Skip to main content
SpringerLink
Log in

Spectroscopic analyses, intra-molecular interaction, chemical reactivity and molecular docking of imerubrine into bradykinin receptor

  • Original Research
  • Published:
Medicinal Chemistry Research Aims and scope Submit manuscript

Abstract

Imerubrine, a biologically active natural product, is one of the initial members of tropoloisoquinolines and biosynthetically related to the more common azafluoranthene alkaloids. We perform a comprehensive quantum chemical analysis on imerubrine using density functional theory at B3PW91/6-311 + G(d,p) level. The equilibrium molecular structure of imerubrine has been obtained. The weak intra-molecular C–H⋯O interactions are recognized, characterized and quantified by quantum theory of atoms in molecule and relaxed force constants. The chemical reactivity of imerubrine is explained and discussed with the help of highest occupied molecular orbital, lowest unoccupied molecular orbital and molecular electro static potential surfaces as well as a number of reactivity descriptors. The infrared spectrum of imerubrine has been calculated and the vibrational modes have been assigned on the basis of the potential energy distribution with the highest possible accuracy. The nuclear magnetic resonance spectra of imerubrine have been calculated, analyzed and compared with available experimental data. A good agreement between experimental and calculated values has been observed. The molecular docking of imerubrine into B1 bradykinin receptor (PDB ID: 1HZ6) shows that it is capable to bind with the receptor and hence, it can act as an effective bradykinin receptor agonist.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Aakeroy CB, Seddon KR (1993) The hydrogen bond and crystal engineering. Chem Soc Rev 22:397–407

    Article  CAS  Google Scholar 

  • Arivazhagan M, Jevavijayan S (2011) Vibrational spectroscopic, first-order hyperpolarizability and HOMO, LUMO studies of 1,2-dichloro-4-nitrobenzene based on Hartree–Fock, and DFT calculations. Spectrochim Acta A 79:376–38

    Article  CAS  Google Scholar 

  • Arjunan V, Sakiladevi S, Marchewka MK, Mohan S (2013) FT-IR, FT-Raman, FT-NMR and quantum chemical investigations of 3-acetylcoumarin. Spectrochim Acta A 109:79

    Article  CAS  Google Scholar 

  • Arjunan V, Subramaniam S, Mohan S (2004) Synthesis, Fourier transform infrared and Raman spectra, assignments and analysis of N-(phenyl)- and N-(chloro substituted phenyl)-2,2-dichloroacetamides. Spectrochim Acta A 60:1141–1159

    Article  CAS  Google Scholar 

  • Bader RFW (1990) Atoms in Molecules. A Quantum Theory, 2nd ed. Oxford, New York

    Google Scholar 

  • Baker J (2006) A critical assessment of the use of compliance constants as bond strength descriptors for weak interatomic interactions. J Chem Phys 125:014103

    Article  PubMed  Google Scholar 

  • Baker J, Pulay P (2006) The interpretation of compliance constants and their suitability for characterizing hydrogen bonds and other weak interactions. J Am Chem Soc 128:11324–11325

    Article  CAS  PubMed  Google Scholar 

  • Becke AD (1993) Density functional thermochemistry.III. The role of exact exchange. J Chem Phys 98:5648

    Article  CAS  Google Scholar 

  • Boger DL, Brotherton CE (1984) Plementary use of 3-Methoxycarbonyl-2-pyrones. J Org Chem 49:4050

    Article  CAS  Google Scholar 

  • Boger DL, Takahashi K (1995) Total Synthesis of granditropone, grandirubrine, imerubrine and isoimerubrine. J Am Chem Soc 117:12452–12459

    Article  CAS  Google Scholar 

  • Brandhorst K, Grunenberg J (2008) How strong is it? The interpretation of force and compliance constants as bond strength descriptors. Chem Soc Rev 37:1558–1567

    Article  CAS  PubMed  Google Scholar 

  • Buck KT (1984) The Alkaloids: Chemistry and Pharmacology 23:301–325

  • Dennington R, Keith T and Millam J (2009) GaussView Version 5.0. Semichem Inc. Shawnee Mission, KS, USA

  • Desiraju GR, Kashino S, Coombs MM, Glusker JP (1993) C-H--O packing motifs in some cyclopenta[a]phenanthrenes. Acta Cryst B 49:880–892

    Article  Google Scholar 

  • Espinosa E, Molins E, Lecomte C (1998) Hydrogen bond strength revealed by topological analyses of experimentally observed electron densities. Chem Phys Lett 285:170

