Maria Atanassova MITEVA (Mrs.) Senior Scientist INSERM MTi ...

Maria Atanassova MITEVA (Mrs.)
Senior Scientist
INSERM MTi
University Paris Diderot
5 rue Lagroua, Bat. Lamarck
75013 Paris, France
email : maria.miteva@univ-paris-diderot.fr
http://www.mti.univ-paris-diderot.fr/en/index.html
http://www.vls3d.com/
Research topics
Structural bioinformatics, biophysical chemistry, protein electrostatics, molecular modeling, protein
engineering, drug design and virtual ligand screening, chemoinformatics, in silico ADMETox.
Current position
Senior Scientist in MTI (Molécules Thérapeutiques in silico) research Unit (permanent position CR1 at the
Inserm (Institut National de la santé et de la recherché médicale; Inserm is the only French public organization
entirely dedicated to biological, medical and public health research)
Other positions
2005–2007: Senior Scientist (Chargée de recherche Première classe CR1) Inserm Unit 648, University Paris
Descartes, France
2002–2005: Visiting scientist («poste vert» Inserm), Inserm Unit 428, Fac. Pharmacie, Paris,
France
2001-2002: Visiting scientist («chercheur associé» CNRS), Lab. MIP, Université Paris-Sud, Bat 430, Orsay,
France
1997 and 1998: Fellowships (3 months) (Electrostatics) Karolinska Institute, NOVUM, Huddinge, Sweden
1993–2001: Scientific researcher (permanent position), Institute of Organic Chemistry, Bulgarian Academy of
Sciences, Sofia, Bulgaria
Diplomas
1991: Engineer of biotechnique , M.Sc. degree, Technical University, Sofia, Bulgaria
Thesis title: Electrostatic interactions in Bacteriorhodopsin”.
2000: PhD degree in structural bioinformatics and biophysical chemistry, Institute of Organic Chemistry,
Bulgarian Academy of Sciences, Sofia, Bulgaria
Thesis title: “Theoretical analysis of pH dependent effects in proteins”
2008: HDR Habilitation à Diriger des Recherches, University Paris Diderot
« Recherche de nouveaux agents thérapeutiques par criblage virtuel hiérarchique:
développement et application d'une approche bioinformatique »

Teaching
Univ.Paris 5/Univ.Paris 7 (master & PhD programs, 2003-present):
Structural Bioinformatics - Electrostatic interactions – Virtual Screening - Drug Design
International Summer School on Protein Science Sofia, Bulgaria (2005-present):
Structural Bioinformatics - Protein Flexibility - Virtual screening -Drug Design- ADMET
Member of:
Editorial Advisory Board of Computational Biology and Chemistry (Dove Medical Press)
Scientific Board of a FEBS meeting “Sofia school of protein science 2009”
French Society of Chemoinformatics
French Society “Groupe de Graphisme et Modélisation Moléculaire”
Expert for:
French ANR “physique-chimie du vivant” 2006 (Grant Reviewing)
Committee “Workshops Inserm” 2008 (Invited Expert on Drug Design)
Ad hoc reviewer for :
Expert Opinion on Drug Discovery, J Chem Inf Model, Current Computer-Aided Drug Design, Current
Protein Peptide Science, Nucleic Acid Research etc.
Developed programs available for academic scientists:
Multiconf-DOCK: http://dock.compbio.ucsf.edu/Contributed_Code/multiconfdock.htm
(generator of multiple conformations for small drug-like molecules)
AMMOS: http://www.vls3d.com/programs.html
(Automated Molecular Mechanics Optimization for in silico screening: minimization of conformations of
chemicals of a library; minimization of protein-ligand complexes)
On-line tools:
PCE: http://bioserv.rpbs.jussieu.fr/Help/PCE.html
(Protein Continuum electrostatics)
FAFDrugs: http://bioserv.rpbs.jussieu.fr/RPBS/cgi-bin/Ressource.cgi?chzn_lg=an&chzn_rsrc=ADMETox
(In silico ADMETox filtering of chemical libraries)
Publications:
Over 35 research publications, 9 reviews, 2 book chapters, 1 patent (pending) “Inhibiteurs de Phosphatase”
Pencheva T, Lagorce D, Pajeva I, Villoutreix BO and Miteva MA. AMMOS: Automated Molecular Mechanics
Optimization tool for in silico Screening. BMC Bioinformatics 2008 9:438
Nilsson SC, Trouw LA, Renault N, Miteva MA, Genel F, Zelazko M, Marquart H, Muller K, Sjöholm AG,
Truedsson L, Villoutreix BO and Blom AM. Genetic. Molecular and Functional Analysis of

Complement Factor I Deficiency. European Journal of Immunology 2008 in press
Sauton N, Lagorce D, Villoutreix BO, Miteva MA. MS-DOCK: Accurate multiple conformation generator and
rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics. 2008 9:184
Sperandio O, Souaille M, Delfaud F, Miteva MA, Villoutreix BO. MED-3DMC: A New tool to generate 3D
conformation ensembles of small molecules with an efficient Monte Carlo sampling of the
conformational space. Eur J Med Chem 2008 in press
Lagorce D, Sperandio O, Galons H, Miteva MA, Villoutreix BV. FAF-Drugs2: free ADME/tox filtering tool to
assist drug discovery and chemical biology projects. BMC Bioinformatics 2008, 9:396.
