1
|
Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RDC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [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: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
Collapse
Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
| |
Collapse
|
2
|
Umaña E, Solano G, Zamora G, Tamayo-Castillo G. Costa Rican Propolis Chemical Compositions: Nemorosone Found to Be Present in an Exclusive Geographical Zone. Molecules 2023; 28:7081. [PMID: 37894560 PMCID: PMC10609476 DOI: 10.3390/molecules28207081] [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: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND The chemistry of Costa Rican propolis from Apis mellifera remains underexplored despite its potential applications. This study identified its chemical composition, linking chemotypes to antioxidant potential. METHODS Proton nuclear magnetic resonance (1H NMR) spectra were obtained for 119 propolis extracts and analyzed using multivariate analyses. In parallel, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay was used to assess antioxidant activity. A generalized linear regression model (GLM) correlated this with its chemical profiles and geographical origin. Chromatographic methods were used to isolate active and inactive compounds, which were identified using nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS). RESULTS Principal component analysis (PCA) revealed three chemical profile groups for the 119 propolis extracts, explaining 73% of the total variance with two components. Radical scavenging activity was found to correlate with chemical composition. Isolation yielded n-coniferyl benzoate in type I (EC50 = 190 µg/mL, ORAC = 0.60 µmol TE/µmol) and nemorosone in type II (EC50 = 300 µg/mL, ORAC = 0.7 µmol TE/µmol). Type III was represented in terpene-like components, which exhibited lower antioxidant activity. CONCLUSIONS This study categorizes Costa Rican propolis into three chemical types and identifies two key components linked to antioxidant activity. Notably, nemorosone, a valuable natural product, was found to be highly concentrated in a particular region of Costa Rica.
Collapse
Affiliation(s)
- Eduardo Umaña
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501, Costa Rica; (E.U.); (G.S.)
- Centro de Investigaciones Apícolas Tropicales (CINAT), Universidad Nacional, Heredia 3000, Costa Rica;
| | - Godofredo Solano
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501, Costa Rica; (E.U.); (G.S.)
| | - Gabriel Zamora
- Centro de Investigaciones Apícolas Tropicales (CINAT), Universidad Nacional, Heredia 3000, Costa Rica;
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501, Costa Rica; (E.U.); (G.S.)
- Escuela de Química, Universidad de Costa Rica, San José 11501, Costa Rica
| |
Collapse
|
3
|
Escudero-Leyva E, Quirós-Guerrero L, Vásquez-Chaves V, Pereira-Reyes R, Chaverri P, Tamayo-Castillo G. Differential Volatile Organic Compound Expression in the Interaction of Daldinia eschscholtzii and Mycena citricolor. ACS Omega 2023; 8:31373-31388. [PMID: 37663497 PMCID: PMC10468842 DOI: 10.1021/acsomega.3c03865] [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] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
Fungi exhibit a wide range of ecological guilds, but those that live within the inner tissues of plants (also known as endophytes) are particularly relevant due to the benefits they sometimes provide to their hosts, such as herbivory deterrence, disease protection, and growth promotion. Recently, endophytes have gained interest as potential biocontrol agents against crop pathogens, for example, coffee plants (Coffea arabica). Published results from research performed in our laboratory showed that endophytic fungi isolated from wild Rubiaceae plants were effective in reducing the effects of the American leaf spot of coffee (Mycena citricolor). One of these isolates (GU11N) from the plant Randia grandifolia was identified as Daldinia eschscholtzii (Xylariales). Its antagonism mechanisms, effects, and chemistry against M. citricolor were investigated by analyzing its volatile profile alone and in the presence of the pathogen in contactless and dual culture assays. The experimental design involved direct sampling of agar plugs in vials for headspace (HS) and headspace solid-phase microextraction (HS-SPME) gas chromatography-mass spectrometry (GC-MS) analysis. Additionally, we used ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS/MS) to identify nonvolatile compounds from organic extracts of the mycelia involved in the interaction. Results showed that more volatile compounds were identified using HS-SPME (39 components) than those by the HS technique (13 components), sharing only 12 compounds. Statistical tests suggest that D. eschscholtzii inhibited the growth of M. citricolor through the release of VOCs containing a combination of 1,8-dimethoxynapththalene and terpene compounds affecting M. citricolor pseudopilei. The damaging effects of 1,8-dimethoxynaphthalene were corroborated in an in vitro test against M. citricolor pseudopilei; scanning electron microscopy (SEM) photographs confirmed structural damage. After analyzing the UHPLC-HRMS/MS data, a predominance of fatty acid derivatives was found among the putatively identified compounds. However, a considerable proportion of features (37.3%) remained unannotated. In conclusion, our study suggests that D. eschscholtzii has potential as a biocontrol agent against M. citricolor and that 1,8-dimethoxynaphthalene contributes to the observed damage to the pathogen's reproductive structures.
Collapse
Affiliation(s)
- Efraín Escudero-Leyva
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
- Escuela
de Biología, Universidad de Costa
Rica, 11520-2060 San José, Costa Rica
| | - Luis Quirós-Guerrero
- Institute
of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland
- School
of Pharmaceutical Sciences, University of
Geneva, 1205 Geneva, Switzerland
| | - Víctor Vásquez-Chaves
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
| | - Reinaldo Pereira-Reyes
- Laboratorio
Nacional de Nanotecnología (LANOTEC), Centro Nacional de Alta Tecnología, 10109 San Jose, Costa Rica
| | - Priscila Chaverri
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
- Escuela
de Biología, Universidad de Costa
Rica, 11520-2060 San José, Costa Rica
- Department
of Natural Sciences, Bowie State University, Bowie, Maryland 20715, United States
| | - Giselle Tamayo-Castillo
- Centro
de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11520-2060 San José, Costa Rica
- Escuela
de Química, Universidad de Costa
Rica, 11520-2060 San José, Costa Rica
| |
Collapse
|
4
|
Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SLL, Barbera GL, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O’Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Res Sq 2023:rs.3.rs-3189768. [PMID: 37577622 PMCID: PMC10418563 DOI: 10.21203/rs.3.rs-3189768/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.
