Selected research articles, reviews & meeting abstracts among over 220 (ISI Web of Science); 10 book chapters, 7 patents & strong contributions to the rational design of a new anti-metastatic presently in phase 1b clinical trial

 

Patents
COMPOUNDS TARGETING THE BFL-1 ANTI-APOPTOTIC PROTEIN AND USES THEREOF FOR THE TREATMENT OF CANCER.
Inventeurs : BONNEFOY-BERARD N; DEPREZ B; SPERANDIO O; DEBAUD AL; VILLOUTREIX Bruno; LEROUX F.
Numéro de brevet : WO/2014/EP77041 2014-12-09

MOLECULES INHIBITING A METABOLIC PATHWAY INVOLVING THE SYK PROTEIN TYROSINE KINASE AND METHOD FOR IDENTIFYING SAID MOLECULES.
Inventeurs : DARIAVACH Piona ; MARTINEAU Pierre,Emile,Ulysse ; VILLOUTREIX Bruno
Numéro de brevet : WO/2009/133294 and European Patent Office, Feb 25, 2015 number 2285366

PIPERAZINES DERIVATIVES AS PROTEASOME MODULATORS.
Inventeurs : VILLOUTREIX Bruno; REBOUD-RAVAUX Michèle; BASSE Nicolas; VIDAL Joëlle; MONTES Matthieu
Numéro de brevet : WO/2010/001366

NITROGEN HETEROCYCLE DERIVATIVES AS PROTEASOME MODULATORS.
Inventeurs : VILLOUTREIX Bruno; REBOUD-RAVAUX Michèle; BASSE Nicolas; VIDAL Joëlle; MONTES Matthieu
Numéro de brevet : WO/2010/001365

USE OF DERIVATIVES OF 3-OXO-2,3-DIHYDRO-5H-THIAZOLOF[3,2-A]PYRIMIDINE OR OF 3-OXO-2,3-DIHYDRO-5H-SELENAZOLO[3,2-A]PYRIMIDINE OR OF 3-OXO-1,2,3-TRIHYDRO-5H-IMIDAZOLO[1,2-A]PYRIMIDINE FOR THE PREPARATION OF PHARMACEUTICAL COMPOSITIONS INTENDED FOR THE TREATMENT OF CANCER.
Inventeurs : GARBAY Christiane; VILLOUTREIX Bruno; BRAUD Emmanuelle; GODDARD Mary-Lorène; KOLB Stéphanie; MITEVA Maria
Numéro de brevet : WO/2008/149311

POLYPEPTIDES FOR THE TREATMENT OF ANGIOGENESIS OR LYMPHANGIOGENESIS-RELATED DISEASES (WO2016083409 (A1)) (2016)
Mourah Samia; Villoutreix Bruno; Khayati Farah; Menashi Suzanne; Lebbe Celeste; Fernandez-Recio Juan; Calvo Fabien 

NOUVEAUX COMPOSES, COMPOSITIONS ET METHODES POUR LE TRAITEMENT DE LA RESISTANCE A L’INSULINE
Miteva M, Villoutreix BO, Aitken DJ, Burnol AF, Gondoin A, Issad T. (just filed April 2017)

 

Some publications

  • AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.
    Labbé CM, Pencheva T, Jereva D, Desvillechabrol D, Becot J, Villoutreix BO, Pajeva I, Miteva MA.
    Nucleic Acids Res. 2017 May 9. doi: 10.1093/nar/gkx397. [Epub ahead of print]

    Gly74Ser mutation in protein C causes thrombosis due to a defect in protein S-dependent anticoagulant function.
    Chen C, Yang L, Villoutreix BO, Wang X, Ding Q, Rezaie AR.
    Thromb Haemost. 2017 Apr 13. doi: 10.1160/TH17-01-0043. [Epub ahead of print]

    Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors.
    Lagorce D, Douguet D, Miteva MA, Villoutreix BO.
    Sci Rep. 2017 Apr 11;7:46277. doi: 10.1038/srep46277.

    Computational Biology and Chemistry in MTi: Emphasis on the Prediction of Some ADMET Properties.
    Miteva MA, Villoutreix BO.
    Mol Inform. 2017 Feb 21. doi: 10.1002/minf.201700008. [Epub ahead of print] Review.

