1
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Kurmayer R, Morón Asensio R. Real-Time Observation of Clickable Cyanotoxin Synthesis in Bloom-Forming Cyanobacteria Microcystis aeruginosa and Planktothrix agardhii. Toxins (Basel) 2024; 16:526. [PMID: 39728784 DOI: 10.3390/toxins16120526] [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] [Academic Contribution Register] [Received: 10/12/2024] [Revised: 11/28/2024] [Accepted: 12/01/2024] [Indexed: 12/28/2024] Open
Abstract
Recently, the use of click chemistry for localization of chemically modified cyanopeptides has been introduced, i.e., taking advantage of promiscuous adenylation (A) domains in non-ribosomal peptide synthesis (NRPS), allowing for the incorporation of clickable non-natural amino acids (non-AAs) into their peptide products. In this study, time-lapse experiments have been performed using pulsed feeding of three different non-AAs in order to observe the synthesis or decline of azide- or alkyne-modified microcystins (MCs) or anabaenopeptins (APs). The cyanobacteria Microcystis aeruginosa and Planktothrix agardhii were grown under maximum growth rate conditions (r = 0.35-0.6 and 0.2-0.4 (day-1), respectively) in the presence of non-AAs for 12-168 h. The decline of the azide- or alkyne-modified MC or AP was observed via pulse-feeding. In general, the increase in clickable MC/AP in peptide content reached a plateau after 24-48 h and was related to growth rate, i.e., faster-growing cells also produced more clickable MC/AP. Overall, the proportion of clickable MC/AP in the intracellular fraction correlated with the proportion observed in the dissolved fraction. Conversely, the overall linear decrease in clickable MC/AP points to a rather constant decline via dilution by growth instead of a regulated or induced release in the course of the synthesis process.
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Affiliation(s)
- Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria
| | - Rubén Morón Asensio
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria
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2
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Cheng L, Yan J, Shi W, Zhang J, Dong Q, Hu Y, Zhou Z, Ye Q. Exploring the causal link between serum amino acids and Parkinson's disease: a Mendelian randomization approach. Sci Rep 2024; 14:30271. [PMID: 39632961 PMCID: PMC11618358 DOI: 10.1038/s41598-024-81787-z] [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] [Academic Contribution Register] [Received: 05/28/2024] [Accepted: 11/28/2024] [Indexed: 12/07/2024] Open
Abstract
This study aimed to explore the causal relationships between multiple blood amino acids (BAAs) and the Parkinson's disease (PD). We downloaded genome-wide association study (GWAS) data for BAAs and PD from the OpenGWAS database, screened single nucleotide polymorphisms (SNPs) from the data, and evaluated the causal relationship between BAA levels and PD using the inverse variance weighted (IVW) method. The sensitivity analysis was also conducted. After SNP screening, three amino acid indicators were identified: met-a-308 (phenylalanine), met-a-584 (X-12100 hydroxytryptophan), and met-a-337 (5-hydroxyproline), which showed significant causal relationship with the occurrence of PD. There was no significant heterogeneity or horizontal pleiotropy, and the results were stable. The multivariate MR analysis showed that the mediating effects generated by the introduction of multiple variables were not significant. In conclusion, phenylalanine, X-12,100 hydroxytryptophan, and 5-hydroxyproline have a causal relationship with the occurrence of PD and may be potential early screening biomarkers and blocking targets.
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Affiliation(s)
- Lei Cheng
- Department of Tuina, Longhua Hospital Shanghai University of Traditional Chinese Medicine, NO.725, South Wanping Road, Xuhui District, Shanghai, 200032, China
| | - Juntao Yan
- Department of Tuina, Yueyang Hospital of Integrated Traditional Chinese Medicine and Western Medicine, Shanghai University of Traditional Chinese Medicine, NO.110, Ganhe Road, Hongkou District, Shanghai, 200437, China
| | - Wenting Shi
- Longhua Hospital Shanghai University of Traditional Chinese Medicine, NO.725, South Wanping Road, Xuhui District, Shanghai, 200032, China
| | - Jing Zhang
- Longhua Hospital Shanghai University of Traditional Chinese Medicine, NO.725, South Wanping Road, Xuhui District, Shanghai, 200032, China
| | - Qingjun Dong
- Longhua Hospital Shanghai University of Traditional Chinese Medicine, NO.725, South Wanping Road, Xuhui District, Shanghai, 200032, China
| | - Yiren Hu
- University College London, Gower Street, WC1E 6BT, London, UK
| | - Zhongyan Zhou
- Department of Pharmacology and Pharmacy & State Key Labratory of Pharmaceutical Biotechnology, LKS Faculty of Medicine, The University of Hong Kong, 2/F, Laboratory Block, 21 Sassoon, Hong Kong, China.