    Article  CAS  Google Scholar 

  • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zheng G, Petersson GA, Voth GA, Scalmani G, Nakatsuji H, Nakai H, Hratchian HP, Brothers E, Ogliaro F, Bloino J, Cioslowski J, Foresman JB, Burant JC, Cross JB, Jaramillo J, Knox JE, Montgomery JA, Millam JM, Normand J, Peralta JE, Heyd JJ, Dannenberg JJ, Sonnenberg JL, Hasegawa J, Tomasi J, Ortiz JV, Ochterski JW, Salvador P, Morokuma K, Raghavachari K, Toyota K, Kudin KN, Bearpark M, Caricato M, Cossi M, Ehara M, Hada M, Ishida M, Klene M, Rega N, Farkas O, Kitao O, Yazyev O, Cammi R, Fukuda R, Gomperts R, Kobayashi R, Stratmann RE, Martin RL, Iyengar SS, Dapprich S, Keith T, Nakajima T, Vreven T, Barone V, Bakken V, Rendell V, Staroverov VN, Zakrzewski VG, Li X, Honda Y, Daniels AD, Izmaylov AF, Austin AJ, Mennucci B, Adamo C, Pomelli C, Fox DJ (2010) Gaussian 09 Revision B.01. Gaussian Inc., Wallingford CT

    Google Scholar 

  • George S (2001) Infrared and Raman characteristic group frequencies-Tables and Charts, 3rd ed. Wiley, Chichester

    Google Scholar 

  • Gfeller D, Michielin O and Zoete V (2013) Bioinformatics 29: 3073

  • Grosdidier A, Zoete V and Michielin O (2011) Nucleic Acids Res. 39: 270

  • Jamroz MH (2004) Vibrational energy distribution analysis, VEDA 4 Program. Warsaw, Poland

  • Jamroz MH (2013) Vibrational Energy Distribution Analysis (VEDA): Scopes and limitations. Spectrochim Acta A 114:220–230

    Article  CAS  Google Scholar 

  • Jeffrey GA, Saenger W (1991) Hydrogen Bonding in Biological Structures. Springer–Verlag, Berlin Heidelberg

    Book  Google Scholar 

  • Jones LH, Swanson BI (1976) Bonding in Metal Carbonyls. Acc Chem Res 9:128

    Article  CAS  Google Scholar 

  • Keith TA (2012) AIMAll Version 12.09.23 TK Gristmill Software Overland Park KS USA

  • Krishnakumar V, Balachandran V (2005) Analysis of vibrational spectra of 5-fluoro, 5-chloro and 5-bromo-cytosines based on density functional theory calculations. Spectrochim Acta A 61:1001–1006

    Article  CAS  Google Scholar 

  • Kumar A, Srivastava AK, Mondal A, Brahmachari G, Misra N, Gangwar S (2015) Combined experimental (FT-IR, UV-visible spectra, NMR) and theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, reactivity descriptor and molecular docking of Phomarin. J Mol Struct 1096:94–101

    Article  CAS  Google Scholar 

  • Lee JC, Cha JK (2001) Total synthesis of tropoloisoquinolines: imerubrine, isoimerubrine, and grandirubrine. J Am Chem Soc 123:3243–3246

    Article  CAS  PubMed  Google Scholar 

  • Lewis WH, Stonard RJ, Porras-Reyes B and Mustoe TA (1992) (US Patent No. 5,156,847)

  • Luqul FJ, Lopez JM, Orozco M (2000) Perspective on electrostatic interactions of a solute with a continuum, a direct utilization of ab initio molecular potentials for the prevision of solvent effects. Theor Chem Acc 103:343

    Article  Google Scholar 

  • Madhav MV, Manogaran S (2009) A relook at the compliance constants in redundant internal coordinates and some new insights. J Chem Phys 131:174112–174116

    Article  Google Scholar 

  • Majumder M, Manogaran S (2013) Redundant internal coordinates, compliance constants and non-bonded interactions-Some new insights. J Chem Sci 125:9–15

    Article  CAS  Google Scholar 

  • Manolopoulos DE, May JC, Down SE (1991) Systematic relationships between fullerenes without spirals. Chem Phys Lett 181:105

    Article  CAS  Google Scholar 

  • Merrick JP, Moran D, Radom L (2007) An evaluation of harmonic vibration frequency scale factors. J Phys Chem A 111:11683–11700

    Article  CAS  PubMed  Google Scholar 

  • Mukherjee KM, Mishra TN (1996) Surface-enhanced raman spectra of 2- and 3-hydroxypyridines in silver sol. J Raman Spectrosc 27:595–600

    Article  CAS  Google Scholar 

  • Parr RG, Yang W (1989) Density Functional Theory of Atoms and Molecules. Oxford University Press and Clarendon Press, New York and Oxford

    Google Scholar 

  • Perdew JP, Wang Y (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys Rev B 45:13244

