Chemistry and Modelling for Protein Recognition

Team Publications

Year of publication 2017

J Santo, C Lopez-Herrera, C Apolit, Y Bareche, L Lapasset, C Chavey, S Capozi, F Mahuteau-Betzer, R Najman, P Fornarelli, I C Lopez-Mejía, G Béranger, F Casas, E-Z Amri, B Pau, D Scherrer, J Tazi (2017 Feb 14)

Pharmacological modulation of LMNA SRSF1-dependent splicing abrogates diet-induced obesity in mice.

International journal of obesity : 41 : 390-401 : DOI : 10.1038/ijo.2016.220 Learn more
Summary

Bakground/Objectives:

Intense drug discovery efforts in the metabolic field highlight the need for novel strategies for the treatment of obesity. Alternative splicing (AS) and/or polyadenylation enable the LMNA gene to express distinct protein isoforms that exert opposing effects on energy metabolism and lifespan. Here we aimed to use the splicing factor SRSF1 that contribute to the production of these different isoforms as a target to uncover new anti-obesity drug.

Subjects/Methods:

Small molecules modulating SR protein activity and splicing were tested for their abilities to interact with SRSF1 and to modulate LMNA (AS). Using an LMNA luciferase reporter we selected molecules that were tested in diet-induced obese (DIO) mice. Transcriptomic analyses were performed in the white adipose tissues from untreated and treated DIO mice and mice fed a chow diet.

Results:

We identified a small molecule that specifically interacted with the RS domain of SRSF1. ABX300 abolished DIO in mice, leading to restoration of adipose tissue homeostasis. In contrast, ABX300 had no effect on mice fed a standard chow diet. A global transcriptomic analysis revealed similar profiles of white adipose tissue from DIO mice treated with ABX300 and from untreated mice fed a chow diet. Mice treated with ABX300 exhibited an increase in O2 consumption and a switch in fuel preference toward lipids.

Conclusions:

Targeting SRSF1 with ABX300 compensates for changes in RNA biogenesis induced by fat accumulation and consequently represents a novel unexplored approach for the treatment of obesity.

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Year of publication 2016

Chaput L., Martinez-Sanz J., Saettel N., Mouawad L. (2016 Oct 17)

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

Journal of Cheminformatics : 8:56 : DOI : 10.1186/s13321-016-0167-x Learn more
Summary

Abstract
In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken on a large variety of protein targets. Here, the performance of four popular virtual screening programs, Gold, Glide, Surflex and FlexX, is compared using the Directory of Useful Decoys-Enhanced database (DUD-E), which includes 102 targets with an average of 224 ligands per target and 50 decoys per ligand, generated to avoid biases in the benchmarking. Then, a relationship between these program performances and the properties of the targets or the small molecules was investigated.
Results
The comparison was based on two metrics, with three different parameters each. The BEDROC scores with α = 80.5, indicated that, on the overall database, Glide succeeded (score > 0.5) for 30 targets, Gold for 27, FlexX for 14 and Surflex for 11. The performance did not depend on the hydrophobicity nor the openness of the protein cavities, neither on the families to which the proteins belong. However, despite the care in the construction of the DUD-E database, the small differences that remain between the actives and the decoys likely explain the successes of Gold, Surflex and FlexX. Moreover, the similarity between the actives of a target and its crystal structure ligand seems to be at the basis of the good performance of Glide. When all targets with significant biases are removed from the benchmarking, a subset of 47 targets remains, for which Glide succeeded for only 5 targets, Gold for 4 and FlexX and Surflex for 2.
Conclusion
The performance dramatic drop of all four programs when the biases are removed shows that we should beware of virtual screening benchmarks, because good performances may be due to wrong reasons. Therefore, benchmarking would hardly provide guidelines for virtual screening experiments, despite the tendency that is maintained, i.e., Glide and Gold display better performance than FlexX and Surflex. We recommend to always use several programs and combine their results.

