Team « Biomolecules: Syntheses and Mechanisms of Action » (BSMA)

Coordinator: A. Haudrechy

Research studies of BSMA team are organised around three groups (CIE, C2R, GeM):

"Design of Enzymatic Inhibitors" group (in french: Conception d’Inhibiteurs Enzymatiques / CIE)

Keywords: Heterocyclic Chemistry, Chemodiversity, Pharmacochemistry (Structure-Activity Relationships, «hits detection »,…).

Coordinator: S. Gérard

Thematic Scopes: The "Design of Enzymatic Inhibitors" group focuses its activities on the research of structural chemo-diversity in order to develop innovative pharmacophores answering to problematics submitted by biologist collaborators.

Project: The "Design of Enzymatic Inhibitors" group is interested in the development of new heterocyclic entities contributing to a better understanding of the role of phosphodiesterases in the physiopathological mechanisms especially associated to chronic obstructive pulmonary diseases (COPD, asthma, cystic fibrosis…) as well as tumor processes.

Human Perimeter: Erika Bourguet Assistant Professor, Marie Cochard Assistant Professor, Stéphane Gérard Assistant Professor, Janos Sapi Professor.

Collaborators associated to the project: F. Vélard (BIOS, EA 4691), L. Meyer (Roscoff), A. Bentaher (CIRI U1111), J.-P. Bouillon (COBRA, UMR 6014), G. Nowicka (Medical University of Warsaw) and B. Brassart (MEDyC, UMR 7369)

"Conformation, Restriction and Rationalisation" group (C2R)

Keywords: Photochemistry, Atropoisomers, Modelling, Biomolecules.

Coordinator: C. Denhez

Thematic Scopes: The "Conformation, Restriction and Rationalisation" group is committed to fundamental and applied study of the conformational impact governing biological phenomena such as the formation of DNA photoproducts and interaction with their biological target of synthetic molecules having a constrained axis of rotation.

Projects: i) Study of the impact of the introduction of conformational constraints on the formation of DNA photoproducts; iii) Synthesis and conformational study of cannabidiol derivatives for anti-tumoral purposes; iii) Photochemical synthesis, conformational study and biological activity of inhibitors of neutrophil elastase (NE) with a alpha,beta-dicarbonylepoxide backbone. NE is a prime target in many chronic conditions such as COPD, atherosclerosis, invasive cancers and bullous pemphigoid.

Human Perimeter: Hatice Berber Assistant Professor, Pascale Clivio Research Director, Clément Denhez Assistant Professor, Dominique Guillaume Professor.

Collaborators associated to the project: H. Morjani (BioSpecT, EA 7506), A. Bentaher (CIRI U1111), P. Lameiras (ICMR), T. Douki (SCIB – UMR E3) and J. Chattopadhyaya (Uppsala)

"Glycoscience and Molecular Modelling" group (in french: Glycoscience et Modélisation / GeM)

Keywords: Glycochemistry, Synthesis, Inhibition, Molecular modelling.

Coordinator: A. Haudrechy

Thematic Scopes: The "Glycoscience and Molecular Modelling" group focuses its activities on the understanding of biomolecular recognitions for therapeutic, phytosanitary or cosmetic applications especially through studies of receptors and active sites, combining skills centered on the (bio)chemistry of sugars and molecular modelling simulation in a broad sense.

Project: Study, development and optimization of specific inhibitors of human Neuraminidase-1, first-rate pharmacological target in the context of various cardiovascular pathologies and melanoma.

Human Perimeter: Marie-Charlotte Belhomme Assistant Professor, Stéphanie Coantic-Castex Research Engineer, Sylvain Gatard Assistant Professor, Arnaud Haudrechy Professor, Eric Hénon Professor, Hassan Khartabil Assistant Professor, Murielle Muzard Assistant Professor, Miguel Ponce-Vargas Assistant Professor, Richard Plantier-Royon Professor.

Collaborators associated to the project: S. Baud, A. Bennasroune, L. Duca, L. Debelle, P. Maurice (MEDyC, UMR 7369), P. Goekjian (Lyon, ICBMS, UMR 5246) and P. Chavatte (Lille, ICPAL LIRIC UMR U995).

