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Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
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Gahl M, Kim HW, Glukhov E, Gerwick WH, Cottrell GW. PECAN Predicts Patterns of Cancer Cell Cytostatic Activity of Natural Products Using Deep Learning. J Nat Prod 2024; 87:567-575. [PMID: 38349959 PMCID: PMC10960629 DOI: 10.1021/acs.jnatprod.3c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Many machine learning techniques are used as drug discovery tools with the intent to speed characterization by determining relationships between compound structure and biological function. However, particularly in anticancer drug discovery, these models often make only binary decisions about the biological activity for a narrow scope of drug targets. We present a feed-forward neural network, PECAN (Prediction Engine for the Cytostatic Activity of Natural product-like compounds), that simultaneously classifies the potential antiproliferative activity of compounds against 59 cancer cell lines. It predicts the activity to be one of six categories, indicating not only if activity is present but the degree of activity. Using an independent subset of NCI data as a test set, we show that PECAN can reach 60.1% accuracy in a six-way classification and present further evidence that it classifies based on useful structural features of compounds using a "within-one" measure that reaches 93.0% accuracy.
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Affiliation(s)
- Martha Gahl
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Hyun Woo Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Gyeonggi-do 04620, Republic of Korea
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Garrison W Cottrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
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3
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Ngo TE, Ecker A, Ryu B, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Thomas L, Dahesh S, Nizet V, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from Marine Cyanobacterium Moorena producens JHB Discovered via Coculture with Candida albicans. ACS Chem Biol 2024; 19:619-628. [PMID: 38330248 PMCID: PMC10949194 DOI: 10.1021/acschembio.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies on this strain led to the discovery of several novel compounds such as hectochlorins and jamaicamides. However, bioinformatic analyses of its genome indicate the presence of numerous cryptic biosynthetic gene clusters that have yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was cocultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that coculture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrew Ecker
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Byeol Ryu
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Aurora Guild
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ariana Remmel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul D. Boudreau
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of BioMolecular Sciences,University of Mississippi,
School of Pharmacy, University, Mississippi 38677, United States
| | - Kelsey L. Alexander
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Chemistry, University of California San
Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - C. Benjamin Naman
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Science and Conservation, San Diego Botanic
Garden, 300 Quail Gardens
Drive, Encinitas, California 92024, United States
| | - Evgenia Glukhov
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nicole E. Avalon
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vikram V. Shende
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lamar Thomas
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Samira Dahesh
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Victor Nizet
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lena Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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Esposito G, Glukhov E, Gerwick WH, Medio G, Teta R, Lega M, Costantino V. Lake Avernus Has Turned Red: Bioindicator Monitoring Unveils the Secrets of "Gates of Hades". Toxins (Basel) 2023; 15:698. [PMID: 38133202 PMCID: PMC10747548 DOI: 10.3390/toxins15120698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Lake Avernus is a volcanic lake located in southern Italy. Since ancient times, it has inspired numerous myths and legends due to the occurrence of singular phenomena, such as coloring events. Only recently has an explanation been found for them, i.e., the recurring color change over time is due to the alternation of cyanobacterial blooms that are a consequence of natural nutrient inputs as well as pollution resulting from human activities. This current report specifically describes the red coloring event that occurred on Lake Avernus in March 2022, the springtime season in this region of Italy. Our innovative multidisciplinary approach, the 'Fast Detection Strategy' (FDS), was devised to monitor cyanobacterial blooms and their toxins. It integrates remote sensing data from satellites and drones, on-site sampling, and analytical/bioinformatics analyses into a cohesive information flow. Thanks to FDS, we determined that the red color was attributable to a bloom of Planktothrix rubescens, a toxin-producing cyanobacterium. Here, we report the detection and identification of 14 anabenopeptins from this P. rubescens strain, seven of which are known and seven are newly reported herein. Moreover, we explored the mechanisms and causes behind this cyclic phenomenon, confirming cyanobacteria's role as reliable indicators of environmental changes. This investigation further validates FDS's effectiveness in detecting and characterizing cyanobacterial blooms and their associated toxins, expanding its potential applications.
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Affiliation(s)
- Germana Esposito
- The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (G.E.); (V.C.)
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (E.G.); (W.H.G.)
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (E.G.); (W.H.G.)
| | - Gabriele Medio
- Department of Engineering, University of Naples Parthenope, 80133 Napoli, Italy;
| | - Roberta Teta
- The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (G.E.); (V.C.)
| | - Massimiliano Lega
- Department of Engineering, University of Naples Parthenope, 80133 Napoli, Italy;
| | - Valeria Costantino
- The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (G.E.); (V.C.)
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5
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Ngo TE, Ecker A, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from the Marine Cyanobacterium Moorena producens JHB Discovered via Co-culture with Candida albicans. bioRxiv 2023:2023.07.06.547815. [PMID: 37461655 PMCID: PMC10350029 DOI: 10.1101/2023.07.06.547815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies of this strain led to the discovery of several novel compounds such as the hectochlorins and jamaicamides; however, bioinformatic analyses of its genome suggested that there were many more cryptic biosynthetic gene clusters yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was co-cultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that co-culture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrew Ecker
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Aurora Guild
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ariana Remmel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of BioMolecular Sciences, University of Mississippi School of Pharmacy, University, Mississippi 38677, USA
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Science and Conservation, San Diego Botanic Garden, 300 Quail Gardens Drive, Encinitas, CA, 92024, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nicole E Avalon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vikram V Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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6
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Almaliti J, Fajtová P, Calla J, LaMonte GM, Feng M, Rocamora F, Ottilie S, Glukhov E, Boura E, Suhandynata RT, Momper JD, Gilson MK, Winzeler EA, Gerwick WH, O'Donoghue AJ. Development of Potent and Highly Selective Epoxyketone-Based Plasmodium Proteasome Inhibitors. Chemistry 2023; 29:e202203958. [PMID: 36617500 PMCID: PMC10894724 DOI: 10.1002/chem.202203958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/10/2023]
Abstract
Here, we present remarkable epoxyketone-based proteasome inhibitors with low nanomolar in vitro potency for blood-stage Plasmodium falciparum and low cytotoxicity for human cells. Our best compound has more than 2,000-fold greater selectivity for erythrocytic-stage P. falciparum over HepG2 and H460 cells, which is largely driven by the accommodation of the parasite proteasome for a D-amino acid in the P3 position and the preference for a difluorobenzyl group in the P1 position. We isolated the proteasome from P. falciparum cell extracts and determined that the best compound is 171-fold more potent at inhibiting the β5 subunit of P. falciparum proteasome when compared to the same subunit of the human constitutive proteasome. These compounds also significantly reduce parasitemia in a P. berghei mouse infection model and prolong survival of animals by an average of 6 days. The current epoxyketone inhibitors are ideal starting compounds for orally bioavailable anti-malarial drugs.
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Affiliation(s)
- Jehad Almaliti
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
- Department Pharmaceutical Sciences, College of Pharmacy, University of Jordan, Amman, 11942, Jordan
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610, Prague, Czech Republic
| | - Jaeson Calla
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Gregory M LaMonte
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Mudong Feng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
- Calibr, a division of The Scripps Research Institute, 11119 N Torrey Pines Rd, La Jolla, California, 92093, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610, Prague, Czech Republic
| | - Raymond T Suhandynata
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Jeremiah D Momper
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093, USA
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7
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Leão TF, Wang M, da Silva R, Gurevich A, Bauermeister A, Gomes PWP, Brejnrod A, Glukhov E, Aron AT, Louwen JJR, Kim HW, Reher R, Fiore MF, van der Hooft JJJ, Gerwick L, Gerwick WH, Bandeira N, Dorrestein PC. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS Nexus 2022; 1:pgac257. [PMID: 36712343 PMCID: PMC9802219 DOI: 10.1093/pnasnexus/pgac257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/25/2022] [Indexed: 06/02/2023]
Abstract
Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.
