Scientific Publications

Our research contributions to the field of computational biology

108 publications

SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations.

Corentin Bedart, Nicolas Renault, Philippe Chavatte, Adeline Porcherie, Abderrahim Lachgar, Monique Capron, Amaury Farce
Journal of chemical information and modeling March 2022 Vol. 62(6) Pages: 1425-1436

As long as the structural study of molecular mechanisms requires multiple molecular dynamics reflecting contrasted bioactive states, the subsequent analysis of molecular interaction networks remains a bottleneck to be fairly treated and requires a user-friendly 3D view of key interactions. Structural Interaction Network Analysis Protocols (SINAPs) is a proprietary python …

In vitro and in silico approach to study the hormonal activities of the alternative plasticizer tri-(2-ethylhexyl) trimellitate TEHTM and its metabolites.

Laurence Dahbi, Amaury Farce, Nicolas Kambia, Isabelle Séverin, Thierry Dine, Emmanuel Moreau, Valérie Sautou, Marie-Christine Chagnon
Archives of toxicology March 2022 Vol. 96(3) Pages: 899-918

Tri-(2-ethylhexyl) trimellitate (TEHTM) is a plasticizer for polyvinyl chloride (PVC) material used in medical devices. It is an alternative to di-(2-ethylhexyl) phthalate (DEHP), a well-known reprotoxic and endocrine disruptor. As plasticizers are known to easily migrate when in contact with fatty biological fluids, patient exposure to TEHTM is highly probable. …

The EGF Domains of MUC4 Oncomucin Mediate HER2 Binding Affinity and Promote Pancreatic Cancer Cell Tumorigenesis.

Nicolas Stoup, Maxime Liberelle, Céline Schulz, Sumeyye Cavdarli, Romain Vasseur, Romain Magnez, Fatima Lahdaoui, Nicolas Skrypek, Fabien Peretti, Frédéric Frénois, Xavier Thuru, Patricia Melnyk, Nicolas Renault, Nicolas Jonckheere, Nicolas Lebègue, Isabelle Van Seuningen
Cancers November 2021 Vol. 13(22)

The HER2 receptor and its MUC4 mucin partner form an oncogenic complex via an extracellular region of MUC4 encompassing three EGF domains that promotes tumor progression of pancreatic cancer (PC) cells. However, the molecular mechanism of interaction remains poorly understood. Herein, we decipher at the molecular level the role and …

Combretastatin A-4 sulfur-containing heterocyclic derivatives: Synthesis, antiproliferative activities and molecular docking studies.

Abdelfattah Faouzi, Alexandre Arnaud, Alexandre Bancet, Caroline Barette, Jordane Preto, Cong Viet Do, Lars Petter Jordheim, Zineb Bousfiha, Thi Thanh Binh Nguyen, Marion Verrière, Amaury Farce, Marie-Odile Fauvarque, Roland Barret, Thierry Lomberget
European journal of medicinal chemistry April 2021 Vol. 215 Pages: 113275

Combretastatin A-4 inspired heterocyclic derivatives were synthesized and evaluated for their biological activities on tubulin polymerization and cell proliferation. Among the 19 described sulfur-containing compounds, derivatives (Z)-4h and (Z)-4j exhibited interesting in cellulo tubulin polymerization inhibition and antiproliferative activities with IC50 values for six different cell lines between 8 and …

Comparative Effects of Di-(2-ethylhexyl)phthalate and Di-(2-ethylhexyl)terephthalate Metabolites on Thyroid Receptors: In Vitro and In Silico Studies.

Nicolas Kambia, Isabelle Séverin, Amaury Farce, Laurence Dahbi, Thierry Dine, Emmanuel Moreau, Valérie Sautou, Marie-Christine Chagnon
Metabolites February 2021 Vol. 11(2)

Plasticizers added to polyvinylchloride (PVC) used in medical devices can be released into patients' biological fluids. Di-(2-ethylhexyl)phthalate (DEHP), a well-known reprotoxic and endocrine disruptor, must be replaced by alternative compounds. Di-(2-ethylhexyl) terephthalate (DEHT) is an interesting candidate due to its lower migration from PVC and its lack of reprotoxicity. However, …

A small-molecule P2RX7 activator promotes anti-tumor immune responses and sensitizes lung tumor to immunotherapy.

