ENP Group
Erode N. Prabhakaran is currently an Associate Professor in Indian Institute of Science, Department of Organic Chemistry.
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.
Selected Publications.
Banerjee, S.; Gupta, S. K.; Pal, S.; Prabhakaran, E. N., Crystal structures reveal that the sterically hindered pivaloyl‐cisProlyl amide bond is energetically frustrated. Peptide Sci. 2024, e24337 (DOI: 10.1002/pep2.24337).
Banerjee, S.; Gupta, S. K.; Prabhakaran, E. N., Direct Evidence for Synchronicity between Rotation along Cα−C′ and Pyramidalization of C′ in Amides. ChemistrySelect 2023, 8 (17), e202301105.
Gupta, S. K.; Banerjee, S.; Prabhakaran, E. N., van der Waals interactions to control amide cis–trans isomerism. New J. Chem. 2022, 46 (26), 12470-12473.
Gupta, S. K.; Banerjee, S.; Prabhakaran, E. N., Understanding the anomaly of cis–trans isomerism in Pro-His sequence. Bioorg. Med. Chem. Lett. 2022, 76, 128985.
Reddy, S. S.; Pal, S.; Ghosh, S.; Prabhakaran, E. N., Hydrogen Bond Surrogate‐Constrained Dynamic Anti‐parallel β‐Sheets. ChemBioChem. 2021, 2021, 22, 2111–2115.
Prabhakaran E.N., Pal S., Kumar A., Mahajan S., Large Scale Synthesis of Native Turn and Helix Mimics Stabilized by a Generic Hydrogen Bond Surrogate. Protocol Exchange, 2021, (DOI: 10.21203/rs.3.pex-1537/v1).
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, 1714-1719.
Pal, S.; Banerjee, S.; Prabhakaran, E. N., Helix-Coil Transition at a glycine following a nascent α-helix: A synergetic guidance mechanism for helix growth. J. Phys. Chem. A. 2020, 124, 7478–7490.
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.