Montes M, Braud E, Miteva MA, Goddard ML, Mondesert O, Kolb S, Brun MP, Ducommun B, Garbay C,
Villoutreix BO. Receptor-based virtual ligand screening for the identification of novel CDC25
phosphatase inhibitors. J Chem Inf Model. 2008 48:157-65
Segers K, Sperandio O, Sack M, Fischer R, Miteva MA, Rosing J, Nicolaes GA, Villoutreix BO. Design of
protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2
domain of factor V. Proc Natl Acad Sci U S A. 2007 104:12697-702
Leite TB, Gomes D, Miteva MA, Chomilier J, Villoutreix BO, Tuffery P. Frog: a FRee Online druG 3D
conformation generator. Nucleic Acids Res. 2007 35:W568-72.
Sperandio O, Andrieu O, Miteva MA, Vo M-Q, Souaille M, Delfaud F, Villoutreix BO. MED-SuMoLig: A
new ligand-based screening tool for efficient scaffold hopping. J Chem Inf Model. 2007 47:1097-110
Montes M, Miteva MA, Villoutreix BO. Structure-based virtual ligand screening with Ligand Fit: pose
prediction and enrichment of compound collections. Proteins 2007. 68:712-25
Hanna N, Montagner A, Lee WH, Miteva M, Vidal M, Vidaud M, Parfait B, Raynal P. Reduced phosphatase
activity of SHP-2 in LEOPARD syndrome: consequences for PI3K binding on Gab1. FEBS Lett. 2006
580:2477-82
Miteva MA, Violas S, Montes M, Gomez D, Tuffery P, Villoutreix BO. FAF-Drugs: free ADME/tox filtering
of compound collections. Nucleic Acids Res. 2006 34:W738-44
Autin L, Miteva MA, Lee WH, Mertens K, Radtke KP, Villoutreix BO. Molecular models of the procoagulant
factor VIIIa-factor IXa complex. J Thromb Haemost. 2005 3:2044-56
Miteva MA, Lee WH, Montes MO, Villoutreix BO. Fast structure-based virtual ligand screening combining
FRED, DOCK, and Surflex. J Med Chem. 2005 48:6012-22
Brun MP, Braud E, Angotti D, Mondésert O, Quaranta M, Montes M, Miteva M, Gresh N, Ducommun B,
Garbay C. Design, synthesis, and biological evaluation of novel naphthoquinone derivatives with
CDC25 phosphatase inhibitory activity. Bioorg Med Chem. 2005 13:4871-9
Miteva MA, Tuffery P, Villoutreix BO. PCE: web tools to compute protein continuum electrostatics. Nucleic
Acids Res. 2005 33 :W372-5
Lee WH, Raas-Rotschild A, Miteva MA, Bolasco G, Rein A, Gillis D, Vidaud D, Vidaud M, Villoutreix BO,
Parfait B. Noonan syndrome type I with PTPN11 3 bp deletion: structure-function implications.
Proteins. 2005 58:7-13
Akhavan S, Miteva MA, Villoutreix BO, Venisse L, Peyvandi F, Mannucci PM, Guillin MC, Bezeaud A. A
critical role for Gly25 in the B chain of human thrombin. J Thromb Haemost. 2005 3:139-45
Miteva MA, Brugge JM, Rosing J, Nicolaes GA, Villoutreix BO. Theoretical and experimental study of the
D2194G mutation in the C2 domain of coagulation factor V. Biophys J. 2004 86:488-98
Steen M, Miteva M, Villoutreix BO, Yamazaki T, Dahlback B. Factor V New Brunswick: Ala221Val
associated with FV deficiency reproduced in vitro and functionally characterized. Blood. 2003
102:1316-22
Shosheva A, Miteva M, Christova P, Atanasov B. pH-dependent stability of sperm whale myoglobin in waterguanidine
hydrochloride solutions. Eur Biophys J. 2003 31:617-25
Miteva MA, Shosheva A, Sose Al, Makinen M, Atanasov B. Theoretical treatment of spectrophotometric
tyrosine titration of two beta-lactamases of class A. Comp Ren Bulg Sci. 2001 54:93-6
Miteva M, Shosheva A, Atanasov B. Spectrophotometric titration of ionisable groups in proteins: a theoretical
study. Spectrochimica Acta A: Mol Biomol Spectrosc. 2000 56:2033-41
Miteva M, M. Andersson, A.Karshikoff, G. Otting. Molecular electroporation: a unifying concept for the

description of membrane pore formation by antibacterial peptides, exemplified with NK-lysin. FEBS
Lett. 1999 462:155-8
Miteva M, Alexov E, Atanasov B. Numerical simulation of aldolase tetramer stability. Eur Biophys J. 1998
28:67-73
Miteva M, Demirev P, Karshikoff A. Multiply-protonated protein ions in the gas phase: Calculation of the
electrostatic interactions between charged sites. J Phys Chem B: 1997 101:9645-50
Atanasov B, Miteva M. Prediction and structural analysis of the enthalpy of ionization of proteins.