Collapse
Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paulo Wender P. Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Andres M. Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States
| | - Emily C. Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nicole E. Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mirte C. M. Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, 178 Montecasino Boulevard, Fourways, Johannesburg, Gauteng, 2191, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Private Bag X5050, Thohoyandou, Limpopo, 950, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paula C. Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Rua Carvalho de Mendonça, 144, Santos, SP, 11070-100, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 319 Life Sciences Building, University Park, PA, 16802, United States
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 320 Life Sciences Building, University Park, PA, 16802, United States
| | - Matthew F. Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Daniel Alvarado-Villalobos
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) & Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, 20715, United States
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Department of Biology, University of Fribourg, Chemin du Musée, 10, Fribourg, FR, 1700, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Josep Massana-Codina
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Berenike C. Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Daniel Petras
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Auf der Morgenstelle 24, Tuebingen, 72076, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, United States
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Cheongpa-ro 47 gil 100, Seoul, 04310, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- King’s College London, Strand, London, WC2R 2LS, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 110 Scripps Way, Jupiter, FL, 33458, United States
| | - Mariana Silva dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet B202, Lyngby, 2800, Denmark
| | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Technikerstr. 25, Innsbruck, 6020, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14,, Vienna, 1090, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02142, United States
| | - Ellis Charles O’Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Xueli Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, Singapore, 636921, Singapore
| | - Jerry J. Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Infectious Diseases Institute, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | | | - Hector H. F. Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, 1777 Carvalho Leal Avenue, Manaus, AM, 69065-001, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jason A. Clement
- Baruch S. Blumberg Institute, 3805 Old Easton Rd., Doylestown, PA, 18902, United States
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, United States
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Weniger Hall, room 341, Corvallis, OR, 97331, United States
| | - Sidnee E. Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, 1255 E 13th Ave, Basement, Eugene, OR, 97402, United States
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, CA, 92521, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| |
Collapse
|
5
|
Garlick JM, Sturlis SM, Bruno PA, Yates JA, Peiffer AL, Liu Y, Goo L, Bao L, De Salle SN, Tamayo-Castillo G, Brooks CL, Merajver SD, Mapp AK. Norstictic Acid Is a Selective Allosteric Transcriptional Regulator. J Am Chem Soc 2021; 143:9297-9302. [PMID: 34137598 DOI: 10.1021/jacs.1c03258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inhibitors of transcriptional protein-protein interactions (PPIs) have high value both as tools and for therapeutic applications. The PPI network mediated by the transcriptional coactivator Med25, for example, regulates stress-response and motility pathways, and dysregulation of the PPI networks contributes to oncogenesis and metastasis. The canonical transcription factor binding sites within Med25 are large (∼900 Å2) and have little topology, and thus, they do not present an array of attractive small-molecule binding sites for inhibitor discovery. Here we demonstrate that the depsidone natural product norstictic acid functions through an alternative binding site to block Med25-transcriptional activator PPIs in vitro and in cell culture. Norstictic acid targets a binding site comprising a highly dynamic loop flanking one canonical binding surface, and in doing so, it both orthosterically and allosterically alters Med25-driven transcription in a patient-derived model of triple-negative breast cancer. These results highlight the potential of Med25 as a therapeutic target as well as the inhibitor discovery opportunities presented by structurally dynamic loops within otherwise challenging proteins.
Collapse
Affiliation(s)
- Julie M Garlick
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steven M Sturlis
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul A Bruno
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joel A Yates
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Amanda L Peiffer
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yejun Liu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Laura Goo
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - LiWei Bao
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Samantha N De Salle
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sofia D Merajver
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
6
|
Matarrita-Carranza B, Murillo-Cruz C, Avendaño R, Ríos MI, Chavarría M, Gómez-Calvo ML, Tamayo-Castillo G, Araya JJ, Pinto-Tomás AA. Streptomyces sp. M54: an actinobacteria associated with a neotropical social wasp with high potential for antibiotic production. Antonie Van Leeuwenhoek 2021; 114:379-398. [PMID: 33587228 DOI: 10.1007/s10482-021-01520-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 11/28/2022]
Abstract
Streptomyces symbionts in insects have shown to be a valuable source of new antibiotics. Here, we report the genome sequence and the potential for antibiotic production of "Streptomyces sp. M54", an Actinobacteria associated with the eusocial wasp, Polybia plebeja. The Streptomyces sp. M54 genome is composed of a chromosome (7.96 Mb), and a plasmid (1.91 Kb) and harbors 30 biosynthetic gene clusters for secondary metabolites, of which only one third has been previously characterized. Growth inhibition bioassays show that this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans. Analyses through TLC-bioautography, LC-MS/MS and NMR allowed the identification of five macrocyclic ionophore antibiotics, with previously reported antibacterial, antitumor and antiviral properties. Phylogenetic analyses placed Streptomyces sp. M54 in a clade of other host-associated strains taxonomically related to Streptomyces griseus. Pangenomic and ANI analyses confirm the identity of one of its closest relatives as Streptomyces sp. LaPpAH-199, a strain isolated from an ant-plant symbiosis in Africa. In summary, our results suggest an insect-microbe association in distant geographic areas and showcase the potential of Streptomyces sp. M54 and related strains for the discovery of novel antibiotics.
Collapse
Affiliation(s)
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - María Isabel Ríos
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - María Luisa Gómez-Calvo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Juan J Araya
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.
| |
Collapse
|
7
|
Montoya-Arroyo A, Díaz C, Vaillant F, Tamayo-Castillo G. Oral administration of Costa Rican guava (Psidium friedrichsthalianum) juice induces changes in urinary excretion of energy-related compounds in Wistar rats determined by 1H NMR. NFS Journal 2020. [DOI: 10.1016/j.nfs.2020.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
8
|
Gómez-Rodríguez L, Schultz PJ, Tamayo-Castillo G, Dotson GD, Sherman DH, Tripathi A. Adipostatins E-J, New Potent Antimicrobials Identified as Inhibitors of Coenzyme-A Biosynthesis. Tetrahedron Lett 2019; 61. [PMID: 32863451 DOI: 10.1016/j.tetlet.2019.151469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 01/04/2023]
Abstract
Phosphopantetheine is a key structural element in biological acyl transfer reactions found embedded within coenzyme A (CoA). Phosphopantothenoylcysteine synthetase (PPCS) is responsible for installing a cysteamine group within phosphopantetheine. Therefore, it holds considerable potential as a drug target for developing new antimicrobials. In this study, we adapted a biochemical assay specific for bacterial PPCS to screen for inhibitors of CoA biosynthesis against a library of marine microbial derived natural product extracts (NPEs). Analysis of the NPE derived from Streptomyces blancoensis led to the isolation of novel antibiotics (10-12, and 14) from the adipostatin class of molecules. The most potent molecule (10) displayed in vitro activity with IC50= 0.93 μM, against S. pneumoniae PPCS. The whole cell antimicrobial assay against isolated molecules demonstrated their ability to penetrate bacterial cells and inhibit clinically relevant pathogenic strains. This establishes the validity of PPCS as a pertinent drug target, and the value of NPEs to provide new antibiotics.