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Affiliation(s)
- Tiago F Leão
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13400-970, SP, Brazil
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA 92093, USA
| | - Ricardo da Silva
- NPPNS, Physic and Chemistry Department, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, St. Petersburg State University, St Petersburg 199004, Russia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do 10326, Korea
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, 35043 Marburg, Germany
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13400-970, SP, Brazil
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA 92093, USA
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Phan VV, Mosier C, Yoon MC, Glukhov E, Caffrey CR, O’Donoghue AJ, Gerwick WH, Hook V. Discovery of pH-Selective Marine and Plant Natural Product Inhibitors of Cathepsin B Revealed by Screening at Acidic and Neutral pH Conditions. ACS Omega 2022; 7:25346-25352. [PMID: 35910167 PMCID: PMC9330179 DOI: 10.1021/acsomega.2c02287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Dysregulation of cathepsin B, which involves the translocation of the enzyme from acidic pH lysosomes to the neutral pH cytosol, followed by the initiation of cell death and inflammation, occurs in numerous brain disorders. The wide difference in the acidic pH (4.6) of lysosomes compared to the neutral pH (7.2) of the cytosol suggests that screening at different pH conditions may identify pH-selective modulators of cathepsin B. Therefore, a collection of pure marine and plant natural product (NP) compounds, with synthetic compounds, was screened at pH 4.6 and pH 7.2 in cathepsin B assays, which led to the identification of GER-12 (Crossbyanol B) and GER-24 ((7Z,9Z,12Z)-octadeca-7,9,12-trien-5-ynoic acid) marine NP inhibitors at acidic pH but not at neutral pH. GER-12 was effective for the reversible inhibition of cathepsin B, with an IC50 of 3 μM. GER-24 had an IC50 of 16 μM and was found to be an irreversible inhibitor. These results show that NP screening at distinct biological pH conditions can lead to the identification of pH-selective cathepsin B modulators. These findings suggest that screening efforts for molecular probes and drug discovery may consider the biological pH environment of the target in the disease process.
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Affiliation(s)
- Von V. Phan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, California 92093, United States
| | - Charles Mosier
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Michael C. Yoon
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Scripps
Institution of Oceanography, University
of California, San Diego, La Jolla, California 92093, United States
| | - Conor R. Caffrey
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Scripps
Institution of Oceanography, University
of California, San Diego, La Jolla, California 92093, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department
of Neurosciences and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California 92093, United States
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He Y, Suyama TL, Kim H, Glukhov E, Gerwick WH. Discovery of Novel Tyrosinase Inhibitors From Marine Cyanobacteria. Front Microbiol 2022; 13:912621. [PMID: 35910604 PMCID: PMC9329053 DOI: 10.3389/fmicb.2022.912621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
Tyrosinase, an important oxidase involved in the primary immune response in humans, can sometimes become problematic as it can catalyze undesirable oxidation reactions. Therefore, for decades there has been a strong pharmaceutical interest in the discovery of novel inhibitors of this enzyme. Recent studies have also indicated that tyrosinase inhibitors can potentially be used in the treatment of melanoma cancer. Over the years, many new tyrosinase inhibitors have been discovered from various natural sources; however, marine natural products (MNPs) have contributed only a small number of promising candidates. Therefore, in this study we focused on the discovery of new MNP tyrosinase inhibitors of marine cyanobacterial and algal origins. A colorimetric tyrosinase inhibitory assay was used to screen over 4,500 marine extracts against mushroom tyrosinase (A. bisporus). Our results revealed that scytonemin monomer (ScyM), a pure compound from our compound library and also the monomeric last-step precursor in the biosynthesis of the well-known cyanobacterial sunscreen pigment “scytonemin,” consistently showed the highest tyrosinase inhibitory score. Determination of the half maximal inhibitory concentration (IC50) further indicated that ScyM is more potent than the commonly used commercial inhibitor standard “kojic acid” (KA; IC50 of ScyM: 4.90 μM vs. IC50 of KA: 11.31 μM). After a scaled-up chemical synthesis of ScyM as well as its O-methyl analog (ScyM-OMe), we conducted a series of follow-up studies on their structures, inhibitory properties, and mode of inhibition. Our results supported ScyM as the second case ever of a novel tyrosinase inhibitory compound based on a marine cyanobacterial natural product. The excellent in vitro performance of ScyM makes it a promising candidate for applications such as a skin-whitening agent or an adjuvant therapy for melanoma cancer treatment.
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Affiliation(s)
- Yifan He
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- *Correspondence: Yifan He,
| | - Takashi L. Suyama
- Department of Chemistry and Forensic Science, Waynesburg University, Waynesburg, PA, United States
- Takashi L. Suyama,
| | - Hyunwoo Kim
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- College of Pharmacy, Dongguk University, Goyang, South Korea
| | - Evgenia Glukhov
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - William H. Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- William H. Gerwick,
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Castro-Falcón G, Creamer KE, Chase AB, Kim MC, Sweeney D, Glukhov E, Fenical W, Jensen PR. Structure and Candidate Biosynthetic Gene Cluster of a Manumycin-Type Metabolite from Salinispora pacifica. J Nat Prod 2022; 85:980-986. [PMID: 35263117 PMCID: PMC9209988 DOI: 10.1021/acs.jnatprod.1c01117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new manumycin-type natural product named pacificamide (1) and its candidate biosynthetic gene cluster (pac) were discovered from the marine actinobacterium Salinispora pacifica CNT-855. The structure of the compound was determined using NMR, electronic circular dichroism, and bioinformatic predictions. The pac gene cluster is unique to S. pacifica and found in only two of the 119 Salinispora genomes analyzed across nine species. Comparative analyses of biosynthetic gene clusters encoding the production of related manumycin-type compounds revealed genetic differences in accordance with the unique pacificamide structure. Further queries of manumycin-type gene clusters from public databases revealed their limited distribution across the phylum Actinobacteria and orphan diversity that suggests additional products remain to be discovered in this compound class. Production of the known metabolite triacsin D is also reported for the first time from the genus Salinispora. This study adds two classes of compounds to the natural product collective isolated from the genus Salinispora, which has proven to be a useful model for natural product research.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Kaitlin E Creamer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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Wang Y, Glukhov E, He Y, Liu Y, Zhou L, Ma X, Hu X, Hong P, Gerwick WH, Zhang Y. Secondary Metabolite Variation and Bioactivities of Two Marine Aspergillus Strains in Static Co-Culture Investigated by Molecular Network Analysis and Multiple Database Mining Based on LC-PDA-MS/MS. Antibiotics (Basel) 2022; 11:antibiotics11040513. [PMID: 35453264 PMCID: PMC9031932 DOI: 10.3390/antibiotics11040513] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Co-culture is known as an efficient way to explore the metabolic potential of fungal strains for new antibiotics and other therapeutic agents that could counter emerging health issues. To study the effect of co-culture on the secondary metabolites and bioactivities of two marine strains, Aspergillus terreus C23-3 and Aspergillus. unguis DLEP2008001, they were co-cultured in live or inactivated forms successively or simultaneously. The mycelial morphology and high-performance thin layer chromatography (HPTLC) including bioautography of the fermentation extracts were recorded. Furthermore, the agar cup-plate method was used to compare the antimicrobial activity of the extracts. Based on the above, liquid chromatography-photodiode array-tandem mass spectrometry (LC-PDA-MS/MS) together with Global Natural Products Social molecular networking (GNPS) and multiple natural products database mining were used to further analyze their secondary metabolite variations. The comprehensive results showed the following trends: (1) The strain first inoculated will strongly inhibit the growth and metabolism of the latter inoculated one; (2) Autoclaved A. unguis exerted a strong inducing effect on later inoculated A. terreus, while the autoclaved A. terreus showed high stability of its metabolites and still potently suppressed the growth and metabolism of A. unguis; (3) When the two strains are inoculated simultaneously, they both grow and produce metabolites; however, the A. terreus seemed to be more strongly induced by live A. unguis and this inducing effect surpassed that of the autoclaved A. unguis. Under some of the conditions, the extracts showed higher antimicrobial activity than the axenic cultures. Totally, A. unguis was negative in response but potent in stimulating its rival while A. terreus had the opposite effect. Fifteen MS detectable and/or UV active peaks showed different yields in co-cultures vs. the corresponding axenic culture. GNPS analysis assisted by multiple natural products databases mining (PubChem, Dictionary of Natural Products, NPASS, etc.) gave reasonable annotations for some of these peaks, including antimicrobial compounds such as unguisin A, lovastatin, and nidulin. However, some of the peaks were correlated with antagonistic properties and remain as possible novel compounds without mass or UV matching hits from any database. It is intriguing that the two strains both synthesize chemical ‘weapons’ for antagonism, and that these are upregulated when needed in competitive co-culture environment. At the same time, compounds not useful in this antagonistic setting are downregulated in their expression. Some of the natural products produced during antagonism are unknown chlorinated metabolites and deserve further study for their antimicrobial properties. In summary, this study disclosed the different responses of two Aspergillus strains in co-culture, revealed their metabolic variation, and displayed new opportunities for antibiotic discovery.
