Production scientifique de l'équipe Bioinformatique structurale

Gyulkhandanyan A, Rezaie AR, Roumenina L, Lagarde N, Fremeaux-Bacchi V, Miteva MA, Villoutreix BO. « Analysis of protein missense alterations by combining sequence- and structure-based methods », Molecular Genetics & Genomic Medicine. 2020, e1166. doi:10.1002/mgg3.1166

Ricco C, Abdmouleh F, Riccobono C, Guenineche L, Martin F, Goya-Jorge E, Lagarde N, Liagre B, Ben Ali M, Ferroud C, El Arbi M, Sylla-Iyarreta Veitía M. « Pegylated Triarylmethanes: Synthesis, Antimicrobial Activity, Anti-Proliferative Behavior and in Silico Studies », Bioorganic Chemistry, 2020, 96, 103591: 13p. doi:10.1016/j.bioorg.2020.103591

Bouchara T, Montes M. Immersive sonification of protein surfaces. IEEE VR Workshop on Sonic Interactions in Virtual Environments, 2020

1: Réau M, Lagarde N, Zagury JF, Montes M. Hits Discovery on the Androgen Receptor: In Silico Approaches to Identify Agonist Compounds. Cells. 2019 Nov13;8(11). pii: E1431. doi: 10.3390/cells8111431. PubMed PMID: 31766271; PubMed Central PMCID: PMC6912550.

2: Lagarde N, Zagury JF, Montes M. Importance of the pharmacological profile of the bound ligand in enrichment on nuclear receptors: toward the use of experimentally validated decoy ligands. J Chem Inf Model. 2014 Oct 27;54(10):2915-44. doi: 10.1021/ci500305c. Epub 2014 Oct 9. PubMed PMID: 25250508.

3: Lagarde N, Delahaye S, Zagury JF, Montes M. Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores. J Cheminform. 2016 Sep 6;8(1):43. doi: 10.1186/s13321-016-0154-2. eCollection 2016. PubMed PMID: 27602059; PubMed Central PMCID: PMC5011875.

4: Lagarde N, Delahaye S, Jérémie A, Ben Nasr N, Guillemain H, Empereur-Mot C, Laville V, Labib T, Réau M, Langenfeld F, Zagury JF, Montes M. Discriminating Agonist from Antagonist Ligands of the Nuclear Receptors Using Different Chemoinformatics Approaches. Mol Inform. 2017 Oct;36(10). doi: 10.1002/minf.201700020. Epub 2017 Jul 3. PubMed PMID: 28671755.

5: Réau M, Langenfeld F, Zagury JF, Lagarde N, Montes M. Decoys Selection in Benchmarking Datasets: Overview and Perspectives. Front Pharmacol. 2018 Jan 24;9:11. doi: 10.3389/fphar.2018.00011. eCollection 2018. Review. PubMed PMID: 29416509; PubMed Central PMCID: PMC5787549.

6: Réau M, Lagarde N, Zagury JF, Montes M. Nuclear Receptors Database Including Negative Data (NR-DBIND): A Database Dedicated to Nuclear Receptors Binding Data Including Negative Data and Pharmacological Profile. J Med Chem. 2019 Mar 28;62(6):2894-2904. doi: 10.1021/acs.jmedchem.8b01105. Epub 2018 Nov 6. PubMed PMID: 30354114.

7: Réau M, Langenfeld F, Zagury JF, Montes M. Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study. J Comput Aided Mol Des. 2018 Jan;32(1):231-238. doi: 10.1007/s10822-017-0063-0. Epub 2017 Sep 14. PubMed PMID: 28913743. 

8: Mouhsine H, Guillemain H, Moreau G, Fourati N, Zerrouki C, Baron B, Desallais L, Gizzi P, Ben Nasr N, Perrier J, Ratsimandresy R, Spadoni JL, Do H, England P, Montes M, Zagury JF. Identification of an in vivo orally active dual-binding protein-protein interaction inhibitor targeting TNFα through combined in silico/in vitro/in vivo screening. Sci Rep. 2017 Jun 13;7(1):3424. doi: 10.1038/s41598-017-03427-z. PubMed PMID: 28611375; PubMed Central PMCID: PMC5469758.

9: Lagarde N, Ben Nasr N, Jérémie A, Guillemain H, Laville V, Labib T, Zagury JF, Montes M. NRLiSt BDB, the manually curated nuclear receptors ligands and structures benchmarking database. J Med Chem. 2014 Apr 10;57(7):3117-25. doi: 10.1021/jm500132p. Epub 2014 Mar 25. PubMed PMID: 24666037.

10: Empereur-Mot C, Guillemain H, Latouche A, Zagury JF, Viallon V, Montes M. Predictiveness curves in virtual screening. J Cheminform. 2015 Nov 4;7:52. doi: 10.1186/s13321-015-0100-8. eCollection 2015. PubMed PMID: 26539250; PubMed Central PMCID: PMC4631717.

11: Rayar AM, Lagarde N, Martin F, Blanchard F, Liagre B, Ferroud C, Zagury JF, Montes M, Sylla-Iyarreta Veitía M. New selective cyclooxygenase-2 inhibitors from cyclocoumarol: Synthesis, characterization, biological evaluation and molecular modeling. Eur J Med Chem. 2018 Feb 25;146:577-587. doi: 10.1016/j.ejmech.2018.01.054. Epub 2018 Jan 31. PubMed PMID: 29407982.