| | - Qing Ye
- Department of Neurology, Longhua Hospital Shanghai University of Traditional Chinese Medicine, NO.725, South Wanping Road, Xuhui District, 200032, Shanghai, China.
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3
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Payne S, Wick S, Carr PA, Guido NJ. A Methodology for the Assessment and Prioritization of Genetic Biocontainment Technologies for Engineered Microbes. APPLIED BIOSAFETY 2024; 29:108-119. [PMID: 39144101 PMCID: PMC11319856 DOI: 10.1089/apb.2023.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 08/16/2024]
Abstract
Introduction Organisms engineered with synthetic genes and genomes have the potential to play critical roles to address important issues in the environment, human health, and manufacturing. Engineered genetic biocontainment technologies are needed to manage the risks of unintended consequences when deploying these biological systems in consultation with the biosafety and biosecurity communities. Metrics measuring genetic biocontainment and a methodology to apply them are required to determine which genetic biocontainment technologies warrant further development for real-world applications. In this study, we develop and apply a systems analysis of the current technical landscape using expert opinion and a metric-based scoring system resulting in a semiquantitative comparative assessment of genetic biocontainment technologies in microorganisms. Methods Genetic biocontainment technologies were evaluated according to multiple metrics, falling into two broad classes: feasibility and applicability. Specific genetic biocontainment example scenarios and generalized categories were scored with these metrics. Gap analysis was carried out, indicating particular areas where genetic biocontainment can be improved. Results Metric analysis scoring of feasibility and applicability enabled prioritization of genetic biocontainment technologies for real-world applications. Gap analysis showed that technology readiness and containment stability scored low for a number of scenarios and categories, indicating a general need for further development before they can be ready for deployment. Conclusion Developing an assessment framework with defined metrics produced a straightforward system for evaluating genetic biocontainment strategies intended for various real-world applications. Use of the methodology also provided insights into existing gaps in genetic biocontainment strategies, and by altering the metrics, can be applied to other biotechnologies.
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Affiliation(s)
- Stephen Payne
- MIT Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Scott Wick
- MIT Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Peter A. Carr
- MIT Lincoln Laboratory, Lexington, Massachusetts, USA
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4
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Valentini A, Schultz-Knudsen K, Højgaard Hansen A, Tsakoumagkou A, Jenkins L, Christensen HB, Manandhar A, Milligan G, Ulven T, Rexen Ulven E. Discovery of Potent Tetrazole Free Fatty Acid Receptor 2 Antagonists. J Med Chem 2023; 66:6105-6121. [PMID: 37129317 PMCID: PMC10547238 DOI: 10.1021/acs.jmedchem.2c01935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/25/2022] [Indexed: 05/03/2023]
Abstract
The free fatty acid receptor 2 (FFA2), also known as GPR43, mediates effects of short-chain fatty acids and has attracted interest as a potential target for treatment of various metabolic and inflammatory diseases. Herein, we report the results from bioisosteric replacement of the carboxylic acid group of the established FFA2 antagonist CATPB and SAR investigations around these compounds, leading to the discovery of the first high-potency FFA2 antagonists, with the preferred compound TUG-2304 (16l) featuring IC50 values of 3-4 nM in both cAMP and GTPγS assays, favorable physicochemical and pharmacokinetic properties, and the ability to completely inhibit propionate-induced neutrophil migration and respiratory burst.
