Violeta Isabel Pérez Nueno

I joined the Orpailleur team at the LORIA in March 2010 as a Post-Doc with a Marie Curie Intra-European Fellowship for Career Development (IEF) from the European Comission CORDIS FP7.

I joined Harmonic Pharma SAS from July 2012 to July 2015.

Projects

Development of Virtual Screening Algorithms: Exploring Multiple Ligand Binding Modes Using Spherical Harmonic Consensus Clustering

My Marie Curie IEF fellowship focused on developing novel spherical harmonic-based consensus clustering algorithms. The GES (Gaussian Ensemble Screening) polypharmacology approach developed in this project is quite generic and it can be broadly applicable to all kind of targets. The approach has been tested and validated using 40 well-known drug targets from the DUD dataset and ligands belonging to 633 annotations (a group of ligands that share an
annotation define a set of functionally related molecules) present in MDDR (MDL Drug Data Report) database. It can be used to screen other libraries to help finding novel polypharmacology relationships between ligand sets. This project provides a generic tool to help deal with cases where multiple ligands may be associated with multiple pocket sub-sites or which may bind multiple targets

GES (Gaussian Ensemble Screening) Approach

Polypharmacology describes the binding of a ligand to multiple protein targets (a promiscuous ligand) or multiple diverse ligands binding to a given target (a promiscuous target). Pharmaceutical companies are discovering increasing numbers of both promiscuous drugs and drug targets. Hence, polypharmacology is now recognised as an important aspect of drug design. The Gaussian Ensemble Screening (GES) is a new and fast way to predict polypharmacological relationships between drug classes quantitatively. This approach represents a cluster of molecules with similar molecular properties as a Gaussian distribution with respect to a selected centre molecule. The similarity score between two clusters of ligands, or “ligand sets”, is calculated from the overlap of their Gaussian distribution functions, and this is then transformed into a probability score, or “p-value”. A large Gaussian overlap between two ligand sets indicates a high probability that these drug classes might be related, whereas a small Gaussian overlap between ligand sets indicates that those drug classes are very unlikely to be related.

GESSE: Predicting Drug Side Effects From Drug-Target Relationships

The in silico prediction of unwanted side effects (SEs) caused by the promiscuous behavior of drugs and their targets is highly relevant to the pharmaceutical industry. Considerable effort is now being put into the computational and experimental screening of several suspected off-target proteins in the hope that SEs might be identified early, before the cost associated with developing a drug candidate rises steeply. Following this need, we present a new method called GESSE to predict potential SEs of drugs from their physico-chemical properties (3D shape plus chemistry) and to target protein data extracted from predicted drug-target relationships. The GESSE approach uses a canonical correlation analysis of the full drug-target and drug-SE matrices, and it then calculates a probability that each drug in the resulting drug-target matrix will have a given SE using a Bayesian discriminant analysis (DA) technique. The performance of GESSE is quantified using retrospective (external database) analysis and literature examples, using area under the ROC curve (AUC), “top hit rates”, misclassification rates, and a Chi-square independence test. Overall, the robust and very promising retrospective statistics obtained and the many SE predictions that have experimental corroboration demonstrate that GESSE can successfully predict potential drug-SE profiles of candidate drug compounds from their predicted drug-target relationships.

Biographical Data

Date of birth: 16 February 1982. Nationality: Spanish.

Academic Degrees

EU official Master in Health Economics and Pharmacoeconomics (Feb 2016-Jan 2018), Universitat Pompeu Fabra and Barcelona School of Management (4th internationally ranked in health economics), online.
European PhD (cum laude) in Computational Chemistry (2009), Ramon LLull University, Barcelona, Spain.
Certificate of pedagogical competence, physics and chemistry specialities (2008), UB, Barcelona, Spain.
DEA in computational chemistry (2007), IQS, Ramon Llull University, Barcelona, Spain.
BSc in Engineering Chemistry IQS (2006), IQS, Ramon Llull University, Barcelona, Spain.
BSc in Organic Chemistry (2005), IQS, Ramon Llull University, Barcelona, Spain.
Piano Teacher degree (2002), Higher Music Conservatory of Barcelona (Liceo), Barcelona, Spain.

