Erode N. Prabhakaran

Associate Professor

Phone : +91-80-2293-3380 
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  • PhD (2000): Indian Institute of Technology, Kanpur, U.P., India (Advisor: Prof. Javed Iqbal)
  • MSc (1995): Sri Sathya Sai Institute of Higher Learning, Prasantinilayam, Anantpur, AP, India (Thesis Advisor: Prof. K Anil Kumar)
  • BSc (1993): Sri Sathya Sai Institute of Higher Learning, Prasantinilayam, Anantpur, AP, India

Professional Positions

  • 2013-present: Associate Professor, Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
  • 2006 to 2013: Assistant Professor, Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
  • 2003 to 2006: Research Scientist at Texas A&M University, College Station, Texas, USA (Advisors: Prof. J. Martin Scholtz and C. Nick Pace)
  • 2000 to 2003: Postdoctoral Fellow at Indiana University, Bloomington, Indiana, USA (Advisor: Prof. Jeffrey N. Johnston)

Research Interests

Our research program includes, the design, synthesis and investigation of Artificial Transcription Factors; Quorum sensing agents in Bacteria; N-Acyl Homoserinelactones (AHLs); Amyloid Inhibition; Induced Amyloid Fragmentation – Hydrogen Bond Reversal Mechanism; Hydrogen Bond Surrogates; Helical Models for Helix-Coil Transition and Helix growth mechanisms; Dynamic β-Sheet Models; Spectral signatures of Constrained β-turns; Weak interactions in Proteins – CH…π, charge→acceptor, cation…π, van der Waals, electrostatic interactions; Charge Transfer Mechanisms in Proteins; Disallowed Conformations in Proteins; Synthetic Organic Chemistry; Chemical Biology; Physical Organic Chemistry; Chemical Kinetics and Equilibrium; Peptidyl Prolyl Isomerase (Chaperone-Mediated) mechanisms; Self-Assembled Organic Microtubes; Metal Nanorod Protein Sensors; Organic Nanoforests; Peptidomimetics; Drug Design; Protein-Protein and Protein-DNA interaction inhibitors. We extensively use 1D and 2D NMR, Far-UV and Vibrational Circular Dichroism, FT-IR, Fluorescence, Mass Spectroscopy; X-Ray Crystallography; Electron Microscopy; Light Scattering; High-Performance Chromatographic and Calorimetric; Computational – DFT, Molecular Dynamics Simulation (GROMACS), NBO, AIMS, NCI, etc. techniques.

Representative Publications

  • Reddy, S. S.; Pal, S.; Ghosh, S.; Prabhakaran, E. N., Hydrogen Bond Surrogate‐Constrained Dynamic Anti‐parallel β‐Sheets. ChemBioChem2021, (  
  • Pal, S.; Prabhakaran, E. N., Trimodular solution phase protocol for rapid large-scale synthesis of hydrogen bond surrogate-constrained α-helicomimics. Eur. J. Org. Chem. 202111, 1714-1719. (  
  • Pal S; Banerjee, S.; Kumar A, Prabhakaran E.N., H-Bond Surrogate-Stabilized Shortest Single-Turn α-Helices: sp2 Constraints and Residue Preferences for the Highest α-Helicities. ACS Omega. 20205, 13902-13912.
  • Prabhakaran E. N., Tumminakatti, S., Vats K, Ghosh, S.  Spectral evidence for generic charge → acceptor interactions in carbamates and esters. RSC Adv.. 202010, 11871-11875.
  • Pal S, Prabhakaran E.N., Hydrogen bond surrogate stabilized water soluble 310-helix from a disordered pentapeptide containing coded α-amino acids.  Tetrahedron Lett. 201859, 2515-2519.
  • Vats K, Prabhakaran E.N., Disallowed conformations of Amino Acids in Proteins and Peptides, Cutting Edge2017, 9 -13.
  • Tumminakatti, S., Khatri, B., Krishnamurthi, V., Athavale, V., Prabhakaran, E. N. Solution Structural Features of N-Acyl Homoserine Lactones. Tetrahedron Letters201556, 5771-5775.
  • Tumminakatti, S., Reddy, D. N., & Prabhakaran, E. N., Exploring the consequences of a representative “disallowed” conformation of Aib on a 310‐helical fold. Peptide Science2015­104, 21-36.
  • Thirupathi, R., Prabhakaran, E. N., Estimation of the 2.05 helix type i→ i hydrogen bond energy at Aib∗-Oxa motif: an isodesmic approach. Tetrahedron Letters201455, 3418-3421.
  • Reddy, D. N., George, G., Prabhakaran, E. N. Crystal-Structure Analysis of cis-X-Pro-Containing Peptidomimetics: Understanding the Steric Interactions at cis X-Pro Amide Bonds.  Angew. Chem. Int. Ed. Engl. 201352, 3935.
  • Reddy, D. N., Prabhakaran, E. N. Steric and Electronic Interactions Controlling the cis/trans Isomer Equilibrium at X-Pro Tertiary Amide Motifs in Solution. Biopolymers. 2013101(1), 66-77.
  • A method for stabilizing the cis prolyl peptide bond: influence of an unusual nπ* interaction in 1,3-oxazine and 1,3-thiazine containing peptidomimetics. Reddy, D. N., Thirupathi, R., Tumminakatti, S., Prabhakaran, E. N. Tet. Lett. 201253, 4413-4417.
  • Accessing the disallowed conformations of peptides employing amide-to-imidate modification. Reddy, D. N., Thirupathi, R., Prabhakaran, E. N. Chem. Commun.2011, 47, 9417–9419.
  • Synthesis and Isolation of 5,6-Dihydro-4H-1,3- Oxazine Hydrobromides by Autocyclization of N-(3-Bromopropyl)amides. Reddy, D. N., Prabhakaran, E. N. J. Org. Chem., 201176, 680–683.

Awards / Honours / Affiliations

  • “Best invention of the year” award by “Intellectual ventures”, USA (2008, 2009)  “The Most prolific inventor of Asia” award by “Intellectual ventures”, USA (2008, 2009)
  • NIH Postdoctoral Fellowship at Texas A&M University, College Station, Texas, USA (2003)
  • Boehringer Ingelheim Postdoctoral Fellowship from Indiana University, Bloomington, Indiana, USA (2000)
  • Best Student Award, for Overall Excellence in Academics (SSSIHL) (1993-95)
  • Guru Prasad University Gold Medal for Academic Excellence in Chemistry, at Sri Sathya Sai Institute of Higher Learning, Prasantinilayam, Anantpur, AP, India (1995)