PhD position – Towards an artificial INTelligence appRoach for the discovEry of metal-chelating PeptIDes for Emulsions applications

Title of the PhD: “towards an artificial INTelligence appRoach for the discovEry of metal-chelating PeptIDes for Emulsions applications”

Key words: peptides, enzymatic hydrolysis of proteins, screening, metal-chelating peptides, coordination chemistry, emulsions.

Modalities of supervision, follow-up of the training and progress of the doctoral student’s research.

This thesis attached to the doctoral school SIMPPE of the Université de Lorraine (UL) will be directed by Laetitia Canabady-Rochelle (CNRS Research scientist, HDR, attached to LRGP, UMR 7274 CNRS-UL) and co-directed by Katalin Selmeczi (Associate Professor, UL, HDR, attached to L2CM, UMR 7053 CNRS-UL). It also involves other UL scientists, notably Roda Bounaceur (LRGP, IR developing the computer code) and Cédric Paris (IR, PASM platform manager). An international mobility of 4 to 6 months is planned in the team of Professor Charlotte Jacobsen (Danish Technological University, DTU, Denmark) in order to study the capacity of metal complexing peptides to inhibit lipid oxidation in emulsions. The student will carry out his thesis between these two laboratories and some of his experiments will be carried out on state-of-the-art equipment present on the platforms of the University of Lorraine (PASM, ASIA, B2S, PhotoNS). Regular follow-ups will be made with his/her supervisors. An individual follow-up committee of the PhD thesis will be carried out each year.

Summary of the PhD. In an ecological transition context related to the bioeconomy, there is a huge importance to discover new biomolecules while exploiting and valorizing coproducts generated by the agro and food industries. Indeed, such by-products are rich in proteins, that can be transformed by proteolysis in peptide hydrolysate. These peptide hydrolysates constitute a bank of peptides in which to screen bioactivities and biofunctionalities. Among them, metal-complexing peptides (MCPs) are of specific interest since they can find various applications according to the target metal ion. While complexing Fe2+ or Cu2+, they can act as an indirect antioxidant and find notably some applications in emulsions for inhibiting lipid oxidation. In our scientific consortium, we developed various experimental strategies for screening and separating Metal-Chelating Peptides from peptide hydrolysate. Currently another approach is under development with the building of a software. This latter one will serve as an IA guided approach to screen the presence of MCPs in various theoretical hydrolysate produced in silico from various theoretical proteins sequences, submitted to various theoretical hydrolysis treatment and complexation rules. In this context, the aim of this PhD thesis is to validate experimentally the construction of this internal software enabling the theoretical screening of MCPs in hydrolysate and enrich it in various enzymatic and complexation rules.

Themes: Proteolysis, peptide hydrolysate, peptide, metal complexation, screening, SPR, mass spectrometry

Field: Biochemistry of proteins and peptides, biotechnology, coordination chemistry, physicochemical analysis.

Context. In a context of ecological transition linked to the bioeconomy, it is essential to discover new biomolecules while exploiting and valorizing the co-products generated by the agro-food industries. The cakes co-generated during oil production are rich in proteins (~30% by mass). Commonly used for animal feed, the proteins contained in these co-products could be extracted and valorized after proteolysis for the bio-functional peptides they contain. Indeed, the presence of such target peptides has been reported in protein hydrolysates for their antioxidant, antihypertensive or antimicrobial properties (1,2). Among the functional properties, some studies have highlighted the presence of metal-chelating peptides (MCP) in protein hydrolysates (3, 4). However, depending on the nature of the complexed metal ion, MCPs may have different bioactivities beneficial for nutraceuticals, cosmetics or health (5). For example, by complexing iron and copper, PCMs could inhibit lipid oxidation in emulsion systems and serve as an alternative to EDTA-type preservative (6).

Objectives. The objective of this thesis is (i) to continue the development of an in-house software for in-silico screening of metal complexing peptides with the help of a computer scientist and (ii) to validate its performances by various experiments (proteolysis, SPR screening, mass spectrometry, IMAC separation), to guide the experimental approach for the screening/separation/identification of metal-complexing peptides in various protein resources (performed at UL, France) and (iii) to evaluate their ability to inhibit lipid oxidation in emulsions (DTU partnership, Denmark).

Method. After a first step of bibliography, allowing to define the rules of proteolysis and complexation of metals, these will be coded in a specific software under construction in the French laboratory. This software, built with the help of a computer scientist, will allow the in-silico screening of metal complexing peptides. In a second step, these theoretical results obtained via this software will have to be validated using various experiments of proteolysis (different sources of proteins and proteolytic enzymes), screening (optical techniques by SPR and SwithSENSE, mass spectrometry, study of complexation by spectroscopy) and separation (affinity chromatography of IMAC type). These validation experiments will be carried out both on peptide hydrolysates but also on synthetic peptides to have a more detailed knowledge of the complexation phenomena. In a third phase of the project, the most promising metal complexing peptides will be evaluated for their ability to inhibit lipid oxidation in emulsions, during an international mobility carried out at DTU.

The expected results are (i) the internal computer code of the LRGP implemented for proteolysis and metal complexation rules allowing an in-silico screening of metal complexing peptides, (ii) the experimental validation of the in-silico rules implemented in the code and its application for the screening of the best hydrolysates in terms of MCPs and (iii) the stabilization of emulsions against oxidation phenomena using MCPs and hydrolysates.

Scientific, material (specific security conditions) and financial conditions of the research project. The student will be recruited on a thesis contract (3-year fixed-term contract) according to the regulations applied in France.

