Erode N. Prabhakaran

Education

• 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)

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.

• Reddy, S. S.; Pal, S.; Ghosh, S.; Prabhakaran, E. N., Hydrogen Bond Surrogate‐Constrained Dynamic Anti‐parallel β‐Sheets. ChemBioChem. 2021, (https://doi.org/10.1002/cbic.202100028).  
• 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. 2021, 11, 1714-1719. (https://doi.org/10.1002/ejoc.202001359).  
• 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. 2020, 5, 13902-13912.
• Prabhakaran E. N., Tumminakatti, S., Vats K, Ghosh, S.  Spectral evidence for generic charge → acceptor interactions in carbamates and esters. RSC Adv.. 2020, 10, 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. 2018, 59, 2515-2519.
• Vats K, Prabhakaran E.N., Disallowed conformations of Amino Acids in Proteins and Peptides, Cutting Edge, 2017, 9 -13.
• Tumminakatti, S., Khatri, B., Krishnamurthi, V., Athavale, V., Prabhakaran, E. N. Solution Structural Features of N-Acyl Homoserine Lactones. Tetrahedron Letters, 2015, 56, 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 Science, 2015­, 104, 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 Letters, 2014, 55, 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. 2013, 52, 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. 2013, 101(1), 66-77.
• A method for stabilizing the cis prolyl peptide bond: influence of an unusual n→π* interaction in 1,3-oxazine and 1,3-thiazine containing peptidomimetics. Reddy, D. N., Thirupathi, R., Tumminakatti, S., Prabhakaran, E. N. Tet. Lett. 2012, 53, 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., 2011, 76, 680–683.
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• “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)