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 Curriculum Vitae 
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Jagadeesh Mavinahalli N., Ph.D.

Aurigene Discovery Technologies Limited

39-40, KIADB Industrial Area

Electronic City Phase II, Hosur Road

Bangalore-560100, India.

Ph: +91-80 2852 1314 Ext: 120/411

Fax: +91-80 2852 6285

E-mail: JagadeeshMN[at]gmail[dot]com

Professional Experience

  • Sr. Scientist: Aurigene Discovery Technologies Ltd., Bangalore, India

Oct 2003-Present

Structure Based Drug Discovery

Research: Molecular recognition and inhibitor design for Proteases and Kinases.

Academic Background

  • Postdoctoral Fellow: College of Pharmacy, University of Michigan, Ann Arbor, USA

Dec. 2001 - Sept. 2003

Mentor: Prof. Heather A. Carlson

Research: Ligand Recognition in Folyl Polyglutamate Synthetase (FPGS).

  • Postdoctoral Fellow: Max-Planck-Institute, Muelheim an der Ruhr, Germany

Oct. 1999 - Nov. 2001

Mentor: Prof. Dr. Walter Thiel

Research: Design of Catalysts for Hydrosilylation Reaction. And, DFT investigation of the single-center, two-state model for the broken rate order of transition metal catalyzed olefin polymerization.

  • Ph.D. : Department of Organic Chemistry, Indian Institute of Science, Bangalore, India

Oct. 2004 - July 2000

Mentor: Prof. Jayaraman Chandrasekhar

Thesis: Theoretical Studies of Electronic Effects on Structure and Reactivity of Highly Unsaturated Organic Systems.

  • M.Sc.: Organic Chemistry; Bangalore University, Bangalore, India

1992 – 1994

Research Interests

  • Structure, mechanism and reactivity of organic, organometallic and enzyme catalyzed reactions.

  • Molecular modeling and Computer aided drug discovery.

  • Protein structure, function and recognition; protein folding; Bioinformatics.

Professional Capabilities

  • Computational Chemistry:

  • In-depth experience with various quantum chemical programs such as, Gaussian 98, GAMESS (US), NWChem, and MOPAC and molecular dynamics packages AMBER and GROMACS.

  • Good experience with Molecular Dynamics and Monte Carlo simulations techniques, force field development and implementation.

  • Expertise in programming (with appropriate scripting languages) and applying following suite of computational tools for solving various research problems in particular drug discovery:

    • Sybyl: FlexX, CombiLibMaker, DVS-solutions, BioPolymer, UNITY, Gasp etc.

    • Molecular Operating Environment (MOE): Dock, Pharmacophore Modeling, Sequence Alignment, etc.

  • Very skillful in locating transition states for molecular reactions and studying reaction mechanisms.

  • Experience in using multiple protein structures, for considering protein flexibility, for pharmacophore design and docking.

  • Experience in target based focused library design using various filters like ADME, docking, diversity analysis and molecular clustering.

  • Power user of visualization softwares like PyMOL, VMD, Gauss View, and MOLDEN.

  • Computing:

  • Programming: Experience in scripting languages like Scientific Vector Language (SVL related to MOE) and Sybyl Scripting Language (SSL). FORTRAN, C, Python, HTML, CSS and PHP.

  • System administration: Unix and derived systems [Silicon Graphics, HP-RISC & Itanium Workstations, Linux Clusters and PCs].

  • Operating Systems: Unix, Linux, HP-UX, IRIX, Mac OS X, and MS Windows.

  • Text and Chemical Structure Processing: Micro Soft-Office suite, OpenOffice, ChemDraw, ChemSketch.


  • Ph.D. Thesis

  • M.N. Jagadeesh: Theoretical Studies of Electronic Effects on Structure and Reactivity of Highly Unsaturated Organic Systems. PhD Thesis (Number: “THESIS” G15592), Indian Institute of Science, Department of Organic Chemistry, Bangalore, India, 1999 iv, 228p.

  • Journal Papers

  1. V.R. Jensen, D. Koley, M.N. Jagadeesh and W. Thiel: DFT investigation of the single-center, two-state model for the broken rate order of transition metal catalyzed olefin polymerization. Macromolecules, 2005 (In Press).

  2. M.N. Jagadeesh, W. Thiel, J. Koehler and A. Fehn: Hydrosilylation with bis(alkynyl)(1,5-cyclooctadiene)platinum catalysts: A density functional study of the initial activation. Organometallics, 2002, 21, 2076-2087.

  3. M.N. Jagadeesh, A. Makur and J. Chandrasekhar: The interplay of angle strain and aromaticity: Molecular and electronic structures of [0(n)]paracyclophanes. J. Mol. Model., 2000, 6, 226-233.

  4. M.N. Jagadeesh and J. Chandrasekhar: Computational studies on C36 and its dimmer. Chem. Phys. Lett., 1999, 305, 298-302.

  5. G. Mehta, R. Uma, M.N. Jagadeesh and J. Chandrasekhar: New paradigms in cycloaddition face-selectivities: Remarkable effects of remote substituents in singlet oxygen addition to hexacyclo[,6.06,13.08,12.010,14]pentadeca-2,4-diene system. J. Chem. Soc., Chem. Commun., 1998, 1813-1814.

  6. D. Ramkumar, M. Kalpana, B. Varghese, S. Sankararaman, M.N. Jagadeesh and J. Chandrasekhar: Cyclization of enediyne radical cations through chemical, photochemical, and electrochemical oxidation: The role of state symmetry. J. Org. Chem., 1996, 61, 2247-2250.

