Objectives: To determine the mechanism ClpXP protease contribute to intrinsic resistance to cell wall antibiotics and the role of autolysins in killing by b-lactams.

Expected Results: 1) The molecular mechanism behind the emergence of Clp mutants emerge against clinically applied antibiotics (e.g., β-lactams, vancomycin, daptomycin) has been elucidated, 2) The role of autolysins in b-lactam mediated killing of G+ pathogens (MRSA) has been determined.

PhD fellowship in “Bacterial Antibiotic Resistance Mechanisms” | EURAXESS (europa.eu)

Objectives: To construct a map of interactions of major cell wall proteins including the PBPs and those involved in teichoic acid synthesis.

Expected results: 1) A protein interaction map pointing to key interaction points linking cell envelope biosynthesis with central components of the cell division machinery, 2) prediction of key proteins to be mined as potential hits.

Objectives: To identify novel antimicrobial activities from variants of poorly explored classes of known metabolites and of metabolites predicted not to be associated with known classes.

Expected Results: 1) Chemical structures of at least 3 metabolites and 2) their antimicrobial activities of the identified molecules.

Position available at Naicons, IT | EURAXESS (europa.eu)

Pablo C. Hisbert

Education and experience:

I graduated with a BSc in Biochemistry and Pharmacology from The University of Strathclyde in Glasgow. For my thesis project I screened Actinobacteria extracts for antimicrobial substances active against ESKAPE pathogens.

I proceeded to complete an MSc in Industrial Biotechnology organised by the Industrial Biotechnology & Innovation Centre of Scotland (IBioIC). During my MSc placement I investigated the potential of including biomass-derived materials in hydrogels for drug delivery.

Later I moved into industry and worked for 3 years at MiAlgae Ltd, a biotechnology start-up based in Edinburgh that produces Omega-3 and other value-added products from industry byproducts. As part of the R&D and Tech Transfer teams I contributed to the development, optimisation, and scale-up of a bespoke fermentation platform, expanding upon the Scottish circular economy.

I am now excited to join Naicons Srl and the CLEAR doctoral consortium to work towards the discovery of antibiotics and other novel microbial natural products of industrial relevance.

Project brief overview:

This project will mine metabolomic data from the MICRO4ALL platform – a microbial database & gateway recently developed by Naicons Srl - and will use a paired omics approach to identify, purify, and characterise novel active antimicrobials to later determine their mode of action.

Project Description

Clostridioides difficile is the leading cause of antibiotic-associated diarrhea worldwide, contributing to significant mortality. This bacterium exhibits resistance to several beta-lactam antibiotics, which inhibit the transpeptidation of peptidoglycan, a crucial component of the bacterial cell envelope. C.difficile peptidoglycan has a unique composition, consisting of 3-3 cross-links catalyzed by L,D-transpeptidases (Ldts). These enzymes are poorly inhibited by beta-lactams, suggesting that their activity may underlie the observed antibiotic resistance. The C. difficile genome encodes three Ldts with canonical YkuD domains and two with VaW domains. Despite their structural and evolutionary differences, both enzyme classes perform the same transpeptidation reaction, offering intriguing insights into their functional convergence.

In my project, I will focus on determining the protein structures of C. difficile L,D-transpeptidases. This will involve protein expression and purification, crystallization, X-ray data collection at synchrotron radiation facilities, and analysis of protein-protein and protein-ligand interactions. Using insights from the catalytic mechanisms derived, I aim to design new molecules that specifically inhibit L,D-transpeptidase activity and assess the impact on sporulation and resistance to cell wall antibiotics in vancomycin-resistant C. difficile.

Sara Ait Ikene, Email: sikene@iqf.csic.es

Affiliation:
Instituto de Química-Física Rocasolano
Department of Cristallography and Structural biology
Calle de Serrano 119
28006 Madrid

Education and Experience

I have a bachelor degree in Biological Science and a master degree in Molecular and Cell Biology.  I conducted my bachelor's thesis at CIBIO within Professor Vito D’Agostino's laboratory. The internship focused on investigating the interaction between two proteins, TDP-43 and VAPB, linked to the development of amyotrophic lateral sclerosis (ALS) in humans.