Research Training

PostDoctoral Fellow Marie Curie (2010), FP7-PEOPLE-2009-IEF.
PostDoctoral Fellow (2010), BE-DGR 2009- 2n termini, Research outside Catalonia Grant, Catalan Parliament, Barcelona, Spain.
Graduate Fellow (2008), FI 2008, Young researcher contract, Catalan Parliament, Barcelona, Spain.
Graduate Fellow (2005), IQS, Ramon LLull University, Barcelona, Spain.

Employment History

2012-2015: Harmonic Pharma SAS Senior Scientist.
2011-2012: Member of the scientific committee for Harmonic Pharma SAS.
2010-2012: Research Scientist, Orpailleur Team, LORIA (INRIA), Nancy, France.
2009-2010: Associate Professor, computational chemistry, IQS, Ramon LLull University, Barcelona, Spain.
2008-2010: Research Scientist, Organic Chemistry Department, Grup d′Enginyeria Molecular (GEM), IQS, Ramon LLull University, Barcelona, Spain.
2005-2007: Assistant Professor, basic programming, numerical calculus, and computational chemistry, IQS, Ramon LLull University, Barcelona, Spain.

Languages

Spanish and Catalan: native.
English: proficient user.
French: independent user.
Greek: basic user.

International Collaborations

Organic Chemistry Department, Grup d′Enginyeria Molecular (GEM), IQS, Ramon LLull University, Barcelona, (SPAIN).
Dipartimento Farmaco-Chimico, Università degli Studi di Bari, Bari (ITALY).
Department of Computing Science, University of Aberdeen, Aberdeen (UK; for fulfillment of European PhD).
IGMM-CNRS and IBMM, Montpellier, (FRANCE).
INRIA Grand Est, LORIA, Vandoeuvre-lès-Nancy (FRANCE).

Patent Publications

ES Patent ES200602764. Oct. 26, 2006 (PCT/ES2007/000613. Oct. 26, 2007). WO2008/04995002 May 2008 (02.05.2008). NOVEL POLYNITROGENATED SYSTEMS AS ANTI-HIV AGENTS. Jordi Teixidó, José I. Borrell, Santiago Nonell, Xavier Batllori, Sofia Pettersson, Laia Ros, Raimon Puig de la Bellacasa, María Obdulia Rabal, Violeta I. Pérez-Nueno, José Esté, Imma Clotet, Mercedes Armand-Ugón.
European patent EP14305 487.2 – 1464. May 28, 2015. New derivatives of cephalosporin for treatment of cancer. Arnaud Sinan Karaboga, Violeta I. Pérez-Nueno, Michel Souchet.
Curie-Cancer and Harmonic Pharma sign a partnership agreement for exploring the anti-cancer activity of several compounds.

Peer-Reviewed Journal Publications (35 Publications, RG Score 26.31, h-index=13)

