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Nuñez Santiago I, Machushynets NV, Mladic M, van Bergeijk DA, Elsayed SS, Hankemeier T, van Wezel GP. nanoRAPIDS as an analytical pipeline for the discovery of novel bioactive metabolites in complex culture extracts at the nanoscale. Commun Chem 2024; 7:71. [PMID: 38561415 PMCID: PMC10984978 DOI: 10.1038/s42004-024-01153-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Microbial natural products form the basis of most of the antibiotics used in the clinic. The vast majority has not yet been discovered, among others because the hidden chemical space is obscured by previously identified (and typically abundant) antibiotics in culture extracts. Efficient dereplication is therefore key to the discovery of our future medicines. Here we present an analytical platform for the efficient identification and prioritization of low abundance bioactive compounds at nanoliter scale, called nanoRAPIDS. NanoRAPIDS encompasses analytical scale separation and nanofractionation of natural extracts, followed by the bioassay of interest, automated mass spectrometry identification, and Global Natural Products Social molecular networking (GNPS) for dereplication. As little as 10 μL crude extract is fractionated into 384 fractions. First, bioactive congeners of iturins and surfactins were identified in Bacillus, based on their bioactivity. Subsequently, bioactive molecules were identified in an extensive network of angucyclines elicited by catechol in cultures of Streptomyces sp. This allowed the discovery of a highly unusual N-acetylcysteine conjugate of saquayamycin, despite low production levels in an otherwise abundant molecular family. These data underline the utility and broad application of the technology for the prioritization of minor bioactive compounds in complex extracts.
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Affiliation(s)
- Isabel Nuñez Santiago
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Marija Mladic
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- DSM-Firmenich, Delft, The Netherlands
| | - Doris A van Bergeijk
- Department of Microbiology, KU Leuven, Immunology and Transplantation (Laboratory of Molecular Bacteriology), Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
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Affiliation(s)
- Cemil Aydoğan
- Biochemistry Division, Department of Chemistry, Bingöl University, Bingöl 12000,Turkey
- Department of Food Engineering, Bingöl University, Bingöl 12000,Turkey
| | - Francesca Rigano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
| | - Lenka Kujovská Krčmová
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, Hradec Králové 500 05, Czech Republic
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Sokolská 581, Hradec Králové 500 05, Czech Republic
| | - Doo Soo Chung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Mirek Macka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00Brno, Czech Republic
- School of Natural Sciences and Australian Centre for Research on Separation Science (ACROSS), University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
- Department of Sciences and Technologies for Human and Environment, University Campus Bio-Medico of Rome, Rome I-00128, Italy
- BeSep s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98168, Italy
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Xie C, Slagboom J, Albulescu LO, Bruyneel B, Still KBM, Vonk FJ, Somsen GW, Casewell NR, Kool J. Antivenom Neutralization of Coagulopathic Snake Venom Toxins Assessed by Bioactivity Profiling Using Nanofractionation Analytics. Toxins (Basel) 2020; 12:E53. [PMID: 31963329 PMCID: PMC7020444 DOI: 10.3390/toxins12010053] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
Venomous snakebite is one of the world's most lethal neglected tropical diseases. Animal-derived antivenoms are the only standardized specific therapies currently available for treating snakebite envenoming, but due to venom variation, often this treatment is not effective in counteracting all clinical symptoms caused by the multitude of injected toxins. In this study, the coagulopathic toxicities of venoms from the medically relevant snake species Bothropsasper, Calloselasmarhodostoma, Deinagkistrodonacutus, Daboiarusselii, Echiscarinatus and Echisocellatus were assessed. The venoms were separated by liquid chromatography (LC) followed by nanofractionation and parallel mass spectrometry (MS). A recently developed high-throughput coagulation assay was employed to assess both the pro- and anticoagulant activity of separated venom toxins. The neutralization capacity of antivenoms on separated venom components was assessed and the coagulopathic venom peptides and enzymes that were either neutralized or remained active in the presence of antivenom were identified by correlating bioassay results with the MS data and with off-line generated proteomics data. The results showed that most snake venoms analyzed contained both procoagulants and anticoagulants. Most anticoagulants were identified as phospholipases A2s (PLA2s) and most procoagulants correlated with snake venom metalloproteinases (SVMPs) and serine proteases (SVSPs). This information can be used to better understand antivenom neutralization and can aid in the development of next-generation antivenom treatments.
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Affiliation(s)
- Chunfang Xie
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.X.); (J.S.); (B.B.); (K.B.M.S.); (G.W.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.X.); (J.S.); (B.B.); (K.B.M.S.); (G.W.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Laura-Oana Albulescu
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK (N.R.C.)
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Ben Bruyneel
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.X.); (J.S.); (B.B.); (K.B.M.S.); (G.W.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Kristina B. M. Still
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.X.); (J.S.); (B.B.); (K.B.M.S.); (G.W.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Freek J. Vonk
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands;
| | - Govert W. Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.X.); (J.S.); (B.B.); (K.B.M.S.); (G.W.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK (N.R.C.)
