-Kaufman KJ, Haase HS, Boersma MD, Lee EF, Fairlie WD, Gellman SH. Residue-Based Preorganization of BH3-Derived α/β-Peptides: Modulating Affinity, Selectivity and Proteolytic Susceptibility in α-Helix Mimics. ACS Chem Biol 2015; 10:1667-75. [PMID: 25946900 DOI: 10.1021/acschembio.5b00109] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report progress toward a general strategy for mimicking the recognition properties of specific α-helices within natural proteins through the use of oligomers that are less susceptible than conventional peptides to proteolysis. The oligomers contain both α- and β-amino acid residues, with the density of the β subunits low enough that an α-helix-like conformation can be adopted but high enough to interfere with protease activity. Previous studies with a different protein-recognition system that suggested ring-constrained β residues can be superior to flexible β residues in terms of maximizing α/β-peptide affinity for a targeted protein surface. Here, we use mimicry of the 18-residue Bim BH3 domain to expand the scope of this strategy. Two significant advances have been achieved. First, we have developed and validated a new ring-constrained β residue that bears an acidic side chain, which complements previously known analogues that are either hydrophobic or basic. Second, we have discovered that placing cyclic β residues at sites that make direct contact with partner proteins can lead to substantial discrimination between structurally homologous binding partners, the proteins Bcl-xL and Mcl-1. Overall, this study helps to establish that α/β-peptides containing ring-preorganized β residues can reliably provide proteolytically resistant ligands for proteins that naturally evolved to recognize α-helical partners.
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Affiliation(s)
| | - Holly S. Haase
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Melissa D. Boersma
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Erinna F. Lee
- Structural
Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - W. Douglas Fairlie
- Structural
Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, 1101 University Ave., Madison, Wisconsin 53706, United States
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14
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Sambasivan R, Ball ZT. Studies of Asymmetric StyreneCyclopropanation with a Rhodium(II) Metallopeptide Catalyst Developed with a High-Throughput Screen. Chirality 2013; 25:493-7. [DOI: 10.1002/chir.22144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/16/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Ramya Sambasivan
- Department of Chemistry MS60; Rice University; 6100 Main Street Houston TX 77005
| | - Zachary T. Ball
- Department of Chemistry MS60; Rice University; 6100 Main Street Houston TX 77005
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15
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Abstract
This chapter provides an introduction to and an overview of current instrumentation for solid-phase peptide synthesis (SPPS). Presently, the two most common designs differ in their mode of liquid handling: the first relies on valves and valve blocks for distribution of reagents, while the second uses a robotic platform. They also differ in their mode of mixing the reactants in the reaction vessel, where the former can utilize sparging, 180° rotational shaking, or vortexing, while the latter typically uses vortexing. Valve-based instruments are often single channel (one peptide at a time), but can also be expanded to allow parallel synthesis of up to 12 and even 24 peptides, however, at the price of added complexity. Valve systems often use inert gas for their operation. The X-Y robotic platforms are ideal for parallel synthesis of large numbers of peptides up to 192 and even peptide libraries. However, although less common, the robotic platform is also very suitable for single-channel operation and can also be used for operations under inert gas. Some single-channeled synthesizers are available with UV feedback monitoring of the Fmoc removal which can be useful for some applications. Importantly, single-channel synthesizers can be equipped with fast and precise microwave heating to accelerate the synthesis and to overcome synthetic difficulties. A whole range of synthesizers with different designs are commercially available. The choice of peptide synthesizer will depend on intended application, for example on the type of chemistry, scale, and the number of peptides that are required and so on.
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Affiliation(s)
- Søren L Pedersen
- IGM, Faculty of Life Sciences, University of Copenhagen, Gubra, Hørsholm, Denmark
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16
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Hussein WM, Liu TY, Toth I, Skwarczynski M. Microwave-assisted synthesis of difficult sequence-containing peptides using the isopeptide method. Org Biomol Chem 2013; 11:2370-6. [DOI: 10.1039/c3ob00030c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Mahindra A, Nooney K, Uraon S, Sharma KK, Jain R. Microwave-assisted solution phase peptide synthesis in neat water. RSC Adv 2013. [DOI: 10.1039/c3ra43040e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Abstract
The tool chest of techniques, methodologies, and equipment for conducting parallel chemistry is larger than ever before. Improvements in the laboratory and developments in computational chemistry have enabled compound library design at the desks of medicinal chemists. This unit includes a brief background in combinatorial/parallel synthesis chemistry, along with a discussion of evolving technologies for both solid- and solution-phase chemistry. In addition, there are discussions on designing compound libraries, acquisition/procurement of compounds and/or reagents, the chemistry and equipment used for chemical production, purification, sample handling, and data analysis.
