Chimie, Modélisation pour la Reconnaissance des Protéines

Publications de l’équipe

Année de publication : 2021

Marc Lavigne, Olivier Helynck, Pascal Rigolet, Rofia Boudria-Souilah, Mireille Nowakowski, Bruno Baron, Sébastien Brülé, Sylviane Hoos, Bertrand Raynal, Lionel Guittat, Claire Beauvineau, Stéphane Petres, Anton Granzhan, Jean Guillon, Geneviève Pratviel, Marie-Paule Teulade-Fichou, Patrick England, Jean-Louis Mergny, Hélène Munier-Lehmann (2021 Jul 7)

SARS-CoV-2 Nsp3 unique domain SUD interacts with guanine quadruplexes and G4-ligands inhibit this interaction.

Nucleic Acids Research : 49 : 7695–7712 : DOI : 10.1093/nar/gkab571 En savoir plus
Résumé

The multidomain non-structural protein 3 (Nsp3) is the largest protein encoded by coronavirus (CoV) genomes and several regions of this protein are essential for viral replication. Of note, SARS-CoV Nsp3 contains a SARS-Unique Domain (SUD), which can bind Guanine-rich non-canonical nucleic acid structures called G-quadruplexes (G4) and is essential for SARS-CoV replication. We show herein that the SARS-CoV-2 Nsp3 protein also contains a SUD domain that interacts with G4s. Indeed, interactions between SUD proteins and both DNA and RNA G4s were evidenced by G4 pull-down, Surface Plasmon Resonance and Homogenous Time Resolved Fluorescence. These interactions can be disrupted by mutations that prevent oligonucleotides from folding into G4 structures and, interestingly, by molecules known as specific ligands of these G4s. Structural models for these interactions are proposed and reveal significant differences with the crystallographic and modeled 3D structures of the SARS-CoV SUD-NM/G4 interaction. Altogether, our results pave the way for further studies on the role of SUD/G4 interactions during SARS-CoV-2 replication and the use of inhibitors of these interactions as potential antiviral compounds.

Replier
Piguel S., Le Bescont J., Mouawad L., Boddaert T., Bombard S. (2021 Jun 29)

Photoactivatable small-molecule inhibitors for light-controlled TAM kinase activity

ChemPhotoChem : Accepted Author Manuscript : DOI : 10.1002/cptc.202100131 En savoir plus
Résumé

The TAM kinase family arises as a promising therapeutical target for cancer therapy, auto-immune, and viral diseases. In this study, we report the first photoactivatable caged inhibitors of Tyro3 and Mer. This strategy enables spatial and temporal control of the biological activity of the inhibitor upon irradiation with UV light. We describe the design, the synthesis, the photocleavage properties, and the inhibitory activity of four Tyro3 and Mer photoactivatable small molecules. The proof of concept on the TAM kinase family was achieved in vitro , since irradiation by UV light restored the full inhibitory activity of two prodrugs.

Replier
Laura Fourmois, Florent Poyer, Aude Sourdon, Delphine Naud-Martin, Sounderya Nagarajan, Rahima Chennoufi, Eric Deprez, Marie-Paule Teulade-Fichou, Florence Mahuteau-Betzer (2021 May 19)

Modulation of cellular fate of vinyl triarylamines through structural fine tuning: to stay or not to stay in the mitochondria?

Chembiochem : a European journal of chemical biology : Accepted Article : DOI : 10.1002/cbic.202100168 En savoir plus
Résumé

Mitochondria is involved in many cellular pathways and dysfunctional mitochondria are linked to various diseases. Hence efforts have been driven to design mitochondria-targeted fluorophores for monitoring the mitochondria status. However, the factors that govern the mitochondria-targeted potential of dyes are not well-understood. In this context, we synthesized analogues of the TP-2Bzim probe belonging to the vinyltriphenylamine (TPA) class and already described for its capacity to bind nuclear DNA in fixed cells and mitochondria in live cells. These analogues ( TP-1Bzim, TP n -2Bzim, TP 1+ -2Bzim, TN-2Bzim ) differ by the cationic charge, the number of vinylbenzimidazolium branches and the nature of the triaryl core. Using microscopy, we demonstrated that the cationic derivatives accumulate in mitochondria but do not reach mtDNA. Under depolarisation of the mitochondrial membrane, TP-2Bzim and TP 1+ -2Bzim translocate to the nucleus in direct correlation with their strong DNA affinity. This reversible phenomenon emphasizes that these probes can be used to monitor ΔΨ m variations.