Collapse
Affiliation(s)
- Lyanne Gómez-Rodríguez
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Pamela J Schultz
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Giselle Tamayo-Castillo
- Escuela de Química & CIPRONA, Universidad de Costa Rica, 2060 San Pedro de Costa Rica & INBio, Santo Domingo de Heredia, Heredia, Costa Rica
| | - Garry D Dotson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - David H Sherman
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ashootosh Tripathi
- UM Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
9
|
Quirós-Guerrero L, Albertazzi F, Araya-Valverde E, Romero RM, Villalobos H, Poveda L, Chavarría M, Tamayo-Castillo G. Phenolic variation among Chamaecrista nictitans subspecies and varieties revealed through UPLC-ESI(-)-MS/MS chemical fingerprinting. Metabolomics 2019; 15:14. [PMID: 30830463 DOI: 10.1007/s11306-019-1475-8] [Citation(s) in RCA: 4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Comparative analysis of metabolic features of plants has a high potential for determination of quality control of active ingredients, ecological or chemotaxonomic purposes. Specifically, the development of efficient and rapid analytical tools that allow the differentiation among species, subspecies and varieties of plants is a relevant issue. Here we describe a multivariate model based on LC-MS/MS fingerprinting capable of discriminating between subspecies and varieties of the medicinal plant Chamaecrista nictitans, a rare distributed species in Costa Rica. METHODS Determination of the chemical fingerprint was carried out on a LC-MS (ESI-QTOF) in negative ionization mode, main detected and putatively identified compounds included proanthocyanidin oligomers, several flavonoid C- and O-glycosides, and flavonoid acetates. Principal component analysis (PCA), partial least square-discriminant analysis (PLS-DA) and cluster analysis of chemical profiles were performed. RESULTS Our method showed a clear discrimination between the subspecies and varieties of Chamaecrista nictitans, separating the samples into four fair differentiated groups: M1 = C. nictitans ssp. patellaria; M2 = C. nictitans ssp. disadena; M3 = C. nictitans ssp. nictitans var. jaliscensis and M4 = C. nictitans ssp. disadena var. pilosa. LC-MS/MS fingerprint data was validated using both morphological characters and DNA barcoding with ITS2 region. The comparison of the morphological characters against the chemical profiles and DNA barcoding shows a 63% coincidence, evidencing the morphological similarity in C. nictitans. On the other hand, genetic data and chemical profiles grouped all samples in a similar pattern, validating the functionality of our metabolomic approach. CONCLUSION The metabolomic method described in this study allows a reliably differentiation between subspecies and varieties of C. nictitans using a straightforward protocol that lacks extensive purification steps.
Collapse
Affiliation(s)
- Luis Quirós-Guerrero
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
| | - Federico Albertazzi
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
| | - Emanuel Araya-Valverde
- Centro Nacional de Innovaciones Biotecnológicas (CENiBiot), CeNAT-CONARE, San Jose, 1174-1200, Costa Rica
- Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, 159-7050, Costa Rica
| | - Rosaura M Romero
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
| | - Heidy Villalobos
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
| | - Luis Poveda
- Herbario Juvenal Valerio Rodríguez, Universidad Nacional, Heredia, Costa Rica
| | - Max Chavarría
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
- Centro Nacional de Innovaciones Biotecnológicas (CENiBiot), CeNAT-CONARE, San Jose, 1174-1200, Costa Rica
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica.
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica.
| |
Collapse
|
10
|
Mike LA, Tripathi A, Blankenship CM, Saluk A, Schultz PJ, Tamayo-Castillo G, Sherman DH, Mobley HLT. Discovery of nicoyamycin A, an inhibitor of uropathogenic Escherichia coli growth in low iron environments. Chem Commun (Camb) 2018; 53:12778-12781. [PMID: 29139494 DOI: 10.1039/c7cc07732g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
High-throughput screening and activity-guided purification identified nicoyamycin A, a natural product comprised of an uncommon 3-methyl-1,4-dioxane ring incorporated into a desferrioxamine-like backbone via a spiroaminal linkage. Nicoyamycin A potently inhibits uropathogenic Escherichia coli growth in low iron medium, a promising step toward developing novel antibiotics to treat recalcitrant bacterial infections.
Collapse
Affiliation(s)
- Laura A Mike
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Lee S, Tamayo-Castillo G, Pang C, Clardy J, Cao S, Kim KH. Diketopiperazines from Costa Rican endolichenic fungus Colpoma sp. CR1465A. Bioorg Med Chem Lett 2016; 26:2438-2441. [PMID: 27080179 DOI: 10.1016/j.bmcl.2016.03.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 02/12/2016] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 11/16/2022]
Abstract
Three new diketopiperazines (1-3), cyclo(l-Pro-d-trans-Hyp) (1), cyclo(l-Pro-d-Glu) (2), and cyclo(d-Pro-d-Glu) (3) and five known diketopiperazines (4-8) were isolated from the endolichenic fungus Colpoma sp. CR1465A identified from the Costa Rican plant Henriettea tuberculosa (Melatomataceae). The structures of the new compounds 1-3 were elucidated using a combination of extensive spectroscopic analyses, including 2D NMR and HR-MS, and their absolute configurations were determined by a combination of NOESY analysis and Marfey's method. Cyclo(l-Pro-d-allo-Thr) (4) was recently isolated from a South China Sea marine sponge Callyspongia sp., but its NMR spectroscopic data were not reported, and cyclo(l-Pro-l-Asp) (5) was previously reported but only as a synthetic product. The NMR data assignments of compounds 4 and 5 are reported for the first time. All of the isolated compounds were tested for antifungal and antimicrobial properties.
Collapse
Affiliation(s)
- Seulah Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, 440-746, Republic of Korea
| | - Giselle Tamayo-Castillo
- Unidad Estratégica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Costa Rica & CIPRONA-Escuela de Química, Universidad de Costa Rica, 2060 San Pedro, Costa Rica
| | - Changhyun Pang
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 440-746, Republic of Korea
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K Inouye College of Pharmacy, University of Hawaii at Hilo, 924 Stainback Hwy, Hilo, HI 96720, USA.
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, 440-746, Republic of Korea.
| |
Collapse
|
12
|
Sidhu A, Miller JR, Tripathi A, Garshott DM, Brownell AL, Chiego DJ, Arevang C, Zeng Q, Jackson LC, Bechler SA, Callaghan MU, Yoo GH, Sethi S, Lin HS, Callaghan JH, Tamayo-Castillo G, Sherman DH, Kaufman RJ, Fribley AM. Borrelidin Induces the Unfolded Protein Response in Oral Cancer Cells and Chop-Dependent Apoptosis. ACS Med Chem Lett 2015; 6:1122-7. [PMID: 26617965 DOI: 10.1021/acsmedchemlett.5b00133] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 03/31/2015] [Accepted: 09/08/2015] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common cancer affecting the oral cavity, and US clinics will register about 30,000 new patients in 2015. Current treatment modalities include chemotherapy, surgery, and radiotherapy, which often result in astonishing disfigurement. Cancers of the head and neck display enhanced levels of glucose-regulated proteins and translation initiation factors associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Previous work demonstrated that chemically enforced UPR could overwhelm these adaptive features and selectively kill malignant cells. The threonyl-tRNA synthetase (ThRS) inhibitor borrelidin and two congeners were discovered in a cell-based chemical genomic screen. Borrelidin increased XBP1 splicing and led to accumulation of phosphorylated eIF2α and UPR-associated genes, prior to death in panel of OSCC cells. Murine embryonic fibroblasts (MEFs) null for GCN2 and PERK were less able to accumulate UPR markers and were resistant to borrelidin. This study demonstrates that UPR induction is a feature of ThRS inhibition and adds to a growing body of literature suggesting ThRS inhibitors might selectively target cancer cells.