Laetitia Douguet, Serena Janho Dit Hreich, Jonathan Benzaquen, Laetitia Seguin, Thierry Juhel, Xavier Dezitter, Christophe Duranton, Bernhard Ryffel, Jean Kanellopoulos, Cecile Delarasse, Nicolas Renault, Christophe Furman, Germain Homerin, Chloé Féral, Julien Cherfils-Vicini, Régis Millet, Sahil Adriouch, Alina Ghinet, Paul Hofman, Valérie Vouret-Craviari
Nature communications January 2021 Vol. 12(1) Pages: 653

Only a subpopulation of non-small cell lung cancer (NSCLC) patients responds to immunotherapies, highlighting the urgent need to develop therapeutic strategies to improve patient outcome. We develop a chemical positive modulator (HEI3090) of the purinergic P2RX7 receptor that potentiates αPD-1 treatment to effectively control the growth of lung tumors in …

Indolizine-phenothiazine hybrids as the first dual inhibitors of tubulin polymerization and farnesyltransferase with synergistic antitumor activity.

Iuliana-Monica Moise, Elena Bîcu, Amaury Farce, Joëlle Dubois, Alina Ghinet
Bioorganic chemistry October 2020 Vol. 103 Pages: 104184

In the incessant search for innovative cancer control strategies, this study was devoted to the design, synthesis and pharmacological evaluation of dual inhibitors of farnesyltransferase and tubulin polymerization (FTI/MTIs). A series of indolizine-phenothiazine hybrids 16 (amides) and 17 (ketones) has been obtained in a 4-step procedure. The combination of the …

Ultrasounds-mediated 10-seconds synthesis of chalcones as potential farnesyltransferase inhibitors.

Germain Homerin, Adrian Sorin Nica, Amaury Farce, Joëlle Dubois, Alina Ghinet
Bioorganic & medicinal chemistry letters June 2020 Vol. 30(11) Pages: 127149

A broad range of chalcones and derivatives were easily and rapidly synthesized, following Claisen-Schmidt condensation of (hetero)aryl ketones and (hetero)aryl aldehydes using a ultrasound probe. A comparison was made with classical magnetic stirring experiments, and an optimization study was realized, showing lithium hydroxide to be the best basic catalyst of …

Pyroglutamide-Based P2X7 Receptor Antagonists Targeting Inflammatory Bowel Disease.

Germain Homerin, Samir Jawhara, Xavier Dezitter, Davy Baudelet, Pierrick Dufrénoy, Benoît Rigo, Régis Millet, Christophe Furman, Guillaume Ragé, Emmanuelle Lipka, Amaury Farce, Nicolas Renault, Boualem Sendid, Rogatien Charlet, Jordan Leroy, Mélodie Phanithavong, Camille Richeval, Jean-François Wiart, Delphine Allorge, Sahil Adriouch, Valérie Vouret-Craviari, Alina Ghinet
Journal of medicinal chemistry March 2020 Vol. 63(5) Pages: 2074-2094

This report deals with the design, the synthesis, and the pharmacological evaluation of pyroglutamide-based P2X7 antagonists. A dozen were shown to possess improved properties, among which inhibition of YO-PRO-1/TO-PRO-3 uptake and IL1β release upon BzATP activation of the receptor and dampening signs of DSS-induced colitis on mice, in comparison with …

Enhanced antitumor potential induced by chloroacetate-loaded benzophenones acting as fused tubulin-pyruvate dehydrogenase kinase 1 (PDHK1) ligands.

Alina Ghinet, Xavier Thuru, Emilie Floquet, Joëlle Dubois, Amaury Farce, Benoît Rigo
Bioorganic chemistry March 2020 Vol. 96 Pages: 103643

The majority of cancers detected every year are treated with anti-cancer compounds. Unfortunately, many tumors become resistant to antineoplastic drugs. One option is to use cocktails of compounds acting on different targets to try to overcome the resistant cells. This type of approach can produce good results, but is often …

New piperazine multi-effect drugs prevent neurofibrillary degeneration and amyloid deposition, and preserve memory in animal models of Alzheimer's disease.

