The ABX registry is a network of researchers across the UK and Ireland academic community working in antibiotic discovery. The intention is to try and improve the first steps in the antibiotic discovery process and increase the number of novel antibiotics entering the pre-clinical development phase.Here you will find a list of ABX members with expertise in antibiotic discovery. Many members will be attending our kick-off event in July (please see main ABX page for details) which will give you the chance to meet the other members, encourage knowledge exchange and foster collaborative projects.
A – D
Dr Dyan Ankrett
University of Exeter
College of Medicine and Health, Living Systems Institute (LSI), University of Exeter, Streatham Campus, Stocker Road, Exeter, EX4 4QD.
Overview: Develop antibacterial conjugate therapies by combining small molecule antibiotics with membrane-targeting peptides in order to improve selectivity and potency towards the target organism.
Target: Our current model includes several strains of E.Coli but this will be widened to include other pathogenic, drug resistant organisms.
Where are you looking: Peptide libraries, short peptide sequences, natural peptides, synthetic/substituted peptides.
Expertise required: Regular contact with the network for support and potential collaboration.
Expertise offered: Wet laboratory/practical skills.
Issues: Peptide synthesis: commercial peptides are expensive and in-house peptide synthesis can be slow.
Antibacterial conjugate therapies, peptide-lipid bilayer interaction, membrane pore formation
Dr Catherine Back
Post-doctoral Research Associate
School of Biochemistry, University of Bristol, Bristol, UK.Overview: Bioprospecting deep-sea environments to discover new natural products with antimicrobial activity.
Target: Mainly bacterial, Gram negative particularly.
Where are you looking: Natural products from sponge-associated bacterial species.
Expertise required: Knowledge transfer through meetings/discussions, equipment access and joint grant applications.
Expertise offered: A wide knowledge base from initial isolation of active bacterial strains through to active compound purification and identification. Also working on using the iChip for use with sponge bacteria.
Issues: Purification and identification of natural product compounds from crude extracts.
Keywords: Antibiotics; deep-sea; sea sponge; bioprospecting; natural products; secondary metabolites; biosynthetic gene clusters; genome mining.
Professor Ibrahim Banat
Professor of Microbial Biotechnology
Biomedical Sciences, Ulster University, Cromore Road, Coleraine BT52 1SA, Northern Ireland.
Our lab specialises in bacterial biofilms, biosurfactants as antimicrobial and adjuvants to antibiotics and antibiotic discovery mainly through Streptomyces species
Target: We test our antibiotics mainly on different Gram + and Gram – bacteria and on multi-resistant pathogens like the ESKAPE pathogens but we also have expertise in bacterial biofilms and have recently added fungal biofilms to our repertoire.
Where are you looking: Unusual environments, extremes of physiological stresses and even ethnopharmacological recipe’s.
Expertise required: Small molecule separation and identification techniques. Project collaborations.
Expertise offered: New strains of antibacterial producing Streptomyces . New methods of isolation of environmental antibiotic producing bacteria. Multiresistant pathogens tests for both planktonic and biofilm physiologies finally biosurfactants production.
Issues: New classes of antibiotic discovery, dereplication of useful antibiotics found, combinatorial therapeutic approaches, ie combinations of therapies that are effective against planktonic and biofilm physiologies.
Keywords: Natural Products, biosurfactants, Novel Streptomyces, Bacterial Biofilms.
Dr Manuel Banzhaf
Birmingham Fellow (Group leader), University of Birmingham
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT
Overview: I work as a group leader in the Institute for Microbiology and Infection at the University of Birmingham. My research explores the use of high-throughput approaches to phenotype pathogens. Those methods allow me to study a) the bacterial cell envelope, a cellular compartment harbouring many determinants and processes related to antimicrobial resistance; b) how differences in DNA sequence result in phenotypic variability of pathogens to improve antimicrobial treatment regimens.
Target: No, but I mostly work with Gram-negative bacteria.
Where are you looking: I can work with all.
Expertise required: Getting novel compounds to perform mode of actions studies.
Expertise offered: High-throughput phenotypic approaches.
Keywords: Gram-negative cell envelope; Systems Biology; Antimicrobial resistance; Biofilms; High-throughput screening.
Dr Vassiliy N Bavro
University of Essex
School of Biosciences; University of Essex; Wivenhoe Park, Colchester, CO43SQ, UK.
Overview: Our team focuses on the functional and structural characterisation of tripartite efflux pumps as well as on the wider structure of outer membrane in Gram-negative bacteria, with regards to antibiotic permeability and by proxy resistance. To that end we utilise a multidisciplinary integrative approach combining in vivo genetic and functional assays with in vitro biophysical and structural techniques including X-ray crystallography, surface plasmon resonance (SPR) and structural mass-spectrometry. We also use molecular modelling approaches to analyse potential drug-antibiotic docking interactions.
Target: At the moment we work predominantly on Gram negative bacteria and tripartite pumps associated with them. Our current research targets include Salmonella and Neisseria but we are investigating pump proteins from other organisms as well.
Where are you looking: We are investigating the potential antimicrobial properties of compounds that bind to efflux pumps or interfere with their assembly. We are also interested in efflux pump inhibitors (EPIs) which can augment the action available antibiotics. We combine in silico drug design and docking with chemical library screening to identify compounds.
Expertise required: We are always happy to collaborate on functional characterisation of novel protein pumps and pump components. We are looking for complementary structural platforms to our own facilities and expertise, which may include e.g. NMR and cryo-EM facility access; We are also looking for any lead compounds that exhibit efflux pump binding properties, which may need optimisation and/or structural characterisation.
Expertise offered: Beyond our immediate research topics on efflux pumps, we can provide general structural biology support and characterisation of protein samples, including membrane proteins using a combination of X-ray crystallography and biophysical approaches. We have a lot of experience in heterologous production, optimisation and scaling up of membrane protein expression, as well as purification and membrane extraction, including detergent alternatives such as styrene maleic acid copolymers (SMA). We are also happy to provide bioinformatics support and structural modelling/docking of compounds and proteins in silico. We are also well set-up for in vivo efflux assays using recombinant E.coli.
