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De Novo Biosynthesis of Terminal Alkyne-Labeled Natural Products
De novo biosynthesis of terminal alkyne-labeled natural products Xuejun Zhu1,2, Joyce Liu2,3, Wenjun Zhang1,2,4* 1Department of Chemical and Biomolecular Engineering, 2Energy Biosciences Institute, 3Department of Bioengineering, University of California, Berkeley, CA 94720, USA. 4Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. *e-mail:[email protected] 1 Abstract: The terminal alkyne is a functionality widely used in organic synthesis, pharmaceutical science, material science, and bioorthogonal chemistry. This functionality is also found in acetylenic natural products, but the underlying biosynthetic pathways for its formation are not well understood. Here we report the characterization of the first carrier protein- dependent terminal alkyne biosynthetic machinery in microbes. We further demonstrate that this enzymatic machinery can be exploited for the in situ generation and incorporation of terminal alkynes into two natural product scaffolds in E. coli. These results highlight the prospect for tagging major classes of natural products, including polyketides and polyketide/non-ribosomal peptide hybrids, using biosynthetic pathway engineering. 2 Natural products are important small molecules widely used as drugs, pesticides, herbicides, and biological probes. Tagging natural products with a unique chemical handle enables the visualization, enrichment, quantification, and mode of action study of natural products through bioorthogonal chemistry1-4. One prevalent bioorthogonal reaction is -
Phospholipid:Diacylglycerol Acyltransferase: an Enzyme That Catalyzes the Acyl-Coa-Independent Formation of Triacylglycerol in Yeast and Plants
Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants Anders Dahlqvist*†‡, Ulf Ståhl†§, Marit Lenman*, Antoni Banas*, Michael Lee*, Line Sandager¶, Hans Ronne§, and Sten Stymne¶ *Scandinavian Biotechnology Research (ScanBi) AB, Herman Ehles Va¨g 2 S-26831 Svaloˆv, Sweden; ¶Department of Plant Breeding Research, Swedish University of Agricultural Sciences, Herman Ehles va¨g 2–4, S-268 31 Svalo¨v, Sweden; and §Department of Plant Biology, Uppsala Genetic Center, Swedish University of Agricultural Sciences, Box 7080, S-750 07 Uppsala, Sweden Edited by Christopher R. Somerville, Carnegie Institution of Washington, Stanford, CA, and approved March 31, 2000 (received for review February 15, 2000) Triacylglycerol (TAG) is known to be synthesized in a reaction that acid) and epoxidated fatty acid (vernolic acid) in TAG in castor uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, bean (Ricinus communis) and the hawk’s-beard Crepis palaestina, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol respectively. Furthermore, a similar enzyme is shown to be acyltransferase. We have found that some plants and yeast also present in the yeast Saccharomyces cerevisiae, and the gene have an acyl-CoA-independent mechanism for TAG synthesis, encoding this enzyme, YNR008w, is identified. which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:dia- Materials and Methods cylglycerol acyltransferase, or PDAT. PDAT was characterized in Yeast Strains and Plasmids. The wild-type yeast strains used were microsomal preparations from three different oil seeds: sunflower, either FY1679 (MAT␣ his3-⌬200 leu2-⌬1 trp1-⌬6 ura3-52) (9) or castor bean, and Crepis palaestina. -
The. Reactions Op Semicarbazones, Thiosbmicarbazonbs
THE. REACTIONS OP SEMICARBAZONES, THIOSBMICARBAZONBS AMD RELATED COMPOUNDS, IMCLTJDIMG THE ACTION OF AMINES ON AMINOCARBOCARBAZONES. A THESIS PRESENTED BY JOHN MCLEAN B.So. IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY OF THE UNIVERSITY OF GLASGOW. / MAY *936. THE ROYAL TECHNICAL COLLEGE, GLASGOW. ProQuest Number: 13905234 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 13905234 Published by ProQuest LLC(2019). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106- 1346 This research was carried out in the Royal Technical College, Glasgow, under the supervision of Professor F.J. Wilson, whose helpful advice was greatly appreciated by the author. CONTENTS. Page General Introduction, PART 1. The Action of Amines on Amino Carhocarbazones. Introduction... ..... ,..................... 4 Benzylamine......... Theoretical.............. 11 ......... Experimental............. 15 Aniline............. Theoretical............ 21 ............. Experimental............ 22 B-Naphthylamine..... Theoretical............... 27 -