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Affiliation(s)
- Yuan Wang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yifan He
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yayue Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Longjian Zhou
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xiaoxiang Ma
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xueqiong Hu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
| | - Pengzhi Hong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yi Zhang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
- Correspondence: or ; Tel.: +86-759-2396046
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Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol 2021; 17:363-368. [PMID: 33589842 PMCID: PMC7987574 DOI: 10.1038/s41589-020-00724-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.
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Affiliation(s)
- Michelle A Schorn
- Laboratory of Microbiology, Department of Agricultural and Food Sciences, Wageningen University, Wageningen, the Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Lars Ridder
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Florian Huber
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Deepa D Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jamshid Amiri Moghaddam
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Saefuddin Aziz
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Microbiology Department, Biology Faculty, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Katherine D Bauman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - J Michael Beman
- Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA
- Sierra Nevada Research Institute, University of California Merced, Merced, CA, USA
| | - María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Alex A Blacutt
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Anne Boullie
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra Calteau
- Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Liu Cao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Shaurya Chanana
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Bart Cuypers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tam Dang
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Anna Edlund
- J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Harald Gross
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Dulce G Guillén Matus
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Eric J N Helfrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Benjamin-Florian Hempel
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
- Charité, University Medicine Berlin, Berlin-Brandenburg Center for Regenerative Therapy (BCRT), Campus Virchow Klinikum, Berlin, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea
| | | | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Leonard Kaysser
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Tiago Leao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Yi-Yuan Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xuanji Li
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Daniel Männle
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Christian Martin H
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Willam W Metcalf
- Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Mitchell Muskat
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Elizabeth I Parkinson
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Karine Pires
- Instituto Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hamada Saad
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Carmen Saenz
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | | | | | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Nicholas J Tobias
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Amaro E Trindade-Silva
- Departamento de Fisiologia e Farmacologia, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, UK
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
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Abstract
Laucysteinamide A (4) is a marine natural product isolated from the cyanobacterium Caldora penicillata and contains structural motifs found in promising cancer drug leads. The first total synthesis of 4 and its analogues was achieved, which also enabled a concise formal synthesis of somocystinamide A (3), a dimeric congener of 4 that previously showed extremely potent antiproliferative activities. This work provides further insights on structure-activity relationships in this class of natural products.
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Affiliation(s)
- Kimberly S Taylor
- Department of Chemistry and Forensic Science, Waynesburg University, 51 W College Street, Waynesburg, Pennsylvania 15370, United States
| | - Chen Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Takashi L Suyama
- Department of Chemistry and Forensic Science, Waynesburg University, 51 W College Street, Waynesburg, Pennsylvania 15370, United States
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Yang JM, Liu YY, Yang WC, Ma XX, Nie YY, Glukhov E, Gerwick L, Gerwick WH, Lei XL, Zhang Y. An anti-inflammatory isoflavone from soybean inoculated with a marine fungus Aspergillus terreus C23-3. Biosci Biotechnol Biochem 2020; 84:1546-1553. [PMID: 32434451 DOI: 10.1080/09168451.2020.1764838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/30/2020] [Indexed: 02/08/2023]
Abstract
A new isoflavone derivative compound 1 (psoralenone) was isolated from soybean inoculated with a marine fungus Aspergillus terreus C23-3, together with seven known compounds including isoflavones 2-6, butyrolactone I (7) and blumenol A (8). Their structures were elucidated by MS, NMR, and ECD. Psoralenone displayed moderate in vitro anti-inflammatory activity in the LPS-induced RAW264.7 cell model. Compound 2 (genistein) showed moderate acetylcholinesterase (AChE) inhibitory activity whereas compounds 2, 5 (biochanin A), 6 (psoralenol), and 7 exhibited potent larvicidal activity against brine shrimp. Compounds 3 (daidzein), 4 (4'-hydroxy-6,7-dimethoxyisoflavone), and 5-7 showed broad-spectrum anti-microbial activity, and compound 7 also showed moderate 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity.
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Affiliation(s)
- Jing-Ming Yang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University , Zhanjiang, China
- Marine Medicine Research and Development Center, Shenzhen Institute of Guangdong Ocean University , Shenzhen, China
| | - Ya-Yue Liu
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University , Zhanjiang, China
| | - Wen-Cong Yang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University , Zhanjiang, China
| | - Xiao-Xiang Ma
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University , Zhanjiang, China
| | - Ying-Ying Nie
- Marine Medicine Research and Development Center, Shenzhen Institute of Guangdong Ocean University , Shenzhen, China
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego, CA, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego, CA, USA
| | - Xiao-Ling Lei
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University , Zhanjiang, China
| | - Yi Zhang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University , Zhanjiang, China
- Marine Medicine Research and Development Center, Shenzhen Institute of Guangdong Ocean University , Shenzhen, China
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego, CA, USA
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15
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Li Y, Yu HB, Zhang Y, Leao T, Glukhov E, Pierce ML, Zhang C, Kim H, Mao HH, Fang F, Cottrell GW, Murray TF, Gerwick L, Guan H, Gerwick WH. Pagoamide A, a Cyclic Depsipeptide Isolated from a Cultured Marine Chlorophyte, Derbesia sp., Using MS/MS-Based Molecular Networking. J Nat Prod 2020; 83:617-625. [PMID: 31916778 PMCID: PMC7210564 DOI: 10.1021/acs.jnatprod.9b01019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A thiazole-containing cyclic depsipeptide with 11 amino acid residues, named pagoamide A (1), was isolated from laboratory cultures of a marine Chlorophyte, Derbesia sp. This green algal sample was collected from America Samoa, and pagoamide A was isolated using guidance by MS/MS-based molecular networking. Cultures were grown in a light- and temperature-controlled environment and harvested after several months of growth. The planar structure of pagoamide A (1) was characterized by detailed 1D and 2D NMR experiments along with MS and UV analysis. The absolute configurations of its amino acid residues were determined by advanced Marfey's analysis following chemical hydrolysis and hydrazinolysis reactions. Two of the residues in pagoamide A (1), phenylalanine and serine, each occurred twice in the molecule, once in the d- and once in the l-configuration. The biosynthetic origin of pagoamide A (1) was considered in light of other natural products investigations with coenocytic green algae.