Issues: High-throughput screening approaches for ligand binding - e.g. multichannel SPR. Access to cryo-EM facilities and large scale fermentors/protein purification set-ups. Availability of facilities to work on certain organisms beyond category 2 and genetic manipulation of such organisms.
Keywords: Multidrug resistance; Efflux pumps; Efflux Pump Inhibitors (EPIs); Gram-negative bacteria; Outer membrane; RND-transporters; TolC; membrane fusion proteins; AcrB; Neisseria; Salmonella; X-ray crystallography; membrane proteins; in silico docking.
Dr Dany JV Beste
Lecturer in Microbial Metabolomics, University of Surrey
Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH
Overview: The Beste group uses an integrated approach of genetics, metabolomics, biochemical assays, transcriptomics, chemostat cultures to study the metabolism of a pathogen (Mycobacterium tuberculosis) in the host environment. Understanding metabolism of pathogens such as Mycobacterium tuberculosis presents an opportunity not only to identify novel drug targets but also potentiating metabolism has emerged as a potential route for overcoming antimicrobial resistance.
Target: Mycobacterium tuberculosis
Where are you looking: We have been screening natural products and in collaboration compounds from chemical libraries.
Expertise required: Collaboration with mathematical modellers, Medicinal Chemists and pharmaceutical companies.
Expertise offered: Developing chemostat models for generating high quality data to inform mathematical modelling; generating and studying mutant strains of (M. tuberculosis) in a range of physiologically relevant conditions in vitro and ex vivo conditions; metabolomics including 13C isotopomer analysis; macrophage models of TB; developing and using fluorescent reporter strains to measure growth, transcriptional responses and redox potential; medium through-put antibiotic assays to test novel antimicrobial compounds against mycobacteria.
Issues: Obtaining suitable compounds to screen. Elucidating the mechanisms of action of compounds.
Keywords: Tuberculosis; Metabolomics; Microbial metabolism; Systems Biology
Professor Sanjib Bhakta
University of London and UCL
Mycobacteria Research Laboratory, The Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London and UCL, Malet Street, Bloomsbury, London WC1E 7HX.
Overview: Our research interest is primarily focused on characterising the physiology of the different metabolic states of Mycobacterium spp., tackling antimicrobial resistance through validating novel therapeutic targets, from identifying hits to optimising novel leads and repurposing existing immunomodulatory drugs to cure TB. Our lab is specialised in molecular microbiology and biochemistry techniques to manipulate DNA, RNA, proteins and lipids to characterise therapeutic targets and elucidate their structure, function, regulation and inhibition. We have integrated high-throughput enzymatic and whole-cell phenotypic assays for screening biological properties of natural or synthetic chemical inhibitors of mycobacterial morphology, growth and viability in vitro as well as in infected macrophage models mimicking the intracellular host-environment. Our expertise in microbiology enables us to generate genetically-modified and/or chemically-derived mutants and perform phenotypic and genotypic evaluation on these infectious pathogens of global interest.
Target: Bacteria especially Acid Fast Bacilli such as Mycobacterium tuberculosis and Mycobacterium leprae.
Where are you looking: Both natural products, synthetic chemical libraries and repurposing existing drugs (i.e. pain-killers).
Expertise required: Need support for animal testing, clinical trial, and industrial development.
Expertise offered: Whole-cell phenotypic evaluation of inhibitors, mode(s)/mechanism(s) of action studies for novel chemical entities, high through put target-based enzyme assays, therapeutic target identification and validation.
Issues: New lead optimisation.
Keywords: Mycobacterium tuberculosis, cell-wall metabolism, antimicrobial resistance, whole-cell phenotypic assays.
Professor Melody Clark
British Antarctic Survey
British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET
Overview: Adaptations of Antarctic marine species and their responses to climate change.
Targets: No specific targets, but currently looking at cultivatable bacteria.
Where are you looking: Environmental organisms.
Expertise required: We are looking to initiate partnerships to develop this area of work at BAS (rather than just hand over samples) in all areas from initial cultivation through to screening.
Expertise offered: Remote access to organisms from the Antarctic marine and terrestrial environments around the UK research bases depending on requirements and support request.
Keywords: Adaptations, transcriptomics, invertebrate, marine, Antarctic.
Dr Jonathan Cox
School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK B4 7ET
Overview: I lead the Mycobacterial Research Group at Aston University. We are a team composed of 3 PhD Students and a Post Doctoral Research Fellow with the objective of improving the understanding of the physiology of mycobacterial pathogens such as Mycobacterium tuberculosis. Our aim is to discover and develop new antibiotics for the treatment of mycobacterial diseases that are able to circumvent current antibiotic resistance mechanisms.
Target: We exclusively work on mycobacteria. In addition to tuberculosis, we have recently been working closely with clinicians at Birmingham Children’s Hospital on an aggressive pathogen called Mycobacterium abscessus that infects children and young adults with cystic fibrosis. This infection is becoming increasingly difficult to treat so we are engaged with developing new treatment regimes to overcome resistance mechanisms in this organism.
Where are you looking: We collaborate with medicinal chemists at University of Hertfordshire, University of Bradford and at Aston University. Furthermore we are engaged in drug repurposing and natural product drug discovery.
Expertise required: My team are always on the hunt for new chemical space that has the potential for antimicrobial activity. We are specialists in identifying the mechanism of action of antimicrobials and this information helps to discover new drug targets and refine the inhibitory chemicals into druggable antibiotics.
Expertise offered: Mechanistic knowledge of microbial physiology, resistance mechanisms and drug discovery.
Keywords: Mycobacteria, Antibiotic drug discovery, Microbial physiology, Mechanism of action.
Professor of Microbiology, Ulster University
School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland. BT52 1SA.