Replier
Abegão L.M., Santos F.A., Piguel S., Rodrigues J.J., Mendonça C.R., De Boni L. (2021 Apr 15)

The ability of 2,5-disubstituted oxazole dyes derivatives to generate two-photon upconversion photoluminescence and its brightness evaluation

Journal of Photochemistry and Photobiology A: Chemistry : 411 : 113214 : DOI : 10.1016/j.jphotochem.2021.113214 En savoir plus
Résumé

S1010603021000873-ga1_lrgThe brightness study of emissive compounds is one of the fundamental spectroscopic characterizations. In this work, we assessed the brightness values of eight 2,5-disubstituted oxazole dyes derivatives by combining linear and nonlinear spectroscopic parameters. The range of the brightness values obtained is from 0.26 GM to 15.15 GM. The highest value belongs to compound 14 m, which, compared to previously investigated compounds of similar π-conjugation length, is at least two times higher. Brightness values were determined in the spectral region between 700 nm–720 nm, revealing this class of dyes’ potential to be used as photoluminescence bioprobes excited by two-photons.

Replier
Sylvie Gory-Fauré, Rebecca Powell, Julie Jonckheere, Fabien Lanté, Eric Denarier, Leticia Peris, Chi Hung Nguyen, Alain Buisson, Laurence Lafanechère, Annie Andrieux (2021 Mar 12)

Pyr1-Mediated Pharmacological Inhibition of LIM Kinase Restores Synaptic Plasticity and Normal Behavior in a Mouse Model of Schizophrenia.

Frontiers in pharmacology : 12 : 627995 : DOI : 10.3389/fphar.2021.627995 En savoir plus
Résumé

The search for effective treatments for neuropsychiatric disorders is ongoing, with progress being made as brain structure and neuronal function become clearer. The central roles played by microtubules (MT) and actin in synaptic transmission and plasticity suggest that the cytoskeleton and its modulators could be relevant targets for the development of new molecules to treat psychiatric diseases. In this context, LIM Kinase – which regulates both the actin and MT cytoskeleton especially in dendritic spines, the post-synaptic compartment of the synapse – might be a good target. In this study, we analyzed the consequences of blocking LIMK1 pharmacologically using Pyr1. We investigated synaptic plasticity defects and behavioral disorders in MAP6 KO mice, an animal model useful for the study of psychiatric disorders, particularly schizophrenia. Our results show that Pyr1 can modulate MT dynamics in neurons. In MAP6 KO mice, chronic LIMK inhibition by long-term treatment with Pyr1 can restore normal dendritic spine density and also improves long-term potentiation, both of which are altered in these mice. Pyr1 treatment improved synaptic plasticity, and also reduced social withdrawal and depressive/anxiety-like behavior in MAP6 KO mice. Overall, the results of this study validate the hypothesis that modulation of LIMK activity could represent a new therapeutic strategy for neuropsychiatric diseases.

Replier
Auvray M., Bolze F., Clavier G., Mahuteau-Betzer F. (2021 Mar 1)

Silafluorene as a promising core for cell-permeant, highly bright and two-photon excitable fluorescent probes for live-cell imaging

Dyes and Pigments : 187 : 109083 : DOI : 10.1016/j.dyepig.2020.109083 En savoir plus
Résumé

ImageJ=1.52a

In this study, we report the synthesis, linear and non-linear photophysical studies and live-cell imaging of two two-photon activatable probes based on a silafluorene core: SiFluo-V and SiFluo-L. Thanks to their quadrupolar (A-π-D-π-A) design, these probes exhibit respectively good to impressive two-photon cross-sections (from 210 GM to 2150 GM). TD-DFT calculations support the experimental evidence that SiFluo-L displays far better two-photon absorption properties than SiFluo-V. Moreover, SiFluo-L possesses all requirements for bioimaging as it is water soluble, cell-permeant and presents a low cytotoxicity (IC80 ≥ 10 μM). It labels mitochondria in live-cell imaging at low laser power with high brightness, contrast and photostability. This study demonstrates that silafluorene is a promising core to develop new two-photon fluorophores for live-cell imaging.

