1
|
JIANG B, GAO B, WEI S, LIANG Z, ZHANG L, ZHANG Y. [Progress in enrichment methods for protein N-phosphorylation]. Se Pu 2024; 42:623-631. [PMID: 38966971 PMCID: PMC11224942 DOI: 10.3724/sp.j.1123.2024.04029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Indexed: 07/06/2024] Open
Abstract
Protein phosphorylation is one of the most common and important post-translational modifications that regulates almost all life processes. In particular, protein phosphorylation regulates the development of major diseases such as tumors, neurodegenerative diseases, and diabetes. For example, excessive phosphorylation of Tau protein can cause neurofibrillary tangles, leading to Alzheimer's disease. Therefore, large-scale methods for identifying protein phosphorylation must be developed. Rapid developmentin efficient enrichment methods and biological mass spectrometry technologies have enabled the large-scale identification of low-abundance protein O-phosphorylation modifications in, allowing for a more thorough study of their biological functions. The N-phosphorylation modifications that occur on the side-chain amino groups of histidine, arginine, and lysine have recently received increased attention. For example, the biological function of histidine phosphorylation in prokaryotes has been well studied; this type of modification regulates signal transduction and sugar metabolism. Two mammalian pHis kinases (NME1 and NME2) and three pHis phosphatases (PHPT1, LHPP, and PGAM5) have been successfully identified using various biological methods. N-Phosphorylation is involved in multiple biological processes, and its functions cannot be ignored. However, N-phosphorylation is unstable under acidic and thermal conditions owing to the poor chemical stability of the P-N bond. Unfortunately, the current O-phosphorylation enrichment method, which relies on acidic conditions, is unsuitable for N-phosphorylation enrichment, resulting in a serious lag in the large-scale identification of protein N-phosphorylation. The lack of enrichment methods has also seriously hindered studies on the biological functions of N-phosphorylation. Therefore, the development of efficient enrichment methods that target protein N-phosphorylation is an urgent undertaking. Research on N-phosphorylation proteome enrichment methods is limited, hindering functional research. Thus, summarizing such methods is necessary to promote further functional research. This article introduces the structural characteristics and reported biological functions of protein N-phosphorylation, reviews the protein N-phosphorylation modification enrichment methods developed over the past two decades, and analyzes the advantages and disadvantages of each method. In this study, both antibody-based and nonantibody-dependent methods are described in detail. Owing to the stability of the molecular structure of histidine, the antibody method is currently limited to histidine phosphorylation enrichment research. Future studies will focus on the development of new enrichment ligands. Moreover, research on ligands will promote studies on other nonconventional phosphorylation targets, such as two acyl-phosphates (pAsp, pGlu) and S-phosphate (pCys). In summary, this review provides a detailed analysis of the history and development directions of N-phosphorylation enrichment methods.
Collapse
|
2
|
Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
Collapse
Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| |
Collapse
|
3
|
Jaiswal MK, Gupta A, Ansari FJ, Pandey VK, Tiwari VK. Recent Progress on Synthesis of Functionalized 1,5-Disubstituted Triazoles. Curr Org Synth 2024; 21:513-558. [PMID: 38804327 DOI: 10.2174/1570179420666230418123350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/13/2022] [Accepted: 01/12/2023] [Indexed: 05/29/2024]
Abstract
Immediately after the invention of 'Click Chemistry' in 2002, the regioselective 1,2,3- triazole scaffolds resulted from respective organic azides and terminal alkynes under Cu(I) catalysis have been well recognized as the functional heterocyclic core at the centre of modern organic chemistry, medicinal chemistry, and material sciences. This CuAAC reaction has several notable features including excellent regioselectivity, high-to-excellent yields, easy to execute, short reaction time, modular in nature, mild condition, readily available starting materials, etc. Moreover, the resulting regioselective triazoles can serve as amide bond isosteres, a privileged functional group in drug discovery and development. More than hundreds of reviews had been devoted to the 'Click Chemistry' in special reference to 1,4-disubstituted triazoles, while only little efforts were made for an opposite regioisomer i.e., 1,5-disubstituted triazole. Herein, we have presented various classical approaches for an expeditious synthesis of a wide range of biologically relevant 1,5- disubstituted 1,2,3-triazole analogues. The syntheses of such a class of diversly functionalized triazoles have emerged as a crucial investigation in the domain of chemistry and biology. This tutorial review covers the literature assessment on the development of various synthetic protocols for the functionalized 1,5-disubstituted triazoles reported during the last 12 years.
Collapse
Affiliation(s)
- Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Abhishek Gupta
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Faisal J Ansari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vinay K Pandey
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| |
Collapse
|
4
|
Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [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: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
Collapse
Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| |
Collapse
|
5
|
Xin T, Cummins CC. Mechanochemical Phosphorylation of Acetylides Using Condensed Phosphates: A Sustainable Route to Alkynyl Phosphonates. ACS CENTRAL SCIENCE 2023; 9:1575-1580. [PMID: 37637745 PMCID: PMC10451036 DOI: 10.1021/acscentsci.3c00725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 08/29/2023]
Abstract
In pursuit of a more sustainable route to phosphorus-carbon (P-C) bond-containing chemicals, we herein report that phosphonates can be prepared by mechanochemical phosphorylation of acetylides using polyphosphates in a single step, redox-neutral process, bypassing white phosphorus (P4) and other high-energy, environmentally hazardous intermediates. Using sodium triphosphate (Na5P3O10) and acetylides, alkynyl phosphonates 1 can be isolated in yields of up to 32%, while reaction of sodium pyrophosphate (Na4P2O7) and sodium carbide (Na2C2) engendered, in an optimized yield of 63%, ethynyl phosphonate 2, an easily isolable compound that can be readily converted to useful organophosphorus chemicals. Highly condensed phosphates like Graham's salt and bioproduced polyphosphate were also found to be compatible after reducing the chain length by grinding with orthophosphate. These results demonstrate the possibility of accessing organophosphorus chemicals directly from condensed phosphates and may offer an opportunity to move toward a "greener" phosphorus industry.