Overview: We are interested in how environmental pressures influence the spread of antibiotic resistance by horizontal gene transfer. We have been working a lot with filter feeding organisms and have shown that freshwater sponges, Daphnia, and various mussels all facilitate transfer of vancomycin resistance in members of the genus Enterococcus. We believe that by understanding the mechanisms at work here we can develop ways to slow down the inexorable spread of resistance and, ultimately, protect the next generations of antibiotics. In the course of our work we have identified some antibacterial activities among the filter feeding organisms that may have the potential for exploitation. In addition we have been looking at the conjugation mechanisms employed by the enterococci using whole genome sequencing approaches and we believe it may be possible to harness some of the signalling systems as antibacterial agents.
Target: Currently we are mostly focused on gram positive bacteria but we have an interest, and direct expertise, in bacterial communication systems across both gram positive and gram negative species. At present our group works with Enterococcus spp. , Pseudomonas aeruginosa, Clostridium difficile, Salmonella spp. and Campylobacter spp.
Where are you looking: We have two approaches to searching for new antibiotics.
(A) We are looking for antimicrobial activity in freshwater and marine filter feeding organisms. We are testing extracts for activity against a range of antibiotic resistant bacteria.
(B) We believe that disruption of communication offers a realistic opportunity to 1. develop narrow spectrum agents and 2. to develop agents that should not generate excessive selective pressure to promote resistance. Therefore we are also focused heavily on the antibiotic resistant bacteria themselves and are trying to dissect their communication systems at the molecular level.
Expertise required: The primary goal of participating in the network for us would be to gain access to open minded collaborators. We have no specific technique or enterprise in mind. We need help with everything! We currently work with a few multidisciplinary projects involving engineers, public health professionals and nutritional biochemists and we see the value of such an approach in generating new ideas.
Expertise offered: We can offer a range of microbiological assays including; biofilm cultivation, cultivation of anaerobes and microaerophiles, electron microscopy and whole genome sequencing.
Issues: Access to expertise that we currently do not have in the form of meaningful collaborations. We are concerned however that collaboration may be hindered by the desire of institutions and investigators to protect their intellectual property. Clearly this is necessary but it is something that needs to be addressed at the outset in a new collaborative network.
Keywords: bacterial communication, horizontal gene transfer, quorum sensing, antimicrobial peptides, environmental resistance reservoirs.
Ulster University (6th from Ulster)
Ulster University, Coleraine Campus, NI
Overview: My research group’s work is centralised around biosurfactants focusing on the production of microbial biosurfactants, their biosynthesis and their biotechnological and industrial applications, especially in environmental, medical, pharmaceutical and health related areas.
Target: Biosurfactants are produced by various bacterial, yeast and fungal species. My research is focusing on a range of Gram positive and Gram negative bacteria associated with skin infections and wounds.
Where are you looking: I have tested the antibacterial properties of two well established biosurfactants; mannosylerythritol lipids (MELs) and rhamnolipids which are produced naturally. They have shown activity against Gram negative bacteria and when combined with antibiotics they have demonstrated some activity against Gram positive bacteria.
Expertise required: I am currently identifying the mechanism of action of the biosurfactants on bacterial cells using scanning electron microscopy. In the future I want to use molecular biology to explore and elucidate this further. I would love to learn more about this and meet possible connections with other researchers who have focused their research on this. I would also like to meet other researchers with in vivo experience and drug formulation experience to enhance my research further by developing an effective combination topical antibiotic/biosurfactant treatment to test on laboratory animal models.
Expertise offered: With a wide range of skills and expertise I can assist in the development of new ideas and trouble shoot problems that may arise. I am extremely resilient in my career and this is something I can lend to others through sharing my experiences. I have a wide range of scientific skills such microbiological testing, small scale and large scale fermentation skills and in vitro assay experience both on bacteria and human keratinocyte skin cells.
Issues: Current literature focuses on optimising the production of biosurfactants and understanding their biosynthesis. My works relates to their application as a combination therapy with antibiotics and this novel work branches across many specialisms from biotechnology to AMR to industry. Due to this, it can be difficult to portray the impact of my research as each specialism are interested in different aspects of my research. Attending the ABX networking event will give me the possibility to bridge the gaps between the specialisms.
Keywords: AMR, Biotechnology, Microbiology, Biosurfactants, Combination Therapy.
Dr Katherine Duncan
Chancellor's Fellow and Lecturer, University of Strathclyde
University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral St, Glasgow G4 0RE. www.medicinesfromthesea.com
Overview: We are interested in marine microbial natural products, specifically the chemical language of bacteria and microalgae in the oceans to help us discover new antibiotics.
Target: Actinobacteria and microalgae.
Where are you looking: Marine microbial natural products from environmental isolates.
Expertise required: Chemical ecology collaborations to understand the function of specialised metabolites in the environment.
Expertise offered: Environmental isolation, molecular biology, whole genome sequencing and mining for biosynthetic gene clusters, bioactivity screening against clinically relevant pathogens, natural products chemistry including mass spectrometry and comparative metabolomics.
Issues: Biological and chemical dereplication.
Keywords: Actinobacteria, specialised metabolite, biosynthetic gene clusters, marine.
Professor Paul Dyson
Swansea University Medical School, Singleton Park, Swansea, SA2 8PP
Overview: Discovery, isolation and characterisation (genome sequencing, antibiotic assays versus ESKAPE bacteria and fungi) of new antibiotic-producing Streptomyces.
Target: Bacteria (especially those resistant to frontline antibiotics) and fungi.
Where are you looking: Environmental soil organisms.
Expertise required: Expertise in isolation and structural determination of antibiotics.
Expertise offered: Expertise in where to find new antibiotic-producing Streptomyces; genome sequencing.
Issues: Isolation and structural determination of antibiotics; toxicity testing.
Keywords: Molecular microbiology, Streptomyces, gene expression analysis.
E – H
Dr RuAngelie Edrada-Ebel
Senior Lecturer, University of Strathclyde
University of Strathclyde, 161 Cathedral Street, G4 0RE, Glasgow
Overview: Our expertise is on secondary Metabolomics of potential antimicrobials from marine sponge symbionts from extreme environments.
Target: We do work both on actinomyces and fungi.
Where are you looking: Natural. Products from microbes from extreme environments.
Expertise required: Imaging mass Spectrometry and bioreactor facilities for scale up.
