1
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Venrooij KR, de Bondt L, Bonger KM. Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously. Top Curr Chem (Cham) 2024; 382:24. [PMID: 38971884 PMCID: PMC11227474 DOI: 10.1007/s41061-024-00467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.
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Affiliation(s)
- Kevin R Venrooij
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lucienne de Bondt
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kimberly M Bonger
- Chemical Biology Group, Department of Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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2
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Svatunek D. Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions. Top Curr Chem (Cham) 2024; 382:17. [PMID: 38727989 PMCID: PMC11087259 DOI: 10.1007/s41061-024-00461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.
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Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, Technische Universität Wien (TU Wien), Getreidemarkt 9, 1060, Vienna, Austria.
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3
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Vargiu M, Xu Y, Kuipers OP, Roelfes G. Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides. Chembiochem 2024; 25:e202400043. [PMID: 38334959 DOI: 10.1002/cbic.202400043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity remained good, albeit lower than the unmodified peptide. Also the lanthipeptide nisin could be modified using this method.
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Affiliation(s)
- Michela Vargiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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4
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Tanimoto H, Adachi R, Tanisawa K, Tomohiro T. Amphos-Mediated Conversion of Alkyl Azides to Diazo Compounds and One-Pot Azide-Site Selective Transient Protection, Click Conjugation, and Deprotective Transformation. Org Lett 2024. [PMID: 38502004 DOI: 10.1021/acs.orglett.4c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
A one-pot conversion of alkyl azides to diazo compounds is outlined. After the reaction of α-azidocarbonyl compounds with Amphos, treatment of the resulting phosphazides with silica gel in a wet solvent afforded α-diazo carbonyl products. Through the azido group protection property of Amphos, inter- and intramolecular azide-site selective reactions of azido group protection, click functionalization, and deprotection of the diazo group have been demonstrated in one pot.
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Affiliation(s)
- Hiroki Tanimoto
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ryo Adachi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kodai Tanisawa
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takenori Tomohiro
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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5
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Lv J, Hua R. LiO tBu-Promoted Intramolecular 1,3-Dipolar Cycloaddition of the 2'-Alkynyl-biaryl-2-aldehyde N-Tosylhydrazones Approach to 3-Substituted 1 H-Dibenzo[ e, g]indazoles. Molecules 2023; 28:8061. [PMID: 38138554 PMCID: PMC10745680 DOI: 10.3390/molecules28248061] [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: 10/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
A two-step, one-pot synthesis of 3-substituted 1H-dibenzo[e,g]indazoles in good to high yields via a LiOtBu-promoted intramolecular 1,3-dipolar cyclization of 2'-alkynyl-biaryl-2-aldehyde N-tosylhydrazones was developed. The N-Ts-hydrazones used were prepared in situ via the reactions of 2'-alkynyl-biaryl-2-aldehydes and TsNHNH2(p-methylbenzenesulfonohydrazide). Two types of signals related to the hydrogen bonds, forming in several products, were observed in the 1H NMR spectra recorded in DMSO-d6, assigned to N-H bonds in their dimeric species of product and tautomer.
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Affiliation(s)
- Jiaying Lv
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China;
| | - Ruimao Hua
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China;
- State Key Laboratory of Chemistry and Utilization of Carbon-Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, China
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6
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Phanumartwiwath A, Kesornpun C, Chokchaichamnankit D, Khongmanee A, Diskul-Na-Ayudthaya P, Ruangjaroon T, Srisomsap C, Kittakoop P, Svasti J, Ruchirawat S. Protein Modification via Nitrile Oxide-Dehydroalanine Cycloaddition: Formation of Isoxazoline Ring on the Protein Backbone. Chembiochem 2023; 24:e202300268. [PMID: 37199473 DOI: 10.1002/cbic.202300268] [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: 04/03/2023] [Revised: 04/26/2023] [Accepted: 05/18/2023] [Indexed: 05/19/2023]
Abstract
Here we describe a novel catalyst-free 1,3-dipolar cycloaddition bioconjugation approach for chemical modification of proteins. The dehydroalanine (Dha)-containing protein reacts with nitrile oxides generated in situ through 1,3-dipolar cycloaddition in fully aqueous-buffered systems. This leads to the formation of a new isoxazoline ring at a pre-defined site (Dha) of the protein. Furthermore, the 1-pyrene isoxazoline-installed annexin V acts as a fluorescent probe, which successfully labels the outer cellular membranes of human cholangiocarcinoma (HuCCA-1) cells for detection of apoptosis.
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Affiliation(s)
- Anuchit Phanumartwiwath
- College of Public Health Sciences, Chulalongkorn University, Phyathai Road, Bangkok, 10330, Thailand
- Chemical Biology Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Centre of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10400, Thailand
| | - Chatchai Kesornpun
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | | | - Amnart Khongmanee
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | | | - Theetat Ruangjaroon
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Chantragan Srisomsap
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Prasat Kittakoop
- Chemical Biology Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Centre of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10400, Thailand
| | - Jisnuson Svasti
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Somsak Ruchirawat
- Chemical Biology Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Centre of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10400, Thailand
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
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7
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Zhang M, He P, Li Y. Light-initiated 1,3-dipolar cycloaddition between dehydroalanines and tetrazoles: application to late-stage peptide and protein modifications. Chem Sci 2023; 14:9418-9426. [PMID: 37712045 PMCID: PMC10498508 DOI: 10.1039/d3sc02818f] [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: 06/02/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
As an easily introduced noncoded amino acid with unique electrophilicity distinct from the 20 natural amino acids, dehydroalanine (Dha) is not only a precise protein post-translational modification (PTM) insertion tool, but also a promising multifunctional labelling site for peptides and proteins. However, achieving a balance between the reaction rate and mild reaction conditions has been a major challenge in developing novel Dha-modified strategies. Rapid, efficient, and mild Dha modification strategies are highly desired. Additionally, catalyst-free photocontrollable reactions for Dha-containing peptide and protein modification have yet to be developed. Here, we report a photoinitiated 1,3-dipolar cycloaddition reaction between Dha and 2,5-diaryl tetrazoles. Under low-power UV lamp irradiation, this reaction is completed within minutes without catalysis, resulting in a fluorescent pyrazoline-modified peptide or protein with excellent chemoselectivity for Dha residues. Notably, this reaction exhibits complete site-specificity in the modification of thiostrepton, a natural antimicrobial peptide containing multiple Dha residues (Dha3, Dha16, and Dha17), within 20 minutes in high yields. This is currently the fastest reaction for modifying the Dha residue in thiostrepton with clear site-specificity towards Dha16. This photoinitiated reaction also provides a chemoselective strategy for precise functionalization of proteins. Additionally, the rapidity and efficiency of the reaction minimize UV light damage to the biological reaction system. Combined with fluorogenic properties, this photo-controllable methodology can be applied to live cell imaging, further broadening the application scope of the Dha modification methodology.