    Acute genetic ablation of pendrin lowers blood pressure in mice.
    Trepiccione F, Soukaseum C, Baudrie V, Kumai Y, Teulon J, Villoutreix B, Cornière N, Wangemann P, Griffith AJ, Byung Choi Y, Hadchouel J, Chambrey R, Eladari D.
    Nephrol Dial Transplant. 2017 Jan 7. pii: gfw393. doi: 10.1093/ndt/gfw393. [Epub ahead of print]

    Blockade of the malignant phenotype by β-subunit selective noncovalent inhibition of immuno- and constitutive proteasomes.
    Villoutreix BO, Khatib AM, Cheng Y, Miteva MA, Maréchal X, Vidal J, Reboud-Ravaux M.
    Oncotarget. 2017 Feb 7;8(6):10437-10449. doi: 10.18632/oncotarget.14428.

    Pharmacogenomics of the cytochrome P450 2C family: impacts of amino acid variations on drug metabolism.
    Isvoran A, Louet M, Vladoiu DL, Craciun D, Loriot MA, Villoutreix BO, Miteva MA.
    Drug Discov Today. 2017 Feb;22(2):366-376. doi: 10.1016/j.drudis.2016.09.015. Epub 2016 Sep 28. Review.

    A Cell-Penetrating Peptide Targeting AAC-11 Specifically Induces Cancer Cells Death.
    Jagot-Lacoussiere L, Kotula E, Villoutreix BO, Bruzzoni-Giovanelli H, Poyet JL.
    Cancer Res. 2016 Sep 15;76(18):5479-90. doi: 10.1158/0008-5472.CAN-16-0302. Epub 2016 Jul 12.

    Discoidin Domains as Emerging Therapeutic Targets. (cover page)
    Villoutreix BO, Miteva MA.
    Trends Pharmacol Sci. 2016 Aug;37(8):641-59. doi: 10.1016/j.tips.2016.06.003. Epub 2016 Jun 29. Review.

    Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation.
    Villoutreix BO.
    Ann Pharm Fr. 2016 Jul;74(4):253-66. doi: 10.1016/j.pharma.2016.03.006. Epub 2016 Apr 28. Review.

    Genetic polymorphisms associated with increased risk of developing chronic myelogenous leukemia.
    Bruzzoni-Giovanelli H, González JR, Sigaux F, Villoutreix BO, Cayuela JM, Guilhot J, Preudhomme C, Guilhot F, Poyet JL, Rousselot P.
    Oncotarget. 2015 Nov 3;6(34):36269-77. doi: 10.18632/oncotarget.5915.

    iPPI-DB: an online database of modulators of protein-protein interactions.
    Labbé CM, Kuenemann MA, Zarzycka B, Vriend G, Nicolaes GA, Lagorce D, Miteva MA, Villoutreix BO, Sperandio O.
    Nucleic Acids Res. 2016 Jan 4;44(D1):D542-7. doi: 10.1093/nar/gkv982. Epub 2015 Oct 1.

    Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6.
    Martiny VY, Carbonell P, Chevillard F, Moroy G, Nicot AB, Vayer P, Villoutreix BO, Miteva MA.
    Bioinformatics. 2015 Dec 15;31(24):3930-7. doi: 10.1093/bioinformatics/btv486. Epub 2015 Aug 26.

 

  • I was pleased to contribute with Pharma's colleagues to two chapters of the 4th Edition of The Practice of Medicinal Chemistry by Prof C. Wermuth and to the book "In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications" edited by my colleague and friend, Prof C. Cavasotto
  • Computational investigations of hERG channel blockers: new insights and current predictive models. Villoutreix BO, Taboureau O. Advanced Drug Delivery Reviews 2015; 86:72-82
  • MTiOpenScreen: a web server for structure-based virtual screening. Labbe C, Rey J, Lagorce D, Vavruaa M, Becot J, Sperandio O, Villoutreix BO, Tuffery P, Miteva M. NAR 2015; 43(W1):W448-54
  • FAF-Drugs3: a web-server for compound property calculation and chemical library design. Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO. NAR 2015; 43(W1):W200-7
  • Therapeutic targeting of nuclear gamma-tubulin in RB1-negative tumors. Lindstrom L, Villoutreix BO, Lehn S, Hellsten R, Nilsson E, Crneta E, Olsson R, Alvarado-Kristensson M. Molecular Cancer Research 2015; 13(7):1073-82
  • Theileria parasites secrete a prolyl isomerase to maintain host leukocyte transformation. Marsolier J, Perichon M, DeBarry JD, Villoutreix BO, Chluba J, Garrido C, Zhou XZ, Lu KP, Ait-Si-Ali S, Fritsch L, Mhadhbi M, Medjkane S, Weitzman JB. Nature 2015; 520(7547):378-82

