1
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Chen XM, Zhang XY, He FL, Pan J, Jia GK. Crystal structure of (2 E,4 Z)-dimethyl 4-((phenylamino)methylene)pent-2-enedioate, C 14H 15N 1O 4. Z KRIST-NEW CRYST ST 2018. [DOI: 10.1515/ncrs-2018-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C14H15N1O4, triclinic, P1̄, a = 8.2018(4) Å, b = 11.5512(5) Å, c = 14.4121(7) Å, α = 79.242(2)°, β = 78.647(3)°, γ = 85.496(3)°, V = 1313.93(11) Å3, Z = 2, R
gt(F) = 0.0548, wR
ref(F
2) = 0.1805, T = 296(2) K.
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Affiliation(s)
- Xiao-Ming Chen
- Department of Biology and Chemistry , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
- Hunan Hengwei Pharmaceutical Co., LTD , Yongzhou Hunan 425199 , P.R. China
| | - Xing-Yu Zhang
- Department of Biology and Chemistry , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
- Hunan Key Laboratory of Comprehensive Utilization of Advantage Plants Resources of Hunan South , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
| | - Fu-Lin He
- Department of Biology and Chemistry , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
- Hunan Provincial Engineering Research Center for Ginkgo Biloba , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
| | - Jun Pan
- Department of Biology and Chemistry , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
- Hunan Provincial Engineering Research Center for Ginkgo Biloba , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
| | - Guo-Kai Jia
- Department of Biology and Chemistry , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
- Hunan Key Laboratory of Comprehensive Utilization of Advantage Plants Resources of Hunan South , Hunan University of Science and Engineering , Yongzhou Hunan 425199 , P.R. China
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2
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Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:034702. [PMID: 27191010 PMCID: PMC4851618 DOI: 10.1063/1.4948539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.
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Affiliation(s)
- Hongnan Cao
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Lance Bigelow
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | | | - Robert Jedrzejczak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Gyorgy Babnigg
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA
| | - Andrzej Joachimiak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Madan K Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Shanteri Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - George N Phillips
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
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3
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Elshahawi SI, Ramelot TA, Seetharaman J, Chen J, Singh S, Yang Y, Pederson K, Kharel MK, Xiao R, Lew S, Yennamalli RM, Miller MD, Wang F, Tong L, Montelione GT, Kennedy MA, Bingman CA, Zhu H, Phillips GN, Thorson JS. Structure-guided functional characterization of enediyne self-sacrifice resistance proteins, CalU16 and CalU19. ACS Chem Biol 2014; 9:2347-58. [PMID: 25079510 PMCID: PMC4201346 DOI: 10.1021/cb500327m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Calicheamicin γ1I (1)
is an enediyne antitumor compound produced by Micromonospora
echinospora spp. calichensis, and its biosynthetic gene cluster
has been previously reported. Despite extensive analysis and biochemical
study, several genes in the biosynthetic gene cluster of 1 remain functionally unassigned. Using a structural genomics approach
and biochemical characterization, two proteins encoded by genes from
the 1 biosynthetic gene cluster assigned as “unknowns”,
CalU16 and CalU19, were characterized. Structure analysis revealed
that they possess the STeroidogenic Acute Regulatory protein related
lipid Transfer (START) domain known mainly to bind and transport lipids
and previously identified as the structural signature of the enediyne
self-resistance protein CalC. Subsequent study revealed calU16 and calU19 to confer resistance to 1, and reminiscent of the prototype CalC, both CalU16 and CalU19 were
cleaved by 1in vitro. Through site-directed
mutagenesis and mass spectrometry, we identified the site of cleavage
in each protein and characterized their function in conferring resistance
against 1. This report emphasizes the importance of structural
genomics as a powerful tool for the functional annotation of unknown
proteins.