During my master thesis I decided to focus on plant biology for research because I was always fascinated with their intricate biology and numerous possibility they offer. I wanted also to make an experience abroad, as I knew I would benefit from an international context and seeing new research realities.  For these reasons I started an internship of 1 year in the laboratory of prof. Yasin Dagdas at the Gregor Mendel Institute in Vienna. The aim of this internship was to establish an evolutionary framework that elucidates the mechanisms by which conserved protein complexes, such as the exocyst, evolve over time and acquire novel functionalities within the cell while maintaining their original function. To accomplish this goal, I employed a trans-species approach, combining immunoprecipitation coupled with mass-spectrometry to study the interactome of the plant exocyst subunit, Exo70, using three model organisms: Arabidopsis thaliana, Marchantia polymorpha, and Chlamydomonas reinhardtii. After completing my master's degree, I participated in a three-month summer school at the laboratory of Prof. Jiri Friml at the Institute of Science and Technology Austria in Klosterneuburg, near Vienna. During this period, I explored the roles of MAKR 2/6 in auxin canalization and auxin activation of ROPs, utilizing Arabidopsis thaliana and Nicotiana benthamiana for my research.

In pursuing my PhD, I was eager to try something new from my previous studies, driven by my curiosity to learn more and desire to expand my expertise. During my master’s work, I was interested in structural biology, particularly  Cryo-electron microscopy and X-ray crystallography, which were used by some colleagues. I want to dive deeper into this field and specialize in it because I find it intriguing to understand the complex architectures of biological molecules and their functional implications and for this reason I applied for a PhD position in the group of prof. Juan Hermoso in Madrid inside the CLEAR consortium.

Objectives: To demonstrate efficacy of computer assisted drug design (CADD) methods on antimicrobial targets in the bacterial envelope with focus on LD-transpeptidase from C. difficile. Preliminary synthetic optimization of hits to select most promising for further development.

Expected Results: 1) To have identified novel inhibitors of LD-transpeptidases of C. difficile and of two targets identified in the project; 2) To have derivatized hits obtained by analysis of at least one LD-transpeptidase.

Project Description

The liberal use of antibiotics in the past decades has resulted in a growth of antibacterial resistance. Gram-positive bacteria have shown to be able to acquire resistance to virtually all antibiotics, while at the same time, the arsenal of effective antibiotics is shrinking. The rise of multi-antibiotic resistant bacteria represents one of the most urgent challenges to global human health. The effects of antibiotic resistance are devastating, with at least 1.2 million yearly deaths worldwide.

Antibiotics like penicillin, target the bacterial cell wall synthesizing enzymes of the DD-transpeptidase class (Penicillin binding proteins, PBPs). These beta-lactams inactivate the DD-transpeptidase (PBP), thereby disabling their functioning. This renders bacteria unable to construct enough peptido-glycan bonds per second to constitute an effective cell wall. Loss of cell wall barrier function kills the bacterium.

Recent discoveries suggest that certain strains of gram-positive bacteria can employ another class of cell wall synthesizing enzymes, LD-Transpeptidases (LDts), in the construction of alternative peptido-glycan motifs. This bypasses the lethal effects of antibiotics that inactivate their PBPs. These bacterial LDt proteins seem to be unaffected by beta-lactam antibiotics that normally target PBPs. This secures survival of the bacterium through continued cell wall synthesis even when their DD-transpeptidases are taken out of action by (for instance) beta-lactam antibiotics as penicillin.

Recent studies have pointed towards the effectiveness of LD-transpeptidases to confer resistance to beta-lactam antibiotics in bacteria such as (but not limited to) Staphylococcus aureus, Mycobacterium tuberculosis, Clostridioides difficile.
Investigation of inhibitors towards LD-transpeptidases would therefore possibly result in finding novel inhibitors that provide an alternative to defeating drug-resistant strains of these gram positive bacteria.

In our research, I will employ computer aided drug design (CADD) to analyse protein models of LDts arising from models which include X-ray protein crystal structures from an array of species. These protein models will be applied to in silico docking studies of putative inhibitors of LDts. Modelling results will enable the design of inhibitors which will be synthesised and validated in enzymatic assay by project CLEAR partners from CSIC (Spain). The validated hits will be used as templates for design of improved analogues by input of co-crystallisation X-ray crystallography studies using LDts, performed by collaboration partners from CSIC (Spain). The designed compounds will be synthetically prepared leading to potent LDt inhibitors. These will be used as tool compounds for investigation of their antibacterial potency and will serve as leads for extended drug discovery programs.

