Production scientifique de l'équipe Bioinformatique structurale

2022

Goldwaser E, Laurent C, Lagarde N, Fabrega S, Nay L, Villoutreix BO, Jelsch C, Nicot AB, Loriot MA, Miteva MA. Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. PLoS Comput. Biol., 2022

El Khoury L, Jing Z, Cuzzolin A, Deplano A, Loco D, Sattarov B, Hedin F, Wendeborn S, Ho C, El Ahdab D, Jaffrelot Inizan T, Sturleze M, Sosic A, Volpiana M, Lugato A, Barone M, Gatto B, Macchia ML, Bellanda M, Battistutta R, Salata C, Kondratov I, Iminov R, Khairulin A, Mykhalonok Y, Pochepko A, Chashka-Ratushmyi V, Kos I, Moro S, Montes M, Ren P, Ponder JW, Lagardere L, Piquemal JP, Sabbadin D. Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation. Chem Sci, 2022, in press

Langenfeld, F, Aderinwale T, Christoffer C, Shin WH, Terashi G, Wang X, Kihara D, Benhabiles H, Hammoudi K, Cabani A, Windal F, Melkemi M, Otu E, Zwiggelaar R, Hunter D, Liu Y, Sirugue L, Nguyen HN, Nguyen TDH, Nguyen-Truong VT, Le D, Nguyen HD, Tran MT, Montes M. Surface-based protein domains retrieval methods from a SHREC2021 challenge. J Mol Graph Model, 2021

2021

Lessigiarska I, Peng Y, Tsakovska I, Alov P, Lagarde N, Jereva D, Villoutreix BO, Nicot AB, Pajeva I, Pencheva T, Miteva MA. Computational Analysis of Chemical Space of Natural Compounds Interacting with Sulfotransferases. Molecules, 2021

Langenfeld, F, Aderinwale T, Christoffer C, Shin WH, Terashi G, Wang X, Kihara D, Benhabiles H, Hammoudi K, Cabani A, Windal F, Melkemi M, Otu E, Zwiggelaar R, Hunter D, Liu Y, Sirugue L, Nguyen HN, Nguyen TDH, Nguyen-Truong VT, Le D, Nguyen HD, Tran MT, Montes M. SHREC 2021: Surface-based protein domains retrieval. Eurographics Workshop on 3D Object Retrieval 2021

Machat M, Langenfeld F, Craciun D, Sirugue L, Labib T, Lagarde N, Maria M, Montes M. Comparative Evaluation of Shape Retrieval Methods on Macromolecular Surfaces: An Application of Computer Vision Methods in Structural Bioinformatics. Bioinformatics 2021, 1-8

Sellami A, Montes M, Lagarde N. Predicting Potential Endocrine Disrupting Chemicals Binding to Estrogen Receptor α (ERα) Using a Pipeline Combining Structure-Based and Ligand-Based in Silico Methods, Int. J. Mol. Sci. 2021, 22(6), 2846

Jaffrelot Inizan T, Célerse, F, Adjoua, O, El Ahdab, D, Jolly, LH, Liu, C, Ren, P, Montes, M, Lagarde, N, Lagardère, L, Monmarché, P, Piquemal, JP, High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling. Chem. Sci., 2021, Advance Article

Dumond A, Brachet E, Durivault J, Vial V, Puszko A, Lepelletier Y, Montemagno C, Pagnuzzi-Boncompagni M, Hermine O, Garbay C, Lagarde N, Montes M, Demange L, Grepin R, Pages G. Neuropilin 1 and Neuropilin 2 gene invalidation or pharmacological inhibition reveals their relevance for the treatment of metastatic renal cell carcinoma. J Exp Clin Cancer Res, 2021, 80: 33

Sellami A, Reau M, Langenfeld F, Lagarde N, Montes M. Virtual Libraries for Docking Methods: Guidelines for the Selection and the Preparation, Molecular Docking for Computer-Aided Drug Design, Elsevier, in press

2020

Langenfeld F. Peng Y, Lai YK, Rosin PL, Aderinwale T, Terashi G, Christoffer C, Kihara D, Benhabiles H, Hammoudi K, Cabani A, Windal F, Melkemi M, Giachetti A, Mylonas S, Axenopoulos A, Daras P, Otu E, Zwiggelaar R, Hunter D, Liu H, Montes M. "SHREC2020 track: Multi-domain protein shape retrieval challenge." Computer & Graphics, 2020, 91:189-198

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" 2020 IEEE Conference on Virtual Reality and 3D User Interfaces Abstracts and Workshops (VRW), 2020, 380-383

2019

Langenfeld F, Axenopoulos A, Benhabiles H, Daras P, Giachetti A, Han X, Hammoudi K, Kihara D, Lai T, Liu H, Melkemi M, Mylonas S, Terashi G, Wang Y, Windal F, Montes M. "SHREC’19 Protein Shape Retrieval Contest. Eurographics Workshop on 3D Objects Retrieval" 2019; 25-31

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.

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.

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.

2018

Langenfeld F, Axenopoulos A, Chtziofis A, Craciun D, Daras P, Du B, Giachetti A, Lai YK, Li H, Li Y, Masoumi M, Peng Y, Rosin PL, Sirugue J, Sun L, Thermos S, Toews M, Wei Y, Wu Y, Zhai Y, Zhao T, Zhen Y, Montes M. "SHREC’18 – Protein Shape Retrieval. Eurographics Workshop on 3D Objects Retrieval" 2018; 53-61

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

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 32, 231-238. doi: 10.1007/s10822-017-0063-0. PubMed PMID: 28913743.

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. PubMed PMID: 29111348

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. PubMed PMID: 29407982.

2017

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.

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.

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.

Craciun D, Sirugue J, Montes M, Global-to-Local Protein Shape Similarity System driven by Digital Elevation Models, IEEE Biosmart, 2017

Craciun D, Levieux G, Montes M. Shape Similarity System driven by Digital Elevation Models for Non-Rigid Shape Retrieval. Eurographics Workshop on 3D Object Retrieval, 2017.

Song N, Craciun D, Christoffer CW, Han X, Kihara D, Levieux G, Montes M, Qin H, Sahu P, Terashi T, Liu H. SHREC 2017 – Classification of Protein Shapes. Eurographics Workshop on 3D Object Retrieval, 2017

2015-2016

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.

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.

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.

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

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.

Levieux, G.; Montes, M., "Towards real-time interactive visualization modes of molecular surfaces: examples with Udock," Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015:19-23