Thermochemical, PASS, Molecular Docking, Drug-Likeness  and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase

Kawsar, Sarkar Mohammad Abe; Hosen, Mohammed Anowar; Chowdhury, Tasneem Sultana; Rana, Kazi Masud; Fujii, Yuki; Ozeki, Yasuhiro

Sarkar Mohammad Abe Kawsar, Mohammed Anowar Hosen, Tasneem Sultana Chowdhury, Kazi Masud Rana, Yuki Fujii, Yasuhiro Ozeki

Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase

Abstract:

In recent, millions of people are living with the human immunodeficiency virus type 1 (HIV-1), which causes acquired immunodeficiency syndrome. HIV-1 reverse transcriptase (RT) is one of the main viral targets for HIV-1 inhibition. Pyrimidine nucleoside derivative, 3′-azido-3′-deoxythymidine (AZT) is a highly active nucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). In this work, hydroxyl (-OH) groups of cytidine structure were modified with different aliphatic and aromatic groups to get 5´-O-acyl- and 2´,3´-di-O-acyl derivatives and then employed for molecular modeling, molecular docking, biological prediction, and pharmacological studies. Herein, we relate the optimization of cytidine and its acylated analogues applying density functional theory (DFT) with B3LYP/3-21G level theory to explore their thermochemical and molecular electrostatic potential (MEP) properties. Prediction of activity spectra for substances (PASS) indicated promising antiviral, anti-carcinogenic, and antifungal functionality of these cytidine esters compared to the antibacterial activities. To support this observation, their cytotoxic prediction and molecular docking studies have been performed against HIV-1 reverse transcriptase (RT) (PDB: 3V4I). Most of the molecules studied out here could bind near the crucial catalytic binding site, Tyr181, Ile94, Ile382, Lys374, Val381, Val90, and Tyr34 of the HIV-1 reverse transcriptase (RT), and the molecules were surrounded by other active site residues like Gln332, Trp406, Asn265, Gly93, His96, Pro95, and Thr165. Finally, these novel molecules were analyzed for their pharmacokinetic properties which expressed that the combination of in silico ADMET prediction, toxicity prediction, and drug-likeness had shown a promising result. The study discusses the performance of molecular docking to suggest the novel molecules active against resistance mutants of RT and/or recombinant strains of HIV-1.

Keywords:
cytidine; density functional theory; HIV-1 reverse transcriptase (RT); MEP; PASS; in silico ADMET

Issue: 2021, Volume 72, Issue 3

Pages: 159-178

Publication date: 2021/7/29

https://doi.org/10.37358/RC.21.3.8446

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This article is published under the Creative Commons Attribution 4.0 International License

Citation Styles

Cite this article as:
KAWSAR, S.M.A., HOSEN, M.A., CHOWDHURY, T.S., RANA, K.M., FUJII, Y., OZEKI, Y., Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase, Rev. Chim., 72(3), 2021, 159-178.

Vancouver
Kawsar SMA, Hosen MA, Chowdhury TS, Rana KM, Fujii Y, Ozeki Y. Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase. Rev. Chim.[internet]. 2021 Mar;72(3):159-178. Available from: https://doi.org/10.37358/RC.21.3.8446

APA 6th edition
Kawsar, S.M.A., Hosen, M.A., Chowdhury, T.S., Rana, K.M., Fujii, Y. & Ozeki, Y. (2021). Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase. Revista de Chimie, 72(3), 159-178. https://doi.org/10.37358/RC.21.3.8446

Harvard
Kawsar, S.M.A., Hosen, M.A., Chowdhury, T.S., Rana, K.M., Fujii, Y., Ozeki, Y. (2021). 'Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase', Revista de Chimie, 72(3), pp. 159-178. https://doi.org/10.37358/RC.21.3.8446

IEEE
S.M.A. Kawsar, M.A. Hosen, T.S. Chowdhury, K.M. Rana, Y. Fujii, Y. Ozeki, "Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase". Revista de Chimie, vol. 72, no. 3, pp. 159-178, 2021. [online]. https://doi.org/10.37358/RC.21.3.8446

Text
Sarkar Mohammad Abe Kawsar, Mohammed Anowar Hosen, Tasneem Sultana Chowdhury, Kazi Masud Rana, Yuki Fujii, Yasuhiro Ozeki,
Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase,
Revista de Chimie,
Volume 72, Issue 3,
2021,
Pages 159-178,
ISSN 2668-8212,
https://doi.org/10.37358/RC.21.3.8446.
(https://revistadechimie.ro/Articles.asp?ID=8446)
Keywords: cytidine; density functional theory; HIV-1 reverse transcriptase (RT); MEP; PASS; in silico ADMET

RIS
TY - JOUR
T1 - Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase
A1 - Kawsar, Sarkar Mohammad Abe
A2 - Hosen, Mohammed Anowar
A3 - Chowdhury, Tasneem Sultana
A4 - Rana, Kazi Masud
A5 - Fujii, Yuki
A6 - Ozeki, Yasuhiro
JF - Revista de Chimie
JO - Rev. Chim.
PB - Revista de Chimie SRL
SN - 2668-8212
Y1 - 2021
VL - 72
IS - 3
SP - 159
EP - 178
UR - https://doi.org/10.37358/RC.21.3.8446
KW - cytidine
KW - density functional theory
KW - HIV-1 reverse transcriptase (RT)
KW - MEP
KW - PASS
KW - in silico ADMET
ER -

BibTex
@article{RevCh2021P159,
author = {Kawsar Sarkar Mohammad Abe and Hosen Mohammed Anowar and Chowdhury Tasneem Sultana and Rana Kazi Masud and Fujii Yuki and Ozeki Yasuhiro},
title = {Thermochemical, PASS, Molecular Docking, Drug-Likeness and In Silico ADMET Prediction of Cytidine Derivatives against HIV-1 Reverse Transcriptase},
journal = {Revista de Chimie},
volume = {72},
number = {3},
pages = {159-178},
year = {2021},
issn = {2668-8212},
doi = {https://doi.org/10.37358/RC.21.3.8446},
url = {https://revistadechimie.ro/Articles.asp?ID=8446}
}

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