Collapse
Affiliation(s)
- Tiansi Xin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
6
|
Makwana MV, Dos Santos Souza C, Pickup BT, Thompson MJ, Lomada SK, Feng Y, Wieland T, Jackson RFW, Muimo R. Chemical Tools for Studying Phosphohistidine: Generation of Selective τ-Phosphohistidine and π-Phosphohistidine Antibodies. Chembiochem 2023; 24:e202300182. [PMID: 37183567 DOI: 10.1002/cbic.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
Nonhydrolysable stable analogues of τ-phosphohistidine (τ-pHis) and π-pHis have been designed, aided by electrostatic surface potential calculations, and subsequently synthesized. The τ-pHis and π-pHis analogues (phosphopyrazole 8 and pyridyl amino amide 13, respectively) were used as haptens to generate pHis polyclonal antibodies. Both τ-pHis and π-pHis conjugates in the form of BSA-glutaraldehyde-τ-pHis and BSA-glutaraldehyde-π-pHis were synthesized and characterized by 31 P NMR spectroscopy. Commercially available τ-pHis (SC56-2) and π-pHis (SC1-1; SC50-3) monoclonal antibodies were used to show that the BSA-G-τ-pHis and BSA-G-π-pHis conjugates could be used to assess the selectivity of pHis antibodies in a competitive ELISA. Subsequently, the selectivity of the pHis antibodies generated by using phosphopyrazole 8 and pyridyl amino amide 13 as haptens was assessed by competitive ELISA against His, pSer, pThr, pTyr, τ-pHis and π-pHis. Antibodies generated by using phosphopyrazole 8 as a hapten were found to be selective for τ-pHis, and antibodies generated by using pyridyl amino amide 13 were found to be selective for π-pHis. Both τ- and π-pHis antibodies were shown to be effective in immunological experiments, including ELISA, western blot, and immunofluorescence. The τ-pHis antibody was also shown to be useful in the immunoprecipitation of proteins containing pHis.
Collapse
Affiliation(s)
- Mehul V Makwana
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK
- Department of Infection Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Cleide Dos Santos Souza
- Sheffield Instituate of Translational Neuroscience, The University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK
| | - Barry T Pickup
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK
| | - Mark J Thompson
- Department of Oncology and Metabolism, Medical School, The University Of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Santosh K Lomada
- Experimental Pharmacology, European Center of Angioscience, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Yuxi Feng
- Experimental Pharmacology, European Center of Angioscience, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Thomas Wieland
- Experimental Pharmacology, European Center of Angioscience, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Richard F W Jackson
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK
| | - Richmond Muimo
- Department of Infection Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| |
Collapse
|
7
|
Zhang B, Zhou WQ, Liu XT, Sun Y, Zhang QW. A Ni-catalyzed asymmetric C(sp)-P cross-coupling reaction for the synthesis of P-stereogenic alkynylphosphines. Chem Sci 2023; 14:1286-1290. [PMID: 36756330 PMCID: PMC9891383 DOI: 10.1039/d2sc05841c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023] Open
Abstract
Due to the high reactivity of the triple bond, P-stereogenic alkynylphosphines could be easily derivatized, serving as universal building blocks for structurally diverse phosphine compounds. However, the synthesis of alkynylphosphines via direct P-C bond formation was unprecedented. Here, we report an efficient method for the synthesis of P-stereogenic alkynylphosphines with high enantioselectivity via a Ni-catalyzed asymmetric cross-coupling reaction. The reaction could tolerate a variety of functional groups, affording products that can be converted into useful phosphine derivatives.
Collapse
Affiliation(s)
- Bin Zhang
- Department of Chemistry, University of Science and Technology of China Hefei 230026 China
| | - Wen-Qing Zhou
- Department of Chemistry, University of Science and Technology of China Hefei 230026 China
| | - Xu-Teng Liu
- Department of Chemistry, University of Science and Technology of China Hefei 230026 China
| | - Yingying Sun
- Department of Chemistry, University of Science and Technology of China Hefei 230026 China
| | - Qing-Wei Zhang
- Department of Chemistry, University of Science and Technology of China Hefei 230026 China
| |
Collapse
|
8
|
Ji SH, Kim S, Nam G, Lee DH, Han SJ. Synthetic Strategy for Aryl(alkynyl)phosphinates by a Three-Component Coupling Reaction Involving Arynes, Phosphites, and Alkynes. Org Lett 2022; 24:8295-8299. [DOI: 10.1021/acs.orglett.2c03231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Su Hyun Ji
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department of Chemistry, Sogang University, 35 Baekbeom Ro, Seoul 04107, Republic of Korea
| | - Soomin Kim
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Ghilsoo Nam
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Duck-Hyung Lee
- Department of Chemistry, Sogang University, 35 Baekbeom Ro, Seoul 04107, Republic of Korea
| | - Seo-Jung Han
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| |
Collapse
|
9
|
Mele L, Luc Pirat J, Ayad T, Virieux D. New Approaches toward Building C
sp
−P bond: A Two‐Decade Overview. Chemistry 2022; 28:e202200957. [DOI: 10.1002/chem.202200957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Lucas Mele
- ICGM Univ Montpellier, CNRS, ENSCM Montpellier France
| | | | - Tahar Ayad
- ICGM Univ Montpellier, CNRS, ENSCM Montpellier France
| | - David Virieux
- ICGM Univ Montpellier, CNRS, ENSCM Montpellier France
| |
Collapse
|
10
|
Hu Y, Jiang B. Selective enrichment tandem β-elimination assisted strategy for N-phosphorylation analysis. Talanta 2022; 247:123580. [DOI: 10.1016/j.talanta.2022.123580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/27/2022]
|
11
|
Squair DR, Virdee S. A new dawn beyond lysine ubiquitination. Nat Chem Biol 2022; 18:802-811. [PMID: 35896829 DOI: 10.1038/s41589-022-01088-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/21/2022] [Indexed: 01/18/2023]
Abstract
The ubiquitin system has become synonymous with the modification of lysine residues. However, the substrate scope and diversity of the conjugation machinery have been underappreciated, bringing us to an epoch in ubiquitin system research. The striking discoveries of metazoan enzymes dedicated toward serine and threonine ubiquitination have revealed the important role of nonlysine ubiquitination in endoplasmic reticulum-associated degradation, immune signaling and neuronal processes, while reports of nonproteinaceous substrates have extended ubiquitination beyond the proteome. Bacterial effectors that bypass the canonical ubiquitination machinery and form unprecedented linkage chemistry further redefine long-standing dogma. While chemical biology approaches have advanced our understanding of the canonical ubiquitin system, further study of noncanonical ubiquitination has been hampered by a lack of suitable tools. This Perspective aims to consolidate and contextualize recent discoveries and to propose potential applications of chemical biology, which will be instrumental in unraveling this new frontier of ubiquitin research.
