Project 1: Isolation of new bioactive secondary metabolites from marine bacteria

Host institution: UiT – The Arctic University of Norway

Objectives: The main objective is the discovery of novel antibacterial molecules in (Arctic) marine bacteria. The specific objectives are:

1) Nomination of talented producers (marine bacteria) of secondary metabolites. Combining chemical analysis with genome analysis. 2) Fermentation of bacteria under different culturing conditions, including co-culturing to search for antibacterial compounds. 3) Chemical analysis of fermentation broths to identify potential new compounds. 4) Isolation and structure elucidation of compounds. 5) Bioactivity profiling of isolated and chemically characterized compounds (anti-infectives, anticancer, anti-diabetic).

We have now recruited a student for this position, so it is no longer available.

Project 2: Discovery of novel bioactive compounds from marine microorganisms

Host institution: University of Aberdeen, UK

Objectives: 1) Fermentation of bacterial strains using a range of media. The addition of stresses (toxins, metals etc) to elicit expression will be tried as well as the use of co-cultivation in a specially designed vessel separating cultures with a membrane permeable to small molecules. 2) Extraction and fractionation of the fermentation broth and cell mass using solvents followed by dereplication using GNPS and other MS-MS networking tools. Extracts/fractions will be tested for bioactivity. 3) Compound purification and structural elucidation. Fractions with high bioactivity that show chemical novelty will be prioritised for chromatographic purification. Pure compounds will be structurally characterised using spectroscopic methods (NMR/MS). 4) Pure compounds will be tested to establish their mechanism of action and their ADMET profile determined to confirm their drug-likeness.

Project 3: Exploitation of a collection of marine-derived microbial extracts as source of new antibiotics useful in human, plant, and fish infections

Host institution: Fundación MEDINA, Spain

Objectives: A collection of microbial extracts from ~200 marine derived strains already available at MEDINA, generated using a One Strain Many Compounds (OSMAC) approach by growing each strain in 5 different selected culture media will be used as starting point for: 1) Testing of this extract collection against human, plant and fish pathogens. 2) Dereplication of the best bioactive hits using LC-HRMS and LC-MS/MS analyses combined with the use of internal spectral databases, the Dictionary of Natural Products (DNP) and the Global Natural Products Social Molecular Networking (GNPS) and selection of the best candidates for fractionation 3) Scaled-up fermentation, extraction, and fractionation of best candidates (3-30 L) for the purification of the bioactive molecules. 4) Structural elucidation of new molecules obtained using HRMS and NMR techniques. 5) Full profiling of the bioactive compounds against an extended panel of pathogens and other assays available from different consortium partners as well ADME-Tox assessment of the new molecules. 6) Genome mining of the strains yielding the most interesting candidates to identify the biosynthetic gene clusters (BGC) responsible for their production.

The position is now available for applicants! See the announcment here.

Project 4: Microbiology, novel strains isolation, and exploitation of a collection of marine-derived microbial extracts as source of new compounds

Host institution: Stazione Zoologica Anthon Dohrn, Italy

Objectives: Isolation and characterization of promising marine bacteria and improvement of secondary metabolites production (especially antimicrobials, siderophores and biosurfactants) by exploring different cultivation approaches. Strains will be collected from different extreme locations and isolated applying a wide range of conditions and substrates to maximise the biodiversity. Then the most diverse will be identified and initially cultivated in 96xDeepwell plates (OSMAC approach, axenic cultures and co-cultivation). A wide range of screening will be applied in order to select promising candidates for the lab scale-up. Genomes of the best microbial candidates will be sequenced and subjected to a genome mining approach for the identification of novel biosynthetic gene clusters (BGCs). Along with the OSMAC (One Strain MAny Compounds) approach, special co-cultivation systems will be explored to induce the expression of silent BGCs which will be further chemically analysed. As a matter of fact, this part of the project will be followed by the extraction and metabolic profiling of the samples in order to apply a fast dereplication approach. Mass spectrometry and the use of molecular networking will allow the selection of new potential molecules which will be further purified and identified by NMR.