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Baladi T., Granzhan A., Piguel S. (2016 May 1)

Microwave-Assisted C-2 Direct Alkenylation of Imidazo[4,5-b]pyridines: Access to Fluorescent Purine Isosteres with Remarkably Large Stokes Shifts

European Journal of Organic Chemistry : 2016 : 2421-2434 : DOI : 10.1002/ejoc.201600166 Learn more
Summary

We describe herein the first C-2 direct alkenylation of the valuable 3H-imidazo[4,5-b]pyridine promoted by microwave-assisted Pd/Cu co-catalysis. The reaction is rapid and compatible with a wide range of functional groups either on the imidazo[4,5-b]pyridine ring or on the styryl bromides thereby leading to the isolation of 23 compounds with moderate to good yields. The relevance of this method is demonstrated by its application to the synthesis of new cross-conjuguated push-pull 2-vinyl- and 2-alkynylimidazo[4,5-b]pyridines characterized by satisfactory fluorescence quantum yields and remarkable solvatofluorochromic properties.

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Jessy Aziz, Tom Baladi, Sandrine Piguel (2016 Apr 26)

Direct Alkynylation of 3H-Imidazo[4,5-b]pyridines Using gem-Dibromoalkenes as Alkynes Source.

The Journal of organic chemistry : 81 : 4122-4133 : DOI : 10.1021/acs.joc.6b00406 Learn more
Summary

C2 direct alkynylation of 3H-imidazo[4,5-b]pyridine derivatives is explored for the first time. Stable and readily available 1,1-dibromo-1-alkenes, electrophilic alkyne precursors, are used as coupling partners. The simple reaction conditions include an inexpensive copper catalyst (CuBr·SMe2 or Cu(OAc)2), a phosphine ligand (DPEphos) and a base (LiOtBu) in 1,4-dioxane at 120 °C. This C-H alkynylation method revealed to be compatible with a variety of substitutions on both coupling partners: heteroarenes and gem-dibromoalkenes. This protocol allows the straightforward synthesis of various 2-alkynyl-3H-imidazo[4,5-b]pyridines, a valuable scaffold in drug design.

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Morgan Pellerano, Delphine Naud-Martin, Marion Peyressatre, Camille Prével, Marie-Paule Teulade-Fichou, May Morris, Florence Mahuteau-Betzer (2016 Mar 17)

TP-2Rho Is a Sensitive Solvatochromic Red-Shifted Probe for Monitoring the Interactions between CDK4 and Cyclin D.

Chembiochem : a European journal of chemical biology : 17 : 737-744 : DOI : 10.1002/cbic.201500641 Learn more
Summary

Understanding the intricate steps of protein kinase regulation requires characterization of protein-protein interactions between the catalytic subunit, its regulatory partners and the substrate. Fluorescent probes are useful tools with which to study such interactions and to gain insight into their affinities and specificities. Solvatochromic probes, which display changes in their fluorescence emission in response to changes in the polarity of the medium, are particularly attractive. Here we describe conjugation of a switchable fluorescent dye, TP-2Rho, to peptide and protein derivatives of cyclin-dependent kinase 4 (CDK4) and its application to characterization of the interactions between the catalytic subunit of this kinase, its regulatory partner cyclin D1 and a peptide substrate. We demonstrate the sensitivity of TP-2Rho in relation to of those other dyes used for monitoring peptide-protein and protein-protein interactions. Moreover, we show that TP-Rho-labelled peptides can be introduced into living cells to probe endogenous CDK4/cyclin D.

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Rahima Chennoufi, Houcine Bougherara, Nathalie Gagey-Eilstein, Blaise Dumat, Etienne Henry, Frédéric Subra, Stéphanie Bury-Moné, Florence Mahuteau-Betzer, Patrick Tauc, Marie-Paule Teulade-Fichou, Eric Deprez (2016 Mar 8)

Mitochondria-targeted Triphenylamine Derivatives Activatable by Two-Photon Excitation for Triggering and Imaging Cell Apoptosis.