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Affiliation(s)
- Alan Long
- SCYNEXIS, Research Triangle Park, NC, USA
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19
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20
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Deverakonda M, Mailavaram RP, Deb PK, Banda N, Vedula GS. Rapid and Efficient, Microwave-Assisted, Base-Catalyzed Synthesis of Some Novel 2,7-Disubstituted Pyrrolopyrimidinones. SYNTHETIC COMMUN 2012. [DOI: 10.1080/00397911.2011.576324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Douat-Casassus C, Pulka K, Claudon P, Guichard G. Microwave-Enhanced Solid-Phase Synthesis of N,N′-Linked Aliphatic Oligoureas and Related Hybrids. Org Lett 2012; 14:3130-3. [DOI: 10.1021/ol3012106] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Céline Douat-Casassus
- Université de Bordeaux–CNRS UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Karolina Pulka
- Université de Bordeaux–CNRS UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Paul Claudon
- Université de Bordeaux–CNRS UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Gilles Guichard
- Université de Bordeaux–CNRS UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
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22
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Pedersen SL, Tofteng AP, Malik L, Jensen KJ. Microwave heating in solid-phase peptide synthesis. Chem Soc Rev 2012; 41:1826-44. [DOI: 10.1039/c1cs15214a] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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23
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Murray JK, Aral J, Miranda LP. Solid-phase peptide synthesis using microwave irradiation. Methods Mol Biol 2011; 716:73-88. [PMID: 21318901 DOI: 10.1007/978-1-61779-012-6_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Since the advent of solid-phase peptide synthesis (SPPS) in the late 1950s, numerous advancements in the underlying chemistry (i.e., orthogonal protection strategy, coupling reagents, and solid support matrices) have greatly improved the efficiency of the technique. More recently, application of microwave radiation to SPPS has been found to reduce reaction time and/or increase the initial purity of synthetic peptide products. In this protocol, conditions are described to accomplish rapid peptide coupling and 9-fluorenylmethoxycarbonyl (Fmoc) removal reactions under temperature-controlled conditions in either a manual or automated synthesis format using a microwave reactor. These microwave-assisted peptide synthesis procedures have been used to rapidly prepare a "difficult" peptide sequence from the acyl carrier protein, ACP(65-74), in less than 3 h and the reduced, linear precursor to human hepcidin, in high initial purity.
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24
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Sawada T, Gellman SH. Structural mimicry of the α-helix in aqueous solution with an isoatomic α/β/γ-peptide backbone. J Am Chem Soc 2011; 133:7336-9. [PMID: 21520956 PMCID: PMC3141811 DOI: 10.1021/ja202175a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artificial mimicry of α-helices offers a basis for development of protein-protein interaction antagonists. Here we report a new type of unnatural peptidic backbone, containing α-, β-, and γ-amino acid residues in an αγααβα repeat pattern, for this purpose. This unnatural hexad has the same number of backbone atoms as a heptad of α residues. Two-dimensional NMR data clearly establish the formation of an α-helix-like conformation in aqueous solution. The helix formed by our 12-mer α/β/γ-peptide is considerably more stable than the α-helix formed by an analogous 14-mer α-peptide, presumably because of the preorganized β and γ residues employed.
