Physical Chemistry Research

TD-DFT, Vibrational Spectra, Molecular Docking, ADMET, and PASS Assessment as Potential Inhibitors of SARS-CoV-2 Alpha and Beta Variants of Uridine Derivatives

Document Type : Special issue in the honor of Prof. Pakiari

Authors

Md. Rithoan Hossain
S M Abe Kawsar

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

https://doi.org/10.22036/pcr.2025.513955.2661
Abstract
The synthesis of innovative pharmaceuticals and their pharmacological advancements are attracting the interest of chemists and biochemists because of the importance of uridine derivatives as primary scaffolds for various chemical molecules. To explain the thermal (electronic energy, enthalpy, Gibb's free energy), molecular orbital (HOMO-LUMO gap, hardness, and softness), and molecular electrostatic potential (MEP) properties of uridine and its synthesized derivatives, density functional theory (DFT) with B3LYP/6-31G level theory was utilized in this study. The majority of the derivatives are more chemically reactive and thermodynamically stable and exhibit greater binding affinities than the parent compound. To investigate the binding modes and affinities of uridine and its derivatives (1–7), which exhibit enhanced antibacterial action, molecular docking was performed against the SARS-CoV-2 alpha version 7EKF and the SARS-CoV-2 beta variant 7ekg. Compound 5 demonstrates enhanced efficacy with both proteins by establishing hydrogen bonds with the TRP69 amino acid within the binding pocket. Furthermore, ADMET parameters are anticipated to predict the enhanced pharmacokinetic properties of each analyzed derivative. This acquaintance may be significant in comprehending the roles of uridine and its derivatives, together with the intensity of other chemical and quantum characteristics.

Graphical Abstract

TD-DFT, Vibrational Spectra, Molecular Docking, ADMET, and PASS Assessment as Potential Inhibitors of SARS-CoV-2 Alpha and Beta Variants of Uridine Derivatives

Keywords

TD-DFT
SARS-CoV-2
Vibrational spectra
Uridine
Docking

Subjects

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Physical Chemistry Research
Volume 13, Issue 4
Autumn 2025
Pages 643-668

  • Receive Date 25 March 2025
  • Revise Date 27 July 2025
  • Accept Date 16 August 2025