12: Levieux G, Tiger G, Mader S, Zagury JF, Natkin S, Montes M. Udock, the interactive docking entertainment system. Faraday Discuss. 2014;169:425-41. doi: 10.1039/c3fd00147d. Epub 2014 May 22. PubMed PMID: 25341068.

13: Dufies M, Grytsai O, Ronco C, Camara O, Ambrosetti D, Hagege A, Parola J, Mateo L, Ayrault M, Giuliano S, Grépin R, Lagarde N, Montes M, Auberger P, Demange L, Benhida R, Pagès G. New CXCR1/CXCR2 inhibitors represent an effective treatment for kidney or head and neck cancers sensitive or refractory to reference treatments. Theranostics. 2019 Jul 9;9(18):5332-5346. doi: 10.7150/thno.34681. eCollection 2019. Review. PubMed PMID: 31410218; PubMed Central PMCID: PMC6691587.

14: Borriello L, Montès M, Lepelletier Y, Leforban B, Liu WQ, Demange L, Delhomme B, Pavoni S, Jarray R, Boucher JL, Dufour S, Hermine O, Garbay C, Hadj-Slimane R, Raynaud F. Structure-based discovery of a small non-peptidic Neuropilins antagonist exerting in vitro and in vivo anti-tumor activity on breast cancer
model. Cancer Lett. 2014 Jul 28;349(2):120-7. doi: 10.1016/j.canlet.2014.04.004. Epub 2014 Apr 19. PubMed PMID: 24752068.

15: Ben Nasr N, Guillemain H, Lagarde N, Zagury JF, Montes M. Multiple structures for virtual ligand screening: defining binding site properties-based criteria to optimize the selection of the query. J Chem Inf Model. 2013 Feb 25;53(2):293-311. doi: 10.1021/ci3004557. Epub 2013 Jan 29. PubMed PMID: 23312043. 

16: Lagarde N, Zagury JF, Montes M. Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives. J Chem Inf Model. 2015 Jul 27;55(7):1297-307. doi: 10.1021/acs.jcim.5b00090. Epub 2015 Jun 18. Review. PubMed PMID: 26038804.

17: Empereur-Mot C, Zagury JF, Montes M. Screening Explorer-An Interactive Tool for the Analysis of Screening Results. J Chem Inf Model. 2016 Dec 27;56(12):2281-2286. doi: 10.1021/acs.jcim.6b00283. Epub 2016 Nov 22. PubMed PMID: 27808512.

18: Liu WQ, Lepelletier Y, Montès M, Borriello L, Jarray R, Grépin R, Leforban B, Loukaci A, Benhida R, Hermine O, Dufour S, Pagès G, Garbay C, Raynaud F, Hadj-Slimane R, Demange L. NRPa-308, a new neuropilin-1 antagonist, exerts in vitro anti-angiogenic and anti-proliferative effects and in vivo anti-cancer effects in a mouse xenograft model. Cancer Lett. 2018 Feb 1;414:88-98. doi: 10.1016/j.canlet.2017.10.039. Epub 2017 Oct 28. PubMed PMID: 29111348.

19: Liu WQ, Megale V, Borriello L, Leforban B, Montès M, Goldwaser E, Gresh N, Piquemal JP, Hadj-Slimane R, Hermine O, Garbay C, Raynaud F, Lepelletier Y, Demange L. Synthesis and structure-activity relationship of non-peptidic antagonists of neuropilin-1 receptor. Bioorg Med Chem Lett. 2014 Sep 1;24(17):4254-9. doi: 10.1016/j.bmcl.2014.07.028. Epub 2014 Jul 17. PubMed PMID: 25091928.

20: Desallais L, Bouchez C, Mouhsine H, Moreau G, Ratsimandresy R, Montes M, Do H, Quintin-Colonna F, Zagury JF. Immunization against an IL-6 peptide induces anti-IL-6 antibodies and modulates the Delayed-Type Hypersensitivity reaction in cynomolgus monkeys. Sci Rep. 2016 Jan 19;6:19549. doi: 10.1038/srep19549. PubMed PMID: 26782790; PubMed Central PMCID: PMC4726013.

21: Limou S, Delaneau O, van Manen D, An P, Sezgin E, Le Clerc S, Coulonges C, Troyer JL, Veldink JH, van den Berg LH, Spadoni JL, Taing L, Labib T, Montes M, Delfraissy JF, Schachter F, O'Brien SJ, Buchbinder S, van Natta ML, Jabs DA, Froguel P, Schuitemaker H, Winkler CA, Zagury JF. Multicohort genomewide
association study reveals a new signal of protection against HIV-1 acquisition. J Infect Dis. 2012 Apr 1;205(7):1155-62. doi: 10.1093/infdis/jis028. Epub 2012 Feb 23. PubMed PMID: 22362864; PubMed Central PMCID: PMC3295605.

22: Rayar AM, Lagarde N, Ferroud C, Zagury JF, Montes M, Sylla-Iyarreta Veitia M. Update on COX-2 Selective Inhibitors: Chemical Classification, Side Effects and their Use in Cancers and Neuronal Diseases. Curr Top Med Chem. 2017;17(26):2935-2956. doi: 10.2174/1568026617666170821124947. Review. PubMed
PMID: 28828990.