Applied Enzymology and Glycochemistry

Our services are based on a combination of state-of-the-art expertise in enzymology and glycoscience. 

Enzymology and the glycosciences field (coupling glycochemistry and glycobiology) inspire many and varied academic and industrial innovations. Our experts in these fields develop powerful molecular tools for applications in agri-food, health, nutraceuticals, cosmetics, biotechnology and green chemistry.

 

Our core skills are to be found in the field of glycochemistry, focussing on the following areas: the synthesis and study of the structure of sugars, oligosaccharides and glycans; glyco-enzymology, specialising in the activity of glyco-specific enzymes; glyco-recognition (or glyco-binding).

Services

Screening

Modeling and simulations

Molecular design

Chemical synthesis

R&D projects

Whatever your challenges, our experts deliver functional and innovative solutions.

Biocatalysis: enzymatic assay and transformation

We cater for the chemical and biotech industries, as well the agri-food and health sectors, with a view to: validating an enzymatic assay method, improving the physico-chemical and rheological properties of an industrial product, and creating a functioning extraction process.

In a nutshell
SCREENING ENZYME IMMOBILISATION MOLECULAR INTERACTION PROTEINS LIGANDS ENZYMATIC ASSAY

High-throughput screening strategy of enzymatic activities

  • Collection of 300 strains: marine fungi, bacteria and microalgae
  • Search for innovative enzymatic candidates that are free to exploit
  • Analysis of genomic databases and phylogeny (ancestral genes)
  • Identification of candidate enzyme genes
  • Design of screening strategies for enzymatic diversity
  • Screening of enzymatic activities (FACS-FRET)
  • High throughput screening by cell sorting or medium throughput

Immobilization of enzymes

  • Analysis of the immobilization matrix and the type of immobilization
  • Covalent enzymatic immobilization
  • Chemical activation of commercial matrix surfaces
  • Co-immobilization and colocalization of enzymes on porous matrix

Modeling of protein-ligand interactions

  • Structural prediction
  • Docking, molecular dynamics and deep learning
  • Screening of candidates: chemical reactivity, duplicates, physicochemical properties
  • Classification of molecules: drug design, interaction modeling (ligand-protein)

Optimization of enzymatic activities

  • Directed evolution: random mutagenesis, directed and semi-directed mutagenesis
  • Creation of mutant libraries
  • Development of biocatalytic processes
  • Integration of biocatalysis strategy into existing production processes
  • Development of enzymatic assays
  • Enzyme inhibitor testing

Development of enzymatic inhibitors

  • Characterization of inhibitors on model enzymes
  • Development of new methods for the determination of enzymatic activities
  • Analysis of enzyme-substrate interaction and affinity measurements
  • Measurement of functional performance and enzymatic activities on different formulations

Production of functional enzymes

  • Identification of the expression gene
  • Study of the adaptation of strains to culture conditions
  • Stability improvement, recycling and DownStream Process
  • Optimization of enzyme production conditions: temperature, pH, salinity

Principales réactions enzymatiques utilisées pour des synthèses moléculaires

  • Hydrolyse (hydrolases)
  • Isomérisation, addition, élimination (isomérases, lyases, hydratases)
  • Création de liaisons C-N (transaminases)
  • Formation d’esters sulfate (sulfotransférases)
  • Formation et hydrolyse d’esters phosphate (phosphorylases, phosphatases)
  • Formation d’esters ATP-dépendant (kinases)
  • Formation de liaisons glucoside (glycosyltransférases, glucosidases)
  • Formation de liaisons C-C (aldolases, transcétolases)
  • Oxydation (oxydases, peroxydases)
  • Oxydoréduction des alcools et cétones (déshydrogénases)
  • Liaison amide : amidases (protéases, acylases)
  • Liaison ester (estérase, lipase)

Recombinant protein production

Our experts, who are specialised in producing recombinant proteins and synthesising peptides, possess outstanding know-how in protein engineering and bioinformatics.