Using quantitative systems pharmacology for novel drug discovery.
Pérez-Nueno, V. I.(2015)
Expert Opin. Drug Discov.,10,1-17.
GESSE: Predicting Drug Side Effects From Drug-Target Relationships.
Pérez-Nueno, V. I. ;Souchet, M.; Karaboga,A.S.; Ritchie, D.W.(2015)
J. Chem. Inf. Model.,55,1804-1823, and Front Cover Illustration.
Studying the Binding Interactions of Allosteric Agonists and Antagonists of the CXCR4 Receptor.
Planesas, J.M.;Pérez-Nueno, V. I.;Borrell, J. I.; Teixidó, J. (2015)
Journal of Molecular Graphics and Modelling,60,1-14.
Polypharmacology within CXCR4: Multiple binding sites and allosteric behavior.
Planesas, J.M.;Pérez-Nueno, V. I.;Borrell, J. I.; Teixidó, J.(2014)
AIP Conf.Proc.,1618,1036,DOI:10.1063/1.4898789
GES polypharmacology fingerprints: A novel approach for drug repositioning.
Pérez-Nueno, V. I.; Karaboga,A.S.;Souchet, M.; Ritchie, D.W. (2014)
J. Chem. Inf. Model.,54,720-734, and Front Cover Illustration.
Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology.
Carrieri, A.; Pérez-Nueno, V. I.; Lentini, G.; Ritchie, D.W. (2013)
Current Topics in Medicinal Chemistry,13,1069-1097.
A highly specific and sensitive pharmacophore model for identifying CXCR4 antagonists. Comparison with docking and shape-matching virtual screening performance.
Karaboga,A.S.; Planesas, J.M.; Petronin, F.; Teixidó, J.; Souchet, M.; Pérez-Nueno, V. I. (2013)
J. Chem. Inf. Model.,53,DOI: 10.1021/ci400037y
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report.
Yasset Perez-Riverola, Henning Hermjako, Oliver Kohlbacher, Lennart Martens, David Creasy, Jürgen Cox, Felipe Leprevost, Baozhen Paul Shan,Pérez-Nueno, V. I., Michal Blazejczyk, Marco Punta, Klemens Vierlinger, Pedro Valiente, Kalet Leon, Glay Chinea, Osmany Guirola, Ricardo Bringas, Gleysin Cabrera, Gerardo Guillen, Gabriel Padron, Luis Javier Gonzalez, Vladimir Besada. (2013)
Journal of Proteomics, DOI :10.1016/j.jprot.2013.01.019.
Detecting Drug Promiscuity using Gaussian Ensemble Screening.
Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. (2012)
J. Chem. Inf. Model.,52,1948-1961.
Recent Trends and Applications in 3D Virtual Screening.
Ghemtio, L.; Pérez-Nueno, V. I.; Leroux, V.; Asses, Y.; Souchet, M.; Mavridis, L.; Ritchie, D.W. (2012)
Combinatorial Chemistry & High Throughput Screening,15,749-769.
Impact of the CXCR4 structure on docking-based virtual screening of HIV entry inhibitors.
Planesas, J. M.; Pérez-Nueno, V. I.;Borrell, J. I.; Teixidó, J. (2012)
Journal of Molecular Graphics and Modelling,38,123-136.
Identifying and characterizing promiscuous targets: Implications for virtual screening.
Pérez-Nueno, V. I.; Ritchie, D.W. (2012)
Expert Opinion On Drug Discovery,7,1-17.
Predicting drug promiscuity using spherical harmonic (SH) shape-based similarity comparisons.
Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. (2011)
The Open Conference Proceedings Journal,2,113-129.
Using Consensus-Shape Clustering to Identify Promiscuous Ligands and Protein targets and to Choose the Right Query for Shape-Based Virtual Screening.
Pérez-Nueno, V. I.; Ritchie, D.W. (2011)
J. Chem. Inf. Model. 51, 1233-1248.
Predicting drug polypharmacology using a novel surface property similarity-based approach.
Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W. (2011)
Journal of Cheminformatics 3 (Suppl 1), O19.
Using spherical harmonic surface property representations for ligand-based virtual screening.
Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Clark, T.; Ritchie, D.W. (2011)
Molecular Informatics 30, 151-159.
Improving VEGFR-2 docking-based screening by pharmacophore post-filtering and similarity search post-processing.
Planesas, J. M.; Claramunt, R. M.; Borrell, J. I.; Pérez-Nueno, V. I. (2011)
J. Chem. Inf. Model. 51, 777-787.
A Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Dataset Reveals Limitations of Current 3D Methods.
Venkatraman, V.; Pérez-Nueno, V. I.; Mavridis, L.; Ritchie, D.W. (2010)
J. Chem. Inf. Model. 50, 2079-2093.
Applying in silico Tools to the Discovery of Novel CXCR4 Inhibitors.
Pérez-Nueno, V. I.; Ritchie, D. W. (2010)
Drug Discovery Development Research 72, 95-111.
Novel Monocyclam Derivatives as HIV Entry Inhibitors: Design, Synthesis, Anti-HIV Evaluation, and Their Interaction with the CXCR4 Coreceptor.
Pettersson, S.; Pérez-Nueno, V. I.; Mena, M. P.; Clotet, B.; Esté, J.; Borrell, J. I.; Teixidó, J. (2010)
ChemMedChem 5, 1272-1285.
Virtual screening tools applied to HIV entry inhibitors. Design of novel anti-HIV compounds.
Pérez-Nueno, V. I., PhD Thesis , (2009).
Biological profiling of anti-HIV agents and insights into CCR5 antagonist binding using in silico techniques.
Carrieri, A.; Pérez-Nueno, V. I.; Fano, A.; Pistone, C.; Ritchie, D. W.; Teixidó, J. (2009)
ChemMedChem. 4, 1153-1163.
APIF: A New Interaction Fingerprint Based on Atom Pairs and its Application to Virtual Screening.
Pérez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixidó, J. (2009)
J. Chem. Inf. Model. 49, 1245-1260.
Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening.
Pérez-Nueno, V. I.; Pettersson, S.; Ritchie, D. W.; Borrell, J. I.; Teixidó, J. (2009)
J. Chem. Inf. Model. 49, 810-823.
Clustering and classifying diverse HIV entry inhibitors using a novel consensus shape based virtual screening approach: Further evidence for multiple binding sites within the CCR5 extracellular pocket.
Pérez-Nueno, V. I.; Ritchie, D. W.; Borrell, J. I.; Teixidó, J. (2008)
J. Chem. Inf. Model. 48, 2146-2165.
Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape matching and Ligand-Receptor Docking.
Pérez-Nueno, V. I.; Ritchie, D. W.; Rabal, O.; Pascual, R.; Borrell, J. I.; Teixidó, J. (2008)
J. Chem. Inf. Model. 48, 509-533, and Front Cover Illustration.
Discovery of novel non-cyclam polynitrogenated CXCR4 coreceptor inhibitors.
Pettersson, S.; Pérez-Nueno, V. I.; Ros-Blanco, L.; Puig de la Bellacasa, R.; Rabal,O.; Batllori, X.; lotet, B.; Clotet-Codina, I.; Armand-Ugón, M.; Esté, J.; Borrell, J. I.; Teixidó, J. (2008)
ChemMedChem 3, 1549-1557.. In Spotlights (Antiviral Agents), Angew. Chem. Int. Ed. 2008,47, 8554-8555.
Nous fàrmacs per bloquejar l′entrada del VIH a les cèl·lules.
Pérez-Nueno, V. I.; Pettersson, S.; Borrell, J. I.; Teixidó, J. (2007)
Teraflop 94, 14-15..
Molècules Contra la Sida.
Pettersson, S.; Pérez-Nueno, V. I.; Ros-Blanco, L.; Puig de la Bellacasa, R.; Tejedor, R.; Alavedra, R.; Borrell, J. I.; Teixidó, J. (2007)

