Research Article
BibTex RIS Cite

Year 2023, Volume: 6 Issue: 2, 138 - 144, 18.12.2023

Özlem İşcan

https://doi.org/10.54565/jphcfum.1402117

Abstract

References

  • Nehlig, A., Daval, J. L., & Debry, G. (1992). Caffeine and the central nervous system: mechanisms of action, biochemical, metabolic and psychostimulant effects. Brain research reviews, 17(2), 139-170.
  • Camfield, D. A., Stough, C., Farrimond, J., & Scholey, A. B. (2014). Acute effects of tea constituents L-theanine, caffeine, and epigallocatechin gallate on cognitive function and mood: a systematic review and meta-analysis. Nutrition reviews, 72(8), 507-522.
  • Wood, S., Sage, J. R., Shuman, T., & Anagnostaras, S. G. (2014). Psychostimulants and cognition: a continuum of behavioral and cognitive activation. Pharmacological reviews, 66(1), 193-221.
  • Ribeiro, J. A., & Sebastiao, A. M. (2010). Caffeine and adenosine. Journal of Alzheimer's Disease, 20(s1), S3-S15.
  • Hillis DM, Sadava D, Hill RW, Price MV (2015). Principles of Life (2 ed.). Macmillan Learning. pp. 102–103.
  • Faudone, G., Arifi, S., & Merk, D. (2021). The medicinal chemistry of caffeine. Journal of Medicinal Chemistry, 64(11), 7156-7178.
  • Bhailume Meenal V. and Shinde Shubhangi R (2020) Biodegradation of Caffeine, International Journal of Science and Research, Vol 9, Issue 10.
  • Tzenios, N. (2023). Obesity as a risk factor for cancer. EPRA International Journal of Research and Development (IJRD), 8(2), 101-104.
  • Perone, F., Pingitore, A., Conte, E., Halasz, G., Ambrosetti, M., Peruzzi, M., & Cavarretta, E. (2023, March). Obesity and Cardiovascular Risk: Systematic Intervention Is the Key for Prevention. In Healthcare (Vol. 11, No. 6, p. 902). MDPI.
  • Jia, G., Fu, Y. E., Zhao, X. U., Dai, Q., Zheng, G., Yang, Y., ... & He, C. (2011). N 6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nature chemical biology, 7(12), 885-887.
  • Mauer, J., Sindelar, M., Despic, V., Guez, T., Hawley, B. R., Vasseur, J. J., ... & Jaffrey, S. R. (2019). FTO controls reversible m6Am RNA methylation during snRNA biogenesis. Nature chemical biology, 15(4), 340-347.
  • Gerken, T., Girard, C. A., Tung, Y. C. L., Webby, C. J., Saudek, V., Hewitson, K. S., ... & Schofield, C. J. (2007). The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science, 318(5855), 1469-1472.
  • Shishodia, S., Demetriades, M., Zhang, D., Tam, N. Y., Maheswaran, P., Clunie-O’Connor, C., ... & Schofield, C. J. (2021). Structure-based design of selective fat mass and obesity associated protein (FTO) inhibitors. Journal of Medicinal Chemistry, 64(22), 16609-16625.
  • Gulati, P., Cheung, M. K., Antrobus, R., Church, C. D., Harding, H. P., Tung, Y. C. L., ... & Yeo, G. S. (2013). Role for the obesity-related FTO gene in the cellular sensing of amino acids. Proceedings of the National Academy of Sciences, 110(7), 2557-2562.
  • http://pubchem.ncbi.nlm.nih.gov/
  • Thompson MA. (2004). Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScoring function. ACS meeting Philadelphia 172, CINF 42, PA.
  • Peng C, Ayali PY, Schlegel HB and Frisch MJ, (1995) J. Comp Chem., 16: 49-51.
  • Cramer CJ and Truhlar DG(1992), Computer-Aided Mol. Design, 6: 629-666.
  • https://www.rcsb.org/
  • Martin YC (1998). Perspective in drug discovery and design. Springer Publisher, USA, 12th Volume, pp.3- 23.
  • Cruciani G, Clementi S and Pastor M (1998). GOLPEguided region selection. Perspectives in
  • Drug Discovery and Design, 12-14(16): 71-86.
  • Dunn III and Hopfinger AJ (1998). Drug Discovery, Kluwer Academic Publishers. Chapter 12, pp.167-182
  • Dewar MJS, Zoobisch EG, Healy EF and Stewart JJP (1985). AM1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107: 3902-3910.
  • James J. P. Stewart, J. (1989) Comp. Chem., 10, 209-220 and 221-264, (1989)
  • Thompson, M. A., Zerner M. C. J. Am. Chem. Soc., 113,
  • Mark A. Thompson, Eric D. Glendening, and David Feller (1994). J. Phys. Chem. 98, 10465-10476
  • Mark A. Thompson, and Gregory K. Schenter J. (1995). Phys. Chem. 99, 6374-6386,
  • Mark A. Thompson, (1996). J. Phys. Chem. 100, 14492-14507,
  • https://plip-tool.biotec.tu-dresden.de/plipweb/plip/result /47049a63-a21b-4f90-9705 2218ba8be383