Collapse
Affiliation(s)
- Alpa Sidhu
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Justin R. Miller
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Ashootosh Tripathi
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Danielle M. Garshott
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Amy L. Brownell
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Daniel J. Chiego
- Cariology,
Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, Michigan 48109, United States
| | - Carl Arevang
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Qinghua Zeng
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Leah C. Jackson
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Shelby A. Bechler
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Michael U. Callaghan
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - George H. Yoo
- Department
of Otolaryngology, Wayne State University and Karmanos Cancer Institute, Detroit, Michigan 48201, United States
| | - Seema Sethi
- Department
of Pathology, Wayne State University and Karmanos Cancer Institute, Detroit, Michigan 48201, United States
| | - Ho-Sheng Lin
- Department
of Otolaryngology, Wayne State University and Karmanos Cancer Institute, Detroit, Michigan 48201, United States
| | - Joseph H. Callaghan
- School of
Business Administration, Oakland University, Rochester, Michigan 48309, United States
| | - Giselle Tamayo-Castillo
- Instituto
Nacional de Biodiversidad, CIPRONA-Escuela de Química, Universidad de Costa Rica, 3100 Heredia, Costa Rica
| | - David H. Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Randal J. Kaufman
- Degenerative Disease Research Program,
Center for Cancer Research, Sanford
- Burnham Medical Research Institute, La
Jolla, California 92037, United States
| | - Andrew M. Fribley
- Carmen
and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
- Department
of Otolaryngology, Wayne State University and Karmanos Cancer Institute, Detroit, Michigan 48201, United States
- Developmental Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
| |
Collapse
|
13
|
Cheng KCC, Cao S, Raveh A, MacArthur R, Dranchak P, Chlipala G, Okoneski MT, Guha R, Eastman RT, Yuan J, Schultz PJ, Su XZ, Tamayo-Castillo G, Matainaho T, Clardy J, Sherman DH, Inglese J. Actinoramide A Identified as a Potent Antimalarial from Titration-Based Screening of Marine Natural Product Extracts. J Nat Prod 2015; 78:2411-2422. [PMID: 26465675 PMCID: PMC4633019 DOI: 10.1021/acs.jnatprod.5b00489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Methods to identify the bioactive diversity within natural product extracts (NPEs) continue to evolve. NPEs constitute complex mixtures of chemical substances varying in structure, composition, and abundance. NPEs can therefore be challenging to evaluate efficiently with high-throughput screening approaches designed to test pure substances. Here we facilitate the rapid identification and prioritization of antimalarial NPEs using a pharmacologically driven, quantitative high-throughput-screening (qHTS) paradigm. In qHTS each NPE is tested across a concentration range from which sigmoidal response, efficacy, and apparent EC50s can be used to rank order NPEs for subsequent organism reculture, extraction, and fractionation. Using an NPE library derived from diverse marine microorganisms we observed potent antimalarial activity from two Streptomyces sp. extracts identified from thousands tested using qHTS. Seven compounds were isolated from two phylogenetically related Streptomyces species: Streptomyces ballenaensis collected from Costa Rica and Streptomyces bangulaensis collected from Papua New Guinea. Among them we identified actinoramides A and B, belonging to the unusually elaborated nonproteinogenic amino-acid-containing tetrapeptide series of natural products. In addition, we characterized a series of new compounds, including an artifact, 25-epi-actinoramide A, and actinoramides D, E, and F, which are closely related biosynthetic congeners of the previously reported metabolites.
Collapse
Affiliation(s)
- Ken Chih-Chien Cheng
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI 96720, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, C-643, Boston, Massachusetts 021151, USA
| | - Avi Raveh
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ryan MacArthur
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Patricia Dranchak
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - George Chlipala
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Matthew T. Okoneski
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Rajarshi Guha
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Richard T. Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Jing Yuan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Costa Rica & CIPRONA-Escuela de Química, Universidad de Costa Rica, 2060 San Pedro, Costa Rica
| | - Teatulohi Matainaho
- School of Medicine and Health Sciences, University of Papua New Guinea, Boroko, Papua New Guinea
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, C-643, Boston, Massachusetts 021151, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - James Inglese
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| |
Collapse
|
14
|
Cruz PG, Fribley AM, Miller JR, Larsen MJ, Schultz PJ, Jacob RT, Tamayo-Castillo G, Kaufman RJ, Sherman DH. Novel Lobophorins Inhibit Oral Cancer Cell Growth and Induce Atf4- and Chop-Dependent Cell Death in Murine Fibroblasts. ACS Med Chem Lett 2015; 6:877-81. [PMID: 26288688 DOI: 10.1021/acsmedchemlett.5b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 03/24/2015] [Accepted: 07/06/2015] [Indexed: 12/15/2022] Open
Abstract
As part of the International Cooperative Biodiversity Groups (ICBG) Program, we were interested in identifying biologically active unfolded protein response (UPR) inducing compounds from marine microorganisms isolated from Costa Rican biota. With this aim in mind we have now generated more than 33,000 unique prefractionated natural product extracts from marine and terrestrial organisms that have been submitted to the Center of Chemical Genomics (CCG) at the University of Michigan for high throughput screening (HTS). An effective complementary cell-based assay to identify novel modulators of UPR signaling was used for screening extracts. Active fractions were iteratively subjected to reverse-phase HPLC chromatographic analysis, and together with lobophorin A, B, E, and F (1-4), three new lobophorin congeners, designated as CR1 (5), CR2 (6), and CR3 (7) were isolated. Herein, we report that secondary assays revealed that the new lobophorins induced UPR-associated gene expression, inhibited oral squamous cell carcinoma cell growth, and led to UPR-dependent cell death in murine embryonic fibroblast (MEF) cells.