Expertise offered: Metabolomics profiling analysis of mass and nmr spectral data. We have coupled the analysis of our mass spectral data to a natural product database for automated dereplication study.
Issues: Bioreactor scale up.
Keywords: Secondary Metabolomics, structure elucidatoon.
Anglia Ruskin University
School of Life Sciences, Anglia Ruskin University, East Road, Cambridge, CB1 1PT
Overview: Discovery of agents of low toxicity with capacity to reverse mechanisms of antibiotic resistance.
Target: Gram-negative bacteria (E. coli, A. baumannii, P. aeruginosa, K. pneumoniae).
Where are you looking: Primarily natural products from screens of traditional medicines.
Expertise required: Open to any collaboration.
Expertise offered: Screening of natural product libraries, activity guided separation, compound isolation.
Issues: Too much time spent teaching!
Keywords: Natural products, screening, drug discovery, resistance blockers.
Dr Lorena Fernández-Martínez
Reader in Microbial genetics, Edge Hill University
Biology Department, Edge Hill University, Ormskirk, L39 4QP, UK.
Overview: Research in my laboratory is focused on understanding the production of natural products from Actinomycetes. Actinomycetes are a wonderful and diverse group of gram positive bacteria present in almost all environments. In particular my research group is interested in the genus Streptomyces because this genus alone is responsible for the production of a high number of clinically relevant specialised metabolites including antibiotics, anti-fungal, anti-helminthic and anti-cancer drugs.
Target: We look at a variety of target organisms but regularly focus on the ESKAPE strains.
Where are you looking: We look in environmental Streptomyces (and other actinomycete) isolates.
Expertise required: Collaborations with natural product chemists and bioinformaticians would be really relevant to my research group as I am a microbial geneticist.
Expertise offered: Genetic manipulation of actinomycete strains.
Issues: Production of sufficient yield and lack of chemistry facilities at my institution.
Keywords: Antibiotic discovery; Actinomycetes; Streptomycetes; Gene regulation; Genetic manipulation to increase yields of natural products.
I – L
University of Aberdeen
Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE, Scotland, UK.
Overview: The Marine Biodiscovery Centre (MBC) Was established in 2010 and its research predominantly concerns marine natural product chemistry including microbial strain isolation, chemical isolation, and structural determination using spectroscopic methods. There are exciting projects focused on the discovery of biologically active molecules in a range of disease areas such treatments for parasitic infections, cancer, bacterial/fungal infections, and inflammation. The MBC is a £2.5 M, 400 m2 integrated facility with state-of-the-art equipment for the discovery of new products from marine bioresources as well as their synthesis and modification. It houses unique analytical facilities for structural characterisation. The MBC is at the vanguard of exploration of bioresources for medical and non-medical applications. The MBC co-locates synthetic chemists, medicinal chemists, natural product chemists, analytical chemists, molecular biologists and microbiologists. It incorporates work on natural products from marine invertebrates, plants, bacteria and fungi.
Target: No – we are focused on the discovery of molecules so we work with others to provide assays and targets.
Where are you looking: Natural products, mainly from marine invertebrates, deep sea and cold adapted bacteria and fungi as well as microorganisms from arid environments.
Expertise required: Biological assay capacity, development of new targets.
Expertise offered: Extract, fraction and compound libraries.
Issues: Compound rediscovery.
Keywords: Natural products; isolation and purification; spectroscopy; compound identification; molecular genetics of biosynthetic gene clusters.
Dr Thamarai K Janganan
Lecturer in Microbiology and Biotechnology, University of Bedfordshire
School of Life Sciences, University of Bedfordshire, Luton, Bedfordshire, UK, LU1 3JU
Overview: My lab is mainly focusing AMR in the context of a) multi-drug efflux pumps from the dangerous pathogen Neisseria gonorrhoeae and emerging pathogen Acinetobacter baumannii b) finding an alternative antimicrobial compound for the above pathogen.
Target: Gram-negative – Neisseria gonorrhoeae and Acinetobacter baumannii.
Where are you looking: Natural products and synthetic.
Expertise required: A constructive feedback/discussion to expand my idea.
Expertise offered: Characterizing new antibiotics or antimicrobial compounds. Investigate whether the new antimicrobial agents are substrates for multidrug efflux pumps. Characterizing the structure and function of multidrug-resistant pumps.
Issues: Finding a potential new antimicrobial agent whether natural or synthetic. How to inhibit the efflux pumps, because efflux pumps are diverse and most of the bacterial cells have more than one class of efflux pumps such as RND, SMR, ABC and MATE family, identifying an agent to inhibit all these pumps is really challenging.
Keywords: Multidrug efflux pumps from Gram-negative bacteria. Neisseria gonorrhoeae & Acinetobacter efflux pumps. Alternative antimicrobial compounds.
NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen AB21 9YA
Overview: NCIMB provides specialist microbiology, chemical analysis and biomaterial storage products and services to support clients in their quality control procedures, research and development projects, intellectual property protection and compliance with environmental regulations.
My department maintains the National Collection of Industrial Food and Marine Bacteria, the biggest reference collection of over 10,000 industrially and environmentally valuable microorganisms in the UK. We are looking for partnerships to untap the potential of this genetic resource. NCIMB is an International Depository Authority (IDA) for bacteria, fungi, bacteriophages, plasmids and plant seeds that are the subject of patent applications and we also offer a confidential secure storage facility where we store our clients’ strains as part of their disaster recovery plans.
Target: We have a collection of over 10,000 bacterial strains – Gram negative and Gram positive. The most likely candidates are the large number of Actinobacteria that we hold.
Where are you looking: For us, we are happy to look for many natural products from antibiotics to industrially relevant enzymes.
Expertise required: We have the knowledge to grow and maintain these strains and we are able to carry out NGS however we do not have the equipment, knowledge and skills to investigate the potential of the strains we have.
Expertise offered: We have the knowledge to grow and maintain these strains and we are able to carry out NGS. We are also a patent repository and we can act as a back-up storage for any researchers strains being used in projects.
Issues: As a commercial company it is difficult for us to get funding without an academic partner. We also do not have the equipment, knowledge and skill to untap the potential of the strains within our open collection.