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Affiliation(s)
- Mengqian Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Peiyang He
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Yanmei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
- Beijing Institute for Brain Disorders Beijing 100069 P. R. China
- Center for Synthetic and Systems Biology, Tsinghua University Beijing 100084 P. R. China
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8
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Holzmann MJ, Khanal N, Yamanushkin P, Gold B. Remote Strain Activation in a Sulfate-Linked Dibenzocycloalkyne. Org Lett 2023; 25:309-313. [PMID: 36455206 DOI: 10.1021/acs.orglett.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cycloalkynes and their utilization in cycloaddition reactions enable modular strategies spanning the molecular sciences. Strain─imparted by deviation from linearity─enables sufficient alkyne reactivity without the need for a catalyst (e.g., copper); however, the design and synthesis of stable reagents with suitable reactivity remains an ongoing challenge. We report the incorporation of an endocyclic sulfate within a dibenzocyclononyne scaffold to generate a cyclononyne displaying remarkable reactivity and stability. Through computational analyses, we revealed that the endocyclic sulfate group shares nearly half the total strain energy, providing an activation strategy that reduces alkyne bending. Rehybridization of alkyne carbons in the formation of the heterocyclic product relieves strain both at the reactive site and in the transannular sulfate group. This mode of remote activation enables rapid reactivity while minimizing distortion─and strain─at the reactive site (the alkyne). The result: a design strategy for a new class of cycloalkynes with increased stability and reactivity.
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Affiliation(s)
- Michael J Holzmann
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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9
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Beutick SE, Vermeeren P, Hamlin TA. The 1,3-Dipolar Cycloaddition: From Conception to Quantum Chemical Design. Chem Asian J 2022; 17:e202200553. [PMID: 35822651 PMCID: PMC9539489 DOI: 10.1002/asia.202200553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/08/2022] [Indexed: 11/12/2022]
Abstract
The 1,3-dipolar cycloaddition (1,3-DCA) reaction, conceptualized by Rolf Huisgen in 1960, has proven immensely useful in organic, material, and biological chemistry. The uncatalyzed, thermal transformation is generally sluggish and unselective, but the reactivity can be enhanced by means of metal catalysis or by the introduction of either predistortion or electronic tuning of the dipolarophile. These promoted reactions generally go with a much higher reactivity, selectivity, and yields, often at ambient temperatures. The rapid orthogonal reactivity and compatibility with aqueous and physiological conditions positions the 1,3-DCA as an excellent bioorthogonal reaction. Quantum chemical calculations have been critical for providing an understanding of the physical factors that control the reactivity and selectivity of 1,3-DCAs. In silico derived design principles have proven invaluable for the design of new dipolarophiles with tailored reactivity. This review discusses everything from the conception of the 1,3-DCA all the way to the state-of-the-art methods and models used for the quantum chemical design of novel (bioorthogonal) reagents.
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Affiliation(s)
- Steven E. Beutick
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Pascal Vermeeren
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
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10
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Yamanushkin P, Kaya K, Feliciano MAM, Gold B. SuFExable NH-Pyrazoles via 1,3-Dipolar Cycloadditions of Diazo Compounds with Bromoethenylsulfonyl Fluoride. J Org Chem 2022; 87:3868-3873. [PMID: 35143195 DOI: 10.1021/acs.joc.1c03105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
"Click" reactions have transformed the molecular sciences. Augmenting cycloaddition reactions, sulfur(VI) fluoride exchange (SuFEx) chemistry has diversified the landscape of molecular assembly. Herein, we report a facile strategy to access SuFExable NH-pyrazoles via strain and catalyst-free 1,3-dipolar cycloadditions of stabilized diazo compounds under mild conditions. Subsequent SuFEx proceeds efficiently with various N- and O-nucleophiles. Access to SuFExable NH-pyrazoles─a class of compounds containing two common pharmacophores─enables future opportunities within drug discovery, chemical biology, materials chemistry, and related fields.
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Affiliation(s)
- Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Kemal Kaya
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Biochemistry, Kütahya Dumlupınar University, 43100 Kütahya, Turkey
| | - Mark Aldren M Feliciano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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11
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Chandrasekharan SP, Dhami A, Kumar S, Mohanan K. Recent advances in pyrazole synthesis employing diazo compounds and synthetic analogues. Org Biomol Chem 2022; 20:8787-8817. [DOI: 10.1039/d2ob01918c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review summarizes the recent developments in the construction of pyrazoles using diazo compounds, nitrile imines and their synthetic equivalents.
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Affiliation(s)
- Sanoop P. Chandrasekharan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Anamika Dhami
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Sandeep Kumar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kishor Mohanan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad-201002, India
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12
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Giri P, Pagar AD, Patil MD, Yun H. Chemical modification of enzymes to improve biocatalytic performance. Biotechnol Adv 2021; 53:107868. [PMID: 34774927 DOI: 10.1016/j.biotechadv.2021.107868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022]
Abstract
Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.