Nicolet Condensed Phase Academic Sampler
Nicolet Condensed Phase Academic Sampler Library Listing – 1,000 spectra This high resolution format library is suited to the needs of academic institutions and small QC labs. Chosen by chemistry professors from many disciplines, it includes spectra of chemicals used in a wide range of common laboratory experiments. The Nicolet Condensed Phase Academic Sampler includes 1,000 spectra of common chemicals representing the major functional groups and combinations of functional groups which are most likely to be observed in academic chemistry laboratories. These chemicals are also important building blocks commonly found in industrial applications. Thermo Nicolet Condensed Phase Academic Sampler Index Compound Name Index Compound Name 353 (+)-2-Phenyl-1-propanol, 97% 164 1,2,4,5-Tetramethylbenzene, 98% 768 (+)-4-Cholesten-3-one 161 1,2,4-Trimethylbenzene, 99+% 290 (+)-a-Lactose 254 1,2-Butanediol, 98% 262 (+)-b-Citronellol, 95% 499 1,2-Diaminopropane, 99% 344 (+/-)-1-Phenyl-1-propanol, 99% 128 1,2-Dibromoethylene, 98%, (Z) + (E) 101 (+/-)-2-Bromopentane, 97% 106 1,2-Dichloroethane, 99+% 228 (+/-)-2-Butanol, 99% 110 1,2-Dichloropropane, 99% 233 (+/-)-2-Heptanol, 96% 258 1,2-Pentanediol, tech., 95% 402 (+/-)-Camphor, 97% 550 1,2-Phenylenediamine, 98% 553 (+/-)-Epinephrine, 99% 77 1,3,5,7-Cyclooctatetraene, 98% 280 (+/-)-Isoborneol, 85% 45 1,3,5-Hexatriene 706 (+/-)-Warfarin, 98% 74 1,3-Cycloheptadiene, 97% 648 (+/-)-sec-Butyl acetate, 99% 72 1,3-Cyclohexadiene, 96% 490 (+/-)-sec-Butylamine, 99% 388 1,3-Cyclohexanedione, 97% 279 (-)-Borneol, -
Synthetic and Mechanistic Investigations in Organophosphorus Chemistry Towards an Alternative Mitsunobu Protocol
Synthetic and Mechanistic Investigations of Some Novel Organophosphorus Reagents Author Fairfull-Smith, Kathryn Elizabeth Published 2004 Thesis Type Thesis (PhD Doctorate) School School of Science DOI https://doi.org/10.25904/1912/3875 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/367534 Griffith Research Online https://research-repository.griffith.edu.au SYNTHETIC AND MECHANISTIC INVESTIGATIONS OF SOME NOVEL ORGANOPHOSPHORUS REAGENTS KATHRYN ELIZABETH FAIRFULL-SMITH (née ELSON) BSc (Hons) School of Science Faculty of Science Griffith University Submitted in fulfilment of the requirements of the Degree of Doctor of Philosophy May 2004 i Statement of Originality This work has not previously been submitted for a degree or diploma in any University. To the best of my knowledge and belief, this thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. Kathryn Fairfull-Smith (née Elson) BSc (Hons) ii Preface Unless otherwise stated, the results in this thesis are those of the author. Parts of this work have appeared elsewhere. Refereed journal publications are submitted with the dissertation and are presented in Appendix Two. Refereed Journal Publications ‘The Hendrickson reagent and the Mitsunobu reaction : a mechanistic study’ Kathryn E. Elson, Ian D. Jenkins and Wendy A. Loughlin, Org. Biomol. Chem., 2003, 1, 2958-2965. ‘Cyclic analogues of the Hendrickson ‘POP’ reagent’ Kathryn E. Elson, Ian D. Jenkins and Wendy A. Loughlin, Aust. J. Chem., 2004, 57, 371-376. ‘Polymer-supported triphenylphosphine ditriflate : a novel dehydrating reagent’ Kathryn E. Elson, Ian D. -
Aldehydes and Ketones