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Affiliation(s)
- Alice Valentini
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Katrine Schultz-Knudsen
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anders Højgaard Hansen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Argyro Tsakoumagkou
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Laura Jenkins
- Centre
for Translational Pharmacology, School of Molecular Biosciences, College
of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Henriette B. Christensen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Asmita Manandhar
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Graeme Milligan
- Centre
for Translational Pharmacology, School of Molecular Biosciences, College
of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Trond Ulven
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Elisabeth Rexen Ulven
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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5
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Zhang X, Galenkamp NS, van der Heide NJ, Moreno J, Maglia G, Kjems J. Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor. ACS NANO 2023; 17:9167-9177. [PMID: 37127291 PMCID: PMC10184537 DOI: 10.1021/acsnano.2c12733] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 05/03/2023]
Abstract
Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Julián Moreno
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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6
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Rein J, Meinhardt JM, Hofstra Wahlman JL, Sigman MS, Lin S. A Physical Organic Approach towards Statistical Modeling of Tetrazole and Azide Decomposition. Angew Chem Int Ed Engl 2023; 62:e202218213. [PMID: 36823344 PMCID: PMC10079611 DOI: 10.1002/anie.202218213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 12/09/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Nitrogen atom-rich heterocycles and organic azides have found extensive use in many sectors of modern chemistry from drug discovery to energetic materials. The prediction and understanding of their energetic properties are thus key to the safe and effective application of these compounds. In this work, we disclose the use of multivariate linear regression modeling for the prediction of the decomposition temperature and impact sensitivity of structurally diverse tetrazoles and organic azides. We report a data-driven approach for property prediction featuring a collection of quantum mechanical parameters and computational workflows. The statistical models reported herein carry predictive accuracy as well as chemical interpretability. Model validation was successfully accomplished via tetrazole test sets with parameters generated exclusively in silico. Mechanistic analysis of the statistical models indicated distinct divergent pathways of thermal and impact-initiated decomposition.
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Affiliation(s)
- Jonas Rein
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jonathan M Meinhardt
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Song Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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7
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Xie Y, Lopez-Silva TL, Schneider JP. Hydrophilic Azide-Containing Amino Acid to Enhance the Solubility of Peptides for SPAAC Reactions. Org Lett 2022; 24:7378-7382. [PMID: 36190801 PMCID: PMC10673676 DOI: 10.1021/acs.orglett.2c02906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Abstract
We report a new positively charged azidoamino acid for strain-promoted azide-alkyne cycloaddition (SPAAC) applications that overcomes possible solubility limitations of commonly used azidolysine, especially in systems with numerous ligation sites. The residue is easily synthesized, is compatible with Fmoc-based solid-phase peptide synthesis employing a range of coupling conditions, and offers efficient second-order rate constants in SPAAC ligations employing DBCO (0.34 M-1 s-1) and BCN (0.28 M-1 s-1).
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Affiliation(s)
- Yixin Xie
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Tania L Lopez-Silva
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Joel P Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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8
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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9
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Mandler MD, Degnan AP, Zhang S, Aulakh D, Georges K, Sandhu B, Sarjeant A, Zhu Y, Traeger SC, Cheng PT, Ellsworth BA, Regueiro-Ren A. Structural and Thermal Characterization of Halogenated Azidopyridines: Under-Reported Synthons for Medicinal Chemistry. Org Lett 2022; 24:799-803. [PMID: 34714083 DOI: 10.1021/acs.orglett.1c03201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Abstract
Owing to their participation in Click reactions, bifunctional azides are valuable intermediates in the preparation of medicines and biochemical tool compounds. Despite the privileged nature of pyridines among pharmaceutical scaffolds, reports of the synthesis and characterization of azidopyridines bearing a halogen substituent for further elaboration are almost completely unknown in the literature. As azidopyridines carry nearly equal numbers of nitrogen and carbon atoms, we hypothesized that safety concerns limited the application of these useful bifunctional building blocks in medicinal and biological chemistry. To address this concern, we prepared and characterized nine azidopyridines bearing a single fluorine, chlorine, or bromine atom. All were examined by differential scanning calorimetry (DSC), in which they demonstrated exotherms of 228-326 kJ/mol and onset temperatures between 119 and 135 °C. Selected azidopyridines were advanced to mechanical stress testing, in which impact sensitivity was noted for one regioisomer of C5H3FN4. The utility of these versatile intermediates was demonstrated through their use in a variety of Click reactions and the diversification of the halogen handles.