Collapse
Affiliation(s)
- Daniel R Squair
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
| |
Collapse
|
12
|
Maas MN, Hintzen JCJ, Mecinović J. Probing lysine posttranslational modifications by unnatural amino acids. Chem Commun (Camb) 2022; 58:7216-7231. [PMID: 35678513 DOI: 10.1039/d2cc00708h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
Collapse
Affiliation(s)
- Marijn N Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| |
Collapse
|
13
|
Bilbrough T, Piemontese E, Seitz O. Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem Soc Rev 2022; 51:5691-5730. [PMID: 35726784 DOI: 10.1039/d1cs00991e] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
Collapse
Affiliation(s)
- Tim Bilbrough
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| |
Collapse
|
14
|
Hunter T. A journey from phosphotyrosine to phosphohistidine and beyond. Mol Cell 2022; 82:2190-2200. [PMID: 35654043 DOI: 10.1016/j.molcel.2022.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Protein phosphorylation is a reversible post-translational modification. Nine of the 20 natural amino acids in proteins can be phosphorylated, but most of what we know about the roles of protein phosphorylation has come from studies of serine, threonine, and tyrosine phosphorylation. Much less is understood about the phosphorylation of histidine, lysine, arginine, cysteine, aspartate, and glutamate, so-called non-canonical phosphorylations. Phosphohistidine (pHis) was discovered 60 years ago as a mitochondrial enzyme intermediate; since then, evidence for the existence of histidine kinases and phosphohistidine phosphatases has emerged, together with examples where protein function is regulated by reversible histidine phosphorylation. pHis is chemically unstable and has thus been challenging to study. However, the recent development of tools for studying pHis has accelerated our understanding of the multifaceted functions of histidine phosphorylation, revealing a large number of proteins that are phosphorylated on histidine and implicating pHis in a wide range of cellular processes.
Collapse
Affiliation(s)
- Tony Hunter
- Molecular Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
15
|
Hintzen JCJ, Ma H, Deng H, Witecka A, Andersen SB, Drozak J, Guo H, Qian P, Li H, Mecinović J. Histidine methyltransferase
SETD3
methylates structurally diverse histidine mimics in actin. Protein Sci 2022; 31:e4305. [PMID: 35481649 PMCID: PMC9004244 DOI: 10.1002/pro.4305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 01/05/2023]
Abstract
Actin histidine Nτ‐methylation by histidine methyltransferase SETD3 plays an important role in human biology and diseases. Here, we report integrated synthetic, biocatalytic, biostructural, and computational analyses on human SETD3‐catalyzed methylation of actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N‐nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical molecular dynamics and free‐energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic, and functional insight into actin histidine methylation by SETD3. PDB Code(s): 7W28 and 7W29
Collapse
Affiliation(s)
- Jordi C. J. Hintzen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| | - Huida Ma
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua‐Peking Center for Life Sciences Tsinghua University Beijing China
| | - Hao Deng
- Chemistry and Materials Science Faculty Shandong Agricultural University Tai'an Shandong China
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology University of Warsaw Warsaw Poland
| | - Steffen B. Andersen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology University of Warsaw Warsaw Poland
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Ping Qian
- Chemistry and Materials Science Faculty Shandong Agricultural University Tai'an Shandong China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua‐Peking Center for Life Sciences Tsinghua University Beijing China
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| |
Collapse
|
16
|
The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins. Biochem J 2021; 478:3575-3596. [PMID: 34624072 DOI: 10.1042/bcj20210533] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 01/12/2023]
Abstract
Histidine phosphorylation is an important and ubiquitous post-translational modification. Histidine undergoes phosphorylation on either of the nitrogens in its imidazole side chain, giving rise to 1- and 3- phosphohistidine (pHis) isomers, each having a phosphoramidate linkage that is labile at high temperatures and low pH, in contrast with stable phosphomonoester protein modifications. While all organisms routinely use pHis as an enzyme intermediate, prokaryotes, lower eukaryotes and plants also use it for signal transduction. However, research to uncover additional roles for pHis in higher eukaryotes is still at a nascent stage. Since the discovery of pHis in 1962, progress in this field has been relatively slow, in part due to a lack of the tools and techniques necessary to study this labile modification. However, in the past ten years the development of phosphoproteomic techniques to detect phosphohistidine (pHis), and methods to synthesize stable pHis analogues, which enabled the development of anti-phosphohistidine (pHis) antibodies, have accelerated our understanding. Recent studies that employed anti-pHis antibodies and other advanced techniques have contributed to a rapid expansion in our knowledge of histidine phosphorylation. In this review, we examine the varied roles of pHis-containing proteins from a chemical and structural perspective, and present an overview of recent developments in pHis proteomics and antibody development.
Collapse
|
17
|
Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| |
Collapse
|
18
|
Heiss TK, Dorn RS, Prescher JA. Bioorthogonal Reactions of Triarylphosphines and Related Analogues. Chem Rev 2021; 121:6802-6849. [PMID: 34101453 PMCID: PMC10064493 DOI: 10.1021/acs.chemrev.1c00014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.
Collapse
|
19
|
Agouram N, El Hadrami EM, Bentama A. 1,2,3-Triazoles as Biomimetics in Peptide Science. Molecules 2021; 26:2937. [PMID: 34069302 PMCID: PMC8156386 DOI: 10.3390/molecules26102937] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/05/2021] [Indexed: 01/10/2023] Open
Abstract
Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.
Collapse
Affiliation(s)
- Naima Agouram
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology, Sidi Mohammed Ben Abdellah University, Immouzer Road, Fez 30050, Morocco; (E.M.E.H.); (A.B.)
| | | | | |
Collapse
|
20
|
Incel A, Arribas Díez I, Wierzbicka C, Gajoch K, Jensen ON, Sellergren B. Selective Enrichment of Histidine Phosphorylated Peptides Using Molecularly Imprinted Polymers. Anal Chem 2021; 93:3857-3866. [PMID: 33591162 PMCID: PMC8023515 DOI: 10.1021/acs.analchem.0c04474] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Protein histidine
phosphorylation
(pHis) is involved in molecular signaling networks in bacteria, fungi,
plants, and higher eukaryotes including mammals and is implicated
in human diseases such as cancer. Detailed investigations of the pHis
modification are hampered due to its acid-labile nature and consequent
lack of tools to study this post-translational modification (PTM).
We here demonstrate three molecularly imprinted polymer (MIP)-based
reagents, MIP1–MIP3, for enrichment of pHis peptides and subsequent
characterization by chromatography and mass spectrometry (LC–MS).
The combination of MIP1 and β-elimination provided some selectivity
for improved detection of pHis peptides. MIP2 was amenable to larger
pHis peptides, although with poor selectivity. Microsphere-based MIP3
exhibited improved selectivity and was amenable to enrichment and
detection by LC–MS of pHis peptides in tryptic digests of protein
mixtures. These MIP protocols do not involve any acidic solvents during
sample preparation and enrichment, thus preserving the pHis modification.
The presented proof-of-concept results will lead to new protocols
for highly selective enrichment of labile protein phosphorylations
using molecularly imprinted materials.