Keywords: Biorepository, patents, bacterial culture collection.
Dr Wen-Wu Li
Guy Hilton Research Centre, Keele University, Thornburrow drive, Stoke on Trent, ST4 7QB
Overview: Due to the development of multi-drug resistance in cancers and microbial pathogens, there is an urgent need to discover and develop new medicines with novel mechanisms of action to combat these diseases. Currently, we are exploring anticancer, antibacterial and antimalarial compounds from natural sources, which include traditional Chinese and African medicinal plants, endemic plants and marine organisms from Mauritius. We use various techniques in chemistry (extraction, purification, isolation, structure elucidation using mass spectrometry and nuclear magnetic resonance spectroscopy, chemical and enzymatic synthesis), pharmacology (mammalian/bacterial cell cultures, cytotoxicity assay, drug metabolism, immunoblotting, flow cytometry, fluorescence/scanning electron microscopy, and epigenetic analysis), and biochemistry (proteomics and target identification). Our aim is to discover and develop novel bioactive natural products and their semi-synthetic analogues as clinical trial candidates, and eventually as safe and effective medicines.
Target: Mainly, biofilm-related bacteria.
Where are you looking: Natural products.
Expertise required: Antibiofilm and antibacterial screening, mechanistic study.
Expertise offered: Isolation, structural elucidation and semi-synthesis.
Issues: Funding and microbiological facility.
Keywords: Antibiolilm, natural products, marine organism, peptides and synthesis.
M – P
Dr Marta Martins
Assistant Professor in Microbiology, University of Dublin
Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, the University of Dublin, Dublin 2, Ireland.
Overview: My research addresses the significant problem of antibiotic resistance in bacteria along with aspects of the infection biology. For that, we use a combination of classical microbiology, biochemistry, cell biology, immunology and functional genomic techniques. I am particularly interested in developing novel therapeutic approaches (adjuvant therapy; modulation of infected macrophages) to treat multidrug resistant bacteria and their associated infections.
Target: Mainly Gram-negative and -positive bacteria.
Where are you looking: Natural products, chemical libraries, repurpose of known drugs and chemical synthesis (rational design) of new drugs.
Expertise required: New antibacterial compounds rationally designed; knockouts in specific bacterial genes related to antibiotic resistance; sequencing; bioinformatics analysis.
Expertise offered: Testing of compounds for assessing antibacterial activity in vitro against Gram-negative and -positive bacteria in reference strains and in human clinical isolates; testing of compounds for efflux inhibition in bacteria; synergy testing with antibiotics and adjuvant compounds (for example: efflux pump inihibitors); metabolic profiling of bacterial isolates; toxicity assays in human cell lines; testing of compounds in cell lines, such as the human macrophages THP-1 for intracellular killing of phagocytosed bacteria or for cell activation (production of cytokines; production of reactive oxygen species, etc); Testing of compounds in epithelial cell lines, among others.
Issues: Identification/discovery of active compounds that are physiologically/clinically relevant (low toxicity; soluble in water, etc).
Keywords: New antibacterial compounds; Efflux pump inhibitors; Macrophage activation; Immunomodulation of infected macrophages.
Professor Tony Maxwell
John Innes Centre, Norwich
Dept. Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH
Overview: My lab is expert in DNA topoisomerases, which are targets for a number of antibacterial agents (e.g. fluoroquinolones). We carry out structure/function studies on topoisomerases, and look at the molecular mode of action of antibiotics, as well as being involved in aspects of the discovery process. We are also working on insect gut bacteria, particularly in relation to the effects of antibiotics on the gut microbiome.
Target: We are working on enzymes from Mycobacteria, Staphylococcus aureus, Escherichia coli, and other Gram-negative pathogens.
Where are you looking: Natural products and outputs from library screens.
Expertise required: Access to new chemical libraries; computational chemistry; access to novel natural products.
Expertise offered: Enzymology; structural biology.
Issues: Funding; access to expertise that could form part of a discovery pipeline.
Keywords: DNA gyrase; DNA topoisomerase; supercoiling; fluoroquinolones; aminocoumarins.
Dr Marie Lisandra Zepeda Mendoza
University of Birmingham
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT.
Overview: My main driver is bridging the gap between different disciplines for the design of analysis pipelines and the biological interpretation of the results. Her specific research objectives are: 1. Alternatives to the use of antibiotics 2. Understanding of antibiotic resistance (AR) from a metabolic network and evolution point of view 3. Identification and characterization of microbiomes with relevant pathogenic traits To accomplish these objectives I use high-throughput data (DNA, RNA, metabolites) and metabolic/regulatory modelling methods. I use genome scale metabolic and regulatory modelling to better guide hypothesis testing in the laboratory to understand metabolic network rewiring leading to AR, thus finding complex genotype-phenotype associations. High-throughput sequencing data is analysed with metagenomic approaches for characterization of different natural and clinical environments.
Target: I have both specific targets and general microbiome targets. For the computational modeling, my target is Pseudomonas aeruginosa and Clostridium difficile. And for the microbiomes, I aim to focus on characterizing the environmental role not only bacteria, but also of phages.
Where are you looking: Environmental organisms (mined from the microbiomes).
Expertise required: Experimental validation of my computational predictions/hypotheses. Since my laboratory is (so far) only computational based, I rely on collaborators for the wet-lab work.
Expertise offered: Computational analysis of high-throughput data, and multi-omics data integration (computational models are an invaluable tool to integrate data and to drive hypothesis-making).
Issues: The experimental validation.
Keywords: Metagenomics, genome-scale metabolic modeling, transcriptional regulatory network modeling, genomics, bioinformatics.
Dr Gavin J Miller
Lecturer in Organic Chemistry, Keele University
Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK.
Overview: We are a group of organic chemists focused on carbohydrate synthesis. We are interested in making tools for glycobiology, new glycomaterials and carbohydrates in medicinal chemistry. Most relenvnt to this network, we are developing the synthesis of sugar-nucleotide tools to probe the structure and function of enzymes regulating the biosynthesis of alginate. Alginate is a component of the exopolysaccharide coating secreted by the Gram-negative bacterium and opportunistic pathogen P. aeruginosa.
