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Erode N. Prabhakaran is currently a 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.
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