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Affiliation(s)
- Yueying Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People’s Republic of China
- University of California, San Diego, La Jolla, California 92093, United States
| | - Hao-Bing Yu
- University of California, San Diego, La Jolla, California 92093, United States
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, People’s Republic of China
| | - Yi Zhang
- University of California, San Diego, La Jolla, California 92093, United States
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, People’s Republic of China
| | - Tiago Leao
- University of California, San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- University of California, San Diego, La Jolla, California 92093, United States
| | - Marsha L. Pierce
- Department of Pharmacology, School of Medicine, Creighton University, Omaha, Nebraska 68178, United States
| | - Chen Zhang
- University of California, San Diego, La Jolla, California 92093, United States
- Department of Computer Sciences and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Hyunwoo Kim
- University of California, San Diego, La Jolla, California 92093, United States
| | - Huanru Henry Mao
- Department of Computer Sciences and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Fang Fang
- University of California, San Diego, La Jolla, California 92093, United States
| | - Garrison W. Cottrell
- Department of Computer Sciences and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Thomas F. Murray
- Department of Pharmacology, School of Medicine, Creighton University, Omaha, Nebraska 68178, United States
| | - Lena Gerwick
- University of California, San Diego, La Jolla, California 92093, United States
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People’s Republic of China
| | - William H. Gerwick
- University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- To whom correspondence should be addressed. Tel: (858)-534-0578.
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16
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Keller L, Canuto KM, Liu C, Suzuki BM, Almaliti J, Sikandar A, Naman CB, Glukhov E, Luo D, Duggan BM, Luesch H, Koehnke J, O’Donoghue AJ, Gerwick WH. Tutuilamides A-C: Vinyl-Chloride-Containing Cyclodepsipeptides from Marine Cyanobacteria with Potent Elastase Inhibitory Properties. ACS Chem Biol 2020; 15:751-757. [PMID: 31935054 DOI: 10.1021/acschembio.9b00992] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Marine cyanobacteria (blue-green algae) have been shown to possess an enormous capacity to produce structurally diverse natural products that exhibit a broad spectrum of potent biological activities, including cytotoxic, antifungal, antiparasitic, antiviral, and antibacterial activities. Using mass-spectrometry-guided fractionation together with molecular networking, cyanobacterial field collections from American Samoa and Palmyra Atoll yielded three new cyclic peptides, tutuilamides A-C. Their structures were established by spectroscopic techniques including 1D and 2D NMR, HR-MS, and chemical derivatization. Structure elucidation was facilitated by employing advanced NMR techniques including nonuniform sampling in combination with the 1,1-ADEQUATE experiment. These cyclic peptides are characterized by the presence of several unusual residues including 3-amino-6-hydroxy-2-piperidone and 2-amino-2-butenoic acid, together with a novel vinyl chloride-containing residue. Tutuilamides A-C show potent elastase inhibitory activity together with moderate potency in H-460 lung cancer cell cytotoxicity assays. The binding mode to elastase was analyzed by X-ray crystallography revealing a reversible binding mode similar to the natural product lyngbyastatin 7. The presence of an additional hydrogen bond with the amino acid backbone of the flexible side chain of tutuilamide A, compared to lyngbyastatin 7, facilitates its stabilization in the elastase binding pocket and possibly explains its enhanced inhibitory potency.
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Affiliation(s)
- Lena Keller
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Kirley Marques Canuto
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Embrapa Agroindústria Tropical, Fortaleza, Ceará 60511-110, Brazil
| | - Chenxi Liu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Brian M. Suzuki
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Asfandyar Sikandar
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken 66123, Germany
| | - C. Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, People’s Republic of China
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Danmeng Luo
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida 32610, United States
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida 32610, United States
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken 66123, Germany
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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17
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Reher R, Kim HW, Zhang C, Mao HH, Wang M, Nothias LF, Caraballo-Rodriguez AM, Glukhov E, Teke B, Leao T, Alexander KL, Duggan BM, Van Everbroeck EL, Dorrestein PC, Cottrell GW, Gerwick WH. A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products. J Am Chem Soc 2020; 142:4114-4120. [PMID: 32045230 DOI: 10.1021/jacs.9b13786] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This report describes the first application of the novel NMR-based machine learning tool "Small Molecule Accurate Recognition Technology" (SMART 2.0) for mixture analysis and subsequent accelerated discovery and characterization of new natural products. The concept was applied to the extract of a filamentous marine cyanobacterium known to be a prolific producer of cytotoxic natural products. This environmental Symploca extract was roughly fractionated, and then prioritized and guided by cancer cell cytotoxicity, NMR-based SMART 2.0, and MS2-based molecular networking. This led to the isolation and rapid identification of a new chimeric swinholide-like macrolide, symplocolide A, as well as the annotation of swinholide A, samholides A-I, and several new derivatives. The planar structure of symplocolide A was confirmed to be a structural hybrid between swinholide A and luminaolide B by 1D/2D NMR and LC-MS2 analysis. A second example applies SMART 2.0 to the characterization of structurally novel cyclic peptides, and compares this approach to the recently appearing "atomic sort" method. This study exemplifies the revolutionary potential of combined traditional and deep learning-assisted analytical approaches to overcome longstanding challenges in natural products drug discovery.
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Affiliation(s)
- Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Hyun Woo Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Chen Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Huanru Henry Mao
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andres Mauricio Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Bahar Teke
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Tiago Leao
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brendan M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ezra L Van Everbroeck
- Director's Office, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Garrison W Cottrell
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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18
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Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst 2019; 9:600-608.e4. [PMID: 31629686 DOI: 10.1016/j.cels.2019.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.
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Affiliation(s)
- Liu Cao
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Tiago Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Robby Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Rodolfo A S Benitez
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Md-Nafiz Hamid
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | | | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Hosein Mohimani
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA.
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19
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Yu HB, Glukhov E, Li Y, Iwasaki A, Gerwick L, Dorrestein PC, Jiao BH, Gerwick WH. Cytotoxic Microcolin Lipopeptides from the Marine Cyanobacterium Moorea producens. J Nat Prod 2019; 82:2608-2619. [PMID: 31468974 DOI: 10.1021/acs.jnatprod.9b00549] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nine new linear lipopeptides, microcolins E-M (1-9), together with four known related compounds, microcolins A-D (10-13), were isolated from the marine cyanobacterium Moorea producens using bioassay-guided and LC-MS/MS molecular networking approaches. Catalytic hydrogenation of microcolins A-D (10-13) yielded two known compounds, 3,4-dihydromicrocolins A and B (14, 15), and two new derivatives, 3,4-dihydromicrocolins C and D (16, 17), respectively. The structures of these new compounds were determined by a combination of spectroscopic and advanced Marfey's analysis. Structurally unusual amino acid units, 4-methyl-2-(methylamino)pent-3-enoic (Mpe) acid and 2-amino-4-methylhexanoic acid (N-Me-homoisoleucine), in compounds 1-3 and 8, respectively, are rare residues in naturally occurring peptides. These metabolites showed significant cytotoxic activity against H-460 human lung cancer cells with IC50 values ranging from 6 nM to 5.0 μM. The variations in structure and attendant biological activities provided fresh insights concerning structure-activity relationships for the microcolin class of lipopeptides.