Organic Lecture Series Aldehydes And Ketones Chap 16 111 Organic Lecture Series IUPAC names • the parent alkane is the longest chain that contains the carbonyl group • for ketones, change the suffix -e to -one • number the chain to give C=O the smaller number • the IUPAC retains the common names acetone, acetophenone, and benzophenone O O O O Propanone Acetophenone Benzophenone 1-Phenyl-1-pentanone (Acetone) Commit to memory 222 Organic Lecture Series Common Names – for an aldehyde , the common name is derived from the common name of the corresponding carboxylic acid O O O O HCH HCOH CH3 CH CH3 COH Formaldehyde Formic acid Acetaldehyde Acetic acid – for a ketone , name the two alkyl or aryl groups bonded to the carbonyl carbon and add the word ketone O O O Ethyl isopropyl ketone Diethyl ketone Dicyclohexyl ketone 333 Organic Lecture Series Drawing Mechanisms • Use double-barbed arrows to indicate the flow of pairs of e - • Draw the arrow from higher e - density to lower e - density i.e. from the nucleophile to the electrophile • Removing e - density from an atom will create a formal + charge • Adding e - density to an atom will create a formal - charge • Proton transfer is fast (kinetics) and usually reversible 444 Organic Lecture Series Reaction Themes One of the most common reaction themes of a carbonyl group is addition of a nucleophile to form a tetrahedral carbonyl addition compound (intermediate). - R O Nu - + C O Nu C R R R Tetrahedral carbonyl addition compound 555 Reaction Themes Organic Lecture Series A second common theme is -
2 Reactions Observed with Alkanes Do Not Occur with Aromatic Compounds 2 (SN2 Reactions Never Occur on Sp Hybridized Carbons!)
Reactions of Aromatic Compounds Aromatic compounds are stabilized by this “aromatic stabilization” energy Due to this stabilization, normal SN2 reactions observed with alkanes do not occur with aromatic compounds 2 (SN2 reactions never occur on sp hybridized carbons!) In addition, the double bonds of the aromatic group do not behave similar to alkene reactions Aromatic Substitution While aromatic compounds do not react through addition reactions seen earlier Br Br Br2 Br2 FeBr3 Br With an appropriate catalyst, benzene will react with bromine The product is a substitution, not an addition (the bromine has substituted for a hydrogen) The product is still aromatic Electrophilic Aromatic Substitution Aromatic compounds react through a unique substitution type reaction Initially an electrophile reacts with the aromatic compound to generate an arenium ion (also called sigma complex) The arenium ion has lost aromatic stabilization (one of the carbons of the ring no longer has a conjugated p orbital) Electrophilic Aromatic Substitution In a second step, the arenium ion loses a proton to regenerate the aromatic stabilization The product is thus a substitution (the electrophile has substituted for a hydrogen) and is called an Electrophilic Aromatic Substitution Energy Profile Transition states Transition states Intermediate Potential E energy H Starting material Products E Reaction Coordinate The rate-limiting step is therefore the formation of the arenium ion The properties of this arenium ion therefore control electrophilic aromatic substitutions (just like any reaction consider the stability of the intermediate formed in the rate limiting step) 1) The rate will be faster for anything that stabilizes the arenium ion 2) The regiochemistry will be controlled by the stability of the arenium ion The properties of the arenium ion will predict the outcome of electrophilic aromatic substitution chemistry Bromination To brominate an aromatic ring need to generate an electrophilic source of bromine In practice typically add a Lewis acid (e.g. -
Thesis Has Been Carried out in the School of Pharmacy and Pharmacology and in the School of Biology and Biochemistry, Under the Supervision of Dr Michael D