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Affiliation(s)
- Tomohisa Sawada
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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25
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Sammond DW, Joce C, Takeshita R, McQuate SE, Ghosh N, Martin JM, Yin H. Transmembrane peptides used to investigate the homo-oligomeric interface and binding hotspot of latent membrane protein 1. Biopolymers 2011; 95:772-84. [PMID: 21560118 DOI: 10.1002/bip.21672] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/15/2011] [Accepted: 04/29/2011] [Indexed: 12/30/2022]
Abstract
Epstein-Barr virus (EBV), a human γ-herpesvirus, establishes lifelong infection by targeting the adaptive immune system of the host through memory B cells. Although normally benign, EBV contributes to lymphoid malignancies and lymphoproliferative syndromes in immunocompromised individuals. The viral oncoprotein latent membrane protein 1 (LMP-1) is essential for B lymphocyte immortalization by EBV. The constitutive signaling activity of LMP-1 is dependent on homo-oligomerization of its six-spanning hydrophobic transmembrane domain (TMD). However, the mechanism driving LMP-1 intermolecular interaction is poorly understood. Here, we show that the fifth transmembrane helix (TM5) of LMP-1 strongly self-associates, forming a homotrimeric complex mediated by a polar residue embedded in the membrane, D150. Replacement of this aspartic acid residue with alanine disrupts TM5 self-association in detergent micelles and bacterial cell membranes. A full-length LMP-1 variant harboring the D150A substitution is deficient in NFκB activation, supporting the key role of the fifth transmembrane helix in constitutive activation of signaling by this oncoprotein.
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Affiliation(s)
- Deanne W Sammond
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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26
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Chanda K, Maiti B, Yellol GS, Chien MH, Kuo ML, Sun CM. Polymer supported synthesis of novel benzoxazole linked benzimidazoles under microwave conditions: in vitro evaluation of VEGFR-3 kinase inhibition activity. Org Biomol Chem 2011; 9:1917-26. [PMID: 21283915 DOI: 10.1039/c0ob00547a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An efficient soluble polymer-supported method has been developed for the parallel synthesis of substituted benzimidazole linked benzoxazoles using focused microwave irradiation. The key step involves the amidation of 4-hydroxy-3-nitrobenzoic acid with polymer-immobilized o-phenylenediamine. Application of mild acidic conditions promoted the ring closure to furnish the benzimidazole ring. After hydrogenation of the nitro-group to amine, the resulted polymer conjugates underwent efficient ring closure with various alkyl, aryl and heteroaryl isothiocyanates to generate the polymer-bound benzimidazolyl benzoxazoles. The polymer-bound compounds were finally cleaved from the support to furnish benzimidazole linked benzoxazole derivatives. The efficacy of the resultant angular bis-heterocyclic library was studied against vascular endothelial growth factor receptor (VEGFR-3). The preliminary screening of these novel compounds exhibits moderate to high inhibition (IC(50) = 0.56-1.42 μM). This protocol provides an easy access to novel angular bis-heterocycles which have potential for the discovery of novel leads for targeted cancer therapeutics.
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Affiliation(s)
- Kaushik Chanda
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300-10, Taiwan
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27
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Helliwell PA, Fake RE, Kerr KG, Santry B, Speakman A, Routledge A. Microwave-Assisted Synthesis of Aryl Amide Bonds on Solid Phase. SYNTHETIC COMMUN 2010. [DOI: 10.1080/00397910903370618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Ruth E. Fake
- a Department of Chemistry , University of York , Heslington, York, UK
| | - Kevin G. Kerr
- b Department of Microbiology , Harrogate District Hospital , Harrogate, UK
| | - Barbara Santry
- a Department of Chemistry , University of York , Heslington, York, UK
| | - Austen Speakman
- a Department of Chemistry , University of York , Heslington, York, UK
| | - Anne Routledge
- a Department of Chemistry , University of York , Heslington, York, UK
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28
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Park S, Gunasekera S, Aboye TL, Göransson U. An Efficient Approach for the Total Synthesis of Cyclotides by Microwave Assisted Fmoc-SPPS. Int J Pept Res Ther 2010. [DOI: 10.1007/s10989-010-9221-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Synthesis of alkyl- and aryl-amino-substituted anthraquinone derivatives by microwave-assisted copper(0)-catalyzed Ullmann coupling reactions. Nat Protoc 2010; 5:945-53. [DOI: 10.1038/nprot.2010.63] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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30
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Facile construction of fluorescent peptide microarrays: One-step fluorescent derivatization of sub-microscale peptide aldehydes for selective terminal immobilization. Anal Biochem 2010; 398:132-4. [PMID: 19903446 DOI: 10.1016/j.ab.2009.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/30/2009] [Accepted: 11/04/2009] [Indexed: 11/20/2022]
Abstract
In this note, we demonstrate the utility of bifunctional fluorescent linkers to facilitate the construction of peptide microarrays with either an N- or a C-terminal alkylamine for directionally preferred peptide immobilization. Significantly, these small tags facilitate high-performance liquid chromatography (HPLC) profiling while limiting interference with antigen-antibody interactions after peptide immobilization. In a model peptide-antibody binding assay, a sequence-dependent orientation effect of antibody binding to a series of peptide ligands was demonstrated. This approach provides a strategy that can be applied to a variety of peptide microarray-based detection systems.