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Affiliation(s)
- Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mahesh D Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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13
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Ruffell K, Smith FR, Green MT, Nicolle SM, Inman M, Lewis W, Hayes CJ, Moody CJ. Diazophosphonates: Effective Surrogates for Diazoalkanes in Pyrazole Synthesis. Chemistry 2021; 27:13703-13708. [PMID: 34425034 DOI: 10.1002/chem.202101788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 01/04/2023]
Abstract
Diazophosphonates, readily prepared from α-ketophosphonates by oxidation of the corresponding hydrazones in batch or in flow, are useful partners in 1,3-dipolar cycloaddition reactions to alkynes to give N-H pyrazoles, including the first intramolecular examples of such a process. The phosphoryl group imbues a number of desirable properties into the diazo 1,3-dipole. The electron-withdrawing nature of the phosphoryl stabilizes the diazo compound making it easier to handle, whilst the ability of the phosphoryl group to migrate readily in a [1,5]-sigmatropic rearrangement enables its transfer from C to N to aromatize the initial cycloadduct, and hence its facile removal from the final pyrazole product. Overall, the diazophosphonate acts as a surrogate for the much less stable diazoalkane in cycloadditions, with the phosphoryl group playing a vital, but traceless, role. The cycloaddition proceeds more readily with alkynes bearing electron-withdrawing groups, and is regiospecific with asymmetrical alkynes. The potential of diazophosphonates for use in bioorthogonal cycloadditions is demonstrated by their facile addition to strained alkynes.
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Affiliation(s)
- Katie Ruffell
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - Frances R Smith
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - Michael T Green
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - Simon M Nicolle
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - Martyn Inman
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - William Lewis
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - Christopher J Hayes
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
| | - Christopher J Moody
- School of Chemistry, University of Nottingham University Park, Nottingham, NG7 2RD, U.K
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14
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Su Y, Dong K, Zheng H, Doyle MP. Generation of Diazomethyl Radicals by Hydrogen Atom Abstraction and Their Cycloaddition with Alkenes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yong‐Liang Su
- Department of Chemistry The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Kuiyong Dong
- Department of Chemistry The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Haifeng Zheng
- Department of Chemistry The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Michael P. Doyle
- Department of Chemistry The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
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15
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Su YL, Dong K, Zheng H, Doyle MP. Generation of Diazomethyl Radicals by Hydrogen Atom Abstraction and Their Cycloaddition with Alkenes. Angew Chem Int Ed Engl 2021; 60:18484-18488. [PMID: 34043866 DOI: 10.1002/anie.202105472] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/23/2021] [Indexed: 12/16/2022]
Abstract
A general catalytic methodology for the synthesis of pyrazolines from α-diazo compounds and conjugated alkenes is reported. The direct hydrogen atom transfer (HAT) process of α-diazo compounds promoted by the tert-butylperoxy radical generates electrophilic diazomethyl radicals, thereby reversing the reactivity of the carbon atom attached with the diazo group. The regiocontrolled addition of diazomethyl radicals to carbon-carbon double bonds followed by intramolecular ring closure on the terminal diazo nitrogen and tautomerization affords a diverse set of pyrazolines in good yields with excellent regioselectivity. This strategy overcomes the limitations of electron-deficient alkenes in traditional dipolar [3+2]-cycloaddition of α-diazo compounds with alkenes. Furthermore, the straightforward formation of the diazomethyl radicals provides umpolung reactivity, thus opening new opportunities for the versatile transformations of diazo compounds.
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Affiliation(s)
- Yong-Liang Su
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Kuiyong Dong
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Haifeng Zheng
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Michael P Doyle
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
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16
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Dones JM, Abularrage NS, Khanal N, Gold B, Raines RT. Acceleration of 1,3-Dipolar Cycloadditions by Integration of Strain and Electronic Tuning. J Am Chem Soc 2021; 143:9489-9497. [PMID: 34151576 DOI: 10.1021/jacs.1c03133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The 1,3-dipolar cycloaddition between azides and alkynes provides new means to probe and control biological processes. A major challenge is to achieve high reaction rates with stable reagents. The optimization of alkynyl reagents has relied on two strategies: increasing strain and tuning electronics. We report on the integration of these strategies. A computational analysis suggested that a CH → N aryl substitution in dibenzocyclooctyne (DIBO) could be beneficial. In transition states, the nitrogen of 2-azabenzo-benzocyclooctyne (ABC) engages in an n→π* interaction with the C=O of α-azidoacetamides and forms a hydrogen bond with the N-H of α-diazoacetamides. These dipole-specific interactions act cooperatively with electronic activation of the strained π-bond to increase reactivity. We found that ABC does indeed react more quickly with α-azidoacetamides and α-diazoacetamides than its constitutional isomer, dibenzoazacyclooctyne (DIBAC). ABC and DIBAC have comparable chemical stability in a biomimetic solution. Both ABC and DIBO are accessible in three steps by the alkylidene carbene-mediated ring expansion of commercial cycloheptanones. Our findings enhance the accessibility and utility of 1,3-dipolar cycloadditions and encourage further innovation.
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Affiliation(s)
- Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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17
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Sorbelli D, Belanzoni P, Belpassi L. Tuning the Gold(I)‐Carbon σ Bond in Gold‐Alkynyl Complexes through Structural Modifications of the NHC Ancillary Ligand: Effect on Spectroscopic Observables and Reactivity. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Diego Sorbelli
- Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
| | - Paola Belanzoni
- Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
- CNR Institute of Chemical Science and Technologies “Giulio Natta” (CNR-SCITEC) c/o Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
| | - Leonardo Belpassi
- CNR Institute of Chemical Science and Technologies “Giulio Natta” (CNR-SCITEC) c/o Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
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18
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Bao G, Wang P, Li G, Yu C, Li Y, Liu Y, He Z, Zhao T, Rao J, Xie J, Hong L, Sun W, Wang R. 1,3‐Dipolar Cycloaddition between Dehydroalanines and C,N‐Cyclic Azomethine Imines: Application to Late‐Stage Peptide Modification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Guangjun Bao
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Peng Wang
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Guofeng Li
- School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Changjun Yu
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Yiping Li
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Yuyang Liu
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Zeyuan He
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Tiantian Zhao
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Jing Rao
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Junqiu Xie
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Liang Hong
- School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Wangsheng Sun
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
| | - Rui Wang
- School of Life Sciences Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science Chinese Academy of Medical Sciences, 2019RU066 Lanzhou University 199 West Donggang Rd Lanzhou 730000 Gansu P. R. China
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19
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de Vries RH, Viel JH, Kuipers OP, Roelfes G. Rapid and Selective Chemical Editing of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) via Cu II -Catalyzed β-Borylation of Dehydroamino Acids. Angew Chem Int Ed Engl 2021; 60:3946-3950. [PMID: 33185967 PMCID: PMC7898795 DOI: 10.1002/anie.202011460] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 12/22/2022]
Abstract
We report the fast and selective chemical editing of ribosomally synthesized and post-translationally modified peptides (RiPPs) by β-borylation of dehydroalanine (Dha) residues. The thiopeptide thiostrepton was modified efficiently using CuII -catalysis under mild conditions and 1D/2D NMR of the purified product showed site-selective borylation of the terminal Dha residues. Using similar conditions, the thiopeptide nosiheptide, lanthipeptide nisin Z, and protein SUMO_G98Dha were also modified efficiently. Borylated thiostrepton showed an up to 84-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity was maintained in thiostrepton and nosiheptide. The introduced boronic-acid functionalities were shown to be valuable handles for chemical mutagenesis and in a reversible click reaction with triols for the pH-controlled labeling of RiPPs.
