Investigation of pyrazole linked carbonitrile based Schiff Bases through molecular dynamic simulation as promising urease and thymidine phosphorylase inhibitors: Synthesis in-vitro biological screening, DFT and computational approaches

Twelve new pyrazole-linked carbonitrile-based Schiff base derivatives have been prepared in the present study following a two-step pathway of reactions and tested as a dual inhibitor of urease and thymidine phosphorylase. The main target of this study was to develop structurally simple yet biologically active pyrazole-based scaffolds for targeting enzymes involved in bacterial infections and cancer-related angiogenesis. The originality of the present research lies in the rational synthesis of a pyrazole-carbonitrile core bearing Schiff base functionality, and in the thorough examination of the structure-activity relationship (SAR) through the in vitro, in silico, and quantum chemical studies. The compounds synthesized were structurally verified by the use of the NMR spectroscopy of 1 H and 13 C and screened against enzyme inhibition. Some of the derivatives showed better activity than the standard inhibitors, with compounds 4 (13.47 ± 1.12 μM for urease; 4.04 ± 1.78 μM for thymidine phosphorylase), 11 (14.75 ± 1.53 μM; 4.42 ± 0.98 μM), and 8 (17.93 ± 1.98 μM; 5.73 ± 2.16 μM). The results of molecular docking showed favorable binding interactions in the active sites of urease (PDB ID: 4UBP) and thymidine phosphorylase (PDB ID: 4EAD). In order to confirm binding stability, 100 ns molecular dynamics simulations were conducted, which confirmed stable ligand protein complexes, especially between compound 8 and urease and compound 4 and thymidine phosphorylase. DFT calculations were used to understand electronic stability and reactivity, and ADME analysis identified drug-like properties acceptable for the lead compounds.