Collapse
Affiliation(s)
- Patricia G. Cruz
- Center for Chemical Genomics, Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| | - Andrew M. Fribley
- Carmen
and Ann Adams Department of Pediatrics, Division of Hematology and
Oncology, and the Karmanos Cancer Institute Molecular Therapeutics
Program, Wayne State University, 2228 Elliman Building, 421 East
Canfield, Detroit, Michigan 48201, United States
| | - Justin R. Miller
- Carmen
and Ann Adams Department of Pediatrics, Division of Hematology and
Oncology, and the Karmanos Cancer Institute Molecular Therapeutics
Program, Wayne State University, 2228 Elliman Building, 421 East
Canfield, Detroit, Michigan 48201, United States
| | - Martha J. Larsen
- Center for Chemical Genomics, Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| | - Pamela J. Schultz
- Center for Chemical Genomics, Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| | - Renju T. Jacob
- Center for Chemical Genomics, Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| | - Giselle Tamayo-Castillo
- Instituto Nacional de Biodiversidad (INBio), Heredia, Costa Rica & CIPRONA-Escuela de Química, Universidad de Costa Rica (UCR), 2061-San José, Costa Rica
| | - Randal J. Kaufman
- Degenerative
Disease Research Program, Center for Cancer Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - David H. Sherman
- Center for Chemical Genomics, Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| |
Collapse
|
15
|
Delekta PC, Raveh A, Larsen MJ, Schultz PJ, Tamayo-Castillo G, Sherman DH, Miller DJ. The combined use of alphavirus replicons and pseudoinfectious particles for the discovery of antivirals derived from natural products. ACTA ACUST UNITED AC 2014; 20:673-80. [PMID: 25550354 DOI: 10.1177/1087057114564868] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 08/19/2014] [Accepted: 11/28/2014] [Indexed: 11/15/2022]
Abstract
Alphaviruses are a prominent class of reemergent pathogens due to their globally expanding ranges, potential for lethality, and possible use as bioweapons. The absence of effective treatments for alphaviruses highlights the need for innovative strategies to identify antiviral agents. Primary screens that use noninfectious self-replicating RNAs, termed replicons, have been used to identify potential antiviral compounds for alphaviruses. Only inhibitors of viral genome replication, however, will be identified using replicons, which excludes many other druggable steps in the viral life cycle. To address this limitation, we developed a western equine encephalitis virus pseudoinfectious particle system that reproduces several crucial viral life cycle steps in addition to genome replication. We used this system to screen a library containing ~26,000 extracts derived from marine microbes, and we identified multiple bacterial strains that produce compounds with potential antiviral activity. We subsequently used pseudoinfectious particle and replicon assays in parallel to counterscreen candidate extracts, and followed antiviral activity during biochemical fractionation and purification to differentiate between inhibitors of viral entry and genome replication. This novel process led to the isolation of a known alphavirus entry inhibitor, bafilomycin, thereby validating the approach for the screening and identification of potential antiviral compounds.
Collapse
Affiliation(s)
- Phillip C Delekta
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Avi Raveh
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Martha J Larsen
- Center for Chemical Genomics, University of Michigan, Ann Arbor, MI, USA
| | - Pamela J Schultz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | | | - David H Sherman
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA Department of Chemistry and Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - David J Miller
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
16
|
Kim KH, Beemelmanns C, Murillo C, Guillén A, Umaña L, Tamayo-Castillo G, Kim SN, Clardy J, Cao S. Naphthalenones and Isocoumarins from a Costa Rican Fungus Xylariaceae sp. CR1546C. Journal of Chemical Research 2014. [DOI: 10.3184/174751914x14175406270662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new naphthalenone, ( R)-4,6,8-trihydroxy-3,4-dihydro-1(2 H)-naphthalenone and a new isocoumarin, 6,8-dihydroxy-(3 R)-(2-oxopropyl)-3,4-dihydroisocoumarin, together with eight related known compounds were isolated from the endolichenic fungal species, CR1546C from Costa Rican lichen Sticta fuliginosa (Lobariaceae). Their structures were elucidated by spectroscopic methods, including extensive 1D- and 2D-NMR techniques and chemical methods. All of the isolated compounds exhibited moderate antifungal activity against the yeast Candida albicans.
Collapse
Affiliation(s)
- Ki Hyun Kim
- Natural Product Research Laboratory, School of Pharmacy, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Catalina Murillo
- Unidad Estratégica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Costa Rica
| | - Anny Guillén
- Unidad Estratégica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Costa Rica
| | - Loengrin Umaña
- Unidad Estratégica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Costa Rica
| | - Giselle Tamayo-Castillo
- Unidad Estratégica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Costa Rica
- Escuela de Química, & CIPRONA Universidad de Costa Rica, San José, Costa Rica
| | - Su-Nam Kim
- Natural Products Research Center, KIST Gangneung Institute, Gangneung 210-340, Republic of Korea
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shugeng Cao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Natural Products & Experimental Therapeutics, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawaii, 96813, USA
| |
Collapse
|
17
|
Raveh A, Schultz PJ, Aschermann L, Carpenter C, Tamayo-Castillo G, Cao S, Clardy J, Neubig RR, Sherman DH, Sjögren B. Identification of protein kinase C activation as a novel mechanism for RGS2 protein upregulation through phenotypic screening of natural product extracts. Mol Pharmacol 2014; 86:406-16. [PMID: 25086086 DOI: 10.1124/mol.114.092403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Biochemical high-throughput screening is widely used in drug discovery, using a variety of small molecule libraries. However, broader screening strategies may be more beneficial to identify novel biologic mechanisms. In the current study we used a β-galactosidase complementation method to screen a selection of microbial-derived pre-fractionated natural product extracts for those that increase regulator of G protein signaling 2 (RGS2) protein levels. RGS2 is a member of a large family of proteins that all regulate signaling through G protein-coupled receptors (GPCRs) by accelerating GTPase activity on active Gα as well as through other mechanisms. RGS2(-/-) mice are hypertensive, show increased anxiety, and are prone to heart failure. RGS2 has a very short protein half-life due to rapid proteasomal degradation, and we propose that enhancement of RGS2 protein levels could be a beneficial therapeutic strategy. Bioassay-guided fractionation of one of the hit strains yielded a pure compound, Indolactam V, a known protein kinase C (PKC) activator, which selectively increased RGS2 protein levels in a time- and concentration-dependent manner. Similar results were obtained with phorbol 12-myristate 13-acetate as well as activation of the Gq-coupled muscarinic M3 receptor. The effect on RGS2 protein levels was blocked by the nonselective PKC inhibitor Gö6983 (3-[1-[3-(dimethylamino)propyl]-5-methoxy-1H-indol-3-yl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione), the PKCβ-selective inhibitor Ruboxastaurin, as well as small interfering RNA-mediated knockdown of PKCβ. Indolactam V-mediated increases in RGS2 protein levels also had functional effects on GPCR signaling. This study provides important proof-of-concept for our screening strategy and could define a negative feedback mechanism in Gq/Phospholipase C signaling through RGS2 protein upregulation.