Replier
Thomas Barbot, Veronica Beswick, Cédric Montigny, Éric Quiniou, Nadège Jamin and Liliane Mouawad (2021 Feb 4)

Deciphering the mechanism of inhibition of SERCA1a by sarcolipin using molecular simulations

Frontiers in Molecular Biosciences : 7 : 606254 : DOI : 10.3389/fmolb.2020.606254 En savoir plus
Résumé

SERCA1a is an ATPase calcium pump that transports Ca2+ from the cytoplasm to the sarco/endoplasmic reticulum lumen. Sarcolipin (SLN), a transmembrane peptide, regulates the activity of SERCA1a by decreasing its Ca2+ transport rate, but its mechanism of action is still not well understood. To decipher this mechanism, we have performed normal mode analysis in the all-atom model, with the SERCA1a-SLN complex, or the isolated SERCA1a, embedded in an explicit membrane. The comparison of the results allowed us to provide an explanation at the atomic level for the action of SLN that is in good agreement with experimental observations. In our analyses, the presence of SLN locally perturbs the TM6 transmembrane helix and as a consequence modifies the position of D800, one of the key metal-chelating residues. Additionally, it reduces the flexibility of the gating residues, V304 and E309 in TM4, at the entrance of the Ca2+ binding sites, which would decrease the affinity for Ca2+. Unexpectedly, SLN has also an effect on the ATP binding site more than 35 Å away, due to the straightening of TM5, a long helix considered as the spine of the protein. The straightening of TM5 modifies the structure of the P-N linker that sits above it, and which comprises the 351DKTG354 conserved motif, resulting in an increase of the distance between ATP and the phosphorylation site. As a consequence, the turn-over rate could be affected. All this gives SERCA1a the propensity to go toward a Ca2+ low-affinity E2-like state in the presence of SLN and toward a Ca2+ high-affinity E1-like state in the absence of SLN. In addition to a general mechanism of inhibition of SERCA1a regulatory peptides, this study also provides an insight into the conformational transition between the E2 and E1 states.

Replier

Année de publication : 2020

Breton-Patient C., Naud-Martin D., Mahuteau-Betzer F., Piguel S. (2020 Nov 15)

Three-component C-H bond sulfonylation of imidazoheterocycles via visible-light organophotoredox catalysis.

European Journal of Organic Chemistry : 2020 : 6653-6660 : DOI : 10.1002/ejoc.202001219 En savoir plus
Résumé

10.1002-ejoc202001219

The first entirely visible-light photoredox catalyzed sulfonylation of imidazoheterocycles has been developed. This transformation demonstrates an efficient C-H functionalization for the straightforward synthesis of novel C-3 sulfonylated imidazoheterocycles from various imidazopyridines and diaryliodonium salts with different electronic and steric properties and easy handled DABCO- bis (sulfur dioxide). The reaction proceeds in moderate to good yields under mild conditions at room temperature using the inexpensive organophotocatalyst EosinY.Na 2 and shows a high functional group tolerance (37 examples).

Replier
Küssau T., Van Wyk N., Johansen M.D., Alsarraf H.M.A.B., Neyret A., Hamela C., Sørensen K.K., Thygesen M.B., Beauvineau C., Kremer L., Blaise M. (2020 Nov 4)

Functional Characterization of the N-Acetylmuramyl-l-Alanine Amidase, Ami1, from Mycobacterium abscessus

Cells : 9 : 2410 : DOI : 10.3390/cells9112410 En savoir plus
Résumé

Peptidoglycan (PG) is made of a polymer of disaccharides organized as a three-dimensional mesh-like network connected together by peptidic cross-links. PG is a dynamic structure that is essential for resistance to environmental stressors. Remodeling of PG occurs throughout the bacterial life cycle, particularly during bacterial division and separation into daughter cells. Numerous autolysins with various substrate specificities participate in PG remodeling. Expression of these enzymes must be tightly regulated, as an excess of hydrolytic activity can be detrimental for the bacteria. In non-tuberculous mycobacteria such as Mycobacterium abscessus, the function of PG-modifying enzymes has been poorly investigated. In this study, we characterized the function of the PG amidase, Ami1 from M. abscessus. An ami1 deletion mutant was generated and the phenotypes of the mutant were evaluated with respect to susceptibility to antibiotics and virulence in human macrophages and zebrafish. The capacity of purified Ami1 to hydrolyze muramyl-dipeptide was demonstrated in vitro. In addition, the screening of a 9200 compounds library led to the selection of three compounds inhibiting Ami1 in vitro. We also report the structural characterization of Ami1 which, combined with in silico docking studies, allows us to propose a mode of action for these inhibitors.