The research activities of the BSMA team are historically oriented towards the design, synthesis and biological evaluation of therapeutically interesting molecules. The BSMA team is partner of the CAP-Health federative research structure (in french: SFR CAP-Santé), involved in the tumor progression, aging and repair and neuroscience areas, as well as in Condorcet federative research structure (in french: SFR Condorcet), through the valorisation of agro-resources section.

The value chain of the BSMA team (Biomolecules: Syntheses and Mechanisms of Action) covers, as the name suggests:

- The marked implications in the valorization of agricultural resources of regional interest (use of carbohydrates such as L-Arabinose, D-Xylose, L-Sorbose and levoglucosenone, or levulinic acid…);

- The development of new approaches to access skeletons encountered in natural structures (poly(hetero)cyclic systems for example);

- The sophisticated analysis (interaction with the PlAneT platform and CSN ("Chemistry and Natural Substances" team) in order to highlight structural subtleties, especially in the study of conformations of nucleotide patterns or entities with atropoisomeric properties;

- The custom-made synthesis of specific inhibitors targeting enzymes of interest, especially for anti-tumoral and anti-inflammatory purposes…;

- The development of new Molecular Modelling tools to identify, characterize and quantify molecular interactions, but also application aspects supporting experimental studies, whether upstream, for predictive molecular dynamics or docking approaches (drug design), or downstream, for the understanding of reaction mechanisms via quantum calculations.

1 – Implications for valorization of agro-resources and environment

Aware of the need to participate in an evolution of concepts to contribute to the energy transition (replacement of fossil carbon), the BSMA team pays attention to the use of:

- Carbohydrates in diverse syntheses: D-Xylose and derivatives for various applications, DMDP from L-Sorbose (Figure 1), bio-inspired rhamnolipids for eliciting activities (see paragraphs 3 and 7 for more informations),

- Levulinic acid: development of serotonergic receptor ligands (Figure 2) for applications oriented towards sectors with medium or high added value,

This attention is formalized in particular by participation in a general article on ICMR activities in materials chemistry, fine chemicals, agrochemicals, health and cosmetics,1 but also by a proposal of depollution methods regarding pesticides observed in aquifers (centrifugal partition extraction with ionic liquids derived from biobased betaine, Figure 3),2 or involvment in the huge field of investigation of lignin derivatives (conception of a trimeric model to study the degradation of lignin, Figure 4).3

Figures 1 - 4

Several projects are carried out in collaboration with the UMR 614 INRA / FARE (Fractionation of Agroresources and Environment, Pr. C. Rémond), in particular by using D-Xylose and L-Arabinose as platform molecules derived from lignocellulosic biomass. The work consists in developing rapid and efficient lignocellulosic enzymatic or chemo-enzymatic synthesis pathways to access molecules with high added value for different applications. For example, new ionic liquids derived from beta-D-xylosides and xylobiosides (Figure 5)4 were obtained via enzymatic transglycosylation reactions from xylans. These ionic liquids have a modular amphiphilic anionic structure with either tetraalkylphosphonium cations or tetraalkylammoniums. The aim of this work was to produce "greener" ionic liquids from renewable resources but also to assess how the physicochemical properties of liquids could vary according to the different anion / cation associations. After a "click chemistry" reaction, propargyl xylosides and xylobiosides allowed to obtain initiators for the biosynthesis of glycosaminoglycans (active on pgsA-745 ovarian cell lines deficient in xylosyltransferase, Figure 6).5 An exploratory work on mutation on the aglycone subsite of a xylanase to improve the transglycosylation reaction in the presence of aromatic acceptors helped identify a more effective mutant (W126A, Figure 7).6

Figure 5
Figure 6
Figure 7

Using supported lipase, lauryl esters of D-Xylose and L-Arabinose (Figure 8),7 and also xylo-oligosaccharides (xylobiose to xylotetraose) (Figure 9) have been prepared8 and their respective structures determined. These lauryl esters have interesting physicochemical properties, and in particular, critical aggregation concentrations (green surfactants).

