Gaining insights into Enzymes Transition States: Superacid as new tool to design specific CAZymes inhibitors.

Project Information

GLYCOMIMIC

Grant agreement ID: 101026396

DOI

10.3030/101026396

Project closed

EC signature date 7 April 2021

Start date 1 September 2022

End date 31 August 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 184 707,84

EU contribution

€ 184 707,84

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 1 - GLYCOMIMIC (Gaining insights into Enzymes Transition States: Superacid as new tool to design specific CAZymes inhibitors.)

Reporting period: 2022-09-01 to 2024-08-31

Summary of the context and overall objectives of the project

Glycosciences study the structural and functional roles of carbohydrates in biology and have an increasing impact on many areas of our economy (health, food, natural resources). Carbohydrate Active enZymes (CAZymes), which catalyse the assembly (Glycosyl transferases, GTs) and breakdown (Glycosidases, GHs) of glycosidic linkage in carbohydrates, are essential to life, being involved in key cell functions. Their pharmacological modulation by means of selective CAZymes’ inhibitors can also have multiple applications (e.g. antiviral TamifluTM, antidiabetic GlysetTM, molecular chaperone GalafoldTM). The mechanism of the glycosylation reaction is believed to involve a species with substantial oxocarbenium ion character as reactive intermediate (glycosyl cations). Because of the chemical environment within the sugar ring, the stability and lifetime of the oxocarbenium ions in solutions are very low. The extreme reactivity of these cations has thus precluded for decades their direct observation and characterization in the deprotected form. Understanding the structure, conformation, reactivity, and interactions of glycosyl cations is essential to predict the outcome of glycosylation and to design selective inhibitors of CAZymes. In this context, GLYCOMIMIC general scientific objective was to develop an innovative superacid-based approach to gain insights into CAZymes’ transition states (glycosyl cations). Non-nucleophilic superacids, which constitute a powerful tool to take snapshots of transient superelectrophilic cations in solution, were used at this aim to generate and stabilize “naked” glycosyl cations. Our approach was developed across 3 work-packages (WP1 to WP3).

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In WP1, non-nucleophilic superacid environment was used to generate, accumulate and fully characterize by low-temperature NMR spectroscopy non-protected glycosyl cations. A panel of natural and non-natural carbohydrates were synthetised and submitted to in situ NMR studies. The results were supported by DFT calculations, performed by our collaborators in Bilbao (Pr. J. Jiménez Barbero (CICbioGUNE, Spain)). Estimation of their electrophilic character/reactivity through stability (t°, time) studies and trapping experiments was also performed.
In WP2 we wanted to explore the possibility that some glycosyl cations generated in superacid environment could mimic the cationic TS core of the related glycosyl processing enzymes. At this aim, we turned to QM/MM MD simulations, modelling a superacidic ionic environment. A conformational energy landscape (CEL) map of this cation in superacid was produced and compared to the same glycosyl cations modelled in the relevant enzymes. This work, which necessitates a strong expertise in quantum calculations and access to calculation facilities, was supervised by Dr. C. Rovira at University of Barcelona. This step of the project was also very successful, confirming that structural and electronic properties of the observed glycosyl cations in superacid solution can parallel those observed in the active site of relevant enzymes. This finding led to the conclusion that the strong confinement effect played by superacid can mimic the enzymatic cavity of carbohydrate-active enzyme. Moreover, the persistence of the cations in a preferential conformation in superacid medium led to the stereoselective formation of deuterated and/or fluorinated products after aqueous quenching. This phenomenon confirmed again the analogy between superacid and enzymatic media, opening the way for the use of superacid chemistry to catalyse stereoselective reactions in an enzymatic fashion (Armand M, Nin-Hill A, Ardá A, Berrino E, Désiré J, Martin-Mingot A, Michelet B, Jiménez-Barbero J, Blériot Y, Rovira C, Thibaudeau S, Glycosylium ions in superacid mimic the transition state of enzyme reactions. JACS, just accepted, doi.org/10.1021/jacs.4c11677).
Therefore, in WP3 we aimed gathering more information about conformation and reactivity of glycosyl cations. A first objective was to apply the novel methodology developed herein, combining superacid-DFT-QM/MM dynamic simulations, to stereoselective glycosylation (manuscript in preparation). The second objective was to explore the possibility to exploit the stereoselective generation of cyclic ammonium oxocarbenim dications in superacid to access diastereoenriched amines. In superacid, reactions involving polycationic superelectrophiles have been exploited to generate innovative molecules in bioactive series. However, these reactions are limited by the absence of stereoselective versions (Berrino E. et al, Journal of Medicinal Chemistry Article ASAP, DOI: 10.1021/acs.jmedchem.4c01795). This approach aimed to overcome this limitation, opening the way for the diastereoselective hydrofunctionalization of non-activated alkenes in superacid exploiting in situ generation of chiral cyclic oxocarbenium ions. The study was supported by DFT calculations applied to the determination of reaction mechanisms (Berrino E, Cantin T, Artault M, Beck S, Jessen C, Marrot J, Guégan F, Mingot A, Kornath A, Thibaudeau S. Accumulation, Characterization and Reactivity of Chiral Ammonium-Carboxonium Dications in Superacid. Angew Chem Int Ed Engl. 2024 Jun 3;63(23):e202404066. doi: 10.1002/anie.202404066).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Overall, GLYCOMIMIC offered an innovative approach based on superacid chemistry to gain insights into CAZymes’ transition states (TS), paving the way for short-term impact on drug discovery. Superacid chemistry was applied for the first time to naked carbohydrates. In collaboration with Univ. Barcelona and CIC bioGUNE (Spain), GLYCOMIMIC (Figure 1) blended multidisciplinary states of the art research training in carbohydrate chemistry (Pr. Y. Bleriot), superacids (Pr. S. Thibaudeau), low-temperature NMR analysis, DFT calculations (Pr. J. J. Barbero), and QM/MM dynamic simulation of enzymes (Dr. C. Rovira). The interest of the scientific community for this original approach explored during GLYCOMIMIC is reflected in the presentation of the achieved work in two international conferences and in the publication of 3 research papers in high-ranking journal (one manuscript in preparation). The impact on the scientific community is expected to be large, as the methodology here presented allowed to get more insights into the conformation and reactivity of naked glycosyl cations, opening the way for selective reactions on glycosyl cations and, more in general, on oxocarbenium ion-type intermediates.