Nicolas Sergeant, Valérie Vingtdeux, Sabiha Eddarkaoui, Marion Gay, Caroline Evrard, Nicolas Le Fur, Cyril Laurent, Raphaelle Caillierez, Hélène Obriot, Paul-Emmanuel Larchanché, Amaury Farce, Mathilde Coevoet, Pascal Carato, Mostafa Kouach, Amandine Descat, Patrick Dallemagne, Valérie Buée-Scherrer, David Blum, Malika Hamdane, Luc Buée, Patricia Melnyk
Neurobiology of disease September 2019 Vol. 129 Pages: 217-233

Alzheimer's Disease is a devastating dementing disease involving amyloid deposits, neurofibrillary tangles, progressive and irreversible cognitive impairment. Today, only symptomatic drugs are available and therapeutic treatments, possibly acting at a multiscale level, are thus urgently needed. To that purpose, we designed multi-effects compounds by synthesizing drug candidates derived by substituting …

In vitro and in silico hormonal activity studies of di-(2-ethylhexyl)terephthalate, a di-(2-ethylhexyl)phthalate substitute used in medical devices, and its metabolites.

Nicolas K Kambia, Isabelle Séverin, Amaury Farce, Emmanuel Moreau, Laurence Dahbi, Claire Duval, Thierry Dine, Valérie Sautou, Marie-Christine Chagnon
Journal of applied toxicology : JAT July 2019 Vol. 39(7) Pages: 1043-1056

Plasticizers added to polyvinylchloride used in medical devices can be released into patients' biological fluids. The substitution of di-(2-ethylhexyl)phthalate (DEHP) by alternative plasticizers is essential but their safety must be demonstrated. DEHP, di-(2-ethylhexyl)terephthalate (DEHT) and their metabolites were investigated using level 2 Organization for Economic Co-operation and Development bioassays to …

Exploring isoxazoles and pyrrolidinones decorated with the 4,6-dimethoxy-1,3,5-triazine unit as human farnesyltransferase inhibitors.

Liliana Lucescu, Alina Ghinet, Sergiu Shova, Romain Magnez, Xavier Thuru, Amaury Farce, Benoît Rigo, Dalila Belei, Joëlle Dubois, Elena Bîcu
Archiv der Pharmazie May 2019 Vol. 352(5) Pages: e1800227

Unprecedented triazinyl-isoxazoles were afforded via an effective cycloaddition reaction between nitrile oxides and the scarcely described 2-ethynyl-4,6-dimethoxy-1,3,5-triazine as dipolarophile. The biological evaluation of the newly synthesized compounds showed that the inhibition of human farnesyltransferase by zinc complexation could be improved with triazine-isoxazole moieties. The replacement of the isoxazole unit by …

Access to 3-spiroindolizines containing an isoindole ring through intra-molecular arylation of spiro-N-acyliminium species: a new family of potent farnesyltransferase inhibitors.

Anthony Pesquet, Hamid Marzag, Michael Knorr, Carsten Strohmann, Ata Martin Lawson, Alina Ghinet, Joëlle Dubois, Farce Amaury, Adam Daïch, Mohamed Othman
Organic & biomolecular chemistry March 2019 Vol. 17(10) Pages: 2798-2808

Based on N-acyliminium species, two efficient and rapid approaches to diversify spirocyclic systems connected by two different carbon centers to the isoindole ring have been developed. The imide reduction and the tandem oxidative cleavage of olefin/formyl-amide equilibration were at first selected as the key steps for these strategies. Ultimately the …

Benzo[d]thiazol-2(3H)-ones as new potent selective CB2 agonists with anti-inflammatory properties.

Natascha Leleu-Chavain, Davy Baudelet, Valéria Moas Heloire, Diana Escalante Rocha, Nicolas Renault, Amélie Barczyk, Madjid Djouina, Mathilde Body-Malapel, Pascal Carato, Régis Millet
European journal of medicinal chemistry March 2019 Vol. 165 Pages: 347-362

The high distribution of CB2 receptors in immune cells suggests their important role in the control of inflammation. Growing evidence offers this receptor as an attractive therapeutic target: selective CB2 agonists are able to modulate inflammation without triggering psychotropic effects. In this work, we report a new series of selective …

Chlorinated and brominated bisphenol A derivatives: Synthesis, characterization and determination in water samples.