International opening. The student will spend 4-6 months at DTU in Denmark in Prof. Charlotte Jacobsen’s team in order to study the ability of the most promising hydrolysates and peptide sequences to inhibit lipid oxidation in emulsion-like systems.

Envisaged collaborations: An international collaboration is envisaged with the group of Pr. Charlotte Jacobsen at DTU.

Objectives of the valorization of the PhD student’s research work: diffusion, publication and confidentiality, intellectual property rights. The results of this thesis will be valorized in different forms: scientific publications, oral and poster presentations during various scientific events (doctoral school day, workshop, national and international congresses). If the results prove to be interesting from an application point of view, they will be valorized in the form of a patent before publication. In addition, the PhD student will be asked to participate in various scientific mediation events to promote the science-society dialogue.

Profile and skills required: The recruited candidate will ideally have a biochemist/biotechnology engineer background with an interest in chemistry, in particular with regard to the study of peptide-metal interactions (coordination chemistry). He/she should be able to communicate with the computer engineer who will code the software according to the rules of proteolysis and peptide/metal complexation as defined in the literature. Having an experimental profile, the recruited candidate will have to be able to carry out various physicochemical analyses. He/she will have good writing and communication skills in English. Knowledge of bioinformatics software would be a plus.

Confidentiality of the work: NO

Web link with additional information on the subject

Application deadline: June 26, 2023. 

Following the evaluation of the applications, the selected candidates will be auditioned (conditions of the audition given later).

Application file: the application file must include the following elements 

– M1 and M2 grades

– CV

– Letter of motivation

– Letter(s) of recommendation from teachers and scientific supervisors

– Activity report on the research internship carried out in M2 in English of a maximum of 2 pages, in order to demonstrate one’s ability to communicate on the progress of this research work.

The whole file should be sent to Laetitia Canabady-Rochelle and Katalin Selmeczi.

laetitia.canabady-rochelle@univ-lorraine.fr

katalin.selmeczi@univ-lorraine.fr

Références bibliographiques

[1]  Chalamaiahet al., Regulatory requirements of bioactive peptides (protein hydrolysates) from food proteins. Journal of Functional Foods, 2019, 58, 123–129. https://doi.org/10.1016/j.jff.2019.04.050

[2] Liu et al., Safety considerations on food protein-derived bioactive peptides. Trends in Food Science and Technology, 2020, 96, 199–207. https://doi.org/10.1016/j.tifs.2019.12.022

[3] Wang et al., Separation and identification of zinc-chelating peptides from sesame protein hydrolysate using IMAC-Zn2+ and LC-MS/MS. Food Chemistry, 2012, 134(2), 1231–1238. https://doi.org/10.1016/j.foodchem.2012.02.204

[4] Megías et al., Production of copper-chelating peptides after hydrolysis of sunflower proteins with pepsin and pancreatin. LWT – Food Science and Technology, 2008, 41(10), 1973–1977. https://doi.org/10.1016/j.lwt.2007.11.010

[5] El Hajj et al., Application in Nutrition: Mineral-Binding. 2021. Elsevier Book chapter 19 in Wu, J. and Toldra, F. Book title: Biologically Active Peptides. In press.

[6] Irankunda et al., Inhibition of lipid oxidation in oil-in-water emulsion by metal-chelating peptides and pea hydrolysates. Article in progress.

Autres références de l’équipe en lien avec le sujet : 

[10] El Hajj et al., Application in Nutrition: Mineral-Binding. 2021. Elsevier Book chapter 19 in Wu, J. and Toldra, F. Book title: Biologically Active Peptides. In press.

[11] El Hajj et al., Metal-chelating activity of soy and pea protein hydrolysates obtained after different enzymatic treatments from protein isolate. Food Chemistry, 2022, 405(2023) 134788. https://doi.org/10.1016/j.foodchem.2022.134788

[12] Canabady-Rochelle et al., SPR Screening of Metal-chelating Peptides for their Antioxidant Properties. Food Chemistry, 2018, 239, 478–485. http://dx.doi.org/10.1016/j.foodchem.2017.06.116

[13] El-Hajj et al., Electrically switchable nanolever technology for the screening of metal-chelating peptides in hydrolysates. Journal of Agricultural and Food Chemistry, 2021, 69, 8819–8827. https://doi.org/10.1021/acs.jafc.1c02199

[14] Paris et al., Metabolomic approach based on LC-HRMS for the fast screening of iron-(II)-chelating peptides in protein hydrolysates. Analytical and Bioanalytical Chemistry, 2021, 413, 315–329. https://rdcu.be/ccYI4

[15] Muhr et al., Chromatographic separation simulation of metal-chelating peptides from surface plasmon resonance. Journal of Separation Sciences, 2020, 43, 2031–2041. http://doi.wiley.com/10.1002/jssc.201900882

[16] Irankunda et al., Metal-chelating peptides separation using immobilized metal ion affinity chromatography: experimental methodology and simulation. Separations, 2022, 9, 370. https://doi.org/10.3390/separations9110370

[30] Csire et al., Both metal-chelating and free radical-scavenging synthetic pentapeptides as efficient inhibitors of reactive oxygen species generation. Metallomics, 2020, 1–10. http://doi:10.1039/d0mt00103a

[31] Csire et al., Bio-inspired casein-derived antioxidant peptides exhibiting a dual direct/indirect mode of action. Inorganic Chemistry, 2022, 1941-1948. https://doi.org/10.1021/acs.inorgchem.1c03085