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Affiliation(s)
- Reinder H. de Vries
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jakob H. Viel
- Department of Molecular GeneticsGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Oscar P. Kuipers
- Department of Molecular GeneticsGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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20
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Bao G, Wang P, Li G, Yu C, Li Y, Liu Y, He Z, Zhao T, Rao J, Xie J, Hong L, Sun W, Wang R. 1,3-Dipolar Cycloaddition between Dehydroalanines and C,N-Cyclic Azomethine Imines: Application to Late-Stage Peptide Modification. Angew Chem Int Ed Engl 2021; 60:5331-5338. [PMID: 33179384 DOI: 10.1002/anie.202012523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Indexed: 12/12/2022]
Abstract
A non-catalytic, mild, and easy-to-handle protecting group switched 1,3-dipolar cycloaddition (1,3-DC) between bi- or mono-N-protected Dha and C,N-cyclic azomethine imines, which afford various quaternary amino acids with diverse scaffolds, is disclosed. Specifically, normal-electron-demand 1,3-DC reaction occurs between bi-N-protected Dha and C,N-cyclic azomethine imines, while inverse-electron-demand 1,3-DC reaction occurs between mono-N-protected Dha and C,N-cyclic azomethine imines. Above all, the reactions can be carried out between peptides with Dha residues at the position of interest and C,N-cyclic azomethine imines, both in homogeneous phase and on resins in SPPS. It provides a new toolkit for late-stage peptide modification, labeling, and peptide-drug conjugation. To shed light on the high regioselectivity of the reaction, DFT calculations were carried out, which were qualitatively consistent with the experimental observations.
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Affiliation(s)
- Guangjun Bao
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Peng Wang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Guofeng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Changjun Yu
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Yiping Li
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Yuyang Liu
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Zeyuan He
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Tiantian Zhao
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Jing Rao
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Junqiu Xie
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Liang Hong
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Wangsheng Sun
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
| | - Rui Wang
- School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences & Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, 199 West Donggang Rd, Lanzhou, 730000, Gansu, P. R. China
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21
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Deb T, Tu J, Franzini RM. Mechanisms and Substituent Effects of Metal-Free Bioorthogonal Reactions. Chem Rev 2021; 121:6850-6914. [DOI: 10.1021/acs.chemrev.0c01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Titas Deb
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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22
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Boto A, González CC, Hernández D, Romero-Estudillo I, Saavedra CJ. Site-selective modification of peptide backbones. Org Chem Front 2021. [DOI: 10.1039/d1qo00892g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.
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Affiliation(s)
- Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Iván Romero-Estudillo
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
- Catedrático CONACYT-CIQ-UAEM, Mexico
| | - Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain
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23
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Vries RH, Viel JH, Kuipers OP, Roelfes G. Rapid and Selective Chemical Editing of Ribosomally Synthesized and Post‐Translationally Modified Peptides (RiPPs) via Cu
II
‐Catalyzed β‐Borylation of Dehydroamino Acids. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Reinder H. Vries
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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24
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van Lier RCW, de Bruijn AD, Roelfes G. A Water-Soluble Iridium Photocatalyst for Chemical Modification of Dehydroalanines in Peptides and Proteins. Chemistry 2020; 27:1430-1437. [PMID: 32896943 PMCID: PMC7898865 DOI: 10.1002/chem.202002599] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/04/2020] [Indexed: 12/27/2022]
Abstract
Dehydroalanine (Dha) residues are attractive noncanonical amino acids that occur naturally in ribosomally synthesised and post-translationally modified peptides (RiPPs). Dha residues are attractive targets for selective late-stage modification of these complex biomolecules. In this work, we show the selective photocatalytic modification of dehydroalanine residues in the antimicrobial peptide nisin and in the proteins small ubiquitin-like modifier (SUMO) and superfolder green fluorescent protein (sfGFP). For this purpose, a new water-soluble iridium(III) photoredox catalyst was used. The design and synthesis of this new photocatalyst, [Ir(dF(CF3 )ppy)2 (dNMe3 bpy)]Cl3 , is presented. In contrast to commonly used iridium photocatalysts, this complex is highly water soluble and allows peptides and proteins to be modified in water and aqueous solvents under physiologically relevant conditions, with short reaction times and with low reagent and catalyst loadings. This work suggests that photoredox catalysis using this newly designed catalyst is a promising strategy to modify dehydroalanine-containing natural products and thus could have great potential for novel bioconjugation strategies.
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Affiliation(s)
- Roos C W van Lier
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - A Dowine de Bruijn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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25
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Hu Y, Roberts JM, Kilgore HR, Lani ASM, Raines RT, Schomaker JM. Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes. J Am Chem Soc 2020; 142:18826-18835. [PMID: 33085477 PMCID: PMC7891878 DOI: 10.1021/jacs.0c06725] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jessica M. Roberts
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Henry R. Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amirah S. Mat Lani
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jennifer M. Schomaker
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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26
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Pellegrino S, Erba E, Bucci R, Clerici F. Diastereoselective Synthesis of Pyrazolines by Metal-Free Rearrangement of Bicyclic Triazolines. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1707173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The metal-free preparation of diazoalkanes through the ring rearrangement of bicyclic triazolines is reported here. Their use in 1,3-dipolar cycloaddition reactions with electron-withdrawing alkenes was investigated. This synthetic procedure allows differently substituted pyrazolines to be obtained in few steps and with high atom economy.