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Affiliation(s)
- Hao-Bing Yu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , People's Republic of China
- Center for Marine Biotechnology and Biomedicine , Scripps Institution of Oceanography, University of California, San Diego , La Jolla , California 92093 , United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine , Scripps Institution of Oceanography, University of California, San Diego , La Jolla , California 92093 , United States
| | - Yueying Li
- Center for Marine Biotechnology and Biomedicine , Scripps Institution of Oceanography, University of California, San Diego , La Jolla , California 92093 , United States
| | - Arihiro Iwasaki
- Center for Marine Biotechnology and Biomedicine , Scripps Institution of Oceanography, University of California, San Diego , La Jolla , California 92093 , United States
- Department of Chemistry , Keio University , 3-14-1, Hiyoshi, Kohoku-ku , Yokohama , Kanagawa 223-8522 , Japan
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine , Scripps Institution of Oceanography, University of California, San Diego , La Jolla , California 92093 , United States
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Bing-Hua Jiao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , People's Republic of China
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine , Scripps Institution of Oceanography, University of California, San Diego , La Jolla , California 92093 , United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
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20
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Almaliti J, Miller B, Pietraszkiewicz H, Glukhov E, Naman CB, Kline T, Hanson J, Li X, Zhou S, Valeriote FA, Gerwick WH. Exploration of the carmaphycins as payloads in antibody drug conjugate anticancer agents. Eur J Med Chem 2019; 161:416-432. [PMID: 30384045 PMCID: PMC6248884 DOI: 10.1016/j.ejmech.2018.10.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/25/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023]
Abstract
Antibody-drug conjugates (ADCs) represent a new dimension of anticancer chemotherapeutics, with warheads to date generally involving either antitubulin or DNA-directed agents to achieve low-to sub-nanomolar potency. However, other potent cytotoxins working by different pharmacological mechanisms are under investigation, such as α,β-epoxyketone based proteasome inhibitors. These proteasome active agents are an emerging class of anticancer drug that possesses ultra-potent cytotoxicity to some cancer cell lines. The carmaphycins are representatives of this latter class that we isolated and characterized from a marine cyanobacterium, and these as well as several synthetic analogues exhibit this level of potency. In the current work, we investigated the use of these highly potent cytotoxic compounds as warheads in the design of novel ADCs. We designed and synthesized a library of carmaphycin B analogues that contain amine handles, enabling their attachment to an antibody linker. The basicity of these incorporated amine handles was shown to strongly affect their cytotoxic properties. Linear amines resulted in the greatest reduction in cytotoxicity whereas less basic aromatic amines retained potent activity as demonstrated by a 4-sulfonylaniline derivative. These investigations resulted in identifying the P2 residue in the carmaphycins as the most suitable site for linker attachment point, and hence, we synthesized a highly potent analogue of carmaphycin B that contained a 4-sulfonylaniline handle as an attachment point for the linker antibody.
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Affiliation(s)
- Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States; Department Pharmaceutical Sciences, College of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Bailey Miller
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States
| | - Halina Pietraszkiewicz
- Department of Internal Medicine, Division of Hematology and Oncology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - Evgenia Glukhov
- Department Pharmaceutical Sciences, College of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States; College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Toni Kline
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Jeffrey Hanson
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Xiaofan Li
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Sihong Zhou
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Frederick A Valeriote
- Department of Internal Medicine, Division of Hematology and Oncology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States.
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21
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Ding CYG, Pang LM, Liang ZX, Goh KKK, Glukhov E, Gerwick WH, Tan LT. MS/MS-Based Molecular Networking Approach for the Detection of Aplysiatoxin-Related Compounds in Environmental Marine Cyanobacteria. Mar Drugs 2018; 16:md16120505. [PMID: 30551660 PMCID: PMC6315786 DOI: 10.3390/md16120505] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022] Open
Abstract
Certain strains of cyanobacteria produce a wide array of cyanotoxins, such as microcystins, lyngbyatoxins and aplysiatoxins, that are associated with public health issues. In this pilot study, an approach combining LC-MS/MS and molecular networking was employed as a rapid analytical method to detect aplysiatoxins present in four environmental marine cyanobacterial samples collected from intertidal areas in Singapore. Based on 16S-ITS rRNA gene sequences, these filamentous cyanobacterial samples collected from Pulau Hantu were determined as Trichodesmium erythraeum, Oscillatoria sp. PAB-2 and Okeania sp. PNG05-4. Organic extracts were prepared and analyzed on LC-HRMS/MS and Global Natural Product Social Molecular Networking (GNPS) for the presence of aplysiatoxin-related molecules. From the molecular networking, six known compounds, debromoaplysiatoxin (1), anhydrodebromoaplysiatoxin (2), 3-methoxydebromoaplysiatoxin (3), aplysiatoxin (4), oscillatoxin A (5) and 31-noroscillatoxin B (6), as well as potential new analogues, were detected in these samples. In addition, differences and similarities in molecular networking clusters related to the aplysiatoxin molecular family were observed in extracts of Trichodesmium erythraeum collected from two different locations and from different cyanobacterial species found at Pulau Hantu, respectively.
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Affiliation(s)
- Chi Ying Gary Ding
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Kau Kiat Kelvin Goh
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, (K.K.K.G.).
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
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22
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Via CW, Glukhov E, Costa S, Zimba PV, Moeller PDR, Gerwick WH, Bertin MJ. The Metabolome of a Cyanobacterial Bloom Visualized by MS/MS-Based Molecular Networking Reveals New Neurotoxic Smenamide Analogs (C, D, and E). Front Chem 2018; 6:316. [PMID: 30094232 PMCID: PMC6071517 DOI: 10.3389/fchem.2018.00316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 11/29/2022] Open
Abstract
Members of the cyanobacterial genus Trichodesmium are well known for their substantial impact on nitrogen influx in ocean ecosystems and the enormous surface blooms they form in tropical and subtropical locations. However, the secondary metabolite composition of these complex environmental bloom events is not well known, nor the possibility of the production of potent toxins that have been observed in other bloom-forming marine and freshwater cyanobacteria species. In the present work, we aimed to characterize the metabolome of a Trichodesmium bloom utilizing MS/MS-based molecular networking. Furthermore, we integrated cytotoxicity assays in order to identify and ultimately isolate potential cyanotoxins from the bloom. These efforts led to the isolation and identification of several members of the smenamide family, including three new smenamide analogs (1-3) as well as the previously reported smenothiazole A-hybrid polyketide-peptide compounds. Two of these new smenamides possessed cytotoxicity to neuro-2A cells (1 and 3) and their presence elicits further questions as to their potential ecological roles. HPLC profiling and molecular networking of chromatography fractions from the bloom revealed an elaborate secondary metabolome, generating hypotheses with respect to the environmental role of these metabolites and the consistency of this chemical composition across genera, space and time.
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Affiliation(s)
- Christopher W. Via
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States
| | - Samuel Costa
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Paul V. Zimba
- Center for Coastal Studies and Department of Life Sciences, Texas A&M Corpus Christi, Corpus Christi, TX, United States
| | - Peter D. R. Moeller
- Emerging Toxins Program, Hollings Marine Laboratory, National Ocean Service/NOAA, Charleston, SC, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States
| | - Matthew J. Bertin
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
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23
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Moss NA, Leao T, Glukhov E, Gerwick L, Gerwick WH. Collection, Culturing, and Genome Analyses of Tropical Marine Filamentous Benthic Cyanobacteria. Methods Enzymol 2018; 604:3-43. [PMID: 29779657 DOI: 10.1016/bs.mie.2018.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Decreasing sequencing costs has sparked widespread investigation of the use of microbial genomics to accelerate the discovery and development of natural products for therapeutic uses. Tropical marine filamentous cyanobacteria have historically produced many structurally novel natural products, and therefore present an excellent opportunity for the systematic discovery of new metabolites via the information derived from genomics and molecular genetics. Adequate knowledge transfer and institutional know-how are important to maintain the capability for studying filamentous cyanobacteria due to their unusual microbial morphology and characteristics. Here, we describe workflows, procedures, and commentary on sample collection, cultivation, genomic DNA generation, bioinformatics tools, and biosynthetic pathway analysis concerning filamentous cyanobacteria.