A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software

Year 2023, Volume: 6 Issue: 2, 138 - 144, 18.12.2023

Özlem İşcan

https://doi.org/10.54565/jphcfum.1402117

Abstract

In this study, the quasi-experimental molecular computational studies of the caffeine compound found in many herbal and the binding properties of the 4QHO protein to the active site were investigated by molecular docking method. For molecular docking, first of all, caffeine molecule, geometry optimization was done in ArgusLab program with semi-experimental PM3 method. The HOMO, LUMO, HOMO-LUMO energy differences and potential energy surface of all optimized molecules were calculated. The selected 4QHO protein crystal structure was obtained from the protein database in *.pdb format and optimized ligand interaction with this crystal structure was studied using ArgusLab. As a result of molecular docking studies, ligand-protein binding energies, hydrogen bond sites and number that can occur between ligand-protein were determined and evaluated.

Keywords

Caffeine ArgusLab Molecular Docking

Supporting Institution

Bartın Üniversitesi

Thanks

Bartın Üniversitesine katkılarından dolayı teşekkür ederim.

References

  • Nehlig, A., Daval, J. L., & Debry, G. (1992). Caffeine and the central nervous system: mechanisms of action, biochemical, metabolic and psychostimulant effects. Brain research reviews, 17(2), 139-170.
  • Camfield, D. A., Stough, C., Farrimond, J., & Scholey, A. B. (2014). Acute effects of tea constituents L-theanine, caffeine, and epigallocatechin gallate on cognitive function and mood: a systematic review and meta-analysis. Nutrition reviews, 72(8), 507-522.
  • Wood, S., Sage, J. R., Shuman, T., & Anagnostaras, S. G. (2014). Psychostimulants and cognition: a continuum of behavioral and cognitive activation. Pharmacological reviews, 66(1), 193-221.
  • Ribeiro, J. A., & Sebastiao, A. M. (2010). Caffeine and adenosine. Journal of Alzheimer's Disease, 20(s1), S3-S15.
  • Hillis DM, Sadava D, Hill RW, Price MV (2015). Principles of Life (2 ed.). Macmillan Learning. pp. 102–103.
  • Faudone, G., Arifi, S., & Merk, D. (2021). The medicinal chemistry of caffeine. Journal of Medicinal Chemistry, 64(11), 7156-7178.
  • Bhailume Meenal V. and Shinde Shubhangi R (2020) Biodegradation of Caffeine, International Journal of Science and Research, Vol 9, Issue 10.
  • Tzenios, N. (2023). Obesity as a risk factor for cancer. EPRA International Journal of Research and Development (IJRD), 8(2), 101-104.
  • Perone, F., Pingitore, A., Conte, E., Halasz, G., Ambrosetti, M., Peruzzi, M., & Cavarretta, E. (2023, March). Obesity and Cardiovascular Risk: Systematic Intervention Is the Key for Prevention. In Healthcare (Vol. 11, No. 6, p. 902). MDPI.
  • Jia, G., Fu, Y. E., Zhao, X. U., Dai, Q., Zheng, G., Yang, Y., ... & He, C. (2011). N 6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nature chemical biology, 7(12), 885-887.
  • Mauer, J., Sindelar, M., Despic, V., Guez, T., Hawley, B. R., Vasseur, J. J., ... & Jaffrey, S. R. (2019). FTO controls reversible m6Am RNA methylation during snRNA biogenesis. Nature chemical biology, 15(4), 340-347.
  • Gerken, T., Girard, C. A., Tung, Y. C. L., Webby, C. J., Saudek, V., Hewitson, K. S., ... & Schofield, C. J. (2007). The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science, 318(5855), 1469-1472.
  • Shishodia, S., Demetriades, M., Zhang, D., Tam, N. Y., Maheswaran, P., Clunie-O’Connor, C., ... & Schofield, C. J. (2021). Structure-based design of selective fat mass and obesity associated protein (FTO) inhibitors. Journal of Medicinal Chemistry, 64(22), 16609-16625.
  • Gulati, P., Cheung, M. K., Antrobus, R., Church, C. D., Harding, H. P., Tung, Y. C. L., ... & Yeo, G. S. (2013). Role for the obesity-related FTO gene in the cellular sensing of amino acids. Proceedings of the National Academy of Sciences, 110(7), 2557-2562.
  • http://pubchem.ncbi.nlm.nih.gov/
  • Thompson MA. (2004). Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScoring function. ACS meeting Philadelphia 172, CINF 42, PA.
  • Peng C, Ayali PY, Schlegel HB and Frisch MJ, (1995) J. Comp Chem., 16: 49-51.
  • Cramer CJ and Truhlar DG(1992), Computer-Aided Mol. Design, 6: 629-666.
  • https://www.rcsb.org/
  • Martin YC (1998). Perspective in drug discovery and design. Springer Publisher, USA, 12th Volume, pp.3- 23.
  • Cruciani G, Clementi S and Pastor M (1998). GOLPEguided region selection. Perspectives in
  • Drug Discovery and Design, 12-14(16): 71-86.
  • Dunn III and Hopfinger AJ (1998). Drug Discovery, Kluwer Academic Publishers. Chapter 12, pp.167-182
  • Dewar MJS, Zoobisch EG, Healy EF and Stewart JJP (1985). AM1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107: 3902-3910.
  • James J. P. Stewart, J. (1989) Comp. Chem., 10, 209-220 and 221-264, (1989)
  • Thompson, M. A., Zerner M. C. J. Am. Chem. Soc., 113,
  • Mark A. Thompson, Eric D. Glendening, and David Feller (1994). J. Phys. Chem. 98, 10465-10476
  • Mark A. Thompson, and Gregory K. Schenter J. (1995). Phys. Chem. 99, 6374-6386,
  • Mark A. Thompson, (1996). J. Phys. Chem. 100, 14492-14507,
  • https://plip-tool.biotec.tu-dresden.de/plipweb/plip/result /47049a63-a21b-4f90-9705 2218ba8be383
There are 30 citations in total.

