Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF

Kelly, Samantha P.; Shende, Vikram V.; Flynn, Autumn R.; Dan, Qingyun; Ye, Ying; Smith, Janet L.; Tsukamoto, Sachiko; Sigman, Matthew S.; Sherman, David H.

doi:10.1021/jacs.2c06631

Title: Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF

Journal Article · 01 October 2022 · J. Am. Chem. Soc.

DOI:https://doi.org/10.1021/jacs.2c06631· OSTI ID:1901248

Kelly, Samantha P.; Shende, Vikram V.; Flynn, Autumn R.; Dan, Qingyun; Ye, Ying; Smith, Janet L.; Tsukamoto, Sachiko; Sigman, Matthew S.; Sherman, David H.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH); National Science Foundation (NSF)

OSTI ID:: 1901248

Journal Information:: J. Am. Chem. Soc., Vol. 144, Issue (42)

Country of Publication:: United States

Language:: ENGLISH

References (73)

Concise syntheses of the 1,7-dihydropyrano[2,3-g]indole ring system of the stephacidins, aspergamides and norgeamides Grubbs, Alan W.; Artman, Gerald D.; Williams, Robert M. Tetrahedron Letters, Vol. 46, Issue 52 https://doi.org/10.1016/j.tetlet.2005.10.112	journal	December 2005
Concise, biomimetic total synthesis of d,l-marcfortine C Greshock, Thomas J.; Grubbs, Alan W.; Williams, Robert M. Tetrahedron, Vol. 63, Issue 27 https://doi.org/10.1016/j.tet.2007.03.016	journal	July 2007
Biomimetic Total Synthesis of Malbrancheamide and Malbrancheamide B Miller, Kenneth A.; Welch, Timothy R.; Greshock, Thomas J. The Journal of Organic Chemistry, Vol. 73, Issue 8 https://doi.org/10.1021/jo800116y	journal	March 2008
Applications of dimethylallyltryptophan synthases and other indole prenyltransferases for structural modification of natural products Li, Shu-Ming Applied Microbiology and Biotechnology, Vol. 84, Issue 4 https://doi.org/10.1007/s00253-009-2128-z	journal	July 2009
Prenylated indole derivatives from fungi: structure diversity, biological activities, biosynthesis and chemoenzymatic synthesis Li, Shu-Ming Nat. Prod. Rep., Vol. 27, Issue 1 https://doi.org/10.1039/B909987P	journal	January 2010
Stereoselective Synthesis of Brevianamide E Zhao, Liang; May, Jonathan P.; Huang, Jack Organic Letters, Vol. 14, Issue 1 https://doi.org/10.1021/ol202880y	journal	November 2011
An Artificial Pathway for Isoprenoid Biosynthesis Decoupled from Native Hemiterpene Metabolism Lund, Sean; Hall, Rachael; Williams, Gavin J. ACS Synthetic Biology, Vol. 8, Issue 2 https://doi.org/10.1021/acssynbio.8b00383	journal	January 2019
Total synthesis of (−)-penicimutanin a and related congeners Yu, Haiyong; Zong, Yan; Xu, Tao Chemical Science, Vol. 11, Issue 3 https://doi.org/10.1039/C9SC05252F	journal	January 2020
Prenyltransferases as key enzymes in primary and secondary metabolism Winkelblech, Julia; Fan, Aili; Li, Shu-Ming Applied Microbiology and Biotechnology, Vol. 99, Issue 18 https://doi.org/10.1007/s00253-015-6811-y	journal	July 2015
Prenylation of Aromatic Secondary Metabolites: A New Frontier for Development of Novel Drugs Alhassan, Am; Abdullahi, Mi; Uba, A. Tropical Journal of Pharmaceutical Research, Vol. 13, Issue 2 https://doi.org/10.4314/tjpr.v13i2.22	journal	February 2014
Evolutionary Relationships of Microbial Aromatic Prenyltransferases Bonitz, Tobias; Alva, Vikram; Saleh, Orwah PLoS ONE, Vol. 6, Issue 11 https://doi.org/10.1371/journal.pone.0027336	journal	November 2011
The ABBA family of aromatic prenyltransferases: broadening natural product diversity Tello, M.; Kuzuyama, T.; Heide, L. Cellular and Molecular Life Sciences, Vol. 65, Issue 10 https://doi.org/10.1007/s00018-008-7579-3	journal	February 2008
Evolution of aromatic prenyltransferases in the biosynthesis of indole derivatives Li, Shu-Ming Phytochemistry, Vol. 70, Issue 15-16 https://doi.org/10.1016/j.phytochem.2009.03.019	journal	October 2009