Scientific reports : 6 : 21458 : DOI : 10.1038/srep21458 Learn more
Summary

Photodynamic therapy (PDT) leads to cell death by using a combination of a photosensitizer and an external light source for the production of lethal doses of reactive oxygen species (ROS). Since a major limitation of PDT is the poor penetration of UV-visible light in tissues, there is a strong need for organic compounds whose activation is compatible with near-infrared excitation. Triphenylamines (TPAs) are fluorescent compounds, recently shown to efficiently trigger cell death upon visible light irradiation (458 nm), however outside the so-called optical/therapeutic window. Here, we report that TPAs target cytosolic organelles of living cells, mainly mitochondria, triggering a fast apoptosis upon two-photon excitation, thanks to their large two-photon absorption cross-sections in the 760-860 nm range. Direct ROS imaging in the cell context upon multiphoton excitation of TPA and three-color flow cytometric analysis showing phosphatidylserine externalization indicate that TPA photoactivation is primarily related to the mitochondrial apoptotic pathway via ROS production, although significant differences in the time courses of cell death-related events were observed, depending on the compound. TPAs represent a new class of water-soluble organic photosensitizers compatible with direct two-photon excitation, enabling simultaneous multiphoton fluorescence imaging of cell death since a concomitant subcellular TPA re-distribution occurs in apoptotic cells.

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Chaput L., Martinez-Sanz J., Quiniou E., Rigolet P., Saettel N., Mouawad L. (2016 Jan 18)

vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available

Journal of Cheminformatics : 8:1 : DOI : 10.1186/s13321-016-0112-z Learn more
Summary

Background: In drug design, one may be confronted to the problem of finding hits for targets for which no small inhibiting molecules are known and only low-throughput experiments are available (like ITC or NMR studies), two common difficulties encountered in a typical academic setting. Using a virtual screening strategy like docking can alleviate some of the problems and save a considerable amount of time by selecting only top-ranking molecules, but only if the method is very efficient, i.e. when a good proportion of actives are found in the 1-10 % best ranked molecules.

Results: The use of several programs (in our study, Gold, Surflex, FlexX and Glide were considered) shows a divergence of the results, which presents a difficulty in guiding the experiments. To overcome this divergence and increase the yield of the virtual screening, we created the standard deviation consensus (SDC) and variable SDC (vSDC) methods, consisting of the intersection of molecule sets from several virtual screening programs, based on the standard deviations of their ranking distributions.

Conclusions: SDC allowed us to find hits for two new protein targets by testing only 9 and 11 small molecules from a chemical library of circa 15,000 compounds. Furthermore, vSDC, when applied to the 102 proteins of the DUD-E benchmarking database, succeeded in finding more hits than any of the four isolated programs for 13-60 % of the targets. In addition, when only 10 molecules of each of the 102 chemical libraries were considered, vSDC performed better in the number of hits found, with an improvement of 6-24 % over the 10 best-ranked molecules given by the individual docking programs.

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Blaise Dumat, Elodie Faurel-Paul, Pauline Fornarelli, Nicolas Saettel, Germain Metgé, Céline Fiorini-Debuisschert, Fabrice Charra, Florence Mahuteau-Betzer, Marie-Paule Teulade-Fichou (2016 Jan 7)

Influence of the oxazole ring connection on the fluorescence of oxazoyl-triphenylamine biphotonic DNA probes.

Organic & biomolecular chemistry : 14 : 358-370 : DOI : 10.1039/c5ob02225h Learn more
Summary

On the basis of our previous work on DNA fluorophores derived from vinylpyridinium-triphenylamine, we explored the structure space around the electron-rich triphenylamine (TP) core by changing the vinyl bond to an oxazole ring. As 2,5-diaryloxazoles are known to be highly fluorescent and efficient two photon absorbers, we synthesized analogues with two different connections of the oxazole to the triphenylamine core: TP-Ox2Py and TP-Ox5Py sets. Since the benzimidazolium group was proven to be more effective in the TP series than the pyridinium, we also synthesized a TP-Ox5Bzim set. The TP-Ox5Py series retains the TP-Py properties: on/off behavior on DNA, good two-photon cross-section and bright staining of nuclear DNA by microscopy under both one or two-photon excitation. On the other hand, the TP-Ox2Py series does not display fluorescence upon binding to DNA. The TP-Ox5Bzim set is fluorescent even in the absence of DNA and displays lower affinity than the corresponding TP-Ox5Py. CD experiments and docking were performed to understand these different behaviors.

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Year of publication 2015

Tom Baladi, Valentina Abet, Sandrine Piguel (2015 Nov 13)

State-of-the-art of small molecule inhibitors of the TAM family: the point of view of the chemist.