From structural modelling to the genetic modification of enzymes, Capacités offers tailor-made services: screening enzyme strains, developing and refining new enzymes and producing functional and modified enzymes.

There are innumerable fields of application that cover not only the agri-food sector, but also extend to chemistry, biotechnology, cosmetics, nutraceuticals and health.

In a nutshell
MOLECULAR CLONING MUTAGENESIS AMINO ACIDS PROTEIN CHARACTERISATIONPROTEIN PURIFICATION FUNCTIONALISATION

Molecular cloning

  • Molecular cloning and subcloning of vectors
  • Custom design of strain-dependent expression vectors: host-specific promoter, selection gene, tag insertion
  • Study of strain adaptation to culture conditions
  • Optimization of enzyme production conditions: temperature, pH, medium
  • Stability improvement and DownStream Process

Directed mutagenesis and directed evolution

  • Sequence analysis: in silico structure/activity study
  • Molecular modeling: regioselectivity improvement
  • Generation of mutant libraries
  • Screening of enzymatic activities / substrate
  • Substrate characterization
  • Random mutagenesis
  • DNA shuffling

Incorporation of non-natural amino acids

  • In vitro incorporation: by pre-coupling of tRNA or by chemical synthesis
  • In cellulo incorporation, via cellular tRNA synthetases: residue-specific method and site-specific method
  • Optimization, development of specific strains

Protein characterization and purification

  • Protein purity evaluation: electrophoresis, spectroscopy (Nanodrop), Bioanalyzer
  • Structural prediction
  • Candidate screening: chemical reactivity, duplicates, physicochemical properties, docking, molecular dynamics and deep learning
  • Molecule ranking: drug design, interaction modeling (ligand-protein)

Functionalization of proteins and biomolecules

  • Click chemistry and macromolecular engineering
  • Bioconjugation (biodetection, FRET, …)
  • Chemical/electrochemical modification of residues in situ (Lys, Tyr, Cys)
  • Incorporation of activatable chemical functions
  • Modification of the physicochemical properties of biomolecules by enzymatic way
  • Immobilization or biological marking

Glycochemistry

In the form of either a service or a collaboration, we provide the chemical synthesis and functionalisation of saccharide structures. Our activities are centered on developing glycoconjugates, glycoclusters and glycovaccines, as well as lectin and glycosidases modulation.

In a nutshell
GLYCOSIDE SYNTHESIS CREATING GLYCOCONJUGATES GLYCOMOLECULE ASSAY FUNCTIONALISATIONBIOCONJUGATION

Synthesis of glycosides

  • Orthogonal protection/deprotection
  • Selective functionalizations
  • O, S, C, N-glycosides
  • Cyclodextrin chemistry
  • Multivalence/polymers
  • Glycosidase inhibitors/activators
  • Glyco-nanoparticles

Development of glycoconjugates

  • Lys, Tyr, Cys functionalizations by bioconjugation
  • Electrochemical functionalizations
  • Affinity-guided bioconjugations
  • Site-selective conjugation (site-directed mutagenesis, incorporation of non-natural amino acids, metabolic functionalization)

Determination of glycomolecules

  • Analysis of reaction mixtures
  • Capillary electrophoresis
  • HPAEC-PAD…

Glycobinding

Sugar/protein (enzyme/lectin) interactions are at the heart of cellular communication: with cell-cell, cell-matrix and host-pathogen interactions on an extracellular level; and GlcNAcylation, as a post-translational modification, on an intracellular level.
Our teams are renowned for their expertise in the fields of Glycobinding and sugar-protein interaction analysis.