  • Selected Posters

  1. M.N. Jagadeesh, J. Chandrasekhar; Title: "Reliable Modeling of Structural and Strain Effects on Bergman Cyclization Rates" Sixth Biennial Discussion Meeting in Theoretical Chemistry, Dec. 26-28, 1998, School of Chemistry University of Hyderabad, Hyderabad, India.

  2. M.N. Jagadeesh, H.A. Carlson; Title: “Ligand recognition in Folyl poly glutamate synthetase” 225th ACS National Meeting, Mar. 22-27, 2003, New Orleans, LA, USA.


  • Coordinated research and development activities of computational chemistry group with other groups like Protein Sciences, X-Ray, NMR and Medicinal Chemistry.

  • Coordinated with support scientists of various software companies for fixing problems and to keep all the softwares in working condition.

  • Played key role in decision making to choose suitable software/hardware for computational chemistry group.


Aurigene Discovery Technologies Ltd., Bangalore, India

(Oct. 2003 - present)

Continuously applied various computational chemistry and chemo-informatics techniques like Ab initio, Semiempirical, MD/MC (Molecular Dynamics and Monte Carlo) simulations, QSAR, CoMFA modeling, pharmacophore modeling, database search/screening, database building, homology modeling, and diversity analysis using various software applications like NWChem, MOPAC, MOE, SYBYL, GROMACS, Catalyst, and DVS-Solutions. I effectively interact with medicinal chemists, aiding them or seeking valuable inputs to design better compounds having therapeutic value.

Worked in close collaboration with synthetic chemists, biologists, X-ray crystallographers and NMR scientists to design focused library of small compounds for various protein targets in the class of proteases and kinases. ADME-property screening, Protein Ligand Docking (FlexX), Diversity analysis and Cluster analysis were employed intensively for designing focused library of small molecules. It was gratifying to note that many of my focused library yielded good leads, which we are presently optimizing. Close interaction with other members of multidisciplinary 'structure guided drug discovery' group gave me good idea about lead optimization techniques.

Designed and maintained database of diverse set of small molecular scaffolds. Applied various computational techniques to tackle problems related to drug discovery. Gained in depth experience with ligand based and receptor based pharmacophore generation and screening. Taught basic molecular modeling techniques to medicinal chemists. Did system administration of UNIX workstations. Installed and maintained various softwares for the computational chemistry group.

Used Python for writing compter programs for our routine tasks and also for adding modules, plugins for software package PyMOL.

University of Michigan, Ann Arbor, MI, USA

Department: College of Pharmacy

(Dec. 2001 - Sept. 2003)

Research focused on improving procedures for creating receptor-based pharmacophore models using the protein Folylpolyglutamate synthetase (FPGS). Study aimed in understanding the structure, function and ligand recognition of FPGS. Gained in-depth experience with Molecular Operating Environment (MOE) and SVL commands for working with proteins for ligand docking, homology modeling, sequence alignment and other techniques which assist in small molecular inhibitor design. Also, got exposed to developing force field parameters and for performing Molecular Dynamics simulation for understanding dynamics of protein structures using AMBER suite of programs. Developed force field parameters for the ligand Folate for the MD simulation with the protein FPGS and ATP.

Max-Planck-Institute, Mülheim an der Ruhr, NRW, Germany

Department: Computational Theoretical Chemistry

(Oct. 1999 - Nov. 2001)

Worked in close collaboration with industry (Consortium für elektrochemische Industrie GmbH, Munich, Germany). Exposed to direct application of quantum chemical techniques to tackle industrial research problems. In particular, in the field of Organometallic catalysis for polymerization reactions. Extended my help to industrial collaborators to fine-tune their working catalyst with substituents to obtain quality catalyst with desired activity. Diversified my experience to compute electronic properties of organometallic systems in addition to previous knowledge with organic systems. Programs used for this research work were Gaussian 98, GAMESS (US) and NWChem.

Indian Institute of Science, Bangalore, Karnataka, India

Department: Organic Chemistry

(Oct. 1994 - Jul. 2000)

THESIS: Theoretical Studies of Electronic Effects on Structure and Reactivity of Highly Unsaturated Organic Systems.

  1. Introduction: Importance of molecular and electronic structures and brief summary of the methodologies employed.

  2. Design of planar cyclooctatetraene derivatives.

  3. Study of smaller fullerenes and fullerene fragments.

  4. Reliable modeling of structural and strain effects on bergman cyclization rates.

  5. Electronic effects on the mode of cyclization of enediyne radical cations.

  6. Remote substituent effects on –facial selectivity in cycloadditions involving hexacyclo[,6.06,13.08,12.010,14]pentadeca-2,4 diene system.

    Gained extensive experience in electronic structure calculations using various methodologies like Ab Initio, Density Functional Theory, Semi-empirical as well as molecular mechanics. Research focused on the elucidation of molecular and electronic structures, energetics, as well as reactivity patterns in organic molecules with many multiple bonds. The systems examined were uniformly of considerable experimental interest. Located transition states for various stereo selective, stereo specific reactions. Quantitative interpretation of electronic effects such as, hyper conjugation, negative hyper conjugation (through NBO analysis) and aromaticity (employing Nucleus Independent Chemical Shift values). Carried out calculation to prediction of band structure on cyclic polyenes and phenylenes.

Wrote programs for routine tasks using Fortran and C. Prepared assignments for Fortran course and taught course students to get started to work with UNIX work stations.

Reference List

Dr. Jayaraman Chandrasekhar
Neurogen Corporation
35 Northeast Industrial Rd. Branford, CT 06405, USA

Phone: +1-203-488-8201, Fax: +1-203-488-9540

E-mail: Jayaraman_Chandrasekhar[at]nrgn[dot]com

Prof. Dr. Walter Thiel

Max-Planck-Institut für Kohlenforschung

Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr, Germany

Phone: +49-208-306-2150, Fax: +49-208-306-2996


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