European journal of medicinal chemistry : 105 : 220-37 : DOI : 10.1016/j.ejmech.2015.10.003 Learn more
Summary

The TAM family of tyrosine kinases receptors (Tyro3, Axl and Mer) is implicated in cancer development, autoimmune reactions and viral infection and is therefore emerging as an effective and attractive therapeutic target. To date, only a few small molecules have been intentionally designed to block the TAM kinases, while most of the inhibitors were developed for blocking different protein kinases and then identified through selectivity profile studies. This minireview will examine in terms of chemical structure the different compounds able to act on either one, two or three TAM kinases with details about structure-activity relationships, drug-metabolism and pharmacokinetics properties where they exist.

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Guillaume Kellermann, Markus Kaiser, Florent Dingli, Olivier Lahuna, Delphine Naud-Martin, Florence Mahuteau-Betzer, Damarys Loew, Evelyne Ségal-Bendirdjian, Marie-Paule Teulade-Fichou, Sophie Bombard (2015 Sep 3)

Identification of human telomerase assembly inhibitors enabled by a novel method to produce hTERT.

Nucleic acids research : 43 : e99 : DOI : 10.1093/nar/gkv425 Learn more
Summary

Telomerase is the enzyme that maintains the length of telomeres. It is minimally constituted of two components: a core reverse transcriptase protein (hTERT) and an RNA (hTR). Despite its significance as an almost universal cancer target, the understanding of the structure of telomerase and the optimization of specific inhibitors have been hampered by the limited amount of enzyme available. Here, we present a breakthrough method to produce unprecedented amounts of recombinant hTERT and to reconstitute human telomerase with purified components. This system provides a decisive tool to identify regulators of the assembly of this ribonucleoprotein complex. It also enables the large-scale screening of small-molecules capable to interfere with telomerase assembly. Indeed, it has allowed us to identify a compound that inhibits telomerase activity when added prior to the assembly of the enzyme, while it has no effect on an already assembled telomerase. Therefore, the novel system presented here may accelerate the understanding of human telomerase assembly and facilitate the discovery of potent and mechanistically unique inhibitors.

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Kathleen Solmont, Hamza Boufroura, Amel Souibgui, Pauline Fornarelli, Anne Gaucher, Florence Mahuteau-Betzer, Béchir Ben Hassine, Damien Prim (2015 May 13)

Divergent strategy for the synthesis of original dihydrobenzo- and dihydronaphtho-acridines.

Organic & biomolecular chemistry : 13 : 6269-6277 : DOI : 10.1039/c5ob00456j Learn more
Summary

A straightforward access to numerous novel substituted dihydrobenzo- and dihydronaphthoacridines is described using a unique molecular platform in two key steps. A large range of carbon-based substituents such as aromatic, vinyl, alkynyl fragments through Pd-catalysed couplings has been installed. The molecular diversity is extended to the introduction of aza-heterocycles and further authorizes the installation of alkylamino chains by means of Cu-promoted C-N bond formation. Possible access to quinolinium salts is also described. The methodology revealed convenient preparation of a wide panel of molecules that display various rigidity/flexibility and lipophilic/hydrophilic balances. Finally, the influence of structural modulations on the photophysical properties of these novel architectures is also studied. It is noteworthy that styryl and alkynyl derivatives are emissive in water (ΦF up to 12%).


Divergent_strategy

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Florence Mahuteau-Betzer (2015 May 12)

The French National Compound Library: advances and future prospects.

Médecine sciences : M/S : 31 : 417-422 : DOI : 10.1051/medsci/20153104016 Learn more
Summary

The French National Compound Library (Chimiothèque Nationale) has been created in 2003 and is the federation of local collections. It contains more than 56 000 small molecules and natural compounds synthesised or isolated in different laboratories over the past years. This explains the diversity of the collection. The strength of this initiative is the ability to connect chemists and biologists for the development of hits. This development involves the synthesis of analogues or/and chemical tools to find new targets. These collaborations lead to the identification of new chemical probes. These probes able to modulate a biological function are essential to study biological pathways. They can also be useful for therapeutic applications. This article will describe the major achievements and perspectives of the French Chemical Library.