Consciència URL, divendres 14 de setembre de 2007.

Book chapters

Spherical Harmonic Molecular Surfaces (ParaFit).
D.W.Ritchie; Pérez-Nueno, V. I.(2013)
in Scaffold Hopping in Medicinal Chemistry, chapter 3d (editor Nathan Brown). Methods and Principles in Medicinal Chemistry series,”Bioisosteres in Medicinal Chemistry”. Wiley-VCH Publishing,London,UK.

Presentations

“Relating drugs targets and side effects using GES and GESSE”,4th International Work-Conference on Bioinformatics and Biomedical Engineering 2016 (IWBBIO), 20th-22th April 2016, Granada, (SPAIN) Pérez-Nueno, V. I.
“Detecting drug polypharmacology.Towards systems pharmacology and an understanding of drug action”,Séminaire, Molécules Thérapeutiques in silico (MT,24th September 2015, Paris, (FRANCE) Pérez-Nueno, V. I.
“GESSE: Side Effects Prediction from GES Ligand-Target Relationships”,3rd International Work-Conference on Bioinformatics and Biomedical Engineering 2015 (IWBBIO), 15th-17th April 2015, Granada, (SPAIN) Pérez-Nueno, V. I.
Polypharmacology Within CXCR4: Multiple Binding Sites And Allosteric Behavior,10th International Conference of Computational Methods in Sciences and Engineering 2014 (ICCMSE), 4th-7th April 2014, Athens, (GREECE) Planesas, J.M.; Pérez-Nueno, V. I.; Borrell, J.I.; Teixidó, J.
GES polypharmacology fingerprints: A novel approach for drug repositioning,10th International Conference of Computational Methods in Sciences and Engineering 2014 (ICCMSE), 4th-7th April 2014, Athens, (GREECE) Pérez-Nueno, V. I.; Karaboga, A.S.; Souchet, M.; Ritchie, D.W.
A novel and powerful preclinical compound profiling and drug repositioning tool: GES polypharmacology fingerprints,Journées de la Société Francophone de Chémoinformatique, Nancy (FRANCE), October 10-11, 2013 Pérez-Nueno, V. I.; Karaboga, A.S.; Souchet, M.; Ritchie, D.W.
GES polypharmacology fingerprint: A novel and powerful drug repositioning tool,246th ACS National Meeting, Indianapolis, Indiana,(USA), September 8-12, 2013 Pérez-Nueno, V. I.; Karaboga, A.S.; Souchet, M.; Ritchie, D.W.
Preclinical Compound Profiling and Drug Repositioning,Bioinformatics and OMICS, 8th-11th December 2012, La Havana (CUBA) Pérez-Nueno, V. I.
An Overview of Modeling Molecular Interactions at INRIA Nancy. Detecting Drug Promiscuity using Gaussian Ensemble Screening,Bioinformatics and OMICS, 8th-11th December 2012, La Havana (CUBA) Pérez-Nueno, V. I.
Detecting drug promiscuity using Gaussian ensemble screening,Journees Ouvertes MBI. Modélisation des Biomoécules et de leurs Interactio, 25-26 Octobre 2012, Vandoeuvre-lès-Nancy (FRANCE), May 25-27, 2012. Pérez-Nueno, V. .
Gaussian Ensemble Screening: A novel way to analize virtual screening in a systems pharmacology context,15th Hellenic Symposium on Medicinal Chemistry,Athens, (Greece), May 25-27, 2012. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Gaussian ensemble screening (GES): A new approach to polypharmacology and virtual screening,243rd ACS National Meeting that will be held in San Diego, California, (USA), March 25-29, 2012. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Diseño computacional de compuestos activos.Estudio de cases aplicados, Diseño y síntesis de nuevas moléculas farmacológicamente activas: introducción a drug discovery, 5-16 March 2012. Pérez-Nueno, V. I.
Gaussian ensemble screening (GES): A new approach to polypharmacology and
virtual screening,Medicinal Chemistry Conference, Lanzarote, (SPAIN), March 2-5, 2012. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Predicting Drug Promiscuity using Gaussian Ensemble Screening, Institute for Research in Biomedicine – Barcelona Science Park, Barcelona, (SPAIN). 1 March 2012. Pérez-Nueno, V. I.; Ritchie, D.W.
VS approaches and successful applications ,
Séminaires & Conférences Chimie École Doctorale 459, Jeudi 24 Novembre 2011, Université Montpellier II, Montpellier (FRANCE),
Pérez-Nueno, V. I.; Ritchie,
D.W.
Using consensus shape-based clustering to help understand how multiple ligands might bind multiple target sites,Chemoinformatics seminar in Master en Chemoinformatique et Master « In silico drug design », October 27h 2011, Strasbourg (FRANCE), Pérez-Nueno, V. I.; Ritchie, D.W.
Using shape-based clustering to predict relationships between drug classes, 5emes Journées Nationales de Chémoinformatique, October 13-14 2011, Cabourg (FRANCE), Pérez-Nueno, V. I.; Venkatraman, V.; Ritchie, D.W.
Identifying and quantifying drug promiscuity by correlating ligand and target shape similarities,9th International Conference on Chemical Structures, June 5-9 2011, Noordwijkerhout (NETHERLANDS), Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Diseño computacional de compuestos activos., Introducción al proceso de drug discovery, 7-18 March 2011. Pérez-Nueno, V. I.
Predicting drug polypharmacology by correlating ligand and target shape similarities,3rd International Conference on Drug Discovery & Therapy, 7-10 February 2011, Dubai (UAE), Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Predicting drug polypharmacology using a novel surface property similarity-based approach, Chemoinformatics seminar in IMIM (Institut Municipal d′Investigació Mèdica), Barcelona, 24 November 2010. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Predicting drug polypharmacology using a novel surface property similarity-based approach, 6th German Conference on Chemoinformatics, November 2010. Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
Using “Consensus clustering” to help understand how multiple ligands might bind to multiple target sites. How this helps to choose the Right Query in Shape-Based Virtual Screening, 5th Joint Sheffield Conference on Chemoinformatics, July 2010. Pérez-Nueno, V. I.; Ritchie, D. W.
Diseño computacional de compuestos activos., Diseño y síntesis de nuevas moléculas farmacológicamente activas: introducción a drug discovery, March 2010. Pérez-Nueno, V. I.
ParaFit – Clustering and Classifying HIV Entry Inhibitors, Cepos Symposium 2010. Ritchie, D. W.; Pérez-Nueno, V. I.
Using Spherical Harmonic Virtual Screening Tools to Compare and Classify HIV Entry Inhibitors for the CXCR4 and CCR5 Co-Receptors, Modeling-09, CCC Erlangen, 2009. Ritchie, D. W.; Pérez-Nueno, V. I.
Biological profiling of anti-HIV agents using in silico techniques: insights into CCR5 ligands binding through homology buildings, 3D-QSAR, docking and shape matching virtual screening,
XXth International Symposium on Medicinal Chemistry (EFMC-ISMC 2008), September 2008. Carrieri, A.; Pérez-Nueno, V. I.; Ritchie, D. W.
Virtual screening tools applied to the discovery of novel HIV entry inhibitors for the CXCR4 and CCR5 receptors,
Seminaire Bioinformatique en Lorraine, LORIA, Vandoeuvre-lès-Nancy, January 2008. Pérez-Nueno, V. I.
The state of the art in Computational Chemistry,
Congress of the ISJACHEM, July 2006. Tejedor, R.; Rabal,O.; Pérez-Nueno, V. I.; Teixidó, J.