Collapse
Affiliation(s)
- Anıl Incel
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Ignacio Arribas Díez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Celina Wierzbicka
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Katarzyna Gajoch
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 205 06 Malmö, Sweden
| |
Collapse
|
21
|
Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies. Proc Natl Acad Sci U S A 2021; 118:2010644118. [PMID: 33547238 PMCID: PMC8017925 DOI: 10.1073/pnas.2010644118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 2015, monoclonal antibodies (mAbs) that selectively recognize the 1-pHis or 3-pHis isoforms of phosphohistidine were developed by immunizing rabbits with degenerate Ala/Gly peptides containing the nonhydrolyzable phosphohistidine (pHis) analog- phosphotriazolylalanine (pTza). Here, we report structures of five rabbit mAbs bound to cognate pTza peptides: SC1-1 and SC50-3 that recognize 1-pHis, and their 3-pHis-specific counterparts, SC39-4, SC44-8, and SC56-2. These cocrystal structures provide insights into the binding modes of the pTza phosphate group that are distinct for the 1- and 3-pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl ring. The mode of phosphate recognition in the 3-pHis mAbs recapitulates the Walker A motif, as present in kinases. The complementarity-determining regions (CDRs) of four of the Fabs interact with the peptide backbone rather than peptide side chains, thus conferring sequence independence, whereas SC44-8 shows a proclivity for binding a GpHAGA motif mediated by a sterically complementary CDRL3 loop. Specific hydrogen bonding with the triazolyl ring precludes recognition of pTyr and other phosphoamino acids by these mAbs. Kinetic binding experiments reveal that the affinity of pHis mAbs for pHis and pTza peptides is submicromolar. Bound pHis mAbs also shield the pHis peptides from rapid dephosphorylation. The epitope-paratope interactions illustrate how these anti-pHis antibodies are useful for a wide range of research techniques and this structural information can be utilized to improve the specificity and affinity of these antibodies toward a variety of pHis substrates to understand the role of histidine phosphorylation in healthy and diseased states.
Collapse
|
22
|
Huang B, Zhao Z, Zhao Y, Huang S. Protein arginine phosphorylation in organisms. Int J Biol Macromol 2021; 171:414-422. [PMID: 33428953 DOI: 10.1016/j.ijbiomac.2021.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Protein arginine phosphorylation (pArg), a novel molecular switch, plays a key role in regulating cellular processes. The intrinsic acid lability, hot sensitivity, and hot-alkali instability of "high-energy" phosphoamidate (PN bond) in pArg, make the investigation highly difficult and challenging. Recently, the progress in identifying prokaryotic protein arginine kinase/phosphatase and assigning hundreds of pArg proteins and phosphosites has been made, which is arousing scientists' interest and passions. It shows that pArg is tightly connected to bacteria stress response and pathogenicity, and is probably implied in human diseases. In this review, we highlight the strategies for investigation of this mysterious modification and its momentous physiological functions, and also prospect for the potentiality of drugs development targeting pArg-relative pathways.
Collapse
Affiliation(s)
- Biling Huang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China.
| | - Zhixing Zhao
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China; Department of Chemical Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, PR China; Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, PR China.
| | - Shaohua Huang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China.
| |
Collapse
|
23
|
Cao H, Li J, Zhang F, Cahard D, Ma J. Asymmetric Synthesis of Chiral Amino Carboxylic‐Phosphonic Acid Derivatives. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202001345] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hao‐Qiang Cao
- Department of Chemistry Tianjin Key Laboratory of Molecular Optoelectronic Sciences Frontiers Science Center for Synthetic Biology (Ministry of Education) and Tianjin Collaborative Innovation Center of Chemical Science & Engineering Tianjin University Tianjin 300072 People's Republic of China
| | - Jun‐Kuan Li
- Department of Chemistry Tianjin Key Laboratory of Molecular Optoelectronic Sciences Frontiers Science Center for Synthetic Biology (Ministry of Education) and Tianjin Collaborative Innovation Center of Chemical Science & Engineering Tianjin University Tianjin 300072 People's Republic of China
| | - Fa‐Guang Zhang
- Department of Chemistry Tianjin Key Laboratory of Molecular Optoelectronic Sciences Frontiers Science Center for Synthetic Biology (Ministry of Education) and Tianjin Collaborative Innovation Center of Chemical Science & Engineering Tianjin University Tianjin 300072 People's Republic of China
- Joint School of National University of Singapore and Tianjin University International Campus of Tianjin University, Binhai New City Fuzhou 350207 People's Republic of China
| | - Dominique Cahard
- CNRS UMR 6014 COBRA Normandie Université 76821 Mont Saint Aignan France
| | - Jun‐An Ma
- Department of Chemistry Tianjin Key Laboratory of Molecular Optoelectronic Sciences Frontiers Science Center for Synthetic Biology (Ministry of Education) and Tianjin Collaborative Innovation Center of Chemical Science & Engineering Tianjin University Tianjin 300072 People's Republic of China
- Joint School of National University of Singapore and Tianjin University International Campus of Tianjin University, Binhai New City Fuzhou 350207 People's Republic of China
| |
Collapse
|
24
|
Ahn S, Jung H, Kee JM. Quest for the Crypto-phosphoproteome. Chembiochem 2020; 22:319-325. [PMID: 33094900 DOI: 10.1002/cbic.202000583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/14/2020] [Indexed: 11/05/2022]
Abstract
Protein phosphorylation is one of the most studied post-translational modifications (PTMs). Despite the remarkable advances in phosphoproteomics, a chemically less-stable subset of the phosphosites, which we call the crypto-phosphoproteome, has remained underexplored due to technological challenges. In this Viewpoint, we briefly summarize the current understanding of these elusive protein phosphorylations and identify the missing pieces for future studies.
Collapse
Affiliation(s)
- Seungmin Ahn
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Hoyoung Jung
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Jung-Min Kee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| |
Collapse
|
25
|
Conibear AC. Deciphering protein post-translational modifications using chemical biology tools. Nat Rev Chem 2020; 4:674-695. [PMID: 37127974 DOI: 10.1038/s41570-020-00223-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Proteins carry out a wide variety of catalytic, regulatory, signalling and structural functions in living systems. Following their assembly on ribosomes and throughout their lifetimes, most eukaryotic proteins are modified by post-translational modifications; small functional groups and complex biomolecules are conjugated to amino acid side chains or termini, and the protein backbone is cleaved, spliced or cyclized, to name just a few examples. These modifications modulate protein activity, structure, location and interactions, and, thereby, control many core biological processes. Aberrant post-translational modifications are markers of cellular stress or malfunction and are implicated in several diseases. Therefore, gaining an understanding of which proteins are modified, at which sites and the resulting biological consequences is an important but complex challenge requiring interdisciplinary approaches. One of the key challenges is accessing precisely modified proteins to assign functional consequences to specific modifications. Chemical biologists have developed a versatile set of tools for accessing specifically modified proteins by applying robust chemistries to biological molecules and developing strategies for synthesizing and ligating proteins. This Review provides an overview of these tools, with selected recent examples of how they have been applied to decipher the roles of a variety of protein post-translational modifications. Relative advantages and disadvantages of each of the techniques are discussed, highlighting examples where they are used in combination and have the potential to address new frontiers in understanding complex biological processes.
