Kalyan Das, Ph. D.

Office

Research Professor

Center for Advanced Biotechnology & Medicine and

Department of Chemistry, Rutgers University

679 Hoes Lane, Piscataway, NJ 08854-5638, U.S.A.

Phone: (732) 235-5634; Fax : (732) 235-5788

E-mail : kalyan@cabm.rutgers.edu

Web Site: http://www.cabm.rutgers.edu/~kalyan

Home

716 Cranbury Road

East Brunswick, NJ 08816, USA

Phone: (908) 720-8099

Research Interest

       Structure-based drug design, exploring and targeting protein:protein interactions, structural and functional genomics, molecular modeling, structural studies and biophysical/biochemical characterization of macromolecules.

Education and Positions Held

* M.S.(Physics): Berhampur University, India (1984). Solid State Physics (specialization).

* Ph.D.: Indian Institute of Tech. (IIT), Bombay (1986-1991). X-ray crystallography.

* Post Doc.-1: Molecular Biophysics Unit, Indian Institute of Science, Bangalore (1992-1994).

* Post Doc.-2: Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University (1994-1996).

* Research Associate: CABM and Rutgers University Chemistry Department (1996-1998).

Research Projects

            1. HIV-1 reverse transcriptase (RT) drug resistance, 2. Structure-based drug design (involved in discovery of the HIV-1 drug Etravirine), 3. Molecular modeling studies on drug targets, 4. Structural study of bacterial RNA polymerase(RNAP) and structure-based drug design targeting bacterial RNAP including that of mycobacterium tuberculosis(mTB), 5. Structure-based drug design targeting influenza A Non-structural Protein (NS1) by disrupting of its interaction with CPSF30 and other host factors, 6. Structural and functional genomics, 7. Structural study of human capping enzyme etc.

Technical profile

      Fifteen years of experience in pharmaceutical industries sponsored structure-based design of antivirals targeting HIV reverse transcriptase (RT), HIV protease, Hepatitis B polymerase, Hepatitis C protease, bacterial RNA polymerase, and influenza A NS1 protein.  Pattern applications on key finding from HIV-1 RT, RNA polymerase, and influenza NS1A projects.  Contributor to the discovery and charactrization of DAPY (diarylpyrimidine) class of NNRTI including etravirine (Intelence) which is approved for treating NNRTI-resistant HIV-1 infections.

X-ray crystallography:  Crystallization including micro-crystallization and optimization, crystal freezing, data collection for proteins and viruses using various synchrotron and rotating anode x-ray sources, MIR, MAD, and MR techniques for determining crystal structures, and various techniques associated with phase improvement and structure refinement etc.

Molecular modeling: Protein and DNA sequence analysis, homology modeling, molecular mechanics and dynamics calculations, docking of small molecules etc.

Computation: Programming in Pascal, C, FORTRAN, JAVA, HTML, and SQL; O/S - Unix, Linux, VAX/VMS, and NOS/VE. Implementing, maintaining, and upgrading crystallographic software in Silicon Graphics, Linux, and Mac Workstations.

Crystallography and molecular modeling software: Implementation, maintenance, and extensive uses of DENZO, HKL 2000, XPLOR, CNS, COOT, CCP4, WARP, Solve/Resolve, Phases, Phenix, O, Sybyl, Schrödinger, Pymol etc.

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Selected Publications

• Das, Kalyan, Ma, L.-C., Xiao, R., Radvansky, B., Aramini, J., Zhao, L. , Marklung, J., Kuo, R.-L., Twu, K., Arnold, E., Krug, R., Montelione, G. (2008). Proc. Natl. Acad. Sci. USA. 105:13092-13097. “Structural basis for suppression of a host antiviral response by influenza A virus.”
• Mukhopadhyay, J., Das, Kalyan, Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Höfle, G., Arnold, E., Ebright, R.H. (2008). Cell 135:295-307. ‘The RNA Polymerase “Switch Region” is a Target for Inhibitors.’
• Das, Kalyan, Bauman, J.D., Clark Jr., A.D., Frenkel, Y.V., Lewi, P.J., Shatkin, A.J., Hughes, S.H., Arnold, E. (2008). Proc. Natl. Acad. Sci. USA. 105:1466-1471. ‘High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.’
• Das, Kalyan, Acton, T., Chiang, Y., Shih, L., Arnold, E., and Montelione, G.T. (2004). Proc. Natl. Acad. Sci. USA. 101:4041-4046. “Crystal. Structure of RlmA^I: Implications for Understanding the 23S rRNA G745/G748-Methylation at the Macrolide Antibiotic Binding Site.”
• Das, Kalyan, Butler, G.H., Kwiatkowski, V., Clark, Jr. A.D.Jr, Yadav, P., Arnold, E. (2004). Structure (Camb.). 12:657-667. ‘Crystal Structures of Arginine Deiminase with Covalent Reaction Intermediates: Implications for Catalytic Mechanism.’
• Das, Kalyan , Clark, Jr., A.D., Lewi, P., Heeres, J., de Jonge, M., Koymans, L., Vinkers, M., Daeyaert, F., Ludovici, D.W., Kukla, M.J., De Corte, B., Kavash, R.W., Ho, C., Ye, H., Lichtenstein, M.A., Andries, K., Pauwels, R., de Bethune, M.-P., Boyer, P.L., Clark, P., Hughes, S.H., Janssen, P.A.J., and Arnold. E. (2004). J. Med. Chem. 47:2550-2560. ‘Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants.’

[Complete list of publications in scientific journals]

[List of abstract presented at conferences and meetings as talk or posters]

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