Multisite Prenylation of 4-Substituted Tryptophans by Dimethylallyltryptophan Synthase Rudolf, Jeffrey D.; Wang, Hong; Poulter, C. Dale Journal of the American Chemical Society, Vol. 135, Issue 5 https://doi.org/10.1021/ja310734n	journal	January 2013
Enzymatic studies on aromatic prenyltransferases Mori, Takahiro Journal of Natural Medicines, Vol. 74, Issue 3 https://doi.org/10.1007/s11418-020-01393-x	journal	March 2020
Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides Yin, Suqin; Yu, Xia; Wang, Qing Applied Microbiology and Biotechnology, Vol. 97, Issue 4 https://doi.org/10.1007/s00253-012-4130-0	journal	June 2012
Structure and Catalytic Mechanism of a Cyclic Dipeptide Prenyltransferase with Broad Substrate Promiscuity Schuller, Jan Michael; Zocher, Georg; Liebhold, Mike Journal of Molecular Biology, Vol. 422, Issue 1 https://doi.org/10.1016/j.jmb.2012.05.033	journal	September 2012
Reinvestigation of the substrate specificity of a reverse prenyltransferase NotF from Aspergillus sp. MF297-2 Yang, Keyan; Li, Shu-Ming; Liu, Xiaoqing Archives of Microbiology, Vol. 202, Issue 6 https://doi.org/10.1007/s00203-020-01854-7	journal	March 2020
Biosynthesis of Complex Indole Alkaloids: Elucidation of the Concise Pathway of Okaramines Lai, Chen-Yu; Lo, I-Wen; Hewage, Ranuka T. Angewandte Chemie International Edition, Vol. 56, Issue 32 https://doi.org/10.1002/anie.201705501	journal	July 2017
Biosynthesis and Structure–Activity Relationship Studies of Okaramines That Target Insect Glutamate-Gated Chloride Channels Kato, Naoki; Furutani, Shogo; Otaka, Junnosuke ACS Chemical Biology, Vol. 13, Issue 3 https://doi.org/10.1021/acschembio.7b00878	journal	January 2018
Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway Fraley, Amy E.; Caddell Haatveit, Kersti; Ye, Ying Journal of the American Chemical Society, Vol. 142, Issue 5 https://doi.org/10.1021/jacs.9b09070	journal	January 2020
Flavin‐Dependent Monooxygenases NotI and NotI′ Mediate Spiro‐Oxindole Formation in Biosynthesis of the Notoamides Fraley, Amy E.; Tran, Hong T.; Kelly, Samantha P. ChemBioChem, Vol. 21, Issue 17 https://doi.org/10.1002/cbic.202000004	journal	May 2020
Fungal-derived brevianamide assembly by a stereoselective semipinacolase Ye, Ying; Du, Lei; Zhang, Xingwang Nature Catalysis, Vol. 3, Issue 6 https://doi.org/10.1038/s41929-020-0454-9	journal	May 2020
Function and Structure of MalA/MalA′, Iterative Halogenases for Late-Stage C–H Functionalization of Indole Alkaloids Fraley, Amy E.; Garcia-Borràs, Marc; Tripathi, Ashootosh Journal of the American Chemical Society, Vol. 139, Issue 34 https://doi.org/10.1021/jacs.7b06773	journal	August 2017
Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels–Alderase Dan, Qingyun; Newmister, Sean A.; Klas, Kimberly R. Nature Chemistry, Vol. 11, Issue 11 https://doi.org/10.1038/s41557-019-0326-6	journal	September 2019
Comparative analysis of the biosynthetic systems for fungal bicyclo[2.2.2]diazaoctane indole alkaloids: the (+)/(−)-notoamide, paraherquamide and malbrancheamide pathways Li, Shengying; Srinivasan, Krithika; Tran, Hong MedChemComm, Vol. 3, Issue 8 https://doi.org/10.1039/c2md20029e	journal	January 2012
Enzyme evolution in fungal indole alkaloid biosynthesis Fraley, Amy E.; Sherman, David H. The FEBS Journal, Vol. 287, Issue 7 https://doi.org/10.1111/febs.15270	journal	April 2020
Genome-Based Characterization of Two Prenylation Steps in the Assembly of the Stephacidin and Notoamide Anticancer Agents in a Marine-Derived Aspergillus sp. Ding, Yousong; Wet, Jeffrey R. de; Cavalcoli, James Journal of the American Chemical Society, Vol. 132, Issue 36 https://doi.org/10.1021/ja1049302	journal	September 2010