Details

Primary Language English
Subjects Classical Physics (Other)
Journal Section Articles
Authors

Özlem İşcan 0000-0003-3282-1121

Publication Date December 18, 2023
Submission Date December 8, 2023
Acceptance Date December 16, 2023
Published in Issue Year 2023 Volume: 6 Issue: 2

Cite

APA İşcan, Ö. (2023). A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software. Journal of Physical Chemistry and Functional Materials, 6(2), 138-144. https://doi.org/10.54565/jphcfum.1402117
AMA İşcan Ö. A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software. Journal of Physical Chemistry and Functional Materials. December 2023;6(2):138-144. doi:10.54565/jphcfum.1402117
Chicago İşcan, Özlem. “A Insilico Study on Structural Aspects of Caffeine by ArgusLab 4 Software”. Journal of Physical Chemistry and Functional Materials 6, no. 2 (December 2023): 138-44. https://doi.org/10.54565/jphcfum.1402117.
EndNote İşcan Ö (December 1, 2023) A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software. Journal of Physical Chemistry and Functional Materials 6 2 138–144.
IEEE Ö. İşcan, “A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software”, Journal of Physical Chemistry and Functional Materials, vol. 6, no. 2, pp. 138–144, 2023, doi: 10.54565/jphcfum.1402117.
ISNAD İşcan, Özlem. “A Insilico Study on Structural Aspects of Caffeine by ArgusLab 4 Software”. Journal of Physical Chemistry and Functional Materials 6/2 (December 2023), 138-144. https://doi.org/10.54565/jphcfum.1402117.
JAMA İşcan Ö. A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software. Journal of Physical Chemistry and Functional Materials. 2023;6:138–144.
MLA İşcan, Özlem. “A Insilico Study on Structural Aspects of Caffeine by ArgusLab 4 Software”. Journal of Physical Chemistry and Functional Materials, vol. 6, no. 2, 2023, pp. 138-44, doi:10.54565/jphcfum.1402117.
Vancouver İşcan Ö. A Insilico Study on Structural aspects of Caffeine by ArgusLab 4 software. Journal of Physical Chemistry and Functional Materials. 2023;6(2):138-44.