    Article  Google Scholar 

  • Ponnala S, Harding WW (2013) A route to azafluoranthene natural products through direct arylation. Eur J Org Chem 6:1107

    Article  Google Scholar 

  • Rozas I, Alkorta I, Elguero J (2000) Behavior of ylides containing N, O and C atoms as hydrogen bond acceptors. J Am Chem Soc 122:11154

    Article  CAS  Google Scholar 

  • Saenger W (1984) Principles of Nucleic Acid Structure. Springer, Berlin

    Book  Google Scholar 

  • Scherowsky G, Frackowiak E, Adam D (1997) 4,5,6,7,8,9-Hexamethoxyindeno[1,2,3-ij] isoquinoline. Acta Cryst C 53:5

    Article  Google Scholar 

  • Schlick T (2010) Molecular modelling and simulation: An Interdisciplinary Guide Vol. 21, 2nd ed. New York

  • Schwan TJ (1976) (US Patent No. 3,971,788)

  • Scrocco E, Tomasi J (1973) The electrostatic molecular potential as a tool for the interpretation of molecular properties. Top Curr Chem 42:95–170

    CAS  Google Scholar 

  • Silveira CC, Larghi EL, Mendes SR, Bracca ABJ, Rinaldi F, Kaufman TS (2009) Electrocyclization-mediated approach to 2-methyltriclisine, an unnatural analog of the azafluoranthene alkaloid triclisine. Eur J Org Chem 2:4637

    Article  Google Scholar 

  • Srivastava AK, Baboo V, Narayana B, Sarojini BK, Misra N (2014a) Comparative DFT study on reactivity, acidity and vibrational spectra of halogen substituted phenylacetic acids. Indian J Pure Appl Phys 52:507–519

    Google Scholar 

  • Srivastava AK, Narayana B, Sarojini BK, Misra N (2014b) Vibrational, structural and hydrogen bonding analysis of N’-[(E)-4-hydroxybenzylidene]-2-(naphthalene-2-yloxy) acetohydrazide: combined density functional and atoms-in-molecule based theoretical studies. Indian J Phys 88:547–556

    Article  CAS  Google Scholar 

  • Srivastava AK, Pandey AK, Gangwar SK, Misra N (2014c) Structural, vibrational and electronic properties of cis and trans conformers of 4-hydroxy-l-proline: a density functional approach. J At Mol Sci 5:279–288

    Google Scholar 

  • Srivastava AK, Pandey AK, Misra N, Jain S (2015) FT-IR spectroscopy, intra-molecular C-H--O interactions, HOMO, LUMO, MESP analysis and biological activity of two natural products, triclisine and rufescine: DFT and QTAIM approaches. Spectrochim Acta A 136:682–689

    Article  CAS  Google Scholar 

  • Steiner T, Saenger W (1992) Geometry of C–H---O Hydrogen bonds in Carbohydrate crystal structures, Analysis of neutron diffraction data. J Am Chem Soc 114:10146–10154

    Article  CAS  Google Scholar 

  • Sundaraganesan N, Ilakiamani S, Joshua BD (2007) FT-Raman and FT-IR spectra, ab initio and density functional studies of 2-amino-4,5-difluorobenzoic acid. Spectrochim Acta A 67:287–297

    Article  CAS  Google Scholar 

  • Swanson BI (1976) Minimum energy coordinates. A relation between molecular vibrations and reaction coordinates. J Am Chem Soc 98:3067–3071

    Article  CAS  Google Scholar 

  • Zhao B, Snieckus V (1984) Integrated aromatic metalation—cross coupling methodologies. A concise synthesis of the azafluoranthene alkaloid imeluteine. Tetrahedron Lett 32:5277–5278

    Article  Google Scholar 

Download references

Acknowledgments

A.K. Srivastava is thankful to Council of Scientific and Industrial Research (CSIR), New Delhi, India for providing a research fellowship via grant no. 09/107(0359)/2012-EMR-I. The Central Facility for Computational Research (CFCR), Department of Chemistry, University of Lucknow is also acknowledged.

Author information

Authors and Affiliations

  1. Department of Physics, University of Lucknow, Lucknow, 226007, India

    Ambrish Kumar Srivastava, Abhishek Kumar & Neeraj Misra

  2. Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India

    Sarvesh Kumar Pandey

Authors
  1. Ambrish Kumar Srivastava
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Abhishek Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sarvesh Kumar Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Neeraj Misra
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Neeraj Misra.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Srivastava, A.K., Kumar, A., Pandey, S.K. et al. Spectroscopic analyses, intra-molecular interaction, chemical reactivity and molecular docking of imerubrine into bradykinin receptor. Med Chem Res 25, 2832–2841 (2016). https://doi.org/10.1007/s00044-016-1710-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00044-016-1710-z

Keywords

Search

Navigation