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.X.); (J.S.); (B.B.); (K.B.M.S.); (G.W.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
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Zietek BM, Still KBM, Jaschusch K, Bruyneel B, Ariese F, Brouwer TJF, Luger M, Limburg RJ, Rosier JC, V Iperen DJ, Casewell NR, Somsen GW, Kool J. Bioactivity Profiling of Small-Volume Samples by Nano Liquid Chromatography Coupled to Microarray Bioassaying Using High-Resolution Fractionation. Anal Chem 2019; 91:10458-10466. [PMID: 31373797 PMCID: PMC6706796 DOI: 10.1021/acs.analchem.9b01261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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High-throughput
screening platforms for the identification of bioactive
compounds in mixtures have become important tools in the drug discovery
process. Miniaturization of such screening systems may overcome problems
associated with small sample volumes and enhance throughput and sensitivity.
Here we present a new screening platform, coined picofractionation
analytics, which encompasses microarray bioassays and mass spectrometry
(MS) of components from minute amounts of samples after their nano
liquid chromatographic (nanoLC) separation. Herein, nanoLC was coupled
to a low-volume liquid dispenser equipped with pressure-fed solenoid
valves, enabling 50-nL volumes of column effluent (300 nL/min) to
be discretely deposited on a glass slide. The resulting fractions
were dried and subsequently bioassayed by sequential printing of nL-volumes
of reagents on top of the spots. Unwanted evaporation of bioassay
liquids was circumvented by employing mineral oil droplets. A fluorescence
microscope was used for assay readout in kinetic mode. Bioassay data
were correlated to MS data obtained using the same nanoLC conditions
in order to assign bioactives. The platform provides the possibility
of freely choosing a wide diversity of bioassay formats, including
those requiring long incubation times. The new method was compared
to a standard bioassay approach, and its applicability was demonstrated
by screening plasmin inhibitors and fibrinolytic bioactives from mixtures
of standards and snake venoms, revealing active peptides and coagulopathic
proteases.
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Affiliation(s)
- Barbara M Zietek
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Kristina B M Still
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Kevin Jaschusch
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Ben Bruyneel
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Freek Ariese
- LaserLaB , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Tinco J F Brouwer
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Matthijs Luger
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Rob J Limburg
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Joost C Rosier
- Fine Mechanics and Engineering Beta-VU , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Dick J V Iperen
- Fine Mechanics and Engineering Beta-VU , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions , Liverpool School of Tropical Medicine , Pembroke Place , Liverpool L3 5QA , U.K.,Centre for Drugs and Diagnostics , Liverpool School of Tropical Medicine , Pembroke Place , Liverpool L3 5QA , U.K
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
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Zietek BM, Mayar M, Slagboom J, Bruyneel B, Vonk FJ, Somsen GW, Casewell NR, Kool J. Liquid chromatographic nanofractionation with parallel mass spectrometric detection for the screening of plasmin inhibitors and (metallo)proteinases in snake venoms. Anal Bioanal Chem 2018; 410:5751-5763. [PMID: 30090989 PMCID: PMC6096707 DOI: 10.1007/s00216-018-1253-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/22/2018] [Accepted: 07/06/2018] [Indexed: 02/05/2023]
Abstract
To better understand envenoming and to facilitate the development of new therapies for snakebite victims, rapid, sensitive, and robust methods for assessing the toxicity of individual venom proteins are required. Metalloproteinases comprise a major protein family responsible for many aspects of venom-induced haemotoxicity including coagulopathy, one of the most devastating effects of snake envenomation, and is characterized by fibrinogen depletion. Snake venoms are also known to contain anti-fibrinolytic agents with therapeutic potential, which makes them a good source of new plasmin inhibitors. The protease plasmin degrades fibrin clots, and changes in its activity can lead to life-threatening levels of fibrinolysis. Here, we present a methodology for the screening of plasmin inhibitors in snake venoms and the simultaneous assessment of general venom protease activity. Venom is first chromatographically separated followed by column effluent collection onto a 384-well plate using nanofractionation. Via a post-column split, mass spectrometry (MS) analysis of the effluent is performed in parallel. The nanofractionated venoms are exposed to a plasmin bioassay, and the resulting bioassay activity chromatograms are correlated to the MS data. To study observed proteolytic activity of venoms in more detail, venom fractions were exposed to variants of the plasmin bioassay in which the assay mixture was enriched with zinc or calcium ions, or the chelating agents EDTA or 1,10-phenanthroline were added. The plasmin activity screening system was applied to snake venoms and successfully detected compounds exhibiting antiplasmin (anti-fibrinolytic) activities in the venom of Daboia russelii, and metal-dependent proteases in the venom of Crotalus basiliscus. Graphical abstract ᅟ.
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Affiliation(s)
- Barbara M Zietek
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Morwarid Mayar
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Ben Bruyneel
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Freek J Vonk
- Naturalis Biodiversity Center, 2333 CR, Leiden, The Netherlands
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Nicholas R Casewell
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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