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Affiliation(s)
- Sara Pellegrino
- DISFARM-Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano
| | - Emanuela Erba
- DISFARM-Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano
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27
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de Vries RH, Roelfes G. Cu(II)-Catalysed β-silylation of dehydroalanine residues in peptides and proteins. Chem Commun (Camb) 2020; 56:11058-11061. [PMID: 32812557 DOI: 10.1039/d0cc05026a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report the efficient and selective Cu(ii)-catalysed β-silylation of naturally occurring dehydroalanine (Dha) residues in various ribosomally synthesized and post-translationally modified peptides (RiPPs). The method is also applicable to proteins, as was shown by the modification of a Dha residue that was chemically introduced into Small Ubiquitin-like Modifier (SUMO).
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Affiliation(s)
- Reinder H de Vries
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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28
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Nguyen SS, Prescher JA. Developing bioorthogonal probes to span a spectrum of reactivities. Nat Rev Chem 2020; 4:476-489. [PMID: 34291176 DOI: 10.1038/s41570-020-0205-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.
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Affiliation(s)
- Sean S Nguyen
- Departments of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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29
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Breugst M, Reissig H. The Huisgen Reaction: Milestones of the 1,3-Dipolar Cycloaddition. Angew Chem Int Ed Engl 2020; 59:12293-12307. [PMID: 32255543 PMCID: PMC7383714 DOI: 10.1002/anie.202003115] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Indexed: 12/21/2022]
Abstract
The concept of 1,3-dipolar cycloadditions was presented by Rolf Huisgen 60 years ago. Previously unknown reactive intermediates, for example azomethine ylides, were introduced to organic chemistry and the (3+2) cycloadditions of 1,3-dipoles to multiple-bond systems (Huisgen reaction) developed into one of the most versatile synthetic methods in heterocyclic chemistry. In this Review, we present the history of this research area, highlight important older reports, and describe the evolution and further development of the concept. The most important mechanistic and synthetic results are discussed. Quantum-mechanical calculations support the concerted mechanism always favored by R. Huisgen; however, in extreme cases intermediates may be involved. The impact of 1,3-dipolar cycloadditions on the click chemistry concept of K. B. Sharpless will also be discussed.
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Affiliation(s)
- Martin Breugst
- Department für ChemieUniversität zu KölnGreinstrasse 450939KölnGermany
| | - Hans‐Ulrich Reissig
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
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30
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DeMeester KE, Liang H, Zhou J, Wodzanowski KA, Prather BL, Santiago CC, Grimes CL. Metabolic Incorporation of N-Acetyl Muramic Acid Probes into Bacterial Peptidoglycan. ACTA ACUST UNITED AC 2020; 11:e74. [PMID: 31763799 DOI: 10.1002/cpch.74] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells utilize small carbohydrate building blocks to construct peptidoglycan (PG), a highly conserved mesh-like polymer that serves as a protective coat for the cell. PG production has long been a target for antibiotics, and its breakdown is a source for human immune recognition. A key component of bacterial PG, N-acetyl muramic acid (NAM), is a vital element in many synthetically derived immunostimulatory compounds. However, the exact molecular details of these structures and how they are generated remain unknown due to a lack of chemical probes surrounding the NAM core. A robust synthetic strategy to generate bioorthogonally tagged NAM carbohydrate units is implemented. These molecules serve as precursors for PG biosynthesis and recycling. Escherichia coli cells are metabolically engineered to incorporate the bioorthogonal NAM probes into their PG network. The probes are subsequently modified using copper-catalyzed azide-alkyne cycloaddition to install fluorophores directly into the bacterial PG, as confirmed by super-resolution microscopy and high-resolution mass spectrometry. Here, synthetic notes for key elements of this process to generate the sugar probes as well as streamlined user-friendly metabolic labeling strategies for both microbiology and immunological applications are described. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of peracetylated 2-azido glucosamine Basic Protocol 2: Synthesis of 2-azido and 2-alkyne NAM Basic Protocol 3: Synthesis of 3-azido NAM methyl ester Basic Protocol 4: Incorporation of NAM probes into bacterial peptidoglycan Basic Protocol 5: Confirmation of bacterial cell wall remodeling by mass spectrometry.