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Affiliation(s)
- Michael D Mandler
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Andrew P Degnan
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Shasha Zhang
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Darpandeep Aulakh
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Ketleine Georges
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Bhupinder Sandhu
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Yeheng Zhu
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Sarah C Traeger
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Peter T Cheng
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Bruce A Ellsworth
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Alicia Regueiro-Ren
- Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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10
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Allian AD, Flanagan RC, Mentzer R, Sperry JB, Xia H, Zhao R. Precompetitive Collaborations in the Pharmaceutical Industry: Process Safety Groups Work Together to Reduce Hazards, from R&D Laboratories to Manufacturing Facilities. ACS CHEMICAL HEALTH & SAFETY 2021. [DOI: 10.1021/acs.chas.1c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ayman D. Allian
- Eli Lilly and Company, Synthetic Molecule Design & Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Roy C. Flanagan
- GlaxoSmithKline, Clinical Supply Chain, 1011 North Arendell Avenue, Zebulon, North Carolina 27597, United States
| | - Ray Mentzer
- Purdue University, 480 Stadium Mall Drive, FRNY Building, Rm 3019, West Lafayette, Indiana 47907-2050, United States
| | - Jeffrey B. Sperry
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Han Xia
- Eli Lilly and Company, Synthetic Molecule Design & Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Ralph Zhao
- Process Research & Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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11
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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12
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13
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Green S, Wheelhouse KM, Payne AD, Hallett JP, Miller PW, Bull JA. Thermal Stability and Explosive Hazard Assessment of Diazo Compounds and Diazo Transfer Reagents. Org Process Res Dev 2020; 24:67-84. [PMID: 31983869 PMCID: PMC6972035 DOI: 10.1021/acs.oprd.9b00422] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/27/2019] [Indexed: 11/29/2022]
Abstract
Despite their wide use in academia as metal-carbene precursors, diazo compounds are often avoided in industry owing to concerns over their instability, exothermic decomposition, and potential explosive behavior. The stability of sulfonyl azides and other diazo transfer reagents is relatively well understood, but there is little reliable data available for diazo compounds. This work first collates available sensitivity and thermal analysis data for diazo transfer reagents and diazo compounds to act as an accessible reference resource. Thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and accelerating rate calorimetry (ARC) data for the model donor/acceptor diazo compound ethyl (phenyl)diazoacetate are presented. We also present a rigorous DSC dataset with 43 other diazo compounds, enabling direct comparison to other energetic materials to provide a clear reference work to the academic and industrial chemistry communities. Interestingly, there is a wide range of onset temperatures (T onset) for this series of compounds, which varied between 75 and 160 °C. The thermal stability variation depends on the electronic effect of substituents and the amount of charge delocalization. A statistical model is demonstrated to predict the thermal stability of differently substituted phenyl diazoacetates. A maximum recommended process temperature (T D24) to avoid decomposition is estimated for selected diazo compounds. The average enthalpy of decomposition (ΔH D) for diazo compounds without other energetic functional groups is -102 kJ mol-1. Several diazo transfer reagents are analyzed using the same DSC protocol and found to have higher thermal stability, which is in general agreement with the reported values. For sulfonyl azide reagents, an average ΔH D of -201 kJ mol-1 is observed. High-quality thermal data from ARC experiments shows the initiation of decomposition for ethyl (phenyl)diazoacetate to be 60 °C, compared to that of 100 °C for the common diazo transfer reagent p-acetamidobenzenesulfonyl azide (p-ABSA). The Yoshida correlation is applied to DSC data for each diazo compound to provide an indication of both their impact sensitivity (IS) and explosivity. As a neat substance, none of the diazo compounds tested are predicted to be explosive, but many (particularly donor/acceptor diazo compounds) are predicted to be impact-sensitive. It is therefore recommended that manipulation, agitation, and other processing of neat diazo compounds are conducted with due care to avoid impacts, particularly in large quantities. The full dataset is presented to inform chemists of the nature and magnitude of hazards when using diazo compounds and diazo transfer reagents. Given the demonstrated potential for rapid heat generation and gas evolution, adequate temperature control and cautious addition of reagents that begin a reaction are strongly recommended when conducting reactions with diazo compounds.
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Affiliation(s)
- Sebastian
P. Green
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K.
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, Exhibition Road, London SW7 2AZ, U.K.
| | - Katherine M. Wheelhouse
- API Chemistry, Product Development & Supply and Process Safety,
Pilot Plant Operations, GlaxoSmithKline,
GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - Andrew D. Payne
- API Chemistry, Product Development & Supply and Process Safety,
Pilot Plant Operations, GlaxoSmithKline,
GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - Jason P. Hallett
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, Exhibition Road, London SW7 2AZ, U.K.
| | - Philip W. Miller
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K.
| | - James A. Bull
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K.