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Affiliation(s)
- Sherif I. Elshahawi
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Theresa A. Ramelot
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Jayaraman Seetharaman
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry & Center for Structural Biology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Shanteri Singh
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yunhuang Yang
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Kari Pederson
- Complex Carbohydrate
Research Center, Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602, United States
| | - Madan K. Kharel
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Rong Xiao
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology
and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Scott Lew
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Ragothaman M. Yennamalli
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Mitchell D. Miller
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Fengbin Wang
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Liang Tong
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Gaetano T. Montelione
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology
and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Michael A. Kennedy
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Craig A. Bingman
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry & Center for Structural Biology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - George N. Phillips
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Jon S. Thorson
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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4
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Sivaramakrishnan S, Breydo L, Sun D, Gates KS. The macrocycle of leinamycin imparts hydrolytic stability to the thiol-sensing 1,2-dithiolan-3-one 1-oxide unit of the natural product. Bioorg Med Chem Lett 2012; 22:3791-4. [PMID: 22560586 DOI: 10.1016/j.bmcl.2012.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/21/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
Abstract
Reaction of cellular thiols with the 1,2-dithiolan-3-one 1-oxide moiety of leinamycin triggers the generation of DNA-damaging reactive intermediates. Studies with small, synthetic analogues of leinamycin reveal that the macrocyclic portion of the natural product imparts remarkable hydrolytic stability to the 1,2-dithiolan-3-one 1-oxide heterocycle without substantially compromising its thiol-sensing property.
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5
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Fekry MI, Price NE, Zang H, Huang C, Harmata M, Brown P, Daniels JS, Gates KS. Thiol-activated DNA damage by α-bromo-2-cyclopentenone. Chem Res Toxicol 2011; 24:217-28. [PMID: 21250671 DOI: 10.1021/tx100282b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Some biologically active chemicals are relatively stable in the extracellular environment but, upon entering the cell, undergo biotransformation into reactive intermediates that covalently modify DNA. The diverse chemical reactions involved in the bioactivation of DNA-damaging agents are both fundamentally interesting and of practical importance in medicinal chemistry and toxicology. The work described here examines the bioactivation of α-haloacrolyl-containing molecules. The α-haloacrolyl moiety is found in a variety of cytotoxic natural products including clionastatin B, bromovulone III, discorahabdins A, B, and C, and trichodenone C, in mutagens such as 2-bromoacrolein and 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX), and in the anticancer drug candidates brostallicin and PNU-151807. Using α-bromo-2-cyclopentenone (1) as a model compound, the activation of α-haloacrolyl-containing molecules by biological thiols was explored. The results indicate that both low molecular weight and peptide thiols readily undergo conjugate addition to 1. The resulting products are consistent with a mechanism in which initial addition of thiols to 1 is followed by intramolecular displacement of bromide to yield a DNA-alkylating episulfonium ion intermediate. The reaction of thiol-activated 1 with DNA produces labile lesions at deoxyguanosine residues. The sequence specificity and salt dependence of this process is consistent with involvement of an episulfonium ion intermediate. The alkylated guanine residue resulting from the thiol-triggered reaction of 1 with duplex DNA was characterized using mass spectrometry. The results provide new insight regarding the mechanisms by which thiols can bioactivate small molecules and offer a more complete understanding of the molecular mechanisms underlying the biological activity of cytotoxic, mutagenic, and medicinal compounds containing the α-haloacrolyl group.