Catalytic Mechanism of Stereospecific Formation of cis-Configured Prenylated Pyrroloindoline Diketopiperazines by Indole Prenyltransferases Yu, Xia; Zocher, Georg; Xie, Xiulan Chemistry & Biology, Vol. 20, Issue 12 https://doi.org/10.1016/j.chembiol.2013.10.007	journal	December 2013
Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products Kuzuyama, Tomohisa; Noel, Joseph P.; Richard, Stéphane B. Nature, Vol. 435, Issue 7044 https://doi.org/10.1038/nature03668	journal	June 2005
The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria Metzger, U.; Schall, C.; Zocher, G. Proceedings of the National Academy of Sciences, Vol. 106, Issue 34 https://doi.org/10.1073/pnas.0904897106	journal	August 2009
Structure−Function Analysis of an Enzymatic Prenyl Transfer Reaction Identifies a Reaction Chamber with Modifiable Specificity Jost, Marco; Zocher, Georg; Tarcz, Sylwia Journal of the American Chemical Society, Vol. 132, Issue 50 https://doi.org/10.1021/ja106817c	journal	November 2010
Mechanism of Dimethylallyltryptophan Synthase: Evidence for a Dimethylallyl Cation Intermediate in an Aromatic Prenyltransferase Reaction Luk, Louis Y. P.; Tanner, Martin E. Journal of the American Chemical Society, Vol. 131, Issue 39 https://doi.org/10.1021/ja906485u	journal	September 2009
Purification and properties of dimethylallylpyrophosphate: Tryptophan dimethylallyl transferase, the first enzyme of ergot alkaloid biosynthesis in Claviceps. sp. SD 58 Lee, Siu-Leung; Floss, Heinz G.; Heinstein, Peter Archives of Biochemistry and Biophysics, Vol. 177, Issue 1 https://doi.org/10.1016/0003-9861(76)90418-5	journal	November 1976
Bioinspired Indole Prenylation Reactions in Water Tanaka, Satomi; Shiomi, Shinya; Ishikawa, Hayato Journal of Natural Products, Vol. 80, Issue 8 https://doi.org/10.1021/acs.jnatprod.7b00464	journal	August 2017
Isolation of Talathermophilins from the Thermophilic Fungus Talaromyces thermophilus YM3-4 Guo, Ji-Peng; Tan, Jian-Lin; Wang, Yan-Li Journal of Natural Products, Vol. 74, Issue 10 https://doi.org/10.1021/np200365z	journal	October 2011
Monoisoprenylated cyclo-L-alanyl-L-tryptophanyl. Biosynthetic precursor of echinulin Allen, Charles M. Journal of the American Chemical Society, Vol. 95, Issue 7 https://doi.org/10.1021/ja00788a059	journal	April 1973
New Diketopiperazine Alkaloids from Penicillium fellutanum Kozlovsky, Anatoly G.; Vinokurova, Nataliya G.; Adanin, Vladimir M. Journal of Natural Products, Vol. 63, Issue 5 https://doi.org/10.1021/np9903853	journal	March 2000
Austamide, a new toxic metabolite from Steyn, P. S. Tetrahedron Letters, Vol. 12, Issue 36 https://doi.org/10.1016/S0040-4039(01)97170-9	journal	January 1971
A Mild and General Larock Indolization Protocol for the Preparation of Unnatural Tryptophans Chuang, Kangway V.; Kieffer, Madeleine E.; Reisman, Sarah E. Organic Letters, Vol. 18, Issue 18 https://doi.org/10.1021/acs.orglett.6b02477	journal	September 2016
A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective “Ligation” of Azides and Terminal Alkynes Rostovtsev, Vsevolod V.; Green, Luke G.; Fokin, Valery V. Angewandte Chemie International Edition, Vol. 41, Issue 14, p. 2596-2599 https://doi.org/10.1002/1521-3773(20020715)41:14<2596::AID-ANIE2596>3.0.CO;2-4	journal	July 2002
Bioorthogonal Click Chemistry: Covalent Labeling in Living Systems Baskin, Jeremy M.; Bertozzi, Carolyn R. QSAR & Combinatorial Science, Vol. 26, Issue 11-12 https://doi.org/10.1002/qsar.200740086	journal	December 2007
Tyrosine O -Prenyltransferase SirD Catalyzes S -, C -, and N -Prenylations on Tyrosine and Tryptophan Derivatives Rudolf, Jeffrey D.; Poulter, C. Dale ACS Chemical Biology, Vol. 8, Issue 12 https://doi.org/10.1021/cb400691z	journal	October 2013