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Affiliation(s)
- Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.,Cutaneous Microbiome and Inflammation Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland
| | - Junhui Zhou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | | | - Benjamin L Prather
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Cintia C Santiago
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.,Center for the Study of Organic Compounds, CEDECOR-UNLP-CIC, Department of Chemistry, Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.,Department of Biological Sciences, University of Delaware, Newark, Delaware
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31
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Breugst M, Reißig H. Die Huisgen‐Reaktion: Meilensteine der 1,3‐dipolaren Cycloaddition. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003115] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Martin Breugst
- Department für Chemie Universität zu Köln Greinstraße 4 50939 Köln Deutschland
| | - Hans‐Ulrich Reißig
- Institut für Chemie und Biochemie Freie Universität Berlin Takustr. 3 14195 Berlin Deutschland
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32
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Bernardim B, Dunsmore L, Li H, Hocking B, Nuñez-Franco R, Navo CD, Jiménez-Osés G, Burtoloso ACB, Bernardes GJL. Precise Installation of Diazo-Tagged Side-Chains on Proteins to Enable In Vitro and In-Cell Site-Specific Labeling. Bioconjug Chem 2020; 31:1604-1610. [DOI: 10.1021/acs.bioconjchem.0c00232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Barbara Bernardim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - He Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Brad Hocking
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Reyes Nuñez-Franco
- Computational Chemistry Lab, CIC bioGUNE-BRTA, Derio, Bizkaia, 48160, Spain
| | - Claudio D. Navo
- Computational Chemistry Lab, CIC bioGUNE-BRTA, Derio, Bizkaia, 48160, Spain
| | | | - Antonio C. B. Burtoloso
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Joao Dagnone, 1100, CEP 13563-120, São Carlos, São Paolo, Brazil
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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33
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de Vries RH, Viel JH, Oudshoorn R, Kuipers OP, Roelfes G. Selective Modification of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) through Diels-Alder Cycloadditions on Dehydroalanine Residues. Chemistry 2019; 25:12698-12702. [PMID: 31361053 PMCID: PMC6790694 DOI: 10.1002/chem.201902907] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Indexed: 11/08/2022]
Abstract
We report the late‐stage chemical modification of ribosomally synthesized and post‐translationally modified peptides (RIPPs) by Diels–Alder cycloadditions to naturally occurring dehydroalanines. The tail region of the thiopeptide thiostrepton could be modified selectively and efficiently under microwave heating and transition‐metal‐free conditions. The Diels–Alder adducts were isolated and the different site‐ and endo/exo isomers were identified by 1D/2D 1H NMR. Via efficient modification of the thiopeptide nosiheptide and the lanthipeptide nisin Z the generality of the method was established. Minimum inhibitory concentration (MIC) assays of the purified thiostrepton Diels–Alder products against thiostrepton‐susceptible strains displayed high activities comparable to that of native thiostrepton. These Diels–Alder products were also subjected successfully to inverse‐electron‐demand Diels–Alder reactions with a variety of functionalized tetrazines, demonstrating the utility of this method for labeling of RiPPs.
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Affiliation(s)
- Reinder H de Vries
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Jakob H Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Ruben Oudshoorn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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34
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Derda R, Ng S. Genetically encoded fragment-based discovery. Curr Opin Chem Biol 2019; 50:128-137. [DOI: 10.1016/j.cbpa.2019.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
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35
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Bogart JW, Bowers AA. Dehydroamino acids: chemical multi-tools for late-stage diversification. Org Biomol Chem 2019; 17:3653-3669. [PMID: 30849157 PMCID: PMC6637761 DOI: 10.1039/c8ob03155j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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36
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Aydillo C, Mazo N, Navo CD, Jiménez‐Osés G. Elusive Dehydroalanine Derivatives with Enhanced Reactivity. Chembiochem 2019; 20:1246-1250. [DOI: 10.1002/cbic.201800758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Carlos Aydillo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- Department of Pharmaceutical Technology and ChemistryFaculty of Pharmacy and NutritionUniversity of Navarra Irunlarrea 3 31008 Pamplona Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA) Irunlarrea 3 31008 Pamplona Spain
| | - Nuria Mazo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
| | - Claudio D. Navo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
| | - Gonzalo Jiménez‐Osés
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
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37
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Gerster H, Keim M, Maas G. Cycloaddition reactions of acetylenic iminium salts and diazoacetates leading to pyrazole iminium salts. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2019. [DOI: 10.1515/znb-2019-0001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Acetylenic iminium triflates with the general formula [R–C≡ C–C(Ar)=N+R2 TfO−] were found to be excellent dipolarophiles in [3+ 2] cycloaddition reactions with diazoacetates leading to (1H-pyrazol-3(5)-yl)methanaminium triflates in high yields. The terminal acetylenic iminium salt (propyne iminium salt) [HC≡C–C(Ph)=N+Me2 TfO−] reacted with an equimolar amount of methyl diazoacetate instantaneously at 20°C to form the expected pyrazole in almost quantitative yield. When a 2:1 stoichiometry was applied, subsequent Michael addition of the pyrazole at the alkyne occurred and the bis(iminium) ditriflate 4 was obtained in high yield. By hydride reduction or hydrolysis of the iminium group, some of the highly hygroscopic pyrazole iminium salts were converted into neutral, twofold functionalized, di- and tri-C-substitued 1H-pyrazoles.
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Affiliation(s)
- Holger Gerster
- Institute of Organic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , D-89081 Ulm , Germany
| | - Michael Keim
- Institute of Organic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , D-89081 Ulm , Germany
| | - Gerhard Maas
- Institute of Organic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , D-89081 Ulm , Germany , Fax: +49(0731)5022803
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38
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Maaskant RV, Roelfes G. Bioorthogonal Metalloporphyrin-Catalyzed Selective Methionine Alkylation in the Lanthipeptide Nisin. Chembiochem 2019; 20:57-61. [PMID: 30246492 PMCID: PMC6680192 DOI: 10.1002/cbic.201800493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Bioorthogonal catalytic modification of ribosomally synthesized and post-translationally modified peptides (RiPPs) is a promising approach to obtaining novel antimicrobial peptides with improved properties and/or activities. Here, we present the serendipitous discovery of a selective and rapid method for the alkylation of methionines in the lanthipeptide nisin. Using carbenes, formed from water-soluble metalloporphyrins and diazoacetates, methionines are alkylated to obtain sulfonium ions. The formed sulfonium ions are stable, but can be further reacted to obtain functionalized methionine analogues, expanding the toolbox of chemical posttranslational modification even further.
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Affiliation(s)
- Ruben V. Maaskant
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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39
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Yokoi T, Ueda T, Tanimoto H, Morimoto T, Kakiuchi K. Site-selective conversion of azido groups at carbonyl α-positions into oxime groups leading triazide to a triple click conjugation scaffold. Chem Commun (Camb) 2019; 55:1891-1894. [DOI: 10.1039/c8cc09415b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This paper reports the selective conversion of alkyl azido groups at the carbonyl α-position into oximes, and one-pot triple click conjugation is demonstrated.