Thermochim Acta. 1997 291:141-53
Miteva M, Kossekova G, Villoutreix B, Atanasov B. Local electrostatic potentials in pyridoxal phosphate
labelled horse heart cytochrome c. J Photochem Photobiol B: 1997 37:74-83
Miteva M, Mishonova E, Atanasov B. A theoretical model for evaluation of the ultrasonic velocimetric titration
of proteins. Comp Ren Bulg Sci 1996 5:99-102
Kossekova G, Miteva M, Atanasov B. Characterization of pyridoxal phosphate as optical label for measuring
electrostatic potentials in proteins. J Photochem Photobiol B: 1996 32:71-9
Miteva M, Spassov V, Atanasov B. Computer simulations in bacteriorhodopsin and its mutants. Comp Ren
Bulg Sci. 1994 47:37-40
Reviews
Miteva MA. Hierarchical structure-based virtual screening for drug design. Biotechnol & Biotechnol Equip.
2008 1:634-638
Mitra R, Shyam R., Mitra I, Miteva MA and Emil Alexov. Calculating the Protonation States of Proteins and
Small Molecules: Implications to Ligand-Receptor Interactions. Current Computer-Aided Drug Design
2008 4:169-179
Sperandio O, Miteva MA, Villoutreix BO. Combining structure-based and ligand-based virtual ligand screening:
recent success stories. Current Computer-Aided Drug Design 2008 4:250-258.
Villoutreix BO, Eudes R, Miteva MA. Structure-based virtual ligand screening: recent success stories.
Combinatorial Chemistry and High Throughput Screening. 2008 in press
Villoutreix BO, Bastard K, Sperandio O, Fahraeus R, Poyet JL, Calvo F, Deprez B, Miteva MA. In silico-in
vitro screening of protein-protein interactions: towards the next generation of therapeutics. Curr Pharm
Biotechnol. 2008 9:103-22
Sperandio O, Miteva M, Segers K, Nicolaes G, Villoutreix BO. Screening outside the catalytic site: Inhibition
of macromolecular interactions through structure-based virtual ligand screening experiments. The Open
Biochemistry Journal. 2008 2: 29-37
Miteva MA, Sperandio O, Villoutreix BO. Virtual ligand screening for structure-based drug design:
Approaches and progress. Bioautomation. 2007 7:104 − 121
Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA. Free resources to assist structurebased
virtual ligand screening experiments. Curr Protein Pept Sci. 2007 8:381-411
Sperandio O, Miteva MA, Delfaud F, Villoutreix BO. Receptor-based computational screening of compound
databases: the main docking-scoring engines. Curr Protein Pept Sci. 2006 7:369-93
Book Chapters
Miteva MA, Alexov E, Villoutreix BO. Protein structure analysis online. , John Wiley & Sons, Inc. Curr Protoc
Protein Sci. 2007 Chapter 2:Unit 2.13. 50:2.13.1-2.13.23
Autin L, Montes M, Miteva M, BO Villoutreix. Computer tools to study intermolecular interactions. Recent
Adv. In Structural Bioinformatics. 2007 Chapt.9, p1-51 ISBN: 978-81-308-0208-4 in “Research
Signpost”, Trivandrum, India

Congress Posters and Talks
Miteva M. Protein flexibility in computer-aided drug design. International School of Protein Science Sofia
2008 (Sept 17-19) (plenary lecture, invited)
Pinto E, Mouawad L , Sperandio O, Villoutreix BO, Perahia D, Miteva MA. Protein flexibility in virtual
screening: multiple receptor structures generated by normal mode analysis. International School of
Protein Science, Sofia, Bulgaria 2008 (Sept 17-19)
K.Segers, Sperandio O, Sack M, Fischer R, Miteva MA, Rosing J, Nicolaes GAF, Villoutreix BO.