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31
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Galanis AS, Albericio F, Grøtli M. Solid-phase peptide synthesis in water using microwave-assisted heating. Org Lett 2009; 11:4488-91. [PMID: 19757802 DOI: 10.1021/ol901893p] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An approach using water as a solvent (coupling and deprotection) was developed for the solid-phase synthesis of peptides using the most common Boc-amino acid derivatives. Key aspects of this methodology are the use of a PEG-based resin, EDC-HONB as a coupling method, and microwave irradiation as an energy source.
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Affiliation(s)
- Athanassios S Galanis
- Department of Chemistry, Medicinal Chemistry, University of Gothenburg, SE-412 96 Goteborg, Sweden
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32
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Banerjee J, Hanson AJ, Muhonen WW, Shabb JB, Mallik S. Microwave-assisted synthesis of triple-helical, collagen-mimetic lipopeptides. Nat Protoc 2009; 5:39-50. [PMID: 20057380 DOI: 10.1038/nprot.2009.195] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, we report a rapid microwave-assisted, solid-phase synthetic protocol to prepare the fatty-acid conjugated, triple-helical peptides containing the cleavage site for the enzyme matrix metalloproteinase-9 (MMP-9). We employed a PEG-based resin as the solid support and the amino acids were protected with Fmoc- and tert-butyl groups. The amino acids were coupled at 50 degrees C (25 W of microwave power) for 5 min. The deprotection reactions were carried out at 75 degrees C (35 W of microwave power) for 3 min. Using this protocol, a peptide containing 23 amino acids was synthesized and then conjugated to stearic acid in 14 h.
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Affiliation(s)
- Jayati Banerjee
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota, USA
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33
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34
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35
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Galanis AS, Albericio F, Grøtli M. Enhanced microwave-assisted method for on-bead disulfide bond formation: synthesis of alpha-conotoxin MII. Biopolymers 2009; 92:23-34. [PMID: 19003899 DOI: 10.1002/bip.21116] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A novel enhanced microwave-assisted disulfide bridge formation method has been developed. To optimize the synthesis of the biologically important bicyclic peptide alpha-conotoxin MII (alpha-CtxMII), several cyclization methods have been tested and are discussed herein. By using m.w.-assisted heating, we achieved high yields for the first loop cyclization of alpha-CtxMII on-bead. This method has the advantage of avoiding intermolecular by-products during the cyclization step. Furthermore, the method gives higher yields compared with the common on-bead cyclization methods. The second disulfide bridge of alpha-CtxMII was formed using a simple oxidation method after the cleavage of the intermediate monocyclic peptide from the resin. This method has the potential to be efficient for the synthesis of other disulfide rich biologically important peptides.
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Affiliation(s)
- Athanassios S Galanis
- Department of Chemistry, Medicinal Chemistry, University of Göteborg, SE-41296 Göteborg, Sweden
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36
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37
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Banerjee A, Sergienko E, Vasile S, Gupta V, Vuori K, Wipf P. Triple hybrids of steroids, spiroketals, and oligopeptides as new biomolecular chimeras. Org Lett 2009; 11:65-8. [PMID: 19067551 PMCID: PMC4257705 DOI: 10.1021/ol802247m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An oxidative enol ether rearrangement was the key methodology in the construction of steroid-spiroketal-RGD peptides. Biological studies demonstrated potent integrin CD11b/CD18 antagonistic effects.
