[Cu(dipicolinoylamide)(NO3)(H2O)] as anti-COVID-19 and antibacterial drug candidate: Design, synthesis, crystal structure, DFT and molecular docking

Laila H Abdel-Rahman; Maram T Basha; Badriah Saad Al-Farhan; Mohamed R Shehata; Shaaban K Mohamed; Youssef Ramli

doi:10.1016/j.molstruc.2021.131348

[Cu(dipicolinoylamide)(NO₃)(H₂O)] as anti-COVID-19 and antibacterial drug candidate: Design, synthesis, crystal structure, DFT and molecular docking

J Mol Struct. 2022 Jan 5:1247:131348. doi: 10.1016/j.molstruc.2021.131348. Epub 2021 Aug 22.

Authors

Laila H Abdel-Rahman¹, Maram T Basha², Badriah Saad Al-Farhan³, Mohamed R Shehata⁴, Shaaban K Mohamed^{5

6}, Youssef Ramli⁷

Affiliations

¹ Chemistry Department, Faculty of Science, Sohag University, 82524 Sohag, Egypt.
² University of Jeddah, College of Science, Department of Chemistry, Jeddah, Saudi Arabia.
³ Chemistry Department, Faculty of Girls for Science, King Khalid University, Abha, Saudi Arabia.
⁴ Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt.
⁵ Chemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 6GD, England.
⁶ Chemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt.
⁷ Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco.

Abstract

For first time the new N-picolinoypicolinlamide was obtained as in situ ligand during the reaction of 2,4,6-ris(2-pyridyl)-,3,5-triazine with aqueous solution of CuNO₃·3H₂O and formed the corresponding complex [Cu(dipicolinoylamide)(NO₃)(H₂O)]. The crystal structure of the obtained complex was determined by x-ray structure. The complex crystallizes in space group P2₁/n, a = 10.2782(9) Å, b = 7.5173(6) Å, c = 17.738(2) Å, α = 90.00°, β = 91.368(1)°, γ = 90.00°, V = 1370.1(2) Å3, Z = 4. The copper center has a distorted octahedral geometry. DFT calculations show good agreement between theoretical and X-ray data. The Molecular docking studies were executed to consider the nature of binding and binding affinity of the synthesized compounds with the receptor of COVID-19 main protease viral protein (PDB ID: 6lu7), the receptor of gram -ve bacteria (Escherichia coli, PDB ID: 1fj4) and the receptor of gram +ve bacteria (Staphylococcus aureus, PDB ID: 3q8u and Proteus PDB ID: 5i39) and with human DNA. Finally, in silico ADMET predictions was also examined.

Keywords: 2,4,6-ris(2-pyridyl)-,3,5-triazine; COVID-19, antimicrobial, DFT, docking; Copper (II); N-picolinoylpicolinamide, crystal structure.