Collapse
|
26
|
Unremitting progresses for phosphoprotein synthesis. Curr Opin Chem Biol 2020; 58:96-111. [PMID: 32889414 DOI: 10.1016/j.cbpa.2020.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
Phosphorylation, one of the important protein post-translational modifications, is involved in many essential cellular processes. Site-specifical and homogeneous phosphoproteins can be used as probes for elucidating the protein phosphorylation network and as potential therapeutics for interfering their involved biological events. However, the generation of phosphoproteins has been challenging owing to the limitation of chemical synthesis and protein expression systems. Despite the pioneering discoveries in phosphoprotein synthesis, over the past decade, great progresses in this field have also been made to promote the biofunctional exploration of protein phosphorylation largely. Therefore, in this review, we mainly summarize recent advances in phosphoprotein synthesis, which includes five sections: 1) synthesis of the nonhydrolyzable phosphorylated amino acid mimetic building blocks, 2) chemical total and semisynthesis strategy, 3) in-cell and in vitro genetic code expansion strategy, 4) the late-stage modification strategy, 5) nonoxygen phosphoprotein synthesis.
Collapse
|
27
|
Gong H, Fan Z, Yi D, Chen J, Li Z, Guo R, Wang C, Fang W, Liu S. Histidine kinase NME1 and NME2 are involved in TGF-β1-induced HSC activation and CCl 4-induced liver fibrosis. J Mol Histol 2020; 51:573-581. [PMID: 32860079 DOI: 10.1007/s10735-020-09906-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022]
Abstract
Histidine phosphorylation (pHis) was first reported in 1962. There are few studies on pHis because of the thermal and acidic instability of pHis and the lack of specific methods to detect it. pHis has two isomers of 1-phosphate histidine (1-pHis) and 3-phosphate histidine (3-pHis). pHis antibodies have been developed recently and have promoted research in this field. In this study, we established a CCl4-induced liver fibrosis model in C57 mice and a TGF-β1-induced HSC activation model in LX-2 cells, to study the role of histidine phosphorylation. The expression of histidine kinases NME1 and NME2 was increased, histidine phosphatase PGAM5 and PHPT1 was unchanged, and 1-pHis and 3-pHis were increased in the in vivo and in vitro models. The expression of LHPP was decreased in the in vivo model but not in the in vitro model. To further study the role of NME1, NME2, and histidine phosphorylation in HSC activation, we silenced NME1 or NME2 and administered TGF-β1 in LX-2 cells. The results showed silencing NME1 or NME2 decreased TGF-β1-induced pHis levels and the expression of α-SMA and COL1A1, indicating the activation of HSC was suppressed. Then, we found the inhibitory effect on HSC activation is due to reduced phosphorylation of Smad2 and Smad3. In summary, our studies indicate that NME1 and NME2 are involved in TGF-β1-induced HSC activation and CCl4-induced liver fibrosis, which may be mediated by histidine phosphorylation.
Collapse
Affiliation(s)
- Hui Gong
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Zhiqiang Fan
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Dan Yi
- Center of Drug Clinical Trial, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Junyu Chen
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Zuojun Li
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Ren Guo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Chunjiang Wang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Weijin Fang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Shikun Liu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China. .,Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| |
Collapse
|
28
|
Adam K, Ning J, Reina J, Hunter T. NME/NM23/NDPK and Histidine Phosphorylation. Int J Mol Sci 2020; 21:E5848. [PMID: 32823988 PMCID: PMC7461546 DOI: 10.3390/ijms21165848] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022] Open
Abstract
The NME (Non-metastatic) family members, also known as NDPKs (nucleoside diphosphate kinases), were originally identified and studied for their nucleoside diphosphate kinase activities. This family of kinases is extremely well conserved through evolution, being found in prokaryotes and eukaryotes, but also diverges enough to create a range of complexity, with homologous members having distinct functions in cells. In addition to nucleoside diphosphate kinase activity, some family members are reported to possess protein-histidine kinase activity, which, because of the lability of phosphohistidine, has been difficult to study due to the experimental challenges and lack of molecular tools. However, over the past few years, new methods to investigate this unstable modification and histidine kinase activity have been reported and scientific interest in this area is growing rapidly. This review presents a global overview of our current knowledge of the NME family and histidine phosphorylation, highlighting the underappreciated protein-histidine kinase activity of NME family members, specifically in human cells. In parallel, information about the structural and functional aspects of the NME family, and the knowns and unknowns of histidine kinase involvement in cell signaling are summarized.
Collapse
Affiliation(s)
| | | | | | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (K.A.); (J.N.); (J.R.)
| |
Collapse
|
29
|
Kafarski P. Phosphonopeptides containing free phosphonic groups: recent advances. RSC Adv 2020; 10:25898-25910. [PMID: 35518575 PMCID: PMC9055344 DOI: 10.1039/d0ra04655h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/02/2020] [Indexed: 11/21/2022] Open
Abstract
Phosphonopeptides are mimetics of peptides in which phosphonic acid or related (phosphinic, phosphonous etc.) group replaces either carboxylic acid group present at C-terminus, is located in the peptidyl side chain, or phosphonamidate or phosphinic acid mimics peptide bond. Acting as inhibitors of key enzymes related to variable pathological states they display interesting and useful physiologic activities with potential applications in medicine and agriculture. Since the synthesis and biological properties of peptides containing C-terminal diaryl phosphonates and those with phosphonic fragment replacing peptide bond were comprehensively reviewed, this review concentrate on peptides holding free, unsubstituted phosphonic acid moiety. There are two groups of such mimetics: (i) peptides in which aminophosphonic acid is located at C-terminus of the peptide chain with most of them (including antibiotics isolated from bacteria and fungi) exhibiting antimicrobial activity; (ii) non-hydrolysable analogues of phosphonoamino acids, which are useful tools to study physiologic effects of phosphorylations.