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Affiliation(s)
- Abhisek Banerjee
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Eduard Sergienko
- Burnham Center for Chemical Genomics, Burnham Institute for Medical Research, 10901 North Torrey Pines Rd., La Jolla, California 92037
| | - Stefan Vasile
- Burnham Center for Chemical Genomics, Burnham Institute for Medical Research, 10901 North Torrey Pines Rd., La Jolla, California 92037
| | - Vineet Gupta
- Division of Nephrology and Hypertension, University of Miami, 1600 NW 10 Avenue, Miami, Florida 33136
| | - Kristiina Vuori
- Burnham Center for Chemical Genomics, Burnham Institute for Medical Research, 10901 North Torrey Pines Rd., La Jolla, California 92037
| | - Peter Wipf
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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38
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Lee SS, Lim J, Cha J, Tan S, Heath JR. Rapid microwave-assisted CNBr cleavage of bead-bound peptides. JOURNAL OF COMBINATORIAL CHEMISTRY 2008; 10:807-9. [PMID: 18811218 PMCID: PMC2720530 DOI: 10.1021/cc800113d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Junhoe Cha
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Sylvia Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - James R. Heath
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
- Division of Chemistry and Chemical Engineering, Caltech. MC 127-72, Pasadena, CA 911125
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39
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Bacsa B, Horváti K, Bõsze S, Andreae F, Kappe CO. Solid-Phase Synthesis of Difficult Peptide Sequences at Elevated Temperatures: A Critical Comparison of Microwave and Conventional Heating Technologies. J Org Chem 2008; 73:7532-42. [DOI: 10.1021/jo8013897] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bernadett Bacsa
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, 1117 Budapest, Hungary, and piCHEM Forschungs und EntwicklungsgmbH, Kahngasse 20, A-8045 Graz, Austria
| | - Kata Horváti
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, 1117 Budapest, Hungary, and piCHEM Forschungs und EntwicklungsgmbH, Kahngasse 20, A-8045 Graz, Austria
| | - Szilvia Bõsze
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, 1117 Budapest, Hungary, and piCHEM Forschungs und EntwicklungsgmbH, Kahngasse 20, A-8045 Graz, Austria
| | - Fritz Andreae
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, 1117 Budapest, Hungary, and piCHEM Forschungs und EntwicklungsgmbH, Kahngasse 20, A-8045 Graz, Austria
| | - C. Oliver Kappe
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, 1117 Budapest, Hungary, and piCHEM Forschungs und EntwicklungsgmbH, Kahngasse 20, A-8045 Graz, Austria
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40
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Elegbede AI, Banerjee J, Hanson AJ, Tobwala S, Ganguli B, Wang R, Lu X, Srivastava DK, Mallik S. Mechanistic studies of the triggered release of liposomal contents by matrix metalloproteinase-9. J Am Chem Soc 2008; 130:10633-42. [PMID: 18642903 PMCID: PMC2644422 DOI: 10.1021/ja801548g] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Matrix metalloproteinases (MMPs) constitute a class of extracellular-matrix-degrading enzymes overexpressed in many cancers and contribute to the metastatic ability of the cancer cells. We have recently demonstrated that liposomal contents can be released when triggered by the enzyme MMP-9. Herein, we report the results of our mechanistic studies of the MMP-9-triggered release of liposomal contents. We synthesized peptides containing the cleavage site for MMP-9 and conjugated them with fatty acids to prepare the corresponding lipopeptides. By employing circular dichroism (CD) spectroscopy, we demonstrated that the lipopeptides, when incorporated into liposomes, are demixed in the lipid bilayers and generate triple-helical structures. MMP-9 cleaves the triple-helical peptides, leading to the release of the liposomal contents. Other MMPs, which cannot hydrolyze triple-helical peptides, fail to release the contents from the liposomes. We also observed that the rate and extent of release of the liposomal contents depend on the mismatch between the acyl chains of the synthesized lipopeptide and phospholipid components of the liposomes. CD spectroscopic studies imply that the observed differences in the release reflect the ability of the liposomal membrane to anneal the defects following the enzymatic cleavage of the liposome-incorporated lipopeptides.
