Design, one-pot synthesis, and structural characterization of novel 2-ureido-6-nitrobenzamide derivatives as MTDLs targeting HDAC8/epigenetic-kinase networks.

Abstract

Modulating intersecting pathological pathways via multi-target directed ligands (MTDLs) is an active frontier in drug discovery. Herein, we report the design, one-pot synthesis, and characterization of a novel series of functionalized 2-ureido-6-nitrobenzamide derivatives 4-8 in 72-82% yields. Sequential nitration and imidization of phthalic anhydride 1, followed by sulfonylation, afforded the N-cyclic imide 2 and its sulfonyl ester building block 3. Aminolysis of 3 using various amines and hydrazines furnished target compounds 4-8 via a base-catalyzed Lossen rearrangement/addition-nucleophile ring-opening (ANRO) cascade. The structures were characterized using NMR, FT-IR, and mass spectrometry. In silico SwissADME analysis predicted favorable drug-like profiles adhering to Lipinski's Rule of Five. To normalized binding free energies, multi-parameter optimization (MPO) workflow utilizing, AutoDock Vina converted raw docking energies (ΔGcalc) into calculated logarithmic inhibition constants (pKi,calc) across ten targets proteins. The validated and predicted heavy-atom poses closely matched reference structures, with RMSD values confirming docking reliability, while 2D interaction diagrams verified conserved of key contacts. Compound 6 emerged as a prioritized multi-target template, with a balanced predicted dual-target profile against HDAC8 and JNK1. Compound 7 was identified as a prioritized in silico multi-target hit against HDAC8 and PIM1. Structural modifications shifted other derivatives toward target-biased profiles, such as building block 3 against GSK-3β and compound 8 against JAK2. Overall, these tunable 2-ureido-6-nitrobenzamide scaffold serves as an in silico prioritization starting point for the rational design of dual-action therapeutics targeting complex oncology and neurodegenerative networks, requiring future in vitro and in vivo validation.