Collapse
Affiliation(s)
- Paweł Kafarski
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-305 Wrocław Poland
| |
Collapse
|
30
|
Tripolszky A, Tóth E, Szabó PT, Hackler L, Kari B, Puskás LG, Bálint E. Synthesis and In Vitro Cytotoxicity and Antibacterial Activity of Novel 1,2,3-Triazol-5-yl-phosphonates. Molecules 2020; 25:E2643. [PMID: 32517229 PMCID: PMC7321403 DOI: 10.3390/molecules25112643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 11/18/2022] Open
Abstract
Novel 1,2,3-triazol-5-yl-phosphonates were prepared by the copper(I)-catalyzed domino reaction of phenylacetylene, organic azides and dialkyl phosphites. The process was optimized on the synthesis of the dibutyl (1-benzyl-4-phenyl-1H-1,2,3-triazol-5-yl)phosphonate in respect of the catalyst, the base and the solvent, as well as of the reaction parameters (molar ratio of the starting materials, atmosphere, temperature and reaction time). The method elaborated could be applied to a range of organic azides and dialkyl phosphites, which confirmed the large scope and the functional group tolerance. The in vitro cytotoxicity on different cell lines and the antibacterial activity of the synthesized 1,2,3-triazol-5-yl-phosphonates was explored. According to the IC50 values determined, only modest antibacterial effect was detected, while some derivatives showed moderate activity against human promyelocytic leukemia HL-60 cells.
Collapse
Affiliation(s)
- Anna Tripolszky
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1521 Budapest, Hungary; (A.T.); (E.T.)
| | - Emese Tóth
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1521 Budapest, Hungary; (A.T.); (E.T.)
| | - Pál Tamás Szabó
- MS Metabolomics Laboratory, Instrumentation Center, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117 Budapest, Hungary;
| | - László Hackler
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary; (L.H.J.); (B.K.)
| | - Beáta Kari
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary; (L.H.J.); (B.K.)
| | - László G. Puskás
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary; (L.H.J.); (B.K.)
| | - Erika Bálint
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, H-1521 Budapest, Hungary; (A.T.); (E.T.)
| |
Collapse
|
31
|
Chen L, Liu X, Zou Y. Recent Advances in the Construction of Phosphorus‐Substituted Heterocycles, 2009–2019. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901540] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Long Chen
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Hua Guan Road Chengdu 610052 Peoples's Republic of China
| | - Xiao‐Yan Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Hua Guan Road Chengdu 610052 Peoples's Republic of China
| | - Yun‐Xiang Zou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Hua Guan Road Chengdu 610052 Peoples's Republic of China
| |
Collapse
|
32
|
Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
Collapse
Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
33
|
Hosseini-Sarvari M, Jafari F. TiO 2/Cu 2O nanoparticle-catalyzed direct C(sp)-P bond formation via aerobic oxidative coupling in air and visible light. Dalton Trans 2020; 49:3001-3006. [PMID: 32083623 DOI: 10.1039/c9dt04757c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The synthesis of organophosphorus compounds is one of the important goals in organic chemistry. Among these compounds, alkynylphosphonates are significantly utilized as the main precursors for the synthesis of biologically active molecules in medicinal chemistry and have attracted extensive interest in the past few decades. Although few efforts have been made towards the direct and atom-economical synthesis of alkynylphosphonates, efforts towards the utilization of visible light as a green and renewable energy source have not been made to date. Here, we have promoted a strategy to construct a type of nano metal oxide composite photocatalyst (Cu2O decorated on TiO2) for the synthesis of alkynylphosphonates via direct C-P bond formation between terminal alkyne and H-phosphonate under visible light irradiation. In this p-n heterojunction photocatalyst, Cu2O acted as a visible-light absorber; moreover, the CB (conduction band) of TiO2 was favorable for accepting a photogenerated electron, and the generated electron hole (e-/h+) pair could initiate the reaction. The present study can provide a new way for the synthesis of this important class of phosphorus organic compounds.
Collapse
Affiliation(s)
- Mona Hosseini-Sarvari
- Department of Chemistry, Faculty of Science, Shiraz University, Shiraz, 7194684795 I.R, Iran.
| | - Fattaneh Jafari
- Department of Chemistry, Faculty of Science, Shiraz University, Shiraz, 7194684795 I.R, Iran.
| |
Collapse
|
34
|
Huang B, Liu Y, Yao H, Zhao Y. NMR-based investigation into protein phosphorylation. Int J Biol Macromol 2020; 145:53-63. [DOI: 10.1016/j.ijbiomac.2019.12.171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
|
35
|
Adam K, Hunter T. Subcellular Localization of Histidine Phosphorylated Proteins Through Indirect Immunofluorescence. Methods Mol Biol 2020; 2077:209-224. [PMID: 31707661 PMCID: PMC9717436 DOI: 10.1007/978-1-4939-9884-5_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunofluorescence (IF) takes advantage of biological and physical mechanisms to identify proteins in cell or tissue samples, exploiting the specificity of antibodies and stimulated fluorescence light emission. Here, we describe an immunofluorescence staining method for the identification of histidine phosphorylated proteins that uses neutral/alkaline conditions and targeted reagents to overcome the chemical lability of histidine phosphorylation. This method describes how 1- and 3-phosphohistidine (pHis) monoclonal antibodies can be used to reveal the localization of proteins containing these elusive phosphoramidate bonds in cells. Standard procedures and materials for IF staining with adherent and nonadherent cells are described.
Collapse
Affiliation(s)
- Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
36
|
Arribat M, Cavelier F, Rémond E. Phosphorus-containing amino acids with a P–C bond in the side chain or a P–O, P–S or P–N bond: from synthesis to applications. RSC Adv 2020. [DOI: 10.1039/c9ra10917j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Strategies for the preparation of phosphorus-containing amino acids and their utility in the organic chemistry, physico-chemistry, agrochemistry, and pharmacology fields are reported.
Collapse
Affiliation(s)
| | - Florine Cavelier
- Institut des Biomolécules Max Mousseron
- IBMM
- UMR 5247
- CNRS
- Université de Montpellier
| | - Emmanuelle Rémond
- Institut des Biomolécules Max Mousseron
- IBMM
- UMR 5247
- CNRS
- Université de Montpellier
| |
Collapse
|
37
|
Immunohistochemistry (IHC): Chromogenic Detection of 3-Phosphohistidine Proteins in Formaldehyde-Fixed, Frozen Mouse Liver Tissue Sections. Methods Mol Biol 2020; 2077:193-208. [PMID: 31707660 PMCID: PMC9828869 DOI: 10.1007/978-1-4939-9884-5_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The development of antibodies that specifically detect histidine-phosphorylated proteins is a recent achievement and allows potential roles of histidine phosphorylated proteins in pathological and physiological conditions to be characterized. Immunohistochemical analyses enable the detection of proteins in tissues and can reveal alterations to the quantity and/or localization of these proteins through comparisons of normal and diseased specimens. However, the sensitivity of phosphohistidine modifications to phosphatases, acidic pH, and elevated temperatures poses unique challenges to the detection process and requires a protocol that bypasses traditional procedures utilizing paraffin-embedding and antigen-retrieval methods. Here, we detail a method for a brief fixation by 4% (v/v) paraformaldehyde on freshly collected tissues in the presence of PhosSTOP to block phosphatase activity, followed by a float on sucrose to protect the tissue prior to freezing. Specimens are then embedded in a cryopreservation medium in molds and frozen using an isoflurane, dry ice bath to best preserve the tissue morphology and phosphohistidine signal. We validate this technique in normal mouse liver using SC44-1, a monoclonal anti-3-pHis antibody used to uncover a role for a protein histidine phosphatase as a tumor suppressor in the liver. Furthermore, we demonstrate that the antibody signal can be eliminated by preincubating SC44-1 with a peptide treated with phosphoramidate to phosphorylate histidine residues. Thus, we present an IHC protocol suitable for specific detection of 3-phosphohistidine proteins in mouse liver tissue, and suggest that this can be used as a starting point for optimization of IHC using other phosphohistidine antibodies or in other tissue types, generating information that will enhance our understanding of phosphohistidine in models of disease.