  • In silico design of low molecular weight protein-protein interaction inhibitors: overall concept and recent advances. Kuenemann MA, Sperandio O, Labbe CM, Lagorce D, Miteva MA, Villoutreix BO. Progress in Biophysics and Molecular Biology, in press 2015.
  • Les chimiothèques ciblant les interactions protéine-protéine. Sperandio O, Villoutreix BO, Morelli X, Roche P. Medecine/Sciences 2015; 31(3):312-9
  • Functional characterization of two novel non-synonymous alterations in CD46 and a Q950H change in factor H found in atypical hemolytic uremic syndrome patients.  Mohlin FC, Nilsson SC, Levart TK, Golubovic E, Rusai K, Muller-Sacherer T, Arbeiter K, Pallinger E, Szarvas N, Csuka D, Szilagyi A, Villoutreix BO, Prohaszka Z, Blom AM. Molecular Immunology 2015; 65(2):367-76
  • DNA Damage-Induced Nuclear Translocation of Apaf-1 is Mediated by Nucleoporin Nup107. Jagot-Lacoussiere L, Faye A, Villoutreix B, Rain JC, Poyet JL. Cell Cycle 2015 14(8):1242-51
     
  • Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction. Somajo S, Ahnström J, Fernandez-Recio J, Gierula M, Villoutreix BO, Dahlback B. Thrombosis and Haemostasis 2015; 113(5):976-87
  • Which 3D characteristics make an efficient inhibitor of protein-protein interactions ? Kuenemann M, Bourbon L, Labbe, C, Villoutreix BO, Sperandio O. J Chem Inf Model 2014; 3067-79
  • Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology (review). Villoutreix BO, Kuenemann MA, Poyet J-L, Bruzzoni-Giovanelli H, Labbe C, Lagorce D, Sperandio O, Miteva MA. Molecular Informatics 2014; 6-7: 414-437. (open)
  • Discovery of novel inhibitors of vascular endothelial growth factor-A-neuropilin-1 interaction by structure-based virtual screening. Starzec A, Miteva MA, Ladam P, Villoutreix BO, Perret GY. Bioorganic & Medicinal Chemistry 2014; 22:4042-8.
  • Identification of Small Inhibitory Molecules Targeting the Bfl-1 Anti-Apoptotic Protein That Alleviates Resistance to ABT-737. Mathieu AL, Sperandio O, Pottiez V, Balzarin S, Herlédan A, Elkaïm JO, Fogeron ML, Piveteau C, Dassonneville S, Deprez B, Villoutreix BO, Bonnefoy N, Leroux F. J Biomol Screen 2014; 19:1035-46.
  • Identification of novel small molecule inhibitors of activated protein C. Sperandio O, Wildhagen K, Schrijver R, Wielders S, Villoutreix BO, Nicolaes G. Thrombosis Research. 2014; 133:1105-14.

  • Rational design of small molecules targeting the C2 domain of coagulation factor VIII. Nicolaes GA, Kulharia M, Voorberg J, Kaijen PH, Wroblewska A, Wielders S, Schrijver R, Sperandio O, Villoutreix BO. Blood. 2014; 123:113-20.

  • One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. Villoutreix BO, Lagorce D, Labbé CM, Sperandio O, Miteva MA. Drug Discov Today. 2013; 18:1081-9.

  • iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. Labbé CM, Laconde G, Kuenemann MA, Villoutreix BO, Sperandio O. Drug Discov Today. 2013; 18:958-68.

  • Toward in silico structure-based ADMET prediction in drug discovery. Moroy G, Martiny VY, Vayer P, Villoutreix BO, Miteva MA. Drug Discov Today. 2012; 17:44-55.

  • Targeting the proangiogenic VEGF-VEGFR protein-protein interface with drug-like compounds by in silico and in vitro screening. Gautier B, Miteva MA, Goncalves V, Huguenot F, Coric P, Bouaziz S, Seijo B, Gaucher JF, Broutin I, Garbay C, Lesnard A, Rault S, Inguimbert N, Villoutreix BO, Vidal M. Chem Biol. 2011; 18:1631-9.

  • The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. Lagorce D, Maupetit J, Baell J, Sperandio O, Tufféry P, Miteva MA, Galons H, Villoutreix BO. Bioinformatics. 2011; 27:2018-20.

  • Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Pérot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO. Drug Discov Today. 2010; 15:656-67.