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Affiliation(s)
- Adekunle I. Elegbede
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58105
| | - Jayati Banerjee
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58105
| | - Andrea J. Hanson
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58105
| | - Shakila Tobwala
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Bratati Ganguli
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Rongying Wang
- Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Xiaoning Lu
- Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - D. K. Srivastava
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58105
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41
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Interplay among side chain sequence, backbone composition, and residue rigidification in polypeptide folding and assembly. Proc Natl Acad Sci U S A 2008; 105:9151-6. [PMID: 18587049 DOI: 10.1073/pnas.0801135105] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extent to which polypeptide conformation depends on side-chain composition and sequence has been widely studied, but less is known about the importance of maintaining an alpha-amino acid backbone. Here, we examine a series of peptides with backbones that feature different repeating patterns of alpha- and beta-amino acid residues but an invariant side-chain sequence. In the pure alpha-backbone, this sequence corresponds to the previously studied peptide GCN4-pLI, which forms a very stable four-helix bundle quaternary structure. Physical characterization in solution and crystallographic structure determination show that a variety of alpha/beta-peptide backbones can adopt sequence-encoded quaternary structures similar to that of the alpha prototype. There is a loss in helix bundle stability upon beta-residue incorporation; however, stability of the quaternary structure is not a simple function of beta-residue content. We find that cyclically constrained beta-amino acid residues can stabilize the folds of alpha/beta-peptide GCN4-pLI analogues and restore quaternary structure formation to backbones that are predominantly unfolded in the absence of cyclic residues. Our results show a surprising degree of plasticity in terms of the backbone compositions that can manifest the structural information encoded in a sequence of amino acid side chains. These findings offer a framework for the design of nonnatural oligomers that mimic the structural and functional properties of proteins.
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42
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Application of microwave method to the solid phase synthesis of pseudopeptides containing ester bond. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2007.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Bacsa B, Kappe CO. Rapid solid-phase synthesis of a calmodulin-binding peptide using controlled microwave irradiation. Nat Protoc 2007; 2:2222-7. [PMID: 17853879 DOI: 10.1038/nprot.2007.300] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A rapid and efficient microwave-assisted solid-phase synthesis method for the preparation of a nonapeptide using conventional Fmoc/Bu(t) orthogonal protection strategy is described. In this protocol, the coupling steps are performed within 5 min at 60 degrees C and the Fmoc-deprotection steps are completed within 3 min at 60 degrees C using a dedicated single-mode microwave peptide synthesizer utilizing temperature-controlled conditions. It is demonstrated that the model nonapeptide (containing the calmodulin-binding octapeptide sequence) is synthesized in a shorter time (approximately 3.5 h) and with high purity (>95%) under microwave irradiation conditions in comparison with a reference peptide that is obtained by standard methods at room temperature (within 11 h).
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Affiliation(s)
- Bernadett Bacsa
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Graz, Austria
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44
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Sadowsky JD, Murray JK, Tomita Y, Gellman SH. Exploration of Backbone Space in Foldamers Containing α- and β-Amino Acid Residues: Developing Protease-Resistant Oligomers that Bind Tightly to the BH3-Recognition Cleft of Bcl-xL. Chembiochem 2007; 8:903-16. [PMID: 17503422 DOI: 10.1002/cbic.200600546] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-protein interactions play crucial roles in cell-signaling events and are often implicated in human disease. Molecules that bind tightly to functional protein-surface sites and show high stability to degradative enzymes could be valuable pharmacological tools for dissection of cell-signaling networks and might ultimately lead to therapeutic agents. We recently described oligomers containing both alpha- and beta-amino acid residues that bind tightly to the BH3 recognition site of the anti-apoptotic protein Bcl-x(L). The oligomers with highest affinity had a nine-residue N-terminal segment with a 1:1 alpha:beta residue repeat and a six-residue C-terminal segment containing exclusively proteinogenic alpha-residues. The N-terminal portions of such (alpha/beta+alpha)-peptides are highly resistant to proteolysis, but the C-terminal alpha-segments are susceptible. This study emerged from efforts to modify the alpha-segment in an (alpha/beta+alpha)-peptide in a way that would diminish proteolytic degradation but retain high affinity for Bcl-x(L). Some of the oligomers reported here could prove useful in certain biological applications, particularly those for which extended incubation in a biological milieu is required.
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Affiliation(s)
- Jack D Sadowsky
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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