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Noëlie Campos, Renier Myburgh, Aude Garcel, Audrey Vautrin, Laure Lapasset, Erika Schläpfer Nadal, Florence Mahuteau-Betzer, Romain Najman, Pauline Fornarelli, Katjana Tantale, Eugénia Basyuk, Martial Séveno, Julian P Venables, Bernard Pau, Edouard Bertrand, Mark A Wainberg, Roberto F Speck, Didier Scherrer, Jamal Tazi (2015 Apr 19)

Long lasting control of viral rebound with a new drug ABX464 targeting Rev – mediated viral RNA biogenesis.

Retrovirology : 12 : 30 : DOI : 10.1186/s12977-015-0159-3 Learn more
Summary

Background: Current therapies have succeeded in controlling AIDS pandemic. However, there is a continuing need for new drugs, in particular those acting through new and as yet unexplored mechanisms of action to achieve HIV infection cure. We took advantage of the unique feature of proviral genome to require both activation and inhibition of splicing of viral transcripts to develop molecules capable of achieving long lasting effect on viral replication in humanized mouse models through inhibition of Rev-mediated viral RNA biogenesis.

Results: Current HIV therapies reduce viral load during treatment but titers rebound after treatment is discontinued. We devised a new drug that has a long lasting effect after viral load reduction. We demonstrate here that ABX464 compromises HIV replication of clinical isolates of different subtypes without selecting for drug resistance in PBMCs or macrophages. ABX464 alone, also efficiently compromised viral proliferation in two humanized mouse models infected with HIV that require a combination of 3TC, Raltegravir and Tenofovir (HAART) to achieve viral inhibition in current protocols. Crucially, while viral load increased dramatically just one week after stopping HAART treatment, only slight rebound was observed following treatment cessation with ABX464 and the magnitude of the rebound was maintained below to that of HAART for two months after stopping the treatment. Using a system to visualize single HIV RNA molecules in living cells, we show that ABX464 inhibits viral replication by preventing Rev-mediated export of unspliced HIV-1 transcripts to the cytoplasm and by interacting with the Cap Binding Complex (CBC). Deep sequencing of viral RNA from treated cells established that retained viral RNA is massively spliced but importantly, normal cellular splicing is unaffected by the drug. Consistently ABX464 is non-toxic in humans and therefore represents a promising complement to current HIV therapies.

Conclusions: ABX464 represents a novel class of anti-HIV molecules with unique properties. ABX464 has a long lasting effect in humanized mice and neutralizes the expression of HIV-1 proviral genome of infected immune cells including reservoirs and it is therefore a promising drug toward a functional cure of HIV.

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Year of publication 2014

Vabre R., Legraverend M., Piguel S. (2014 Jun 1)

Synthesis and evaluation of spectroscopic properties of newly synthesized push–pull 6-amino-8-styryl purines

Dyes and Pigments : 105 : 145-151 : DOI : 10.1016/j.dyepig.2014.01.025 Learn more
Summary

New 6-amino-8-styryl purines were synthesized using direct C–H bond functionalization. These push–pull compounds showed strong fluorescence, high quantum yields and a noteworthy fluorosolvatochromism. Deprotected purines 7a–c are promising targets for incorporation into nucleic acids as they are still fluorescent in aqueous media.

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Delphine Naud-Martin, Xavier Martin-Benlloch, Florent Poyer, Florence Mahuteau-Betzer, Marie-Paule Teulade-Fichou (2014 Feb 1)

Acri-2,7-Py, a bright red-emitting DNA probe identified through screening of a distyryl dye library.

Biotechnology journal : 9 : 301-310 : DOI : 10.1002/biot.201300197 Learn more
Summary

The identification of DNA sensors is still a challenge since no DNA probe possesses all the photophysical properties required for live-cell imaging: high fluorescence yield, red emission, permeability, no photobleaching and no cytotoxicity. We describe the preparation of a distyryl dye library and its evaluation on a panel of nucleic acids with various structures (duplex DNA, quadruplex DNA and RNA). The screening involved measuring the modification of the fluorescence properties of the dyes with or without nucleic acids on a microplate reader, and allowed the identification of selective quadruplex DNA ligands with good affinities. Using this screening method we discovered a new bright red-emitting DNA stain, Acri-2,7-Py, for fixed cells. In living cells, the staining was not nuclear and photodamage generated through illumination induced cellular death. These processes require further studies to determine the relevance of Acri-2,7-Py in photodynamic therapy.

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