Project 5: Extremophilic microorganisms against human, agricultural and aquacultural infections

Host institution: GEOMAR Helmholtz Centre for Ocean Research, Germany

Objectives: Microorganisms thriving in previously unexplored extreme marine environments represent a golden opportunity for discovery of novel and potent anti-infectives. Antibiotic discovery efforts have so far focused on Gram-positive marine bacteria (e.g., actinobacteria). This PhD project will aim to focus on less studied marine microbes, such as Gram-negative bacteria that are predominant in ocean bacterioplankton as well as in various extreme marine environments (a large collection available at GEOMAR). Specific objectives: 1) Optimized cultivation of microorganisms (WP2) by e.g., OSMAC approach to activate biosynthetic gene clusters (BGCs). 2) Extraction and screening of microbial cultures against a large panel of pathogens associated with human infections (ESKAPE and others), crop diseases (agriculture) and aquaculture diseases (fish and seaweed pathogens). 3) Deep UPLC-MS and MS/MS based metabolomics for dereplication of microbial extracts using molecular networks/GNPS platform. 4) Genomic mining/screening of the most promising microorganisms (with the highest bioactivity and chemical novelty) to inform the isolation of the secondary metabolites. 5) Purification of bioactive molecules (guided by bioactivity & bioactive molecular networks) and structure elucidation by spectroscopic methods. 6) Analysis of the key components of the biosynthetic pathway (BGCs) leading to hit bioactive molecules. 7)Preclinical studies on compounds, including mechanism of bioactivity and ADMET profiling.

Project 6: Untapped potential of actinobacteria from aquatic environments as a source of novel bioactive compounds

Host institution: Nicolaus Copernicus University, Poland

Objectives: The discovery of unique bioactive compounds is related to research on the taxonomic diversity of actinomycetes isolated from untapped environments. Novel actinobacteria are a source of chemical diversity resulting from their high adaptability to harsh environments. The main objectives of the research project are as follows: 1) Isolation of actinobacteria from aquatic sediments and their dereplication. 2) Screening of established collection of actinobacterial strains for novel taxa with antimicrobial activity against Gram-positive and Gram-negative bacteria, including clinical isolates, and against pathogenic fungi of human and plants (selection of isolates for screening program for bioactive compounds). 3) Genome-mining for identification of natural product-biosynthetic gene clusters (NP-BGCs). 4) Cultivation of actinobacteria and their co-cultivation with other microorganisms to induce synthesis of bioactive compound. 5) The detection of chemical novelty using appropriate analytical chemical procedures (dereplication) and structural analyses of interesting compounds.

Project 7: Towards a collaborative model for IP protection in the marine biodiscovery pipeline

Host institution: ABSInt, Belgium

Objectives: The ESR will study the management of Intellectual Property in the complex environment of marine natural product research. The objectives are: 1) to study existing models of IP projecting that are currently being applied. 2) to map the new requirements regarding IP and benefit-sharing that are coming out of international policy discussions. 3) to develop novel approaches in IP management that support the collaborative nature of MNP research, that respect the benefit-sharing requirements of providers and that are fit-for-purpose given developments in technology and bio-informatics

Project 8: Identification of molecular targets and mode-of-action of bioactive natural products

Host institution: Lead Discovery Centre, Germany

Objectives: In this project, the molecular targets of bioactive natural products will be elucidated. Various methods can be used, such as affinity chromatography (using the compound of interest bound to a matrix and the protein extract to identify binders; binders will be identified via mass-spec and competition experiments), CETSA assays (= cellular temperature shift assay for the identification of thermally shifted proteins in the presence of compound/modulator), cell painting, crosslinking, functional genetic approaches (e.g. si/sh-RNA-, CRISPR/Cas9-, cDNA- Screens, haploid screening), cellular profiling (e.g. metabolomics, proteomics, gene expression analysis), knowledge-based approaches (e.g. analysis of chemical similarities, machine learning methods, computer-based docking studies). From these methods the most appropriate ones will be applied to elucidate unknown molecular target(s) from known bioactive natural products such as Lulworthinone or MBR-322. In the next step, the most promising natural product candidate identified and profiled within Hotbio will also be investigated with regard to its molecular target, using the previously established methods.

Project 9: Preclinical development of bioactive compounds isolated from marine microorganisms

Host institution: UiT -The Arctic University of Norway

Objectives: Bioprofiling of compounds in the securamine series (delivered by WP5) and its derivatives to be able to select the best compounds for further development. ADME profiling, to provide information about in vitro metabolism like plasma stability, microsomal stability, solubility and hepatocyte stability. The ESR will re-ferment the producing organisms to isolate sufficient amount of the bioactive natural products that will be tested in a broad bioassay panel together with the synthetic derivatives provided from WP5. The molecular target and the mode-of-action of the most promising compounds must be identified. The bioactive compounds will be tested for toxicity and their ADME properties to provide input for the chemical synthesis.