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Qi D, Dong W, Peng Z, Zhang Y, An D. Mukaiyama reagent-promoted metal-free preparation of alkynyl sulfones and phosphonates under mild conditions. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.06.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
40
|
Tripolszky A, Németh K, Szabó PT, Bálint E. Synthesis of (1,2,3-triazol-4-yl)methyl Phosphinates and (1,2,3-Triazol-4-yl)methyl Phosphates by Copper-Catalyzed Azide-Alkyne Cycloaddition. Molecules 2019; 24:E2085. [PMID: 31159301 PMCID: PMC6600419 DOI: 10.3390/molecules24112085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/02/2022] Open
Abstract
An efficient and practical method was developed for the synthesis of new (1,2,3triazol4yl)methyl phosphinates and (1,2,3-triazol-4-yl)methyl phosphates by the copper(I)catalyzed azide-alkyne cycloaddition (CuAAC) of organic azides and prop-2-ynyl phosphinate or prop-2-ynyl phosphate. The synthesis of (1benzyl-1H-1,2,3-triazol-4-yl)methyl diphenylphosphinate was optimized with respect to the reaction parameters, such as the temperature, reaction time, and catalyst loading. The approach was applied to a range of organic azides, which confirmed the wide scope and the substituent tolerance of the process. The method elaborated represents a novel approach for the synthesis of the target compounds.
Collapse
Affiliation(s)
- Anna Tripolszky
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1521 Budapest, Hungary.
| | - Krisztina Németh
- MS Metabolomics Laboratory, Instrumentation Center, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary.
| | - Pál Tamás Szabó
- MS Metabolomics Laboratory, Instrumentation Center, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary.
| | - Erika Bálint
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1521 Budapest, Hungary.
| |
Collapse
|
41
|
Prasher P, Sharma M. Tailored therapeutics based on 1,2,3-1 H-triazoles: a mini review. MEDCHEMCOMM 2019; 10:1302-1328. [PMID: 31534652 DOI: 10.1039/c9md00218a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Contemporary drug discovery approaches rely on library synthesis coupled with combinatorial methods and high-throughput screening to identify leads. However, due to the multitude of components involved, a majority of optimization techniques face persistent challenges related to the efficiency of synthetic processes and the purity of compound libraries. These methods have recently found an upgradation as fragment-based approaches for target-guided synthesis of lead molecules with active involvement of their biological target. The click chemistry approach serves as a promising tool for tailoring the therapeutically relevant biomolecules of interest, improving their bioavailability and bioactivity and redirecting them as efficacious drugs. 1,2,3-1H-Triazole nucleus, being a planar and biologically acceptable scaffold, plays a crucial role in the design of biomolecular mimetics and tailor-made molecules with therapeutic relevance. This versatile scaffold also forms an integral part of the current fragment-based approaches for drug design, kinetic target guided synthesis and bioorthogonal methodologies.
Collapse
Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ; .,Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
| |
Collapse
|
42
|
Gao Y, Lee H, Kwon OK, Cheng Z, Tan M, Kim K, Lee S. Profiling of Histidine Phosphoproteome in
Danio rerio
by TiO
2
Enrichment. Proteomics 2019; 19:e1800471. [DOI: 10.1002/pmic.201800471] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/25/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Yan Gao
- BK21 Plus KNU Multi‐Omics based Creative Drug Research TeamCollege of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National University Daegu 41566 Republic of Korea
| | - Hyojin Lee
- Department of Energy and Environmental Engineering and Department of Environmental EngineeringSeoul National University of Science and Technology Seoul 01811 Republic of Korea
| | - Oh Kwang Kwon
- BK21 Plus KNU Multi‐Omics based Creative Drug Research TeamCollege of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National University Daegu 41566 Republic of Korea
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd. Hangzhou 310018 China
| | - Minjia Tan
- Shanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai 201203 China
| | - Ki‐Tae Kim
- Department of Energy and Environmental Engineering and Department of Environmental EngineeringSeoul National University of Science and Technology Seoul 01811 Republic of Korea
- Jingjie PTM BioLab (Hangzhou) Co. Ltd. Hangzhou 310018 China
| | - Sangkyu Lee
- BK21 Plus KNU Multi‐Omics based Creative Drug Research TeamCollege of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National University Daegu 41566 Republic of Korea
| |
Collapse
|
43
|
Hu Y, Weng Y, Jiang B, Li X, Zhang X, Zhao B, Wu Q, Liang Z, Zhang L, Zhang Y. Isolation and identification of phosphorylated lysine peptides by retention time difference combining dimethyl labeling strategy. Sci China Chem 2019. [DOI: 10.1007/s11426-018-9433-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
44
|
Jung H, Shin SH, Kee J. Recent Updates on ProteinN‐Phosphoramidate Hydrolases. Chembiochem 2018; 20:623-633. [DOI: 10.1002/cbic.201800566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Hoyoung Jung
- Department of ChemistryUlsan National Institute of Science and Technology (UNIST) Ulsan 44919 South Korea
| | - Son Hye Shin
- Department of ChemistryUlsan National Institute of Science and Technology (UNIST) Ulsan 44919 South Korea
| | - Jung‐Min Kee
- Department of ChemistryUlsan National Institute of Science and Technology (UNIST) Ulsan 44919 South Korea
| |
Collapse
|
45
|
Nadal S, Raj R, Mohammed S, Davis BG. Synthetic post-translational modification of histones. Curr Opin Chem Biol 2018; 45:35-47. [DOI: 10.1016/j.cbpa.2018.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/17/2018] [Accepted: 02/10/2018] [Indexed: 12/14/2022]
|
46
|
Song W, Zheng N, Li M, Ullah K, Zheng Y. Rhodium(I)-Catalyzed Azide-Alkyne Cycloaddition (RhAAC) of Internal Alkynylphosphonates with High Regioselectivities under Mild Conditions. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800336] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wangze Song
- State Key Laboratory of Fine Chemicals, School of Pharmaceutical Science and Technology; Dalian University of Technology; Dalian 116024 People's Republic of China
| | - Nan Zheng
- State Key Laboratory of Fine Chemicals, School of Pharmaceutical Science and Technology; Dalian University of Technology; Dalian 116024 People's Republic of China
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering; Dalian University of Technology; Dalian 116024 People's Republic of China
| | - Ming Li
- State Key Laboratory of Fine Chemicals, School of Pharmaceutical Science and Technology; Dalian University of Technology; Dalian 116024 People's Republic of China
| | - Karim Ullah
- State Key Laboratory of Fine Chemicals, School of Pharmaceutical Science and Technology; Dalian University of Technology; Dalian 116024 People's Republic of China