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Affiliation(s)
- Taiki Yokoi
- Division of Materials Science
- Graduate School of Science and Technology
- Nara Institute of Science and Technology (NAIST)
- 8916-5 Takayamacho
- Ikoma
| | - Tomomi Ueda
- Division of Materials Science
- Graduate School of Science and Technology
- Nara Institute of Science and Technology (NAIST)
- 8916-5 Takayamacho
- Ikoma
| | - Hiroki Tanimoto
- Division of Materials Science
- Graduate School of Science and Technology
- Nara Institute of Science and Technology (NAIST)
- 8916-5 Takayamacho
- Ikoma
| | - Tsumoru Morimoto
- Division of Materials Science
- Graduate School of Science and Technology
- Nara Institute of Science and Technology (NAIST)
- 8916-5 Takayamacho
- Ikoma
| | - Kiyomi Kakiuchi
- Division of Materials Science
- Graduate School of Science and Technology
- Nara Institute of Science and Technology (NAIST)
- 8916-5 Takayamacho
- Ikoma
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40
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Procacci B, Roy SS, Norcott P, Turner N, Duckett SB. Unlocking a Diazirine Long-Lived Nuclear Singlet State via Photochemistry: NMR Detection and Lifetime of an Unstabilized Diazo-Compound. J Am Chem Soc 2018; 140:16855-16864. [PMID: 30407809 PMCID: PMC6300312 DOI: 10.1021/jacs.8b10923] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Diazirines
are important for photoaffinity labeling, and their
photoisomerization is relatively well-known. This work shows how hyperpolarized
NMR spectroscopy can be used to characterize an unstable diazo-compound
formed via photoisomerization of a 15N2-labeled
silyl-ether-substituted diazirine. This diazirine is prepared in a
nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is
characterized to provide insight into the mechanism. The photochemical
isomerization of the diazirine into the diazo-analogue allows the
NMR invisible nuclear singlet state of the parent compound to be probed.
The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford
bicyclic pyrazolines that also show singlet state character. The presence
of singlet states in the diazirine and the diazo-compound is validated
by comparison of experimental nutation behavior with theoretical simulation.
The magnetic state lifetime of the diazo-compound is determined as
12 ± 1 s in CD3OD solution at room temperature, whereas
its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized
NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.
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Affiliation(s)
- Barbara Procacci
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Soumya S Roy
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Philip Norcott
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Norman Turner
- Accelerator Research Group, University of Huddersfield , Queensgate, Huddersfield HD1 3DH , United Kingdom
| | - Simon B Duckett
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
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41
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Jangra H, Chen Q, Fuks E, Zenz I, Mayer P, Ofial AR, Zipse H, Mayr H. Nucleophilicity and Electrophilicity Parameters for Predicting Absolute Rate Constants of Highly Asynchronous 1,3-Dipolar Cycloadditions of Aryldiazomethanes. J Am Chem Soc 2018; 140:16758-16772. [DOI: 10.1021/jacs.8b09995] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Harish Jangra
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Quan Chen
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Elina Fuks
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Ivo Zenz
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Peter Mayer
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Armin R. Ofial
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Hendrik Zipse
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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42
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Bartoccini F, Mari M, Retini M, Bartolucci S, Piersanti G. Organocatalytic Aza-Friedel-Crafts/Lactonization Domino Reaction of Naphthols and Phenols with 2-Acetamidoacrylate to Naphtho- and Benzofuranones Bearing a Quaternary Center at the C3 Position. J Org Chem 2018; 83:12275-12283. [PMID: 30191715 DOI: 10.1021/acs.joc.8b01774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
N-Acetyl ketimine generated from methyl 2-acetamidoacrylate was explored to develop an unprecedented domino aza-Friedel-Crafts/lactonization reaction with naphthols and phenols (including 5-hydroxyindoles). This novel method requires a catalyst loading of only 5 mol % of a phosphoric acid catalyst and provides a new series of 3-NHAc-naphtho- and benzofuranone derivatives bearing tetra-substituted stereogenic centers in moderate-to-good yields. The enantioselective variant using BINOL-derived phosphoric acids was also explored with 1-naphthol, providing the desired product with moderate enantioselectivities (up to 99:1 following recrystallization).
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Affiliation(s)
- Francesca Bartoccini
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Michele Mari
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Michele Retini
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Silvia Bartolucci
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Giovanni Piersanti
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
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43
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Yokoi T, Tanimoto H, Ueda T, Morimoto T, Kakiuchi K. Site-Selective Conversion of Azido Groups at Carbonyl α-Positions to Diazo Groups in Diazido and Triazido Compounds. J Org Chem 2018; 83:12103-12121. [DOI: 10.1021/acs.joc.8b02074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Taiki Yokoi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Hiroki Tanimoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Tomomi Ueda
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Tsumoru Morimoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Kiyomi Kakiuchi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
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44
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Hamlin TA, Svatunek D, Yu S, Ridder L, Infante I, Visscher L, Bickelhaupt FM. Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800572] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Trevor A. Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Dennis Svatunek
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute of Applied Synthetic Chemistry; Technische Universität Wien (TU Wien); Getreidemarkt 9 1060 Vienna Austria
| | - Song Yu
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Lars Ridder
- Netherlands eScience Center; Science Park 140 1098 XG Amsterdam The Netherlands
| | - Ivan Infante
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lucas Visscher
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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45
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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46
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de Bruijn AD, Roelfes G. Chemical Modification of Dehydrated Amino Acids in Natural Antimicrobial Peptides by Photoredox Catalysis. Chemistry 2018; 24:11314-11318. [PMID: 29939448 PMCID: PMC6099298 DOI: 10.1002/chem.201803144] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 12/29/2022]
Abstract
Dehydroalanine (Dha) and dehydrobutyrine (Dhb) are remarkably versatile non-canonical amino acids often found in antimicrobial peptides. This work presents the selective modification of Dha and Dhb in antimicrobial peptides through photocatalytic activation of organoborates under the influence of visible light. Ir(dF(CF3 )ppy)2 (dtbbpy)PF6 was used as a photoredox catalyst in aqueous solutions for the modification of thiostrepton and nisin. The mild conditions and high selectivity for the dehydrated residues show that photoredox catalysis is a promising tool for the modification of peptide-derived natural products.