In a nutshell
MOLECULAR INTERACTIONS CHEMICAL SYNTHESIS LECTINS/GLYCOSIDASES MOLECULAR AFFINITY ENZYME ACTIVITY

Modeling of molecular interactions

  • Drug design
  • Docking, molecular dynamics
  • Virtual screening
  • Structural (molecular and protein)

Chemical synthesis of glycoligands/glycoconjugates

  • Synthesis of lectin/glycosidase inhibitors
  • Synthesis of oligosaccharides by glycosylations
  • Chemical/electrochemical methods of bioconjugation

Production of lectins/glycosidases

  • Production of recombinant proteins
  • Truncation: production of protein fragments or domains
  • Mutagenesis
  • Incorporation of non-natural amino acids
  • Structural integrity analysis
  • Stability analysis

Molecular affinity measurements

  • Chemical library screening
  • Activity and inhibition measurements
  • IC50, Ki measurements (interaction inhibition)
  • Isothermal microcalorimetry, Surface Plasmon Resonance, FRET
  • Fluorescence polarization
  • Technology a, label free

Measurement of enzymatic activity

  • Determination of kinetic constants
  • Characterization of substrate specificity
  • Enzyme activity screening: lipases, glycoside hydrolases, sulfatases, sulfotransferases, monooxygenases
  • Enzyme stability/reactivity studies (temperature, pH…)

Cyclodextrin micro-encapsulation

The formation of inclusion complexes allows for the modification of a molecule’s physical, chemical and biological characteristics.
Our experts in sugar chemistry and encapsulation constantly strive to provide answers to the complex issues of stability and solubility, as well as the prolonged and controlled release of active ingredients over time. Our specialisation lies in optimising the affinity of cyclodextrin for the ligand. We chemically modify the properties of the cyclodextrin in order to obtain a precise encapsulation of the ligand.

In a nutshell
INCLUSION COMPLEXATION CYCLODEXTRIN-LIGAND AFFINITY SOLUBILITY STABILITY CAPTURE

Improvement of inclusion properties

  • Selective functionalization of cyclodextrins
  • Chemical modification of commercial cyclodextrins
  • Monofunctionalization of cyclodextrins
  • Synthesis of anionic, cationic and ambiphilic cyclodextrins

Complexation studies

  • Preparation of inclusion complexes
  • Encapsulation of molecules of biological interest/active principles, ingredients, agro-foods, peptides
  • Kneading, freeze-drying, co-precipitation, microwave methods
  • Formulation in powders to be reconstituted
  • Characterization of association constants

Determination of cyclodextrin-ligand affinity constants

  • Titration by 1H-NMR
  • Determination by UV
  • Determination of the stoichiometry of complexes
  • Higuchi’s method

Study of the aqueous solubility by phase diagram

  • Setting up of adapted protocols
  • Determination of the types of phase solubility diagrams (Ap, Al, An, Bs)
  • Solubility of complexes formed in aqueous solution
  • Release kinetics under different conditions (pH, temperature)

Stability study of encapsulated molecules

  • Thermal and photochemical degradation
  • Degradation kinetics by HPLC, NMR
  • Thermal analysis: TGA, DTG

Entrapment of active ingredients: antagonistic cyclodextrins

  • Design of cyclodextrins for decorporation
  • Decontamination of water and soil
  • Control of aroma release and entrapment
  • Cyclodextrins for the formulation of cosmetic products or drugs


Engineering at Capacités

Our chemistry and enzymology experts perform their engineering duties in the very research laboratories of Nantes Université themselves, most notably at US2B and CEISAM. They strive to combine technical resources and scientific discovery to meet your R&D needs.

Our projects

Challenges we’ve met

Capacités develops an enzyme for biotech company DNA Script

Sourcing, modeling and high-throughput screening of DNA synthesis enzymes

Read this success story

Enzymes at the Heart of Cell Therapy

A company that manufactures pharmaceutical grade hyaluronic acid contacted Capacités’ enzyme engineering experts: the company aims at developing a new deacetylation process which keeps overall polymer structure while increasing its interactions with stem cells.

Read this success story

Incorporating a biocatalyst into a food product

Cycle Farms asked Capacités experts to support them in the development of the transformation and preservation process of its product.

Read this success story

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