University of Bath PHD Inhibitors of DNA repair processes as potentiating drugs in cancer radiotherapy and chemotherapy Watson, Corrine Yvonne Award date: 1997 Awarding institution: University of Bath Link to publication Alternative formats If you require this document in an alternative format, please contact: [email protected] General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 10. Oct. 2021 Inhibitors of DNA Repair Processes as Potentiating Drugs in Cancer Radiotherapy and Chemotherapy submitted by Corrine Yvonne Watson for the degree of PhD of the University of Bath 1997 The research work in this thesis has been carried out in the School of Pharmacy and Pharmacology and in the School of Biology and Biochemistry, under the supervision of Dr Michael D. Threadgill and Dr William J. D. Whish. COPYRIGHT Attention is drawn to the fact that copyright of this thesis rests with its author. -
Cu(II) Catalyzed Unsymmetrical Di-Oxidation of Gem- Difluoroalkenes to Generate Α,Α-Difluorinated-Α-Phenoxyketones, an Unstudied Substructure
Cu(II) Catalyzed Unsymmetrical Di-oxidation of gem- Difluoroalkenes to Generate α,α-Difluorinated-α-Phenoxyketones, an Unstudied Substructure Suvajit Koley, [a] Kaylee T. Cayton, [b] Gisela A. González-Montiel,[b] M. Ramu Yadav,[c] Douglas L. Orsi,[d] Paul Ha-Yeon Cheong,*[b] and Ryan A. Altman*[a] [a] Dr. S. Koley, Dr. R. A. Altman Department of Medicinal Chemistry and Molecular Pharmacology; Department of Chemistry Purdue University West Lafayette, IN 47907 (USA) E-mail: [email protected] [b] K. T. Cayton, G. A. González-Montiel, Dr. P. H.-Y. Cheong Department of Chemistry Oregon State University 153 Gilbert Hall, Corvallis, OR 97331 (USA) [c] Dr. M. R. Yadav Department of Chemistry Indian Institute of Technology Delhi MS-723, Hauz Khas, New Delhi-110016 (India) [d] Dr. D. L. Orsi Broad Institute of Harvard and MIT Cambridge, MA 02142 (USA) Supporting information for this article is given via a link at the end of the document. Abstract: A Cu-based catalyst system convergently couples gem- conformers versus the parent alkyl-aryl ethers that preferentially difluoroalkenes with phenols under aerobic conditions to deliver α,α- reside in the plane of the arene,[23] and versus trifluoromethyl-aryl difluorinated-α-phenoxy ketones, an unstudied hybrid fluorinated ethers that reside orthogonally to the plane of the arene.[24] functional group. Composed of α,α-difluorinated ketone and α,α- Interestingly, despite the individual significance of the α,α- difluorinated ether moieties, these have only once been previously difluoroketone and α,α-difluoroalkyl ethers components, the reported as a synthetic intermediate en route to pharmacologically hybrid α,α-difluorinated-α-phenoxy-ketone functional group has active compounds. -
Semicarbazone – a Versatile Therapeutic Pharmacophore for Fragment Based Anticonvulsant Drug Design
Acta Pharm. 62 (2012) 263–286 Review DOI: 10.2478/v10007-012-0030-1 Semicarbazone – a versatile therapeutic pharmacophore for fragment based anticonvulsant drug design SURENDRA NATH PANDEYA During the last fifteen years, semicarbazones have been extensively investigated for their anticonvulsant proper- Department of Pharmacy, Saroj Institute ties. 4-(4-Flurophenoxy) benzaldehyde semicarbazone of Technology and Management Ahimamau (C0102862, V102862) was discovered as a lead molecule Lucknow-226002 (U.P.), India and is being developed as a potent antiepileptic drug, with maximal electroshock (MES) ED50 of i.p. 12.9 mg kg-1. In MES (oral screen), this compound has a protec- tive index (PI = TD50/ED50 > 315) higher than carbama- zepine (PI 101), phenytoin (PI > 21.6) and valproate (PI 2.17). The compound is a potent sodium channel blocker. Other semicarbazones have demonstrated activity in va- rious chemoshock screens, like subcutaneous pentylene- tetrazole, subcutaneous strychnine, subcutaneous picro- toxin and subcutaneous bicculine. Semicarbazones are also GABA-transaminase inhibitors. Extensive structure- -activity relationship has demonstrated that F, Cl, Br and NO2 substituents in the arylhydrophobic pocket and a hydrogen bonding domain (HBD) are generally found in active anticonvulsant agents. Keywords: semicarbazone, anticonvulsant, Na+ channel Accepted July 17, 2012 blocker Epilepsy is a brain disorder that causes people to have recurring seizures. Epilepsy affects 50 million people worldwide, and 50 % of them live in the developing world (1, 2). Many options are available, from different chemical classes such as hydantoins (3) barbiturates (4), benzodiazepines (5), gamma-aminobutyric acid (GABA) analogs (6), di- benzepines (7) and carbamates (8). All of these compounds are used in the treatment of epilepsy. -