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Affiliation(s)
- Mostafa I Fekry
- Department of Chemistry, University of Missouri, 125 Chemistry Building Columbia, Missouri 65211, United States
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6
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Lahiri D, Majumdar R, Patra AK, Chakravarty AR. Anaerobic DNA cleavage in red light by dicopper(II) complexes on disulphide bond activation. J CHEM SCI 2010. [DOI: 10.1007/s12039-010-0037-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Basak A, Das S, Mallick D, Jemmis ED. Which One Is Preferred: Myers−Saito Cyclization of Ene-Yne-Allene or Garratt−Braverman Cyclization of Conjugated Bisallenic Sulfone? A Theoretical and Experimental Study. J Am Chem Soc 2009; 131:15695-704. [DOI: 10.1021/ja9023644] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amit Basak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India, and Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Thiruvananthapuram, 695 016 Kerala, India
| | - Sanket Das
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India, and Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Thiruvananthapuram, 695 016 Kerala, India
| | - Dibyendu Mallick
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India, and Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Thiruvananthapuram, 695 016 Kerala, India
| | - Eluvathingal D. Jemmis
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India, and Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Thiruvananthapuram, 695 016 Kerala, India
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8
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9
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Singh S, Hager MH, Zhang C, Griffith BR, Lee MS, Hallenga K, Markley JL, Thorson JS. Structural insight into the self-sacrifice mechanism of enediyne resistance. ACS Chem Biol 2006; 1:451-60. [PMID: 17168523 DOI: 10.1021/cb6002898] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent discovery of the first "self-sacrifice" mechanism for bacterial resistance to the enediyne antitumor antibiotics, where enediyne-induced proteolysis of the resistance protein CalC inactivates both the highly reactive metabolite and the resistance protein, revealed yet another ingenious bacterial mechanism for controlling reactive metabolites. As reported herein, the first 3D structures of CalC and CalC in complex with calicheamicin (CLM) divulge CalC to be a member of the steroidogenic acute regulatory protein (StAR)-related transfer (START) domain superfamily. In contrast to previous studies of proteins known to bind DNA-damaging natural products ( e.g ., bleomycins, mitomycins, and nine-membered chromoprotein enediynes), this is the first demonstrated involvement of a START domain fold. Consistent with the CalC self-sacrifice mechanism, CLM in complex with CalC is positioned for direct hydrogen abstraction from Gly113 to initiate the oxidative proteolysis-based resistance mechanism. These structural studies also illuminate, for the first time, a small DNA-binding region within CalC that may serve to localize CalC to the enediyne target (DNA). Given the role of START domains in nuclear/cytosolic transport and translocation, this structural study also may implicate START domains as post-endocytotic intracellular chaperones for enediyne-based therapeutics such as MyloTarg.
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Affiliation(s)
- Shanteri Singh
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA
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10
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Biggins JB, Onwueme KC, Thorson JS. Resistance to enediyne antitumor antibiotics by CalC self-sacrifice. Science 2003; 301:1537-41. [PMID: 12970566 DOI: 10.1126/science.1086695] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Antibiotic self-resistance mechanisms, which include drug elimination, drug modification, target modification, and drug sequestration, contribute substantially to the growing problem of antibiotic resistance among pathogenic bacteria. Enediynes are among the most potent naturally occurring antibiotics, yet the mechanism of resistance to these toxins has remained a mystery. We characterize an enediyne self-resistance protein that reveals a self-sacrificing paradigm for resistance to highly reactive antibiotics, and thus another opportunity for nonpathogenic or pathogenic bacteria to evade extremely potent small molecules.
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Affiliation(s)
- John B Biggins
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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11
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Clive DLJ, Bo Y, Tao Y, Daigneault S, Wu YJ, Meignan G. Synthesis of (±)-Calicheamicinone by Two Methods. J Am Chem Soc 1998. [DOI: 10.1021/ja980292s] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Derrick L. J. Clive
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Yunxin Bo
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Yong Tao
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Sylvain Daigneault
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Yong-Jin Wu
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Gérard Meignan
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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12
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Affiliation(s)
- A L Smith
- Department of Chemistry, Scripps Research Institute, La Jolla, California 92037, USA
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13
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Grissom JW, Gunawardena GU, Klingberg D, Huang D. The chemistry of enediynes, enyne allenes and related compounds. Tetrahedron 1996. [DOI: 10.1016/0040-4020(96)00016-6] [Citation(s) in RCA: 307] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Chatterjee M, Smith PJ, Townsend CA. The Role of the Aminosugar and Helix Binding in the Thiol-Induced Activation of Calicheamicin for DNA Cleavage. J Am Chem Soc 1996. [DOI: 10.1021/ja953162h] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Moneesh Chatterjee
- Contribution from the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Paul J. Smith
- Contribution from the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Craig A. Townsend
- Contribution from the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
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15
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16
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Probing the Underlying Basis for the Binding Specificity of Calicheamicin γ1I. A Molecular Dynamics Study. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)80625-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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