Manon Doumas, Steeve Rouillon, Nicolas Venisse, Cedric Nadeau, Pascale Pierre Eugene, Amaury Farce, Philippe Chavatte, Antoine Dupuis, Virginie Migeot, Pascal Carato
Chemosphere December 2018 Vol. 213 Pages: 434-442

Bisphenol A (BPA) has been used in the plastics industry for several decades. During the treatment of drinking water with chlorine reagent, the formation of chlorinated derivatives of BPA (ClxBPA) but also bromoBPA and bromochloroBPA is to be expected. Some of these compounds are considered to have an estrogenic effect …

A phenotypic approach to the discovery of compounds that promote non-amyloidogenic processing of the amyloid precursor protein: Toward a new profile of indirect β-secretase inhibitors.

Marion Gay, Caroline Evrard, Florian Descamps, Pascal Carato, Nicolas Renault, Mathilde Coevoet, Sabiha Eddarkaoui, Catherine Baud, Paul-Emmanuel Larchanché, Luc Buée, Jamal El Bakali, Valérie Vingtdeux, Nicolas Sergeant, Patricia Melnyk
European journal of medicinal chemistry November 2018 Vol. 159 Pages: 104-125

Dysregulation of the Amyloid Precursor Protein (APP) processing leading to toxic species of amyloid β peptides (Aβ) is central to Alzheimer's disease (AD) etiology. Aβ peptides are produced by sequential cleavage of APP by β-secretase (BACE-1) and γ-secretase. Lysosomotropic agent, chloroquine (CQ), has been reported to inhibit Aβ peptide production. …

Importance of the second extracellular loop for melatonin MT1 receptor function and absence of melatonin binding in GPR50.

Nathalie Clement, Nicolas Renault, Jean-Luc Guillaume, Erika Cecon, Anne-Sophie Journé, Xavier Laurent, Kenjiro Tadagaki, Francis Cogé, Arnaud Gohier, Philippe Delagrange, Philippe Chavatte, Ralf Jockers
British journal of pharmacology August 2018 Vol. 175(16) Pages: 3281-3297

Recent crystal structures of GPCRs have emphasized the previously unappreciated role of the second extracellular (E2) loop in ligand binding and gating and receptor activation. Here, we have assessed the role of the E2 loop in the activation of the melatonin MT1 receptor and in the inactivation of the closely …

Design and synthesis of 2,6-disubstituted-8-amino imidazo[1,2a]pyridines, a promising privileged structure.

Rajaa Boulahjar, Angela Rincon Arias, Raphaël Bolteau, Nicolas Renault, Mathilde Coevoet, Amélie Barczyk, Romain Duroux, Saïd Yous, Patricia Melnyk, Laurence Agouridas
Bioorganic & medicinal chemistry July 2018 Vol. 26(12) Pages: 3296-3307

Imidazo[1,2a]pyridines have gained much interest in the field of medicinal chemistry research. In the aim of accessing new privileged structure, we decided to design and synthesize 8-aminated-imidazo[1,2a]pyridines substituted on positions 2 and 6. This scaffold, rarely found in the literature, was obtained via palladium-catalyzed coupling reactions (Suzuki reaction or N-hydroxysuccinimidyl …

Toward the Discovery of a Novel Class of YAP⁻TEAD Interaction Inhibitors by Virtual Screening Approach Targeting YAP⁻TEAD Protein⁻Protein Interface.

Floriane Gibault, Mathilde Coevoet, Manon Sturbaut, Amaury Farce, Nicolas Renault, Frédéric Allemand, Jean-François Guichou, Anne-Sophie Drucbert, Catherine Foulon, Romain Magnez, Xavier Thuru, Matthieu Corvaisier, Guillemette Huet, Philippe Chavatte, Patricia Melnyk, Fabrice Bailly, Philippe Cotelle
Cancers May 2018 Vol. 10(5)

Intrinsically disordered protein YAP (yes-associated protein) interacts with TEADs transcriptional factors family (transcriptional enhancer associated domain) creating three interfaces. Interface 3, between the Ω-loop of YAP and a shallow pocket of TEAD was identified as the most important TEAD zone for YAP-TEAD interaction. Using the first X-ray structure of the …