Course Announcement: Chemistry of Proteins and Peptides, 3:0 OC-231 / CD-231 BS, MSc, Int PhD, PhD students, who have passed a course in Fundamentals of Organic Chemistry are eligible. Starting: Aug 3rd 2023. Aug – Dec, 2023. Days: Tue, Thr, Time: 8.30 – 10.00 am. Venue: AG-08, Chemical Sciences Building Once you register for the course, intimate me at

Associate Professor
Department of Organic Chemistry
Indian Institute of Science, Bangalore 560012,INDIA
Tel: 2293-3380 Fax: 2360 0529

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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)

Awards and Fellowships

  • “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)

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, (
  • 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. (
  • 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 nπ* 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.