Figures 8 - 9

This active collaboration with the FARE UMR continues within the Interreg ValBran cross-border project dedicated to the development of wheat bran, an abundant agricultural co-product, by developing biotechnology and green chemistry pathways that respect the environment for the production of high added value surfactant molecules (

2 – Biomolecules and plant extracts

The content of various vegetable oils is a highly reliable marker for defining their origins.9 For example, the analysis of the composition of argan oil (concerning 11 heavy metals and different dietetic elements), traditionally used as an interesting food ingredient for health as well as in the cosmetics, was investigated by atomic emission spectroscopy, the three extractive processes (traditional, mechanical, using solvent) showing no significant variations (Figure 10).10

Figure 10

Three similar studies, carried out on sesame oils from plants grown in Yemen (Figure 11),11 cumin seeds,12 and seeds of Lawsonia inermis, these last two coming from different regions of Morocco (Figure 12),13 can attest that their nutritional quality and their adequacy with the current standards, highlighting a high reproducibility after three years of conservation (physico-chemical groups identified with very low contents in potentially toxic metals,11 in petroselinic acid12 or in phytosterols,13 correlated with specific geographic origins).

Figures 11 - 12

The combination of all these informations then showed that the tin content turns out to be a potential identity marker to discriminate between argan, olive, sesame, mustard, corn, peanut and sunflower oils. Thus, this recommended measure certifies the authenticity of an argan oil.14

Inspired by these analytical works, the contents of Yemenis honeys15 and coffees16 allow long-term identification of the botanical origin of the samples (144 honeys for 5 plant species from 4 geographic areas; 16 coffees collected from 8 producers to compare with Ethiopian coffees). Concerning coffees, a high calcium content is a characteristic of Yemeni coffees.

The Albizia species is a deciduous tree belonging to the fabaceae family. NMR studies (DEPT, COSY, TOCSY, NOESY, ROESY, HSQC, HMBC) of different medicinal varieties of Cameroonian origin show that these trees are sources of many triterpene saponins inducing the apoptosis of cancer cells (glaberrimosides A, B and C isolated from Albizia glaberrima (Figure 13),17 chevalierosides A, B and C from Albizia chevalieri (tested on hematopoietic monocytes THP-1),18 these last 6 structures being tested on pancreatic carcinomas AsPC-1, zygiaosides A, B, C and D from Albizia zygia,19,20 gummiferaosides D and E from Albizia gummifera,21 and adianthifoliosides G, H and I from Albizia adianthifolia,22 these last 9 structures being tested on cancer cells of the human epidermis A431).

Figure 13

3 – Syntheses and Mechanisms of Action / carbohydrates

Extension of our strong involvement in the development of carbohydrates, many contributions have resulted in a book (Figure 14) and a book chapter,23,24 as well as by setting up an interactive online decision support tool to identify the stereochemical relationships between sugars, as well as synthetic shortcuts (Figure 15).25

Figures 14 - 15

Other projects related to our expertise in the chemical synthesis of functionalized xylosides with always the backdrop of the transformation and enhancement of agro-molecules are under development. Substituted chiral allenes (alkyl, silyl or aryl type groups) which can serve as "building blocks" in organic synthesis have thus been prepared in a diastereoselective manner from propargyl xylosides (Figure 16). DFT calculations in collaboration with Dr. Y. Gimbert (Univ. Grenoble) allow to highlight the different reaction intermediates (Figure 17) and the stereoselective mechanism during the formation of these allenes.26 The preparation of chiral phospholes derived from xylosides has also been initiated or applications in homogeneous enantioselective catalysis (collaboration M. Ogasawara, Univ. Tokushima, Japan).