Collapse
Affiliation(s)
- Avi Raveh
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Pamela J Schultz
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Lauren Aschermann
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Colleen Carpenter
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Giselle Tamayo-Castillo
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Shugeng Cao
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Jon Clardy
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Richard R Neubig
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| | - Benita Sjögren
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan (A.R., P.J.S., D.H.S.); Department of Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan (L.A., R.R.N., B.S.); Department of Pharmacology (C.C.), Department of Medicinal Chemistry (D.H.S.), Department of Microbiology and Immunology (D.H.S.), Department of Chemistry (D.H.S.), Center for Chemical Genomics, University of Michigan, Ann Arbor, Michigan (D.H.S.); Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica (G.T-C.); Harvard Medical School, Boston, Massachusetts (S.C., J.C.); and University of Hawaii Cancer Center, Honolulu, Hawaii (S.C.)
| |
Collapse
|
18
|
Tripathi A, Schofield MM, Chlipala GE, Schultz PJ, Yim I, Newmister SA, Nusca TD, Scaglione JB, Hanna PC, Tamayo-Castillo G, Sherman DH. Correction to “Baulamycins A and B, Broad-Spectrum Antibiotics Identified as Inhibitors of Siderophore Biosynthesis in Staphylococcus aureus and Bacillus anthracis”. J Am Chem Soc 2014. [PMCID: PMC4353028 DOI: 10.1021/ja505297x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
19
|
Tripathi A, Schofield MM, Chlipala GE, Schultz PJ, Yim I, Newmister SA, Nusca TD, Scaglione JB, Hanna PC, Tamayo-Castillo G, Sherman DH. Baulamycins A and B, broad-spectrum antibiotics identified as inhibitors of siderophore biosynthesis in Staphylococcus aureus and Bacillus anthracis. J Am Chem Soc 2014; 136:1579-86. [PMID: 24401083 PMCID: PMC4028973 DOI: 10.1021/ja4115924] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [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] [Indexed: 11/29/2022]
Abstract
Siderophores are high-affinity iron chelators produced by microorganisms and frequently contribute to the virulence of human pathogens. Targeted inhibition of the biosynthesis of siderophores staphyloferrin B of Staphylococcus aureus and petrobactin of Bacillus anthracis hold considerable potential as a single or combined treatment for methicillin-resistant S. aureus (MRSA) and anthrax infection, respectively. The biosynthetic pathways for both siderophores involve a nonribosomal peptide synthetase independent siderophore (NIS) synthetase, including SbnE in staphyloferrin B and AsbA in petrobactin. In this study, we developed a biochemical assay specific for NIS synthetases to screen for inhibitors of SbnE and AsbA against a library of marine microbial-derived natural product extracts (NPEs). Analysis of the NPE derived from Streptomyces tempisquensis led to the isolation of the novel antibiotics baulamycins A (BmcA, 6) and B (BmcB, 7). BmcA and BmcB displayed in vitro activity with IC50 values of 4.8 μM and 19 μM against SbnE and 180 μM and 200 μM against AsbA, respectively. Kinetic analysis showed that the compounds function as reversible competitive enzyme inhibitors. Liquid culture studies with S. aureus , B. anthracis , E. coli , and several other bacterial pathogens demonstrated the capacity of these natural products to penetrate bacterial barriers and inhibit growth of both Gram-positive and Gram-negative species. These studies provide proof-of-concept that natural product inhibitors targeting siderophore virulence factors can provide access to novel broad-spectrum antibiotics, which may serve as important leads for the development of potent anti-infective agents.
Collapse
Affiliation(s)
- Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Michael M. Schofield
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - George E. Chlipala
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Isaiah Yim
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Sean A. Newmister
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Tyler D. Nusca
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Jamie B. Scaglione
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Philip C. Hanna
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, 2060 San Pedro, Costa Rica
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
- Departments of Medicinal Chemistry and Chemistry, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
20
|
Tamayo-Castillo G, Vásquez V, Ríos MI, Rodríguez MV, Solano G, Zacchino S, Gupta MP. Isolation of major components from the roots of Godmania aesculifolia and determination of their antifungal activities. Planta Med 2013; 79:1749-1755. [PMID: 24356871 DOI: 10.1055/s-0033-1351025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
From the methanol root extract of Godmania aesculifolia, a species selected in a multinational OAS program aimed at discovering antifungal compounds from Latin American plants, a new chavicol diglycoside (1), the known 3,4-dihydroxy-2-(3-methylbut-2-en-1-yl)-3,4-dihydronaphthalen-1(2H)-one (2), and lapachol (3) were isolated and characterized by 1D and 2D NMR and MS techniques. Only 3 exhibited fairly good activity against a panel of clinical isolates of Cryptococcus neoformans (MIC50 between 7.8 and 31.2 µg/mL) and moderate activities against Candida spp. and non-albicans Candida spp.
Collapse
Affiliation(s)
- Giselle Tamayo-Castillo
- Unidad Estratégica de Acción de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Heredia, Costa Rica
| | - Víctor Vásquez
- Unidad Estratégica de Acción de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Heredia, Costa Rica
| | - María Isabel Ríos
- Unidad Estratégica de Acción de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Heredia, Costa Rica
| | - María Victoria Rodríguez
- Farmacognosia y Biología Vegetal, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional Rosario, Rosario, Argentina
| | - Godofredo Solano
- Unidad Estratégica de Acción de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Heredia, Costa Rica
| | - Susana Zacchino
- Farmacognosia y Biología Vegetal, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional Rosario, Rosario, Argentina
| | - Mahabir P Gupta
- Centro de Investigaciones Farmacognósticas de la Flora Panameña, CIFLORPAN, Universidad de Panamá, Panamá, Panamá
| |
Collapse
|
21
|
Cheng B, Cao S, Vasquez V, Annamalai T, Tamayo-Castillo G, Clardy J, Tse-Dinh YC. Identification of anziaic acid, a lichen depside from Hypotrachyna sp., as a new topoisomerase poison inhibitor. PLoS One 2013; 8:e60770. [PMID: 23593306 PMCID: PMC3620467 DOI: 10.1371/journal.pone.0060770] [Citation(s) in RCA: 31] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/02/2013] [Indexed: 11/18/2022] Open
Abstract
Topoisomerase inhibitors are effective for antibacterial and anticancer therapy because they can lead to the accumulation of the intermediate DNA cleavage complex formed by the topoisomerase enzymes, which trigger cell death. Here we report the application of a novel enzyme-based high-throughput screening assay to identify natural product extracts that can lead to increased accumulation of the DNA cleavage complex formed by recombinant Yersinia pestis topoisomerase I as part of a larger effort to identify new antibacterial compounds. Further characterization and fractionation of the screening positives from the primary assay led to the discovery of a depside, anziaic acid, from the lichen Hypotrachyna sp. as an inhibitor for both Y. pestis and Escherichia coli topoisomerase I. In in vitro assays, anziaic acid exhibits antibacterial activity against Bacillus subtilis and a membrane permeable strain of E. coli. Anziaic acid was also found to act as an inhibitor of human topoisomerase II but had little effect on human topoisomerase I. This is the first report of a depside with activity as a topoisomerase poison inhibitor and demonstrates the potential of this class of natural products as a source for new antibacterial and anticancer compounds.