Project 10: Market potential and market opportunities for MNP

Host institution: ABSInt, Belgium

Objectives: The ESR will study the market potential and the market opportunities for MNPs. For the market potential, the ESR will explore the potential fit between MNPs at final stage of development and on the market with market needs. For the market opportunities, the ESR will also look at market size, competition, pricing power, sustainability, etc.

The objectives are: 1) To map the market landscape of (near) market MNPs and explore the specific market needs they might fulfil. 2) To perform a market analysis of MNPs, compared to existing alternatives. 3)To study the economic drivers of MNPs, such as price elasticity and pricing power.

Project 11: Synthesis and Functional Optimization of Natural Products

Host institution: University of Zürich, Switzerland

Objectives: The main objective of this project is the design and development of a scalable route towards securamine derivatives and the functional optimization of natural products by chemical synthesis. 1) The PhD student will design and develop a chemical route towards securamine by using state-of-the art databases, machine learning using both commercial and open access tools, and swarm intelligence methods. 2) The PhD student will establish structure activity relationship studies on the securamine class of natural products, which will be aided by computational design if possible and evaluated by biological assays. Feedback from these partners will enhance the design and the performance of the newly synthesized compounds in the hit to lead transition. 3) The PhD student will prepare a larger amount of the lead compound for downstream ADMET/Tox studies. 4) After new hits have been identified, the PhD student will perform SAR studies.

Project 12: Functional Optimization and Synthesis of Natural Products

Host institution: University of Zürich, Switzerland

Objectives: The main objective of this project is the design and development of a scalable route towards novel lead compounds identified by this consortium, subsequent functional optimization of natural products by chemical synthesis (hit to lead transition), and synthesis of a larger amount of the lead compound for downstream studies. (1) The PhD student will design and develop a chemical route towards hit compounds by using state-of-the art databases, machine learning using both commercial and open access tools, and swarm intelligence methods. (2) The PhD student will establish structure activity relationship studies, facilitating the hit to lead transition, which will be aided by computational design if possible and evaluated by biological assays. Feedback from these partners will enhance the design and the performance of the newly synthesized compounds in the hit to lead transition. (3) The PhD student will prepare a larger amount of the lead compound for downstream ADMET/Tox studies.

Project 13: Updating the CADD tools SwissTargetPrediction and SwissADME to extend their use to natural compounds

Host institution: University of Lausanne, Switzerland

Objectives: Through the research project we will be aiming at upgrading our CADD tools to support their use with naturally occurring compounds. Indeed, SwissTargetPrediction and SwissADME, for instance, have been trained on different sets of drug like molecules, mainly originating from medicinal chemistry literature. Consequently, they have been little trained on natural compounds. Although a large fraction of natural compounds are drug-like according to general rules like those of Lipinski, they exhibit somewhat different molecular properties compared to synthetic compounds (PMID: 22537178, 29711552, 11350252, 12546556). Consequently, machine-learning based approaches which were trained on synthetic compounds, like SwissADME and SwissTargetPrediction, are expected to perform worse on natural products and possibly necessitate a retraining using libraries of natural molecules (PMID: 34584636). SwissTargetPrediction requires a large amount of small molecules for its training, typically some tens to hundreds of thousands. Consequently, its re-training will necessitate the large numbers of natural products that are currently available in the numerous open-access and freely available databases of natural molecules (PMID: 33431011; http://zinc20.docking.org). Crossing these databases with the bio-activities stored in ChEMBL and PubChem will provide us with a sufficiently large dataset of bioactivities for natural products, allowing the adaptation of SwissTargetPrediction to this class of compounds. The novel data provided by WP4 will be used as an external test set to validate the predictive ability of this alternative version of SwissTargetPredicition. SwissADME contains several machine-learning models to predict for instance gastro-intestinal or BBB crossing, P-gp activity or cytochrome inhibition. Again, these models were established on several sets of synthetic small molecules for which these properties were determined and made publicly available. Of note, these models require smaller amount of molecules for their training (typically a few hundred diverse compounds). Consequently, it could be possible to directly use the experimental data produced in WP6 using always the same well-defined and thus reproducible approaches. Such high-quality and well defined data constitute a training set of choice for such prediction models, since they do not come with the usual ‘noise’ existing when using information from different origin and experiments.
 Importantly, feedback loops will be put in place between predictions made using (the retrained) SwissTargetPrediction and SwissADME and the experimental data obtained in WP4 and WP6 to optimize the predictive ability of these tools.

*PhD project #13 will have a duration of 48 months, where 36 are funded by SERI and 12 months will be funded by UNIL and/or SIB.