Posters

Research Projects

“Evaluation of the antitumor activity of new identified drugs in various primary human cáncer”. Dr Michel SOUCHET, Dr Arnaud Sinan KARABOGA, Dr Violeta I. PEREZ-NUENO; Period: 2011-2015.
“Pograma de investigación antiviral VIH-VHC: diseño y síntesis de antivirales potencial”. Financing institution: MEDU – Ministerio de Educación y Ciencia; Contract: SAF2010-21617-C02-02; Subproject computational part budget: 65.000 €; IP: José Ignacio Borrell Bilbao; Period: 2010-2013.
“Disseny i selecció de nous nuclis d′alta rendiment en recerca de nous fàrmacs pel sistema vascular”. Financing institution: CIDEM; Subcontract computational part budget 22.000 €; IP Josep Castells i Boliart; Period: 2009-2011.
“Diseño y síntesis de nuevos inhibidores del VIH – ENTRINHIV-1”. Program: NBME – Programa Nacional de Biomedicina; Financing institution: MEDU – Ministerio de Educación y Ciencia; Contract: SAF2007-63622-C02-01; IP: José Ignacio Borrell Bilbao; Total budget: 96.800,00 €; Period: 2007- 2010.
“Disseny, síntesi i avaluació de l′activitat antiviral de nous compostos anti-VIH”. Financing institution: Fundació La Marató de TV3; Project: 020930; IP: Jordi Teixidó Closa, José Andrés Esté, Josefa Mallol; Total budget: 309.336 €; Period: 2001-2003.

Master Thesis Supervised

1. Jesus Planesas (2009-2010) “Elaboració de models computacionals ligand-based i structure-based per al garbellat virtual d′inhibidors de vascular epitelial grow factor receptor utilitzant MOE”, UNED & Ramon Llull University (Spain).

2. Elena Escubedo (2010-2011). “Estudi de l′afinitat comparativa de diverses drogues d′abús amb els receptors nicotínics neuronals implicats en l′addicció”, UB & Ramon Llull University (Spain).

Thesis Supervised

Jesus Planesas (2010-2015). “Diseño de compuestos químicos antivirales (VIH). Modelado de potenciales inhibidores alostéricos del co-receptor celular CXCR4”. Ramon Llull University (Spain). Qualification: Excellent cum laude.