Replier
Leandro H. Zucolotto Cocca, Luis M. G. Abegão, Lucas F. Sciuti, Roxane Vabre, Jonathas de Paula Siqueira, Kenji Kamada, Cleber R. Mendonca, Sandrine Piguel, and Leonardo De Boni (2020 Jun 11)

Two-Photon Emissive Dyes Based on Push–Pull Purines Derivatives: Toward the Development of New Photoluminescence Bioprobes

The Journal of Physical Chemistry C : 124 : 12185-12864 : DOI : 10.1021/acs.jpcc.0c01859 En savoir plus
Résumé

Two-Photon Emissive Dyes Based on Push–Pull Purines Derivatives: Toward the Development of New Photoluminescence BioprobesFluorescent organic molecules have received great attention due to their largest applications, for example, in DNA and RNA spectroscopies studies, development of new photoluminescence bioprobes, and applications in fluorescence spectroscopy. In specific, purine base analog molecules present high fluorescence quantum yields and significant Stokes shift. Furthermore, the addition of push–pull structures at the purine core could increase the photoluminescence properties, making candidates for photoluminescence bioprobes. To consider this, a complete spectroscopic study was performed on nine push–pull purines, distinguished by different push–pull structures. In specific, for this research, the two-photon absorption (2PA) study showed that the compounds present induced two-photon fluorescence at the therapeutic window, desired for fluorescence microscopy. The brightness property was evaluated, indicating that all chromospheres are fluorescent by a 2PA process. Additionally, ultrafast transient absorption was performed to elucidate contribution of the excited states on the 2PA spectra, and quantum chemistry calculations were performed to corroborate the experimental results.

Replier
Rahima Chennoufi, Ngoc-Duong Trinh, Françoise Simon, Guillaume Bordeau, Delphine Naud-Martin, Albert Moussaron, Bertrand Cinquin, Houcine Bougherara, Béatrice Rambaud, Patrick Tauc, Céline Frochot, Marie-Paule Teulade-Fichou, Florence Mahuteau-Betzer & Eric Deprez (2020 Apr 23)

Interplay between cellular uptake, intracellular localization and the cell death mechanism in triphenylamine-mediated photoinduced cell death

Scientific Reports : 10 : 6881 : DOI : 10.1038/s41598-020-63991-9 En savoir plus
Résumé

Triphenylamines (TPAs) were previously shown to trigger cell death under prolonged one- or two-photon illumination. Their initial subcellular localization, before prolonged illumination, is exclusively cytoplasmic and they translocate to the nucleus upon photoactivation. However, depending on their structure, they display significant differences in terms of precise initial localization and subsequent photoinduced cell death mechanism. Here, we investigated the structural features of TPAs that influence cell death by studying a series of molecules differing by the number and chemical nature of vinyl branches. All compounds triggered cell death upon one-photon excitation, however to different extents, the nature of the electron acceptor group being determinant for the overall cell death efficiency. Photobleaching susceptibility was also an important parameter for discriminating efficient/inefficient compounds in two-photon experiments. Furthermore, the number of branches, but not their chemical nature, was crucial for determining the cellular uptake mechanism of TPAs and their intracellular fate. The uptake of all TPAs is an active endocytic process but two- and three-branch compounds are taken up via distinct endocytosis pathways, clathrin-dependent or -independent (predominantly caveolae-dependent), respectively. Two-branch TPAs preferentially target mitochondria and photoinduce both apoptosis and a proper necrotic process, whereas three-branch TPAs preferentially target late endosomes and photoinduce apoptosis only.

Replier
Julie Le Bescont, Chloé Breton‐Patient et Sandrine Piguel (2020 Apr 16)

Unconventional Reactivity with DABCO-Bis(sulfur dioxide): C–H Bond Sulfenylation of Imidazopyridines

European Journal of Organic Chemistry : 2020 : 2101-2109 : DOI : 10.1002/ejoc.202000112 En savoir plus
Résumé

Exploring the unexpected reactivity of DABCO‐bis(sulfur dioxide) on various imidazo[1,2‐a ]pyridines expanded the toolbox of the sulfenylation reagent. Starting from three simple building blocks, this three‐component transformation led to various C‐3 sulfenylated substituted imidazo[1,2‐a ]pyridines in moderate to good yields.
Exploring the unexpected reactivity of DABCO‐bis(sulfur dioxide) on various imidazo[1,2‐a ]pyridines expanded the toolbox of the sulfenylation reagent. Starting from three simple building blocks, this three‐component transformation led to various C‐3 sulfenylated substituted imidazo[1,2‐a ]pyridines in moderate to good yields.