Three Novel, Structurally Unique Spirocyclic Alkaloids from the Halotolerant B-17 Fungal Strain ofAspergillus variecolor Wang, Wen-Liang; Zhu, Tian-Jiao; Tao, Hong-Wen Chemistry & Biodiversity, Vol. 4, Issue 12 https://doi.org/10.1002/cbdv.200790240	journal	December 2007
Indole diketopiperazine alkaloids from the deep-sea-derived fungus Aspergillus sp. FS445 Liu, Zhaoming; Chen, Yuchan; Li, Saini Natural Product Research, Vol. 36, Issue 20 https://doi.org/10.1080/14786419.2021.1925271	journal	May 2021
(±)-Uncarilins A and B, Dimeric Isoechinulin-Type Alkaloids from Uncaria rhynchophylla Geng, Chang-An; Huang, Xiao-Yan; Ma, Yun-Bao Journal of Natural Products, Vol. 80, Issue 4 https://doi.org/10.1021/acs.jnatprod.6b00938	journal	February 2017
A New Prenylated Indole Diketopiperazine Alkaloid from Eurotium cristatum Zou, Xianwei; Li, Ying; Zhang, Xiaona Molecules, Vol. 19, Issue 11 https://doi.org/10.3390/molecules191117839	journal	November 2014
Isolation and structure (X-ray analysis) of marcfortine A, a new alkaloid from Penicillium roqueforti Polonsky, Judith; Merrien, Marie-Annick; Prangé, Thierry J. Chem. Soc., Chem. Commun., Issue 13 https://doi.org/10.1039/C39800000601	journal	January 1980
Discovery and Biocatalytic Application of a PLP-Dependent Amino Acid γ-Substitution Enzyme That Catalyzes C–C Bond Formation Chen, Mengbin; Liu, Chun-Ting; Tang, Yi Journal of the American Chemical Society, Vol. 142, Issue 23 https://doi.org/10.1021/jacs.0c03535	journal	May 2020
Total Synthesis of Gypsetin, Deoxybrevianamide E, Brevianamide E, and Tryprostatin B: Novel Constructions of 2,3-Disubstituted Indoles Schkeryantz, Jeffrey M.; Woo, Jonathan C. G.; Siliphaivanh, Phieng Journal of the American Chemical Society, Vol. 121, Issue 51 https://doi.org/10.1021/ja9925249	journal	December 1999
Predictive and mechanistic multivariate linear regression models for reaction development Santiago, Celine B.; Guo, Jing-Yao; Sigman, Matthew S. Chemical Science, Vol. 9, Issue 9 https://doi.org/10.1039/C7SC04679K	journal	January 2018
Pursuit of Noncovalent Interactions for Strategic Site-Selective Catalysis Toste, F. Dean; Sigman, Matthew S.; Miller, Scott J. Accounts of Chemical Research, Vol. 50, Issue 3 https://doi.org/10.1021/acs.accounts.6b00613	journal	March 2017
Multidimensional steric parameters in the analysis of asymmetric catalytic reactions Harper, Kaid C.; Bess, Elizabeth N.; Sigman, Matthew S. Nature Chemistry, Vol. 4, Issue 5 https://doi.org/10.1038/nchem.1297	journal	March 2012
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects Sherman, Woody; Day, Tyler; Jacobson, Matthew P. Journal of Medicinal Chemistry, Vol. 49, Issue 2 https://doi.org/10.1021/jm050540c	journal	January 2006
Use of an Induced Fit Receptor Structure in Virtual Screening Sherman, Woody; Beard, Hege S.; Farid, Ramy Chemical Biology Drug Design, Vol. 67, Issue 1 https://doi.org/10.1111/j.1747-0285.2005.00327.x	journal	January 2006
Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase Chen, Ridao; Gao, Bingquan; Liu, Xiao Nature Chemical Biology, Vol. 13, Issue 2 https://doi.org/10.1038/nchembio.2263	journal	December 2016
5-N-Acetylardeemin, a novel heterocyclic compound which reverses multiple drug resistance in tumor cells. II. Isolation and elucidation of the structure of 5-N-acetylardeemin and two congeners. Hochlowski, Jill E.; Mullally, Mark M.; Spanton, Stephen G. The Journal of Antibiotics, Vol. 46, Issue 3 https://doi.org/10.7164/antibiotics.46.380	journal	January 1993
Reversal of anticancer multidrug resistance by the ardeemins Chou, Ting-Chao; Depew, Kristopher M.; Zheng, Yu-Huang Proceedings of the National Academy of Sciences, Vol. 95, Issue 14 https://doi.org/10.1073/pnas.95.14.8369	journal	July 1998