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Affiliation(s)
- A. Dowine de Bruijn
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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47
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de Bruijn AD, Roelfes G. Catalytic Modification of Dehydroalanine in Peptides and Proteins by Palladium-Mediated Cross-Coupling. Chemistry 2018; 24:12728-12733. [PMID: 29923249 PMCID: PMC6146911 DOI: 10.1002/chem.201802846] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/18/2018] [Indexed: 11/16/2022]
Abstract
Dehydroalanine (Dha) is a remarkably versatile non‐canonical amino acid often found in antimicrobial peptides. Herein, we present the catalytic modification of Dha by a palladium‐mediated cross‐coupling reaction. By using Pd(EDTA)(OAc)2 as water‐soluble catalyst, a variety of arylboronic acids was coupled to the dehydrated residues in proteins and peptides, such as Nisin. The cross‐coupling reaction gave both the Heck product, in which the sp2‐hybridisation of the α‐carbon is retained, as well as the conjugated addition product. The reaction can be performed under mild aqueous conditions, which makes this method an attractive addition to the palette of bio‐orthogonal catalytic methods.
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Affiliation(s)
- A Dowine de Bruijn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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48
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Dadová J, Galan SR, Davis BG. Synthesis of modified proteins via functionalization of dehydroalanine. Curr Opin Chem Biol 2018; 46:71-81. [PMID: 29913421 DOI: 10.1016/j.cbpa.2018.05.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Dehydroalanine has emerged in recent years as a non-proteinogenic residue with strong chemical utility in proteins for the study of biology. In this review we cover the several methods now available for its flexible and site-selective incorporation via a variety of complementary chemical and biological techniques and examine its reactivity, allowing both creation of modified protein side-chains through a variety of bond-forming methods (C-S, C-N, C-Se, C-C) and as an activity-based probe in its own right. We illustrate its utility with selected examples of biological and technological discovery and application.
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Affiliation(s)
- Jitka Dadová
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sébastien Rg Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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49
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Abstract
Chemical tools are transforming our understanding of biomolecules and living systems. Included in this group are bioorthogonal reagents-functional groups that are inert to most biological species, but can be selectively ligated with complementary probes, even in live cells and whole organisms. Applications of these tools have revealed fundamental new insights into biomolecule structure and function-information often beyond the reach of genetic approaches. In many cases, the knowledge gained from bioorthogonal probes has enabled new questions to be asked and innovative research to be pursued. Thus, the continued development and application of these tools promises to both refine our view of biological systems and facilitate new discoveries. Despite decades of achievements in bioorthogonal chemistry, limitations remain. Several reagents are too large or insufficiently stable for use in cellular environments. Many bioorthogonal groups also cross-react with one another, restricting them to singular tasks. In this Account, we describe our work to address some of the voids in the bioorthogonal toolbox. Our efforts to date have focused on small reagents with a high degree of tunability: cyclopropenes, triazines, and cyclopropenones. These motifs react selectively with complementary reagents, and their unique features are enabling new pursuits in biology. The Account is organized by common themes that emerged in our development of novel bioorthogonal reagents and reactions. First, natural product structures can serve as valuable starting points for probe design. Cyclopropene, triazine, and cyclopropenone motifs are all found in natural products, suggesting that they would be metabolically stable and compatible with a variety of living systems. Second, fine-tuning bioorthogonal reagents is essential for their successful translation to biological systems. Different applications demand different types of probes; thus, generating a collection of tools that span a continuum of reactivities and stabilities remains an important goal. We have used both computational analyses and mechanistic studies to guide the optimization of various cyclopropene and triazine probes. Along the way, we identified reagents that are chemoselective but best suited for in vitro work. Others are selective and robust enough for use in living organisms. The last section of this Account highlights the need for the continued pursuit of new reagents and reactions. Challenges exist when bioorthogonal chemistries must be used in concert, given that many exploit similar mechanisms and cannot be used simultaneously. Such limitations have precluded certain multicomponent labeling studies and other biological applications. We have relied on mechanistic and computational insights to identify mutually orthogonal sets of reactions, in addition to exploring unique genres of reactivity. The continued development of mechanistically distinct, biocompatible reactions will further diversify the bioorthogonal reaction portfolio for examining biomolecules.
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50
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Escorihuela J, Das A, Looijen WJE, van Delft FL, Aquino AJA, Lischka H, Zuilhof H. Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies. J Org Chem 2018; 83:244-252. [PMID: 29260879 PMCID: PMC5759032 DOI: 10.1021/acs.joc.7b02614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Indexed: 11/29/2022]
Abstract
Stimulated by its success in both bioconjugation and surface modification, we studied the strain-promoted oxidation-controlled cycloalkyne-1,2-quinone cycloaddition (SPOCQ) in three ways. First, the second-order rate constants and activation parameters (ΔH⧧) were determined of various cyclooctynes reacting with 4-tert-butyl-1,2-quinone in a SPOCQ reaction, yielding values for ΔH⧧ of 4.5, 7.3, and 12.1 kcal/mol, for bicyclo[6.1.0]non-4-yne (BCN), cyclooctyne (OCT), and dibenzoazacyclooctyne (DIBAC), respectively. Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3-8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. Only dispersion-corrected DFT methods like B97D (yielding 4.9, 6.4, and 12.1 kcal/mol for these three reactions) and high-level CCSD(T) and multireference multiconfiguration AQCC ab initio approaches (both yielding 8.2 kcal/mol for BCN) give good approximations of experimental data. Finally, the multireference methods show that the radical character in the TS is rather small, thus rationalizing the use of single-reference methods like B97D and SCS-MP2 as intrinsically valid approaches.
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Affiliation(s)
- Jorge Escorihuela
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Escuela
Técnica Superior de Ingenieros Industriales − Departamento
de Termodinámica Aplicada, Universitat
Politècnica de València, Camino de Vera s/n, 46020 Valencia, Spain
| | - Anita Das
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
| | - Wilhelmus J. E. Looijen
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Floris L. van Delft
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Adelia J. A. Aquino
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
- Institute
for Soil Research, University of Natural Resources and Life Sciences
Vienna, Peter-Jordan-Strasse
82, A-1190 Vienna, Austria
| | - Hans Lischka
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
- Institute
for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Han Zuilhof
- Laboratory
of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- School
of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
- Department
of Chemical and Materials Engineering, King
Abdulaziz University, Jeddah, Saudi Arabia
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