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Pathak P, Zarandi MA, Zhou X, Jayawickramarajah J. Synthesis and Applications of Porphyrin-Biomacromolecule Conjugates. Front Chem 2021; 9:764137. [PMID: 34820357 PMCID: PMC8606752 DOI: 10.3389/fchem.2021.764137] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/25/2021] [Indexed: 01/10/2023] Open
Abstract
With potential applications in materials and especially in light-responsive biomedicine that targets cancer tissue selectively, much research has focused on developing covalent conjugation techniques to tether porphyrinoid units to various biomacromolecules. This review details the key synthetic approaches that have been employed in the recent decades to conjugate porphyrinoids with oligonucleotides and peptides/proteins. In addition, we provide succinct discussions on the subsequent applications of such hybrid systems and also give a brief overview of the rapidly progressing field of porphyrin-antibody conjugates. Since nucleic acid and peptide systems vary in structure, connectivity, functional group availability and placement, as well as stability and solubility, tailored synthetic approaches are needed for conjugating to each of these biomacromolecule types. In terms of tethering to ONs, porphyrins are typically attached by employing bioorthogonal chemistry (e.g., using phosphoramidites) that drive solid-phase ON synthesis or by conducting post-synthesis modifications and subsequent reactions (such as amide couplings, hydrazide-carbonyl reactions, and click chemistry). In contrast, peptides and proteins are typically conjugated to porphyrinoids using their native functional groups, especially the thiol and amine side chains. However, bioorthogonal reactions (e.g., Staudinger ligations, and copper or strain promoted alkyne-azide cycloadditions) that utilize de novo introduced functional groups onto peptides/proteins have seen vigorous development, especially for site-specific peptide-porphyrin tethering. While the ON-porphyrin conjugates have largely been explored for programmed nanostructure self-assembly and artificial light-harvesting applications, there are some reports of ON-porphyrin systems targeting clinically translational applications (e.g., antimicrobial biomaterials and site-specific nucleic acid cleavage). Conjugates of porphyrins with proteinaceous moieties, on the other hand, have been predominantly used for therapeutic and diagnostic applications (especially in photodynamic therapy, photodynamic antimicrobial chemotherapy, and photothermal therapy). The advancement of the field of porphyrinoid-bioconjugation chemistry from basic academic research to more clinically targeted applications require continuous fine-tuning in terms of synthetic strategies and hence there will continue to be much exciting work on porphyrinoid-biomacromolecule conjugation.
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Affiliation(s)
- Pravin Pathak
- Department of Chemistry, Tulane University, New Orleans, LA, United States
| | | | - Xiao Zhou
- Department of Chemistry, Tulane University, New Orleans, LA, United States
| | - Janarthanan Jayawickramarajah
- Department of Chemistry, Tulane University, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University, New Orleans, LA, United States
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Basauri-Molina M, Verhoeven DGA, van Schaik AJ, Kleijn H, Klein Gebbink RJM. Ring-Closing and Cross-Metathesis with Artificial Metalloenzymes Created by Covalent Active Site-Directed Hybridization of a Lipase. Chemistry 2015; 21:15676-85. [PMID: 26346291 DOI: 10.1002/chem.201502381] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/08/2022]
Abstract
A series of Grubbs-type catalysts that contain lipase-inhibiting phosphoester functionalities have been synthesized and reacted with the lipase cutinase, which leads to artificial metalloenzymes for olefin metathesis. The resulting hybrids comprise the organometallic fragment that is covalently bound to the active amino acid residue of the enzyme host in an orthogonal orientation. Differences in reactivity as well as accessibility of the active site by the functionalized inhibitor became evident through variation of the anchoring motif and substituents on the N-heterocyclic carbene ligand. Such observations led to the design of a hybrid that is active in the ring-closing metathesis and the cross-metathesis of N,N-diallyl-p-toluenesulfonamide and allylbenzene, respectively, the latter being the first example of its kind in the field of artificial metalloenzymes.
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Affiliation(s)
- Manuel Basauri-Molina
- Organic Chemistry and Catalysis, Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584CG (The Netherlands)
| | - Dide G A Verhoeven
- Organic Chemistry and Catalysis, Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584CG (The Netherlands)
| | - Arnoldus J van Schaik
- Organic Chemistry and Catalysis, Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584CG (The Netherlands)
| | - Henk Kleijn
- Organic Chemistry and Catalysis, Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584CG (The Netherlands)
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Nanomaterials Science, Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht 3584CG (The Netherlands).