Figure 16
Figure 17

Xylosides functionalized with an ester function have been transformed into ligands in order to complex metallic cations (Au, Fe, etc.) for applications in catalysis or in the biological field with the design of original enzyme inhibitors (collaboration J. Devy, MEDyC UMR 7369). The incorporation of the xyloside part aims to give to these metal complexes a better bioavailability, controlled solubility and specific recognition properties in the body (Figure 18).27

Figure 18

In collaboration with the URD ABI AgroParisTech, (S)-gamma-hydroxymethyl-alpha,beta-butenolide (HBO), obtained from levoglucosenone made from cellulose (renewable and easily accessible), has been valued, in particular to offer access to derivatives of D-(+)-ribonolactone (Figure 19).28 This starting material also offers attractive opportunities for applications as additive, active ingredient, food-grade compound and cosmetic, all this in the context of green chemistry (Figure 20).29

Figures 19 - 20

In order to better understand the phenomena involved into the nucleotide patterns, structure / activity relationship studies, enriched with targeted NMR approaches, helped to clarify the importance of the positioning of substituent groups (example of the fluorine atom in C2’ position, Figure 21)30 and define the GNA entities as very likely prebiotic ancestors, due to their photo-robustness linked to the stacking of intra-strand bases (Figure 22).31 This work is of great importance for the fight against tumors.

Figures 21 - 22

4 – Syntheses and Mechanisms of Action / NMR studies

Enriched by our interaction with the CSN team, heteronuclear NMR studies of small molecules mixed in viscous solvents provide a solution to extract individualized spectra (Figure 23),32 while study of atropoisomerism phenomena at variable temperatures, coupled with DFT calculations (Molecular Modelling), determines the activation energies of these conformational exchanges (influences of the positioning of a methyl group, Figure 24, of the substitution in ortho, Figure 25, as well as intramolecular stabilizations Pi/Pi and CH/Pi, or OH/Pi versus CH/OH, Figure 26).33,34,35

Figures 23 - 26

5 – Syntheses and Mechanisms of Action / enzymatic inhibitions

The therapeutic aim of the BSMA team proves to be the driving force through several themes with a strong interaction between syntheses, Molecular Modelling and biological assessments, revealing, for example, the inhibitory activities of many fluorinated and variously substituted pyridazinones on PDE4, this isoenzyme being a target of choice for the treatment of many bronchopulmonary pathologies (Figure 27).36,37,38

Figure 27

Different isoforms of human carbonic anhydrase (hCA I, II, IX and XII) are studied, some of which being associated with various aggressive tumors (cases of hCA IX and XII). The activities and specificities of inhibitors derived from benzenesulfonamides on these hCAs show nanomolar affinities. In silico modelling highlights the importance of particular positions (Molecular Modelling, Figures 28 and 29).39,40 Effectiveness is conditioned by the coordination of the sulfonamide motif with the zinc of the active site (Figure 30).41 Recently, a new class of structures belonging to the isothiazolinone family, with a binding site external to the active site, suggests a different mechanism.42

Figures 28 - 30

The design, synthesis and biological evaluation of new analogs of nitrogenous sugars (iminosugars) and sulfur (thiosugars and sulfonium derivatives) for the inhibition of glycosidases remain an important theme of the team. In collaboration with the MSO ("Methodology in Organic Synthesis") team, 1-C-perfluoroalkylated iminosugars have been synthesized for inhibition activities against alpha-fucosidases and alpha-glucosidases (Figure 31).43

Figure 31

A new strategy for accessing thioglycals and C-2 substituted thioglycals from a ketene dithioacetal derived from D-erythrose has been developed.44 The functionalization of these thioglycals by alkylation of the intracyclic sulfur atom led to sulfoniums with the aim of developing new alpha-mannosidase inhibitors (Figures 32 and 33).

Figures 32 - 33

Quantum docking experiments performed on a series of sulfoniums synthesized in the laboratory in the active site of mannosidase II of the Golgi apparatus are encouraging and have revealed a positioning and interactions comparable to those observed in the case of a natural GMII inhibitor, swainsonine (Figure 34).