In this project I will perform secondment research at the Institute of Physical Chemistry "Blas Cabrera" (CSIC) Madrid, Spain. At the department of Crystallography and Structural Biology in the research group of Prof. Dr. Juan A. Hermoso Domínguez where I will learn more about protein X-ray crystallography. Later in my PhD I will perform secondment research at the University of Copenhagen where I will apply bacterial studies to discovered lead compounds.

Novel inhibitors capable of defeating drug-resistant strains of these gram positive bacteria will yield us a significant victory in our fight against drug-resistant bacterial disease.

Sjoerd van der Gun
E-mail: sjoerd.van.der.gun@osi.lv

Affiliation:
Latvian Institute of Organic Synthesis
Aizkraukles iela 21
Vidzemes priekšpilsēta
Rīga, LV-1006

Education and Experience

I hold a Bachelors of applied science in Chemistry with minors in Analytical and Organic Chemistry, as well as a Masters of Science in Chemistry, with a specialisation in Research.

In the pursuit of my Bachelor's degree at Avans University ATGM (Breda), I delved into both practical and theoretical aspects of Organic Chemistry. I engaged in a diverse range of classes, while contributing to interdisciplinary research projects.

Across my BSc. and MSc. , I undertook three research internships, each contributing significantly to my growth as a researcher. One of the highlights of my Bachelors was a six-month internship in Japan, where I assisted the exploration of synthetic routes in a total synthesis project. In the Gousei research group at the Graduate School of Pharmaceutical Sciences under Prof. Dr. Takasu & Prof. Dr. Takikawa, I learned the fundamentals of exploratory chemical synthesis, as well as experiencing the unique culture and warm hospitality of Japan. 

Building on the success of my internship in Japan, I further honed my research skills during a subsequent

Internship spanning six months at the Radboud University, Nijmegen.
Here at Institute for Molecules and Materials in the Rutjes research group I explored the synthetic chemistry of octagonal heterocycles. Here I focused on investigating key reactions for the production of starting material for futher photo-flow production of building blocks for orthogonal in vivo anti-tumor medication, which employed click-to-release chemistry. 

Continuing the journey into my Master's program at the University of Leiden, amidst the challenges posed

by the pandemic, I followed a year of classes aimed at widening my skillset. I followed excellent classes on Biochemistry, Immunology and Theoretical Synthetic Chemistry. After which I followed a year-long research internship at the Overkleeft research group of the University of Leiden under Prof. Dr. Jeroen Codee.

During this work, I contributed to the production of promising epitope candidates for the development of glycoconjugate vaccines against drug-resistant s.aureus infections, through successful construction of a robust synthetic method. I finished my MSc. of Chemistry with a large literature thesis that focused on strategies for beating bacterial resistance through deception.

After graduating, I taught for a short period as a chemistry teacher's assistant at Mgr. Frencken College, where I had the privilege of sharing my passion for chemistry.

My interests in developing new synthetic methodologies and strategies in support of solving the problem of bacterial resistance will be central in my work at the Organic Synthesis Methodology group of Professor Doctor Aigars Jirgensons, in the Latvian Institute of Organic Science.

I approach the prospect of a PhD. with enthusiasm and a deep sense of gratitude for the opportunities that education has afforded me. This enthusiasm propels me to contribute meaningfully to the scientific community and, together with my collegues in this Maria Skłodowska-Curie fellowship, find elegant answers to complex questions.

Objectives: To identify and characterize compounds that maintain ticagrelor antibacterial activity but are devoid of antiplatelet effect among a hundred of ticagrelor-derived pyrimidine compounds synthesized by ULiège. About twenty of these molecules, triazolo-pyrimidines and purines, display potential antibacterial activity as ticagrelor. All of these molecules are patented.

Expected Results: 1) Ten derivatives of ticagrelor with antibacterial activity but lacking the antiplatelet activity have been identified and 2) To derivatives have been characterized in detailed in in vivo assays.

Objectives: To determine the mode of action in penicillin/β-lactamase inhibitor killing of MRSA and MDRSE. To identify the optimal penicillin/β-lactamase inhibitor combinations (with and without other potentially potentiating drugs) and dosage regimens using checkerboard assays. To access the efficacy of the best penicillin/β-lactamase inhibitor combination(s) in in vitro and animal models of biofilm- and non-biofilm-related infections.