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14
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Inada H, Furukawa K, Shibuya M, Yamamoto Y. One-pot, two-step synthesis of unnatural α-amino acids involving the exhaustive aerobic oxidation of 1,2-diols. Chem Commun (Camb) 2019; 55:15105-15108. [PMID: 31782427 DOI: 10.1039/c9cc07889d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/04/2023]
Abstract
Herein, we report the nor-AZADO-catalyzed exhaustive aerobic oxidations of 1,2-diols to α-keto acids. Combining oxidation with transamination using dl-2-phenylglycine led to the synthesis of free α-amino acids (AAs) in one pot. This method enables the rapid and flexible preparation of a variety of valuable unnatural AAs, such as fluorescent AAs, photoactivatable AAs, and other functional AAs for bioorthogonal reactions.
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Affiliation(s)
- Haruki Inada
- Department of Basic Medicinal Sciences Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.
| | - Keisuke Furukawa
- Department of Basic Medicinal Sciences Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.
| | - Masatoshi Shibuya
- Department of Basic Medicinal Sciences Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.
| | - Yoshihiko Yamamoto
- Department of Basic Medicinal Sciences Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.
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15
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Abstract
Organic azides are useful synthetic intermediates, which demonstrate broad reactivity. Unlike most organic azides, allylic azides can spontaneously rearrange to form a mixture of isomers. This rearrangement has been named the Winstein rearrangement. Using allylic azides can result in low yields and azide racemization in some synthetic contexts due to the Winstein rearrangement. Effort has been made to understand the mechanism of the Winstein rearrangement and to take advantage of this process. Several guiding principles can be used to identify which azides will produce a mixture of isomers and which will resist rearrangement. Selective reaction conditions can be used to differentiate the azide isomers in a dynamic manner. This review covers all aspects of allylic azides including their synthesis, their reactivity, the mechanism of the Winstein rearrangement, and reactions that can selectively elaborate an azide isomer. This review covers the literature from Winstein's initial report to early 2019.
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Affiliation(s)
- Angela S Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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16
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Tippmann EM, Culpepper S, Bunnel W, Appel N. New perspectives on aryl azide noncanonical amino acid use in yeast. Photochem Photobiol Sci 2019; 18:253-258. [DOI: 10.1039/c8pp00243f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/23/2022]
Abstract
A photochemically chemically active noncanonical amino acidpara-azido-l-phenylalanine widely used in biology was found to be metabolized bySaccharomyces cerevisiae.
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17
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Abstract
Aryl transfer reactions from arenediazonium salts have started to make their impact in chemical biology with initial forays in the arena of arylative modifications and bio-conjugations of amino acids, peptides and proteins.
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Affiliation(s)
- Saumitra Sengupta
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore
- India
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18
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Yang H, Wierzbicki M, Bois DRD, Nowick JS. X-ray Crystallographic Structure of a Teixobactin Derivative Reveals Amyloid-like Assembly. J Am Chem Soc 2018; 140:14028-14032. [PMID: 30296063 PMCID: PMC6356018 DOI: 10.1021/jacs.8b07709] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/18/2022]
Abstract
This paper describes the X-ray crystallographic structure of a derivative of the antibiotic teixobactin and shows that its supramolecular assembly through the formation of antiparallel β-sheets creates binding sites for oxyanions. An active derivative of teixobactin containing lysine in place of allo-enduracididine assembles to form amyloid-like fibrils, which are observed through a thioflavin T fluorescence assay and by transmission electron microscopy. A homologue, bearing an N-methyl substituent, to attenuate fibril formation, and an iodine atom, to facilitate X-ray crystallographic phase determination, crystallizes as double helices of β-sheets that bind sulfate anions. β-Sheet dimers are key subunits of these assemblies, with the N-terminal methylammonium group of one monomer and the C-terminal macrocycle of the other monomer binding each anion. These observations suggest a working model for the mechanism of action of teixobactin, in which the antibiotic assembles and the assemblies bind lipid II and related bacterial cell wall precursors on the surface of Gram-positive bacteria.
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Affiliation(s)
- Hyunjun Yang
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Michał Wierzbicki
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Derek R. Du Bois
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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