Targets: Bacteria, Gram -ve
Where are you looking: We are looking for new enzyme inhibitors, potentially.
Expertise required: Microbiology for P. Aeruginosa
Expertise offered: Synthetic organic chemistry/synthetic carbohydrate chemistry/medicinal chemistry
Issues: Translation from a chemistry driven project.
Keywords: Sugar-nucleotides, carbohydrate active enzymes, chemical synthesis, alginate.
Antimicrobial screening facility and University of Warwick
Antimicrobial screening facility, School of Life Sciences, Faculty of Science, Gibbet Hill Road, Coventry, CV4 7AL
Overview: We offer undertake anything microbiological offering services to academia, industry and medicine. Website
Target: Were currently working with all of the above and hopefully soon to offer virology based testing/screening.
Where are you looking: All of the above, so currently working with natural products (from plant and bacterial origins), targeted drug design and library based screening. Also involved in incorporating novel antimicrobials into various medical devices and efficacy testing.
Expertise required: Increasing network would be the main objective.
Expertise offered: Microbiological screening/testing with a very wide library of organisms both NCTC/ATCC and clinical.
Issues: Finding the right person to progress.
Keywords: Microbiological screening, testing.
School of Biosciences, Ingram Building, Room I321B, University of Kent, CT2 7NJ.
Overview: Natural product biosynthesis, particularly the development of synthetic routes with cell-free systems (purified enzymes, crude-extracts) for the synthesis of antimicrobials, or derivatisation into non-natural analogs.
Target: Largely Gram-positive, Streptomyces bacteria.
Where are you looking: Natural products, biosynthetic gene clusters.
Expertise required: Microbiologists with new compounds (unknown biochemistry), structural biologists with specific targets, medicinal chemists. Also development high-throughput methodologies for screening targets.
Expertise offered: Cell-free systems, combinatorial DNA assembly.
Issues: Biochemical studies on new natural products - >99% of bioinformatic data is unstudied at this level. Identifying new biological targets / bioassays, high-throughput laboratory experiments that demonstrate this.
Keywords: Natural product biosynthesis, cell-free systems, synthetic biology.
Dr Aimee Murray
University of Exeter Medical School, European Centre for Environment and Human Health, Environment & Sustainability Institute, University of Exeter Penryn Campus, Cornwall, TR10 9FE.Overview: Studying evolution of antibiotic resistance, relating findings to environmental risk assessment and environmental policy. Selection and co-selection at low concentrations of antibiotics, antimicrobials and other potentially selective compounds.
Target: Bacterial communities (mixed Gram positive and negative).
Where are you looking: Not looking for antibiotics currently.
Expertise required: Access to compounds currently being developed; or abandoned compounds for proof of concept work.
Expertise offered: Offering to test novel compounds currently under development, to provide information on selective potential, characterisation of resistance genes, mobility of genes and bacterial host in relation to green/sustainable development of novel antimicrobials.
Issues: Access to test compounds and collaborators.
Keywords: Selection, co-selection, evolution, risk assessment, green pharmacy.
Dr Noelle O’Driscoll
Robert Gordon University
School of Pharmacy and Life Sciences, Robert Gordon University, Riverside East, Garthdee Road, Aberdeen.
Overview: The main research work currently is to investigate new sources of antibiotics from soil. We are also investigating the microbial contamination of contact lenses and doing some work on veterinary pharmacy.
Target: Our specific targets are Gram positive and negative bacteria.
Where are you looking: Bacteria that are naturally occurring in the soil.
Expertise required: Collaboration with others who have expertise in unfolding the genomic sequences of bacteria.
Expertise offered: Our group is comprised of 2 microbiologists and 2 pharmacists so we could offer perspectives from both these backgrounds.
Issues: Research time as two of us have heavy teaching loads and our PhD student is part-time.
Keywords: Antimicrobial resistance, innovative methods of treating wounds, veterinary pharmacy, One Health.
Anglia Ruskin University
Sci 008, Science Centre, Anglia Ruskin University, East Road, Cambridge, CB1 1PT.
Overview: Our research group focuses on targeting antimicrobial resistance through the utilization of genetic elements involved in gene regulation. Our main target ae DNA quadruplexes; four stranded structures formed from guanine rich sequences, commonly found in promoter regions. We are particularly interested carbapenem resistance genes of Acinetobacter baumannii.
Target: Acinetobacter baumannii, Klebsiella pneumoniae.
Where are you looking: DNA-based therapeutics.
Expertise required: NMR for structural analysis; Mechanistic determination of proteins involved in genetic regulation.
Expertise offered: Identification and Characterization of Structural Genetic Elements.
Issues: Time constraints; Funding.
Keywords: Quadruplex; Gene regulation; DNA therapuetics.
Dr Soumya Palliyil
Principal Scientist & Facility Manager, University of Aberdeen
Scottish Biologics Facility, Liberty Building, Foresterhill Road, AB25 2ZP.
Overview: The Scottish Biologics Facility specialises in developing recombinant antibodies as diagnostics, therapeutics and research tools. Monoclonal antibodies and their fragments are generated from naïve and immunised phage display antibody libraries. Currently, we have a number of monoclonal antibody development programmes in therapeutic areas such as neurodegenerative diseases, invasive fungal infections, Gram negative bacterial infections and liver diseases.
Target: Gram negative bacteria and Candida albicans
Where are you looking: Our research is focused on developing biologics based novel antibacterials and antifungals mainly using recombinant antibodies
Expertise required: We are interested in collaborating with research groups with expertise in bacterial and fungal pathogenicity to identify druggable bacterial/fungal targets, develop bioassays for screening biologics binders, design proof -of-concept experiments to evaluate resistance development, animal models of infection to evaluate the potential of alternative therapies.
Expertise offered: Recombinant antibodies with high affinity and epitope specificity from naïve human and immunised phage display antibody libraries. Generation of single chain antibodies and fully human mAbs. Co- develop prescreening experiments using non-mammalian in vivo models such as Galleria mellonella.