  • Rationalizing the chemical space of protein-protein interaction inhibitors. Sperandio O, Reynès CH, Camproux AC, Villoutreix BO. Drug Discov Today. 2010; 15:220-9.
  • Novel organic proteasome inhibitors identified by virtual and in vitro screening. Basse N, Montes M, Maréchal X, Qin L, Bouvier-Durand M, Genin E, Vidal J, Villoutreix BO, Reboud-Ravaux M. J Med Chem. 2010; 53:509-13.
  • 1,2,4-Oxadiazoles identified by virtual screening and their non-covalent inhibition of the human 20S proteasome. Maréchal X, Genin E, Qin L, Sperandio O, Montes M, Basse N, Richy N, Miteva MA, Reboud-Ravaux M, Vidal J, Villoutreix BO. Curr Med Chem. 2013; 20:2351-62.

  • A leap into the chemical space of protein-protein interaction inhibitors. Villoutreix BO, Labbé CM, Lagorce D, Laconde G, Sperandio O. Curr Pharm Des. 2012; 18:4648-67.
  • A novel druglike spleen tyrosine kinase binder prevents anaphylactic shock when administered orally. Mazuc E, Villoutreix BO, Malbec O, Roumier T, Fleury S, Leonetti JP, Dombrowicz D, Daëron M, Martineau P, Dariavach P, J Allergy. Clin Immunol. 2008; 122:188-94

  • A novel non-synonymous polymorphism (p.Arg240His) in C4b-binding protein is associated with atypical hemolytic uremic syndrome and leads to impaired alternative pathway cofactor activity. Blom AM, Bergström F, Edey M, Diaz-Torres M, Kavanagh D, Lampe A, Goodship JA, Strain L, Moghal N, McHugh M, Inward C, Tomson C, Frémeaux-Bacchi V, Villoutreix BO, Goodship TH. J Immunol. 2008; 180:6385-91.

  • Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V. Segers K, Sperandio O, Sack M, Fischer R, Miteva MA, Rosing J, Nicolaes GA, Villoutreix BO. Proc Natl Acad Sci U S A. 2007; 104:12697-702.

  • A formylated hexapeptide ligand mimics the ability of Wnt-5a to impair migration of human breast epithelial cells. Säfholm A, Leandersson K, Dejmek J, Nielsen CK, Villoutreix BO, Andersson T. J Biol Chem. 2006; 281:2740-9.

  • Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex. Miteva MA, Lee WH, Montes MO, Villoutreix BO. J Med Chem. 2005; 48:6012-22

  • Regulation of blood coagulation by the protein C anticoagulant pathway: novel insights into structure-function relationships and molecular recognition. Dahlbäck B, Villoutreix BO. Arterioscler Thromb Vasc Biol. 2005; 25:1311-20.

  • 3-Dimensional structure of membrane-bound coagulation factor VIII: modeling of the factor VIII heterodimer within a 3-dimensional density map derived by electron crystallography. Stoilova-McPhie S, Villoutreix BO, Mertens K, Kemball-Cook G, Holzenburg A. Blood. 2002; 99:1215-23.

  • Structural and energetic characteristics of the heparin-binding site in antithrombotic protein C. Friedrich U, Blom AM, Dahlbäck B, Villoutreix BO. J Biol Chem. 2001; 276:24122-8.

  • A structural model for the prostate disease marker, human prostate-specific antigen. Villoutreix BO, Getzoff ED, Griffin JH. Protein Sci. 1994; 3:2033-44.

Book chapters
In silico approaches assisting the rational design of low molecular weight protein-protein interaction modulators. Bruno Villoutreix, Melaine A. Kuenemann, David Lagorce, Olivier Sperandio, Maria A. Miteva. Parution : 2015 In Silico Drug Discovery and Design. Theory, Methods, Challenges, and Applications - August 26, 2015 - ISBN 9781482217834 (CRC Press)

Strategies in the Search for New Lead Compounds or Original Working Hypotheses. Auteurs : Camille Wermuth, Bruno Villoutreix, Serge Grisoni, Anne Olivier et Jean-Philippe Rocher. Sept 2015 The Practice of Medicinal Chemistry - pp 73-96 (Academic Press)

Application Strategies for the Primary Structure-Activity Relationship Exploration. Auteurs : Camille Wermuth, Serge Grisoni, Bruno Villoutreix et Jean-Philippe Rocher. Sept 2015 The Practice of Medicinal Chemistry - pp 302-317 (Academic Press)

Villoutreix B.O, Labbé C. M., Lagorce David, Laconde G., Sperandio O. A leap into the chemical space of Protein-Protein Interaction inhibitors. Wiley-VCH, «Protein-Protein Interactions in Drug Discovery», Ed. A. Doemling, pp 53-63. 2012

Lagorce D, Sperandio O, Miteva MA, Villoutreix BO. Chapter 1: Chemical Libraries for Virtual Screening. Bentham Science Publishers, eBook «In silico lead discovery». 2011

Sperandio O, Villoutreix BO, Miteva MA. Chapter 2: Structure-Based Virtual Screening. Bentham Science Publishers, eBook «In silico lead discovery». 2011.