Collapse
Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Shugeng Cao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Victor Vasquez
- Unidad Estrategica de Bioprospeccion, Instituto Nacional de Biodiversidad (INBio) and Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Thirunavukkarasu Annamalai
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospeccion, Instituto Nacional de Biodiversidad (INBio) and Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yuk-Ching Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- * E-mail:
| |
Collapse
|
22
|
Majmudar CY, Højfeldt JW, Arevang CJ, Pomerantz WC, Gagnon JK, Schultz PJ, Cesa LC, Doss CH, Rowe SP, Vásquez V, Tamayo-Castillo G, Cierpicki T, Brooks CL, Sherman DH, Mapp AK. Sekikaic Acid and Lobaric Acid Target a Dynamic Interface of the Coactivator CBP/p300. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206815] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
23
|
Majmudar CY, Højfeldt JW, Arevang CJ, Pomerantz WC, Gagnon JK, Schultz PJ, Cesa LC, Doss CH, Rowe SP, Vásquez V, Tamayo-Castillo G, Cierpicki T, Brooks CL, Sherman DH, Mapp AK. Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300. Angew Chem Int Ed Engl 2012; 51:11258-62. [PMID: 23042634 DOI: 10.1002/anie.201206815] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Indexed: 12/25/2022]
Abstract
Capturing a coactivator, naturally: the natural products sekikaic acid and lobaric acid, isolated after a high-throughput screen of a structurally diverse extract collection, effectively target the dynamic binding interfaces of the GACKIX domain of the coactivator CBP/p300. These molecules are the most effective inhibitors of the GACKIX domain yet described and are uniquely selective for this domain.
Collapse
|
24
|
Cruz PG, Auld DS, Schultz PJ, Lovell S, Battaile KP, MacArthur R, Shen M, Tamayo-Castillo G, Inglese J, Sherman DH. Titration-based screening for evaluation of natural product extracts: identification of an aspulvinone family of luciferase inhibitors. ACTA ACUST UNITED AC 2012; 18:1442-52. [PMID: 22118678 DOI: 10.1016/j.chembiol.2011.08.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/18/2011] [Accepted: 08/09/2011] [Indexed: 10/15/2022]
Abstract
The chemical diversity of nature has tremendous potential for the discovery of molecular probes and medicinal agents. However, sensitivity of HTS assays to interfering components of crude extracts derived from plants, and macro- and microorganisms has curtailed their use in lead discovery. Here, we describe a process for leveraging the concentration-response curves obtained from quantitative HTS to improve the initial selection of "actives" from a library of partially fractionated natural product extracts derived from marine actinomycetes and fungi. By using pharmacological activity, the first-pass CRC paradigm improves the probability that labor-intensive subsequent steps of reculturing, extraction, and bioassay-guided isolation of active component(s) target the most promising strains and growth conditions. We illustrate how this process identified a family of fungal metabolites as potent inhibitors of firefly luciferase, subsequently resolved in molecular detail by X-ray crystallography.
Collapse
Affiliation(s)
- Patricia G Cruz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Fribley AM, Cruz PG, Miller JR, Callaghan MU, Cai P, Narula N, Neubig RR, Showalter HD, Larsen SD, Kirchhoff PD, Larsen MJ, Burr DA, Schultz PJ, Jacobs RR, Tamayo-Castillo G, Ron D, Sherman DH, Kaufman RJ. Complementary cell-based high-throughput screens identify novel modulators of the unfolded protein response. ACTA ACUST UNITED AC 2011; 16:825-35. [PMID: 21844328 DOI: 10.1177/1087057111414893] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Despite advances toward understanding the prevention and treatment of many cancers, patients who suffer from oral squamous cell carcinoma (OSCC) confront a survival rate that has remained unimproved for more than 2 decades, indicating our ability to treat them pharmacologically has reached a plateau. In an ongoing effort to improve the clinical outlook for this disease, we previously reported that an essential component of the mechanism by which the proteasome inhibitor bortezomib (PS-341, Velcade) induced apoptosis in OSCC required the activation of a terminal unfolded protein response (UPR). Predicated on these studies, the authors hypothesized that high-throughput screening (HTS) of large diverse chemical libraries might identify more potent or selective small-molecule activators of the apoptotic arm of the UPR to control or kill OSCC. They have developed complementary cell-based assays using stably transfected CHO-K1 cell lines that individually assess the PERK/eIF2α/CHOP (apoptotic) or the IRE1/XBP1 (adaptive) UPR subpathways. An 66 K compound collection was screened at the University of Michigan Center for Chemical Genomics that included a unique library of prefractionated natural product extracts. The mycotoxin methoxycitrinin was isolated from a natural extract and found to selectively activate the CHOP-luciferase reporter at 80 µM. A series of citrinin derivatives was isolated from these extracts, including a unique congener that has not been previously described. In an effort to identify more potent compounds, the authors examined the ability of citrinin and the structurally related mycotoxins ochratoxin A and patulin to activate the UPR. Strikingly, it was found that patulin at 2.5 to 10 µM induced a terminal UPR in a panel of OSCC cells that was characterized by an increase in CHOP, GADD34, and ATF3 gene expression and XBP1 splicing. A luminescent caspase assay and the induction of several BH3-only genes indicated that patulin could induce apoptosis in OSCC cells. These data support the use of this complementary HTS strategy to identify novel modulators of UPR signaling and tumor cell death.
Collapse
Affiliation(s)
- Andrew M Fribley
- Carmen and Ann Adams Department of Pediatrics, Division of Hematology/Oncology, Wayne State University, 421 E. Canfield, Detroit, MI 48201, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Solano G, Rojas-Jiménez K, Jaspars M, Tamayo-Castillo G. Study of the diversity of culturable actinomycetes in the North Pacific and Caribbean coasts of Costa Rica. Antonie Van Leeuwenhoek 2009; 96:71-8. [PMID: 19365710 DOI: 10.1007/s10482-009-9337-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 03/25/2009] [Indexed: 11/30/2022]
Abstract
In this study, 137 actinomycetes were isolated from subtidal marine sediments in the North Pacific and Caribbean coasts of Costa Rica. Bioinformatics analysis of the 16S rRNA gene sequences assigned the isolates to 15 families and 21 genera. Streptomyces was the dominant genus while the remaining 20 genera were poorly represented. Nearly 70% of the phylotypes presented a coastal-restricted distribution whereas the other 30% were common inhabitants of both shores. The coastal tropical waters of Costa Rica showed a high diversity of actinomycetes, both in terms of the number of species and phylogenetic composition, although significant differences were observed between and within shores. The observed pattern of species distribution might be the result of several factors including the characteristics of the ecosystems, presence of endemic species and the influence of terrestrial runoff.