Figure 34

Overexpression of matrix metalloproteinases (such as MMP-2) around tumors makes them potential targets in the search for antitumor molecules. Grafting Q-dots on a biotinylated inhibitor provides in vitro visualization, the performed tests showing encouraging results (at nanomolar concentrations, Figures 35 and 36).45

Figures 35 - 36

The study of epigenetic phenomena (modification of gene expression without altering the DNA nucleic sequence) plays an important role in inflammation, one of the main mechanisms involved being the remodeling of chromatin via the modification of histones (Figure 37). Since histone acetylation is a major regulator of chromatin conformation and therefore influences gene expression, inhibitory molecules (HDACI) are studied to try to influence this process, involved for example in alcohol dependence (Figure 38). Cyclodepsipeptides, model pharmacophores for the inhibition of HDAC consist of three elements: a surface recognition domain (head), a hydrophobic arm which occupies the channel of the enzyme to reach the catalytic site, and a metal binding domain which interacts with the Zn2+ ion of the catalytic site (ZBG, Figures 39 and 40).46,47,48,49,50

Figures 37 - 38
Figures 39 - 40

6 – Syntheses and Mechanisms of Action / heterocycles

The development of methods for early diagnosis, anticipating cancer treatment by controlling the targeted release of active ingredients (with real-time monitoring) is supported by the design of semiconductor Q-dots nanocrystals conjugated to a ligand of the acridin family (Figure 41).51,52

Figure 41

Finally, greatly invested in the field of poly(hetero)cyclic derivatives, the BSMA team is developing a radical cascade process including a Smiles rearrangement, a synthetic tool explained in a review of the possibilities offered in modern organic chemistry (Figure 42).53 The first library of indoloquinoleic compounds obtained is notably evaluated for its antimalarial properties.

Figure 42

7 – Syntheses and Mechanisms of Action / elicitation

Bacterial rhamnolipids, especially those produced by Pseudomonas aeruginosa and Burkholderia plantarii have demonstrated promising properties in many areas, particularly those related to environment purposes. It has been demonstrated by our partners in the SDRP (Stress Defenses and Plant Reproduction) that this family of compounds is able to boost plant immunity and could potentially be used in alternative biocontrol strategies. We have recently described a synthetic route to rhamnolipides as well as studies of structure-activity relationships (Figures 43 to 47).54,55,56,57 However, the used methods are not very respectful of the principles of green chemistry and that is the reason why we are currently working with URD ABI on a new approach that is more compatible with a sustainable development.

Figures 43 - 44
Figures 45 - 47

8 – Syntheses and Mechanisms of Action / Molecular Modelling

In support of collaborative projects at the theory-experience interface, our molecular modelling activities are frequently applied to the understanding of reaction mechanisms (mechanism of an original Mitsunobu sequence (Figures 48 and 49),58 domino process investigations (Figures 50 and 51),59 Smiles radical cascade,53 as well as host-guest systems, especially complexes of biological interest (Figures 52 and 53).60,61,62,63,64,65

The rational design via molecular modelling has gradually imposed itself in chemistry as a tool of choice for the discovery and oriented synthesis of new active molecules. This modelling activity strengthens the experimental part of the ICMR, the emphasis being placed here on the possibility of implementing these strategies directly in the concerned experimental team through work combining theory and experience. Four main families of modelling tools are developed here:

• Quantum chemistry and statistical tools for determining reaction profiles / exploration of potential energy surfaces, geometry and energy of stationary points (minima, transition states),

Figure 48
Figure 49
Figure 50
Figures 51 - 52
Figure 53

• Classical mechanics and molecular dynamics for the study of objects of biochemical dimension (ligand-receptor complexes),

• Molecular docking (classical and quantic, Figure 54),

Figure 54

• Identification and quantification of chemical interactions by the IGMPlot tool developed in the laboratory.

In parallel with the modelling application approach coordinated with the experimental efforts, a more fundamental aspect of our activity is focused on the development of new theoretical methods and tools:66,67,68,69

AlgoGen: a quantum molecular docking program; it is sometimes essential to be able to describe ligand-protein interactions at the quantum level like in the case of metalloenzymes, what conventional tools in the field do not allow; this program is developed in collaboration with the CReSTIC laboratory of our university (

IGMPlot: a program dedicated to the identification and quantification of molecular interactions (Figures 55 and 56), essential in biomolecular recognition; this tool is also written in collaboration with the CReSTIC laboratory but also with the LCT laboratory (Sorbonne Université);; this tool has been extended to the study of strong interactions: bond formation / cleavage during reaction mechanisms.

Figures 55 - 56