Awards

Health Economics Grant from UPF Barcelona School of Management for the Master in Health Economics and Pharmacoeconomics, January 2016.
Medicinal Chemistry Conference, Lanzarote, March 2-5, 2012. Best Overall Poster Content Award.
PhD Extraordinary Award from the Ramon Llull University inside the PhD program Chemistry and Engineering Chemistry 2009-2010, for the thesis “Virtual Screening Tools Applied to the Discovery of Novel HIV Entry Inhibitors”.
Honorary mention award in the XII Premio de Investigación Dr. Antonio Esteve for the work “Discovery of novel non-cyclam polynitrogenated CXCR4 coreceptor inhibitors”. ChemMedChem 2008, 3, 1549-1557.
EXPOQUIMIA I+D+i 2011 Award for the work in 4 JCIM papers, the “Discovery of novel non-cyclam polynitrogenated CXCR4 coreceptor inhibitors”. ChemMedChem 2008, 3, 1549-1557, and the patent WO2008049950-A1.

Refereeing

Journal of Chemical Information and Modeling.
European Journal of Medicinal Chemistry.
Journal of Open Access Bioinformatics.
Peptides.
Bioorganic & Medicinal Chemistry Letters.
Molecular Informatics.
Molecular Biosystems.
Anti-Cancer Agents in Medicinal Chemistry.
Current Topics in Medicinal Chemistry.

Editor

Executive Guest Editor Current Pharmaceutical Design (IF_3.452) for the Thematic Issue “Towards the integration of Quantitative and Systems Pharmacology into drug discovery: a systems level understanding of therapeutic and toxic effects of drugs”

Journal covers

Journal of Chemical Information and Modeling (2008), volume 48, issue 3.
Journal of Chemical Information and Modeling (2014), volume 54, issue 3.
Contribution to Journal of Chemical Information and Modeling (2015), volume 55, issue 1.
Journal of Chemical Information and Modeling (2015), volume 55, issue 9.

Others

Steering Committee Member, 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO),Granada,Spain. Organizer of the symposium ” Using quantitative systems pharmacology for novel drug discovery: a ‘systems-level’ perspective to reduce toxicity and increase the therapeutic effect of drugs towards ‘precision medicine’ “.
Member of the ACS CINF Program Committee for San Diego 2016.
Organizer of the symposium ” Quantitative and Systems Pharmacology: Thinking in a wider “systems-level” context accelerates drug discovery and enlightens our understanding of drug action ” at the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2015).
Organizer of the symposium “Drug discovery: Computer models can predict side effect targets” at the International Conference of Computational Methods in Sciences and Engineering 2014 (ICCMSE 2014).
Member of the ACS CINF Program Committee for Indianapolis 2013.Organization of the symposium “Computational Profiling and Repositioning as Promising New Ways of Drug Development”
Member of the scientific committee for Harmonic Pharma SAS 2011-2012.
Session Chair in the 3rd International Conference on Drug Discovery & Therapy, 7-10 February 2011, Dubai (UAE), Anti-Cancer Drug Discovery & Therapy/ Drug Delivery & Targeting Session.
Member of the examining board for the Thesis “In silico methodologies for the design of functional foods that can prevent cardiovascular diseases”, Esther Sala Argüello. Universitat Rovira i Virgili. Department of Biochemistry and Biotechnology (March 2011).
Member of the examining board for the Thesis “Identification of natural products as antidiabetic agents using computer-aided drug design methods”, Laura Guash Pamies. Universitat Rovira i Virgili. Department of Biochemistry and Biotechnology (November 2011).

Contact

Violeta I. Perez-Nueno, Ph.D.

Senior Scientist

615 rue du Jardin Botanique

54600 Villers lès Nancy – France

Cell +33(0) 638 878 547

violeta.pereznueno@loria.fr (please make your own AT sign)

perez.violeta@gmail.com (please make your own AT sign)

https://fr.linkedin.com/in/violetaisabelpereznueno

https://twitter.com/V_I_PerezNueno

https://www.researchgate.net/profile/Violeta_Perez-Nueno

http://scholar.google.es/citations?user=NIewN_UAAAAJ&hl=en

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