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Affiliation(s)
- Nathan A Moss
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - Tiago Leao
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - Evgenia Glukhov
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - Lena Gerwick
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California, San Diego, CA, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States.
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24
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Warmbrunn MV, Schilling JM, Dhanani M, Glukhov E, Gerwick LG, Gerwick WH, Patel HH. Novel Marine Compounds Modulate Mitochondrial Function in H9c2 Cells: Potential New Pharmaceutical Targets to Control Cardiac Metabolism. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.702.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Mehul Dhanani
- AnesthesiologyUniversity of CaliforniaSan DiegoLa JollaCA
| | - Evgenia Glukhov
- Scripps Institution of OceanographyUniversity of CaliforniaSan DiegoLa JollaCA
| | - Lena G. Gerwick
- Scripps Institution of OceanographyUniversity of CaliforniaSan DiegoLa JollaCA
| | - William H. Gerwick
- Scripps Institution of OceanographyUniversity of CaliforniaSan DiegoLa JollaCA
| | - Hemal H. Patel
- AnesthesiologyUniversity of CaliforniaSan DiegoLa JollaCA
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25
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Tao Y, Li P, Zhang D, Glukhov E, Gerwick L, Zhang C, Murray TF, Gerwick WH. Samholides, Swinholide-Related Metabolites from a Marine Cyanobacterium cf. Phormidium sp. J Org Chem 2018; 83:3034-3046. [PMID: 29457979 PMCID: PMC5859247 DOI: 10.1021/acs.joc.8b00028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Cancer cell cytotoxicity was used
to guide the isolation of nine
new swinholide-related compounds, named samholides A–I (1–9), from an American Samoan marine cyanobacterium
cf. Phormidium sp. Their structures were determined
by extensive analysis of 1D and 2D NMR spectroscopic data. The new
compounds share an unusual 20-demethyl 44-membered lactone ring composed
of two monomers, and they demonstrate structural diversity arising
from geometric isomerization of double bonds, sugar units with unique
glyceryl moieties and varied methylation patterns. All of the new
samholides were potently active against the H-460 human lung cancer
cell line with IC50 values ranging from 170 to 910 nM.
The isolation of these new swinholide-related compounds from a marine
cyanobacterium reinvigorates questions concerning the evolution and
biosynthetic origin of these natural products.
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Affiliation(s)
- Yiwen Tao
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital , Guangzhou Medical University , Guangzhou 511436 , People's Republic of China.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Pinglin Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266235 , People's Republic of China.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Daojing Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States.,State Key Laboratory of Bioreactor Engineering , East China University of Science & Technology , Shanghai 200237 , People's Republic of China
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Chen Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Thomas F Murray
- Department of Pharmacology , Creighton University School of Medicine , Omaha , Nebraska 68178 , United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
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26
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Shao CL, Mou XF, Cao F, Spadafora C, Glukhov E, Gerwick L, Wang CY, Gerwick WH. Bastimolide B, an Antimalarial 24-Membered Marine Macrolide Possessing a tert-Butyl Group. J Nat Prod 2018; 81:211-215. [PMID: 29327931 DOI: 10.1021/acs.jnatprod.7b00917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We reported previously the discovery of the potent antimalarial 40-membered macrolide bastimolide A (1) from the tropical marine cyanobacterium Okeania hirsute. Continued investigation has led to the discovery of a new analogue, bastimolide B (2), a 24-membered polyhydroxy macrolide with a long aliphatic chain and unique terminal tert-butyl group. Its complete structure was determined by a combination of extensive spectroscopic methods and comparative analysis of its methanolysis products with those of bastimolide A. A methanolysis mechanism for bastimolide A is proposed, and one unexpected isomerization product of the C2-C3 double bond, 2-(E)-bastimolide A (3), was obtained. Bastimolide B (2) showed strong antimalarial activity against chloroquine-sensitive Plasmodium falciparum strain HB3. A preliminary investigation of the structure-activity relationship based on six analogues revealed the importance of the double bond as well as the 1,3-diol and 1,3,5-triol functionalities.
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Affiliation(s)
- Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266200, China
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, California 92093, United States
| | - Xiao-Feng Mou
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266200, China
| | - Fei Cao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China
| | - Carmenza Spadafora
- Instituto de Investigaciones Cientificas y Servicios de Alta Tecnologia , Clayton, Apartado 0816-02852, Panama
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, California 92093, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, California 92093, United States
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266200, China
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, California 92093, United States
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27
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Pokataev I, Kudaibergenova A, Artemyeva A, Podluzhnyi D, Kudashkin N, Patyutko Y, Moroz E, Kharchenko E, Popova A, Fedyanin M, Rumyantsev A, Bazin I, Tryakin A, Glukhov E, Sekhina O, Chekini D, Tjulandin S. Intratumoral heterogeneity of SMAD4 immunohistochemical (IHC) expression and its role in prediction of recurrence patterns in patients with resectable pancreatic cancer (PC). Ann Oncol 2017. [DOI: 10.1093/annonc/mdx369.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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28
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Naman CB, Almaliti J, Armstrong L, Caro-Díaz EJ, Pierce ML, Glukhov E, Fenner A, Spadafora C, Debonsi HM, Dorrestein PC, Murray TF, Gerwick WH. Discovery and Synthesis of Caracolamide A, an Ion Channel Modulating Dichlorovinylidene Containing Phenethylamide from a Panamanian Marine Cyanobacterium cf. Symploca Species. J Nat Prod 2017; 80:2328-2334. [PMID: 28783331 DOI: 10.1021/acs.jnatprod.7b00367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A recent untargeted metabolomics investigation into the chemical profile of 10 organic extracts from cf. Symploca spp. revealed several interesting chemical leads for further natural product drug discovery. Subsequent target-directed isolation efforts with one of these, a Panamanian marine cyanobacterium cf. Symploca sp., yielded a phenethylamide metabolite that terminates in a relatively rare gem-dichlorovinylidene moiety, caracolamide A (1), along with a known isotactic polymethoxy-1-alkene (2). Detailed NMR and HRESIMS analyses were used to determine the structures of these molecules, and compound 1 was confirmed by a three-step synthesis. Pure compound 1 was shown to have in vitro calcium influx and calcium channel oscillation modulatory activity when tested as low as 10 pM using cultured murine cortical neurons, but was not cytotoxic to NCI-H460 human non-small-cell lung cancer cells in vitro (IC50 > 10 μM).