Issues: Lack of appropriate disease models, expertise in novel antimicrobial targets, networks with a keen focus in developing alternative therapies to combat antimicrobial resistance.
Keywords: Recombinant antibody development, anti-infective biologics, Gram negative drug discovery, antifungal biologics, immunotherapy in infectious diseases.
Professor Vitor B. Pinheiro
Rega Institute for Medical Research, Herestraat, 49, Leuven 3000 Belgium.
Overview: My group focuses on developing platforms for Directed evolution with a particular focus on DNA processing enzymes and unnatural substrates. Nonetheless, those same tools have also enabled us to start developing platforms for the directed evolution of novel antimicrobials both in vitro and in vivo. At present, we focus on ribosomically-translated post-translationally-modified thiazole/oxazole-containing microcins and use the E. coli microcin B17 as our main study platform.
Target: No. Our main focus is on method development.
Where are you looking: The goal is to link unnatural substrates to the natural machinery in search of improved compounds, so closer to natural-like libraries.
Expertise required: Targets and expertise on the mechanism of natural enzymes responsible for the synthesis of antimicrobial compounds.
Expertise offered: Directed evolution, selection and screening platforms, aptamers.
Issues: Lack of students and researchers.
Keywords: Xenobiology (XNA), directed evolution, microcins, biotechnology.
Q – T
Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Northern Ireland.
Overview: Our lab specialises in bacterial biofilms, biosurfactants and antibiotic discovery mainly through Streptomyces species.
Target: We test our antibiotics mainly on multi-resistant pathogens like the ESKAPE pathogens but we also have expertise in bacterial biofilms and have recently added fungal biofilms to our repertoire.
Where are you looking: Unusual environments, extremes of physiological stresses and even ethnopharmacological recipes.
Expertise required: Small molecule separation and identification techniques. Project collaborations.
Expertise offered: New strains of antibacterial producing Streptomyces . New methods of isolation of environmental antibiotic producing bacteria. Multiresistant pathogens tests for both planktonic and biofilm physiologies.
Issues: New classes of antibiotic discovery, dereplication of useful antibiotics found, combinatorial therapeutic approaches, ie combinations of therapies that are effective against planktonic and biofilm physiologies.
Keywords: Natural Products, biosurfactants, Novel Streptomyces, Bacterial Biofilms.
Dr Paul Race
University of Bristol
School of Biochemistry, University of Bristol, Bristol, BS8 1TD
Overview: Antimicrobial natural product drug discovery, pathway engineering for functionally optimised natural product leads and structural enzymology.
Target: Bacteria, both Gram-positive and Gram-negative.
Where are you looking: Natural products from environmental microorganisms (predominantly marine sources) and rationally engineered 'non-natural' natural products.
Expertise required: Metagenomics, high-throughput sequencing, bioinformatics support, natural product pathway expression in heterologous hosts.
Expertise offered: Compound isolation and characterisation, structural enzymology, pathway engineering.
Keywords: Natural product isolation, characterisation and biosynthesis.
Professor Stephen Rimmer
Head of School and Group Lead Polymer and Biomaterials Chemistry Laboratories, University of Bradford
Overview: We are Polymer and Biomaterials Chemists working on polymers that respond to bacteria and fungi for diagnostics; we are looking at the same systems for targeting and delivery to bacteria, fungi and protozoans; Our expertise includes functional wounds dressings. We are are interested in new ligands that bind to microbes and/or working with engineers, clinicians and microbiologists to prepare new devices.
Target: Bacteria, fungi, protozoans.
Where are you looking: We look at all of these sources and are working with bioinformatics teams also.
Expertise required: We are keen to work with any other scientists or engineers and are very interested in finding ligands that bind microorganisms that may not necessarily be active as antibiotics. Compounds that bind to microbes are useful to us for binding targeting and delivery/diagnostics.
Expertise offered: We are polymer chemists and bring expertise in delivery and diagnostics.
Issues: Finding new ligands that selectively bind microbes.
Keywords: Binding, Diagnostics, Responsive Polymers, Ligands, Detection of Infection, Targeted Delivery
Dr Gary Sharples
Department of Biosciences, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE
Overview: My research group is interested in unravelling the molecular mechanisms of genetic recombination and mode of action of novel antibacterial agents and surfaces. Specifically we study molecular mechanisms of genetic rearrangements which contribute to the evolution of bacteria and bacteriophages leading to transmission of antibiotic resistance and virulence functions. We also work with chemists on the antibacterial properties of novel surfaces, peptoids and chelants.
Target: Predominantly bacteria, with most focus at present on Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus.
Where are you looking: Mainly through collaborations with chemists, looking at novel surfaces as antibacterial materials alongside modified peptides and peptoids with antibacterial activity. We are also interested in metal chelating agents and their antibacterial mode of action.
Expertise required: Collaborations with others with differing expertise in chemistry and physics. Also those with expertise in bacterial envelope biology, especially in Pseudomonas and Staphylococcus.
Expertise offered: Significant experience in microbiology, biochemistry, molecular biology with specific expertise in bacterial recombination.
Issues: Understanding the precise cellular targets of the antibacterials and taking projects to the next stage beyond basic science.
Keywords: bacteriophages, genome rearrangements, metal chelants, antibacterial surfaces, peptoids.
Dr Mark Shepherd
Senior Lecturer in Microbial Biochemistry, University of Kent
School of Biosciences, University of Kent, Kent
Overview: We are interested in how stresses encountered during infection can impact upon the efficacy of antibiotics against drug-resistant bacterial pathogens. We have a particular interest in how respiration affects antibiotic toxicity.
Target: Mainly Gram-negative (pathogenic E. coli & Salmonella), but also a little work on Gram-positives (MRSA).
Where are you looking: Environmental organisms (through antibiotics unearthed), and in the past from natural products (e.g. willow extracts).
Expertise required: Animal models, drug libraries, functional annotation of genomes, downstream identification of active compounds.
Expertise offered: Antibiotic susceptibility testing, respiratory assays via oxygen electrode, antibiotic uptake assays (LCMS), bacterial genome editing (e.g. lambda red in E. coli), proteomics, Purification of membrane proteins and ABC transporter assays.