Roquefortine E, a Diketopiperazine from an Australian Isolate of Gymnoascus reessii Clark, Ben; Capon, Robert J.; Lacey, Ernest Journal of Natural Products, Vol. 68, Issue 11 https://doi.org/10.1021/np0503101	journal	October 2005
Shornephine A: Structure, Chemical Stability, and P-Glycoprotein Inhibitory Properties of a Rare Diketomorpholine from an Australian Marine-Derived Aspergillus sp. Khalil, Zeinab G.; Huang, Xiao-cong; Raju, Ritesh The Journal of Organic Chemistry, Vol. 79, Issue 18 https://doi.org/10.1021/jo501501z	journal	September 2014
Distinct mechanisms for spiro-carbon formation reveal biosynthetic pathway crosstalk Tsunematsu, Yuta; Ishikawa, Noriyasu; Wakana, Daigo Nature Chemical Biology, Vol. 9, Issue 12 https://doi.org/10.1038/nchembio.1366	journal	October 2013
Eurotiumins A–E, Five New Alkaloids from the Marine-Derived Fungus Eurotium sp. SCSIO F452 Zhong, Wei-Mao; Wang, Jun-Feng; Shi, Xue-Feng Marine Drugs, Vol. 16, Issue 4 https://doi.org/10.3390/md16040136	journal	April 2018
Structure, Bioactivity and Synthesis of Natural Products with Hexahydropyrrolo[2,3-b]indole Ruiz-Sanchis, Pau; Savina, Svetlana A.; Albericio, Fernando Chemistry - A European Journal, Vol. 17, Issue 5 https://doi.org/10.1002/chem.201001451	journal	January 2011
Lewis Acid Catalyzed Displacement of Trichloroacetimidates in the Synthesis of Functionalized Pyrroloindolines Adhikari, Arijit A.; Chisholm, John D. Organic Letters, Vol. 18, Issue 16 https://doi.org/10.1021/acs.orglett.6b02024	journal	August 2016
Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 Kmunícek, Jan; Hynková, Kamila; Jedlicka, Tomás Biochemistry, Vol. 44, Issue 9 https://doi.org/10.1021/bi047912o	journal	February 2005
Machine Learning in Enzyme Engineering Mazurenko, Stanislav; Prokop, Zbynek; Damborsky, Jiri ACS Catalysis, Vol. 10, Issue 2 https://doi.org/10.1021/acscatal.9b04321	journal	December 2019
Predicting the Substrate Scope of the Flavin‐Dependent Halogenase BrvH Neubauer, Pia R.; Pienkny, Silke; Wessjohann, Ludger ChemBioChem, Vol. 21, Issue 22 https://doi.org/10.1002/cbic.202000444	journal	August 2020
Inversion of Extender Unit Selectivity in the Erythromycin Polyketide Synthase by Acyltransferase Domain Engineering Koryakina, Irina; Kasey, Christian; McArthur, John B. ACS Chemical Biology, Vol. 12, Issue 1 https://doi.org/10.1021/acschembio.6b00732	journal	November 2016
Structure and Function of NzeB, a Versatile C–C and C–N Bond-Forming Diketopiperazine Dimerase Shende, Vikram V.; Khatri, Yogan; Newmister, Sean A. Journal of the American Chemical Society, Vol. 142, Issue 41 https://doi.org/10.1021/jacs.0c06312	journal	August 2020
Computational-Based Mechanistic Study and Engineering of Cytochrome P450 MycG for Selective Oxidation of 16-Membered Macrolide Antibiotics Yang, Song; DeMars, Matthew D.; Grandner, Jessica M. Journal of the American Chemical Society, Vol. 142, Issue 42 https://doi.org/10.1021/jacs.0c04388	journal	October 2020
Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway Newmister, Sean A.; Srivastava, Kinshuk Raj; Espinoza, Rosa V. ACS Catalysis, Vol. 10, Issue 22 https://doi.org/10.1021/acscatal.0c03248	journal	November 2020
Notoamides A–D: Prenylated Indole Alkaloids Isolated from a Marine-Derived Fungus,Aspergillus sp. Kato, Hikaru; Yoshida, Takushi; Tokue, Takanori Angewandte Chemie International Edition, Vol. 46, Issue 13 https://doi.org/10.1002/anie.200604381	journal	March 2007
Bio-mining the microbial treasures of the ocean: New natural products Imhoff, Johannes F.; Labes, Antje; Wiese, Jutta Biotechnology Advances, Vol. 29, Issue 5 https://doi.org/10.1016/j.biotechadv.2011.03.001	journal	September 2011

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