New Pyrimidinone Bearing Aminomethylenes and Schiff Bases as Potent Antioxidant, Antibacterial, SARS-CoV-2, and COVID-19 Main Protease MPro Inhibitors: Design, Synthesis, Bioactivities, and Computational Studies

Abstract

New 2-thioxopyrimidinone derivatives (A1-A10) were synthesized in 87-96% yields via a simple three-component condensation reaction. These compounds were screened extensively through in vitro assays for antioxidant and antibacterial investigations. The DPPH assays resulted in the excellent potency of A6-A10 as antioxidants with IC₅₀ values of 0.83 ± 0.125, 0.90 ± 0.77, 0.36 ± 0.063, 1.4 ± 0.07, and 1.18 ± 0.06 mg/mL, which were much better than 1.79 ± 0.045 mg/mL for the reference ascorbic acid. These compounds exhibited better antibacterial potency against Klebsiella with IC₅₀ values of 2 ± 7, 1.32 ± 8.9, 1.19 ± 11, 1.1 ± 12, and 1.16 ± 11 mg/mL for A6-A10. High-throughput screenings (HTS) of these motifs were carried out including investigation of drug-like behaviors, physiochemical property evaluation, and structure-related studies involving DFT and metabolic transformation trends. The radical scavenging ability of the synthesized motifs was validated through molecular docking studies through ligand-protein binding against human inducible nitric oxide synthase (HINOS) PDB ID: 4NOS, and the results were promising. Furthermore, the antiviral capability of the compounds was examined by in silico studies using two viral proteins PDB ID: 6Y84 and PDB ID: 6LU7. Binding poses of ligands were discussed, and amino acids in the protein binding pockets were investigated, where the tested compounds showed much better binding affinities than the standard inhibitors, proving to be suitable leads for antiviral drug discovery. The stabilities of the molecular docked complexes in real systems were validated by molecular dynamics simulations.

Figure 1

Structures of bioactive natural products and drugs.

Scheme 1. Reaction Scheme for the Single-Step Condensation of 1,3-Diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione, triethyl orthoformate, and Aromatic Amines

Figure 2

Structures of newly synthesized Schiff bases as candidate ligands A1–A5 and aminomethylene-based thiobarbiturates A6–A10.

Figure 3

Graphical representation depicting the results of antibacterial assays of A6–A10, where (A) inhibition (%) at 100 μg/mL, (B) inhibition (%) at 500 μg/mL, and (C) IC₅₀ graphs of screened derivatives.

Figure 4

Frontier molecular orbitals of newly synthesized candidate ligands A1–A10.

Figure 5

TD-DFT-calculated absorption spectra of all the synthesized candidate ligands A1–A10.

Figure 6

Vibration frequency charts of compounds A1–A10.

Figure 7

Correlation graphs of experimental and estimated proton chemical shifts of synthesized compounds A1–A10 at the B3LYP level of theory.

Figure 8

Schematic representation of physiochemical descriptors. The colored zone is the optimal physiochemical space for which molar mass: 100 < MW < 600, number of rigid bonds: 0 < nRig <30, number of heteroatoms: 1 < nHet <15, number of hydrogen bond donors: 0 < nHD < 7, number of hydrogen bond acceptors: 0 < nHA < 12, LogP at physiological pH 7.4:1 < LogD < 3, Log of aqueous solubility: −4 < LogS < 0.5, Log of the octanol/water partition coefficient: 0 < LogP < 3, lipophilicity: −0.7 < LogP_o/w (XLOGP3 < 5.0, topological polar surface area: 0 < TPSA < 140, insaturation: 0.25 < INSATU (Fraction Csp3) < 1, insolubility: −6 < INSOLU (Log S (ESOL)) < 0, Flexibility: 0 < FLEX (Num. rotatable bonds) < 9.

Figure 9

Important metabolites with Pa > Pi of compound A4 estimated to be produced in phase I and phase II metabolism with calculated LogP and metabolite likelihood scores.

Figure 10

Three dimensional representations of binding analysis, the binding pocket of macromolecule, and best docked conformations of compounds A1–A10, and the standard inhibitor ronoptrin against chain A of the HINOS enzyme PDB ID: 4NOS.

Figure 11

Three-dimensional representations of binding analysis, the binding pocket of macromolecule, and best docked conformations of compounds A1–A5 against the SARS-CoV-2 main protease enzyme PDB ID: 6Y84.