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Brath U, Swamy SI, Veiga AX, Tung CC, Van Petegem F, Erdélyi M. Paramagnetic Ligand Tagging To Identify Protein Binding Sites. J Am Chem Soc 2015; 137:11391-8. [PMID: 26289584 PMCID: PMC4583072 DOI: 10.1021/jacs.5b06220] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Transient
biomolecular interactions are the cornerstones of the
cellular machinery. The identification of the binding sites for low
affinity molecular encounters is essential for the development of
high affinity pharmaceuticals from weakly binding leads but is hindered
by the lack of robust methodologies for characterization of weakly
binding complexes. We introduce a paramagnetic ligand tagging approach
that enables localization of low affinity protein–ligand binding
clefts by detection and analysis of intermolecular protein NMR pseudocontact
shifts, which are invoked by the covalent attachment of a paramagnetic
lanthanoid chelating tag to the ligand of interest. The methodology
is corroborated by identification of the low millimolar volatile anesthetic
interaction site of the calcium sensor protein calmodulin. It presents
an efficient route to binding site localization for low affinity complexes
and is applicable to rapid screening of protein–ligand systems
with varying binding affinity.
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Affiliation(s)
- Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Shashikala I Swamy
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Alberte X Veiga
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
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Pentela N, Murugan P, Jaisankar SN, Samanta D, Mandal AB. Immobilization of ruthenium benzylidene on thermoresponsive polymer: Methodology and application. J Organomet Chem 2015. [DOI: 10.1016/j.jorganchem.2014.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Sista P, Ghosh K, Martinez JS, Rocha RC. Metallo-Biopolymers: Conjugation Strategies and Applications. POLYM REV 2014. [DOI: 10.1080/15583724.2014.913063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Lin YA, Boutureira O, Lercher L, Bhushan B, Paton RS, Davis BG. Rapid cross-metathesis for reversible protein modifications via chemical access to Se-allyl-selenocysteine in proteins. J Am Chem Soc 2013; 135:12156-9. [PMID: 23889088 PMCID: PMC3810893 DOI: 10.1021/ja403191g] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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Cross-metathesis (CM) has recently
emerged as a viable strategy for protein modification. Here, efficient
protein CM has been demonstrated through biomimetic chemical access
to Se-allyl-selenocysteine (Seac), a metathesis-reactive
amino acid substrate, via dehydroalanine. On-protein reaction kinetics
reveal a rapid reaction with rate constants of Seac-mediated-CM comparable
or superior to off-protein rates of many current bioconjugations.
This use of Se-relayed Seac CM on proteins has now
enabled reactions with substrates (allyl GlcNAc, N-allyl acetamide) that were previously not possible for the corresponding
sulfur analogue. This CM strategy was applied to histone proteins
to install a mimic of acetylated lysine (KAc, an epigenetic marker).
The resulting synthetic H3 was successfully recognized by antibody
that binds natural H3-K9Ac. Moreover, Cope-type selenoxide elimination
allowed this putative marker (and function) to be chemically expunged,
regenerating an H3 that can be rewritten to complete a chemically
enabled “write (CM)–erase (ox)–rewrite (CM)”
cycle.
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Affiliation(s)
- Yuya A Lin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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Singh R, Vince R. 2-Azabicyclo[2.2.1]hept-5-en-3-one: Chemical Profile of a Versatile Synthetic Building Block and its Impact on the Development of Therapeutics. Chem Rev 2012; 112:4642-86. [DOI: 10.1021/cr2004822] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rohit Singh
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
| | - Robert Vince
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
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Biochemical analysis with the expanded genetic lexicon. Anal Bioanal Chem 2012; 403:2089-102. [PMID: 22322380 DOI: 10.1007/s00216-012-5784-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/17/2012] [Accepted: 01/23/2012] [Indexed: 02/02/2023]
Abstract
The information used to build proteins is stored in the genetic material of every organism. In nature, ribosomes use 20 native amino acids to synthesize proteins in most circumstances. However, laboratory efforts to expand the genetic repertoire of living cells and organisms have successfully encoded more than 80 nonnative amino acids in E. coli, yeast, and other eukaryotic systems. The selectivity, fidelity, and site-specificity provided by the technology have enabled unprecedented flexibility in manipulating protein sequences and functions in cells. Various biophysical probes can be chemically conjugated or directly incorporated at specific residues in proteins, and corresponding analytical techniques can then be used to answer diverse biological questions. This review summarizes the methodology of genetic code expansion and its recent progress, and discusses the applications of commonly used analytical methods.