This work highlights the unexpected and unprecedented outcome of the reactivity with DABCO‐bis(sulfur dioxide). The use of this reagent led to the exclusive introduction of a sulfur atom on the C‐3 position of imidazopyridines instead of a sulfone group. The reaction methodology turned out to be robust, scalable and suitable for various imidazopyridines and aryl iodides both bearing substituents with different electronic and steric properties (38 examples). Beyond the fact that this synthetic method complements the previously reported protocols for sulfenylation reactions, this work is meant to underline the unconventional role of DABCO‐bis(sulfur dioxide).

Replier

Année de publication : 2019

Abegão L.M.G., Fonseca R.D., Santos F.A., Rodrigues J.J., Kamada K., Mendonça C.R., Piguel S., De Boni L. (2019 Aug 23)

First molecular electronic hyperpolarizability of series of π-conjugated oxazole dyes in solution: an experimental and theoretical study

RSC Adv. : 9 : 26476-26482 : DOI : 10.1039/C9RA05246A En savoir plus
Résumé

In this work, we report the experimental and theoretical first molecular electronic hyperpolarizability (βHRS) of eleven π-conjugated oxazoles compounds in toluene medium. The Hyper-Rayleigh Scattering (HRS) technique allowed the determination of the experimental dynamic βHRS values, by exciting the compounds with a picosecond pulse trains from a Q-switched and mode-locked Nd:YAG laser tuned at 1064 nm. Theoretical predictions based on time-dependent density functional theory level using the Gaussian 09 program package were performed with three different functionals (B3LYP, CAM-B3LYP, and M06-2X), to calculate both static and dynamic theoretical βHRS values. Good accordance was found between the experimental and theoretical values, in particular for the CAM-B3LYP and M06-2X functionals.

Replier
El Hassen Mokrani, Abderrahmane Bensegueni, Ludovic Chaput, Claire Beauvineau, Hanane Djeghim, Liliane Mouawad (2019 May 1)

Identification of New Potent Acetylcholinesterase Inhibitors Using Virtual Screening and In Vitro Approaches.

Molecular informatics : 38 : 1800118 : DOI : 10.1002/minf.201800118 En savoir plus
Résumé

Acetylcholinesterase (AChE) is currently the most favorable target for the symptomatic treatment and reduction of Alzheimer’s disease (AD). In order to identify new potent inhibitors of this enzyme, we describe herein a new structure‐based virtual screening (SBVS) using the Institut Curie‐CNRS chemical library (ICCL), which contained at the screening date 14307 compounds. The strategy undertaken in this work consisted of the use of several docking programs in SBVS calculations followed by the application of a consensus method (vSDC) and a scrupulous visual analysis. It allowed us to obtain a high degree of success, with a yield of almost 86 %, since 12 hits were identified among only 14 molecules tested in vitro. Still more remarkably, 6 of these hits were more active than galantamine, the reference inhibitor. These hits were predicted to have good ADMET properties. The two most promising compounds can serve as leads for AD treatment.

Replier
Morgan Pellerano, Delphine Naud-Martin, Florence Mahuteau-Betzer, Marie Morille, May Catherine Morris (2019 Feb 15)

Fluorescent biosensor for detection of the R248Q aggregation-prone mutant of p53.

Chembiochem : a European journal of chemical biology : 20 : 605-613 : DOI : 10.1002/cbic.201800531 En savoir plus
Résumé

The p53 tumour suppressor and guardian of the genome undergoes missense mutations which lead to functional inactivation in 50% human cancers. These mutations occur mostly in the DNA-binding domain of the protein and several of these induce conformational changes which lead to amyloid-like protein aggregation. Here we describe a fluorescent biosensor that reports on the R248Q mutant of p53 in vitro and in living cells, engineered through conjugation of an environmentally-sensitive probe onto a peptide derived from the primary aggregation segment of p53.This biosensor was characterized both in vitro and by fluorescence microscopy following facilitated delivery into cultured cells. We show that this biosensor preferentially reports on the p53 R248Q mutant in PC9 lung cancer cell line compared to other lung cancer cell lines harbouring either wildtype or no p53.

Replier