| | - Yubin Zheng
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering; Dalian University of Technology; Dalian 116024 People's Republic of China
| |
Collapse
|
47
|
Hindupur SK, Colombi M, Fuhs SR, Matter MS, Guri Y, Adam K, Cornu M, Piscuoglio S, Ng CKY, Betz C, Liko D, Quagliata L, Moes S, Jenoe P, Terracciano LM, Heim MH, Hunter T, Hall MN. The protein histidine phosphatase LHPP is a tumour suppressor. Nature 2018; 555:678-682. [PMID: 29562234 DOI: 10.1038/nature26140] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 02/14/2018] [Indexed: 12/13/2022]
Abstract
Histidine phosphorylation, the so-called hidden phosphoproteome, is a poorly characterized post-translational modification of proteins. Here we describe a role of histidine phosphorylation in tumorigenesis. Proteomic analysis of 12 tumours from an mTOR-driven hepatocellular carcinoma mouse model revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the putative histidine phosphatase LHPP was downregulated specifically in the tumours. We demonstrate that LHPP is indeed a protein histidine phosphatase. Consistent with these observations, global histidine phosphorylation was significantly upregulated in the liver tumours. Sustained, hepatic expression of LHPP in the hepatocellular carcinoma mouse model reduced tumour burden and prevented the loss of liver function. Finally, in patients with hepatocellular carcinoma, low expression of LHPP correlated with increased tumour severity and reduced overall survival. Thus, LHPP is a protein histidine phosphatase and tumour suppressor, suggesting that deregulated histidine phosphorylation is oncogenic.
Collapse
Affiliation(s)
| | - Marco Colombi
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Stephen R Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Matthias S Matter
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Yakir Guri
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Marion Cornu
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Charles Betz
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Dritan Liko
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Suzette Moes
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Paul Jenoe
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Markus H Heim
- Department of Biomedicine, University Hospital Basel, 4031 Basel, Switzerland
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Michael N Hall
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
48
|
Makwana MV, Muimo R, Jackson RF. Advances in development of new tools for the study of phosphohistidine. J Transl Med 2018; 98:291-303. [PMID: 29200202 DOI: 10.1038/labinvest.2017.126] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/27/2017] [Accepted: 09/03/2017] [Indexed: 01/04/2023] Open
Abstract
Protein phosphorylation is an important post-translational modification that is an integral part of cellular function. The O-phosphorylated amino-acid residues, such as phosphoserine (pSer), phosphothreonine (pThr) and phosphotyrosine (pTyr), have dominated the literature while the acid labile N-linked phosphorylated amino acids, such as phosphohistidine (pHis), have largely been historically overlooked because of the acidic conditions routinely used in amino-acid detection and analysis. This review highlights some misinterpretations that have arisen in the existing literature, pinpoints outstanding questions and potential future directions to clarify the role of pHis in mammalian signalling systems. Particular emphasis is placed on pHis isomerization and the hybrid functionality for both pHis and pTyr of the proposed τ-pHis analogue bearing the triazole residue.
Collapse
Affiliation(s)
- Mehul V Makwana
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.,Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Richmond Muimo
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | | |
Collapse
|
49
|
Jia K, Li J, Chen Y. Selective P-C(sp 3 ) Bond Cleavage and Radical Alkynylation of α-Phosphorus Alcohols by Photoredox Catalysis. Chemistry 2018; 24:3174-3177. [PMID: 29356137 DOI: 10.1002/chem.201800202] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Indexed: 11/10/2022]
Abstract
Herein the first P-C(sp3 ) bond cleavage and radical alkynylation of α-phosphorus alcohols to construct phosphonoalkynes is reported. The phosphorus radical is generated upon P-C bond cleavage reaction via the alkoxyl radical through photoredox catalysis with cyclic iodine(III) reagents. Various arylphosphinoyl-, alkylphosphinoyl-, phosphonate-, and phosphonic amide alcohols serve as radical phosphorus precursors to construct phosphonoalkynes for the first time.
Collapse
Affiliation(s)
- Kunfang Jia
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
| | - Junzhao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
| |
Collapse
|
50
|
Adam K, Hunter T. Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. J Transl Med 2018; 98:233-247. [PMID: 29058706 PMCID: PMC5815933 DOI: 10.1038/labinvest.2017.118] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation is the most common type of post-translational modification in eukaryotes. The phosphoproteome is defined as the complete set of experimentally detectable phosphorylation sites present in a cell's proteome under various conditions. However, we are still far from identifying all the phosphorylation sites in a cell mainly due to the lack of information about phosphorylation events involving residues other than Ser, Thr and Tyr. Four types of phosphate-protein linkage exist and these generate nine different phosphoresidues-pSer, pThr, pTyr, pHis, pLys, pArg, pAsp, pGlu and pCys. Most of the effort in studying protein phosphorylation has been focused on Ser, Thr and Tyr phosphorylation. The recent development of 1- and 3-pHis monoclonal antibodies promises to increase our understanding of His phosphorylation and the kinases and phosphatases involved. Several His kinases are well defined in prokaryotes, especially those involved in two-component system (TCS) signaling. However, in higher eukaryotes, NM23, a protein originally characterized as a nucleoside diphosphate kinase, is the only characterized protein-histidine kinase. This ubiquitous and conserved His kinase autophosphorylates its active site His, and transfers this phosphate either onto a nucleoside diphosphate or onto a protein His residue. Studies of NM23 protein targets using newly developed anti-pHis antibodies will surely help illuminate the elusive His phosphorylation-based signaling pathways. This review discusses the role that the NM23/NME/NDPK phosphotransferase has, how the addition of the pHis phosphoproteome will expand the phosphoproteome and make His phosphorylation part of the global phosphorylation world. It also summarizes why our understanding of phosphorylation is still largely restricted to the acid stable phosphoproteome, and highlights the study of NM23 histidine kinase as an entrée into the world of histidine phosphorylation.
Collapse
Affiliation(s)
- Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| |
Collapse
|