ELECTRONICS AUTHENTICITY TESTING USING COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY by Joseph C
ELECTRONICS AUTHENTICITY TESTING USING COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY by Joseph C. Cacciatore A Thesis Submitted to the Faculty of Purdue University In Partial Fulfillment of the Requirements for the degree of Master of Science School of Engineering Technology West Lafayette, Indiana December 2019 2 THE PURDUE UNIVERSITY GRADUATE SCHOOL STATEMENT OF COMMITTEE APPROVAL Dr. J. Eric Dietz, Chair Department of Computer and Information Technology Dr. Gozdem Kilaz, Chair School of Engineering Technology Dr. Ken Burbank School of Engineering Technology Approved by: Dr. Duane Dunlap Head of the Graduate Program 2 TABLE OF CONTENTS LIST OF TABLES .......................................................................................................................... 5 LIST OF FIGURES ........................................................................................................................ 6 LIST OF ABBREVIATIONS ......................................................................................................... 7 DEFINITIONS ................................................................................................................................ 8 ABSTRACT .................................................................................................................................... 9 INTRODUCTION .............................................................................................. 10 1.1 Introduction to the Problem ............................................................................................. -
A Simpler Route to Building Photochromic Cinnamaldehyde Semicarbazones Byron R
Eastern Illinois University The Keep Masters Theses Student Theses & Publications 2015 A Simpler Route to Building Photochromic Cinnamaldehyde Semicarbazones Byron R. Ebbert Eastern Illinois University This research is a product of the graduate program in Chemistry at Eastern Illinois University. Find out more about the program. Recommended Citation Ebbert, Byron R., "A Simpler Route to Building Photochromic Cinnamaldehyde Semicarbazones" (2015). Masters Theses. 1721. https://thekeep.eiu.edu/theses/1721 This is brought to you for free and open access by the Student Theses & Publications at The Keep. It has been accepted for inclusion in Masters Theses by an authorized administrator of The Keep. For more information, please contact [email protected]. The Graduate School~ EASTERN lWN(1!5 UNIVERSITY" Thesis Maintenance and Reproduction Certificate FOR: Graduate Candidates Completing Theses in Partial Fulfillment of the Degree Graduate Faculty Advisors Directing the Theses RE: Preservation, Reproduction, and Distribution of Thesis Research Preserving, reproducing, and distributing thesis research is an important part of Booth Library's responsibility to provide access to scholarship. In order to further this goal, Booth Library makes all graduate theses completed as part of a degree program at Eastern Illinois University available for personal study, research, and other not-for-profit educational purposes. Under 17 U.S.C. § 108, the library may reproduce and distribute a copy without infringing on copyright; however, professional courtesy dictates that permission be requested from the author before doing so. Your signatures affirm the following: • The graduate candidate is the author of this thesis. • The graduate candidate retains the copyright and intellectual property rights associated with the original research, creative activity, and intellectual or artistic content of the thesis.