Sperandio O, Miteva MA, Villoutreix BO. Target-based virtual screening to address protein-protein interfaces. Wiley-VCH, «Virtual Screening - Principles, Challenges, and Practical Guidelines», 2011.

David Lagorce, Christelle Reynes, Anne-Claude Camproux, Maria A. Miteva, Olivier Sperandio, Bruno O. Villoutreix. In silico ADME/Tox prediction. John Wiley and Sons, Inc. (Editor K Tsaioun, USA). 2009.

Sperandio O, Miteva MA, Villoutreix BO. Target-based virtual screening to address protein-protein interfaces. Wiley-VCH: Methods and Principles in Medicinal Chemistry (Editor C. Sotriffer). 2009

O. Sperandio, B. O. Villoutreix, MA. Miteva. Structure-based virtual screening. eBook Bentham (Ed. MA Miteva). 2009

Lagorce, D, Sperandio O, Miteva MA, Villoutreix BO. Chemical libraries for virtual screening. eBook Bentham (Ed. MA Miteva). 2009

Miteva, M. A., E. Alexov, Villoutreix BO. 2007. Protein structure analysis online. Curr Protoc Protein Sci Chapter 2:Unit 2 13.

L. Autin, M. Montes, MA. Miteva, BO Villoutreix. Computer tools to study intermolecular interactions. Recent Adv. In Prot. Eng. (2007, Chapt 9. Ed. Research signpost, Trivandrum, India. ISBN:978-81-308-0208-4).

Publication to introduce a topic to non scientists or to scientists working in a very very different field
Villoutreix BO. Bioinformatique structurale, criblage in silico. Sci Tech Anim Lab. Recherche experimentale et protection de l'animal de laboratoire. 22-26 (2006)

Sperandio O, Villoutreix BO, Morelli X, Roche P. [Chemical libraries dedicated to protein-protein interactions]. Med Sci (Paris). 2015 Mar;31(3):312-9. doi: 10.1051/medsci/20153103017. Epub 2015 Apr 8. Review. French. PubMed PMID: 25855285.

De l'algorithme au médicament. Janv - Fev 2014, pp 12-13 - Science et Sante

Cancer, Un parasite aux commandes. Mars - Avril 2015,  pp 8-9 - Science et Sante

Others
Recension du livre Chemoinformatics for Drug Discovery. J. Bajorah, Ed. John Wiley & Sons, Inc., 2014, 415 pages
Auteur: Bruno Villoutreix
Journal: Actualité Chimique, Mai 2015, numéro 396, pages: 59-60

Recent presentations
BO Villoutreix Invited Speaker

a) In silico and in vitro screening of challenging targets: hits modulating transient protein-membrane and protein-protein interactions. UCB Pharma London, Dec 5, 2013, UK
b) Recherche de sondes chimiques anti- et pro-coagulantes en associant le criblage in silico et in vitro. Printemps de la Cardiologie, 24 et 25 avril 2014 au Palais des Congrès de Strasbourg, France
c) Small molecule protein-protein interaction modulators: challenges and opportunities for drug discovery. The 4th International Summer School on Chemoinformatics in Strasbourg (23-27 June 2014), France
d) Design of small non-peptidic molecules targeting protein-protein interactions. GP2A Conference, August 28-29, 2014, Nantes, France
e) EMBO Workshop: Advances in protein–protein interaction analysis and modulation. Modulating PPI with low molecular weight compounds: recent success stories and assistance from in silico approaches. 9-12 September 2014, Hyères, France
g) Nantes, France, CIMATH2, Sept 22-23 2014: Design rationnel de modulateurs non-peptidiques d'interactions proteine-proteine en associant les approches silico et vitro
h) Colloque "Therapeutic innovation" co-organisé par les ITMO Circulation Métabolisme Nutrition et Technologie pour la Santé. 18 et 19 Dec 2014: in silico approaches to assist drug discovery
i) Colloque "Therapeutic innovation", chaire Liliane Bettencourt du Prof B. Meunier, Collège de France, Paris, le 2 -02-2015 : Design rationnel de petites molécules chimiques non peptidiques modulatrices d'interactions protéine-protéine