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Affiliation(s)
- C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan , Amman, 11942, Jordan
| | - Lorene Armstrong
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo , Avenida Do Café, s/n, Campus Universitário, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Eduardo J Caro-Díaz
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Marsha L Pierce
- Department of Pharmacology, Creighton University School of Medicine , 2500 California Plaza, Omaha, Nebraska 68178, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
| | - Amanda Fenner
- Center of Cellular and Molecular Biology of Diseases, City of Knowledge, Instituto de Investigaciones Científicas y Sevicios de Alta Tecnología , Bldg. 219, P.O. Box 7250, Panama 5, Republic of Panama
| | - Carmenza Spadafora
- Center of Cellular and Molecular Biology of Diseases, City of Knowledge, Instituto de Investigaciones Científicas y Sevicios de Alta Tecnología , Bldg. 219, P.O. Box 7250, Panama 5, Republic of Panama
| | - Hosana M Debonsi
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo , Avenida Do Café, s/n, Campus Universitário, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Thomas F Murray
- Department of Pharmacology, Creighton University School of Medicine , 2500 California Plaza, Omaha, Nebraska 68178, United States
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
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29
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Almaliti J, Malloy KL, Glukhov E, Spadafora C, Gutiérrez M, Gerwick WH. Dudawalamides A-D, Antiparasitic Cyclic Depsipeptides from the Marine Cyanobacterium Moorea producens. J Nat Prod 2017; 80:1827-1836. [PMID: 28535042 DOI: 10.1021/acs.jnatprod.7b00034] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A family of 2,2-dimethyl-3-hydroxy-7-octynoic acid (Dhoya)-containing cyclic depsipeptides, named dudawalamides A-D (1-4), was isolated from a Papua New Guinean field collection of the cyanobacterium Moorea producens using bioassay-guided and spectroscopic approaches. The planar structures of dudawalamides A-D were determined by a combination of 1D and 2D NMR experiments and MS analysis, whereas the absolute configurations were determined by X-ray crystallography, modified Marfey's analysis, chiral-phase GCMS, and chiral-phase HPLC. Dudawalamides A-D possess a broad spectrum of antiparasitic activity with minimal mammalian cell cytotoxicity. Comparative analysis of the Dhoya-containing class of lipopeptides reveals intriguing structure-activity relationship features of these NRPS-PKS-derived metabolites and their derivatives.
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Affiliation(s)
- Jehad Almaliti
- Department Pharmaceutical Sciences, College of Pharmacy, The University of Jordan , Amman, 11942, Jordan
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30
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2017; 34:828-837. [PMID: 27504778 DOI: 10.1038/nbt.3597] [Citation(s) in RCA: 2254] [Impact Index Per Article: 322.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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31
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Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. eLife 2017; 6. [PMID: 28492366 PMCID: PMC5441867 DOI: 10.7554/elife.24214] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium. DOI:http://dx.doi.org/10.7554/eLife.24214.001 Cyanobacteria and algae are found in all oceans around the globe. Like plants, they can use sunlight as a source of energy in a process called photosynthesis. As a result, these organisms are important sources of oxygen and another vital nutrient called nitrogen for other marine organisms. Many of these organisms also produce a variety of other chemicals known as “natural products” to help them to survive in their environments. Some of these natural products have shown potential as medicinal drugs. The search for new chemicals with useful medicinal properties has led researchers to collect samples of algae and cyanobacteria from various locations around the world. An approach called mass spectrometry is often used to identify new chemicals because it can provide information about the structure of a molecule based on how much its fragments weigh. Luzzatto-Knaan et al. used mass spectrometry to search for new chemicals in samples of algae and cyanobacteria that had been collected by diving and snorkeling in a wide variety of tropical marine environments over several decades. The experiments reveal that the organisms in these samples produce a diverse range of chemicals, most of which were previously unknown and have not been found in other similar environmental collections. The data were grouped together into eight major collection areas covering different parts of the tropics. The samples from some areas contained a wider variety of chemicals than others. Within each collection area, some molecules were found to be very common whereas others were only present at specific locations. To highlight the distribution of these natural products, Luzzatto-Knaan et al. display the data on a world map. Further experiments used this approach as a guide to extract a previously unknown chemical called yuvalamide A from a marine cyanobacterium. The next challenge would be to associate the geographical patterns of chemicals to their potential ecological roles. This approach offers a new way to explore large-scale collections of environmental samples to discover and study new natural products. DOI:http://dx.doi.org/10.7554/eLife.24214.002
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Mingxun Wang
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, United States
| | - Gail Ackermann
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Amnon Amir
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
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32
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Cummings ME, Barbé D, Leao TF, Korobeynikov A, Engene N, Glukhov E, Gerwick WH, Gerwick L. A novel uncultured heterotrophic bacterial associate of the cyanobacterium Moorea producens JHB. BMC Microbiol 2016; 16:198. [PMID: 27577966 PMCID: PMC5006271 DOI: 10.1186/s12866-016-0817-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 08/19/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Filamentous tropical marine cyanobacteria such as Moorea producens strain JHB possess a rich community of heterotrophic bacteria on their polysaccharide sheaths; however, these bacterial communities have not yet been adequately studied or characterized. RESULTS AND DISCUSSION Through efforts to sequence the genome of this cyanobacterial strain, the 5.99 MB genome of an unknown bacterium emerged from the metagenomic information, named here as Mor1. Analysis of its genome revealed that the bacterium is heterotrophic and belongs to the phylum Acidobacteria, subgroup 22; however, it is only 85 % identical to the nearest cultured representative. Comparative genomics further revealed that Mor1 has a large number of genes involved in transcriptional regulation, is completely devoid of transposases, is not able to synthesize the full complement of proteogenic amino acids and appears to lack genes for nitrate uptake. Mor1 was found to be present in lab cultures of M. producens collected from various locations, but not other cyanobacterial species. Diverse efforts failed to culture the bacterium separately from filaments of M. producens JHB. Additionally, a co-culturing experiment between M. producens JHB possessing Mor1 and cultures of other genera of cyanobacteria indicated that the bacterium was not transferable. CONCLUSION The data presented support a specific relationship between this novel uncultured bacterium and M. producens, however, verification of this proposed relationship cannot be done until the "uncultured" bacterium can be cultured.
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Affiliation(s)
- Milo E Cummings
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Debby Barbé
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tiago Ferreira Leao
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anton Korobeynikov
- Department of Statistical Modelling, St. Petersburg State University, Saint Petersburg, Russia
- Center for Algorithmic Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
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33
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016. [PMID: 27504778 DOI: 10.1038/nbt.3597.sharing] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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Teta R, Sala GD, Glukhov E, Gerwick L, Gerwick WH, Mangoni A, Costantino V. Combined LC-MS/MS and Molecular Networking Approach Reveals New Cyanotoxins from the 2014 Cyanobacterial Bloom in Green Lake, Seattle. Environ Sci Technol 2015; 49:14301-10. [PMID: 26567695 PMCID: PMC4851459 DOI: 10.1021/acs.est.5b04415] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cyanotoxins obtained from a freshwater cyanobacterial collection at Green Lake, Seattle during a cyanobacterial harmful algal bloom in the summer of 2014 were studied using a new approach based on molecular networking analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data. This MS networking approach is particularly well-suited for the detection of new cyanotoxin variants and resulted in the discovery of three new cyclic peptides, namely microcystin-MhtyR (6), which comprised about half of the total microcystin content in the bloom, and ferintoic acids C (12) and D (13). Structure elucidation of 6 was aided by a new microscale methylation procedure. Metagenomic analysis of the bloom using the 16S-ITS rRNA region identified Microcystis aeruginosa as the predominant cyanobacterium in the sample. Fragments of the putative biosynthetic genes for the new cyanotoxins were also identified, and their sequences correlated to the structure of the isolated cyanotoxins.
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Affiliation(s)
- Roberta Teta
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Gerardo Della Sala
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA 92093-0212, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA 92093-0212, USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA 92093-0212, USA
| | - Alfonso Mangoni
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Valeria Costantino
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
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Glukhov E, Stilidi I, Nered S. 212P D2 lymphadenectomy with preservation of the spleen in gastric cancer. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv523.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Brito Â, Gaifem J, Ramos V, Glukhov E, Dorrestein PC, Gerwick WH, Vasconcelos VM, Mendes MV, Tamagnini P. Bioprospecting Portuguese Atlantic coast cyanobacteria for bioactive secondary metabolites reveals untapped chemodiversity. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Ruh Wong W, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. Molecular networking as a dereplication strategy. J Nat Prod 2013; 76:1686-99. [PMID: 24025162 PMCID: PMC3936340 DOI: 10.1021/np400413s] [Citation(s) in RCA: 400] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.