Expected Results: 1) The mode of action has been identified; 2) The efficacy of the best combination(s) has been tested.

Objectives: To determine if combined use of antibiotics and phages can enhance bacterial killing with reduce resistance development, and determine the overlaps in molecular targets of phages and antibiotics, respectively.

Expected Results: 1) Identification of combination treatments that enhance bacterial killing with limited resistance development 2) Knowledge on bacterial pathways that may be triggered to enhance phage therapy against G+ pathogens.

PhD9 – Phage combination therapy

Project Description

Effective treatment of staphylococcus aureus is today currently hindered by the emergence of multi-drug resistant variants and have become a global issue for the clinic. Previously, the use of the drug methicillin and vancomycin was the last line of treatment, however, with the emergence of methicillin- and vancomycin resistant staphylococcus aureus, our options today are limited. The need for new antibiotics and new therapeutic alternatives therefor must be investigated to combat this pressing issue. One possibility is phage therapy, a previous used treatment alternative which vanished with the emergence of antibiotics but have recently reemerged to become a promising candidate. By using bacteriophages that specifically infect staphylococcus aureus, we can alleviate the occurrence of new mutations from use of antibiotics and hopefully solve this issue. 

The aim of my project is to identify bacterial pathways or factors that are determining for the efficacy of phage infection and thereby for the use of phages in phage therapy. To do so, I will screen for a large library of drugs which could support phage infection and identify bacterial pathways that may be triggered to enhance phage mediated killing. Hopefully, this would also lead to identification of secondary phage receptor sites as the wall-teichoic acid is currently the only known receptor site for phage uptake. My Secondment will be conducted at NAICONS (Italy) which is where I will be screening their library of drugs for suitable candidates that could enhance phage killing.

Frederik Pedersen

Email: f.pedersen@sund.ku.dk

Affiliation:
University of Copenhagen
Department for Veterinary and Animal Sciences
Stigbøljen 4
1870 Frederiksberg C 

Education and Experience: 

In June 2021, I acquired a BSc in biology at Linköping’s University, Sweden. During my bachelor’s, I got to experience everything related to cell- and molecular biology, pharmacology, microbiology and physiology. At the time, I really enjoyed medical physiology and therefore made it my specialization. For my bachelor’s thesis, I joined the group of Professor Jordi Altimiras in organ physiology. The project was based on previous data which indicated to survive birth, the organs of neonates must drastically develop to survive leaving the egg or the mother’s womb. My project was therefore to investigate and confirm whether there was a difference in organ mass leading up to hatching by dissecting and analyzing red junglefowls (Gallus Gallus) pre- and post-hatchlings. 

I’ve always loved to learn new things and explore new areas and, I knew from my bachelor’s that I also had a big interest for systems biology, immunology and microbiology. With this, I wanted to expand on my knowledge in medical physiology. I therefore achieved in 2023 a master’s in Immunology and Microbiology with an emphasis on host-pathogen interactions at Uppsala University, Sweden. During my Master’s, I joined Associate Professor Erik Holmqvist’s group at Uppsala University in molecular microbiology. My project revolved around post-transcriptional regulation of Salmonella pathogenicity Island 2 (SPI-2), one of the key regions of genes involved in Salmonella pathogenesis.  More specifically, my project was to investigate whether there was an interaction between the global RNA binding proteins Hfq and ProQ on the phoP 5’UTR. My work also led me to investigate the small RNA ArcZ, to see if it repressed the expression of phoPQ mRNA and if the binding was dependent on Hfq. 

During and after my master’s studies, I also worked in the industry for Olink Proteomics as a laboratory Engineer in proteomics. I always knew I wanted to pursue a PhD and knew it had to be related to microbiology and host-pathogen interactions. After a year in the industry post-graduating, I finally found a PhD I really wanted and started 1^st of May 2024 in Hanne Ingmer’s group at Copenhagen University as part of the CLEAR project. 

Objectives: To develop novel phage based endolysins as antimicrobials against C. difficile and MRSA

Expected Results: 1) At least four endolysins discovered with efficacy against MRSA and C. difficile and 2) two endolysins characterized in gut models and by 3D structure (together with PhD5).

https://euraxess.ec.europa.eu/jobs/190023