Novel pyrimidines as COX-2 selective inhibitors: synthesis, DFT analysis, molecular docking and dynamic simulation studies

Pyrimidine and its derivatives are associated with varieties of biological properties. Therefore, we herein reported the synthesis of four novel pyrimidines (2, 3, and 4a, b) derivatives. The structure of these molecules is confirmed by spectroscopic methods such as IR, NMR, and Mass analysis. The electronic behavior of synthesized compounds 4a, b and in silico drug design 4 c, d was explained by Density Functional Theory estimations at the DFT/B3LYP level via 6-31 G++ (d, p) replicates the structure and geometry. All the synthesized compounds were screened for their in vitro COX-1 and COX-2 inhibitory activity compared to standards Celecoxib and Ibuprofen. Compounds 3 and 4a afforded excellent COX-1 and COX-2 inhibitory activities at IC50 = 5.50 and 5.05 μM against COX-1, 0.85 and 0.65 μM against COX-2, respectively. The standard drugs Celecoxib and Ibuprofen showed inhibitory activity at IC50 = 6.34 and 3.1 μM against COX-1, 0.56 and 1.2 μM against COX-2, respectively. Further, these compounds showed high potential docking with SARS-CoV-2 Omicron protease & COX-2 and predicted drug-likeness for the pyrimidine analogs by using Molinspiration. The protein stability, fluctuations of APO-protein, protein-ligand complexes were investigated through Molecular Dynamics simulations studies using Desmond Maestro 11.3 and potential lead molecules were identified.Communicated by Ramaswamy H. Sarma.

Investigation of embelin synthetic hybrids as potential COVID-19 and COX inhibitors: Synthesis, spectral analysis, DFT calculations and molecular docking studies

Embelin (2, 5-dihydroxy-3-undecyl-1,4-benzoquinone), a benzoquinone isolated from fruits of Embelia ribes has miscellaneous biological potentials including; anticancer, anti-inflammation, antibiotic, and anti-hyperglycemic activities. Also, embelin down-regulates the overexpression of inflammatory pathways like NF-kB, TACE, TNF-α, and other cytokines. Furthermore, embelin fascinated synthetic interest as a pharmacologically active compound. The present article involves the design, synthesis, DFT calculations, and molecular docking studies of embelin derivatives as cyclooxygenase inhibitors. The structure of these derivatives is confirmed by the various spectral analyses such as IR, NMR, and Mass. The DFT calculations were carried out for the molecules (1-8) using CAM-B3LYP hybrid functional with a 6-31+g(d) all-electron basis set using the Gaussian 09 package. Second-order harmonic vibrational calculations are used to check the minimum nature of the geometry. Further, HOMO and LUMO analyses were used for the charge transfer interface between the structures. Based on our previous work and structural activity relationship study, foresaid embelin derivatives were evaluated for in vitro COX-1 and COX-2 inhibitory activity. The compounds 3, 4, 7, and 8 demonstrated excellent COX inhibitions with IC50 values of 1.65, 1.54, 1.56, and 1.23 μM compared to standard drugs Celecoxib and Ibuprofen. Finally, the molecular docking studies carried out with Covid-19 and cyclooxygenase with all the newly synthesized embelin derivatives.

Synthesis, spectral analysis, DFT calculations, biological potential and molecular docking studies of indole appended pyrazolo-triazine

A series of novel 5-(3,5-disubstituted-1H-indol-2-yl)-2,3-dimethyl-1-phenyl-2,6-dihydro-1H-pyrazolo[4,3-e][1,2,4]triazines (3a-l) were synthesized in single step from 3,5-disubstituted indole-2-carbohydrazide and 4-aminoantipyrine under acidic conditions with excellent yields. The various spectroscopic methods were used to prove the formation of all these products. The compounds 3a, 3b, 3e, 3f, 3i and 3j exhibited excellent antibacterial and antifungal activities with an MIC value of 3.125 µg/ml against the tested pathogens and anti-tuberculosis inhibitory potential against M. tuberculosis which is equivalent to standard drug. The antidiabetic activity of the compounds 3a and 3b showed the maximum potential as glucosidase inhibitors with IC₅₀ = 47.21 μg/ml and IC₅₀ = 48.36 μg/ml, respectively. The physicochemical characteristics like ADMET, drug-likeness and bioactivity scores for these molecules were also disclosed. To comprehend the electronic behavior of compound 3a, density functional theory estimations at the DFT/B3LYP level via 6-31G++ (d, p) have been carried out to replicate the structure and geometry. The first-order hyperpolarizability calculation was used to calculate the nonlinear visual feature of compound 3a. The charge transfer interface among the structure is elucidated by the estimated HOMO-LUMO analysis. Further, molecular docking studies were carried out for synthesized compounds with human maltase-glucoamylase (PDB: 2QMJ).