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Giuntini F, Alonso CMA, Boyle RW. Synthetic approaches for the conjugation of porphyrins and related macrocycles to peptides and proteins. Photochem Photobiol Sci 2011; 10:759-91. [DOI: 10.1039/c0pp00366b] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Tiefenbrunn TK, Dawson PE. Chemoselective ligation techniques: modern applications of time-honored chemistry. Biopolymers 2010; 94:95-106. [PMID: 20091876 DOI: 10.1002/bip.21337] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chemoselective ligation techniques enable the selective modification of proteins and other biomolecules in dilute aqueous solution. Importantly, these reactions occur at or near physiological pH and are compatible with the complex array of functional groups commonly found in biological macromolecules including proteins, nucleotides, and carbohydrates, allowing conjugation reactions to be carried out on unprotected substrates. Recently, a growing number of reactions with established utility in synthetic organic chemistry have been shown to have surprising utility in the context of biological molecules in aqueous media. In this review we highlight several promising reactions that may have widespread applicability in the generation of new materials based on biological macromolecules.
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Affiliation(s)
- Theresa K Tiefenbrunn
- Department of Cell Biology, 10550 N. Torrey Pines Road, The Scripps Research Institute, La Jolla, CA 92037, USA
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Hili R, Rai V, Yudin AK. Macrocyclization of Linear Peptides Enabled by Amphoteric Molecules. J Am Chem Soc 2010; 132:2889-91. [PMID: 20155938 DOI: 10.1021/ja910544p] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan Hili
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
| | - Vishal Rai
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
| | - Andrei K. Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
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13
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The chemistry of the carbon-transition metal double and triple bond: Annual survey covering the year 2008. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2009.07.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Ai HW, Shen W, Brustad E, Schultz P. Genetically Encoded Alkenes in Yeast. Angew Chem Int Ed Engl 2009; 49:935-7. [DOI: 10.1002/anie.200905590] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Hughes CC, Yang YL, Liu WT, Dorrestein PC, La Clair JJ, Fenical W. Marinopyrrole A target elucidation by acyl dye transfer. J Am Chem Soc 2009; 131:12094-6. [PMID: 19673475 PMCID: PMC2769490 DOI: 10.1021/ja903149u] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The targeting of marinopyrrole A to actin was identified using a fluorescent dye transfer strategy. The process began by appending a carboxylic acid terminal tag to a phenol in the natural product. The resulting probe was then studied in live cells to verify that it maintained activity comparable to marinopyrrole A. Two-color fluorescence microscopy confirmed that both unlabeled and labeled materials share comparable uptake and subcellular localization in HCT-116 cells. Subsequent immunoprecipitation studies identified actin as a putative target in HCT-116 cells, a result that was validated by mass spectral, affinity, and activity analyses on purified samples of actin. Further data analyses indicated that the dye in the marinopyrrole probe was selectively transferred to a single residue K(115), an event that did not occur with related acyl phenols and reactive labels. In this study, the combination of cell, protein, and amino acid analysis arose from a single sample of material, thereby, suggesting a means to streamline and reduce material requirements involved in mode of action studies.
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Affiliation(s)
- Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego La Jolla, CA 92093-0204, USA
| | - Yu-Liang Yang
- Departments of Chemistry and Biochemistry, the Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego La Jolla, CA 92093-0204, USA
| | - Wei-Ting Liu
- Departments of Chemistry and Biochemistry, the Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego La Jolla, CA 92093-0204, USA
| | - Pieter C. Dorrestein
- Departments of Chemistry and Biochemistry, the Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego La Jolla, CA 92093-0204, USA
| | - James J. La Clair
- Xenobe Research Institute, 3371 Adams Avenue, San Diego, CA 92164-4073
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego La Jolla, CA 92093-0204, USA
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Lin YA, Chalker JM, Davis BG. Olefin Metathesis for Site-Selective Protein Modification. Chembiochem 2009; 10:959-69. [DOI: 10.1002/cbic.200900002] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Chalker JM, Lin YA, Boutureira O, Davis BG. Enabling olefin metathesis on proteins: chemical methods for installation of S-allyl cysteine. Chem Commun (Camb) 2009:3714-6. [DOI: 10.1039/b908004j] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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