Collapse
|
27
|
Chinchilla-Carmona M, Guerrero Bermúdez OM, Tamayo-Castillo G, Appel AS, Jiménez-Somarribas A, Valerio-Campos I. [Natural concentration of antimalaric components in Tropical arthropods (in vitro)]. REV BIOL TROP 2008; 56:473-485. [PMID: 19256421] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Alcohol, hexane and dichlorometane extracts of 751 samples of Costa Rican arthropods were studied for the presence of antimalaric components. With Plasmodium berghei we set an in vitro model in which the effect of the extract was determined by staining of the parasites with cresil brilliant blue. Active extracts at concentration of 50 mg or less, were considered positive. Promissory extracts were found in the orders Lepidoptera (24.1%), Coleoptera (32.8%), Hemiptera (38.5%) and Polydesmida (81.3%). Since most of the Lepidoptera samples were in the immature stages, the relation with the host plant was analyzed. Cannaceae, Flacourtiaceae, Crisobalanaceae, Lauraceae, Fagaceae, Ulmaceae, Rosaceae, Asteraceae, Rubiaceae, Lauraceae and Caprifoliaceae were related with the Lepidoptera larvae, and an antimalaric effect has been reported in most of these families. In the orders Polydesmida, Opiliones and Blattodea, the extract from adults also had some important effect, probably because all of them fed on plants. Polydesmida and Opiliones have chemical substances that probably serve as defensive purposes; these chemicals could also have some antiparasitic effect. Therefore, the detection of antimalaric components in arthropod species led to the identification of plants with promissory antimalaric components.
Collapse
Affiliation(s)
- Misael Chinchilla-Carmona
- Centro de Investigación en Enfermedades Tropicales, Departamento de Parasitologia, Facultad de Microbiologia, Universidad de Costa Rica 2060 San José, Costa Rica.
| | | | | | | | | | | |
Collapse
|
28
|
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007; 5:e77. [PMID: 17355176 PMCID: PMC1821060 DOI: 10.1371/journal.pbio.0050077] [Citation(s) in RCA: 1304] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 01/16/2007] [Indexed: 11/19/2022] Open
Abstract
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS. Marine microbes remain elusive and mysterious, even though they are the most abundant life form in the ocean, form the base of the marine food web, and drive energy and nutrient cycling. We know so little about the vast majority of microbes because only a small percentage can be cultivated and studied in the lab. Here we report on the Global Ocean Sampling expedition, an environmental metagenomics project that aims to shed light on the role of marine microbes by sequencing their DNA without first needing to isolate individual organisms. A total of 41 different samples were taken from a wide variety of aquatic habitats collected over 8,000 km. The resulting 7.7 million sequencing reads provide an unprecedented look at the incredible diversity and heterogeneity in naturally occurring microbial populations. We have developed new bioinformatic methods to reconstitute large portions of both cultured and uncultured microbial genomes. Organism diversity is analyzed in relation to sampling locations and environmental pressures. Taken together, these data and analyses serve as a foundation for greatly expanding our understanding of individual microbial lineages and their evolution, the nature of marine microbial communities, and how they are impacted by and impact our world. TheSorcerer II GOS expedition, data sampling, and analysis is described. The immense diversity in the sequence data required novel comparative genomic assembly methods, which uncovered genomic differences that marker-based methods could not.
Collapse
Affiliation(s)
- Douglas B Rusch
- J. Craig Venter Institute, Rockville, Maryland, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Armbruster JA, Borris RP, Jimenez Q, Zamora N, Tamayo-Castillo G, Harris GH. SEPARATION OF CRUDE PLANT EXTRACTS WITH HIGH SPEED CCC FOR PRIMARY SCREENING IN DRUG DISCOVERY. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100104382] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jean A. Armbruster
- a Department of Natural Products Drug Discovery , Merck Research Laboratories , R80Y-355, P. O. Box 2000, Rahway , NJ , 07065 , U.S.A
| | - Robert P. Borris
- a Department of Natural Products Drug Discovery , Merck Research Laboratories , R80Y-355, P. O. Box 2000, Rahway , NJ , 07065 , U.S.A
| | - Quirico Jimenez
- b Instituto Nacional de Biodiversidad (INBio) , Apdo. 22-3100, Santo Domingo , Heredia , Costa Rica
| | - Nelson Zamora
- b Instituto Nacional de Biodiversidad (INBio) , Apdo. 22-3100, Santo Domingo , Heredia , Costa Rica
| | - Giselle Tamayo-Castillo
- b Instituto Nacional de Biodiversidad (INBio) , Apdo. 22-3100, Santo Domingo , Heredia , Costa Rica
| | - Guy H. Harris
- c Department of Natural Products Drug Discovery , Merck Research Laboratories , R80Y-355, P. O. Box 2000, Rahway , NJ , 07065 , U.S.A
| |
Collapse
|
30
|
Abstract
Fourteen novel sesquiterpene lactones of the germacranolide type have been isolated from the aerial parts of Mikania guaco: six costunolide, two melampolide and six germacra-4-trans,10(14),11(13)-trien-12.6alpha-olide derivatives. Except for one compound all the others possess a carbonyl function at C-9. Eight were obtained in the form of four isomer pairs which were difficult to separate. Structure elucidation was based on mass and ID and 2D NMR measurements. Low energy conformations were obtained by quantum mechanical calculations. Pyrrolizidine alkaloids could not be detected.
Collapse
Affiliation(s)
- P Rüngeler
- nstitut für Pharmazeutische Biologie, Universität Freiburg, Germany
| | | | | | | |
Collapse
|
31
|
Melzig MF, Löser B, Lobitz GO, Tamayo-Castillo G, Merfort I. Inhibition of granulocyte elastase activity by caffeic acid derivatives. Pharmazie 1999; 54:712. [PMID: 10522278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- M F Melzig
- Institute of Pharmacy, Humboldt-University, Berlin, Germany. matthias=
| | | | | | | | | |
Collapse
|
32
|
Goetz MA, Hensens OD, Zink DL, Borris RP, Morales F, Tamayo-Castillo G, Slaughter RS, Felix J, Ball RG. Potent nor-triterpenoid blockers of the voltage-gated potassium channel Kv1.3 from Spachea correae. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|