Issues: Animal models, drug libraries, functional annotation of genomes, downstream identification of active compounds.
Keywords: E. coli, Antibiotic resistance, Respiration, Nitric oxide
Dr William Snelling
Research Associate (Microbiology), Ulster University
Nutrition Innovation Centre for Food and Health (NICHE), ‘Global Excellence in Nutrition Research & Education’, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, BT52 1SA
Overview: Enterococci antibiotic resistance.
Target: Bacteria, including Enterococci, Salmonella and Campylobacter.
Where are you looking: Environmental organisms.
Expertise required: Improvements in conjugation experimental methods and improved genomics analysis tools.
Expertise offered: Culturing difficult to culture pathogens. Working with MinION NGS technology.
Keywords: Enterococci, conjugation, microbiome, water microbiology.
Dr Jem Stach
Senior Lecturer, University of Newcastle
SNES, Devonshire Bld, University of Newcastle, NE1 7RX
Overview: Natural products from actinomycetes. Antisense approaches to antibiotic discovery. Mode-of-action discovery.
Target: Bacteria are the focus, but interested in all.
Where are you looking: Synthetic DNA mimics, natural products of microorganisms.
Expertise required: Networking to enable large multi-institute approaches to research programmes.
Expertise offered: Actinomycete biology, antisense approaches, MoA discovery approaches. If the network wishes to develop a cross-institutional teaching programme, I teach a short module in antibiotic discovery and would be happy to help with that see website.
Issues: Analytic facilities.
Keywords: Antisense antibiotics, actinomycetes, abyssomicins.
Dr Thierry Tonon
Lecturer, University of York
Centre For Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
Overview: Algal physiology and metabolism. Algal metabolic pathways and enzymes. Biotechnological applications of algae and algal genes.
Target: None currently.
Expertise required: I am not currently working on antibiotic discovery. However, if any network collaborator is interested in considering algae for their research, I may be able to help.
Expertise offered: Please see the main current activities of the team.
Keywords: Algae, metabolism, physiology, enzymes.
U – Z
Dr Martin B Ulmschneider
King's College London
King's College London, Department of Chemistry, 7 Trinity Street, London SE1 1DP, UK
Overview: De novo design of antimicrobial peptides and drug-peptide conjugates. We use molecular dynamics simulations to generate atomic detail functional structures that guide the design of new antimicrobial peptides.
Where are you looking: Natural antimicrobial peptides and de novo synthetically designed peptides, as well as peptide-small molecule conjugates.
Expertise required: Libraries of bacterial species to try our antimicrobials on and collaborators with complementary approaches. In vitro pre-clinical assays.
Expertise offered: Atomic detail molecular simulations of antibiotics with known targets and/or the cell membrane. Library-based design approaches and high-throughput screening assays.
Issues: The very small number of bacterial species we use to test our compounds on. Pharmacokinetic and toxicity assays.
Keywords: Antimicrobial peptide, in silico, molecular simulation, peptide design, peptide-drug conjugate.
Dr Michiel Vos
University of Exeter
European Centre for Environment and Human Health, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, Cornwall, UK
Overview: One focus of the lab is the ecology of virulent and antibiotic resistant bacteria. Our work currently uses bioassays isolating potentially emerging environmental human pathogens. We have also quantified antimicrobial activity of environmental bacteria, as well as of seaweeds, a group of antimicrobial producers which is especially diverse and abundant in the SW of the UK, to human (ESKAPE) pathogens.
Target: We are interested in antimicrobial interactions in all microbes as well as in macrobes.
Where are you looking: We have looked at bacterial and seaweed extracts, mainly using a ’black box’ activity approach but have dabbled in metabolomics.
Expertise required: Expertise and infrastructure in chemical elucidation of active compounds mainly, but always interested to collaborate on microbiology, ecology and evolutionary biology topics as well.
Expertise offered: Mainly in evolutionary microbiology, combining field sampling and isolation with lab experiments.
Issues: The genomic and chemical identification of antimicrobial compounds.
Keywords: Evolution, cross-resistance, antimicrobials, species interactions, virulence, emerging pathogens.
Dr Caray Walker
Lecturer in Microbiology, Anglia Ruskin University
Anglia Ruskin University, School of Life Sciences, East Road, Cambridge, CB1 1PT.
Overview: We are specifically involved in surveillance/prevalence of AMR in zoonotic pathogens and the mechanisms of resistance with the view to understanding what is required in a new drug.
Target: Bacteria, zoonotic pathogens and opportunistic pathogens e.g. Acinetobacter baumannii.
Where are you looking: We are looking at natural products and environmental organisms.
Expertise required: Experts in chemical structure of compounds.
Expertise offered: A library of characterized zoonotic pathogens that are multi drug resistant.
Issues: Money and time.
Keywords: Surveillance, zoonotic bacteria, mechanisms of AMR.
Paul Race, C101, School of Biochemistry, Biomedical Science building, University of Bristol.
Overview: Bioprospecting the deep-sea sponge microbiome to identify and isolate novel antimicrobial compounds. Techniques include classical microbiology testing, novel culturing techniques (E.g. iChip), 16S metagenomic analysis, genome assembly and subsequent genome mining.
Where are you looking: Deep-sea sponge associated bacterial metabolites.
Expertise required: Marine culturing expertise, TAR cloning understanding, expression in streptomyces, Large scale fermentation, small molecule isolation and novel bacteria characterisation and taxonomy.
Expertise offered: Chemical compound isolation and characterisation, bacterial genome assembly, bacterial genome mining, culturing deep sea bacteria with focus on actinomycetes, one strain many active compounds testing, 16S community analysis (Qiime2).
Issues: Translating preliminary agar ‘hits’ to isolation of small molecules in a liquid culture. Category 2 space for culturing attempts. Novel bacteria taxonomy and characterisation.
Keywords: Deep-sea bacteria, sponge microbiome, natural product discovery, marine actinomycetes, genome mining, 16S metagenomics, marine natural products.