Inhibition of protein-membrane interactions by compounds selected via structure-based virtual
ligand screening. 4th Joint Sheffield Conference on Chemoinformatics 18th-20th June, 2007,
Sheffield, UK
Miteva M. Bioinformatique Structurale, Drug Design et RPBS. Réunion Annuelle de la platforme RPBS,
EBGM Paris 7, 25 Oct. 2007 (talk)
Segers K, Sperandio O, Sack M, Fischer R, Miteva MA, Rosing J, Nicolaes GAF, Villoutreix BO.
Discovery of compounds that inhibit factor Va-membrane interaction by in silico screening. ISTH
2007 Geneva (July 6-12)
Miteva M. Hierarchical structure-based virtual ligand screening in drug design. International Summer
School on Protein Science, Sofia, 3-5 Oct., 2007 (plenary lecture, invited)
Montes M, Miteva MA, Villoutreix BO. Structure-based virtual ligand screening with LigandFit: pose
prediction and enrichment of compound collections. Europen Science Forum - Accelrys 21
November 2006, Paris
Miteva M. RPBS PCE: web tools to compute Protein Continuum Electrostatics. Réunion Annuelle de la
platforme RPBS, EBGM Univ. Paris 7, 5 Oct. 2006 (talk)
Miteva M. Virtual ligand screening for drug design: an overview. International Summer School on Protein
Science, Sofia, 28-29 Sept. 2006 (plenary lecture, invited)
Montes M, Miteva MA, Lee WH, Villoutreix BO. Impact of Ligandfit docking and scoring functions on
enrichment in structure-based virtual screening of focused libraries Congres de la société de chimie
thérapeutique 6-8 juillet 2005, Paris
Miteva M. Structural Bioinformatics & Drug Design: overview, methods and application International
Summer School "Biophysics methods in protein science”, Sofia, 26-27 Sept. 2005 (plenary lecture,
invited)
Hanna N, Lee WH, Miteva MA, Laurendeau I, Lyonnet S, Villoutreix BO, Vidaud M, Parfait B.
Diminution de l’activité tyrosine phosphatase de SHP-2 dans le syndrome LEOPARD. 3ème
Forum de l’IFR 071 des Sciences du Médicament. Faculté des Sciences Pharmaceutiques et
Biologiques Univ. Paris 5, 3 février 2005
Lee WH, Miteva MA, Villoutreix B, Parfait B, Bolasco G, Raas-Rothschild A, Vidaud M. Structurefunction
analysis of mutation D61del on the enzyme SHP-2 involved in the Noonan Syndrome.
2ème Forum de l’IFR 071 des Sciences du Médicament, Faculté des Sciences Pharmaceutiques et
Biologiques, Univ. Paris 5, 16 janvier 2004
Parfait B, Miteva MA, Bolasco G, Raas-Rotschild A, Lee WH, Villoutreix BO, Vidaud M. Délétion au
sein de la région codante de PTPN11 chez un sujet présentant un syndrome de Noonan. 2eme
Assisses de Génétique Humaine et Médicale. 30.01-01.02.2004, Angers

Autin L, Lee WH, Miteva MA, Mertens K, Radtke P, Villoutreix BO. Molecular models of the
procoagulant intrinsic tenase complex. The American Society of Hematology, 46th Annual Meeting
and Exposition, 4-7 December, 2004, San Diego, California
Miteva MA, Villoutreix BO. Theoretical investigation of the D2194G substitution in the C2 domain of
coagulation factor V. 1 Forum de l’IFR 071 des Sciences du Médicament Faculté des Sciences
Pharmaceutiques et Biologiques Univ. Paris V, 9 janvier 2003
Miteva MA, Brugge JM, Nicolaes G, Villoutreix BO. Theoretical and experimental study of the
Asp2194Gly mutation in the C2 domain of coagulation factor V. XIX Congress of the International
Society on Thrombosis and Haemostasis, 12-18 July 2003, Birmingham UK
Miteva MA, Renault L, Cherfils J, Perahia D. Role of electrostatic interactions in the activation of Ran by
the exchange factor RCC1: A study of molecular dynamics simulations. Troisième Colloque
Francophone “Petites Protéines G”. 27-29 mars 2002, La grande Motte, France
Miteva M. Mechanism of activation of small G-proteins by GEF: Ran-RCC1 complex. Réunion
d’Intergroupe de Modélisation Moléculaire IBPC, Paris, Nov. 2001 ( talk)
Mishonova-Alexova K, Miteva MA, Atanasov B, Kharakoz D, Sarvazyan A. Ultrasonic velocimetric
titration of proteins. Experiments, theoretical prediction and analysis. First East Asian Symposium
on Biophysics 1994, Hyogo, Japan
Miteva MA, Atanasov B. A theoretical evaluation of the enthalpy of ionization of proteins. 10th Balkan
Biochemical Biophysical Days, 22-25 May 1994, Varna, Bulgaria