Synthesis, Biological Activity, and Molecular Dynamics Study of Novel Series of a Trimethoprim Analogs as Multi-Targeted Compounds: Dihydrofolate Reductase (DHFR) Inhibitors and DNA-Binding Agents

Abstract

Eighteen previously undescribed trimethoprim (TMP) analogs containing amide bonds (<b>1-18</b>) were synthesized and compared with TMP, methotrexate (MTX), and netropsin (NT). These compounds were designed as potential minor groove binding agents (MGBAs) and inhibitors of human dihydrofolate reductase (<i>h</i>DHFR). The all-new derivatives were obtained via solid phase synthesis using 4-nitrophenyl Wang resin. Data from the ethidium displacement test confirmed their DNA-binding capacity. Compounds <b>13-14</b> (49.89% and 43.85%) and <b>17-18</b> (41.68% and 42.99%) showed a higher binding affinity to pBR322 plasmid than NT. The possibility of binding in a minor groove as well as determination of association constants were performed using calf thymus DNA, T4 coliphage DNA, poly (dA-dT)², and poly (dG-dC)². With the exception of compounds <b>9</b> (IC50 = 56.05 µM) and <b>11</b> (IC50 = 55.32 µM), all of the compounds showed better inhibitory properties against <i>h</i>DHFR than standard, which confirms that the addition of the amide bond into the TMP structures increases affinity towards <i>h</i>DHFR. Derivatives <b>2</b>, <b>6</b>, <b>13</b>, <b>14</b>, and <b>16</b> were found to be the most potent <i>h</i>DHFR inhibitors. This molecular modelling study shows that they interact strongly with a catalytically important residue Glu-30.