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Affiliation(s)
- Jane Y. Yang
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Laura M. Sanchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Christopher M. Rath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Xueting Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100190, China
| | - Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Nicole Bruns
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Anne Wodtke
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Rafael de Felicio
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Nucleo de Pesquisaem Produtos Naturais e Sinteticos - Departamento de Fisica e Quimica - Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - Amanda Fenner
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Weng Ruh Wong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Lixin Zhang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100190, China
| | - Hosana M. Debonsi
- Nucleo de Pesquisaem Produtos Naturais e Sinteticos - Departamento de Fisica e Quimica - Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Corresponding Author Telephone: 858-534-6607 Fax: 858-822-0041
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38
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Glukhov E, Burrows LL, Deber CM. Membrane interactions of designed cationic antimicrobial peptides: The two thresholds. Biopolymers 2008; 89:360-71. [DOI: 10.1002/bip.20917] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Glukhov E, Shulga YV, Epand RF, Dicu AO, Topham MK, Deber CM, Epand RM. Membrane interactions of the hydrophobic segment of diacylglycerol kinase epsilon. Biochim Biophys Acta 2007; 1768:2549-58. [PMID: 17669357 DOI: 10.1016/j.bbamem.2007.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Revised: 05/26/2007] [Accepted: 06/12/2007] [Indexed: 11/23/2022]
Abstract
Diacylglycerol kinase epsilon (DGKepsilon) is unique among mammalian DGK isoforms in having a segment of hydrophobic amino acids as a putative membrane anchor. To model the conformation, and stoichiometry of this segment in membrane-mimetic environments, we have prepared a peptide corresponding to this hydrophobic segment of DGKepsilon of sequence KKKKLILWTLCSVLLPVFITFWKKKKK-NH(2). Flanking Lys residues mimic the natural setting of this peptide in DGKepsilon, while facilitating peptide synthesis and characterization. Circular dichroism and fluorescence spectroscopic analysis demonstrated that the peptide has increased helical content and significant blue shifts in the presence of anionic--but not zwitterionic--bilayer membranes. When labeled with fluorophores that can undergo fluorescence resonance energy transfer, the peptide was found to dimerize--a result also observed from migration rates on SDS-PAGE gels under both reducing and non-reducing disulfide bridge conditions. The peptide was shown to preferentially interact with cholesterol in lipid films comprised of homogeneous mixtures of cholesterol and phosphatidylcholine, yet the presence of cholesterol in hydrated vesicle bilayers decreases its helical content. The peptide was also able to inhibit the activity of DGKepsilon protein in vitro. Our overall findings suggest that the peptide ultimately cannot leave the bulk water for attachment/insertion into the outer leaflet of an erythrocyte-like bilayer, yet its core sequence is sufficiently hydrophobic to insert into membrane core regions when membrane attachment is promoted by electrostatic attraction to anionic lipid head groups of the inner leaflet of an erythrocyte-like bilayer.
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Affiliation(s)
- Evgenia Glukhov
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
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Burrows LL, Stark M, Chan C, Glukhov E, Sinnadurai S, Deber CM. Activity of novel non-amphipathic cationic antimicrobial peptides against Candida species. J Antimicrob Chemother 2006; 57:899-907. [PMID: 16524895 DOI: 10.1093/jac/dkl056] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Candida species are problematic opportunistic pathogens in the hospital setting, where they are frequently associated with opportunistic infections of indwelling medical devices. There are only a few effective classes of antifungal agents currently available, and some species, such as Candida lusitaniae, Candida glabrata and Candida krusei, are intrinsically resistant to some of these drugs, further reducing existing therapeutic options. We have recently developed synthetic, non-amphipathic cationic antimicrobial peptides (CAPs) based on the structure of native hydrophobic membrane-spanning domains of integral membrane proteins. In this article, we report on the activity of these CAPs and new variants thereof against eight Candida species. METHODS AND RESULTS Using a combination of MIC, haemolysis, time-kill and biofilm killing assays, we demonstrate activity of CAPs in the micromolar range against eight Candida species, with little toxicity to mammalian cells. The synthetic peptides killed both the fluconazole-susceptible and fluconazole-resistant strains of Candida albicans, Candida tropicalis and C. glabrata by 4 logs or more within 3 h, and also killed pre-formed yeast biofilms on plastic surfaces. CONCLUSIONS These peptides show promise as a basis for development of novel, broad-spectrum antimicrobial agents.
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Affiliation(s)
- Lori L Burrows
- Infection, Immunity, Injury and Repair, Hospital for Sick Children Research Institute, Toronto, ON, Canada.
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Abstract
Novel cationic antimicrobial peptides typified by structures such as KKKKKKAAXAAWAAXAA-NH2, where X = Phe/Trp, and several of their analogues display high activity against a variety of bacteria but exhibit no hemolytic activity even at high dose levels in mammalian erythrocytes. To elucidate their mechanism of action and source of selectivity for bacterial membranes, phospholipid mixtures mimicking the compositions of natural bacterial membranes (containing anionic lipids) and mammalian membranes (containing zwitterionic lipids + cholesterol) were challenged with the peptides. We found that peptides readily inserted into bacterial lipid mixtures, although no insertion was detected in model "mammalian" membranes. The depth of peptide insertion into model bacterial membranes was estimated by Trp fluorescence quenching using doxyl groups variably positioned along the phospholipid acyl chains. Peptide antimicrobial activity generally increased with increasing depth of peptide insertion. The overall results, in conjunction with molecular modeling, support an initial electrostatic interaction step in which bacterial membranes attract and bind peptide dimers onto the bacterial surface, followed by the "sinking" of the hydrophobic core segment to a peptide sequence-dependent depth of approximately 2.5-8 A into the membrane, largely parallel to the membrane surface. Antimicrobial activity was likely enhanced by the fact that the peptide sequences contain AXXXA sequence motifs, which promote their dimerization, and possibly higher oligomerization, as assessed by SDS-polyacrylamide gel analysis and fluorescence resonance energy transfer experiments. The high selectivity of these peptides for nonmammalian membranes, combined with their activity toward a wide spectrum of Gram-negative and Gram-positive bacteria and yeast, while retaining water solubility, represent significant advantages of this class of peptides.
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Affiliation(s)
- Evgenia Glukhov
- Division of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario M5S 1A8
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42
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Gazal S, Gellerman G, Glukhov E, Gilon C. Synthesis of novel protected Nalpha(omega-thioalkyl) amino acid building units and their incorporation in backbone cyclic disulfide and thioetheric bridged peptides. J Pept Res 2001; 58:527-39. [PMID: 12005422 DOI: 10.1034/j.1399-3011.2001.00936.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
General methods for the preparation of protected Nalpha(omega-thioalkyl) amino acids building units for backbone cyclization using reductive alkylation and on-resin preparation are described. The synthesis of non-Gly Fmoc-protected S-functionalized N-alkylated amino acids is based on the reaction of readily prepared protected omega-thio aldehyde with the appropriate amino acid. Preparation of Fmoc-protected S-functionalized N-alkylated Gly building units was carried out using two methods: reaction of glyoxylic acid with Acm-thioalkylamine and an on-resin reaction of bromoacetyl resin with Trt-thioalkylamines. Three model peptides were prepared using these building units. The GlyS2 building unit was incorporated into a backbone cyclic analog of somatostatin that contains a disulfide bridge. Formation of the disulfide bridge was performed by on-resin oxidation using 12 or Tl(CF3COO-)3. Both methods resulted in the desired product in a high degree of purity in the crude. The AspS3 building unit was also successfully incorporated into a model peptide. In addition, the in situ generation of sulfur containing Gly building units was demonstrated on a Substance P backbone cyclic analog containing a thioether bridge.
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Affiliation(s)
- S Gazal
- Department of Organic Chemistry, Hebrew University, Jerusalem, Israel
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