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Structural Chemistry

, Volume 30, Issue 5, pp 1899–1910 | Cite as

Synthesis and characterization of oxygen depleted tert-amine calix[4]arene ligands and study the effect on sigma non-opioid intracellular protein receptor

  • Navaneet ChaturvediEmail author
  • Abha Mishra
  • Varun RawatEmail author
Original Research
  • 56 Downloads

Abstract

This study focuses on the biological prospects of oxygen-depleted calix[4]arene ligands on a protein target. Because of their extensive medical relevance, the oxygen-depleted bis(piperdine) (BPD) and bis(pyrazole) (BPZ) ligands were synthesized and characterized by NMR and mass spectrometry. Furthermore, molecular docking followed by molecular dynamics simulation was utilized to understand the behavior of ligands on selection of sigma non-opiod intracellular receptor (SigNOR) as a suitable protein target. The simulations were carried out by three level of complexity: (1) Apo SigNOR, (2) BPD: SigNOR, and (3) BPZ: SigNOR. The three complex systems were subjected to stability check before detail analysis. From the results of the estimation of binding free energy, it follows that both ligands possess the same free energy of binding which, in turn, suggests their similar role; however, energy components such as Van der waal and electrostatic potential recommend BPZ were identified as a competitive drug on SigNOR. In addition, temporal distribution of the clusters suggests that scattering of the cluster’s popularity is a measure of fast structural transitions in both complexes. Current study utilizes modern approach to synthesis, characterization, and simulation of our ligands. This study appropriately highlights the effect of our ligands on SigNOR Protein, which might further be extended to potential in vitro and in vivo bioassay.

Keywords

Calix[4]arene Chemical synthesis NMR Molecular docking Molecular dynamics simulation 

Abbreviations

BPD

Bis(piperdine) calixarene ligand

BPZ

Bis(pyrazole)calixarene ligand

MD

Molecular dynamics

NMR

Nuclear magnetic resonance

ns

Nanosecond

ps

Picosecond

RMSD

Root-mean-square deviation

RMSF

Root-mean-square fluctuation

SigNOR

Sigma non-opiod intracellular receptor

VdW

Van der Waals

Notes

Acknowledgements

NC is thankful for the computational facilities provided by Dr. Yossi Tsfadia, Tel Aviv University, Israel, and VR acknowledges Amity University Haryana, India. NC and VR share equal contribution for this study.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

11224_2019_1324_MOESM1_ESM.doc (71 kb)
ESM 1 (DOC 71 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.School of Biochemical EngineeringIndian Institute of Technology (BHU)VaranasiIndia
  2. 2.Department of Biochemistry and Molecular Biology, Dr George Wise Institute of Life ScienceTel Aviv UniversityTel AvivIsrael
  3. 3.Department of Applied Chemistry, Amity School of Applied SciencesAmity University HaryanaGurugramIndia

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