DFT Study, Physicochemical, Molecular Docking, and ADMET Predictions of some Modified Uridine Derivatives

Document Type : Research Paper

Authors

1 Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh

2 Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh

Abstract

Uridine derivatives are important scaffolds of many organic substances, and are now drawing more and more interests to chemist and biochemist for the synthesis of new drugs and their pharmaceutical development. In this investigation, the optimization of uridine and its synthesized derivatives were employed density functional theory (DFT) with B3LYP/3-21G level theory to elucidate their thermal (electronic energy, enthalpy, Gibb’s free energy), molecular orbital (HOMO-LUMO gap, hardness, and softness) and molecular electrostatic potential (MEP) properties. Molecular docking has been performed against 3C-like protease protein 4YOI to explore the binding mode(s) and affinity with the receptor protein of derivatives (6-9 and 14), which had the better antimicrobial activity. It is found that, most of the derivatives are thermodynamically stable, chemically more reactive, and show better binding affinity than the parent drug. ADMET properties were also calculated to predict the improved pharmacokinetic features of all tested derivatives. This consciousness could be useful in perceiving the functions of uridine and their derivatives, as well as the related fervidity of other chemical and quantum properties.

Keywords

References

[1] M. K. Yates, K. L. Seley-Radtke, Antivir. Res., 162, 5 (2019).
[2] S. Singh, D. Bhattarai, G. Veeraswamy, Y. Choi, K. Lee, Curr. Org. Chem., 20, 856 (2016).
[3] E. De Clercq, Acta Pharm. Sin. B., 2, 535 (2012).
[4] C. Zhou, Curr. Opin. Drug. Discov. Devel., 12, 876 (2009).
[5] C. K. Chu, D. C. Baker, (Eds.), Plenum Press: New York, NY, USA, 245 (1993).
[6] T. P. Prakash, Chem. Biodivers., 8, 1616 (2011).
[7] R. Z. Yu, J. S. Grundy, R. S. Geary, Expert. Opin. Drug. Metab. Toxicol., 9, 169 (2013).
[8] J. K. Watts, Chem. Commun., 49, 5618 (2013).
[9] H. Mitsuya, S. Broder, Proc. Natl. Acad. Sci., USA, 83, 1911 (1986).
[10] T. Gasser, J. D. Moyer, R. E. Handschumacher, Science., 213, 777 (1981).
[11] G. Ronquist, B. Stegmayr, F. Niklasson, A. Androl., 15, 21 (1985).
[12] J. Y. Oh, Y. S. In, M. K. Kim, et al. Invest. Ophthalmol. Vis. Sci., 48, 1102 (2007).
[13] G. L. Patrick, An introduction to medicinal chemistry, 3rd ed. Oxford University press, (2005).
[14] D. Chatfield,  J. Christopher, Theoretica. Chim. Acta., 108, 367 (2002).
[15] S. M. A. Kawsar, M. A. Hosen, Y. Fujii, Y. Ozeki, J. Comput. Chem. Mol. Model., 4, 452 (2020).
[16] R. A. Gaussian09, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, et al., Gaussian, Inc., Wallingford CT., (2009).
[17] A. D. Becke, Phy. Revi., A 38, 3098 (1988).
[18] C. Lee, W. Yang, R. G. Parr, Phys. Rev., B 37, 785 (1988).
[19] R. G. Pearson, Proc. Natl. Acad. Sci., 83, 8440 (1986).
[20] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, Nucleic. Acids. Res., 28, 235 (2000).
[21] W. l. Delano, De-Lano Scientific, San Carlos, CA, USA, (2002).
[22] N. Guex, M. C. Peitsch, Electrophoresis., 18, 2714 (1997).
[23] A. Dallakyan, J. Olson, In: Hempel JE, Williams CH, Hong CC (Eds.). Chemical Biology: Methods and Protocols. Springer New York, USA, 243 (2015).
[24] A. D. S. Version 4.0, Accelrys, San Diego, USA, (2017).
[25] F. Cheng, W. Li, Y. Zhou, J. Shen, Z. Wu, G. Liu, et al., J. Chem. Inf. Model., 52, 3099 (2012).
[26] C. A. Lipinski, F. Lombardo, B. W. Dominy, P. J. Feeney,  Adv. Drug. Deliv. Rev., 46, 3 (2001).
[27] N. Cohen, S. W. Benson, Chem. Rev., 93, 2419 (1993).
[28] E. J. Lien, Z. R. Guo, R. L. Li, C. T. Su, J. Pharm. Sci., 71, 641 (1982).
[29] S. Saravanan, V. Balachandran, Spectrochim. Acta. Part. A. Mol. Biomol. Spectrosc., 120, 351 (2014).
[30] M. M. Hoque, M. A. Halim, M. G. Sarwar, M. Khan, J. Phys. Org. Chem., 28, 732 (2015).
[31] R. G. Parr, Z. Zhou, Acc. Chem. Res., 26:256 (1993).
[32] M. L. Amin, Drug. Target. Insights., 2013, 27 (2013).
[33] P. Politzer, J. S .Murray, Rev. Comput. Chem., 2, 273 (1991).
[34] P. Politzer, D. G. Truhlar, (Eds.), Plenum Press, NY, (1981).
[35] J. Perlstein, J. Am. Chem. Soc., 123, 191 (2001).
[36] M. C. Sanguinetti, M. T. Firouz, Nature., 440, 463 (2006).
International Journal of New Chemistry
Volume 8, Issue 1
Winter 2021
Pages 88-110

Files

Share

How to cite

Statistics